mGWAS Uncovers Gln-Glucosinolate Seed-Specific Interaction ... · 2 47 2Department of Plant...

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Journal Plant Physiology 1

Short title mGWAS reveals Gln-GLS link in Arabidopsis seeds 2

Corresponding author Ruthie Angelovici 3

E-mail angelovicirmissouriedu tel +1 573-882-3440 4

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Article title mGWAS Uncovers Gln-Glucosinolate Seed-Specific Interaction and its 6

Role in Metabolic Homeostasis 7 8 Marianne L Slaten1 9 mleww8mailmissouriedu 10 11 Abou Yobi1 12 yobiamissouriedu 13 14 Clement Bagaza1dagger 15 cb36fmailumsledu 16 17 Yen On Chan1 18 chanyemailmissouriedu 19 20 Vivek Shrestha1 21 vs6d9mailmissouriedu 22 23 Samuel Holden

1 24

slhdmbmailmissouriedu 25 26 Ella Katz2 27 elkatzucdavisedu 28 29 Christa Kanstrup4 30

ckaplenkudk 31

32 Alexander E Lipka3 33 alipkaillinoisedu 34 35 Daniel J Kliebenstein2 36 kliebensteinucdavisedu 37 38 Hussam Hassan Nour-Eldin4 39 huhaplenkudk 40 41 Ruthie Angelovici1 42 angelovicirmissouriedu 43 44

1Division of Biological Sciences Interdisciplinary Plant Group Christopher S Bond Life Sciences 45 Center University of Missouri Columbia MO 65211 USA 46

Plant Physiology Preview Published on April 21 2020 as DOI101104pp2000039

Copyright 2020 by the American Society of Plant Biologists

wwwplantphysiolorgon June 18 2020 - Published by Downloaded from Copyright copy 2020 American Society of Plant Biologists All rights reserved













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2Department of Plant Sciences UC Davis Davis CA 95616 USA 47 3Department of Crop Sciences University of Illinois Urbana IL 61801 USA 48 4DynaMo Center Copenhagen Plant Science Centre Department of Plant and Environmental 49

Sciences University of Copenhagen Frederiksberg Denmark 50 daggerCurrent address Department of Biology University of Missouri Saint Louis MO 63121 USA 51

52

53

Author contributions 54

MS performed the experiments wrote the manuscript and processed and analyzed data AY wrote the 55

manuscript and carried out metabolic analysis CB carried out genotyping experiments YC analyzed data 56

VS analyzed data SH carried out genotyping and metabolic analysis EK performed GLS measurements 57

CK peformed initial gtr12 experiment AL verified analytical methods and assisted with statistical aid H 58

N-E provided gtr12 mutants and initial analysis DK provided all the GLS mutants and GLS related 59

measurements from the population RA conceived the experimental design supervised the work provided 60

funding and wrote the manuscript All authors have reviewed the final version of the manuscript and 61

approved it and therefore are equally responsible for the integrity and accuracy of its content 62

63

Funding information 64 This work was funded by the NSF-IOS 1754201 to Ruthie Angelovici and by Danish National 65

Research Foundation grant DNRF99 to BAH and HHN-E 66

One-sentence summary mGWAS of Gln-related traits reveals an unexpected seed-specific 67

interaction between glutamine and glucosinolates and its potential role in shaping the metabolic 68

homeostasis in Arabidopsis seeds 69

70

71


3

Abstract 72

Glutamine (Gln) is a key player in plant metabolism It is one of the major free amino acids that 73

is transported into the developing seed and is central for nitrogen metabolism However Gln 74

natural variation and its regulation and interaction with other metabolic processes in seeds 75

remain poorly understood To investigate the latter we performed a metabolic genome-wide 76

association study (mGWAS) of Gln-related traits measured from the dry seeds of the 77

Arabidopsis diversity panel using all potential ratios between Gln and the other members of the 78

glutamate (Glu) family as traits This semi-combinatorial approach yielded multiple candidate 79

genes that upon further analysis revealed an unexpected association between the aliphatic 80

glucosinolates (GLS) and the Gln-related traits This finding was confirmed by an independent 81

QTL mapping and statistical analysis of the relationships between the Gln-related traits and the 82

presence of specific GLS in seeds Moreover an analysis of Arabidopsis (Arabidopsis thaliana) 83

mutants lacking GLS showed an extensive seed-specific impact on Gln levels and composition 84

that manifested early in seed development The elimination of GLS in seeds was associated with 85

a large effect on seed nitrogen and sulfur homeostasis which conceivably led to the Gln 86

response This finding indicates that both Gln and GLS play key roles in shaping the seed 87

metabolic homeostasis It also implies that select secondary metabolites might have key 88

functions in primary seed metabolism Lastly our study shows that an mGWAS performed on 89

dry seeds can uncover key metabolic interactions that occur early in seed development 90

Key words glutamine aliphatic glucosinolates mGWAS amino acids QTL seeds 91

92

93


4

Introduction 94

95

Glutamine (Gln) is a free amino acid (FAA) that belongs to the glutamate family which also 96

includes glutamate (Glu) gamma-aminobutyric acid (GABA) proline (Pro) and arginine (Arg) 97

(Skokut et al 1978 Majumdar et al 2016 Okumoto et al 2016) This amino acid family plays 98

a key role in plant cell core metabolism by providing an entry point for inorganic nitrogen 99

Briefly ammonium derived from nitrate or absorbed directly from the soil can be assimilated 100

into Gln via the glutamine synthase (GS)glutamine oxoglutarate aminotransferase (GOGAT) 101

cycle (Lea and Miflin 1974) GSGOGAT is the primary nitrogen assimilation pathway in plants 102

(Ireland 1999) and is involved in the remobilization of nitrogenous compounds and the 103

assimilation of large amounts of ammonium generated by photorespiration in C3 plants (Foyer et 104

al 2009) 105

Gln plays an important role in seed metabolism as one of the main nitrogen carriers it is 106

transported via the xylem and phloem to sink tissues including developing seeds (Zhang et al 107

2010 Zhang et al 2015 Besnard et al 2016) A study of maturing Brassica napus seeds 108

showed that embryos import nitrogen in the form of amino acids (mainly Gln and alanine) to 109

synthesize other amino acids via transaminationdeamination reactions and then incorporation 110

into seed storage proteins (SSP) (Schwender et al 2006) Consistently studies in Arabidopsis 111

have shown that Gln levels are highly elevated prior to the onset of SSP synthesis (Baud et al 112

2002 Fait et al 2006) and then drop substantially during seed maturation (Fait et al 2006) 113

Even though the majority of seed Gln comes from transport several glutamine synthase 114

isozymes are expressed during seed development in the micropillar chalaza embryo and seed 115

coat which suggests that Gln is also actively synthesized in seeds (Winter et al 2007) The 116

content of Gln in dry seeds therefore may be the result of a balance between its incorporation 117

into SSP active synthesis and degradation However its composition may also reflect the 118

environmental conditions encountered by the maternal plant High levels of Gln have been 119

reported in Arabidopsis plants facing sulfur deprivation (Nikiforova et al 2006) and in tobacco 120

plants grown under high nitrogen conditions (Geiger et al 1999) whereas low levels of Gln 121

have been reported in Arabidopsis seedlings grown under nitrate-deficit conditions (Scheible et 122

al 2004) Interestingly extensive variation in free Gln content in dry Arabidopsis seeds has 123

been reported across the various accessions belonging to the Arabidopsis diversity panel 124


5

(Angelovici et al 2017) but the genetic architecture regulating this trait remains poorly 125

understood Knowledge regarding the genes that underlie Gln levels composition and seed 126

partitioning would shed light on its potential seed-specific functions its interaction with other 127

biological processes and its role in downstream metabolism 128

In recent years genome-wide association studies (GWAS) as well as quantitative trait 129

loci (QTL) mapping experiments have facilitated the identification of many loci for both primary 130

and secondary metabolites (Wentzell et al 2007 Chan et al 2011 Riedelsheimer et al 2012 131

Angelovici et al 2013 Gonzalez-Jorge et al 2013 Chen et al 2014 Verslues et al 2014 132

Angelovici et al 2017) In-depth analyses of these QTLs have facilitated the further discovery 133

of key structural and regulatory genes that underlie the natural variation of metabolic traits and 134

the identification of various cellular processes involved in metabolic homeostasis Although 135

GWAS and QTL mapping have been conducted on FAAs in both vegetative and seed tissues 136

across several species no major QTLs have been identified for Gln (Riedelsheimer et al 2012 137

Chen et al 2014 Wen et al 2014) The lack of any identifiable loci implies that Gln either has 138

a complex genetic architecture or that these studies possibly utilized ldquounderpoweredrdquo association 139

panels or both 140

The use of metabolic ratios as traits in GWAS has been useful for dealing with several 141

such calcitrant metabolites The approach which relies on biochemical pathways andor 142

represent relationships uncovered by a metabolic network correlation analysis has yielded 143

several significant associations even when the absolute levels of metabolites have not (Wentzell 144

et al 2007 Lipka 2013 Angelovici et al 2013 Gonzalez-Jorge et al 2013 Angelovici et al 145

2017) It has been postulated that metabolic ratios are less complex (since they only represent the 146

metabolite partitioning within biochemical pathways) and therefore are more tractable in 147

association mapping studies (Angelovici et al 2017) Still even this approach has failed to 148

identify QTLs for Gln in dry seeds (Angelovici et al 2017) 149

A different approach is clearly needed to uncover the genetic architecture of Gln 150

Notably the metabolic ratios used in previous studies do not represent all the potential ratios of 151

Gln-related traits since they were based principally on a priori pathway information which is 152

often incomplete 153

In theory performing a metabolic genome-wide association study (mGWAS) on all 154

possible Gln-related metabolic ratios would potentially resolve its genetic architecture In 155


6

practice however such an endeavor would be challenging given the enormous number of 156

metabolic ratios that could be derived from the relationships between Gln and all 20 proteogenic 157

amino acids Therefore as a point of departure from previous studies we derived all possible 158

metabolic ratios of Gln only to its proteogenic amino acid family members thus theoretically 159

representing all potential biologically relevant partitioningrelationship of Gln within the Glu 160

family (Fig 1) By combining this approach with a Fixed and Random Model Circulating 161

Probability Unification (FarmCPU) which uses fixed and random effect models for powerful 162

and efficient GWAS studies (Liu et al 2016) we uncovered many significant QTLs for various 163

Gln-derived traits in dry seeds More importantly our analysis of the candidate genes revealed a 164

surprising enrichment for genes residing in the glucosinolate (GLS) biosynthesis pathway 165

suggesting a potential interplay between two metabolic pathways that are not known to be 166

directly linked (Fig 1) We validated this association by using an independent QTL mapping 167

approach as well as by characterizing Gln and other FAAs in mutant plants that have a disrupted 168

GLS composition and loading to the seeds Our data support an association between GLS natural 169

diversity and Gln levels and composition in seeds and also reveal that GLS loading to the seeds 170

has a profound effect on seed nitrogen and sulfur homeostasis as well as Gln levels and 171

composition Our results strongly suggest that an interaction between Gln and GLS plays a key 172

role in seed metabolic homeostasis 173

174

175

Results 176

177

The Four Glu Family Members Vary in Abundance Relative Composition and Broad-178

Sense Heritability Across the Arabidopsis Diversity Panel 179

In a previous study we quantified and described the natural variation of 18 out of the 20 180

proteogenic FAAs (excluding cysteine and asparagine) measured from dry seeds of three 181

biological repeats of a 313-accession Arabidopsis diversity panel (Angelovici et al 2013 182

Angelovici et al 2016) In the current study we used that data to assess the natural variation 183

among only the proteogenic FAAs in the Glu family ie Glu Pro Gln and Arg 184

Our analysis showed that the four Glu family members vary in abundance relative 185

composition and broad-sense heritability (Supplemental Table S1A) Glu was the most abundant 186


7

amino acid with a relative composition mean of 035 whereas Gln was the least abundant with a 187

relative composition mean of 0015 We defined relative composition as the ratio of an individual 188

amino acid to the sum of the 18 measured amino acids (eg GlnTotal GluTotal) Arg and Pro 189

had a relative composition means (ArgTotal ProTotal) of 004 and 0017 respectively Gln 190

demonstrated moderate heritability (052) along with Pro and Glu (048 and 063 respectively) 191

whereas Arg had the highest heritability (074) Interestingly Gln had the largest relative 192

standard deviation whereas Glu had the smallest despite its high abundance (~61 and 23 193

RSD respectively) 194

To evaluate the relationship between Gln and the other Glu family members we 195

performed a correlation-based network analysis among the four FAAs and visualized the results 196

using Cytoscape version 361 (Supplemental Fig S1) All correlations (r) were significant at = 197

0001 and ranged from 012 to 054 Gln was moderately correlated with Arg and Glu and 198

weakly correlated with Pro which had a significant but weak correlation with all Glu family 199

members 200

201

mGWAS Identified Significant SNP-Trait Associations for Six Gln-related traits 202

In our previous study no significant associations were identified when seed Gln traits or any 203

Gln-related traits derived from a priori knowledge of the Glu metabolic pathway or correlation-204

based network analysis were used for the mGWAS (Angelovici et al 2017) Therefore we took 205

a slightly different approach in this study by using all possible Gln metabolic ratios that could be 206

derived from Gln relationships with the other members of the glutamate family The various 207

relationships were represented by calculating all the possible ratios in which Gln is the numerator 208

and is divided by a sum of every combination of the four Glu family members including Gln 209

itself ie Gln(Gln|Arg|Pro|Gu) | = (and or) We consider this a semi-combinatorial approach 210

since it relies on both a priori knowledge of the Glu family as well as all the possible 211

combinations of the Glu family FAAs in the denominator The traits and their corresponding 212

means ranges and broad-sense heritability scores are listed in Supplemental Table S1B For 213

simplicity we used a one letter code in our trait representations The sum of the FAA in the 214

denominator of each trait is represented by a string of one letter codes For example QEP is Gln 215

divided by the sum of Glu and Pro This approach yielded 16 Gln-related traits 14 ratio-based 216

traits (Supplemental Table S1B) one free Gln absolute level and the Gln relative composition 217


8

(GlnTotal) (Supplemental Table S1A) Of all these 16 traits QQP had the highest heritability 218

(053) and QRP had the lowest (035) In general the derived traits had low to moderate 219

heritability 220

We used the FarmCPU package in R (version 102) (Liu et al 2016) to perform an 221

mGWAS on the 16 Gln-related traits Since FarmCPU may be prone to a type I error we chose 222

to use the more conservative Bonferroni multiple testing correction procedure instead of the 223

Benjamini-Hochberg (1995) false discovery rate-controlling procedure We also considered 224

SNP-trait associations significant only at an = 001 Bonferroni correction level At this 225

significance threshold we identified 21 SNPndashtrait associations for six traits QP QR QQP 226

QRP QRQ and QRQP (Fig 2 Supplemental Dataset S1) only 16 SNPs were identified from 227

the 21 signals None of the six traits included Glu in their denominator but did include either Arg 228

or Pro or both The heritability of these six traits ranged from low to moderate (035ndash053) 229

(Supplemental Table S1B) No significant associations were observed on chromosome 1 One 230

was observed on chromosome 2 and three on chromosome 3 The majority of significant SNPs 231

were identified on either chromosome 4 or 5 (Fig 2 Supplemental Dataset S1) The five SNPs 232

with the lowest p-values were located on chromosomes 4 or 5 (Table 1) three of these SNPs fell 233

within a gene whereas the remaining two were located in a transposable element and an 234

intragenic region The three genes are annotated as encoding Brassinosteroid suppressor 1 235

(BSU1) a MATE efflux family protein and methylthioalkylmalate synthase 1 (MAM1) 236

237

Genes Within Haploblocks Spanning Significant SNPs Are Enriched for Glucosinolate 238

Biosynthetic Process 239

We compiled a candidate gene list based first on genes that contain a significant SNP We then 240

expanded the list to include those genes that are in strong linkage disequilibrium (LD defined as 241

regions with non-random associations calculated using a 95 confidence bounds on D prime) 242

with the significant SNPs identified by our mGWAS since significant SNPs identified by 243

GWAS may tag causal variants in neighboring genes that are in LD (Atwell et al 2010) To that 244

end we identified haploblocks that spanned the 16 SNPs using Haploview version 42 (See 245

Materials and Methods) (Barrett et al 2004) and considered all spanned genes as candidates If a 246

haploblock was not identified for a given SNP and did not fall within a gene then the gene 247


9

directly upstream or downstream was recorded Overall we found 27 unique genes The entire 248

list of genes associated with all 16 SNPs is summarized in Supplemental Table S2A 249

Next we used agriGO (httpbioinfocaueducnagriGO) to perform a GO enrichment 250

analysis of the 27 genes We analyzed all genes identified across the six traits since collectively 251

they represent the potential genetic architecture of the Gln partition within the Glu family and its 252

relationships to the other members The analysis revealed a significant enrichment for the 253

following terms secondary metabolic process carbohydrate metabolic process sulfur metabolic 254

process S-glycoside biosynthetic process and glucosinolates biosynthetic process (Supplemental 255

Table S2B) 256

All the significant enrichment terms resulted from three genes MAM1 (AT5G23010) 257

AOP1 (AT4G03070) and AOP3 (AT4G03050) all of which are annotated as involved in the 258

biosynthesis of aliphatic GLS Notably one of our top five significant SNPs fell within MAM1 259

(QP) (Table 1) AOP1 was associated with traits QRQ and QRQP and AOP3 was associated 260

with trait QRQ (Fig 2 Supplemental Dataset S1) Although these genes are located in three 261

different haploblocks AOP1 and AOP3 are in very close proximity within the genome the end 262

of AOP3 and the beginning of AOP1 are 11831 base pairs apart (Fig 3) The three genes are 263

located in two well-characterized QTLs GS-ELONG and GS-AOP (Fig 3 and Fig 4) The GS-264

ELONG locus controls variation in the side-chain length of aliphatic GLS and is characterized by 265

three genes MAM1 MAM2 and MAM3 (previously MAM-L) (Kroymann et al 2001 Kroymann 266

et al 2003) GS-AOP is the collective name of two tightly linked loci GS-ALK and GS-OHP 267

and controls GLS side-chain modifications (Kliebenstein et al 2001) The GS-AOP locus 268

represents the branching point in the biosynthesis of aliphatic GLS that includes two 2-269

oxoglutarate dependent dioxygenases AOP2 localized in the GS-ALK locus and AOP3 270

localized in the GS-OHP locus The presenceabsence of genes in the GS-AOP and GS-ELONG 271

loci account for much of the natural variation in aliphatic GLS profiles in Arabidopsis (Fig 1) 272

Thus despite having significant SNPs directly associated with MAM1 AOP1 and AOP3 273

because of the high degree of LD in these regions MAM2 MAM3 and AOP2 are also putative 274

genes of interest 275

We next asked whether the three significant SNPs (ie S127050 S127076 S175365) 276

identified in the two GLS-related QTLs tagged the additional GLS genes in the GS-ELONG and 277

GS-AOP regions To that end we performed a pairwise LD analysis between the three identified 278


10

SNPs and the SNPs +-5 kb to either side of the first and last MAM or AOP genes in the GS-279

ELONG and GS-AOP regions (ie flanking the regions) respectively (Supplemental Fig S2 and 280

Supplemental Fig S3) SNP S127076 which resides within the BSU1 gene but is located within 281

the haploblock containing AOP1 is in high LD with AOP1 (S127071 and S127075 r2 = 0934 282

and 0934) as well as with the SNPs residing in both AOP2 (S127058 r2 = 0918) and AOP3 283

(S127048 S127050 and S127050 r2 = 0902 0918 and 0918 respectively) The high LD with 284

neighboring SNPs suggests that this SNP may tag a causal variation in one or both of these AOP 285

genes (Supplemental Fig S2A) Similarly SNP S127050 which resides in the same haploblock 286

as AOP3 is in perfect LD with a SNP from AOP2 (S127058 r2 = 1) and in high LD with SNPs 287

in AOP1 (S127071 S127075 and S127076 r2 = 0983 0983 and 0918 respectively) which 288

suggests that this SNP may tag the additional AOP genes in the region (Supplemental Fig S2B) 289

Finally SNP S175365 which resides in the same haploblock as MAM1 is in strong to moderate 290

LD with SNPs associated with MAM2 (S175355 r2 = 0908) and MAM3 (S175394 r

2 = 0649) 291

(Supplemental Fig S3) 292

Overall we found six genes involved in aliphatic GLS biosynthesis that are in moderate 293

(gt 05) to strong (gt 08) LD with three of significant SNPs in the region It is likely that either 294

one or an allelic combination of all six genes contributes to the natural variation of free Gln and 295

its related traits in dry seeds 296

297

QTL Analysis of the Bayreuth-0 and Shahdara Mapping Population Supports the GWAS 298

Finding 299

The finding of an association between Gln and GLS in dry seeds was surprising Glucosinolates 300

are not synthesized in seeds but rather are transported to the seed from the maternal plant 301

(Magrath and Mithen 1993) Therefore to independently confirm our results from the mGWAS 302

and to further support the association between Gln and the two GLS-related QTLs we performed 303

a biparental QTL mapping using the Bayreuth-0 (Bay) and Shahdara (Sha) recombinant inbred 304

population (Loudet et al 2002) Previous work has shown that Bay and Sha segregate at the GS-305

ELONG and GS-AOP loci and have an epistatic relationship (Kliebenstein et al 2001 306

Kroymann et al 2003 Textor et al 2004 Kliebenstein et al 2007 Wentzell et al 2007) We 307

hypothesized that if these GLS-related QTLs are indeed responsible for the natural variation of 308


11

Gln in dry seeds then the Bay x Sha mapping population should recapitulate the QTL for the 309

Gln-related traits 310

To test this hypothesis we used the FAA quantifications from 158 recombinant inbred 311

lines of the Bay x Sha population as described previously (Angelovici et al 2013 Angelovici et 312

al 2017) and performed a QTL analysis of our 16 Gln-related traits using Multiple QTL 313

Mapping (MQM) in the Rqtl2 package in R (Arends et al 2010) This approach yielded a total 314

of 25 QTLs for eight traits (for the full list see Supplemental Dataset S2) Six traits had 315

significant LOD maxima on chromosome 5 at marker MSAT514 (position 7498509 bp) QRQ 316

QRQP QR QRP QQP and QP The supporting interval overlapped with the GS-ELONG 317

locus (Table 2) Both the highest percent of total phenotypic variation and the highest LOD were 318

observed for QQP and QP These two traits also had a LOD maxima on chromosome 4 at 319

marker MSAT443 with supporting intervals spanning the GS-AOP locus 320

Interaction between the two QTLs has been observed previously in GLS traits 321

(Kliebenstein Lambrix et al 2001 Kliebenstein et al 2007) Therefore we tested whether 322

interactions between the two loci existed for our Gln-related traits Visual inspection of the 323

interaction plots between markers MSAT443 and MSAT514 clearly indicated interaction 324

between these markers that seem to heavily influence the QQP and QP trait means 325


327

The Presence or Absence of Specific GLS Has a Significant Effect on the Levels of the Gln-328

Related Traits in Dry Seeds 329

To further validate the association between GLS natural variation and the Gln-related traits we 330

grew 133 accessions from the Arabidopsis diversity panel and measured both FAA and GLS 331

levels in the dry seeds (Supplemental Dataset S3) Next we tested whether the presence or 332

absence of one of the four GLS which result from the different allelic combinations at the GS-333

ELONG and GS-AOP loci (Fig 1) were associated with high or low levels of our traits of 334

interest (ie the 16 Gln-related traits analyzed in our mGWAS) The four GLS analyzed for 335

presenceabscence were 3ohp (requiring the presence of MAM2 and AOP3) 2-propenyl 336

(requiring the presence of MAM2 and AOP2) 4ohb (requiring the presence of MAM1 and 337

AOP3) and 3butenylOH-3-butenyl (requiring the presence of MAM1 and AOP2) To evaluate 338

this association we performed t-tests on the levels of the Gln-related traits measured from 339


12

accessions that either had a specific GLS chemotype (ie 3ohp or 4ohb) or completely lacked it 340

(see Materials and Methods for more details regarding the statistical analysis) 341

Our results showed that Gln absolute levels were significantly less in the presence of 2-propenyl 342

(Supplemental Table S3) However the presenceabsence of both 3ohp and 4ohb had the most 343

significant effect on our traits The presence of 3ohp had a negative effect on most of the Gln-344

related ratios and had a positive effect on the absolute levels of Arg Glu and Pro By contrast 345

the presence of 4ohb had the opposite effect on most of the Gln-related traits in addition to the 346

absolute levels of Glu and Pro (Supplemental Table S3) Taken collectively these results both 347

confirm that GLS diversity can significantly affect the Gln-related traits and further supports the 348

association between these two pathways 349

350

FAA Characterization of Mutants in GLS Genes Present in the GS-ELONG and GS-AOP 351

Showed Only Small Effects on Gln-Related Traits in the Col-0 Background 352

We performed a transgenic approach to further confirm the association between aliphatic GLS 353

and Gln content in dry Arabidopsis seeds We obtained null and overexpression (OX) mutants of 354

the six relevant genes located in the GS-ELONG or GS-AOP locus and involved in aliphatic GLS 355

biosynthesis All plants were grown to maturity and their dry seeds harvested and analyzed for 356

FAA content and composition We also obtained and quantified the dry seed FAA content of a 357

bsu1 null mutant which lacks the BSU1 genes that contain the significant SNP (ie S127076) 358

identified for traits QRP and QRQP (Fig 4 Table 1) The T-DNA insertion lines were ordered 359

from the SALK and WISC T-DNA collections and included insertions in the AT4G03070 360

(aop1) AT4G03050 (aop3) AT5G23020 (mam3) and AT4G03080 (bsu1) genes The T-DNA 361

insertion locations are summarized in Supplemental Fig S5 Null homozygous mutants were 362

isolated and confirmed by the absence of the full transcript in a tissue of high expression 363

(Supplemental Fig S5 and Supplemental Fig S6) Based on the eFP browser expression data 364

(Schmid et al 2005 Winter et al 2007) AOP1 expression was evaluated in imbibed seeds 365

AOP3 was evaluated in young siliques MAM1 and MAM3 were evaluated in seedlings and 366

BSU1 was evaluated in leaves The RT-PCR primers used are listed in Supplemental Table S4 367

Interestingly all genes excluding AOP2 showed some transcript expression during seed 368

development despite a lack of GLS synthesis at the seed level MAM2 does not exist in the 369

Columbia-0 (Col-0) ecotype and does not have any publicly available expression profiles 370


13

In addition to null mutants we also obtained mutants with altered GLS composition in 371

the Col-0 background These mutants included gsm1 which accumulates C3 GLS and has large 372

reductions in 4-methyl sulfinylbutyl and 6-methylsulfinyl glucosinolates (Haughn et al 1991 373

Kroymann et al 2001) Since the Col-0 accession does not contain MAM2 and has a truncated 374

non-functional AOP2 protein (Kroymann et al 2001 Wentzell et al 2007 Jensen et al 2015) 375

we also analyzed a previously characterized AOP2 overexpression mutant in the Col-0 376

background that accumulates alkene GLS (Rohr et al 2009 Burow et al 2015) Collectively 377

these mutants represent some of the potential GLS composition alterations that can occur in the 378

Col-0 background The ability of any single gene mutant to capture the diversity of GLS is 379

limited since it arises from a complex allelic combination (Kliebenstein et al 2001) 380

We quantified the dry seed FAA for each of these single gene mutants and then assessed 381

the fold change (FC) as compared to its respective WT control (Col-0 or Col-3) for 16 Gln-382

related traits (Supplemental Dataset S4A) Gln absolute levels in the aop1 aop3 and AOP2-OX 383

mutants did not change significantly An elevated amount of Arg in the aop3 mutant led to 384

reductions in two Gln-related traits QR and QRQ (054 and 075 FC respectively Fig 5 385

Supplemental Table S5A Supplemental Dataset S4B) In addition Glu and Pro were reduced in 386

the AOP2-OX mutant but did not lead to any significant changes in the Gln-related ratios (Fig 387

5B Supplemental Table S5B) The bsu1 mutant had significantly high levels of Arg and Glu (a 388

162 and 143 FC respectively) but the levels of Gln and related ratios were unchanged (Fig 5 389

Supplemental Table S5B) The FAA quantifications of the AOP-related mutants showed that in 390

addition to minor alterations in the Glu family FAAs few other FAAs changed significantly 391

(Fig 5A Supplemental Table 5B) Our analysis of the MAM-related mutants showed that levels 392

of Gln Glu and Pro were slightly elevated (a 139 119 and 135 FC respectively) in the gsm1 393

mutant which led to slight increases in nine traits Gln related ratios (Fig 5B Supplemental 394

Table S5) In sum the single gene mutants showed only a small effect of the altered GLS 395

composition on the Gln-related traits 396

397

Elimination of Aliphatic GLS Triggers a Strong Seed-Specific Increase in Free Gln 398

To further characterize the association between aliphatic GLS and the Gln-related traits we 399

quantified the absolute levels of each FAA in the dry seeds of three null mutants (myb2829 400

myb3451 and grt12) with altered GLS compositions and the Col-0 ecotype The log2 of the 401


14

average FC defined as the ratios between individual amino acid levels in the mutants and their 402

levels in their respective controls were calculated and used to create heat maps of the FAAs (Fig 403

6 Supplemental Dataset S4) The myb2829 double knockout mutant is a null mutant of two 404

transcription factors that regulate the aliphatic GLS in Arabidopsis MYB28 (AT5G61420) and 405

MYB29 (AT5G07690) This double knockout eliminates all aliphatic GLS from the entire plant 406

including the seed (Sonderby et al 2007) A double knockout of GTR1 (AT3G47960) and GTR2 407

(AT5G62680) resulting in the gtr12 mutant abolishes the transport of all GLS to the seeds 408

(Nour-Eldin et al 2012) Finally a double knockout of the two transcription factors MYB51 409

(AT1G18570) and MYB34 (AT5G60890) resulting in the myb3451 mutant eliminates the 410

indole GLS from the entire plant (Frerigmann and Gigolashvili 2014) 411

The FAA analysis revealed that Gln levels were significantly higher in the myb2829 and 412

gtr12 mutants but not in the myb3451 mutant as compared to Col-0 (Fig 6 Supplemental 413

Table S5A Supplemental Dataset S4A) In fact Gln showed the most pronounced FC among all 414

FAAs measured a 97 FC in the myb2829 mutant and a 598 FC in the gtr12 mutant (Fig 6 415

Supplemental Table S5A B) In addition to Gln three other Glu family members increased 416

significantly in the myb2829 and gtr12 mutants a 351 and 645 FC for Arg a 33 and 47 FC 417

for Glu and a 13 and 4 FC for Pro respectively (Supplemental Table S5A B) Alterations in 418

these Glu family FAAs led to significant FC increases in all Gln-related ratios ranging from a 419

15ndash19 FC in QRQ and a 763 and 1507 FC in QP in the myb2829 and gtr12 mutants 420

respectively (Fig 6B Supplemental Table S5A) In the myb2829 and gtr12 mutants we also 421

observed increases in Asn (1040 and 987 FC respectively) and His (878 and 4728 FC 422

respectively) Glu and Asp also showed a consistent elevation (~3ndash5 FC) in both mutants (Fig 423

6A Supplemental Table S5B) The total sum of the FAAs (TFAA) measured also increased 424

significantly in both myb2829 and gtr12 by 473 and 1258 respectively (Supplemental Table 425

S5B) 426

Since TFAA changed in both mutants we also calculated the percent of each FAA to the 427

sum of the TFAA measured in all genotypes including Col-0 (Supplemental Dataset S4C 428

Supplemental Table S5C) In both mutants the largest increase was in the relative composition 429

of Gln which increased from ~1 in Col-0 to 2282 in the myb2829 mutant and to 5310 in 430

the gtr12 mutant (Fig 6C Supplemental Table S5C) Arg and His were the only other FAAs 431

that consistently increased in both the myb2829 and gtr12 mutants from ~1 of the total FAA 432


15

in Col-0 to 882 and 610 respectively for Arg and to 244 and 495 respectively for 433

His The relative compositions of the remaining FAAs were consistently lower in both mutants 434

(excluding Asn which showed opposite trends in the two mutants) (Fig 6C Supplemental Table 435

S5C) The largest decreases were in the two most abundant FAAs in the Col-0 seeds Glu and 436

Gly which had relative abundances of 2881 and 1877 in Col-0 1994 and 1065 in 437

myb2829 and 666 and 283 in gtr12 respectively (Fig 6C Supplemental Table S5C) 438

Next we tested whether a reduction in GLS (rather than its complete elimination) would result in 439

significant alterations in Gln levels We quantified the dry seed FAA levels from the myb28 and 440

myb29 single mutants which have approximately half the seed GLS as the Col-0 ecotype 441

(Francisco et al 2016) The myb28 mutant had significant FCs only in Pro levels (a 123 FC 442

increase) (Supplemental Table S5A B) The myb29 mutant by contrast showed minor but 443

significant increases in both Gln absolute levels (155 FC) and relative composition (GlnTotal 444

126 FC) as well as FCs (17ndash147) in several Gln-related traits (ie QREP QE QP QRE 445

QQE QQP QEP QRQE QQEP QRQEP) in the myb29 mutant (Fig 6B Supplemental 446

Table S5A) Nevertheless levels of Asp Gly Leu and Phe were also elevated significantly in 447

this mutant with FCs of 123ndash142 (Fig 6A Supplemental Table S5B) Collectively this genetic 448

analysis indicated to us that Gln levels were extensively altered in response to a complete 449

absence of aliphatic GLS either in the plant or specifically in the seed 450

To evaluate if the response was seed specific we analyzed the FAA content in the rosette leaves 451

and stems of the myb2829 and gtr12 double mutants and the respective Col-0 control Tissues 452

were collected approximately 20 days after bolting in order to capture the metabolic steady state 453

of the FAA in these tissues during seed setting and filling Neither mutant had significant fold 454

changes in Gln levels in either its leaves or stems (Supplemental Dataset S5 Supplemental Table 455

S6) In contrast to the seeds we also found no elevation in TFAA (as explained above) in either 456

mutant The results support the genetic evidence that the elevated Gln levels in the mutant seeds 457

are occurring at the seed level rather than resulting from specific increases in the maternal tissue 458

459

460

461

462


16

463

Gln Levels Are Elevated During Early Seed Maturation in Both the myb2829 and the 464

gtr12 Mutants 465

During seed maturation FAAs (especially Gln) are incorporated into the SSPs especially during 466

seed fillingmaturation (Fait et al 2006) Hence we assessed whether Gln levels are elevated 467

during the early stages of seed development To do this we isolated developing seeds at 12 14 468

16 and 18 days after flowering (DAF) and at the dry seed stage from the myb2829 and gtr12 469

mutants and the Col-0 ecotype and analyzed the FC in FAA levels across these time points 470

(Supplemental Dataset S6) Our analysis indicated that as compared to the Col-0 control the 471

seeds from both mutants had substantial increases in Gln as early as 12 DAF (Fig 7 472

Supplemental Table S7) At 12 DAF there was a 24 FC increase of Gln in the myb2829 mutant 473

and a 37 FC increase in the gtr12 mutant (Supplemental Table S7) Gln levels were higher 474

across all the developmental time points in both mutants Although Gln levels in all genotypes 475

showed an overall reduction trend the FC observed in the mutants continued to increase as the 476

seed progressed to desiccation (Fig 7A B Supplemental Table S7) Gln absolute levels at all 477

time points exceeded the levels of any other amino acid (Supplemental Dataset S6) 478

Since the TFAA changed in both mutants we also evaluated the changes in FAA relative 479

composition as described above The relative composition of Gln dropped from 95 (12 DAF) 480

to ~111 (dry seed) in the Col-0 and dropped from ~541 (12 DAF) to 2282 (dry seed) in 481

the myb2829 mutant (Supplemental Table S7B) Surprisingly the Gln content in the gtr12 482

mutant remained between 5453 and 6140 throughout the entire seed maturation process 483

despite a drop in Gln absolute levels (Fig 7C Supplemental Table S7B) Hence Gln is only a 484

minor amino acid in Col-0 but the most abundant one in the mutants By contrast Glu is most 485

abundant in the seeds and its levels increased from 213 (12 DAF) to 288 (dry seed) in the 486

Col-0 remained constant at ~20 in the myb2829 mutant throughout development and 487

decreased from 139 (12 DAF) to 106 (dry seed) in the gtr12 mutant (Supplemental Table 488

S7B) Very pronounced changes were also recorded in the composition of Gly which had a 489

lower relative composition as compared to the Col-0 throughout seed development (Fig 7C 490

Supplemental Table S7) Notably at all seed developmental stages the FC never exceeded 2 for 491

Gly or 6 for Glu (Supplemental Table S7A) 492


17

Collectively these results show that compositional alteration to FAAs in the 493

glucosinolate mutants occurs very early in seed maturation and persists in the dry seeds 494

495

Both Sulfur and Nitrogen Significantly Changed in Seeds that Lacked GLS 496

GLS are high in nitrogen and sulfur compounds A lack of GLS in seeds may cause a change in 497

their homeostasis which is known to have a substantial impact on Gln levels (Nikiforova et al 498

2005 Nikiforova et al 2006) To test this possibility we measured nitrogen carbon and sulfur 499

in the myb2829 and gtr12 mutants and in the Col-0 control (Table 3) 500

We found that as compared to Col-0 nitrogen was higher in both mutants (by 8 and 15 501

respectively) sulfur was significantly lower (by 79 and 90 respectively) and carbon was 502

unaltered (Table 3) Finally we assessed whether the elevated levels of Gln and other FAAs 503

reflected any changes in the levels or composition of proteins To do this we analyzed the 504

protein-bound amino acids (PBAA) in the dry seeds of the two mutants and in Col-0 The 505

analysis revealed no significant or consistent alterations in PBAA levels (Supplemental Dataset 506

S7 Supplemental Table S8) 507

508

Discussion 509

Genome-wide association studies have successfully uncovered many genes involved in the 510

natural variation and regulation of various metabolic traits including FAAs in seeds (Magrath 511

1994 Parkin et al 1994 Chan et al 2011 Angelovici et al 2013 Lipka et al 2013 512

Diepenbrock et al 2017) Yet none of these studies have identified any significant SNP 513

associations with free Gln in dry seeds The intractability of this trait would suggest that Gln has 514

a highly complex genetic architecture When faced with such complex metabolic traits some 515

researchers have enlisted metabolic ratios based on a priori knowledge or unbiased network 516

analysis an approach that has yielded additional QTLs that could not be retrieved using direct 517

measurements of the absolute traits (Angelovici et al 2013 Angelovici et al 2017 518

Diepenbrock et al 2017) Unfortunately for free Gln in seeds neither absolute measurements 519

nor specific metabolic ratios have resulted in significant associations 520

In this study we used a semi-combinatorial approach to formulate metabolic ratios as 521

traits in a mGWAS Unlike previous studies this approach yielded several novel SNP-trait 522


18

associations Interestingly we identified unique SNP-trait associations across the different Gln-523

related traits suggesting a slightly different genetic architecture for each metabolic ratio (Fig 2 524

Supplemental Dataset 1) Since all the traits represent the Gln partition or a relationship to the 525

other Glu family members we treated all the SNPs as contributing to one genetic architecture of 526

Gln metabolism This collective analysis enabled us to compile a comprehensive candidate gene 527

list that upon further analysis revealed a strong association between Gln and an unexpected 528

metabolic pathway the GLS biosynthesis We argue that this approach could help elucidate the 529

genetic basis of other complex metabolites and further reveal unexpected metabolic pathway 530

associations 531

532

Unexpected Association Between the Gln-Related Traits and the Aliphatic GLS Natural 533

Diversity is Supported by Multiple Independent Lines of Evidence 534

Our semi-combinatorial mGWAS analysis revealed that the natural variation of the Gln-related 535

traits measured from dry seeds is strongly associated with natural variation of aliphatic GLS Not 536

only did we identify an enrichment of GLS biosynthesis genes in our collective candidate gene 537

list but we also identified two aliphatic GLS biosynthetic genes in our top significant SNP-trait 538

associations analysis (Table 1 Supplemental Table 2B) This association is surprising because 539

GLS biosynthesis has three main steps (chain elongation of either methionine branched chain or 540

aromatic amino acids core structure formation secondary modifications Kliebenstein et al 541

2001) none of which involve Gln In general GLS are nitrogen- and sulfur-containing 542

compounds that likely evolved from cyanogen glucosides but are largely limited to the 543

Brassicales (Halkier and Gershenzon 2006) Their breakdown products display a variety of 544

biological activities explaining their defensive roles (Johnson et al 2009) Although GLS 545

accumulate to very high levels in seeds they are synthesized in the vegetative tissue and 546

transported from the maternal plant to the seed (Magrath and Mithen 1993) Nevertheless our 547

study provides multiple lines of evidence confirming an association between the natural variation 548

of Gln-related traits and the natural diversity of aliphatic GLS Firstly it is important to note that 549

the three significant SNPs associated with aliphatic GLS fell within two well characterized 550

QTLs the GS-ELONG and the GS-AOP (Magrath 1994) Previous studies have shown that the 551

presence and absence of five genes within these QTLs account for much of the diversity in the 552

aliphatic GLS profile in Arabidopsis These genes are MAM1ndash3 AOP2 and AOP3 (Halkier and 553


19

Gershenzon 2006) Pairwise LD analysis of the three significant SNPs identified in these two 554

regions revealed that these SNPs are likely tagging all five genes within these two key QTLs 555

(Supplemental Fig S2 and Supplemental Fig S3) Secondly an independent QTL mapping of 556

the Gln-related traits measured from the BaySha mapping population (which segregates for 557

these two key QTLs (Wentzell et al 2007) also identified significant associations of both GS-558

ELONG and GS-AOP loci with several Gln-related traits (Table 2 Supplemental Dataset 2) 559

Lastly the presenceabsence of various chemotypes arising from different allelic combinations 560

of the MAM and AOP genes (Fig 1) resulted in significantly different levels in the Gln-related 561

traits (Supplemental Table S3) GLS 3ohp and 4ohb in particular showed strong associations 562

with the Gln-related traits and are among the most abundant class of GLS in seeds (Petersen et 563

al 2002 Velasco et al 2008) In addition the aliphatic GLS are the most abundant GLS in 564

Arabidopsis seeds (Kliebenstein et al 2001) Interestingly their precise function in this tissue is 565

unclear Taken together our results show that although unexpected the pathway level 566

association revealed by our mGWAS approach is strongly supported by multiple independent 567

approaches 568

569

The Nature of the Association Between the Gln-Related Traits and the GLS Natural Diversity 570

is Complex and Seed Specific 571

The precise nature of the association between GLS and the Gln-related traits is unclear Our data 572

indicate that the association is not simple Analysis of known single gene mutants of the genes 573

related to GLS in the GS-ELONG and GS-AOP regions in the Col-0 background (which lacks the 574

expression of AOP2 and MAM2) (Kroymann et al 2001) showed relatively small changes in the 575

Gln-related traits (Fig 5 Supplemental Table 5) This finding is perhaps not surprising since 576

GLS diversity relies on the presence of a complex epistatic interaction network of different GLS 577

QTLs (Burow et al 2010) and the ability of a single gene elimination in a set genotypic 578

background to capture all the potential allelic combinations is very limited In addition a 579

reduction of about half of the aliphatic GLS through single mutations in either the myb28 or 580

myb29 mutants (Francisco et al 2016) did not result in any large effects on the Gln-related traits 581

(Fig 6 Supplemental Table 5) However the elimination of all GLS transported to the seeds in 582

the gtr12 double mutant or removal of the aliphatic GLS in the myb2829 from the entire plant 583

had a profound effect on the composition of all FAAs and most prominently on Gln (Fig 6 584


20

Supplemental Table 5) These findings emphasize that the association between Gln and GLS 585

relies on a complete elimination of specific GLS in the seed This observation is further 586

supported by our statistical analysis of the association between levels of the Gln-related traits and 587

the presenceabsence of specific GLS in a natural population (Supplemental Table S3) More 588

importantly lack of FAA alteration in the stem and leaf measured from the double mutant clearly 589

showed that the association between GLS and Gln is seed specific and is not the cause of a 590

pleotropic effect that could arise from a lack of GLS in the mother plant or a direct interaction of 591

the MYB genes with any Gln-related pathway genes (Supplemental Table S6) In line with our 592

observation a study of the perturbation of aliphatic GLS biosynthesis in Arabidopsis showed 593

mild alteration in leaf FAA including free Gln in fact the study found that Gln levels in leaves 594

slightly decreased (Chen et al 2012) Interestingly our FAA analysis performed during early 595

seed maturation further indicated that the response of Gln to the lack of GLS especially 596

aliphatic occurs early (Fig 7 Supplemental Table 7) Overall this early seed-specific 597

interaction strongly suggests that both GLS and Gln have key functions in seed metabolic 598

homeostasis that are not manifested in the vegetative tissues Moreover it also demonstrates that 599

an mGWAS of FAA in dry seeds can reveal associations of biological processes taking place in 600

early development 601

602

The Association between Gln and GLS Is Likely Indirect and Induced by Alterations in the 603

Seed Metabolic Homeostasis 604

The molecular mechanism that underlies the interaction between GLS and Gln in the seeds is not 605

clear The Gln response appears to depend on the presenceabsence of aliphatic GLS that is 606

manifested in a specific tissue and is not dosage dependent This suggests that the interaction is 607

likely indirect and is potentially mediated through alteration of signalingsensing pathways or 608

other aspects of cell metabolism Consistently previous studies in Arabidopsis leaves have 609

shown that perturbation of the aliphatic GLS alter several proteins and metabolites involved in 610

various physiological processes including photosynthesis oxidative stress hormone 611

metabolism and specific amino acids (Chen et al 2012) It also has been shown in Arabidopsis 612

specific that indole GLS activation products can interact with the conserved TIR auxin receptor 613

to alter auxin sensitivity (Katz et al 2015) Furthermore exogenous application of a specific 614

aliphatic GLS (3ohp) causes an alteration in root meristem growth in an array of plant lineages 615


21

even those that have never been reported to produce GLS (Malinovsky et al 2017) These 616

authors have established that this response is due to the interaction between GLS and the TOR 617

pathway which is a key primary metabolic sensor that controls growth and development and is 618

conserved back to the last common eukaryotic ancestor (Henriques et al 2014) These findings 619

highlight the potential interactions of aliphatic GLS with primary metabolism and a conserved 620

sensing mechanism Consistent with these observations our data show that the presence of 621

specific GLS compounds has a significant effect on the levels of the Gln-related ratios 3ohp had 622

a negative effect on most of the Gln-related ratios whereas 4ohb had the opposite effect 623

(Supplementary Table S3) These two GLS may possibly interact with distinct conserved 624

metabolic regulatory pathways that affect Gln metabolism 625

Our data also indicate that the strong seed-specific association between the Gln-related 626

traits and GLS in the seeds lacking aliphatic GLS (ie myb2829 and gtr12) may be induced 627

due to substantial alteration in the overall cell metabolic homeostasis Our analysis of the carbon 628

nitrogen and sulfur contents of the two double mutants lacking aliphatic GLS in seeds support 629

this hypothesis The results show that carbon remains relatively stable whereas both the nitrogen 630

and sulfur homeostasis is severely altered total sulfur is dramatically decreased and nitrogen is 631

increased (Table 3) GLS are compounds rich in both nitrogen and sulfur which are present in 632

high levels in seeds It was previously suggested that GLS may function as a sulfur storage due 633

to the large induction of the GLS breakdown pathway during broccoli (Brassica oleracea var 634

italic) seed germination (Gao et al 2014) Gln is also known to increase upon both high nitrogen 635

availability and sulfur deficiency (Nikiforova et al 2005 Nikiforova et al 2006) A study of 636

sulfur starvation in Arabidopsis seedlings showed that plants convert the accumulated excess 637

nitrogen into nitrogenous compounds including Gln (reviewed in (Nikiforova et al 2006)) 638

Hence it is possible that the lack of stored sulfur in the form of GLS in seeds may lead to sulfur 639

deficiency in turn leading to an elevation in FAAs especially Gln It is worth mentioning that no 640

coherent pattern of alteration of the PBAA composition was observed in the myb2829 and the 641

gtr12 mutants as compared to the Col-0 ecotype indicating that the elevation in Gln is not due 642

to a lack of incorporation of Gln into SSP (Supplemental Table 8) The latter finding further 643

supports the conclusions that sulfur reduction is due mainly to GLS reduction and that the 644

interaction between the pathways is mediated through signalingsensing cascades that are 645

induced in response to the alterations to seed metabolic homeostasis 646


22

647

Conclusions 648

In this study we demonstrated that free glutamine in Arabidopsis seeds is strongly affected by 649

glucosinolate diversity and presence in this organ This finding clearly highlights that the 650

presence of specific secondary metabolites can profoundly affect primary metabolism in seeds 651

and that selected specialized metabolites may play a larger role in the metabolic homeostasis of 652

this tissue than originally believed Evolutionary theory predicts that the diversity and 653

composition of plant defense compounds such as the glucosinolates in the different plant tissues 654

reflect past selection pressures imposed on plants by their environment (Jones and Firn 1991) 655

pressures that are believed to be key driving forces of compound diversity and composition 656

(Benderoth et al 2006) Our study supports this claim and further suggests that the GLS effect 657

on core metabolism may have played a role in shaping its diversity and composition further 658

studies are needed to reveal the extent of this phenomenon and its implication for seed fitness 659

Our study also aligns with previous work that has shown that although defense mechanisms 660

such as GLS although evolutionarily more recent and often species- and taxa-specific have 661

established connections with conserved regulatorysignaling pathways involved in core 662

metabolism and other essential cellular processes The latter was suggested to be evolutionarily 663

advantageous in helping plants coordinate both defense metabolism and growth (Malinovsky et 664

al 2017) Finally this study demonstrates that performing a semi-combinatorial ratio based 665

mGWAS using metabolites measured in dry seeds can capture events occurring early in seed 666

development This finding has practical implications for future metabolic analyses since it is 667

easier to perform an mGWAS on dry seeds than on developing seeds 668

669

Materials and Methods 670

671

Plant growth and seed collection 672

All Arabidopsis (Arabidopsis thaliana) genotypes were grown at 22degC24degC (daynight) under 673

long-day conditions (16 h of light8 h of dark) Growth of the Arabidopsis diversity panel 674

(Nordborg et al 2005 Platt et al 2010 Horton et al 2012) was as described (Angelovici et al 675

2013) 676

677


23

Seed and tissue collection 678

Developing siliques were marked to track their developmental stage Siliques were harvested at 679

12 14 16 or 18 days after flowering (DAF) as well as from dry seeds flash frozen in liquid 680

nitrogen upon collection and stored at -80C Siliques were lyophilized and the seeds were 681

isolated and ground for the metabolic analysis 682

Sample leaf and stem tissues were collected from the same plants at approximately 20 683

days after bolting Only green tissue was collected Tissues were flash frozen in liquid nitrogen 684

upon collection and stored at -80C Tissues were lyophilized and ground for the metabolic 685

analysis 686

687

Isolation of T-DNA insertion mutants and genotypic characterization 688

The mutant lines SAIL_181_F06 (aop1) SALK_001655C (aop3) SALK_004536C (mam3) and 689

WiscDsLoxHs043_06G (bsu1) were obtained from the Arabidopsis Biological Resource Center 690

(httpsabrcosuedu) The SALK and WiscDsLoxHs043_06G insertions are in the Col-0 691

background and the SAIL_181_F06 mutant is in the Col-3 background Homozygous mutant 692

lines were validated by genomic PCR using gene-specific primers in combination with the T-693

DNA left border primer Primers spanning the full-length transcript were used to confirm lack of 694

transcripts for respective genes The list of primers can be found in Supplemental Table S4 695

The AOP2 overexpression line (Burow et al 2015) the myb28 and myb29 single 696

mutants the myb2829 and myb3451 knockout mutants (Sonderby et al 2010 Frerigmann and 697

Gigolashvili 2014) and the GSM1 mutant (Haughn et al 1991) were provided by Dr Dan 698

Kliebenstein with the University of California Davis The GLS transporter mutant gtr12 (Nour-699

Eldin et al 2012) was provided by Dr Hussam Hassan Nour-Eldin with Copenhagen 700

University 701

702

Transcript analysis 703

Total RNA extracted from dry and developing seeds was isolated using a hot borate method 704

(Birtic and Kranner 2006) and purified using Direct-zol RNA Miniprep Plus filter columns 705

(Zymo Research) Total RNA from leaves was extracted using the Direct-zol RNA Miniprep 706

Plus Kit (Zymo Research) First-strand cDNA was synthesized from 1 microg of purified total RNA 707

using the iScript cDNA Synthesis Kit (Bio-rad) RT-PCR was used to determine transcript levels 708


24

using the Dream Taq Green Master Mix (Thermo Fisher Scientific) with ACTIN2 (AT3G18780) 709

as a control (For primers see Supplemental Table S4) 710

711

Data analysis and mGWAS 712

mGWAS was performed using the genotypic data from the 250K single nucleotide 713

polymorphism (SNP) chip that was performed on the Arabidopsis diversity panel (Horton et al 714

2012) SNPs with a minor allele frequency (MAF) lt005 were removed leaving 214052 SNPs 715

for our association mapping The 14 derived ratios and glutamine absolute value and relative 716

composition were used as trait inputs The association tests were conducted in R 332 (Team 717

2014) using the R package Fixed and Random Model Circulating Probability Unification 718

(FarmCPU) (Liu et al 2016) The Bonferroni correction was used to control the experiment 719

wise type I error rate at 120572 = 001 720

721

Statistical analysis of the Gln-related trait levels in accessions harboring specific GLS 722

A subset of 133 accessions from the 313-accession population were grown in single replicates 723

and analyzed for FAA and GLS contents Accessions were grouped based on the presence or 724

absence of four GLS chemotypes 3ohp 2-propenyl 4ohb and 3-butenylOH-3-butenyl A t-test 725

was used to test for the presenceabsence of the group based on levels of Gln-related traits 726

Because sample sizes of some groups were small a 1000 permutations procedure was conducted 727

to determine statistical significance at 120572 = 005 (Churchill and Doerge 1994) 728

GO enrichment 729

For the candidate genes associated with the SNPs a GO enrichment analysis was performed 730

using agriGO (Zhou et al 2010) with the following parameters a hypergeometric test with a = 731

005 FDR correction (n = 3) an agriGO suggested background Arabidopsis as the select 732

organism and a complete GO ontology 733

734

Correlation analysis 735

A Spearmanrsquos rank correlation was used to calculate an r correlation matrix between all raw 736

absolute levels of FAA in the glutamate family after one round of outlier removal was performed 737

in R A p-value was calculated to reflect the significance of each correlation Results were 738

filtered using a r2 = 01 threshold and a p-value = 0001 Results were visualized with 739


25

Cystoscope (Shannon et al 2003) using the method previously described in (Batushansky et al 740

2016) 741

742

Haplotype analysis and pairwise LD analysis 743

Since the average LD in Arabidopsis is 10 kb (Kim et al 2007) the haploblock analysis was 744

performed on a 10-kb window where the 5 kb to the left and right of each significant SNP were 745

used as inputs The haploblock analysis was completed using Haploview version 42 (Barrett et 746

al 2004) Pairwise LD values (r2) were calculated between the significant SNP of interest and 747

neighboring (upstream and downstream) SNPs in a +-5 kb window All SNPs were filtered at a 748

5 MAF Default Gabriel block parameters were used resulting in blocks that contained at least 749

95 of the SNPs in strong LD Any genes contained or partially contained in the haploblock 750

with a significant SNP were saved as putative genes of interest If no haploblock was identified 751

for a respective SNP then the genes immediately upstream and downstream of the SNP were 752

saved 753

754

QTL analysis 755

A QTL analysis was conducted on the 158 RILs from the Bay x Sha population (Loudet et al 756

2002) in R 332 (Team 2014) using the Rqtl2 package (Broman et al 2019) Data were 757

previously quantified and described in Angelovici et al (2013) Publicly available genotype 758

markers spanned the five chromosomes for a total of 69 markers The mqmaugment function in R 759

was used to calculate genotype probabilities using a step value and an assumed genotyping error 760

rate of 0001 Missing values were replaced with the most probable values using the fillgeno 761

function unsupervised cofactor selection was completed through backward elimination 762

Genome-wide LOD significance thresholds were determined using 1000 permutations for each 763

trait For each QTL confidence intervals were determined by a 15 LOD drop from peak marker 764

Percent variance explained (PVE) was calculated using the following formula PVE = 1 - 10^(-765

(2n)LOD) where n is the sample size Epistatic interactions were explored using the effectplot 766

function 767

768

Metabolic analyses 769


26

Amino acid analysis Amino acids were analyzed from four biological replicates (n = 3ndash4) for 770

seed tissues and from five biological replicates (n = 5) for leaf and stem tissues The PBAAs 771

were extracted from ~3 mg of dry seed by performing acid hydrolysis (200 microl 6N HCl at 110degC 772

for 24 h) followed by the FAA extraction method described in (Yobi and Angelovici 2018) 773

FAAs were extracted with 1 mM of perfluoroheptanoic acid (PFHA) from ~6 mg tissue as 774

described previously (Yobi et al 2019) The analyses were performed using an ultra-775

performance liquid chromatography-tandem mass spectrometer (UPLC-MSMS) instrument 776

(Waters Corporation Milford MA) as detailed previously (Yobi and Angelovici 2018 Yobi et 777

al 2019) 778

GLS analysis GLS identification and quantification were completed using high-performance 779

liquid chromatography with diode-array detection (HPLCDAD) as previously described 780

previously (Kliebenstein et al 2001) 781

Nitrogen and carbon analyses Nitrogen and carbon levels were determined using an ECS 4010 782

CHNSO analyzer (Costech Analytical Technologies Inc) following the instructions in the 783

manufacturerrsquos manual Briefly ~2 mg tissue from five biological replicates (n = 5) were placed 784

in tin capsules (Costech Analytical Technologies Inc) and analyzed along with 2 mg of 25-bis-785

2-(5-tert-butylbenzoxazolyl)thiophene (BBOT Thermo Fisher Scientific) as an internal standard 786

Helium was used as a carrier gas and separation was performed on a GC column maintained at 787

110degC Detection was based on a TCD detector and quantification was carried out by plotting 788

against external standards for both molecules 789

Sulfur analysis Sulfur measurements were performed using the procedure described in Ziegler 790

et al (2013) Briefly ~50 mg of seed from six biological replicates (n = 6) were digested with a 791

concentrated HNO3 with an internal standard Seeds were soaked at room temperature overnight 792

and then incubated at 105degC for 2 h After cooling the samples were diluted and analyzed with 793

an Elan 6000 DRC (dynamic reaction cell)-e mass spectrometer (PerkinElmer SCIEX) connected 794

to a Perfluoroalkoxy (PFA) microflow nebulizer (Elemental Scientific) and Apex HF desolvator 795

(Elemental Scientific) as described in (Ziegler et al 2013) 796

797

Accession numbers 798

At4g03070 (AOP1) At4g03060 (AOP2) At4g03050 (AOP3) At5g23010 (MAM1) At5g23020 799

(MAM3) At4g03063 (BSU1) At5g61420 (MYB28) At5g07690 (MYB29) At3g47960 (GTR1) 800

At5g62680 (GTR2) AT1G18570 (MYB51) AT5G60890 (MYB34) 801


27

802

803

Supplemental Data 804

805

Supplemental Figure S1 Correlation analysis of the four Glu family FAAs 806

Supplemental Figure S2 Pairwise LD estimates (r2) of S127076 with SNPs spanning all the 807

GLS-related genes in the region 808



Supplemental Figure S4 Interaction plots from QTL associated with the GS-AOP and GS-811

ELONG loci showing epistatic interactions between markers MSAT443 and MSAT514 for 812

traits QP and QQP respectively 813

Supplemental Figure S5 AOP1 AOP3 MAM3 and BSU1 genomic structures and transcript 814

levels in tissues of high expression from the respective knockout mutants 815

Supplemental Figure S6 Heatmap of expression data for AOP1 AOP2 AOP3 MAM1 MAM3 816

and BSU1 across various Arabidopsis tissues and seed developmental stages 817

Supplemental Table S1 Mean relative content standard deviation relative standard deviation 818

range and broad-sense heritability of the Glu family and the Gln-related traits 819

Supplemental Table S2 List of all unique genes that are included in the haploblocks spanning 820

all the identified significant SNPs 821

Supplemental Table S3 Statistical analysis summary of the Gln-related levels from the 133 822

accessions grouped by GLS chemotypes 823

Supplemental Table S4 A list of primers used to test for the expression of the full transcript of 824

relevant genes involved in GLS biosynthesis in Arabidopsis 825

Supplemental Table S5 Summary of the fold changes (FC) in the average FAA and Gln-related 826

traits measured from the dry mutant seeds as compared to the control (Col-0) 827

Supplemental Table S6 Summary of the fold changes (FC) in the stem and leaf FAA average 828

levels measured from the myb2829 and gtr12 mutants as compared to the Col-0 829

Supplemental Table S7 Summary of the FAA measured from seeds harvested at five time 830

points during seed maturation in the myb2829 and gtr12 mutants and Col-0 ecotype 831


28

Supplemental Table S8 Summary of the fold changes (FC) in the protein-bound amino acid 832

(PBAA) absolute level averages (nmolmg) in myb2829 and gtr12 mutant dry seeds 833

Supplemental Dataset S1 mGWAS results summarizing all significant SNP-trait associations 834

identified at a 1 Bonferroni level from the 16 Gln-related traits 835

Supplemental Dataset S2 The full QTL analysis of the 16 Gln-related traits from the Bay x Sha 836

mapping population 837

Supplemental Dataset S3 Summary of Gln-related traits and GLS measurements from the dry 838

seeds in the 133-accession Arabidopsis panel 839

Supplemental Dataset S4 Summary of the seed FAA quantification from mutants of relevant 840

genes involved in the natural variation of aliphatic GLS in the Col-0 background 841

Supplemental Dataset S5 Summary of the FAA absolute level measurements from the leaf and 842

stem tissues of Arabidopsis myb2829 and gtr12 mutants and the Col-0 ecotype 843

Supplemental Dataset S6 Summary of the FAA measured from seeds harvested at five time 844

points during seed maturation in the myb2829 and gtr12 mutants and the Col-0 ecotype 845

Supplemental Dataset S7 Summary of the protein-bound amino acid (PBAA) absolute levels 846

(nmolmg) measured from the dry seeds of the myb2829 and gtr12 mutants 847

848

849


29

Tables 850

Table 1 Top five SNP-trait associations with the lowest p-values Traits SNP chromosomal position p-value relevant haploblock 851

coordinates the genes that contain significant SNPs or are within a haploblock containing a significant SNP and their annotation are 852

summarized for each SNP An asterisk () designates a gene containing the SNP If a SNP is intergenic and falls within a haploblock 853

with additional genes the additional genes are listed If the SNP is intergenic and does not fall within a haploblock the genes directly 854

upstream (L) and downstream (R) are recorded 855

856

SNP Trait Chr Position p-value Haploblock range Genes within

haploblock Functional annotation

S204486 QP 5 21544586 618E-15 None AT5G53135 transposable element

AT5G53140 protein phosphatase 2C family protein

S127076 QRP 4 1360042 617E-14 1356197-1364333 AT4G03063 Pseudogene of AT4G03070 AOP1 (2-

oxoglutarate-dependent dioxygenase 11)

QRQP AT4G03070 2-oxoglutarate (2OG) and Fe(II)-dependent

oxygenase superfamily protein (AOP1)

AT4G03080 BRI1 suppressor 1 (BSU1)-like 1

S124151 QR 4 152626 532E-13 152604-152640 AT4G00350 MATE efflux family protein

QRQ

S190878 QRP 5 15830557 522E-11 15829858-15830557 AT5G39530 (L) hypothetical protein (DUF1997)

AT5G39532 (R) pseudogene of Bifunctional inhibitorlipid-transfer

proteinseed storage 2S albumin superfamily

protein (computational description)

S175365 QP 5 7704845 379E-10 7703584-7705070 AT5G23010 methylthioalkylmalate synthase 1 (MAM1)

857

858

859


30

Table 2 QTL analysis of the (Gln)-related traits from the Bay x Sha mapping population Only QTL that span the GS-ELONG andor 860

GS-AOP region are shown For full analysis see Supplemental Dataset S2 Genotypic and phenotypic data from 158 recombinant 861

inbred lines were analyzed using the Rqtl2 package to identify significant QTLs An asterisk () indicates traits with significant SNP-862

trait associations in our GWAS 863

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance

GSL genes in supporting interval

Gene name Gene location

QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32

Table 3 Nitrogen carbon and sulfur absolute levels measured from the dry seeds of Arabidopsis myb2829 and gtr12 double 879

mutants and the Col-0 ecotype (n =5) The table lists the averages of the absolute levels the percentage of each absolute level in the 880

mutants relative to Col-0 the percentage of increase or decrease and the significance of the difference after using a Duncanrsquos Multiple 881

Range Test with different lower-case letters indicating significant differences at the = 005 level 882

883

Element Line Av Absolute levels (microgmg) of control Difference Duncan

Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893

Fig 1 Simplified metabolic pathways of the Glu amino acid family and the aliphatic GLS 894

Genes that are within the genomic region of GS-ELONG or GS-AOP loci are represented in red 895

and include MAM1 MAM2 and MAM3 as well as AOP2 and AOP3 These gene products are 896

responsible for most of the GLS natural diversity MAM1 is responsible for the production of C4 897

GLS 4-methylsulfinybutyl GLS (4msb) MAM2 (in the absence of MAM1) is required for the 898

production of C3 GLS 3-methylsulfinypropyl GLS (3msp) MAM3 is responsible for the 899

production of C8 GLS 8-methylsulfinyloctyl (8mso) C3 GLS 3msp can be further converted to 900

3-hydroxypropyl GLS (3ohp) by AOP3 or 2-propenyl by AOP2 C4 GLS 4msb can be converted 901

to 4-hydrozybutyl GLS (4ohb) by AOP3 or 3-butenyl and then OH-3-butenyl by AOP2 902

903

Fig 2 The chromosomal distribution of the 21 significant SNP-trait associations identified by 904

the mGWAS A total of 21 significant SNPs-trait associations were identified at an = 001 905

Bonferroni for six traits SNPs are represented by short lines that are color-coded based on their 906

P-value The histogram on top of the heatmap illustrates the number of occurrences of each SNP 907

identified across all traits Arrows indicate SNPs located within a gene or haploblock of interest 908

An asterisk () designates traits that have a significant association with a SNP in a GLS gene or 909

in high LD with GLS genes Q glutamine R arginine P proline 910

911

Fig 3 mGWAS of traits QRP and QRQ These two representative traits have significant 912

associations with SNPs in LD with genes AOP1 and AOP3 respectively A Scatterplots for 913

QRP (dark blue and black) and QRQ (light blue and grey) show significant associations among 914

multiple SNPs including S127076 and S127050 respectively (red) that reside in haploblocks 915

that contain GLS biosynthesis genes Negative log10-transformed p-values are plotted against 916

the genomic physical position The red line represents the 1 Bonferroni cutoff All SNPs above 917

the red line are significantly associated with other SNPs at that level B A graphical 918

representation of genes and haploblocks within the genomic region (Chr4 1340000ndash1375000 919

bp) spanning SNPs S127076 and S127050 (red arrows) This region also spans the GS-AOP 920

QTL S127050 falls within haploblock 2 which spans AOP3 S127076 falls within haploblock 5 921

which spans BSU1 and AOP1 Genes are represented by wide grey arrow unless they are 922


34

associated with GLS biosynthesis and marked in red Haploblocks in the region are represented 923

by numbered boxes and shaded grey if they contain a SNP of interest 924

925

Fig 4 mGWAS of QP A A scatterplot for QP shows the significant associations among 926

several SNPs including S175365 (marked in red) Negative log10-transformed p-values are 927

plotted against the genomic physical position The red line represents the 1 Bonferroni cutoff 928

All SNPs above the red line are significantly associated with SNPs at that level B A graphical 929

representation of genes and haploblocks within the genomic region spanning SNP S175365 (red 930

arrow) and GLS genes in close proximity (Chr47695000ndash7725000 bp) This region spans the 931

GS-ELONG QTL Genes are represented by wide grey arrows unless they are associated with 932

GLS biosynthesis and marked in red Haploblocks in the region are represented by numbered 933

boxes and shaded grey if they contain a SNP of interest 934

935

Fig 5 Heatmap of the fold changes of FAA and Gln-related traits average in GLS null and OX 936

mutants and the Col-0 ecotype Measurements were obtained from dry seeds and used to 937

calculate the log2 Fold Change (FC) with respect to the Col-0 ecotype for each FAA (A) and 938

each Gln-related trait (B) Blue indicates that the FAA or Gln-related trait decreased relative to 939

Col-0 whereas red indicates that the FAA or Gln-related trait increased relative to Col-0 A t-test 940

was performed to determine the significance of the changes between each mutant and Col-0 (n = 941

3ndash4) Asterisks () represent significant difference between the mutant and the control at a = 942

005 level Q glutamine E glutamate R arginine P proline 943

944

945

Fig 6 Heatmap of the fold changes of FAA and Gln-related traits average in the GLS single and 946

double knockout mutants and the Col-0 ecotype A and B Measurements were obtained from 947

dry seeds and used to calculate the average log2 fold change (FC) with respect to the Col-0 948

ecotype for each FAA (A) and each Gln-related trait (B) Blue indicates that the FAA or Gln-949

related trait decreased relative to Col-0 whereas red indicates that the FAA or Gln-related trait 950

increased relative to Col-0 C A heatmap of the FAA composition of each amino acid ( 951

FAATotal AA) calculated per genotype using the FAA measurements from seeds Red indicates 952

that the amino acid represents a higher percentage of the total composition relative to Col-0 953


35

whereas yellow indicates that the amino acid represents a lower percentage of the total 954

composition relative to Col-0 Asterisks () indicate a significant difference between the mutant 955

and the Col-0 as deduced by t-test at an = 005 level (n = 3ndash4) Q glutamine E glutamate R 956

arginine P proline 957

958

Fig 7 Gln levels and the relative composition of free amino acids across maturation in the GLS 959

double knockout mutants (myb2829 grt12) and the Col-0 ecotype Seeds were harvested at 12 960

14 16 and 18 days after flowering (DAF) and at full maturation (dry seed) and FAA levels and 961

composition were analyzed across these developmental time points A Gln levels (nmolmg) 962

across seed maturation in Col-0 B Gln levels in the double mutants C Composition analysis of 963

the 20 FAAs across the developmental time-points for the three genotypes Relative composition 964

is presented as of each FAA to TFAA in the seed TFAA represents a sum of the 20 FAA 965

measurements Red indicates that the amino acid represents a higher percentage of the total 966

composition relative to Col-0 whereas yellow indicates that the amino acid represents a lower 967

percentage of the total composition relative to Col-0 Asterisks () indicate a significant 968

difference between the mutant and Col-0 as deduced by t-test at an = 005 level (n = 4 except 969

for 18 DAF which is n = 2 for gtr12) 970

971

972

Acknowledgments 973

The authors wish to acknowledge Melody Kroll for assistance with editing the manuscript and 974

Ivan Baxter and Greg Ziegler for sulfur analysis 975

976

Disclosure 977

Authors have no conflict of interest to declare 978

979

980

981

982

983


36

984

Literature cited 985

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Angelovici R Lipka AE Deason N Gonzalez-Jorge S Lin H Cepela J Buell R Gore MA 989 Dellapenna D (2013) Genome-wide analysis of branched-chain amino acid levels in Arabidopsis 990 seeds Plant Cell 25 4827-4843 991

Atwell S Huang YS Vilhjalmsson BJ Willems G Horton M Li Y Meng D Platt A Tarone AM 992 Hu TT (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred 993 lines Nature 465 994

Barrett JC Fry B Maller J Daly MJ (2004) Haploview analysis and visualization of LD and 995 haplotype maps Bioinformatics 21 263-265 996

Batushansky A Toubiana D Fait A (2016) Correlation-based network generation visualization and 997 analysis as a powerful tool in biological studies a case study in cancer cell metabolism Biomed 998 Res Int 2016 1-9 999

Baud S Boutin JP Miquel M Lepiniec L Rochat C (2002) An integrated overview of seed 1000 development in Arabidopsis thaliana ecotype WS Plant Physiology and Biochemistry 40 151-1001 160 1002

Benderoth M Textor S Windsor AJ Mitchell-Olds T Gershenzon J Kroymann J (2006) Positive 1003 selection driving diversification in plant secondary metabolism Proceedings of the National 1004 Academy of Sciences of the United States of America 103 9118-9123 1005

Besnard J Pratelli R Zhao C Sonawala U Collakova E Pilot G Okumoto S (2016) UMAMIT14 is 1006 an amino acid exporter involved in phloem unloading in Arabidopsis roots J Exp Bot 67 6385-1007 6397 1008

Broman KW Gatti DM Simecek P Furlotte NA Prins P Sen Ś Yandell BS Churchill GA (2019) 1009 Rqtl2 Software for mapping quantitative trait loci with high-dimensional data and multiparent 1010 populations Genetics 211 495-502 1011

Burow M Atwell S Francisco M Kerwin RE Halkier BA Kliebenstein DJ (2015) The glucosinolate 1012 biosynthetic gene AOP2 mediates feed-back regulation of jasmonic acid signaling in Arabidopsis 1013 Molecular plant 8 1201-1212 1014

Burow M Atwell S Francisco M Kerwin RE Halkier BA Kliebenstein DJ (2015) The 1015 Glucosinolate Biosynthetic Gene AOP2 Mediates Feed-back Regulation of Jasmonic Acid 1016 Signaling in Arabidopsis Mol Plant 8 1201-1212 1017

Burow M Halkier BA Kliebenstein DJ (2010) Regulatory networks of glucosinolates shape 1018 Arabidopsis thaliana fitness Curr Opin Plant Biol 13 348-353 1019

Chan EK Rowe HC Corwin JA Joseph B Kliebenstein DJ (2011) Combining genome-wide 1020 association mapping and transcriptional networks to identify novel genes controlling 1021 glucosinolates in Arabidopsis thaliana PLoS Biol 9 1022

Chan EK Rowe HC Corwin JA Joseph B Kliebenstein DJ (2011) Combining genome-wide 1023 association mapping and transcriptional networks to identify novel genes controlling 1024 glucosinolates in Arabidopsis thaliana PLoS Biol 9 e1001125 1025

Chen W Gao Y Xie W Gong L Lu K Wang W Li Y Liu X Zhang H Dong H Zhang W Zhang 1026 L Yu S Wang G Lian X Luo J (2014) Genome-wide association analyses provide genetic and 1027 biochemical insights into natural variation in rice metabolism Nat Genet 46 714-721 1028

Chen YZ Pang QY He Y Zhu N Branstrom I Yan XF Chen S (2012) Proteomics and 1029 metabolomics of Arabidopsis responses to perturbation of glucosinolate biosynthesis Mol Plant 1030 5 1138-1150 1031


37

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Velasco P Soengas P Vilar M Cartea ME del Rio M (2008) Comparison of glucosinolate profiles in 1165 leaf and seed tissues of different Brassica napus crops Journal of the American Society for 1166 Horticultural Science 133 551-558 1167

Verslues PE Lasky JR Juenger TE Liu TW Kumar MN (2014) Genome-wide association mapping 1168 combined with reverse genetics identifies new effectors of low water potential-induced proline 1169 accumulation in Arabidopsis Plant Physiol 164 144-159 1170

Wen W Li D Li X Gao Y Li W Li H Liu J Liu H Chen W Luo J Yan J (2014) Metabolome-1171 based genome-wide association study of maize kernel leads to novel biochemical insights Nat 1172 Commun 5 3438 1173

Wentzell AM Rowe HC Hansen BG Ticconi C Halkier BA Kliebenstein DJ (2007) Linking 1174 metabolic QTLs with network and cis-eQTLs controlling biosynthetic pathways PLoS Genet 3 1175 1687-1701 1176

Winter D Vinegar B Nahal H Ammar R Wilson GV Provart NJ (2007) An Electronic Fluorescent 1177 Pictograph browser for exploring and analyzing large-scale biological data sets PLoS One 2 1178 e718 1179

Yobi A Angelovici R (2018) A High-throughput absolute-level quantification of protein-bound amino 1180 acids in seeds Curr Protoc Plant Biol e20084 1181


40

Yobi A Batushansky A Oliver MJ Angelovici R (2019) Adaptive responses of amino acid metabolism 1182 to the combination of desiccation and low nitrogen availability in Sporobolus stapfianus Planta 1183 249 1535-1549 1184

Zhang L Garneau MG Majumdar R Grant J Tegeder M (2015) Improvement of pea biomass and 1185 seed productivity by simultaneous increase of phloem and embryo loading with amino acids 1186 Plant J 81 134-146 1187

Zhang L Tan Q Lee R Trethewy A Lee YH Tegeder M (2010) Altered xylem-phloem transfer of 1188 amino acids affects metabolism and leads to increased seed yield and oil content in Arabidopsis 1189 Plant Cell 22 3603-3620 1190

Ziegler G Terauchi A Becker A Armstrong P Hudson K Baxter I (2013) Ionomic Screening of 1191 Field-Grown Soybean Identifies Mutants with Altered Seed Elemental Composition Plant 1192 Genome 6 1193

1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10

Absolute CompositionC

AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B

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Verslues PE Lasky JR Juenger TE Liu TW Kumar MN (2014) Genome-wide association mapping combined with reverse geneticsidentifies new effectors of low water potential-induced proline accumulation in Arabidopsis Plant Physiol 164 144-159


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Wentzell AM Rowe HC Hansen BG Ticconi C Halkier BA Kliebenstein DJ (2007) Linking metabolic QTLs with network and cis-eQTLscontrolling biosynthetic pathways PLoS Genet 3 1687-1701


Winter D Vinegar B Nahal H Ammar R Wilson GV Provart NJ (2007) An Electronic Fluorescent Pictograph browser for exploringand analyzing large-scale biological data sets PLoS One 2 e718


Yobi A Angelovici R (2018) A High-throughput absolute-level quantification of protein-bound amino acids in seeds Curr Protoc PlantBiol e20084


Yobi A Batushansky A Oliver MJ Angelovici R (2019) Adaptive responses of amino acid metabolism to the combination of desiccationand low nitrogen availability in Sporobolus stapfianus Planta 249 1535-1549


Zhang L Garneau MG Majumdar R Grant J Tegeder M (2015) Improvement of pea biomass and seed productivity by simultaneousincrease of phloem and embryo loading with amino acids Plant J 81 134-146


Zhang L Tan Q Lee R Trethewy A Lee YH Tegeder M (2010) Altered xylem-phloem transfer of amino acids affects metabolism andleads to increased seed yield and oil content in Arabidopsis Plant Cell 22 3603-3620


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Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

2

2Department of Plant Sciences UC Davis Davis CA 95616 USA 47 3Department of Crop Sciences University of Illinois Urbana IL 61801 USA 48 4DynaMo Center Copenhagen Plant Science Centre Department of Plant and Environmental 49

Sciences University of Copenhagen Frederiksberg Denmark 50 daggerCurrent address Department of Biology University of Missouri Saint Louis MO 63121 USA 51

52

53

Author contributions 54

MS performed the experiments wrote the manuscript and processed and analyzed data AY wrote the 55

manuscript and carried out metabolic analysis CB carried out genotyping experiments YC analyzed data 56

VS analyzed data SH carried out genotyping and metabolic analysis EK performed GLS measurements 57

CK peformed initial gtr12 experiment AL verified analytical methods and assisted with statistical aid H 58

N-E provided gtr12 mutants and initial analysis DK provided all the GLS mutants and GLS related 59

measurements from the population RA conceived the experimental design supervised the work provided 60

funding and wrote the manuscript All authors have reviewed the final version of the manuscript and 61

approved it and therefore are equally responsible for the integrity and accuracy of its content 62

63

Funding information 64 This work was funded by the NSF-IOS 1754201 to Ruthie Angelovici and by Danish National 65

Research Foundation grant DNRF99 to BAH and HHN-E 66

One-sentence summary mGWAS of Gln-related traits reveals an unexpected seed-specific 67

interaction between glutamine and glucosinolates and its potential role in shaping the metabolic 68

homeostasis in Arabidopsis seeds 69

70

71


3

Abstract 72




















92

93


4

Introduction 94

95










al 2009) 105





















5
















panels or both 140

















6



















174

175

Results 176

177











7














members 200

201


















8



heritability 220

















237












9









Table S2B) 256
























10














2 = 0649) 291






297


Finding 299











11



















327














12











350






















13



























397






14

























S5B) 426








15



























459

460

461

462


16

463


gtr12 Mutants 465





























17



495













508

Discussion 509















18









associations 531

532























19















approaches 568

569

















20


















602















21

































22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

3

Abstract 72




















92

93


4

Introduction 94

95










al 2009) 105





















5
















panels or both 140

















6



















174

175

Results 176

177











7














members 200

201


















8



heritability 220

















237












9









Table S2B) 256
























10














2 = 0649) 291






297


Finding 299











11



















327














12











350






















13



























397






14

























S5B) 426








15



























459

460

461

462


16

463


gtr12 Mutants 465





























17



495













508

Discussion 509















18









associations 531

532























19















approaches 568

569

















20


















602















21

































22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

4

Introduction 94

95










al 2009) 105





















5
















panels or both 140

















6



















174

175

Results 176

177











7














members 200

201


















8



heritability 220

















237












9









Table S2B) 256
























10














2 = 0649) 291






297


Finding 299











11



















327














12











350






















13



























397






14

























S5B) 426








15



























459

460

461

462


16

463


gtr12 Mutants 465





























17



495













508

Discussion 509















18









associations 531

532























19















approaches 568

569

















20


















602















21

































22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

5
















panels or both 140

















6



















174

175

Results 176

177











7














members 200

201


















8



heritability 220

















237












9









Table S2B) 256
























10














2 = 0649) 291






297


Finding 299











11



















327














12











350






















13



























397






14

























S5B) 426








15



























459

460

461

462


16

463


gtr12 Mutants 465





























17



495













508

Discussion 509















18









associations 531

532























19















approaches 568

569

















20


















602















21

































22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

6



















174

175

Results 176

177











7














members 200

201


















8



heritability 220

















237












9









Table S2B) 256
























10














2 = 0649) 291






297


Finding 299











11



















327














12











350






















13



























397






14

























S5B) 426








15



























459

460

461

462


16

463


gtr12 Mutants 465





























17



495













508

Discussion 509















18









associations 531

532























19















approaches 568

569

















20


















602















21

































22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

7














members 200

201


















8



heritability 220

















237












9









Table S2B) 256
























10














2 = 0649) 291






297


Finding 299











11



















327














12











350






















13



























397






14

























S5B) 426








15



























459

460

461

462


16

463


gtr12 Mutants 465





























17



495













508

Discussion 509















18









associations 531

532























19















approaches 568

569

















20


















602















21

































22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

8



heritability 220

















237












9









Table S2B) 256
























10














2 = 0649) 291






297


Finding 299











11



















327














12











350






















13



























397






14

























S5B) 426








15



























459

460

461

462


16

463


gtr12 Mutants 465





























17



495













508

Discussion 509















18









associations 531

532























19















approaches 568

569

















20


















602















21

































22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

9









Table S2B) 256
























10














2 = 0649) 291






297


Finding 299











11



















327














12











350






















13



























397






14

























S5B) 426








15



























459

460

461

462


16

463


gtr12 Mutants 465





























17



495













508

Discussion 509















18









associations 531

532























19















approaches 568

569

















20


















602















21

































22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

10














2 = 0649) 291






297


Finding 299











11



















327














12











350






















13



























397






14

























S5B) 426








15



























459

460

461

462


16

463


gtr12 Mutants 465





























17



495













508

Discussion 509















18









associations 531

532























19















approaches 568

569

















20


















602















21

































22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

11



















327














12











350






















13



























397






14

























S5B) 426








15



























459

460

461

462


16

463


gtr12 Mutants 465





























17



495













508

Discussion 509















18









associations 531

532























19















approaches 568

569

















20


















602















21

































22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

12











350






















13



























397






14

























S5B) 426








15



























459

460

461

462


16

463


gtr12 Mutants 465





























17



495













508

Discussion 509















18









associations 531

532























19















approaches 568

569

















20


















602















21

































22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

13



























397






14

























S5B) 426








15



























459

460

461

462


16

463


gtr12 Mutants 465





























17



495













508

Discussion 509















18









associations 531

532























19















approaches 568

569

















20


















602















21

































22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

14

























S5B) 426








15



























459

460

461

462


16

463


gtr12 Mutants 465





























17



495













508

Discussion 509















18









associations 531

532























19















approaches 568

569

















20


















602















21

































22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

15



























459

460

461

462


16

463


gtr12 Mutants 465





























17



495













508

Discussion 509















18









associations 531

532























19















approaches 568

569

















20


















602















21

































22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

16

463


gtr12 Mutants 465





























17



495













508

Discussion 509















18









associations 531

532























19















approaches 568

569

















20


















602















21

































22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

17



495













508

Discussion 509















18









associations 531

532























19















approaches 568

569

















20


















602















21

































22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

18









associations 531

532























19















approaches 568

569

















20


















602















21

































22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

19















approaches 568

569

















20


















602















21

































22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

20


















602















21

































22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

21

































22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

22

647

Conclusions 648





















669


671





2013) 676

677


23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

23









analysis 686

687














University 701

702








24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

24



711










721








GO enrichment 729





734







25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

25


2016) 741

742











saved 753

754

QTL analysis 755












function 767

768



26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

26









al 2019) 778



















797






27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

27

802

803


805




























28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

28

















848

849


29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

29

Tables 850






856











QRQ






857

858

859


30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

30





Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QRQ 5 MSAT514 266 7499 177-454 467-1396 349 967

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRQP 5 MSAT514 266 7499 177-418 467-1211 782 2038

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QR 5 MSAT514 266 7499 177-454 467-1396 280 784

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QRP 5 MSAT514 266 7499 177-418 467-1211 597 1597

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

864

865

866

867

868

869


31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

31

Continued 870

Trait Chr Marker

name

Marker

position

(cM)

Marker

position (Mbp)

Suporting

interval (cM)

Supporting

interval (Mbp)

Log of

the odds

Phenotypic

variance



QQP

4 MSAT443 107 2576 2-242 041-755 397 1093

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

AT4G12030 7210807-7213376

5 MSAT514 266 7499 177-418 467-1211 1579 3689

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

QP

4 MSAT443 107 2576 2-158 041-563 588 1575

AT4G03050 (AOP3) 1343845-1346436

AT4G03060 (AOP2) 1351688-1354096

AT4G03063 (AOP1) 1355667-1356018

AT4G03070 (AOP1) 1358267-1359698

5 MSAT514 266 7499 177-418 467-1211 1210 2972

AT5G23010 (MAM1) 7703041-7706973

MAM2

AT5G23020 (MAM3) 7718118-7721866

AT5G26000 9079452-9082384

871

872

873

874

875

876

877

878


32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

32





883


Nitrogen

Col-0 3415 plusmn 032 100 0 b

myb2829 3694 plusmn 048 10817 817 a

gtr12 3918 plusmn 019 11473 1473 a

Carbon

Col-0 52514 plusmn 416 100 0 a

myb2829 5191 plusmn 518 9885 -115 a

gtr12 50876 plusmn 294 9688 -312 a

Sulfur

Col-0 537 plusmn 003 100 0 a

myb2829 115 plusmn 001 2143 -7857 b

gtr12 054 plusmn 002 996 -9004 c

884

885

886

887

888

889

890

891

892


33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

33

Figure legends 893










903








911













34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

34



925










935









944

945










35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

35





958













971

972

Acknowledgments 973



976

Disclosure 977


979

980

981

982

983


36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

36

984



















37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

37





















38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

38





















39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

39



















40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

40





1194

1195

1196

1197


1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

1

GlutamateGlutamine

Arginine Proline

Aspartate

Threonine

IsoleucineSO2

Methionine

Cysteine

Serine

MAM2

3msp

3ohp 2-propenyl

AOP2AOP3

4msb

4ohb 3-butenyl

AOP2AOP3

OH-3-butenyl

MAM1MAM3

8mso

Glutamate family

Aliphatic GLS

Fig 1

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

AOP1BSU-1

AOP3 MAM1

Trai

t

QP

QR

QQP

QRP

QRQ

QRQP

Chromosome Position

1 52 3 4

351E-03

176E-03

618E-10

P-value

SNP

Cou

nt

12

Fig 2

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

A

BAT4G03050AOP3

AT4G03100

AT4G03040 AT4G03060AOP2

AT4G03080BSU1

AT4G03070AOP1

AT4G03063pseudoAOP1

SNP127076SNP127050

1340K

1375K

1350K

1360K

21 4 5 6

3Chr 4

10

6

2

1 2 3 40

4

8

12

14

-log10(P-value)

Chromosome5

SNP127076

SNP127050

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

A

B

Chr 5

7695K

7705K

7725K

7715K

1 2 3 4 5 6 97 8

AM180571MAM2

AT5G23000

AT5G23020MAM3

AT5G23010MAM1 SNP175365

1 2 3 4 50

4

8

12

16

-log10(P-value)

Chromosome

SNP175365

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0

-1

1log2(FC)

Ratios FCA B

AlaAsnAspGly

Ser

His

Total

IleLeuLysMet

TyrThr

ValCys

Phe

Trp

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

2log2(FC)

0

-2

GlnArgGluPro

Absolute FC

aop1

AOP2

OXao

p3gsm1

mam

3bsu1

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

AlaAsn

Gly

PheSerTrp

HisIle

LeuLys

Met

Thr

Val

Asp

Tyr

Cys

Gln

GluPro

Arg

A B

myb28

29

gtr12

myb29

myb28

myb34

51

QRPQQEQQP

QR

QQEP

QEQP

QRQQRE

QRQEQEP

QRQPQREP

QTotalQQREP

0-2

8log2FC)

AA Ratios

4

myb28

29

gtr12

Col-0

60FAATotal AA

0

30

10


AlaAsn

Gly

PheSerTrp

His

Total

IleLeuLys

Met

Thr

Val

Asp

Tyr

Cys

myb28

29

gtr12

myb29

myb28

myb34

51

10log2(FC)

0-2

Gln

GluPro

Arg

6

2

Absolute AA

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

C12 14 16 18 Dry 12 14 16 18 Dry

Ala

AsnAsp

Gly

Phe

Ser

Trp

HisIle

LeuLys

Met

TyrThr

Val

Cys

12 14 16 18 Dry

65FAATFAA

0

30

Gln

Arg

GluPro

FAA Composition

myb2829 gtr12 Col-0

DAF

FAA

12 14 16 18 Dry

0

4Col-0

2100

150

50

myb 2829

gtr12

12 14 16 18 Dry

DAF

Gln

cont

ent (

nmol

mg)

A B





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations





















































































































































Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Parsed Citations

mGWAS Uncovers Gln-Glucosinolate Seed-Specific Interaction ... · 2 47 2Department of Plant...

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Transcript of mGWAS Uncovers Gln-Glucosinolate Seed-Specific Interaction ... · 2 47 2Department of Plant...