From Genes to Twinkies - USDA ARS · 2007 Evaluation of 192 cultivars. Ohio, Indiana, ... Glucose,...
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From Genes to Twinkies
Transcript of From Genes to Twinkies - USDA ARS · 2007 Evaluation of 192 cultivars. Ohio, Indiana, ... Glucose,...
From Genes to Twinkies
Mapping milling and flour traits in soft wheat Edward Souza, USDA-ARS and Clay Sneller, Ohio State University
Review of work with mapping populationsFunding: NRI Wheat CAP – Eastern US Wheat ResearchersWooster – M. Guttieri, D. Hua
Association mapping populationsFunding: OSU, USDA-ARS w/ VA Tech, Cornell, Purdue, U. KyWooster – N. Smith, A. Sturbaum, M. Guttieri, D. Hua, A. Bugaj, S. Carson, S. CroskeyCollaborators – C. Griffey, M. Sorrells, H. Ohm, D. Van Sanford
Genes of Interest – Arabinoxylan compositionFunding: USDA-ARS with Kraft FoodsWooster – M. Guttieri, A. Bugaj
Populations & PhenotypingPedigree Envs done Envs to do Samples
doneSamples to do
Total
1 Foster/Kanqueen NY05, NY06, OH06
NY07 720 240 960
2 SS 550/PIO 26R46 OH02, OH03, OH03, OH04
GA08, GA08
600 300 900
3 MO94-317/Ernie None None 0
4 Jaypee/USG 3209 @VA05, @NC05, VA06
VA07, KY07
650 300 950
5 Foster/PIO 25R26 OH05, OH06, NY06, OH07
OH08 720 180 900
6 92201/91193 NY05, IN05, OH05
IN07 600 200 800
7 Cayuga/Caledonia NY05, NY06*NY03, *NY04
NY08 310 155 465
@, 109 of 130 lines in pop were phenotyped*, only did sodium carbonate on whole grain
77.0
76.0
75.0
74.0
73.0
72.0
71.0
70.0
69.0
68.0
67.0
66.0
65.0
64.0
F/K S/P26R46 J/U F/P25R26 9/9 C/C = Population code3 4 3 4 3 1 = # Environments
Flou
r Yie
ld (
%)
*
*
*
*
*
Parent RangeRIL Range1st QTL2nd QTL
* Range significantlyexceeds parental range
R2= 29%
13%
Effect = | 2a |
14%
13%
2B1B
2A1A
1B2D
4D3A
1B1A
*
*
16%
11%
14%
7%
13%
12%
Presenter
Presentation Notes
Some have large effects that would be useful to breeders. Example, a QTL where efect is ~ 1.5% for FL YLD would be quite important if it proves to be real and transportable across populations.
Chromosome 1B and known genes which segregate in cross
SEH2OPentosanSt. Dam.Fl YLD
Fos/Kanqueen SS/P26R46 Purdue 9/9 Cay/Cal Fos/P25R26 Jaypee/USG
H2OPentosanSt. Dam.Fl YLD
Gl. Str.H2OPentosanSt. Dam.Fl YLD
Gl. Str.H2OPentosanSt. Dam.Fl YLD
H2OPentosanSt. Dam.Fl YLD
PROSETW
1B/1R7+9/13+16
1B/1R Glu-B1?
No rye7/7+9
No ryeNo Glu-B1
Gl. Str.
Gl. Str.PROH2OPentosanSt. Dam.Fl YLD
Gl. Str.H2OPent.St. Dam.Fl YLD
1B/1RBy9/Bx7oe+By8
1B/1RNo GluB1
H2OPentosanSt. Dam.Fl YLDGl. Str.SE
Presenter
Presentation Notes
Note colinearity of effects near Glu-B1. Likely these are from Glu-B1 once we get maps cleaned up and more markers added (especially Glu0-B1 itself) Not unexpected for Gluten strength. But note effect of region on other traits. Fyld in 3/5. Some large effects on H2O, NACO. Note that 9/9 does NOT seg for Glu-B1 alleles, but large effects on water complex traits Region needs more analysis, tweak apart the effects
R2 of QTLs affecting water absorption- flour yield complex
0
5
10
15
20
25
30
1 2 3 4 5 6 7 8
St. Dam.H2OPentosansFl. YLD
0
5
10
15
20
25
30
9 10 11 12 13 14 15 16
St. Dam.H2OPentosansFl. YLD
Presenter
Presentation Notes
R2 values of QTL with a sig (or nearly so) effect on 1 of the four correlated traits (H2O, SUC, NACO, FYLD). The top row of QTL charts are for QTL where NACO had the largest R2 value. For these NACO-dominated QTL, there nearly always a sig effect on one or more of the other 3 traits. A QTL for NACO seemed to always be accompanied by an H2O QTL. The second row of charts are for QTL where one of the other traits had the largest R2 value. Here there are some QTL where it appears just 1 trait affected. In particular, there seems to be several QTL where FYLD is independent of the others. Note there are several where H2O and NACO appear independent, suggesting that the water absorption is affected by a trait other than starch damage.
Ample heritable variation in many soft wheat populationsTransgressive segregants are commonComplex inheritance despite some major genes
Transgressive segregantsMany QTLsMuch of progeny range is not accounted for by QTL analysis
Some consistent effects: HMW glutenins, 2B, others Non-independence of some effects
HMW GluteninsStarch damage and other
Some genetic effects for SRC are large enough for MASLactic acid: 10%, Water: 2%, Na2CO3: 5%, Flour Yield: 1.5%
Conclusions
Association Mapping of Quality in Eastern US Soft Winter Wheat
2007 Evaluation of 192 cultivarsOhio, Indiana, Virginia, New York, Kentucky, and N. Carolina
Association Mapping (AM Study)
Genes that are linked and enter the germplasm pool from the same source will remain linked through cycles of breeding
Mapping across a large number cultivars can identify markers of value in a wide range of breeding programs
Validation of bi-parental mapping populations of Wheat CAP
Composition of the AM StudySource State # Entries Release date range Region
ONT, MI, NY 35 1881 - 2001 North
IN, OH 72 1808 - 2005 Eastern Corn-belt
IL, KS, WI 11 1881 - 2001 Western Corn-belt
VA, NC, MD, PA 28 1837 - 2002 Mid-Atlantic
MO, KY, TN 9 1837 - 2002 Central
GA, SC, FL 23 1881 - 2001 South East
AR, LA, TX 15 1881 - 2003 Delta
Presenter
Presentation Notes
The composition initially based on cultivars present in the Big Green Book and designed to reflect historical development and area of production. Ohio and Indiana favored in the composition as largest wheat growing states. Relative composition decreases from Ohio south and Ohio west. In terms of importance to the SRW production and breeding history, Western Corn-belt is under-represented. However many of the cultivars in other regions overlap with cultivars in these states.
Composition of the AM Study
Release period # EntriesBefore 1900 121900-1949 201950-1969 161970s 281980s 371990s 532000s 27
Presenter
Presentation Notes
The composition initially based on cultivars present in the Big Green Book and designed to reflect historical development and area of production. Ohio and Indiana favored in the composition as largest wheat growing states. Relative composition decreases from Ohio south and Ohio west. In terms of importance to the SRW production and breeding history, Western Corn-belt is under-represented. However many of the cultivars in other regions overlap with cultivars in these states.
Planned Evaluation in 2007 and 2008Quad advanced milling
Four solvent SRC from all locationsCookie bake from 3 locations in 2007 and 2008
Quality Data at Core of New DatabaseSupplement Allis DatabaseCover new cultivars more quicklyInclude more intensive evaluation of samples from other regions – both breeding and extension trials
AM Study 2007 Quad Advanced Flour Yield with Allis Database Straight Grade Flour Yield
y = 0.47x + 44.1R2 = 0.40
74
75
76
77
78
79
80
81
66 67 68 69 70 71 72 73 74 75 76 77
Quad advanced flour yield (%)
Allis
flou
r yie
ld (%
)
AM Study 2007 Quad Advanced Softness Equivalent with Allis Database Break Flour Yield
y = 0.74x - 9.56R2 = 0.56
20
25
30
35
40
45
45 50 55 60 65 70
Softness equivalent (%)
Allis
bre
ak fl
our (
%)
Planned Evaluation in 2007 and 2008
Marker setsDArT analysis for frameworkQTL markers from bi-parental populationsFunctional gene markers, such as glutenins, from USDA-ARS Wooster and RaleighPurified seed production for subsequent mapping will be available later this summer.
Association Mapping Study Wooster and W. Lafayette, 2007 Mean Lactic Acid SRC (Gluten Strength)
1B/1RTranslocation
NoTranslocation
Glu-D1a(2+12)
100.0% 107.7%
Glu-D1d(5+10)
105.1% 117.1%
Presenter
Presentation Notes
The effect of the Glu D1 alleles and the 1B/1R translocations are similar to biparental mapping populations. The effects of the loci are largely additive, similar to bi-parental populations.
Association Mapping Study Wooster and W. Lafayette, 2007 Mean Water, Na2 CO3 , Sucrose SRC 1B QTL
WaterSRC
Na2 CO3
SRCSucrose
SRCLactic acid
SRC
By9 50.6% 65.4% 94.9% 107.9%
Non-By9 51.6% 66.7% 97.9% 110.7%
P-valuesignificance
0.01 0.02 0.01 No difference
Presenter
Presentation Notes
The glutenin By9 appears to be associated with the water/damage starch/pentosan QTL on Chromosome 1B that occurs in multiple bi-parental populations. The glutenin itself does not have a significant effect of glutenin as alternate alleles are either stronger or weaker.
Completion of AM Study
Additional locations for 2007 and 2008Add Quality QTL markers from Wheat CAP studyUse information for
Subsequent fine scale mappingCompositional differences associated with mapped variation…
Arabinoxylans
Compositional Analysis
Arabinoxylans – Pentosans J Delcour – Cereal Chem. 70:324 & J. Cereal Sci. 35:225
A A
[ X-X-…X] - [X] - [X] – X -…
A – [ ] – A -
1-4 xyloses
1-4 xylose, 2 or 3 arabinose
1-4 xylose, 2,3 arabinose
47 to 62%Xylose
28 to 34%arabinose
63-66%Un-substituted
13-21%mono-subst. 16-24%
di-substituted
Enzyme extractable arabinoxylans have more arabinofuranosylresidues than water soluble arabinoxylans.
Increasing the degree of mono- and di-substituted xylopranosyl residuesdecreases flour water absorption.
Ferulatedimer
Presenter
Presentation Notes
Increasing the A/X quotient or ratio should be good for soft wheat because it should reduce water absorption Articles have other first authors but J. Delcour is the principal scientist in the work.
Colorimetric methods
Based on xylose determinationMethodological problem:
Background absorbance caused by glucoseAssumption:
[Arabinoxylan] = C · [Xylose]
Compositional method
Developed in laboratory of Jan Delcour, (Katholieke Universiteit Leuven, Belgium)Trifluoroacetic acid hydrolysisAlditol acetate derivitizationGas chromatographic quantification
Arabinose, Xylose, Mannose, Galactose, Glucose, Allose (Internal Std.)
Minutes
5.0 5.5 6.0 6.5 7.0 7.5 8.0 8.5 9.0 9.5 10.0 10.5 11.0
Vol
t
0.000
0.025
0.050
0.075
0.100
0.125
0.150
0.175
0.200
0.225
0.250
0.275
Vol
t
0.000
0.025
0.050
0.075
0.100
0.125
0.150
0.175
0.200
0.225
0.250
0.275
Ara
bino
se
Xyl
ose
Allo
se
Man
nose
Gal
acto
se
Glu
cose
Detector 1WSP24
Name
ARA
XYL
MAN
GAL
GLU
Int. Std.
Water Extractable ArabinoxylansHopewell SRW – Wooster 2007
Presenter
Presentation Notes
Arabinose to xylose ratio in a soft wheat as detected on a GC with FID. Glucose is a contaminant from starch and galactose is a minor component of cell walls which is mainly in the form of Arabinogalactans.
Experimental Design
6 Wheat genotypes:Hopewell SRW, Caledonia Resel-L SWW, Richland SWW, E0028 SWW, E2017 SWW, NY92039-9065 SWW
2 Locations: Northwest Branch & WoosterMilled on Miag MultomatDuplicate bakes, chemical analyses
Wire Cut Cookie Spread Factor vs. Sucrose SRC
0.34
0.36
0.38
0.40
0.42
0.44
84 86 88 90 92 94 96
Sucrose SRC (%)
Spre
ad fa
ctor
(cm
/mm
)
Sucrose SRC vs WE-Xylose
y = 5.9097x + 75.449R2 = 0.6941
84
86
88
90
92
94
96
1.5 2 2.5 3 3.5
WE-Xylose (mg/g flour)
Sucr
ose
SRC
(%)
Presenter
Presentation Notes
Sucrose SRC is considered to be a predictor of penotsan. We found it to be correlated to water extractable xylose, which should predict water extractable arabinoxylan if the A/X ratio is constant.
Arabinose:Xylose Ratio
0
0.2
0.4
0.6
0.8
1
1.2
Hopewell E2017 E0028 Caled_R Richland NY9065
Northwest Wooster
Presenter
Presentation Notes
The assumption of constant arabinose to xylose ratio is not valid and in fact my obscure some of the GxE which we do find in soft wheat quality.
Wire Cut Spread Factor vs Water- Extractable Arabinoxylan + Arabinogalactan
y = -0.020x + 0.50R2 = 0.88
0.340.350.360.370.380.390.400.410.42
4.5 5 5.5 6 6.5 7 7.5 8
WE - AX + AG (mg/g flour)
Spre
ad fa
ctor
(cm
/mm
)
Presenter
Presentation Notes
Spread to height is tightly predicted by water extractable pentosans when all pentoses are factored. This may be
Relevant Questions for Mapping and Genetic Studies
Milling loci often seem to be loci that also affect sucrose SRC and Na2CO3 SRC
Or….
Arabinoxylan composition and degree of substitution affects sucrose SRC and milling yield, which in turn affects starch damage and Na2CO3 SRC?
Genes coding for synthesis and regulation of arabinoxylan are unknown in wheat
UDP-arabinosyl transferase and UDP-xylosyl transferase are hypothesized but uncharacterized.
Relevant Questions for Mapping and Genetic Studies
Association mapping population follow-upConduct AX composition studies Experimental design based on phenotypic and genotypic information
Positional cloning or gene expression studies may allow identification of genes controlling AX structureThese are the contrasting approaches that are under discussion for Wheat CAPII
![Lect 1 Sucrose [Compatibility Mode]](https://static.fdocuments.in/doc/165x107/577d230e1a28ab4e1e98dd7b/lect-1-sucrose-compatibility-mode.jpg)
