Fine mapping of stay-green QTLs on sorghum chromosome SBI-10L-An approach from Genome to Phenome
1
Abstract Sorghum is the fifth most important C 4 cereal crop grown globally in arid and semi-arid climatic conditions. Drought is the major cause for loss of productivity worldwide. Delayed senescence of plants leads to adaptation to drought stress conditions by staying-green and giving high yields. In order to identify and dissect the stay-green genomic regions we have developed a high resolution fine mapping population from introgression line cross RSG04008-6 (stay-green) × J2614-11 (shoot fly resistant). Nearly 1894 F 2 genotypes were screened with 8 SSR in order to identify double recombinants for both the parents in the sorghum chromosome-10 long arm (SBI-10L). The selected F 2:4 recombinants were GBSed to increase the marker density between flanking markers Xgap001-Xtxp141 for stay-green QTLs on SBI-10L and a high resolution linkage map was developed using GBS SNPs. Out of 182 only 152 recombinants were replicated thrice in field for stay-green screening for two seasons (Summer 2013 and 2014). Fine mapping of the per cent Green Leaf Area (%GLA) traits identified 33 QTLs and 19 QTLs were clustered into 7 groups where 8 genes were identified. These were AP2/ERF transcription factor family (Sb10g025053), Ankyrin-repeat protein (Sb10g025310), WD40 repeat protein (Sb10g025320), NBS-LRR Protein (Sb10g025283), Calcium dependant protein kinase (Sb10g030150), LEA2 protein (Sb10g029570), a putative uncharacterized protein (Sb10g024920) and senescence associated protein (Sb10g030520). With this study SBI-10L stay-green genomic regions were delimited from 15Mb to 8 genes co-localized with GWAS MTAs. Further cloning and expression level studies of the identified candidate genes will improve the development of drought tolerant genotypes. cQTL Nearest marker position cM marker Intervals No. of QTLs Integrated QTLs Gene ID/MTAs Combined R2 Candidate genes SNP effect cQstg10.1 S10_54269620 36.41 36.41 3 Q10GLA14a_14,Q10GLA2 8a_14.Q1049a_across Sb10g025053 12.4 AP2/ERF transcryptional factor Intergenic cQstg10.2 S10_54081973 41.41 39.8 – 42.8 4 Q10GLA7a_13,Q10GLA14 a_13,Q10GL21b_13,Q10G LA28b_14 Sb10g024920 31.3 weakly similar to Putative uncharacterized protein non synonymous cQstg10.3 S10_54535306 45.01 42.8 – 47.4 2 Q10GLA7a_across,Q10GL A14a_across Sb10g025283 16.95 NBS-LRR disease resistance protein Synonimous &non synonimous (Exonic region) cQstg10.4 S10_54585199 44.41 54.58- 54.59 2 Q10GLA14b_14,Q10GLA4 9b_across Sb10g025310, 320 10.57 Ankyrin repeat protein and WD40 repeat family protein (trasducin protein) Intron cQstg10.5 S10_59342820 115.31 114.5 – 115.6 3 Q10GLA21a_13,Q10GLA2 1a_14,Q10GLA21a_acros s Sb10g029570 28 similar to Putative uncharacterized protein P0655A07.24/LEA Synonimous &non synonimous (Exonic region) cQstg10.6 S10_59775456 120.6 121.4 ‒ 122.5 2 Q10GL35a_13,Q10GLA42 a_13 Sb10g030040 6.58 Ca/calmodulin dependant protein kinase Intron cQstg10.7 S10_60194379 125.01 124.7 – 125.5 3 Q10GL21c_13,Q10GLA28 a_13,Q10GLA28a_across Sb10g030520 5.5 similar to Senescence- associated protein 3'UTR+ Exon Sorghum gene ID Description Functional role Reference Sb10g025053 AP2/ERF transcryption factor Over expression of AP2/ERF family genes have been shown to improve stress tolerance under water defect conditions Mawlong et al., 2015 Sb10g025310 Ankyrin repeat protein involved during flower senescence Xu et al., 2007 Sb10g025320 Transducin family protein/ WD40 repeat protein involved in senescence mechanism Guo and Gan, 2012 Sb10g025283 NBS-LRR protein gene Defense response protein leads to increased levels of SA, ABA and cytokinin Sarazin et al., 2015 Sb10g029570 LEA2 protein reported to play a role in late embryogenesis and drought stress mechanisms Gao and Lan, 2016 Sb10g030040 Calcium/calmodulin dependant protein kinase plays a functional role in the identification of drought tolerant locus Franz et al., 2011 Sb10g030520 Senescence associated protein kinase Reported to be involved in senescence mechanisms Liang et al.,2014 Sb10g030770 No apical meristem (NAM) protein Increased expression of NAC transcriptional factors leads to drought stress tolerance Zaho et al ., 2015 Sb10g030776 Starch branching enzyme I precursor Glycogen biosynthesis in seed Peleg et al., 2011 Sb10g031030 similar to Putative AGO1 homologous protein Controls miRNA168 mediated drought tolerance Wang et al., 2014 Sb10g026180, Sb10g029530 similar to Pentatricopeptide (PPR) repeat- containing protein-like involved in chlorophyll degradation mechanism by stabilizing RNA in chloroplasts Manna et al., 2015 Sb10g027640 WRKY transcription factor over expression lead to drought tolerance in rice Cai et al., 2015 Sb10g029810 MADS box transcription factors alterations may lead to stay-green which is involved in many developmental processes Shore and Sharrocks, 1995 Sb10g030620 Exocyst subunit involved in auto phagosome/autolysis associated in programmed cell death Lim et al., 2007 Sb10g026200 Squamosa binding protein family transcriptional factors reported to be involved in leaf, flower, fruit and vegetative phase developmental stages Preston and Hileman, 2013 Sb10g028300 Zinc finger reported to be involved in senescence Griffith et al., 2014 Sb10g022580 CYTOKININ-RESPONSIVE GATA FACTOR 1 involved in chloroplast metabolism Hudson et al., 2013 STAY-GREEN PUTATIVE CANDIDATE GENES STAY-GREEN QTL CLUSTERS ON SBI-10L FINE MAPPING OF STAY-GREEN TRAIT ON SBI-10L WORK FLOW SNP eff on SBI-10L SSR MAP INTEGRATED WITH 260 GBS-SNPs Conclusions • GBS-SNP analysis resulted in identification of genomic regions having candidate genes associated for stay-green trait on chromosome SBI-10L. • In addition, this identified a huge number of SNPs that can be useful for genomics-assisted sorghum breeding. • Further cloning and expression studies of the significantly associated candidate genes may reveal the appropriate role in the biological processes associated with the stay-green (component of both terminal drought tolerance and ruminant livestock feeding value of stover) and can be involved in development of drought tolerant varieties. Acknowledgements • This work is part of PhD work from Department of Genetics, Osmania university Hyderabad • Financial support from ICRISAT ‘s Dryland Cereals research program is greatly acknowledged. • This work has been undertaken as part of the CGIAR Research Program - Dryland Cereals/ Genetic Gains. Horseshoe effect of SNPs Distance matrix of SNPs Usha Kiranmayee K N S 1, 2* , Hash C T 3 , Kavi Kishor P B 2 , Ramu P 4 , Sivasubramani S 1 , Santosh P Deshpande 1 1 International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India 2 Department of Genetics, Osmania University, Hyderabad, India 3 International Crop Research Institute for the Semi-Arid Tropics, Niamey, Niger 4 Cornell university, Ithaca, New York, United States * Email: [email protected] Fine Mapping of stay-green QTLs on sorghum chromosome SBI-10L – An approach from Genome to Phenome About ICRISAT: www.icrisat.org ICRISAT’s scienfic informaon: hp://EXPLOREit.icrisat.org Feb 2017
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Transcript of Fine mapping of stay-green QTLs on sorghum chromosome SBI-10L-An approach from Genome to Phenome
Fine mapping of stay-green QTLs on sorghum chromosome SBI-10L ‒ An approach from Genome to Phenome
Usha Kiranmayee K N S1, 2*, Hash C T 3, Kavi Kishor P B2, Ramu P4, Sivasubramani S1, Santosh P Deshpande1
1 International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India2 Department of Genetics, Osmania University, Hyderabad, India3 International Crop Research Institute for the Semi-Arid Tropics, Niamey, Niger 4 Cornell university, Ithaca, New York, United States*E-mail: [email protected]
Abstract Sorghum is the fifth most important C4 cereal crop grown globally in arid and semi-arid climatic conditions. Drought is the major cause for loss of productivity worldwide.Delayed senescence of plants leads to adaptation to drought stress conditions by staying-green and giving high yields. In order to identify and dissect the stay-green genomicregions we have developed a high resolution fine mapping population from introgression line cross RSG04008-6 (stay-green) × J2614-11 (shoot fly resistant). Nearly 1894 F2genotypes were screened with 8 SSR in order to identify double recombinants for both the parents in the sorghum chromosome-10 long arm (SBI-10L). The selected F2:4recombinants were GBSed to increase the marker density between flanking markers Xgap001-Xtxp141 for stay-green QTLs on SBI-10L and a high resolution linkage map wasdeveloped using GBS SNPs. Out of 182 only 152 recombinants were replicated thrice in field for stay-green screening for two seasons (Summer 2013 and 2014). Fine mappingof the per cent Green Leaf Area (%GLA) traits identified 33 QTLs and 19 QTLs were clustered into 7 groups where 8 genes were identified. These were AP2/ERF transcriptionfactor family (Sb10g025053), Ankyrin-repeat protein (Sb10g025310), WD40 repeat protein (Sb10g025320), NBS-LRR Protein (Sb10g025283), Calcium dependant protein kinase(Sb10g030150), LEA2 protein (Sb10g029570), a putative uncharacterized protein (Sb10g024920) and senescence associated protein (Sb10g030520). With this study SBI-10Lstay-green genomic regions were delimited from 15Mb to 8 genes co-localized with GWAS MTAs. Further cloning and expression level studies of the identified candidate geneswill improve the development of drought tolerant genotypes.
cQTL Nearest marker position cM
marker Intervals
No. of QTLs Integrated QTLs Gene
ID/MTAsCombined
R2 Candidate genes SNP effect
cQstg10.1 S10_54269620 36.41 36.41 3 Q10GLA14a_14,Q10GLA28a_14.Q1049a_across
Sb10g025053 12.4 AP2/ERF transcryptional factor Intergenic
cQstg10.2 S10_54081973 41.41 39.8 – 42.8 4Q10GLA7a_13,Q10GLA14a_13,Q10GL21b_13,Q10G
LA28b_14Sb10g024920 31.3 weakly similar to Putative
uncharacterized proteinnon synonymous
cQstg10.3 S10_54535306 45.01 42.8 – 47.4 2 Q10GLA7a_across,Q10GLA14a_across Sb10g025283 16.95 NBS-LRR disease resistance
protein
Synonimous&non synonimous(Exonicregion)
cQstg10.4 S10_54585199 44.41 54.58- 54.59 2 Q10GLA14b_14,Q10GLA49b_across
Sb10g025310,320 10.57
Ankyrin repeat protein and WD40 repeat family protein (trasducin protein)
Intron
cQstg10.5 S10_59342820 115.31 114.5 – 115.6 3Q10GLA21a_13,Q10GLA21a_14,Q10GLA21a_acros
sSb10g029570 28
similar to Putative uncharacterized protein P0655A07.24/LEA
Synonimous&non synonimous(Exonicregion)
cQstg10.6 S10_59775456 120.6 121.4 ‒ 122.5 2 Q10GL35a_13,Q10GLA42a_13 Sb10g030040 6.58 Ca/calmodulin dependant
protein kinaseIntron
cQstg10.7 S10_60194379 125.01 124.7 – 125.5 3 Q10GL21c_13,Q10GLA28a_13,Q10GLA28a_across Sb10g030520 5.5 similar to Senescence-
associated protein3'UTR+Exon
Sorghum gene ID Description Functional role Reference
Sb10g025053 AP2/ERF transcryption factor Over expression of AP2/ERF family genes have been shown to improve stress tolerance under water defect conditions
Mawlong et al., 2015
Sb10g025310 Ankyrin repeat protein involved during flower senescence Xu et al., 2007
Sb10g025320 Transducin family protein/WD40 repeat protein involved in senescence mechanism Guo and Gan, 2012
Sb10g025283 NBS-LRR protein gene Defense response protein leads to increased levels of SA, ABA and cytokinin Sarazin et al., 2015
Sb10g029570 LEA2 protein reported to play a role in late embryogenesis and drought stress mechanisms Gao and Lan, 2016
Sb10g030040 Calcium/calmodulin dependant protein kinase plays a functional role in the identification of drought tolerant locus Franz et al., 2011
Sb10g030520 Senescence associated protein kinase Reported to be involved in senescence mechanisms Liang et al.,2014
Sb10g030770 No apical meristem (NAM) protein Increased expression of NAC transcriptional factors leads to drought stress tolerance Zaho et al ., 2015
Sb10g030776 Starch branching enzyme I precursor Glycogen biosynthesis in seed Peleg et al., 2011Sb10g031030 similar to Putative AGO1 homologous protein Controls miRNA168 mediated drought tolerance Wang et al., 2014Sb10g026180, Sb10g029530 similar to Pentatricopeptide (PPR) repeat-
containing protein-likeinvolved in chlorophyll degradation mechanism by stabilizing
RNA in chloroplasts Manna et al., 2015
Sb10g027640 WRKY transcription factor over expression lead to drought tolerance in rice Cai et al., 2015
Sb10g029810 MADS box transcription factors alterations may lead to stay-green which is involved in many developmental processes
Shore and Sharrocks, 1995
Sb10g030620 Exocyst subunit involved in auto phagosome/autolysis associated in programmed cell death Lim et al., 2007
Sb10g026200 Squamosa binding protein family transcriptional factors
reported to be involved in leaf, flower, fruit and vegetative phase developmental stages
Preston and Hileman, 2013
Sb10g028300 Zinc finger reported to be involved in senescence Griffith et al., 2014
Sb10g022580 CYTOKININ-RESPONSIVE GATA FACTOR 1 involved in chloroplast metabolism Hudson et al., 2013
STAY-GREEN PUTATIVE CANDIDATE GENES
STAY-GREEN QTL CLUSTERS ON SBI-10L FINE MAPPING OF STAY-GREEN TRAIT ON SBI-10L
WORK FLOW SNP eff on SBI-10L SSR MAP INTEGRATED WITH 260 GBS-SNPs
Conclusions• GBS-SNP analysis resulted in identification of genomic regions having candidate genes associated for stay-green trait on chromosome
SBI-10L.• In addition, this identified a huge number of SNPs that can be useful for genomics-assisted sorghum breeding.• Further cloning and expression studies of the significantly associated candidate genes may reveal the appropriate role in the biological
processes associated with the stay-green (component of both terminal drought tolerance and ruminant livestock feeding value of stover) and can be involved in development of drought tolerant varieties.
Acknowledgements• This work is part of PhD work from Department of Genetics, Osmania university
Hyderabad• Financial support from ICRISAT ‘s Dryland Cereals research program is greatly
acknowledged. • This work has been undertaken as part of the CGIAR Research Program - Dryland Cereals/
Genetic Gains.
Horseshoe effect of SNPs Distance matrix of SNPs
Usha Kiranmayee K N S1, 2*, Hash C T 3, Kavi Kishor P B2, Ramu P4, Sivasubramani S1, Santosh P Deshpande1
1 International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India2 Department of Genetics, Osmania University, Hyderabad, India3 International Crop Research Institute for the Semi-Arid Tropics, Niamey, Niger4 Cornell university, Ithaca, New York, United States* Email: [email protected]
Fine Mapping of stay-green QTLs on sorghum chromosome SBI-10L – An approach from Genome to Phenome
About ICRISAT: www.icrisat.orgICRISAT’s scientific information: http://EXPLOREit.icrisat.org
Feb 2017
