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Functionally Relevant Microsatellite Markers From Chickpea Transcription Factor Genes for Efficient Genotyping Applications and Trait Association Mapping

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Relation http://oar.icrisat.org/6774/
http://dx.doi.org/10.1093/dnares/dst015
10.1093/dnares/dst015
 
Title Functionally Relevant Microsatellite Markers From Chickpea Transcription Factor Genes for Efficient Genotyping Applications and Trait Association Mapping
 
Creator Kujur, A
Bajaj, D
Saxena, M S
Tripathi, S
Upadhyaya, H D
Gowda, C L L
Singh, Sube
Jain, M
Tyagi, A K
Parida, S K
 
Subject Chickpea
Genetics and Genomics
 
Description We developed 1108 transcription factor gene-derived microsatellite (TFGMS) and 161 transcription factor functional domain-associated microsatellite (TFFDMS) markers from 707 TFs of chickpea. The robust amplification efficiency (96.5%) and high intra-specific polymorphic potential (34%) detected by markers suggest their immense utilities in efficient large-scale genotyping applications, including construction of both physical and functional transcript maps and understanding population structure. Candidate gene-based association analysis revealed strong genetic association of TFFDMS markers with three major seed and pod traits. Further, TFGMS markers in the 5′ untranslated regions of TF genes showing differential expression during seed development had higher trait association potential. The significance of TFFDMS markers was demonstrated by correlating their allelic variation with amino acid sequence expansion/contraction in the functional domain and alteration of secondary protein structure encoded by genes. The seed weight-associated markers were validated through traditional bi-parental genetic mapping. The determination of gene-specific linkage disequilibrium (LD) patterns in desi and kabuli based on single nucleotide polymorphism-microsatellite marker haplotypes revealed extended LD decay, enhanced LD resolution and trait association potential of genes. The evolutionary history of a strong seed-size/weight-associated TF based on natural variation and haplotype sharing among desi, kabuli and wild unravelled useful information having implication for seed-size trait evolution during chickpea domestication.
 
Publisher Oxford University Press
 
Date 2013
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
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Identifier http://oar.icrisat.org/6774/1/DNARes_1-19_2013.pdf
Kujur, A and Bajaj, D and Saxena, M S and Tripathi, S and Upadhyaya, H D and Gowda, C L L and Singh, Sube and Jain, M and Tyagi, A K and Parida, S K (2013) Functionally Relevant Microsatellite Markers From Chickpea Transcription Factor Genes for Efficient Genotyping Applications and Trait Association Mapping. DNA Research, 20 (4). pp. 355-374. ISSN 1756-1663