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

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

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Abstract

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.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: association mapping; chickpea; microsatellite; SNP; transcription factor
Subjects: Mandate crops > Chickpea
Others > Genetics and Genomics
Depositing User: Mr Sanat Kumar Behera
Date Deposited: 01 May 2013 03:46
Last Modified: 21 Oct 2016 06:01
URI: http://oar.icrisat.org/id/eprint/6774
Official URL: http://dx.doi.org/10.1093/dnares/dst015
Projects: UNSPECIFIED
Funders: Government of India - Department of Biotechnology , Council of Scientific and Industrial Research(India)
Acknowledgement: The authors gratefully acknowledge the financial support by the Department of Biotechnology (DBT), Government of India. We thank the DNA Sequencing Facility, NIPGR for automated fragment analysis and sequencing. Ms Alice Kujur acknowledges the Council of Scientific and Industrial Research (CSIR) for the award of Junior Research Fellowship (JRF).
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