title: Functionally relevant microsatellite markers from chickpea transcription factor genes for efficient genotyping applications and trait association mapping.
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.
authors: National Institute of Plant Genome Research-NIPGR, Aruna Asaf Ali Marg, New Delhi 110067, India.
authors: Alice
authors: A
authors: Kujur
authors: Deepak
authors: D
authors: Bajaj
authors: Maneesha S
authors: MS
authors: Saxena
authors: Shailesh
authors: S
authors: Tripathi
authors: Hari D
authors: HD
authors: Upadhyaya
authors: C L L
authors: CL
authors: Gowda
authors: Sube
authors: S
authors: Singh
authors: Mukesh
authors: M
authors: Jain
authors: Akhilesh K
authors: AK
authors: Tyagi
authors: Swarup K
authors: SK
authors: Parida
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping / Q000379:methods*; D029863:Cicer / Q000235:genetics*; D020224:Expressed Sequence Tags; D017343:Genes, Plant; D005819:Genetic Markers; D006239:Haplotypes; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D012639:Seeds / Q000235:genetics*; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D005819:Genetic Markers; D014157:Transcription Factors
keywords: SNP; association mapping; chickpea; microsatellite; transcription factor
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