title: A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea.
abstract: The study identified 9045 high-quality SNPs employing both genome-wide GBS- and candidate gene-based SNP genotyping assays in 172, including 93 cultivated (desi and kabuli) and 79 wild chickpea accessions. The GWAS in a structured population of 93 sequenced accessions detected 15 major genomic loci exhibiting significant association with seed coat color. Five seed color-associated major genomic loci underlying robust QTLs mapped on a high-density intra-specific genetic linkage map were validated by QTL mapping. The integration of association and QTL mapping with gene haplotype-specific LD mapping and transcript profiling identified novel allelic variants (non-synonymous SNPs) and haplotypes in a MATE secondary transporter gene regulating light/yellow brown and beige seed coat color differentiation in chickpea. The down-regulation and decreased transcript expression of beige seed coat color-associated MATE gene haplotype was correlated with reduced proanthocyanidins accumulation in the mature seed coats of beige than light/yellow brown seed colored desi and kabuli accessions for their coloration/pigmentation. This seed color-regulating MATE gene revealed strong purifying selection pressure primarily in LB/YB seed colored desi and wild Cicer reticulatum accessions compared with the BE seed colored kabuli accessions. The functionally relevant molecular tags identified have potential to decipher the complex transcriptional regulatory gene function of seed coat coloration and for understanding the selective sweep-based seed color trait evolutionary pattern in cultivated and wild accessions during chickpea domestication. The genome-wide integrated approach employed will expedite marker-assisted genetic enhancement for developing cultivars with desirable seed coat color types in chickpea.
authors.affiliation: National Institute of Plant Genome Research New Delhi, India.
authors.forename: Deepak
authors.initials: D
authors.lastname: Bajaj
authors.affiliation: National Institute of Plant Genome Research New Delhi, India.
authors.forename: Shouvik
authors.initials: S
authors.lastname: Das
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics Telangana, India.
authors.forename: Hari D
authors.initials: HD
authors.lastname: Upadhyaya
authors.affiliation: National Institute of Plant Genome Research New Delhi, India.
authors.forename: Rajeev
authors.initials: R
authors.lastname: Ranjan
authors.affiliation: National Institute of Plant Genome Research New Delhi, India.
authors.forename: Saurabh
authors.initials: S
authors.lastname: Badoni
authors.affiliation: National Research Centre on Plant Biotechnology New Delhi, India.
authors.forename: Vinod
authors.initials: V
authors.lastname: Kumar
authors.affiliation: Division of Genetics, Indian Agricultural Research Institute New Delhi, India.
authors.forename: Shailesh
authors.initials: S
authors.lastname: Tripathi
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics Telangana, India.
authors.forename: C L Laxmipathi
authors.initials: CL
authors.lastname: Gowda
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics Telangana, India.
authors.forename: Shivali
authors.initials: S
authors.lastname: Sharma
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics Telangana, India.
authors.forename: Sube
authors.initials: S
authors.lastname: Singh
authors.affiliation: National Institute of Plant Genome Research New Delhi, India.
authors.forename: Akhilesh K
authors.initials: AK
authors.lastname: Tyagi
authors.affiliation: National Institute of Plant Genome Research New Delhi, India.
authors.forename: Swarup K
authors.initials: SK
authors.lastname: Parida
keywords: GBS; GWAS; QTL; SNP; chickpea; haplotype; seed coat color; wild accession