Genome Wide Association Mapping of yield traits in Chickpea [Cicer arietinum L.]

Abstract

Identification of potential transcription factor (TF) gene-derived natural SNP allelic variants regulating pod and seed yield component traits by large-scale mining and genotyping of SNPs in natural germplasm accessions coupled with high-resolution association mapping is vital for understanding the complex genetic architecture of quantitative yield traits in chickpea. In this perspective, 380 diverse chickpea genotypes formed the association panel and were phenotyped for three consecutive years (2014, 2015 and 2016). Presence of significant difference among the genotypes and sufficient amount of variability in the association panel was indicated by variability study for days to 50% flowering (DTF), days to maturity (DTM), plant height (PH), pods per plant (P/Pl), seeds per plant (S/Pl), hundred seed weight (100SW) and seed yield per plant (SY/Pl). Very high to moderate heritability coupled with high genetic advance was observed for days to 50% flowering, days to maturity, hundred seed weight, number of pods per plant and number of seeds per plant. High positive association and significant positive direct was observed from seeds per plant, pods per plant and hundred seed weight on seed yield per plant indicating direct selections of this trait for yield would be rewarding. Stability analysis by AMMI method revealed ICCV14307 and IG5982 as the most stable genotypes for hundred seed weight and genotypes ICCV00309 and IG5893 for seed number. A genome-wide GBS (genotyping-by-sequencing) and targeted gene amplicon resequencing-based simultaneous SNP discovery and genotyping assays, which discovered 1611 novel SNPs from 736 TF genes physically mapped on eight chromosomes and unanchored scaffolds of Kabuli chickpea genome. A high-resolution genetic association analysis was performed by correlating the genotyping information of 1611 TF gene-based SNPs with multi-location/years field phenotyping data of six major pod and seed yield traits evaluated in a constituted association panel (326 desi and Kabuli germplasm accessions) of chickpea. This essentially identified 27 TF gene-derived SNPs exhibiting significant association with six major yield traits, namely days to 50% flowering (DF), plant height (PH), branch number (BN), pod number (PN), seed number (SN) and seed weight (SW) in chickpea. These trait-associated SNPs individually and in combination explained 10 23% and 32% phenotypic variation respectively for the studied yield component traits. Interestingly, novel non-synonymous coding SNP allelic variants in five potential candidate TF genes encoding SBP (squamosal promoter binding protein), SNF2(sucrose-fermenting2), GRAS [Gibberellic acid insensitive (GAI)-Repressor of GAI (RGA)-SCARECROW (SCR)], bZIP (basic leucine zipper) and LOB (lateral organ boundaries)-domain proteins associated strongly with days to 50% flowering (DTF), plant height (PH), branch number (BN), pod number (PN), seed number (SN) and hundred seed weight (100SW) traits respectively were found most promising in chickpea. Validation study with 21 SSR genic markers in 96 subset panel through association study deciphered five genic microsatellite markers TAA137, CaIISSR25, CaSSR53, GA11 and CEST47 significantly associated with seed weight in chickpea.