Genome wide association studies for flowering time, shelling percentage, harvest index and related traits in chickpea (Cicer arietinum L.)

Grain yield is a product of biomass (BM) and harvest index (HI). HI, not BM, is the major constraint of chickpea productivity in the long season environments of northern Indian plains. This is the first genome wide association study (GWAS) of shelling percentage (Sh.%), HI and related traits in chickpea using genotyping by sequencing approach. Genotyping of 178 germplasm lines involving varieties, trait specific genotypes and advance breeding lines found 35,795 high-throughput single nucleotide polymorphisms (SNPs). The objectives of the study were to unravelling the genomic regions responsible for variation in flowering time, shelling percentage, HI and related traits in chickpea. The phenotypic analysis across three environments showed high variability and connections among HI and related traits. Population structure analysis revealed two sub-populations (k = 2). Linkage disequilibrium (LD) was extensive, and LD decay was relatively low. A total of 172 marker-trait associations (MTAs) were identified for HI and related traits using FarmCPU model, of which days to 50% flowering (DAF), HI and shelling percentage showed significant associations. The current study has identified consistent pleiotropic MTAs, SNC_021165.1_57891716 and SNC_021165.1_57917493, SNC_021164.1_6073633 and SNC_021165.1_33405826 for biomass, pod and seed yield/plant, pod and seed number/plant HI and Sh.%, respectively. All the MTAs observed for SYPL, PYPL and maximum number of MTAs for HI and BM were located on the same chromosome number 6. Further maximum number of MTAs for PPL and SN were distributed on chromosome 5. One of the important findings is that most of the MTAs for SYPL, PYPL, BM, and 100SW are distributed within 25 kb genomic region of chromosome 6. A total of 16 MTAs were retained for Insilco analysis (− log10(p) > 4.0) and searched for their candidate genes in a 100-kb flanking region against the reference genome. The maximum number of genes noticed for DAF (50), followed by Sh.% (48), HI (16), SYPL (13), BM (10), and PYPL (8). The transcripts for DAF, Arabinogalactan proteins and pentatricopeptide repeat were involved in flowering of Arabidopsis. For both PYPL and SYPL, MTA found linked to the genes coding for pentatricopeptide repeat, serine/threonine-protein kinase and E3 ubiquitin-protein ligase. These transcripts played role mainly in pollen maturation, fertilization and flowering time. Chaperone protein DnaJ linked to HI, and receptor-like protein kinase (RLK) for Sh.% were involved in improving yield in Arabidopsis and rice, respectively. The present study also validated one of the MTA linked to DAF which showed r² value of 12.62%.