Abstract
We identified 44844 high-quality SNPs by sequencing 92 diverse chickpea accessions belonging to a seed and pod trait-specific association panel using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays. A GWAS (genome-wide association study) in an association panel of 211, including the 92 sequenced accessions, identified 22 major genomic loci showing significant association (explaining 23–47% phenotypic variation) with pod and seed number/plant and 100-seed weight. Eighteen trait-regulatory major genomic loci underlying 13 robust QTLs were validated and mapped on an intra-specific genetic linkage map by QTL mapping. A combinatorial approach of GWAS, QTL mapping and gene haplotype-specific LD mapping and transcript profiling uncovered one superior haplotype and favourable natural allelic variants in the upstream regulatory region of a CesA-type cellulose synthase (Ca_Kabuli_CesA3) gene regulating high pod and seed number/plant (explaining 47% phenotypic variation) in chickpea. The up-regulation of this superior gene haplotype correlated with increased transcript expression of Ca_Kabuli_CesA3 gene in the pollen and pod of high pod/seed number accession, resulting in higher cellulose accumulation for normal pollen and pollen tube growth. A rapid combinatorial genome-wide SNP genotyping-based approach has potential to dissect complex quantitative agronomic traits and delineate trait-regulatory genomic loci (candidate genes) for genetic enhancement in crop plants, including chickpea.
Highlights
The large-scale SNP genotyping, diversity and LD-based information of natural and mapping populations was further correlated with their robust field phenotyping data to identify functionally relevant potential genomic loci regulating three seed and pod yield-contributing traits using a combinatorial approach of genome-wide association studies (GWAS), QTL mapping, gene haplotype-specific LD mapping and transcript profiling in chickpea
All 44844 genome-wide GBS-based SNPs [submitted to NCBI dbSNP Build (B142)] showing polymorphism among 92 diverse desi and kabuli chickpea accessions were selected for GWAS
Considering disproportionate draft genome assembly and size (Mb) of chromosomal pseudomolecules between desi and kabuli genomes, GWAS needs to be performed separately using desi and kabuli SNPs, which in turn would strengthen the possibility of identifying numerous trait-associated valid genomic loci with wider genome coverage in chickpea. This strategy is essential to access the precise trait association potential of genomic loci by establishing their correlation with chromosomal LD estimates and LD decay separately for desi and kabuli genomes. The implications of such chromosomal LD patterns in GWAS for identification of potential trait-associated genomic loci have been demonstrated in many crop plants including chickpea[70,71]
Summary
The large-scale SNP genotyping, diversity and LD-based information of natural and mapping populations was further correlated with their robust field phenotyping data to identify functionally relevant potential genomic loci (gene-associated targets) regulating three seed and pod yield-contributing traits using a combinatorial approach of GWAS, QTL mapping, gene haplotype-specific LD mapping and transcript profiling in chickpea. These integrated analyses, coupled with our preliminary in vitro pollen tube growth and cellulose estimation assays, were able to identify one superior haplotype and favourable natural allelic variants in the upstream regulatory region of a candidate cellulose synthase (Ca_Kabuli_CesA3) gene. This candidate gene possibly governs high pod and seed number with its increased transcript expression and higher accumulation of cellulose, in pollen and pod tissues, thereby promoting normal pollen and pollen tube growth in chickpea
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