Integrative genome-wide association studies (GWAS) to understand complex genetic architecture of quantitative traits in chickpea uri icon


  • Development of high-yielding stress-tolerant chickpea cultivarsis essential to enhance its yield potential and productivity amidstclimate change scenario. Unfortunately, superior lines/recombinantsproducing higher pod and seed yield under stress are notavailable in world chickpea collection. Therefore, genetic dissectionof complex stress tolerance and yield-contributing quantitativetraits is the prime objective in current chickpea genomicsand breeding research. Our study employed diverse GWAS-assistedintegrated genomic strategies involving classical geneticinheritance analysis, QTL mapping, differential transcript profiling,molecular haplotyping and haplotype-based gene domestication/evolution study for rapid quantitative dissection of complexyield and stress tolerance traits in chickpea. To accomplishthis, multi-location/years replicated yield traits-related fieldphenotyping and high-throughput marker genotyping informationgenerated from numerous natural germplasm accessions(association panel) and multiple intra- and inter-specific mappingpopulations of chickpea were deployed in the aforesaidcombinatorial genomic approaches. These analyses delineated12 novel alleles and six haplotypes from 10 transcription factorgenes and 16 major QTLs/eQTLs governing yield and stress tolerancetraits that were mapped on 10 ultra-high density chickpeagenetic linkage maps. The superior natural alleles/haplotypes oftwo major genes (QTLs) regulating seed weight and pod/seednumber identified from cultivated and wild Cicer gene pools arebeing introduced into multiple high-yielding Indian varieties ofchickpea for its marker-assisted genetic improvement. The potentialmolecular signatures delineated using integrated genomics-assisted breeding strategies have functional significance tounderstand the molecular genetic mechanism and natural allelicdiversity-led domestication pattern underlying these complexquantitative traits at a genome-wide scale, leading to fast-pacedtranslational genomics for chickpea genetic enhancement.These essential outcomes will be useful for devising the mostefficient strategies to produce high-yielding climate-resilientchickpea cultivars for sustaining global food security

publication date

  • 2017