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Development of high-yielding stress-tolerant chickpea cultivars is essential to enhance its yield potential and productivity amidst climate change scenario. Unfortunately, superior lines/recombinants producing higher pod and seed yield under stress are not available in world chickpea collection. Therefore, genetic dissection of complex stress tolerance and yield-contributing quantitative traits is the prime objective in current chickpea genomics and breeding research. Our study employed diverse GWAS-assisted integrated genomic strategies involving classical genetic inheritance analysis, QTL mapping, differential transcript profiling, molecular haplotyping and haplotype-based gene domestication/ evolution study for rapid quantitative dissection of complex yield and stress tolerance traits in chickpea. To accomplish this, multi-location/years replicated yield traits-related field phenotyping and high-throughput marker genotyping information generated from numerous natural germplasm accessions (association panel) and multiple intra- and inter-specific mapping populations of chickpea were deployed in the aforesaid combinatorial genomic approaches. These analyses delineated 12 novel alleles and six haplotypes from 10 transcription factor genes and 16 major QTLs/eQTLs governing yield and stress tolerance traits that were mapped on 10 ultra-high density chickpea genetic linkage maps. The superior natural alleles/haplotypes of two major genes (QTLs) regulating seed weight and pod/seed number identified from cultivated and wild Cicer gene pools are being introduced into multiple high-yielding Indian varieties of chickpea for its marker …