Unraveling the genetics of heat tolerance in chickpea landraces (Cicer arietinum L.) using genome-wide association studies

• DOI: 10.3389/fpls.2024.1376381
• Publication Date: 2024-03-25T04:37:39Z
• Authors: Thippeswamy Danak...; Neeraj Kumar; Basavanagouda Sid...; Tapan Kumar; Chellapilla Bhara...; Pradeep Kumar Jain; Manduparambil Sub...; Nilesh Joshi; Swarup Kumar Parida; Shayla Bindra; Chittaranjan Kole; Rajeev K. Varshney
• Keywords: Genome-wide Association Study; Linkage Disequilibrium; Genetic Association; Association mapping; Pentatricopeptide repeat; Candidate gene; Plant Breeding; Molecular breeding

Chickpea, being an important grain legume crop, is often confronted with the adverse effects of high temperatures at reproductive stage crop growth, drastically affecting yield and overall productivity. The current study deals extensive evaluation chickpea genotypes, focusing on traits associated their response to heat stress. Notably, we observed significant variations for these under both normal high-temperature conditions, forming a robust basis genetic research breeding initiatives. Furthermore, revealed that yield-related exhibited heritability, suggesting potential suitability marker-assisted selection. We carried out single-nucleotide polymorphism (SNP) genotyping using genotyping-by-sequencing (GBS) method genome-wide association (GWAS). Overall, 27 marker–trait associations (MTAs) linked traits, among which identified five common MTAs displaying pleiotropic after applying stringent Bonferroni-corrected p-value threshold <0.05 [−log 10 (p) > 4.95] BLINK (Bayesian-information linkage-disequilibrium iteratively nested keyway) model. Through in-depth in silico analysis markers against CDC Frontier v1 reference genome, discovered majority SNPs were located or proximity gene-coding regions. further explored candidate genes situated near MTAs, shedding light molecular mechanisms governing stress tolerance enhancement chickpeas such as indole-3-acetic acid–amido synthetase GH3.1 GH3 auxin-responsive promoter pentatricopeptide repeat-containing protein, etc. harvest index (HI) trait was marker Ca3:37444451 encoding aspartic proteinase ortholog sequence Oryza sativa subsp. japonica Medicago truncatula , known contributing tolerance. These may serve valuable assets programs dedicated tailoring varieties resilient climate change.