Genome-wide association mapping, phylogenetic study, and multivariate analysis of component traits of grain yield in...

Heat stress negatively impacts key yield-contributing physiological traits in wheat, leading to a decrease in grain yield. Scanning of genomic regions linked to these traits, along with the identification of the most relevant candidate genes (CGs), is an effective strategy for developing heat-tolerant wheat cultivars in the near future. In this context, a genome-wide association mapping approach has been employed to identify chromosomal regions associated with these traits, along with to identify the putative CGs for heat tolerance in wheat. Genotyping was performed using the 35 K Axiom Wheat Breeder Array. From our study, principal component analysis (PCA) revealed that biomass (BM), canopy temperature (CT), and seed weight per pot (SWPP) explained a higher cumulative variance. Population structure and diversity analysis filtered 13,947 markers and revealed three subpopulations with sufficient diversity. A large whole-genome LD block size of 7.15 MB was obtained at a half LD decay value. We have mapped 14 significant MTAs linked to these traits with - log10(p) value > 5.44 after Bonferroni correction and also identified 14 high-confidence CGs. Our study also identified four haplotype groups, suggesting the potential for a haplotype-based breeding program under heat stress. Promoter analysis revealed 174 cis-regulatory elements (CREs). Phylogenetic analysis of the pleiotropic gene TraesCS7A02G200200 revealed three major clades of closely related species. We have also reported several orthologous genes related to our 14 major CGs. Untranslated regions (UTRs) analysis found several upstream Open Reading Frames (uORFs) in few identified genes, which can be employed to understand the stringent mechanism of gene regulation under heat stress. By using the Multitrait-genotype ideotype index (MGIDI), we have selected 13 high-performance genotypes for their use as donor parent for heat tolerance. Henceforth, after successful validation, these SNPs can be utilized for marker-assisted transfer of genes/QTLs to develop heat-tolerant wheat cultivars.