European Journal of Sustainable Agroecosystems

Introduction to the Problem: Climate change is causing unprecedented pressure on wheat production globally, hence, there is a necessity to develop crops with resilience traits. Pan-genome studies provide an effective way to uncover and analyze the diversity of alleles associated with climate-related traits. Aim: The study applies a pan-genome analysis of 127 accessions of Triticum aestivum to discover structural variations in the genome and genes responsible for drought, salinity, and heat tolerance. Materials and Methods: The research integrates whole-genome sequenced data of elite cultivars and varieties and wild relatives with their phenotypic responses observed in different abiotic environments. The definitions of core, soft-core, shell, and cloud genome types are provided, based on presence-absence variations. Structural variants, gene duplications, and gene family expansions have been determined. In addition to that, functional annotations and gene ontology enrichment analyses are undertaken to identify 186 candidate genes associated with stress processes. Results: The pan-genome analysis revealed that 42,847 core genes were identified in 95% of accessions and 18596 accessory genes were found in less than 95% accessions. In addition to that, the pan-genome analysis revealed that 2847 structural variables were mapped out and 247 of them were found essential for improved stress tolerance characteristics. There are 156 genes described that are responsible for improved drought tolerance, 89 genes responsible for heat resistance, and 73 genes responsible for salt tolerance. Variation in copy number was noted in the genes of heat shock proteins and aquaporins. Functional annotation revealed 41 genes associated with positive phenotypic variability of yields. Impact: The obtained results contribute enormously to the comprehension of the molecular mechanisms of climatic adaptation of wheat and provide molecular markers and candidate genes for fast-tracked breeding through genomic selection. The ability to extract beneficial alleles from wild relatives and local varieties opens new avenues for breeding.