Dissecting the Population Structure, Diversity and Genetic Architecture of Disease Resistance in Wild Emmer Wheat (Triticum turgidum subsp. dicoccoides)

Background Wild emmer wheat (WEW) ( Triticum turgidum subsp. dicoccoides ) is one of the important crops domesticated in the Neolithic revolution that shifted humanity to agrarian societies. Leveraging whole-genome sequencing (WGS) data from 291 accessions at ~ 9.5x coverage, we identified 3.4 million high-quality SNP markers and utilized them for population genetics and evolutionary studies. We also conducted Genome-wide association studies (GWAS) for seedling-stage resistance to five races of stem, leaf, and stripe/yellow rust pathogens. We investigated candidate genes using ortholog sequence alignment. Results Phylogenetic clustering, principal component analysis, and population structure assessment revealed distinct genetic subgroups within WEW, specifically the Northern Population, Southern Levant (SL) population, and a highly distinct subgroup near the Sea of Galilee, known as race judaicum . Diversity and pairwise FST analyses highlighted varying levels of genetic diversity and distances among these subpopulations. The SL accessions exhibited higher resistance to all races of the three rust pathogens compared to Northern and judaicum populations. GWAS identified 28, 25, and 32 significant loci associated with stem, leaf, and stripe rust resistance, respectively. Major loci explained up to 60% of phenotypic variation and some loci were linked to multiple races and some were novel. Accessions such as TA11204, TA1041, TA1047, TA11196, TA77, TA93, TA1065, and TA66 demonstrated broad resistance to multiple races. Conclusions In summary, this study provides rust resistance WEW germplasms and guides future research on the selection and introgression of rust resistance loci from WEW into cultivated bread and durum wheat, contributing to the stable production of these important food crops.