Genetic diversity and genome-wide association study of yellow rust resistance in elite spring bread wheat genotypes in Ethiopia

Background Yellow rust, caused by Puccinia striiformis f. sp. Tritici (Pst), is one of the most destructive wheat diseases in the world. It can cause, yield losses of up to 100% during severe outbreaks. The use of resistant wheat varieties is the most effective and environmentally sustainable approach to control yellow rust. This study aimed to assess genetic diversity and identify molecular markers associated with stripe rust resistance. A total of 186 elite bread wheat lines from the International Center for Agricultural Research in the Dry Areas (ICARDA) were investigated for genetic diversity and genome-wide association studies (GWAS) using 17,920 SNP markers. The genotypes were phenotyped for yellow rust resistant under natural infestation condition at five environments in Ethiopia during 2023 and 2024 cropping season. Results Out of 186 genotypes, 8 genotypes were highly resistant with 3–10% level of severity to yellow rust. An average polymorphism information content (PIC) of 0.30 and genetic diversity of 0.37 were observed across the panel. Population structure analysis identified four distinct subpopulations through three different methods. The broad-sense heritability for yellow rust resistance was 86%, indicating the presence of promising alleles in the genotypes that could be deployed to develop yellow rust resistant wheat varieties. The whole genome linkage disequilibrium (LD) declined within an average physical distance of 40.34 Mbp at r2 0.19. GWAS using multi-locus FarmCPU model identified 69 significant marker-trait associations. Five quantitative trait loci (QTLs) identified in this study-qYrS.21, qYrS.22, qYrS.23, qYrS.29, and qYrS.41-were not co-located with any previously reported gene/QTLs regions, indicating that they may represent novel loci associated with yellow rust resistance. Conclusion The highly resistant elite genotypes are recommended for direct release and parentage purposes. The novel QTLs identified in the current study could be potentially used for marker assisted selection after validation using another set of elite wheat genotypes.