Mining disease resistance genes from sitopsis section of Aegilops to broaden wheat’s genetic base

Key message Pan-genomic analysis reveals putative species-specific disease resistance genes in Aegilops Sitopsis, providing valuable resources to enhance wheat genetic diversity and facilitate the deployment of novel resistance genes in breeding. Abstract Wild relatives of wheat ( Triticum aestivum L.) serve as invaluable genetic reservoirs harboring diverse disease resistance genes that exhibit enhanced durability against evolving pathogen populations. Among these wild relatives, the Sitopsis section of genus Aegilops is particularly noteworthy, as it contributed to the B subgenome of wheat and contains numerous elite disease resistance loci that represent critical resources for wheat improvement. In this study, we conducted a comprehensive cross-species pan-genomic analysis of five high-quality Aegilops Sitopsis genomes ( Ae. bicornis , Ae . longissima , Ae. searsii , Ae. sharonensis , and Ae. speltoides ), alongside 30 common wheat genomes. Pan-genomic analysis revealed 5,660 (14.08%), 4,522 (12.17%), 5,043 (13.29%), 5,104 (13.29%), and 4,601 (12.25%) species-specific genes in Ae. bicornis , Ae. longissima , Ae. searsii , Ae. sharonensis , and Ae. speltoides , respectively. Based on functional annotation and domain structures of known cloned disease resistance genes, we identified 136, 159, 115, 141 and 99 species-specific genes that potentially encode a disease resistance function in the respective Sitopsis species. The result revealed that the majority of these putative resistance genes (an average of 41.87%) encode nucleotide-binding and leucine-rich repeat (NLR) proteins, followed by protein kinase-type genes (an average of 41.11%). Transcriptomic profiling further revealed that 33, 43, 27, 35, and 29 of these putative species-specific genes were expressed in at least one tissue, respectively. Notably, among these genes we identified the powdery mildew resistance gene Pm6Sl , which has been cloned from Ae. longissima , as well as homologs of the stripe rust resistance gene YrNAM ( Yr10 ) present in Ae. sharonensis and Ae. longissima . These findings directly facilitate the identification and pyramiding of novel resistance genes from wheat’s wild relatives, providing a solid foundation for enhancing disease resistance in common wheat breeding programs.