The pyramiding of QYr.cib-3AS and YrT14 enhances wheat resistance to stripe rust

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici , is a globally prevalent, wind-borne fungal disease and remains one of the most destructive threats to wheat production. By combining BSA-seq and QTL mapping using the wheat 120K SNP array, we identified two genomic regions associated with stripe rust resistance. Among them, a QTL on the short arm of chromosome 3A, QYr.cib-3AS , was consistently detected across environments, explaining 20.10%–25.21% of the phenotypic variance and showing LOD of 2.57–3.58. QYr.cib-3AS was delimited to an interval flanked by dCAPS-78 and dCAPS-83. Additive-effect analysis showed that RILs pyramiding QYr.cib-3AS with YrT14 increased stripe rust resistance by 77.20% relative to RILs lacking both QYr.cib-3AS and YrT14 , indicating that the pyramiding strategy had a significant impact on stripe rust resistance and underscoring its importance for high-yielding cultivars with durable resistance. The candidate interval exhibited high collinearity. Among the 48 high-confidence genes annotated in this region, an integrated analysis of transcriptome data, functional annotation, and sequence variation suggested that TraesCS3A03G0118200 and TraesCS3A03G0119800 are key candidate genes underlying QYr.cib-3AS . Collectively, these findings provide a foundation for marker-assisted breeding and future cloning and functional characterization of stripe rust resistance genes, which may help accelerate the development of elite stripe rust–resistant wheat cultivars, thereby improving wheat resistance to this destructive pathogen.