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.