High-resolution mapping of Yr78, an adult plant resistance gene to wheat stripe rust

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is responsible for significant yield losses worldwide, which can be minimized by the deployment of Pst resistance genes. Yr78 is an adult plant partial-resistance gene that has remained effective against the post-2000 virulent Pst races. In this study, we generated a high-resolution map of Yr78 based on 6,124 segregating chromosomes. We mapped Yr78 within a 0.05-cM interval on the short arm of chromosome 6B, which corresponds to an 11.16 Mb region between TraesCS6B02G116200 and TraesCS6B02G118000 in the 'Chinese Spring' Ref Seq. v1.1 genome. This interval is likely larger because it includes the unassembled NOR-B2 region, which may have contributed to the low recombination rate detected in this region. The Yr78 candidate region includes 15 genes that were prioritized for future functional studies based on their annotated function and polymorphisms between susceptible and resistant genotypes. Using exome capture data, we identified five major haplotypes in the candidate gene region, with the H1 haplotype associated with Yr78. The H1 haplotype was not detected in tetraploid wheat (Triticum turgidum L.) but was found in ∼30% of the common wheat cultivars (Triticum aestivum L.), suggesting that the associated resistance to stripe rust may have favored the selection of this haplotype. We developed two diagnostic molecular markers for the H1 haplotype that will facilitate the deployment of Yr78 in wheat breeding programs.