Fine mapping of stripe rust resistance gene YrAn1589 in common wheat using Wheat660K SNP array and BSR-Seq.

Key message: A new stripe rust resistance gene YrAn1589 in Chinese wheat Annong1589 was mapped to a 160.9-166.6 kb interval on chromosome arm 3BL and co-segregated with a marker CAPS9 developed from candidate gene TraesCS3B03G1054600.  Stripe rust, caused by Puccinia. striiformis f. sp. tritici (Pst), is a devastating fungal disease that can significantly reduce wheat yield. The Chinese wheat cultivar Annong1589 demonstrates high resistance against the predominant Pst races in the Huang-Huai valley wheat region. The present study aimed to identify the stripe rust resistance gene in Annong1589. Genetic analysis indicated that the resistance in Annong1589 was conferred by a single dominant gene, provisionally designated YrAn1589. Using Wheat660K SNP array, bulked segregant RNA sequencing and new molecular markers developed, the resistance gene was mapped to a 160.9-166.6 kb region between CAPS8 and CAPS10 on chromosome 3BL based on IWGSC CS RefSeq v2.1 and eight other reference genome sequences, including eight high-confidence annotated genes. Transcriptome and qRT-PCR analyses revealed significantly upregulated expression of TraesCS3B03G1054600 in resistant plants following CYR32 inoculation, suggesting it is a potential candidate gene for YrAn1589. A functional marker CAPS9 developed from a A/G polymorphic SNP in the candidate co-segregated with YrAn1589 in the F₂ population. Subcellular localization experiments showed that TraesCS3B03G1054600 protein was localized in the cytoplasm and nucleus, implying its role in immune response and resistance. Our findings establish YrAn1589 as a new stripe rust resistance gene, providing valuable gene resource and molecular markers for improvement of stripe rust resistance in wheat.