Map-based cloning and functional validation of Xa50, a wall-associated kinase gene conferring broad-spectrum bacterial blight resistance in rice

Genetically validated broad-spectrum resistance genes are needed to improve bacterial blight resistance breeding in rice. Here, we identified HP178 as a rice accession showing broad-spectrum resistance to geographically diverse Xanthomonas oryzae pv. oryzae (Xoo) strains and mapped a dominant locus to a 140-kb interval on chromosome 11. Within the mapped interval of the R498 reference genome, annotation and domain analysis identified OsR498G1120741700, which encodes a predicted wall-associated kinase (WAK), as the most likely candidate gene. Genetic complementation in the susceptible cultivar Zhonghua 11 and CRISPR/Cas9-mediated gene editing in HP178 confirmed that OsR498G1120741700 contributes to the resistance phenotype. The largely overlapping mapping intervals and the correspondence of this gene to ORF5, one of the candidates previously proposed for Xa50(t) in CX315, suggest a possible relationship between the two resistance loci. We therefore tentatively adopt the designation Xa50 to refer to the gene identified here, although its relationship to Xa50(t) in CX315 requires further investigation. Natural-variation analysis of 3,970 rice accessions showed that 936 were classified as Xa50-like, including 443 accessions with the resistance-associated Hap1 haplotype. Functional tests showed that the K435N lines exhibited partially attenuated Xa50-mediated resistance, whereas lines carrying a Hap4-type kinase-domain variant showed severely compromised resistance and reduced ROS accumulation. Our results identify Xa50 as a WAK-type resistance gene and provide haplotype information to support the selection of resistance-associatedXa50 alleles in rice breeding.

The online version contains supplementary material available at https://doi.org/10.1007/s11032-026-01739-5.