A new bacterial blight resistance gene Xa50(t) in the Xa4 locus confers resistance against Xanthomonas oryzae pv. oryzae in rice

Rice bacterial leaf blight (BB), caused by Xanthomonas oryzae pv. oryzae ( Xoo ), leads to severe yield losses in rice. Resistance breeding is a sustainable approach to mitigate the impact of this disease. In this study, a novel BB resistance gene, Xa50 ( t ), was identified in the germplasm line CX315. Genetic analysis revealed that the resistance is conferred by a dominant resistant gene, tentatively named Xa50 ( t ), which provides broad-spectrum and robust resistance to multiple Xoo strains. Using an F 2 population derived from a cross between CX315 and IR24, Xa50 ( t ) was fine-mapped to a 147.7 kb region on the long arm of chromosome 11 flanked by InDel markers M11–588 and M11-602. Gene expression analysis identified three candidate genes out of 13 open reading frames (ORFs) predicted in candidate region. ORF5 and ORF9 ( Xa4 ), encoding a wall-associated kinase (WAK)-like protein, and ORF13 , encoding a receptor-like kinase protein, were significantly upregulated in CX315 following Xoo inoculation. While ORF9 is predicted to encode the Xa4 resistance gene, CRISPR/Cas9-based knockout of Xa4 did not abolish Xa50 ( t )-mediated resistance in the CX315 line, indicating that Xa50 ( t ) confers resistance in a complementary manner. Transcriptome analysis further revealed that oxidative stress response and immune signaling pathways were enriched in CX315 at 48 hours post-inoculation. Together, these findings highlight the potential of Xa50 ( t ) as a valuable genetic resource for improving BB resistance in rice, and the transcriptome data provides molecular insight into the BB resistance response.