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 <i>Xanthomonas oryzae</i> pv. <i>oryzae</i> (<i>Xoo</i>), 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, <i>Xa50</i>(<i>t</i>), was identified in the germplasm line CX315. Genetic analysis revealed that the resistance is conferred by a dominant resistant gene, tentatively named <i>Xa50</i>(<i>t</i>), which provides broad-spectrum and robust resistance to multiple <i>Xoo</i> strains. Using an F₂ population derived from a cross between CX315 and IR24, <i>Xa50</i>(<i>t</i>) 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. <i>ORF5</i> and <i>ORF9</i> (<i>Xa4</i>), encoding a wall-associated kinase (WAK)-like protein, and <i>ORF13</i>, encoding a receptor-like kinase protein, were significantly upregulated in CX315 following <i>Xoo</i> inoculation. While <i>ORF9</i> is predicted to encode the <i>Xa4</i> resistance gene, CRISPR/Cas9-based knockout of <i>Xa4</i> did not abolish <i>Xa50</i>(<i>t</i>)-mediated resistance in the CX315 line, indicating that <i>Xa50</i>(<i>t</i>) 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 <i>Xa50</i>(<i>t</i>) as a valuable genetic resource for improving BB resistance in rice, and the transcriptome data provides molecular insight into the BB resistance response.