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

Man Li, Muhammad Sohaib Shafique, Houyu Zhou, Jialu Wang, Yapei Liu, Chunlian Wang, Zhonghua Wang, Zhiyuan Ji

Front Plant Science; 2025 Aug 29: 16:1657476. doi: 10.3389/fpls.2025.1657476.

Abstract

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 F₂ 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.

See https://pmc.ncbi.nlm.nih.gov/articles/PMC12427036/

Figure 2

Fine mapping of Xa50(t) on Chromosome 11. Genetic mapping of the resistance gene Xa50(t) using recombinants from the F2 population. The region was narrowed down to a 147.7 kb interval flanked by markers M11–588 and M11–602 on Chromosome 11. The recombination frequency is displayed for key markers, and the final co-segregating marker (M11-489) is indicated in red. Within the interval, 14 predicted open reading frames were identified.