Bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae is a common, widespread, and highly devastating disease that affects rice yield. Breeding resistant cultivars is considered the most effective measure for controlling this disease. The introgression line G252 derived from Yuanjiang common wild rice (Oryza rufipogon) was highly resistant to all tested strains, including C5, C9, PXO99, PB, T7147Y8, Hzhj19, YM1, YM187, YJdp-2, and YJws-2. To identify the BB resistance gene(s) of G252, we developed an F₂ population from the cross between G252 and 02428. A linkage analysis was performed for the phenotype and genotype of the population. A segregation ratio of 3:1 was observed between the resistant and susceptible individuals in the F₂ progeny, indicating a dominant resistance gene, Xa47(t), in G252. The resistance gene was mapped within an approximately 26.24-kb physical region on chromosome 11 between two InDel markers, R13I14 and 13rbq-71. Moreover, one InDel marker, Hxjy-1, co-segregated with Xa47(t). Three genes were predicted within the target region, including a promising candidate gene encoding a nucleotide-binding domain and leucine-rich repeat (NLR) protein (LOC_Os11g46200) by combining the structure and expression analysis. Physical mapping data suggested that Xa47(t) is a new broad-spectrum BB resistance gene without identified allelic genes.

Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is among the oldest known bacterial diseases found for rice in Asia. It is the most serious bacterial disease in many rice growing regions of the world. A total of 47 resistance (R) genes (Xa1 to Xa47) have been identified. Nonetheless, these R genes could possibly be defeated to lose their qualitative nature and express intermediate phenotypes. The identification of sources of novel genetic loci regulating host plant resistance is crucial to develop an efficient control strategy. Wild ancestors of cultivated rice are a natural genetic resource contain a large number of excellent genes. Medicinal wild rice (Oryza officinalis) belongs to the CC genome and is a well-known wild rice in south China. In this study, O. officinalis was crossed with cultivated rice HY-8 and their hybrids were screened for BB resistance genes deployed through natural selection in wild rice germplasm. The molecular markers linked to R genes for BB were used to screen the genomic regions in wild parents and their recombinants. The gene coding and promoter regions of major R genes were inconsistently found in O. officinalis and its progenies. Oryza officinalis showed resistance to all thirty inoculated Xoo strains with non-availability of various known R genes. The results indicated the presence of novel genomic regions for BB resistance in O. officinalis. The present study not only provides a reference to investigate medicinal rice for R gene(s) identification against BB but also identified it as a new breeding material for BB resistance.

The rice blight poses a significant threat to the rice industry, and the discovery of disease-resistant genes is a crucial strategy for its control. By exploring the rich genetic resources of Yuanjiang common wild rice (Oryza rufipogon) and analyzing their expression patterns, genetic resources can be provided for molecular rice breeding. The target genes’ expression patterns, subcellular localization, and interaction networks were analyzed based on the annotated disease-resistant genes on the 9th and 10th chromosomes in the rice genome database using fluorescent quantitative PCR technology and bioinformatics tools. Thirty-three disease-resistant genes were identified from the database, including 20 on the 9th and 13 on the 10th. These genes were categorized into seven subfamilies of the NLR family, such as CNL and the G subfamily of the ABC family. Four genes were not expressed under the induction of the pathogen Y8, two genes were significantly down-regulated, and the majority were up-regulated. Notably, the expression levels of nine genes belonging to the ABCG, CN, and CNL classes were significantly up-regulated, yet the expression levels varied among roots, stems, and leaves; one was significantly expressed in the roots, one in the stems, and the remaining seven were primarily highly expressed in the leaves. Two interaction network diagrams were predicted based on the seven highly expressed genes in the leaves: complex networks regulated by CNL proteins and specific networks controlled by ABCG proteins. The disease-resistant genes on the 9th chromosome are actively expressed in response to the induction of rice blight, forming a critical gene pool for the resistance of Yuanjiang common wild rice (O. rufipogon) to rice blight. Meanwhile, the disease-resistant genes on the 10th chromosome not only participate in resisting the rice blight pathogen but may also be involved in the defense against other stem diseases.

Background/Objectives: Bacterial blight (BB) represents one of the most devastating diseases threatening global rice production. Exploring and characterizing disease resistance (R) genes provides an effective strategy for controlling BB and enhancing rice resilience. Common wild rice (Oryza rufipogon) serves as a valuable reservoir of genetic diversity and disease resistance resources. In this study, we identified and functionally characterized a novel NLR gene, YPR1, from common wild rice (Oryza rufipogon), which exhibited significant spatial, temporal, and tissue-specific expression patterns. Methods: Using a combination of conventional PCR, RT-PCR, bioinformatics, transgenic analysis, and CRISPR/Cas9 gene-editing approaches, the full-length YPR1 sequence was successfully cloned. Results: The gene spans 4689 bp with a coding sequence (CDS) of 2979 bp, encoding a 992-amino acid protein. Protein domain prediction revealed that YPR1 is a typical CNL-type NLR protein, comprising RX-CC_like, NB-ARC, and LRR domains. The predicted molecular weight of the protein is 112.43 kDa, and the theoretical isoelectric point (pI) is 8.36. The absence of both signal peptide and transmembrane domains suggests that YPR1 functions intracellularly. Furthermore, the presence of multiple phosphorylation sites across diverse residues implies a potential role for post-translational regulation in its signal transduction function. Sequence alignment showed that YPR1 shared 94.02% similarity with Os09g34160 and up to 96.47% identity with its closest homolog in the NCBI database, confirming that YPR1 is a previously unreported gene. To verify its role in disease resistance, an overexpression vector (Ubi–YPR1) was constructed and introduced into the BB-susceptible rice cultivar JG30 via Agrobacterium tumefaciens-mediated transformation. T₁ transgenic lines were subsequently inoculated with 15 highly virulent Xanthomonas oryzae pv. oryzae (Xoo) strains. The transgenic plants exhibited strong resistance to eight strains (YM1, YM187, C1, C5, C6, T7147, PB, and HZhj19), demonstrating a broad-spectrum resistance pattern. Conversely, CRISPR/Cas9-mediated knockout of YPR1 in common wild rice resulted in increased susceptibility to most Xoo strains. Although the resistance of knockout lines to strains C7 and YM187 was comparable to that of the wild type (YP^WT), the majority of knockout plants exhibited more severe symptoms and significantly lower YPR1 expression levels compared with YP^WT. Conclusions: Collectively, these findings demonstrate that YPR1 plays a crucial role in bacterial blight resistance in common wild rice. As a novel CNL-type NLR gene conferring specific resistance to multiple Xoo strains, YPR1 provides a promising genetic resource for the molecular breeding of BB-resistant rice varieties.