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.

Fungal effectors play an important role in plant immunity. The Magnaporthe oryzae effector PWL2 plays a significant role in rice blast disease caused by this fungus. However, the function of PWL2 in rice immunity is not fully understood. In this study, transgenic rice lines overexpressing PWL2 showed resistance to rice blast. Subcellular localization showed that PWL2-GFP fusion protein is localized on the plasma membrane and cytoplasm. Salicylic acid (SA) induces rice resistance to M. oryzae. Notably, the expression of the NPR1 gene exhibited a rhythmic pattern during the early stages of M. oryzae infection in the transgenic rice lines. However, during later stages of infection, transgenic plants showed reduced levels of the NPR1, WRKY45, PR1a and PR10a genes, along with decreased H₂O₂ accumulation, while SA levels remained unchanged. Transcriptome analysis revealed that SA treatment induced the expression of the ARGONAUTE11 (AGO11) gene in rice. Furthermore, during the later infection stage in the transgenic rice lines, the expression levels of both AGO11 and PWL2 genes increased. Intriguingly, PWL2-derived small interfering RNAs (siRNA) were detected in these transgenic rice lines. It suggests that both the SA signaling pathway and PWL2-derived siRNAs function in rice resistance to blast disease caused by M. oryzae.

Rice blast, caused by the fungus Magnaporthe oryzae, is one of the most devastating threatening to global rice production. The narrow genetic background of modern rice cultivars exacerbates the shortage of durable resistance resources. In contrast, the wild rice species Oryza officinalis harbors abundant stress-resistance alleles and represents a valuable gene pool for identifying novel broad blast-resistance genes. The cloned resistance gene Pid2 is encoded in a receptor-like protein kinase conferring race-specific resistance against the M. oryzae isolate ZB15. In this study, three Pid2 homologs were isolated from O. officinalis. The special allele Pid2of-MD33 was transformed into “Yunjing 37(YG37), a blast-susceptible japonica rice cultivar” via Agrobacterium-mediated transformation. Quantitative real-time PCR analysis showed that Pid2of-MD33 was consistently expressed in various tissues of O. officinalis, with the highest transcript abundance detected in leaf mesophyll cells and plasma membranes. Inoculation with the M. oryzae isolate ZB15 revealed that transgenic YG37 lines expressing Pid2of-MD33 displayed significantly reduced lesion size and pathogen proliferation, suggesting recovered race-specific resistance. These results enrich the resistance gene resources for rice blast research and provide a promising candidate gene for rice blast resistance breeding.

Endophytic microbial communities play an important role in plant development, nutrient acquisition, and oxidative stress tolerance. Oryza officinalis and Oryza meyeriana are unique wild rice varieties in China with many high-quality resistance genes, rich endophyte diversity, and potential resources for sustainable agriculture. In the present study, the endophytic microbial community structures of O. officinalis , O. meyeriana , and cultivated rice were compared using metagenomic sequencing. Dechloromonas , Salmonella , Klebsiella , and Listeria were the core microbial groups in wild and cultivated rice. The relative abundances of Ligilactobacillus , Escherichia , and Bradyrhizobium in O. meyeriana were higher than those in cultivated rice. The relative abundances of Listeria , Acinetobacter , Escherichia , and Dechloromonas in O. officinalis were also higher. Compared to that of cultivated rice, the microbiota of wild rice had a more complex and stable community network. At the pathway level 2 based on the Kyoto Encyclopedia of Genes and Genomes classification system, the relative abundance of metabolic categories was dominant. Most pathways showed that the O. officinalis relative abundance was higher than those of the other two species. Our study revealed differences in the leaf endophyte community structure and function between wild and cultivated rice in the same habitat, demonstrating the potential of wild rice in recruiting specific microorganisms to improve crop performance and promote safe and sustainable food production. IMPORTANCE: Under the current climate change environment, plant-beneficial endophytes are of great significance for promoting food production. Modern cultivars may have lost many beneficial endophytes compared to their ancestors. However, relatively few studies have been conducted on the community structure and function of modern ancestral crop endophytes. In this study, the composition and function of the microbial communities of two wild rice species were analyzed; the differences between them and cultivated rice were determined; and the patterns of microbial interactions and their core microbiomes were determined. Our findings can aid in the exploration of the beneficial endophytes in wild rice and use them to improve crop stress resistance and sustainability. These results provide relevant insights into the role of endophytes in the mechanism of high-stress resistance in wild rice.