Bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) 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 Xoo 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 carried out between the phenotype and genotype in the population. A segregation ratio of 3:1 was observed between the resistant and susceptible individuals in 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; and 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) was a new broad-spectrum BB resistance gene.

Background Bacterial blight (BB) caused by Xanthomonas oryzae Pv. oryzae (Xoo) is one of the most serious diseases of rice worldwide. Oryza officinalis Wall ex Watt, harboring abundant genetic diversity and disease resistance features, are important resources of exploring resistance genes with broad-spectrum resistance to BB. However, the molecular mechanisms and genes of BB resistance in O. officinalis have been rarely explored. Results Here, the BB resistance of four different origin O. officinalis populations in Yunnan were identified by seven representative hypervirulent Xoo races, which exhibited different BB resistance among four populations, in which the BB resistance of the Gengma_Lincang population was the strongest. In addition, the pathogenetic ability of seven Xoo races to O. officinalis was different in that the pathogenicity of PXO99 was stronger than that of C5. There were no remarkable differences in leaf microstructures among four O. officinalis populations, revealing the differences in resistance of four O. officinalis to BB are caused by the endogenous resistance genes. Furthermore, our results proved that there were no nine cloned BB resistance genes in four populations but possessed dominant Xa5, dominant Xa13, and recessive xa3/xa26 homologous alleles of xa5, xa13, and Xa3/Xa26 resistance genes. These three homologous genes were isolated and cloned from four populations and named OoXa5, OoXa13, and Ooxa3/xa26. The expression profile revealed that the expression levels of OoXa13 and Ooxa3/xa26 were significantly down-regulated under PXO99 and C5 stress, especially in the Gengma_Lincang population, suggesting the O. officinalis might enhance BB resistance by down-regulating the expression level of OoXa13 and Ooxa3/xa26. Conclusion The BB resistance genes of O. officinalis had its own characteristics by expression pattern and BLAST analysis of OoXa5, OoXa13, and Ooxa3/xa26, which indicated that there might be new genes or molecular mechanism of BB resistance in O. officinalis. Our studies provided a solid foundation and reference for revealing the molecular mechanism of BB resistance in O. officinalis.

Oryza officinalis Wall ex Watt, a very important and special wild rice species, shows abundant genetic diversity and disease resistance features, especially high resistance to bacterial blight. The molecular mechanisms of bacterial blight resistance in O. officinalis have not yet been elucidated. The WRKY transcription factor family is one of the largest gene families involved in plant growth, development and stress response. However, little is known about the numbers, structure, molecular phylogenetics, and expression of the WRKY genes under Xanthomonas oryzae pv. oryzae (Xoo) stress in O. officinalis due to lacking of O. officinalis genome. Therefore, based on the RNA-sequencing data of O. officinalis, we performed a comprehensive study of WRKY genes in O. officinalis and identified 89 OoWRKY genes. Then 89 OoWRKY genes were classified into three groups based on the WRKY domains and zinc finger motifs. Phylogenetic analysis strongly supported that the evolution of OoWRKY genes were consistent with previous studies of WRKYs, and subgroup IIc OoWRKY genes were the original ancestors of some group II and group III OoWRKYs. Among the 89 OoWRKY genes, eight OoWRKYs displayed significantly different expression (>2-fold, p<0.01) in the O. officinalis transcriptome under Xoo strains PXO99 and C5 stress 48 h, suggesting these genes might play important role in PXO99 and C5 stress responses in O. officinalis. QRT-PCR analysis and confirmation of eight OoWRKYs expression patterns revealed that they responded strongly to PXO99 and C5 stress 24 h, 48 h, and 72 h, and the trends of these genes displaying marked changes were consistent with the 48 h RNA-sequencing data, demonstrated these genes played important roles in response to biotic stress and might even involved in the bacterial blight resistance. Tissue expression profiles of eight OoWRKY genes revealed that they were highly expressed in root, stem, leaf, and flower, especially in leaf (except OoWRKY71), suggesting these genes might be also important for plant growth and organ development. In this study, we analyzed the WRKY family of transcription factors in O.officinalis. Insight was gained into the classification, evolution, and function of the OoWRKY genes, revealing the putative roles of eight significantly different expression OoWRKYs in Xoo strains PXO99 and C5 stress responses in O.officinalis. This study provided a better understanding of the evolution and functions of O. officinalis WRKY genes, and suggested that manipulating eight significantly different expression OoWRKYs would enhance resistance to bacterial blight.

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Bacterial blight (BB) induced by Xanthomonas oryzae pv. oryzae (Xoo) is a devastating bacterial disease in rice. The use of disease resistance (R) genes is the most efficient method to control BB. Members of the nucleotide-binding domain and leucine-rich repeat containing protein (NLR) family have significant roles in plant defense. In this study, Xa47, a new bacterial blight R gene encoding a typical NLR, was isolated from G252 rice material, and XA47 was localized in the nucleus and cytoplasm. Among 180 rice materials tested, Xa47 was discovered in certain BB-resistant materials. Compared with the wild-type G252, the knockout mutants of Xa47 was more susceptible to Xoo. By contrast, overexpression of Xa47 in the susceptible rice material JG30 increased BB resistance. The findings indicate that Xa47 positively regulates the Xoo stress response. Consequently, Xa47 may have application potential in the genetic improvement of plant disease resistance. The molecular mechanism of Xa47 regulation merits additional examination.