Xanthomonas oryzaepv.oryzicola(Xoc) andX.oryzaepv.oryzae(Xoo) cause bacterial leaf streak (BLS) and bacterial leaf blight (BLB) in rice, respectively. UnlikeXoo, endogenous avirulence-resistance (avr-R) gene interactions have not been identified in theXoc-rice pathosystem; however, both pathogens possess transcription activator-like effectors (TALEs) that are known to modulateRorSgenes in rice. The transfer of individualtalgenes fromXocRS105 (hypervirulent) intoXocYNB0-17 (hypovirulent) led to the identification oftal7, which suppressedavrXa7-Xa7mediated defense in rice containing anXa7 Rgene. Mobility shift and microscale thermophoresis assays showed that Tal7 bound two EBE sites in the promoters of two rice genes,Os09g29100andOs12g42970, which encode predicted Cyclin-D4-1 and GATA zinc finger family protein, respectively. Assays using designer TALEs and a TALE-free strain ofXoorevealed thatOs09g29100was the biologically relevant target of Tal7. Tal7 activates the expression of rice geneOs09g29100that suppressesavrXa7-Xa7mediated defense in Rice. TALEN editing of the Tal7-binding site in theOs09g29100gene promoter further enhanced resistance to the pathogenXocRS105. The suppression of effector-trigger immunity (ETI) is a phenomenon that may contribute to the scarcity of BLS resistant cultivars.

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.

The total protein contents of rice seeds are significantly higher in the three wild rice species (Oryza rufipogon Grill., Oryza officinalis Wall. and Oryza meyeriana Baill.) than in the cultivated rice (Oryza sativa L.). However, there is still no report regarding a systematic proteomic analysis of seed proteins in the wild rice species. Also, the relationship between the contents of seed total proteins and rice nutritional quality has not been thoroughly investigated. The total seed protein contents, especially the glutelin contents, of the three wild rice species were higher than those of the two cultivated rice materials. Based on the protein banding patterns of SDS-PAGE, O. rufipogon was similar to the two cultivated rice materials, followed by O. officinalis, while O. meyeriana exhibited notable differences. Interestingly, O. meyeriana had high contents of glutelin and low contents of prolamine, and lacked 26 kDa globulin band and appeared a new 28 kDa protein band. However, for O. officinali a 16 kDa protein band was absent and a row of unique 32 kDa proteins appeared. In addition, we found that 13 kDa prolamine band disappeared while special 14 kDa and 12 kDa protein bands were present in O. officinalis. Two-dimensional gel electrophoresis (2-DE) analysis revealed remarkable differences in protein profiles of the wild rice species and the two cultivated rice materials. Also, the numbers of detected protein spots of the three wild rice species were significantly higher than those of two cultivated rice. A total of 35 differential protein spots were found for glutelin acidic subunits, glutelin precursors and glutelin basic subunits in wild rice species. Among those, 18 protein spots were specific and 17 major spots were elevated. Six differential protein spots for glutelin acidic subunits were identified, including a glutelin type-A 2 precursor and five hypothetical proteins. This was the first report on proteomic analysis of the three wild rice species. Overall results suggest that there were many new types of glutelin subunits and precursor in the three wild rice species. Hence, wild rice species are important genetic resources for improving nutritional quality to rice.

Oryza officinalis Wall ex Watt is one of the most important wild relatives of cultivated rice and exhibits high resistance to many diseases. It has been used as a source of genes for introgression into cultivated rice. However, there are limited genomic resources and little genetic information publicly reported for this species. To better understand the pathways and factors involved in disease resistance and accelerating the process of rice breeding, we carried out a de novo transcriptome sequencing of O. officinalis. In this research, 137,229 contigs were obtained ranging from 200 to 19,214 bp with an N50 of 2331 bp through de novo assembly of leaves, stems and roots in O. officinalis using an Illumina HiSeq 2000 platform. Based on sequence similarity searches against a non-redundant protein database, a total of 88,249 contigs were annotated with gene descriptions and 75,589 transcripts were further assigned to GO terms. Candidate genes for plant–pathogen interaction and plant hormones regulation pathways involved in disease-resistance were identified. Further analyses of gene expression profiles showed that the majority of genes related to disease resistance were all expressed in the three tissues. In addition, there are two kinds of rice bacterial blight-resistant genes in O. officinalis, including two Xa1 genes and three Xa26 genes. All 2 Xa1 genes showed the highest expression level in stem, whereas one of Xa26 was expressed dominantly in leaf and other 2 Xa26 genes displayed low expression level in all three tissues. This transcriptomic database provides an opportunity for identifying the genes involved in disease-resistance and will provide a basis for studying functional genomics of O. officinalis and genetic improvement of cultivated rice in the future.

Rice bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the devastating diseases of rice. It is well established that the wild rice Oryza meyeriana is immune to BB. In this study, the transcriptomic analysis was carried out by RNA sequencing of O. meyeriana leaves, inoculated with Xoo to understand the transcriptional responses and interaction between the host and pathogen. Totally, 57,313 unitranscripts were de novo assembled from 58.7 Gb clean reads and 14,143 unitranscripts were identified after Xoo inoculation. The significant metabolic pathways related to the disease resistance enriched by KEGG, were revealed to plant-pathogen interaction, phytohormone signaling, ubiquitin mediated proteolysis, and phenylpropanoid biosynthesis. Further, many disease resistance genes were also identified to be differentially expressed in response to Xoo infection. Conclusively, the present study indicated that the induced innate immunity comprise the basal defence frontier of O. meyeriana against Xoo infection. And then, the resistance genes are activated. Simultaneously, the other signaling transduction pathways like phytohormones and ubiquitin mediated proteolysis may contribute to the disease defence through modulation of the disease-related genes or pathways. This could be an useful information for further investigating the molecular mechanism associated with disease resistance in O. meyeriana.

Plant proteins that belong to the nonexpressor of pathogenesis-related genes (NPR) family are paralogous receptors of the plant defense hormone salicylic acid and essential regulators of the hormone-dependent plant immunity against diseases caused by various pathogens. Previous studies have established NPR1 and NPR3 as a transcriptional activator and a transcriptional repressor, respectively, for defense gene expression to promote and inhibit broad-spectrum resistance against different strains of pathogens. However, the regulatory mechanism underlying the opposite roles of NPR1 and NPR3 in defense gene activation remains unclear. Here we report that a rice transcript splicing factor, Oryza sativa RNA-binding protein 11 (OsRBP11), promotes alternative splicing of OsNPR3 to modulate the defense function of OsNPR1 in rice plants under infection by Xanthomonas oryzae pathovars, which are predominant bacterial pathogens of rice. We discovered that 11 transcription activator-like effectors identified in representative bacterial strains activate OsRBP11 expression. The ensuing OsRBP11 protein, in turn, facilitates alternative splicing of the OsNPR3 mRNA precursor, leading to the production of truncated OsNPR3 protein variants. The OsNPR3 variants aggravate bacterial diseases by sequestering OsNPR1 from defense activation. Contrarily, both artificial and natural variations in OsRBP11 prevent OsNPR3 from alternative splicing, return the defense function to OsNPR1, and enhance rice resistance to different bacterial strains. These findings not only unveil a novel regulatory pathway that is exploited by bacterial pathogens to facilitate their pathogenicity along with subverting plant defense, but also disclose a genetic basis for the biotechnological strategy of developing broad-spectrum resistance in crops in the future.