Xoo Strains Research Articles

Development and Validation of an SNP Marker for Identifying Xanthomonas oryzae pv. oryzae Thai Isolates That Break xa5-Mediated Bacterial Blight Resistance in Rice.

Xanthomonas oryzae pv. oryzae (Xoo) is a pathogenic bacterium responsible for bacterial blight (BB) disease in rice, primarily mediated by the interaction between the plant and pathogen. The virulence mechanism involves the activation of the Sugars Will Eventually be Exported Transporter (SWEET) gene family in rice by transcription activator-like effectors derived from Xoo. The BB resistance gene xa5 has been identified as one of the most effective genes against Thai Xoo isolates, but xa5-mediated resistance-breaking Xoo strains have emerged. This study aimed to develop a single nucleotide polymorphism (SNP) marker for precise identification of xa5-mediated resistance-breaking Xoo. Comparative genomics of Thai Xoo isolates Xoo16PK001 and Xoo16PK002, which were incompatible and compatible with rice variety IRBB5 carrying xa5, respectively, identified eight SNP positions for the development of an SNP marker. The SNP marker XooE6 yields a specific 1,143 bp PCR product unique to Xoo16PK002. Screening 61 Thai isolates using XooE6 identified two positives: Xoo20PL010 and Xoo20UT002. Inoculation tests on rice varieties IRBB5 and IRBB13 demonstrated compatibility with IRBB5 and incompatibility with IRBB13, which bears Xa5 and xa13. Xoo16PK001 (XooE6-negative) showed different virulence. Inoculation on IRBB21 harboring Xa5, Xa13, and Xa21 resulted in partial resistance to both XooE6-positive and -negative strains. XooE6-positive strains up-regulated SWEET11 and suppressed SWEET14 in IRBB5, while Xoo16PK001 slightly induced SWEET11 but activated SWEET14 in IRBB13. This highlights the potential of XooE6 to identify xa5-mediated resistance-breaking Xoo strains and elucidate their pathogenic mechanisms through the upregulation of SWEET11.

Genome-Wide Transcriptome Analysis of a Virulent sRNA, Trans217, in Xanthomonas oryzae pv. oryzae (Xoo), the Causative Agent of Rice Bacterial Blight.

Small non-coding RNAs (sRNAs) act as post-transcriptional regulators to participate in many cellular processes. Among these, sRNA trans217 has been identified as a key virulent factor associated with pathogenicity in rice, triggering hypersensitive reactions in non-host tobacco and facilitating the secretion of the PthXo1 effector in Xanthomonas oryzae pv. oryzae (Xoo) strain PXO99A. Elucidating potential targets and downstream regulatory genes is crucial for understanding cellular networks governing pathogenicity and plant resistance. To explore the targets regulated by sRNA trans217, transcriptome sequencing was carried out to assess differential expression genes (DEGs) between the wild-type strain PXO99A and a mutant lacking the sRNA fragment under both virulence-inducing or normal growth conditions. DEG analysis revealed that sRNA trans217 was responsible for diverse functions, such as type III secretion system (T3SS), glutamate synthase activity, and oxidative stress response. Three genes were selected for further investigation due to their significant differential expression and biological relevance. Deletion of PXO_RS08490 attenuated the pathogenicity of Xoo in rice and reduced the tolerance level of PXO99A to hydrogen peroxide. These findings suggest a regulatory role of sRNA trans217 in modulating bacterial virulence through multiple gene targets, either directly or indirectly.

Effect of mutation of phaC on carbon supply, extracellular polysaccharide production, and pathogenicity of Xanthomonas oryzae pv. oryzae

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight in rice. Polyhydroxyalkanoates (PHAs) consitute a diverse group of biopolyesters synthesized by bacteria under nutrient-limited conditions. The phaC gene is important for PHA polymerization. We investigated the effects of phaC gene mutagensis in Xoo strain PXO99A. The phaC gene knock-out mutant exhibited reduced swarming ability relative to that of the wild-type. Under conditions where glucose was the sole sugar source, extracellular polysaccharide (EPS) production by ΔphaC declined by 44.8%. ΔphaC showed weak hypersensitive response (HR) induction in the leaves of non-host Nicotiana tabacum, concomitant with downregulation of hpa1 gene expression. When inoculated in rice leaves by the leaf-clipping method, ΔphaC displayed reduced virulence in terms of lesion length compared with the wild-type strain. The complemented strain showed no significant difference from the wild-type strain, suggesting that the deletion of phaC in Xoo induces significant alterations in various physiological and biological processes. These include bacterial swarming ability, EPS production, transcription of hrp genes, and glucose metabolism. These changes are intricately linked to the energy utilization and virulence of Xoo during plant infection. These findings revealed involvement of phaC in Xoo is in the maintaining carbon metabolism by functioning in the PHA metabolic pathway.

In planta ANALYSIS OF SALICYLIC ACID MEDIATED MANAGEMENT OF

Bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is a catastrophic bacterial disease of rice, and researchers are facing difficulties in developing the management practices, whereas the continued use of bactericides viz, streptomycin, copper oxychloride leads to the development of resistant Xoo strains. As a consequence, the development of an environmentally safe bactericide for the management of this devastating disease is needed. The present study focused on identification of effective synthetic activators against bacterial leaf blight in rice during their interaction. Survey was conducted to collect different isolates of Xoo and their morphological characters and biochemical properties were determined. All the 10 isolates exhibited circular to flattened slimy yellow colour colonies of the pathogen and showed positive reaction for citrate utilization, lysine utilization and ornithine utilization test. All the ten isolates showed negative reaction for sorbitol utilization. The collected isolates were subjected to PCR for the amplification of 16S-23S intergenic region with the species specific primer and obtained amplicon at ⁓470 bp for the confirmation at molecular level. The virulent isolate was identified by measuring biofilm formation and xanthomonadin pigment which revealed that the isolate ADT 53 strain T3 with the accession number OR121377 recorded maximum OD value of 0.356 for biofilm formation at 570 nm and 0.686 for xanthomonadin pigment at 445 nm. In planta studies revealed that salicylic acid at 100 ppm has the maximum inhibitory effect against bacterial leaf blight disease with the minimal lesion size of 0.7 cm compared to negative control (water). Keywords: Activators, BLB, Biofilm, Characterization, in planta, Xanthomonadin.

A KNOX Ⅱ transcription factor suppresses the NLR immune receptor BRG8-mediated immunity in rice

Nucleotide-binding site and leucine-rich repeat (NLR) proteins are activated by detecting pathogen effectors, which in turn trigger host defenses and cell death. Although many NLRs have been identified, the mechanisms responsible for NLR-triggered defense responses are still poorly understood. In this study, through a genome-wide association study approach, we identified a novel NLR gene, Blast Resistance Gene 8 (BRG8), which confers resistance to rice blast and bacterial blight diseases. BRG8 overexpression and complementation lines exhibit enhanced resistance to both pathogens. Subcellular localization assays showed that BRG8 is localized in both the cytoplasm and the nucleus. Additional evidence revealed that nuclear-localized BRG8 can enhance rice immunity without a hypersensitive response (HR)-like phenotype. We also demonstrated that the coiled-coil domain of BRG8 not only physically interacts with itself but also interacts with the KNOX Ⅱ protein HOMEOBOX ORYZA SATIVA59 (HOS59). Knockout mutants of HOS59 in the BRG8 background show enhanced resistance to Magnaporthe oryzae strain CH171 and Xoo strain CR4, similar to that of the BRG8 background. By contrast, overexpression of HOS59 in the BRG8 background will compromise the HR-like phenotype and resistance response. Further analysis revealed that HOS59 promotes the degradation of BRG8 via the 26S proteasome pathway. Collectively, our study highlights HOS59 as an NLR immune regulator that fine-tunes BRG8-mediated immune responses against pathogens, providing new insights into NLR associations and functions in plant immunity.

Integrative genomic and transcriptomic analysis of Xanthomonas oryzae pv. oryzae pathotype IV, V, and IX in China reveals rice defense-responsive genes

Bacterial blight of rice is a devastating disease caused by the gram-negative bacteria Xanthomonas oryzae pv. oryzae (Xoo). Chinese Xoo strain pathotypes IV, V, and IX are the major virulent Xoo strain types in South China sequentially from the 1990s to the present. Here, we report the isolation of GD0201 and GD0202, which belong to pathotypes IV and IX, respectively, and the complete genome sequence and transcriptomic analysis of GD0201 (IV), GD1358 (V), and GD0202 (IX). We found that resistance genes xa5, Xa23, and Xa27 confer strong resistance to all three Xoo strains, indicating that they are currently good choices for resistance rice breeding. The genome analysis reveals fewer TAL and non-TAL effector coding genes in GD0202 than in the other two strains, potentially contributing to its strong virulence. Transcriptomic analysis of ZH11 inoculated with the three Xoo strains strongly suggests that three Xoo strains for better infection repress the ethylene response factor (ERF) gene family members. Furthermore, weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) analysis revealed 14 hub genes potentially associated with rice response to the three Xoo strains. The expression of several hub genes was validated to be induced by all three Xoo strains, suggesting its role in bacterial blight disease response to Xoo strains. Genomic analysis of the Xoo strains belonging to pathotypes IV, V, and IX, identification of effectors and genes related to Xoo virulence in rice plants will provide insights into understanding the molecular mechanism underlying rice-Xoo interaction and the gene expression pattern in response to Xoo infection.

XA21-mediated resistance to Xanthomonas oryzae pv. oryzae is dose dependent.

The rice receptor kinase XA21 confers broad-spectrum resistance to Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of rice bacterial blight disease. To investigate the relationship between the expression level of XA21 and resulting resistance, we generated independent HA-XA21 transgenic rice lines accumulating the XA21 immune receptor fused with an HA epitope tag. Whole-genome sequence analysis identified the T-DNA insertion sites in sixteen independent T0 events. Through quantification of the HA-XA21 protein and assessment of the resistance to Xoo strain PXO99 in six independent transgenic lines, we observed that XA21-mediated resistance is dose dependent. In contrast, based on the four agronomic traits quantified in these experiments, yield is unlikely to be affected by the expression level of HA-XA21. These findings extend our knowledge of XA21-mediated defense and contribute to the growing number of well-defined genomic landing pads in the rice genome that can be targeted for gene insertion without compromising yield.

Constructed Rice Tracers Identify the Major Virulent Transcription Activator-Like Effectors of the Bacterial Leaf Blight Pathogen

Xanthomonas oryzae pv. oryzae (Xoo) injects major transcription activator-like effectors (TALEs) into plant cells to activate susceptibility (S) genes for promoting bacterial leaf blight in rice. Numerous resistance (R) genes have been used to construct differential cultivars of rice to identify races of Xoo, but the S genes were rarely considered. Different edited lines of rice cv. Kitaake were constructed using CRISPR/Cas9 gene-editing, including single, double and triple edits in the effector-binding elements (EBEs) located in the promoters of rice S genes OsSWEET11a, OsSWEET13 and OsSWEET14. The near-isogenic lines (NILs) were used as tracers to detect major TALEs (PthXo1, PthXo2, PthXo3 and their variants) in 50 Xoo strains. The pathotypes produced on the tracers determined six major TALE types in the 50 Xoo strains. The presence of the major TALEs in Xoo strains was consistent with the expression of S genes in the tracers, and it was also by known genome sequences. The EBE editing had little effect on agronomic traits, which was conducive to balancing yield and resistance. The rice-tracers generated here provide a valuable tool to track major TALEs of Xoo in Asia which then shows what rice cultivars are needed to combat Xoo in the field.

Disease resistance features of the executor R gene Xa7 reveal novel insights into the interaction between rice and Xanthomonas oryzae pv. oryzae.

Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is a widespread and destructive disease in rice production. Previously, we cloned an executor R gene, Xa7, which confers durable and broad-spectrum resistance to BB. Here, we further confirmed that the transcription activator-like effector (TALE) AvrXa7 in Xoo strains could directly bind to the effector-binding element (EBE) in the promoter of the Xa7 gene. Other executor R genes (Xa7, Xa10, Xa23, and Xa27) driven by the promoter of the Xa7 gene could be activated by AvrXa7 and trigger the hypersensitive response (HR) in tobacco leaves. When the expression of the Xa23 gene was driven by the Xa7 promoter, the transgenic rice plants displayed a similar resistance spectrum as the Xa7 gene, demonstrating that the disease resistance characteristics of executor R genes are mainly determined by their induction patterns. Xa7 gene is induced locally by Xoo in the infected leaves, and its induction not only inhibited the growth of incompatible strains but also enhanced the resistance of rice plants to compatible strains, which overcame the shortcomings of its race-specific resistance. Transcriptome analysis of the Xa7 gene constitutive expression in rice plants displayed that Xa7-mediated disease resistance was related to the biosynthesis of lignin and thus enhanced resistance to Xoo. Overall, our results provided novel insights and important resources for further clarifying the molecular mechanisms of the executor R genes.

Genome-wide association mapping in rice MAGIC indica panel detects QTLs and genes for broad-spectrum resistance breeding against African bacterial blight

Rice (Oryza sativa) bacterial blight (BB) is a direct threat to production in Africa. The extent of damage on the continent is not known. We conducted a genome-wide association study (GWAS) to seek out Quantitative trait loci (QTL) that confer the broad-spectrum resistance (BSR) to rice Xanthomonas oryzae pv. oryzae in the rice Multiparent advanced generation intercross (MAGIC) population. The diverse genetic composition and high levels of recombination, are potential resources for the identification of QTL for BSR. Dealing with the ever-evolving Xoo requires identification of novel R gene and resistance quantitative trait loci (QTL). We conducted a genome-wide association study (GWAS) using 250 rice MAGIC indica panel to evaluate for resistance to three Xoo strains from Cote D'Ivoire, namely XooCIkor, XooCIgag and XooCIcii2 which are prevalent highly virulent pathotypes. Using the 3 K RG 4.8mio filtered SNP Dataset, a total of 3 QTL associated with BB resistance on chromosome 9, 6 and 5 were identified. The results of the GWAS identified novel loci that gives useful insight for more investigation and also validated known genes underlying resistance to virulent African strains of BB. Genetic donors identified in this will help plant breeders in improving and broadening resistance to BB.

Ectopic Expression of the Executor-Type R Gene Paralog Xa27B in Rice Leads to Spontaneous Lesions and Enhanced Disease Resistance.

Plant disease resistance (R) gene-mediated effector-triggered immunity (ETI) is usually associated with hypersensitive response (HR) and provides robust and race-specific disease resistance against pathogenic infection. The activation of ETI and HR in plants is strictly regulated, and improper activation will lead to cell death. Xa27 is an executor-type R gene in rice induced by the TAL effector AvrXa27 and confers disease resistance to Xanthomonas oryzae pv. oryzae (Xoo). Here we reported the characterization of a transgenic line with lesion mimic phenotype, designated as Spotted leaf and resistance 1 (Slr1), which was derived from rice transformation with a genomic subclone located 5,125 bp downstream of the Xa27 gene. Slr1 develops spontaneous lesions on its leaves caused by cell death and confers disease resistance to both Xoo and Xanthomonas oryzae pv. oryzicola. Further investigation revealed that the Slr1 phenotype resulted from the ectopic expression of an Xa27 paralog gene, designated as Xa27B, in the inserted DNA fragment at the Slr1 locus driven by a truncated CaMV35Sx2 promoter in reverse orientation. Disease evaluation of IRBB27, IR24, and Xa27B mutants with Xoo strains expressing dTALE-Xa27B confirmed that Xa27B is a functional executor-type R gene. The functional XA27B-GFP protein was localized to the endoplasmic reticulum and apoplast. The identification of Xa27B as a new functional executor-type R gene provides additional genetic resources for studying the mechanism of executor-type R protein-mediated ETI and developing enhanced and broad-spectrum disease resistance to Xoo through promoter engineering. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Pathogen-induced methylglyoxal negatively regulates rice bacterial blight resistance by inhibiting OsCDR1 protease activity

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight (BB), a globally devastating disease of rice (Oryza sativa) that is responsible for significant crop loss. Sugars and sugar metabolites are important for pathogen infection, providing energy and regulating events associated with defense responses; however, the mechanisms by which they regulate such events in BB are unclear. As an inevitable sugar metabolite, methylglyoxal (MG) is involved in plant growth and responses to various abiotic stresses, but the underlying mechanisms remain enigmatic. Whether and how MG functions in plant biotic stress responses is almost completely unknown. Here, we report that the Xoo strain PXO99 induces OsWRKY62.1 to repress transcription of OsGLY II genes by directly binding to their promoters, resulting in overaccumulation of MG. MG negatively regulates rice resistance against PXO99: osglyII2 mutants with higher MG levels are more susceptible to the pathogen, whereas OsGLYII2-overexpressing plants with lower MG content show greater resistance than the wild type. Overexpression of OsGLYII2 to prevent excessive MG accumulation confers broad-spectrum resistance against the biotrophic bacterial pathogens Xoo and Xanthomonas oryzae pv. oryzicola and the necrotrophic fungal pathogen Rhizoctonia solani, which causes rice sheath blight. Further evidence shows that MG reduces rice resistance against PXO99 through CONSTITUTIVE DISEASE RESISTANCE 1 (OsCDR1). MG modifies the Arg97 residue of OsCDR1 to inhibit its aspartic protease activity, which is essential for OsCDR1-enhanced immunity. Taken together, these findings illustrate how Xoo promotes infection by hijacking a sugar metabolite in the host plant.

Genome Resource for the Highly Virulent Xanthomonas oryzae pv. oryzae Strain HN2011 from China

Xanthomonas oryzae pv. oryzae ( Xoo) is the causal bacterium of rice bacterial blight (BB), which is one of the most destructive bacterial diseases of rice worldwide. Although more than 40 BB resistance genes ( Xa genes) have been identified, only a few conferring broad resistance (e.g., Xa4 and Xa21) have been widely used for rice breeding in Asia. The narrow genetic basis for the BB resistance of rice cultivars has resulted in the emergence of new pathogenic strains that can overcome the resistance of commonly grown rice cultivars derived from breeding programs. For example, Xoo strain HN2011, which was isolated in Hainan (China), can overcome the resistance mediated by multiple BB resistance genes, including Xa4 and Xa21. We herein present the complete genome sequence of HN2011 generated by Nanopore sequencing. The genomic data will be useful for elucidating the genomic variations of Xoo and will contribute to clarifying the interaction between Xoo and rice. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Modularly assembled multiplex prime editors for simultaneous editing of agronomically important genes in rice

Prime editing (PE) technology enables precise alterations in the genetic code of a genome of interest. PE offers great potential for identifying major agronomically important genes in plants and editing them into superior variants, ideally targeting multiple loci simultaneously to realize the collective effects of the edits. Here, we report the development of a modular assembly-based multiplex PE system in rice and demonstrate its efficacy in editing up to four genes in a single transformation experiment. The duplex PE (DPE) system achieved a co-editing efficiency of 46.1% in the T0 generation, converting TFIIAγ5 to xa5 and xa23 to Xa23SW11. The resulting double-mutant lines exhibited robust broad-spectrum resistance against multiple Xanthomonas oryzae pathovar oryzae (Xoo) strains in the T1 generation. In addition, we successfully edited OsEPSPS1 to an herbicide-tolerant variant and OsSWEET11a to a Xoo-resistant allele, achieving a co-editing rate of 57.14%. Furthermore, with the quadruple PE (QPE) system, we edited four genes—two for herbicide tolerance (OsEPSPS1 and OsALS1) and two for Xoo resistance (TFIIAγ5 and OsSWEET11a)—using one construct, with a co-editing efficiency of 43.5% for all four genes in the T0 generation. We performed multiplex PE using five more constructs, including two for triplex PE (TPE) and three for QPE, each targeting a different set of genes. The editing rates were dependent on the activity of pegRNA and/or ngRNA. For instance, optimization of ngRNA increased the PE rates for one of the targets (OsSPL13) from 0% to 30% but did not improve editing at another target (OsGS2). Overall, our modular assembly-based system yielded high PE rates and streamlined the cloning of PE reagents, making it feasible for more labs to utilize PE for their editing experiments. These findings have significant implications for advancing gene editing techniques in plants and may pave the way for future agricultural applications.

Complete Genome Resource of a Hypervirulent Xanthomonas oryzae pv. oryzae Strain YNCX Isolated from Yunnan Plateau Japonica Rice.

Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial leaf blight (BLB), is one of the most destructive bacterial pathogens in rice production worldwide. Although several complete genome sequences of Xoo strains have been released in public databases, they are mainly isolated from low-altitude indica rice cultivating areas. Here, a hypervirulent strain, YNCX, isolated from the high-altitude japonica rice-growing region in Yunnan Plateau, was used to extract genomic DNA for PacBio sequencing and Illumina sequencing. After assembly, a high-quality complete genome consisting of a circular chromosome and six plasmids was generated. The genome sequence of YNCX provides a valuable resource for high-altitude races and enables the identification of new virulence TALE effectors, contributing to a better understanding of rice-Xoo interactions.

Pathotyping and Virulence Analysis of Xanthomonas oryzae pv. oryzae Causing Bacterial Blight of Rice in Tamil Nadu

Background-Bacterial leaf blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most destructive diseases affecting rice production worldwide. Resistance breeding is considered a durable, effective, and eco-friendly approach to control BB. Several BB resistance (R) genes have been identified that confer resistance against various strains of Xoo. The dynamic nature of this pathogen needs proper knowledge of pathotype composition and its virulence among the diverse Xoo strains which is imperative for designing a resistance breeding program. Methods-In this study, we conducted an extensive survey to collect BB infected samples from diverse rice-growing regions of Tamil Nadu. Further, the samples were identified as Xoo through morphological and molecular identification methods. The pathotyping and virulence profiling of Xoo isolates was carried out on a set of rice differentials consisting of 22 near-isogenic lines (NILs) of IR24 possessing different BB resistance genes under glasshouse conditions during Kharif 2021-2022. Results-Based on the disease reaction in 22 rice BB differentials (IRBB lines), the Xoo isolates were grouped into six pathotypes (I II, III, IV, V, and VI). Further, the virulence analysis revealed that the near-isogenic lines possessing single R gene and gene pyramids were susceptible to about 20-88% and 4-20% respectively to Xoo isolates. R genes and their pyramids such as (Xa7, Xa21, Xa4+xa5+Xa21, Xa4+xa5+xa13 Xa4+xa13+Xa21, xa5+xa13+Xa21, and Xa4+Xa21+xa5+Xa21) were found to be effective against all the pathotypes in Tamil Nadu. The pathotype III was predominantly distributed (40%) over the Tamil Nadu. The isolates found in the pathotypes I and II are more virulent and in the pathotypes V, VI are less virulent. The current study identified the virulence nature of diverse Xoo isolates and the effectiveness of resistance (R) genes against the Xoo isolates. Therefore, the effective R genes identified in this study could be an effective source for resistance breeding program against BB in Tamil Nadu.

Genetic Structure and TALome Analysis Highlight a High Level of Diversity in Burkinabe Xanthomonas Oryzae pv. oryzae Populations

Bacterial Leaf Blight of rice (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major threat for food security in many rice growing countries including Burkina Faso, where the disease was first reported in the 1980’s. In line with the intensification of rice cultivation in West-Africa, BLB incidence has been rising for the last 15 years. West-African strains of Xoo differ from their Asian counterparts as they (i) are genetically distant, (ii) belong to new races and, (iii) contain reduced repertoires of Transcription Activator Like (TAL) effector genes. In order to investigate the evolutionary dynamics of Xoo populations in Burkina Faso, 177 strains were collected from 2003 to 2018 in three regions where BLB is occurring. Multilocus VNTR Analysis (MLVA-14) targeting 10 polymorphic loci discriminated 24 haplotypes and showed that Xoo populations were structured according to their geographical localization and year of collection. Considering their major role in Xoo pathogenicity, we assessed the TAL effector repertoires of the 177 strains upon RFLP-based profiling. Surprisingly, an important diversity was revealed with up to eight different RFLP patterns. Finally, comparing neutral vs. tal effector gene diversity allowed to suggest scenarios underlying the evolutionary dynamics of Xoo populations in Burkina Faso, which is key to rationally guide the deployment of durably resistant rice varieties against BLB in the country.

T3SS mediated transcriptional reprogramming of rice by the virulent Indian race 4 of Xanthomonas oryzae pv. oryzae

Bacterial blight (BB) incited by Xanthomonas oryzae pv. oryzae (Xoo) is a constant threat to global rice production. Xoo attenuates host defense by directly translocating type III effectors (T3Es) into rice cytosol. The fleeting emergence of new virulent Xoo isolates and subsequent breakdown of resistance in the realm of an erratic climate entails the exploration of befitted resistance to prevent super-races of Xoo from becoming widespread. A comprehensive knowledge of T3Es-mediated transcriptional reprogramming of rice genes in response to Xoo infection remains elusive. Evidently, RNA seq-based transcriptome profiling of rice infected with an Indian virulent Xoo strain Race 4 relative to its T3SS-defective mutant strain (Xoo DhrpX) at early and late hours of bacterial infection yielded an array of differentially expressed genes (DEGs), 49 genes of which were selected for RT-qPCR analysis. The results revealed T3SS-dependent novel defence-related genes belonging to Nucleotide-binding leucine-rich repeat (NLRs), Receptor-like kinases (RLKs), PR proteins, enzymes, cytochrome P450 and secondary metabolites. These genes are direct targets for enhancing BB resistance as well silencing of susceptible targets through gene editing yields durable resistance.

Genome editing of an African elite rice variety confers resistance against endemic and emerging Xanthomonas oryzae pv. oryzae strains.

Bacterial leaf blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), threatens global food security and the livelihood of small-scale rice producers. Analyses of Xoo collections from Asia, Africa and the Americas demonstrated complete continental segregation, despite robust global rice trade. Here, we report unprecedented BB outbreaks in Tanzania. The causative strains, unlike endemic African Xoo, carry Asian-type TAL effectors targeting the sucrose transporter SWEET11a and iTALes suppressing Xa1. Phylogenomics clustered these strains with Xoo from Southern-China. African rice varieties do not carry effective resistance. To protect African rice production against this emerging threat, we developed a hybrid CRISPR-Cas9/Cpf1 system to edit all known TALe-binding elements in three SWEET promoters of the East African elite variety Komboka. The edited lines show broad-spectrum resistance against Asian and African strains of Xoo, including strains recently discovered in Tanzania. The strategy could help to protect global rice crops from BB pandemics.

Novel broad-spectrum bacteriophages against Xanthomonas oryzae and their biocontrol potential in rice bacterial diseases.

Bacterial leaf blight (BLB) and bacterial leaf streak (BLS)-caused by Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), respectively-are two major bacterial diseases that threaten the safe production of rice, one of the most important food crops. Bacteriophages are considered potential biocontrol agents against rice bacterial pathogens, due to their host specificity and environmental safety. It is common for BLB and BLS to occur together in fields, which highlights the need for broad-spectrum phages capable of infecting both Xoo and Xoc. In this study, two lytic broad-spectrum phages (pXoo2106 and pXoo2107) that can infect various strains of Xoo and Xoc were assessed. Both phages belong to the class Caudoviricetes and one of them to the family Autographiviridae, while the other belongs to an unclassified family. Two phages alone or combined in a phage cocktail could effectively inhibit Xoo and Xoc growth in vitro. In an in vivo biocontrol experiment, the phage cocktail reduced the total CFU and significantly eased the symptoms caused by Xoo or Xoc. Our results suggest that pXoo2106 and pXoo2107 have a broad-spectrum host range targeting different X. oryzae strains, and have strong biocontrol potential in field applications against both BLB and BLS.