Sheath blight (ShB), caused by necrotrophic fungus Rhizoctonia solani, is one of the most serious rice diseases worldwide. To the best of our knowledge, no genes with high potential for rice ShB resistance breeding have been previously characterized. Here we identify a ShB resistance receptor-like kinase 1 (SBRR1) gene via a genome-wide association study. The SBRR1-R elite allele, containing a 256-bp insertion in its promoter, is preferentially present in indica varieties in geographical regions with highly favorable conditions for ShB development. Introduction of SBRR1-R into a commercial japonica rice variety significantly reduces yield loss under severe ShB disease pressure. Transcription factor bHLH57 specifically binds to the 256-bp sequence and accounts for highly induced expression and stronger resistance of SBRR1-R. Localization of SBRR1 on plasma membrane, aided by SBRR1-interaction-protein 1, and phosphorylation of SBRR1 are required for SBRR1 to rapidly upregulate downstream chitinase genes for resistance. These findings offer mechanistical insights into ShB resistance hidden in natural rice varieties.

Plants typically activate distinct defense pathways against various pathogens. Heightened resistance to one pathogen often coincides with increased susceptibility to another pathogen. However, the underlying molecular basis of this antagonistic response remains unclear. Here, we demonstrate that mutants defective in the transcription factor ETHYLENE-INSENSITIVE 3-LIKE 2 (OsEIL2) exhibited enhanced resistance to the biotrophic bacterial pathogen Xanthomonas oryzae pv oryzae and to the hemibiotrophic fungal pathogen Magnaporthe oryzae, but enhanced susceptibility to the necrotrophic fungal pathogen Rhizoctonia solani. Furthermore, necrotroph-induced OsEIL2 binds to the promoter of OsWRKY67 with high affinity, leading to the upregulation of salicylic acid (SA)/jasmonic acid (JA) pathway genes and increased SA/JA levels, ultimately resulting in enhanced resistance. However, biotroph- and hemibiotroph-induced OsEIL2 targets OsERF083, resulting in the inhibition of SA/JA pathway genes and decreased SA/JA levels, ultimately leading to reduced resistance. Our findings unveil a previously uncharacterized defense mechanism wherein two distinct transcriptional regulatory modules differentially mediate immunity against pathogens with different lifestyles through the transcriptional reprogramming of phytohormone pathway genes.

Although the antagonistic effects of host resistance against biotrophic and necrotrophic pathogens have been documented in various plants, the underlying mechanisms are unknown. Here, we investigated the antagonistic resistance mediated by the transcription factor ETHYLENE-INSENSITIVE3-LIKE 3 (OsEIL3) in rice. The Oseil3 mutant confers enhanced resistance to the necrotroph Rhizoctonia solani but greater susceptibility to the hemibiotroph Magnaporthe oryzae and biotroph Xanthomonas oryzae pv. oryzae . OsEIL3 directly activates OsERF040 transcription while repressing OsWRKY28 transcription. The infection of R. solani and M. oryzae or Xoo influences the extent of binding of OsEIL3 to OsWRKY28 and OsERF040 promoters, resulting in the repression or activation of both salicylic acid (SA)- and jasmonic acid (JA) -dependent pathways and enhanced susceptibility or resistance, respectively. These results demonstrate that the distinct effects of plant immunity to different pathogen types are determined by two transcription factor modules that control transcriptional reprogramming and the SA and JA pathways.

F-box protein is a subunit of the SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complex, which plays a critical role in regulating different pathways in plant immunity. In this study, we identified the rice (Oryza sativa) F-box protein OsFBX156, which targets the heat shock protein 70 (OsHSP71.1) to regulate resistance to the rice blast fungus Magnaporthe oryzae. Overexpression of OsFBX156 or knockout of OsHSP71.1 in rice resulted in the elevation of pathogenesis-related (PR) genes and an induction burst of reactive oxygen species (ROS) after flg22 and chitin treatments, thereby enhancing resistance to M. oryzae. Furthermore, OsFBX156 can promote the degradation of OsHSP71.1 through the 26S proteasome pathway. This study sheds lights on a novel mechanism wherein the F-box protein OsFBX156 targets OsHSP71.1 for degradation to promote ROS production and PR gene expression, thereby positively regulating rice innate immunity.

Summary Traditional rice blast resistance breeding largely depends on utilizing typical resistance ( R ) genes. However, the lack of durable R genes has prompted rice breeders to find new resistance resources. Susceptibility ( S ) genes are potential new targets for resistance genetic engineering using genome‐editing technologies, but identifying them is still challenging. Here, through the integration of genome‐wide association study (GWAS) and transcriptional analysis, we identified two genes, RNG1 and RNG3 , whose polymorphisms in 3′‐untranslated regions (3′‐UTR) affected their expression variations. These polymorphisms could serve as molecular markers to identify rice blast‐resistant accessions. Editing the 3′‐UTRs using CRISPR/Cas9 technology affected the expression levels of two genes, which were positively associated with rice blast susceptibility. Knocking out either RNG1 or RNG3 in rice enhanced the rice blast and bacterial blight resistance, without impacting critical agronomic traits. RNG1 and RNG3 have two major genotypes in diverse rice germplasms. The frequency of the resistance genotype of these two genes significantly increased from landrace rice to modern cultivars. The obvious selective sweep flanking RNG3 suggested it has been artificially selected in modern rice breeding. These results provide new targets for S gene identification and open avenues for developing novel rice blast‐resistant materials.

Mitochondria are energy factories of cells and are important for intracellular interactions with other organelles. Emerging evidence indicates that mitochondria play essential roles in the response to pathogen infection. During infection, pathogens deliver numerous enzymes and effectors into host cells, and some of these effectors target mitochondria, altering mitochondrial morphology, metabolism, and functions. To defend against pathogen attack, mitochondria are actively involved in changing intracellular metabolism, hormone-mediated signaling, and signal transduction, producing reactive oxygen species and reactive nitrogen species and triggering programmed cell death. Additionally, mitochondria coordinate with other organelles to integrate and amplify diverse immune signals. In this review, we summarize recent advances in understanding how mitochondria function in plant immunity and how pathogens target mitochondria for host defense suppression.

Background Ubiquitination is essential for many cellular processes in eukaryotes, including 26S proteasome-dependent protein degradation, cell cycle progression, transcriptional regulation, and signal transduction. Although numerous ubiquitinated proteins have been empirically identified, their cognate ubiquitin E3 ligases remain largely unknown. Results Here, we generate a complete ubiquitin E3 ligase-encoding open reading frames (UbE3-ORFeome) library containing 98.94% of the 1515 E3 ligase genes in the rice ( Oryza sativa L . ) genome. In the test screens with four known ubiquitinated proteins, we identify both known and new E3s. The interaction and degradation between several E3s and their substrates are confirmed in vitro and in vivo. In addition, we identify the F-box E3 ligase OsFBK16 as a hub-interacting protein of the phenylalanine ammonia lyase family OsPAL1–OsPAL7. We demonstrate that OsFBK16 promotes the degradation of OsPAL1, OsPAL5, and OsPAL6. Remarkably, we find that overexpression of OsPAL1 or OsPAL6 as well as loss-of-function of OsFBK16 in rice displayed enhanced blast resistance, indicating that OsFBK16 degrades OsPALs to negatively regulate rice immunity. Conclusions The rice UbE3-ORFeome is the first complete E3 ligase library in plants and represents a powerful proteomic resource for rapid identification of the cognate E3 ligases of ubiquitinated proteins and establishment of functional E3–substrate interactome in plants.

Cold tolerance at the bud burst stage (CTB) is a key trait for direct-seeded rice. Although quantitative trait loci (QTL) affecting CTB in rice have been mapped using traditional linkage mapping and genome-wide association study (GWAS) methods, the underlying genes remain unknown. In this study, we evaluated the CTB phenotype of 339 cultivars in the Rice Diversity Panel II (RDP II) collection. GWAS identified four QTLs associated with CTB (qCTBs), distributed on chromosomes 1-3. Among them, qCTB-1-1 overlaps with Osa-miR319b, a known cold tolerance micro RNA gene. The other three qCTBs have not been reported. In addition, we characterised the candidate gene OsRab11C1 for qCTB-1-2 that encodes a Rab protein belonging to the small GTP-binding protein family. Overexpression of OsRab11C1 significantly reduced CTB, while gene knockout elevated CTB as well as cold tolerance at the seedling stage, suggesting that OsRab11C1 negatively regulates rice cold tolerance. Molecular analysis revealed that OsRab11C1 modulates cold tolerance by suppressing the abscisic acid signalling pathway and proline biosynthesis. Using RDP II and GWAS, we identified four qCTBs that are involved in CTB and determined the function of the candidate gene OsRab11C1 in cold tolerance. Our results demonstrate that OsRab11C1 is a negative regulator of cold tolerance and knocking out of the gene by genome-editing may provide enhanced cold tolerance in rice.

稻瘟病(rice blast)是水稻生产上最严重的病害之一.抗病相关基因的挖掘对稻瘟病的防治具有重要意义.研究表明植物EIN3/EIL家族基因在抗病过程中发挥着重要作用.本研究采用RNAi技术探究OsEIL6参与的水稻抗稻瘟病反应.稻瘟菌侵染时基因表达谱检测结果表明,OsEIL6在水稻和稻瘟菌非亲和组合中受到诱导表达.稻瘟菌接种结果显示,水稻OsEIL6沉默株系和野生型植株'TG394'相比抗性下降;实时荧光定量RT-PCR结果分析表明,OsEIL6的表达量下降导致乙烯合成途径中OsACO1和乙烯信号传导途径的OsERF063和OsERF073的转录水平下降.亚细胞定位研究发现该基因定位于水稻细胞质.OsEIL6沉默株系中ROS合成途径标记基因OsrbohA和OsrbohB的表达量均明显下调,表明该基因可能通过影响ROS的合成调控水稻抗稻瘟病反应.本研究结果将有助于进一步揭示OsEIL6参与的乙烯信号传导途径介导的水稻抗稻瘟病反应机制.

Since its discovery more than 110years ago, Valsa canker has emerged as a devastating disease of apple in East Asia. However, our understanding of this disease, particularly the identity of the causative agents, has been in a state of confusion. Here we provide a synopsis for the current understanding of Valsa canker and the taxonomy of its causal agents. We highlight the major changes concerning the identity of pathogens and the conflicting viewpoints in moving to "One Fungus = One Name" system for this group of fungal species. We compiled a list of 21 Cytospora species associated with Malus hosts worldwide and curated 12 of them with rDNA-ITS sequences. The inadequacy of rDNA-ITS in discriminating Cytospora species suggests that additional molecular markers, more intraspecific samples and robust methods are required to achieve reliable species recognition.

Reliable knowledge on pathogenic agents contributes to effective plant protection. For most plant pathogens, maintaining protein homeostasis (proteostasis) is essential for unfolding the cellular functions to survive and thrive. However, the fungal proteins involved in proteostasis remain poorly characterized in the process of pathogenesis. In this study, we characterized the function of the nascent polypeptide-associated complex (NAC) in Fusarium graminearum (F. graminearum) (FgNAC), one of the top 10 fungal pathogens with predominant scientific/economic importance. We found that FgNACα, a subunit of FgNAC, manifests high structural and functional similarity to its homologous counterparts in yeast and other species. The mutants of F. graminearum lacking NACα are viable but suffer significant defects in vegetative growth, conidial production, and pathogenesis. In addition, we show here that FgNACα can interact with another subunit of NAC (FgNACβ) in a yeast-two-hybrid assay. The subcellular localization results show that FgNACα and FgNACβ are predominantly localized in the cytoplasm. Future studies should focus on deciphering the mechanism by which NAC orchestrates protein biogenesis and consequentially modulates development and pathogenesis.

Mitochondria are essential for animal and plant immunity. Here, we report that the effector MoCDIP4 of the fungal pathogen Magnaporthe oryzae targets the mitochondria-associated OsDjA9-OsDRP1E protein complex to reduce rice immunity. The DnaJ protein OsDjA9 interacts with the dynamin-related protein OsDRP1E and promotes the degradation of OsDRP1E, which functions in mitochondrial fission. By contrast, MoCDIP4 binds OsDjA9 to compete with OsDRP1E, resulting in OsDRP1E accumulation. Knockout of OsDjA9 or overexpression of OsDRP1E or MoCDIP4 in transgenic rice results in shortened mitochondria and enhanced susceptibility to M. oryzae Overexpression of OsDjA9 or knockout of OsDRP1E in transgenic rice, in contrast, leads to elongated mitochondria and enhanced resistance to M. oryzae Our study therefore reveals a previously unidentified pathogen-infection strategy in which the pathogen delivers an effector into plant cells to target an HSP40-DRP complex; the targeting leads to the perturbation of mitochondrial dynamics, thereby inhibiting mitochondria-mediated plant immunity.

SummaryBecause of the frequent breakdown of major resistance (R) genes, identification of new partial R genes against rice blast disease is an important goal of rice breeding. In this study, we used a core collection of the Rice Diversity Panel II (C‐RDP‐II), which contains 584 rice accessions and are genotyped with 700 000 single‐nucleotide polymorphism (SNP) markers. The C‐RDP‐II accessions were inoculated with three blast strains collected from different rice‐growing regions in China. Genome‐wide association study identified 27 loci associated with rice blast resistance (LABRs). Among them, 22 LABRs were not associated with any known blast R genes or QTLs. Interestingly, a nucleotide‐binding site leucine‐rich repeat (NLR) gene cluster exists in the LABR12 region on chromosome 4. One of the NLR genes is highly conserved in multiple partially resistant rice cultivars, and its expression is significantly up‐regulated at the early stages of rice blast infection. Knockout of this gene via CRISPR‐Cas9 in transgenic plants partially reduced blast resistance to four blast strains. The identification of this new non‐strain specific partial R gene, tentatively named rice blast Partial Resistance gene 1 (PiPR1), provides genetic material that will be useful for understanding the partial resistance mechanism and for breeding durably resistant cultivars against blast disease of rice.

BACKGROUND:Silicon (Si) can confer plant resistance to both abiotic and biotic stress. In the present study, the priming effect of Si on rice (Oryza sativa cv Nipponbare) against the root-knot nematode Meloidogyne graminicola and its histochemical and molecular impact on plant defense mechanisms were evaluated.RESULTS:Si amendment significantly reduced nematodes in rice roots and delayed their development, while no obvious negative effect on giant cells was observed. Increased resistance in rice was correlated with higher transcript levels of defense-related genes (OsERF1, OsEIN2 and OsACS1) in the ethylene (ET) pathway. Si amendment significantly reduced nematode numbers in rice plants with enhanced ET signaling but had no effect in plants deficient in ET signaling, indicating that the priming effects of Si were dependent on the ET pathway. A higher deposition of callose and accumulation of phenolic compounds were observed in rice roots after nematode attack in Si-amended plants than in the controls.CONCLUSION:These findings indicate that the priming effect may partially depend on the production of phenolic compounds and hydrogen peroxide. Further research is required to model the ethylene signal transduction pathway that occurs in the Si-plant-nematode interaction system and gain a better understanding of Si-induced defense in rice.

Rice blast, caused by Magnaporthe oryzae (synonym: Pyricularia oryzae), severely reduces rice production and grain quality. The molecular mechanism of rice resistance to M.oryzae is not fully understood. In this study, we identified a chaperone DnaJ protein, OsDjA6, which is involved in basal resistance to M.oryzae in rice. The OsDjA6 protein is distributed in the entire rice cell. The expression of OsDjA6 is significantly induced in rice after infection with a compatible isolate. Silencing of OsDjA6 in transgenic rice enhances resistance to M.oryzae and also results in an increased burst of reactive oxygen species after flg22 and chitin treatments. In addition, the expression levels of WRKY45, NPR1 and PR5 are increased in OsDjA6 RNAi plants, indicating that OsDjA6 may mediate resistance by affecting the salicylic acid pathway. Finally, we found that OsDjA6 interacts directly with the E3 ligase OsZFP1 invitro and invivo. These results suggest that the DnaJ protein OsDjA6 negatively regulates rice innate immunity, probably via the ubiquitination proteasome degradation pathway.

Rice sheath blight (SB), caused by Rhizoctonia solani ( R. solani ), is a major threat to rice production worldwide. The molecular mechanisms of the SB resistance in rice are poorly understood. The transcriptomes of the SBresistant rice cultivar YSBR1 and the susceptible cultivar Lemont were analyzed after R. solani infection. A total of 7624 differentially expressed genes (DEGs) were identified at one or more timepoints in a cultivar. 5526 and 5618 DEGs were differentially expressed in Lemont and YSBR1, respectively. YSBR1 exhibited stronger and earlier transcriptional response to R. solani than Lemont. Gene ontology enrichment analysis revealed that genes that encode cell wall-modifying and glycosyl-degrading enzymes or anti-microbial proteins were specifically induced in YSBR1 at 6 hpi. MapMan analysis revealed that more DEGs related with cell wall, β-glucanses, respiratory burst, phenylpropanoids and lignin were highly induced by R. solani in YSBR1 than in Lemont. The results also showed that receptor-like kinases and jasmonic acid signaling may play important roles in host resistance to R. solani . This study highlights potential candidate genes and signaling pathways involved in rice sheath resistance and can help to further clarify the mechanistic events underlying resistance and susceptibility to R. solani .

Sheath blight,caused by Rhizoctonia solani ,is one of the three most destructive diseases in rice (Oryza sativa ),which causes severe yield losses and bad quality under favorable disease conditions.Genechip data showed that the expression of OsEIL2,a homolog of the Arabidopsis (Arabidopsis thaliana )ETHYLENE INSENSITIVE 3 (EIN3),was significantly induced in rice by R .solani infection,suggesting a possible involvement of OsEIL2 in the defense against R .solani .In this study,we generated OsEIL2-RNAi transgenic events through agrobacteria-mediated transformation.Quantitative RT-PCR assays showed that the transcription of OsEIL2 was specifically si-lenced in these transgenic events.Inoculation results showed that the OsEIL2 RNAi plants displayed more suscep-tibility to R .solani .Further,subcellular localization analyses revealed that OsEIL2 was localized in the nucleus of rice protoplasts and tobacco leaves.Yeast one-hybrid assays showed that OsEIL2 exhibited transcriptional activity. In addition,the transcripts of OsACO1,a key gene for ethylene biosynthesis,was down-regulated in the OsEIL2-RNAi plants.Taken together,we conclude that OsEIL2,an ortholog of Arabidopsis EIN3,is a transcription fac-tor and positive regulator of rice resistance to R .solani .

水稻是我国主要粮食作物之一,而稻瘟病是影响水稻安全生产的最主要病害之一.为克服抗病基因的抗病性很快消失的弊端,本研究尝试了宿主诱导的基因沉默(HIGS)技术在创制抗稻瘟病水稻新材料上的可行性.HIGS是新发展起来的以RNAi为基础的抗病技术,即在寄主植物中表达可沉默病原物特定基因的HIGS载体,达到控制病原菌扩展的目的.本研究选取了两个稻瘟菌致病关键基因Nox1和NAC为研究靶标,分别克隆其UTR区和CDS区中的特异区段,利用Gateway技术构建这4个片段HIGS表达载体,再利用农杆菌介导法将各载体分别转化水稻,通过鉴定得到转基因阳性植株,为后续开展该技术在水稻抗稻瘟病方面的深入研究奠定了基础.

生物胁迫是影响我国农作物生产的重要因素，也是当前植物界研究方向涉及最为广泛的领域之一。由泛素介导的降解途径是生物体内最为精细的调控体系，涉及对生物体的生长发育以及生物体对周围环境适应的调控等过程。E3泛素连接酶因对底物有特异性识别作用，被认为是泛素化过程中最重要的组成部分。依据其结构和功能的不同可以将 E3泛素连接酶分为4个家族。越来越多的研究表明这些不同的 E3家族成员可以参与植物抗病免疫反应的各个过程。本文在简要概括 E3泛素连接酶分类的基础上综述了目前 E3泛素连接酶参与调控植物抗病害方面研究进展，并对今后研究方向进行了展望，以期对抗病机理解析及抗病品种研发提供新思路。

Fungal diseases are posing tremendous threats to global economy and food safety. Among them, Valsa canker, caused by fungi of Valsa and their Cytospora anamorphs, has been a serious threat to fruit and forest trees and is one of the most destructive diseases of apple in East Asia, particularly. Accurate and robust delimitation of pathogen species is not only essential for the development of effective disease control programs, but also will advance our understanding of the emergence of plant diseases. However, species delimitation is especially difficult in Valsa because of the high variability of morphological traits and in many cases the lack of the teleomorph. In this study, we delimitated species boundary for pathogens causing apple Valsa canker with a multifaceted approach. Based on three independent loci, the internal transcribed spacer (ITS), β-tubulin (Btu), and translation elongation factor-1 alpha (EF1α), we inferred gene trees with both maximum likelihood and Bayesian methods, estimated species tree with Bayesian multispecies coalescent approaches, and validated species tree with Bayesian species delimitation. Through divergence time estimation and ancestral host reconstruction, we tested the possible underlying mechanisms for fungal speciation and host-range change. Our results proved that two varieties of the former morphological species V. mali represented two distinct species, V. mali and V. pyri, which diverged about 5 million years ago, much later than the divergence of their preferred hosts, excluding a scenario of fungi-host co-speciation. The marked different thermal preferences and contrasting pathogenicity in cross-inoculation suggest ecological divergences between the two species. Apple was the most likely ancestral host for both V. mali and V. pyri. Host-range expansion led to the occurrence of V. pyri on both pear and apple. Our results also represent an example in which ITS data might underestimate species diversity.