Transcriptional profiling of rice early response to Magnaporthe oryzae identified OsWRKYs as important regulators in rice blast resistance

Analysis of huanglongbing-associated RNA-seq data reveals disturbances in biological processes within Citrus spp. triggered by Candidatus Liberibacter asiaticus infection

Introduction

Huanglongbing (HLB), a disease that's ubiquitous worldwide, wreaks havoc on the citrus industry. The primary culprit of HLB is the gram-negative bacterium Candidatus Liberibacter asiaticus (CLas) that infects the phloem, but its damaging mechanism is yet to be fully understood.

Methods and results

In this study, a multitude of tools including weighted correlation network analysis (WGCNA), protein-protein interaction (PPI) network analysis and gene expression profiling are employed to unravel the intricacies of its pathogenesis. The investigation pinpoints various central genes, such as the ethylene-responsive transcription factor 9 (ERF9) and thioredoxin reductase 1 (TrxR1), that are associated with CLas invasion and resultant disturbances in numerous biological operations. Additionally, the study uncovers a range of responses through the detection of differential expressed genes (DEGs) across different experiments. The discovery of core DEGs leads to the identification of pivotal genes such as the sieve element occlusion (SEO) and the wall-associated receptor kinase-like 15 (WAKL15). PPI network analysis highlights potential vital proteins, while GO and KEGG pathway enrichment analysis illustrate a significant impact on multiple defensive and metabolic pathways. Gene set enrichment analysis (GSEA) indicates significant alterations in biological processes such as leaf senescence and response to biotic stimuli.

Discussion

This all-encompassing approach extends valuable understanding into the pathogenesis of CLas, potentially aiding future research and therapeutic strategies for HLB.

CRISPR/Cas9-mediated knockout of Bsr-d1 enhances the blast resistance of rice in Northeast China

KEY MESSAGE

The blast resistance allele of OsBsr-d1 does not exist in most japonica rice varieties of Jilin Province in China. The development of Bsr-d1 knockout mutants via CRISPR/Cas9 enhances broad-spectrum resistance to rice blast in Northeast China. Rice blast is a global disease that has a significant negative impact on rice yield and quality. Due to the complexity and variability of the physiological races of rice blast, controlling rice blast is challenging in agricultural production. Bsr-d1, a negative transcription factor that confers broad-spectrum resistance to rice blast, was identified in the indica rice cultivar Digu; however, its biological function in japonica rice varieties is still unclear. In this study, we analyzed the blast resistance allele of Bsr-d1 in a total of 256 japonica rice varieties from Jilin Province in Northeast China and found that this allele was not present in these varieties. Therefore, we generated Bsr-d1 knockout mutants via the CRISPR/Cas9 system using the japonica rice variety Jigeng88 (JG88) as a recipient variety. Compared with those of the wild-type JG88, the homozygous Bsr-d1 mutant lines KO#1 and KO#2 showed enhanced leaf blast resistance at the seedling stage to several Magnaporthe oryzae (M. oryzae) races collected from Jilin Province in Northeast China. Physiological and biochemical indices revealed that the homozygous mutant lines produced more hydrogen peroxide than did JG88 plants when infected with M. oryzae. Comparative RNA-seq revealed that the DEGs were mainly involved in the synthesis of amide compounds, zinc finger proteins, transmembrane transporters, etc. In summary, our results indicate that the development of Bsr-d1 knockout mutants through CRISPR/Cas9 can enhance the broad-spectrum resistance of rice in Northeast China to rice blast. This study not only provides a theoretical basis for disease resistance breeding involving the Bsr-d1 gene in Northeast China, but also provides new germplasm resources for disease-resistance rice breeding.

Mining of Minor Disease Resistance Genes in V. vinifera Grapes Based on Transcriptome

Intraspecific recurrent selection in V. vinifera is an effective method for grape breeding with high quality and disease resistance. The core theory of this method is the substitution accumulation of multi-genes with low disease resistance. The discovery of multi-genes for disease resistance in V. vinifera may provide a molecular basis for breeding for disease resistance in V. vinifera. In this study, resistance to downy mildew was identified, and genetic analysis was carried out in the intraspecific crossing population of V. vinifera (Ecolly × Dunkelfelder) to screen immune, highly resistant and disease-resistant plant samples; transcriptome sequencing and differential expression analysis were performed using high-throughput sequencing. The results showed that there were 546 differential genes (194 up-regulated and 352 down-regulated) in the immune group compared to the highly resistant group, and 199 differential genes (50 up-regulated and 149 down-regulated) in the highly resistant group compared to the resistant group, there were 103 differential genes (54 up-regulated and 49 down-regulated) in the immune group compared to the resistant group. KEGG analysis of differentially expressed genes in the immune versus high-resistance group. The pathway is mainly concentrated in phenylpropanoid biosynthesis, starch and sucrose metabolism, MAPK signaling pathway-plant, carotenoid biosyn-thesis and isoquinoline alkaloid biosynthesis. The differential gene functions of immune and resistant, high-resistant and resistant combinations were mainly enriched in plant-pathogen interaction pathway. Through the analysis of disease resistance-related genes in each pathway, the potential minor resistance genes in V. vinifera were mined, and the accumulation of minor resistance genes was analyzed from the molecular level.

Integrative transcriptomic, proteomic, and phosphoproteomic analysis on the defense response to Magnaporthe oryzae reveals different expression patterns at the molecular level of durably resistant rice cultivar Mowanggu

Rice blast, caused by Magnaporthe oryzae is one of the most destructive diseases of rice (Oryza sativa L.) in most rice-cultivated areas worldwide. Mowanggu (MWG) is a traditional landrace rice variety in Yunnan with broad-spectrum and durable blast resistance against rice blast fungus. However, the underlying disease-resistance mechanisms remain unknown. An integrative transcriptomic, proteomic, and phosphoproteomic analysis of MWG was performed after inoculation with M. oryzae in this study. The transcriptomic and proteomic results revealed that MWG was moderately correlated at the transcriptional and protein levels. Differentially expressed genes and proteins were up-regulated and significantly enriched in protein phosphorylation, peroxisome, plant-pathogen interactions, phenylpropanoid metabolism and phenylalanine biosynthesis pathways. The phosphoproteomic profile and phosphorylated-protein-interaction network revealed that the altered phosphoproteins were primarily associated with reactive oxygen species (ROS), glycolysis, MAPK signaling pathways, and amino acid biosynthesis. In addition, a series of physiological and biochemical parameters, including ROS, soluble sugars, soluble protein and callus accumulation and defense-related enzyme activities, were used to validate the possible blast resistance mechanisms of MWG. The integrative transcriptomic, proteomic, and phosphoproteomic analysis revealed the different expression patterns at the molecular level of the durably resistant rice cultivar MWG after inoculation with M. oryzae, which provides insight into the molecular mechanisms of rice blast resistance.

The OsWRKY63-OsWRKY76-OsDREB1B module regulates chilling tolerance in rice

Rice (Oryza sativa) is sensitive to low temperatures, which affects the yield and quality of rice. Therefore, uncovering the molecular mechanisms behind chilling tolerance is a critical task for improving cold tolerance in rice cultivars. Here, we report that OsWRKY63, a WRKY transcription factor with an unknown function, negatively regulates chilling tolerance in rice. OsWRKY63-overexpressing rice lines are more sensitive to cold stress. Conversely, OsWRKY63-knockout mutants generated using a CRISPR/Cas9 genome editing approach exhibited increased chilling tolerance. OsWRKY63 was expressed in all rice tissues, and OsWRKY63 expression was induced under cold stress, dehydration stress, high salinity stress, and ABA treatment. OsWRKY63 localized in the nucleus plays a role as a transcription repressor and downregulates many cold stress-related genes and reactive oxygen species scavenging-related genes. Molecular, biochemical, and genetic assays showed that OsWRKY76 is a direct target gene of OsWRKY63 and that its expression is suppressed by OsWRKY63. OsWRKY76-knockout lines had dramatically decreased cold tolerance, and the cold-induced expression of five OsDREB1 genes was repressed. OsWRKY76 interacted with OsbHLH148, transactivating the expression of OsDREB1B to enhance chilling tolerance in rice. Thus, our study suggests that OsWRKY63 negatively regulates chilling tolerance through the OsWRKY63-OsWRKY76-OsDREB1B transcriptional regulatory cascade in rice.

Time-series transcriptome of Brachypodium distachyon during bacterial flagellin-induced pattern-triggered immunity

Plants protect themselves from microorganisms by inducing pattern-triggered immunity (PTI) via recognizing microbe-associated molecular patterns (MAMPs), conserved across many microbes. Although the MAMP perception mechanism and initial events during PTI have been well-characterized, knowledge of the transcriptomic changes in plants, especially monocots, is limited during the intermediate and terminal stages of PTI. Here, we report a time-series high-resolution RNA-sequencing (RNA-seq) analysis during PTI in the leaf disks of Brachypodium distachyon. We identified 6,039 differentially expressed genes (DEGs) in leaves sampled at 0, 0.5, 1, 3, 6, and 12 hours after treatment (hat) with the bacterial flagellin peptide flg22. The k-means clustering method classified these DEGs into 10 clusters (6 upregulated and 4 downregulated). Based on the results, we selected 10 PTI marker genes in B. distachyon. Gene ontology (GO) analysis suggested a tradeoff between defense responses and photosynthesis during PTI. The data indicated the recovery of photosynthesis started at least at 12 hat. Over-representation analysis of transcription factor genes and cis-regulatory elements in DEG promoters implied the contribution of 12 WRKY transcription factors in plant defense at the early stage of PTI induction.

Know when and how to die: gaining insights into the molecular regulation of leaf senescence

Senescence is the ultimate phase in the life cycle of leaves which is crucial for recycling of nutrients to maintain plant fitness and reproductive success. The earliest visible manifestation of leaf senescence is their yellowing, which usually commences with the breakdown of chlorophyll. The degradation process involves a gradual and highly coordinated disassembly of macromolecules resulting in the accumulation of nutrients, which are subsequently mobilized from the senescing leaves to the developing organs. Leaf senescence progresses under overly tight genetic and molecular control involving a well-orchestrated and intricate network of regulators that coordinate spatio-temporally with the influence of both internal and external cues. Owing to the advancements in omics technologies, the availability of mutant resources, scalability of molecular analyses methodologies and the advanced capacity to integrate multidimensional data, our understanding of the genetic and molecular basis of leaf ageing has greatly expanded. The review provides a compilation of the multitier regulation of senescence process and the interrelation between the environment and the terminal phase of leaf development. The knowledge gained would benefit in devising the strategies for manipulation of leaf senescence process to improve crop quality and productivity.

Understanding the Dynamics of Blast Resistance in Rice-Magnaporthe oryzae Interactions

Rice is a global food grain crop for more than one-third of the human population and a source for food and nutritional security. Rice production is subjected to various stresses; blast disease caused by Magnaporthe oryzae is one of the major biotic stresses that has the potential to destroy total crop under severe conditions. In the present review, we discuss the importance of rice and blast disease in the present and future global context, genomics and molecular biology of blast pathogen and rice, and the molecular interplay between rice–M. oryzae interaction governed by different gene interaction models. We also elaborated in detail on M. oryzae effector and Avr genes, and the role of noncoding RNAs in disease development. Further, rice blast resistance QTLs; resistance (R) genes; and alleles identified, cloned, and characterized are discussed. We also discuss the utilization of QTLs and R genes for blast resistance through conventional breeding and transgenic approaches. Finally, we review the demonstrated examples and potential applications of the latest genome-editing tools in understanding and managing blast disease in rice.

Transcriptome-wide analysis of North-East Indian rice cultivars in response to Bipolaris oryzae infection revealed the importance of early response to the pathogen in suppressing the disease progression

Brown spot disease (BSD) of rice (Oryza sativa L.) caused by Bipolaris oryzae is one of the major and neglected fungal diseases worldwide affecting rice production. Despite its significance, very limited knowledge on genetics and genomics of rice in response to B. oryzae available. Our study firstly identified moderately resistant (Gitesh) and susceptible (Shahsarang) North-East Indian rice cultivars in response to a native Bipolaris oryzae isolate BO1. Secondly, a systematic comparative RNA seq was performed for both cultivars at four different time points viz. 12, 24, 48, and 72 hours post infestation (hpi). Differential gene expression analysis revealed the importance of early response to the pathogen in suppressing disease progression. The pathogen negatively regulates the expression of photosynthetic-related genes at early stages in both cultivars. Of the cell wall modification enzymes, cellulose synthase and callose synthase are important for signal transduction and defense. Cell wall receptors OsLYP6, OsWAK80 might positively and OsWAK25 negatively regulate disease resistance. Jasmonic acid and/or abscisic acid signaling pathways are presumably involved in disease resistance, whereas salicylic acid pathway, and an ethylene response gene OsEBP-89 in promoting disease. Surprisingly, pathogenesis-related proteins showed no antimicrobial impact on the pathogen. Additionally, transcription factors OsWRKY62 and OsWRKY45 together might negatively regulate resistance to the pathogen. Taken together, our study has identified and provide key regulatory genes involved in response to B. oryzae which serve as potential resources for functional genetic analysis to develop genetic tolerance to BSD of rice.

WAKsing plant immunity, waning diseases

With the requirement to breed more productive crop plants in order to feed a growing global population, compounded by increasingly widespread resistance to pesticides exhibited by pathogens, plant immunity is becoming an increasingly important area of research. Of the genes that contribute to disease resistance, the wall-associated receptor-like kinases (WAKs) are increasingly shown to play a major role, in addition to their contribution to plant growth and development or tolerance to abiotic stresses. Being transmembrane proteins, WAKs form a central pillar of a plant cell's ability to monitor and interact with the extracellular environment. Found in both dicots and monocots, WAKs have been implicated in defence against pathogens with diverse lifestyles and contribute to plant immunity in a variety of ways. Whilst some act as cell surface-localized immune receptors recognizing either pathogen- or plant-derived invasion molecules (e.g. effectors or damage-associated molecular patterns, respectively), others promote innate immunity through cell wall modification and strengthening, thus limiting pathogen intrusion. The ability of some WAKs to provide both durable resistance against pathogens and other agronomic benefits makes this gene family important targets in the development of future crop ideotypes and important to a greater understanding of the complexity and robustness of plant immunity.

Transcriptome analysis of rice response to blast fungus identified core genes involved in immunity

Rice blast disease caused by the filamentous Ascomycetous fungus Magnaporthe oryzae is a major threat to rice production worldwide. The mechanisms underlying rice resistance to M. oryzae, such as transcriptional reprogramming and signalling networks, remain elusive. In this study, we carried out an in-depth comparative transcriptome study on the susceptible and resistant rice cultivars in response to M. oryzae. Our analysis highlighted that rapid, high-amplitude transcriptional reprogramming was important for rice defence against blast fungus. Ribosome- and protein translation-related genes were significantly enriched among differentially expressed genes (DEGs) at 12 hpi in both cultivars, indicating that the protein translation machinery is regulated in the activation of immunity in rice. Furthermore, we identified a core set of genes that are involved in the rice response to both biotic and abiotic stress. More importantly, among the core genes, we demonstrated that the metallothionein OsMT1a and OsMT1b genes positively regulated rice resistance while a peroxidase gene Perox4 negatively regulated rice resistance to M. oryzae. Our study provides novel insight into transcriptional reprogramming and serves as a valuable resource for functional studies on rice immune signalling components in resistance to blast disease.

Differential Regulation of Maize and Sorghum Orthologs in Response to the Fungal Pathogen Exserohilum turcicum

Pathogens that infect more than one host offer an opportunity to study how resistance mechanisms have evolved across different species. Exserohilum turcicum infects both maize and sorghum and the isolates are host-specific, offering a unique system to examine both compatible and incompatible interactions. We conducted transcriptional analysis of maize and sorghum in response to maize-specific and sorghum-specific E. turcicum isolates and identified functionally related co-expressed modules. Maize had a more robust transcriptional response than sorghum. E. turcicum responsive genes were enriched in core orthologs in both crops, but only up to 16% of core orthologs showed conserved expression patterns. Most changes in gene expression for the core orthologs, including hub genes, were lineage specific, suggesting a role for regulatory divergent evolution. We identified several defense-related shared differentially expressed (DE) orthologs with conserved expression patterns between the two crops, suggesting a role for parallel evolution of those genes in both crops. Many of the differentially expressed genes (DEGs) during the incompatible interaction were related to quantitative disease resistance (QDR). This work offers insights into how different hosts with relatively recent divergence interact with a common pathogen. Our results are important for developing resistance to this critical pathogen and understanding the evolution of host-pathogen interactions.

Genome Identification and Expression Analysis of GRAS Family Related to Development, Hormone and Pathogen Stress in Brachypodium distachyon

GRAS transcription factors are widely present in the plant kingdom and play important roles in regulating multiple plant physiological processes. Brachypodium distachyon is a model for grasses for researching plant-pathogen interactions. However, little is known about the BdGRAS family genes involved in plant response to biotic stress. In this study, we identified 63 genes of the GRAS family in B. distachyon. The phylogenetic analysis showed that BdGRAS genes were divided into ten subfamilies and unevenly distributed on five chromosomes. qRT-PCR results showed that the BdGRAS family genes were involved in the growth and development of B. distachyon. Moreover, the expression of the HAM subfamily genes of BdGRAS changed during the interaction between B. distachyon and Magnaporthe oryzae. Interestingly, BdGRAS31 in the HAM subfamily was regulated by miR171 after inoculation with M. oryzae. These results provide insight into the potential functions of the BdGRAS family in disease resistance.

When rice gets the chills: comparative transcriptome profiling at germination shows WRKY transcription factor responses

Rice is vital for food security. Due to its tropical origin, rice suffers from cold temperatures that affect its entire life cycle. Key genes have been identified involved in cold tolerance. WRKYs are generally downstream of the MAPK cascade and can act together with VQ proteins to regulate stress-responsive genes. Chilling treatment was applied at germination to two rice genotypes (tolerant and sensitive). Shoots at S3 stage were collected for RNA-seq to identify OsWRKY, OsMAPKs and OsVQs expression. Relationships among MAPKs, WRKYs and VQs were predicted through correlation analysis. OsWRKY transcriptional regulation was predicted by in silico analysis of cis-regulatory elements. A total of 39 OsWRKYs were differentially expressed. OsWRKY21, OsWRK24 and OsWRKY69 are potential positive regulators, while OsWRKY10, OsWRK47, OsWRKY62, OsWRKY72 and OsWRKY77 are potential negative regulators, of chilling tolerance. 12 OsMAPKs were differentially expressed. OsMAPKs were downregulated and negatively correlated with the upregulated OsWRKYs in the tolerant genotype. 19 OsVQs were differentially expressed, three and six OsVQs were positively correlated with OsWRKYs in the tolerant and sensitive genotypes, respectively. Seven differentially expressed OsWRKYs have cold-responsive elements in their promoters and five upregulated OsWRKYs in the tolerant genotype contained the W-box motif. Chilling causes changes in OsWRKY, OsMAPK and OsVQ gene expression at germination. OsWRKYs may not act downstream of the MAPK cascade to coordinate chilling tolerance, but OsWRKYs may act with VQs to regulate chilling tolerance. Candidate OsWRKYs are correlated and have a W-box in the promoter, suggesting an auto-regulation mechanism.

OsWRKY93 Dually Functions Between Leaf Senescence and in Response to Biotic Stress in Rice

Cross talking between natural senescence and cell death in response to pathogen attack is an interesting topic; however, its action mechanism is kept open. In this study, 33 OsWRKY genes were obtained by screening with leaf aging procedure through RNA-seq dataset, and 11 of them were confirmed a significant altered expression level in the flag leaves during aging by using the reverse transcript quantitative PCR (RT-qPCR). Among them, the OsWRKY2, OsWRKY14, OsWRKY26, OsWRKY69, and OsWRKY93 members exhibited short-term alteration in transcriptional levels in response to Magnaporthe grisea infection. The CRISPR/Cas9-edited mutants of five genes were developed and confirmed, and a significant sensitivity to M. oryzae infection was observed in CRISPR OsWRKY93-edited lines; on the other hand, a significant resistance to M. oryzae infection was shown in the enhanced expression OsWRKY93 plants compared to mock plants; however, enhanced expression of other four genes have no significant affection. Interestingly, ROS accumulation was also increased in OsWRKY93 enhanced plants after flg22 treatment, compared with the controls, suggesting that OsWRKY93 is involved in PAMP-triggered immune response in rice. It indicated that OsWRKY93 was involved in both flag leaf senescence and in response to fungi attack.

Overexpression of ZmWRKY65 transcription factor from maize confers stress resistances in transgenic Arabidopsis

Plant-specific WRKY transcription factors play important roles in regulating the expression of defense-responsive genes against pathogen attack. A multiple stress-responsive WRKY gene, ZmWRKY65, was identified in maize by screening salicylic acid (SA)-induced de novo transcriptomic sequences. The ZmWRKY65 protein was localized in the nucleus of mesophyll protoplasts. The analysis of the ZmWRKY65 promoter sequence indicated that it contains several stress-related transcriptional regulatory elements. Many environmental factors affecting the transcription of ZmWRKY65 gene, such as drought, salinity, high temperature and low temperature stress. Moreover, the transcription of ZmWRKY65 gene was also affected by the induction of defense related plant hormones such as SA and exogenous ABA. The results of seed germination and stomatal aperture assays indicated that transgenic Arabidopsis plants exhibit enhanced sensitivity to ABA and high concentrations of SA. Overexpression of ZmWRKY65 improved tolerance to both pathogen attack and abiotic stress in transgenic Arabidopsis plants and activated several stress-related genes such as RD29A, ERD10, and STZ as well as pathogenesis-related (PR) genes such as PR1, PR2 and PR5; these genes are involved in resistance to abiotic and biotic stresses in Arabidopsis. Together, this evidence implies that the ZmWRKY65 gene is involved in multiple stress signal transduction pathways.

Weighted Gene Co-Expression Network Coupled with a Critical-Time-Point Analysis during Pathogenesis for Predicting the Molecular Mechanism Underlying Blast Resistance in Rice

BACKGROUND

Rice blast, caused by the ascomycete fungus M. oryzae, is one of the most important diseases of rice. Although many blast resistance (R) genes have been identified and deployed in rice varieties, the molecular mechanisms responsible for the R gene-mediated defense responses are yet not fully understood.

RESULTS

In this study, we used comparative transcriptomic analysis to explore the molecular mechanism involved in Piz-t-mediated resistance in a transgenic line containing Piz-t (NPB-Piz-t) compared to Nipponbare (NPB). Clustering and principal component analysis (PCA) revealed that the time-point at 24-h post inoculation (hpi) was the most important factor distinguishing the four time-points, which consisted of four genes of mitogen-activated protein kinases (MAPKs) signaling pathway, one gene related to WRKY DNA-binding domain containing protein, five pathogenesis-related protein (OsPR1s) genes, and three genes of R proteins involving in the most significant protein-protein interaction (PPI) pathway. Using weighted gene co-expression network analysis (WGCNA) to investigate RNA-seq data across 0, 24, 48, and 72 hpi, nine modules with similar patterns expression pattern (SEP) and three modules with differential expression pattern (DEP) between NPB-Piz-t and NPB across 0, 24, 48, and 72 hpi with KJ201 (referred to as Piz-t-KJ201 and NPB-KJ201) were identified. Among these the most representative SEP green-yellow module is associated with photosynthesis, and DEP pink module comprised of two specific expressed nucleotide-binding domain and leucine-rich repeat (NLR) genes of LOC_Os06g17900 and LOC_Os06g17920 of Pi2/9 homologous, three NLR genes of LOC_Os11g11810, LOC_Os11g11770, and LOC_Os11g11920 which are putatively associated with important agronomic traits, and a B3 DNA binding domain containing protein related genes (LOC_Os10g39190). Knockout of LOC_Os10g39190 via CRISPR-Cas9 resulted in plant death at the seedling stage.

CONCLUSIONS

The research suggested that Piz-t and multiple NLR network might play important roles in the regulation of the resistance response in the Piz-t-KJ201 interaction system. The identified genes provide an NLR repository to study the rice-M. oryzae interaction system and facilitate the breeding of blast-resistant cultivars in the future.

BdWRKY38 is required for the incompatible interaction of Brachypodium distachyon with the necrotrophic fungus Rhizoctonia solani

Rhizoctonia solani is a soil-borne necrotrophic fungus that causes sheath blight in grasses. The basal resistance of compatible interactions between R. solani and rice is known to be modulated by some WRKY transcription factors (TFs). However, genes and defense responses involved in incompatible interaction with R. solani remain unexplored, because no such interactions are known in any host plants. Recently, we demonstrated that Bd3-1, an accession of the model grass Brachypodium distachyon, is resistant to R. solani and, upon inoculation with the fungus, undergoes rapid induction of genes responsive to the phytohormone salicylic acid (SA) that encode the WRKY TFs BdWRKY38 and BdWRKY44. Here, we show that endogenous SA and these WRKY TFs positively regulate this accession-specific R. solani resistance. In contrast to a susceptible accession (Bd21), the infection process in the resistant accessions Bd3-1 and Tek-3 was suppressed at early stages before the development of fungal biomass and infection machinery. A comparative transcriptome analysis during pathogen infection revealed that putative WRKY-dependent defense genes were induced faster in the resistant accessions than in Bd21. A gene regulatory network (GRN) analysis based on the transcriptome dataset demonstrated that BdWRKY38 was a GRN hub connected to many target genes specifically in resistant accessions, whereas BdWRKY44 was shared in the GRNs of all three accessions. Moreover, overexpression of BdWRKY38 increased R. solani resistance in Bd21. Our findings demonstrate that these resistant accessions can activate an incompatible host response to R. solani, and BdWRKY38 regulates this response by mediating SA signaling.

Comparative transcriptomic analysis reveals the mechanistic basis of Pib-mediated broad spectrum resistance against Magnaporthe oryzae

Rice blast, caused by the fungus Magnaporthe oryzae, is a highly damaging disease. Introducing genes, which confer a broad spectrum resistance to the disease, such as Pib, makes an important contribution to protecting rice production. However, little is known regarding the mechanistic basis of the products of such genes. In this study, transcriptome of the cultivar Lijiangxintuanheigu (LTH) and its monogenic IRBLb-B which harbors Pib treated with M. oryzae were compared. Among the many genes responding transcriptionally to infection were some encoding products involved in the metabolism of ROS (reactive oxygen species), in jasmonate (JA) metabolism, and WRKY transcription factors, receptor kinases, and resistance response signal modulation. The down-regulation of genes encoding peroxiredoxin and glutathione S transferases implied that the redox homeostasis is essential for the expression of Pib-mediated resistance. The up-regulation of seven disease resistance-related genes, including three encoding a NBS-LRR protein, indicated that disease resistance-related genes are likely tend to support the expression of Pib resistance. These data revealed that potential candidate genes and transcriptional reprogramming were involved in Pib-mediated resistance mechanisms.

New insights into bsr-d1-mediated broad-spectrum resistance to rice blast

bsr-d1, an allele encoding a transcription factor identified from the rice cultivar Digu, confers durable, broad-spectrum resistance to infections by strains of Magnaporthe oryzae. bsr-d1 was predicted to inhibit M. oryzae-induced expression of Bsr-d1 RNA and degradation of hydrogen peroxide to achieve resistance to M. oryzae. However, the global effect of biological process and molecular function on blast resistance mediated by Bsr-d1 remains unknown. In this study, we compared transcriptomic profiling between Bsr-d1 knockout (Bsr-d1KO) lines and the wild type, TP309. Our study revealed that bsr-d1 mainly regulates the redox state of plant cells, but also affects amino acid and unsaturated fatty acid metabolism. We further found that BSR-D1 indirectly regulates salicylic acid biosynthesis, metabolism, and signal transduction downstream of the activation of H₂ O₂ signalling in the bsr-d1-mediated immune response. Furthermore, we identified a novel peroxidase-encoding gene, Perox3, as a new BSR-D1 target gene that reduces resistance to M. oryzae when overexpressed in TP309. These results provide new insights into the bsr-d1-mediated blast resistance.

WRKY10 transcriptional regulatory cascades in rice are involved in basal defense and Xa1-mediated resistance

WRKY proteins play essential roles as negative or positive regulators of pathogen defense. This study explored the roles of different OsWRKY proteins in basal defense and Xa1-mediated resistance to Xanthomonas oryzae pv. oryzae (Xoo) infection in rice. Assays of disease in OsWRKY10KD and OsWRKY88KD lines following infection with an incompatible Xoo race, which induced Xa1-mediated resistance in wild-type plants, showed that OsWRKY10 and OsWRKY88 were positive regulators of Xa1-mediated resistance. OsWRKY10 also acted as a positive regulator in basal defense by directly or indirectly activating transcription of defense-related genes. OsWRKY10 activated the OsPR1a promoter by binding to specific WRKY binding sites. Two transcriptional regulatory cascades of OsWRKY10 were identified in basal defense and Xa1-mediated resistance. In the first transcriptional regulatory cascade, OsWRKY47 acted downstream of OsWRKY10 whereas OsWRKY51 acted upstream. OsWRKY10 activated OsPR1a in two distinct ways: by binding to its promoter and, at the same time, by indirect activation through OsWRKY47. In the second transcriptional regulatory cascade, OsWRKY47 acted downstream of OsWRKY10, and OsWRKY88 acted upstream. These OsWRKY10 transcriptional regulatory cascades played important roles in basal defense and Xa1-mediated resistance to enable the mounting of a rapid immune response against pathogens.

Comparison of defense responses of transgenic potato lines expressing three different Rpi genes to specific Phytophthora infestans races based on transcriptome profiling

Potato late blight, one of the most devastating diseases in potato, is caused by the oomycete Phytophthora infestans. Over 20 resistance genes have been cloned including R1, R3a, and R3b. The distinctions between defense response mechanisms mediated by different resistance genes are still unclear. Here we performed transcriptome profiling in three transgenic lines, R1, R3a, and R3b, and wild-type Desiree under inoculation with two P. infestans isolates, 89148 (race 0) and CN152 (super race), using RNA-seq. Compared with wild type, specific differentially expressed genes (DEGs) were identified in the three transgenic lines. The highest number of DEGs occurred in transgenic R3b, with 779 DEGs in response to isolate 89148 and 864 DEGs in response to infection by CN152, followed by transgenic R1 lines with 408 DEGs for isolate 89148 and 267 DEGs for CN152. Based on gene ontology, the most common GO terms (15 for 89148 and 20 for CN152) were enriched in transgenic R3a and R3b lines. This indicates that the defense pathways mediated by R3a and R3b are more similar than those mediated by R1. Further separate GO analysis of up- or down-regulated DEGs showed that the down-regulated DEGs mainly functioned in mediating the resistance of potato to P. infestans 89148 by response to stress biological process and to CN152 by oxidation reduction biological process. KEGG pathways of DNA replication, plant-pathogen interaction and pentose and glucuronate interconversions are unique for transgenic R1, R3a, and R3b lines in incompatible interactions. Quantitative real-time PCR experimental validation confirmed the induced expression of DEGs in the late blight resistance signaling pathway. Our results will lay a solid foundation for further understanding the mechanisms of plant-pathogen interactions, and provide a theoretical reference for durable resistance in potato.

Phosphate excess increases susceptibility to pathogen infection in rice

Phosphorus (P) is an essential nutrient for plant growth and productivity. Due to soil fixation, however, phosphorus availability in soil is rarely sufficient to sustain high crop yields. The overuse of fertilizers to circumvent the limited bioavailability of phosphate (Pi) has led to a scenario of excessive soil P in agricultural soils. Whereas adaptive responses to Pi deficiency have been deeply studied, less is known about how plants adapt to Pi excess and how Pi excess might affect disease resistance. We show that high Pi fertilization, and subsequent Pi accumulation, enhances susceptibility to infection by the fungal pathogen Magnaporthe oryzae in rice. This fungus is the causal agent of the blast disease, one of the most damaging diseases of cultivated rice worldwide. Equally, MIR399f overexpression causes an increase in Pi content in rice leaves, which results in enhanced susceptibility to M. oryzae. During pathogen infection, a weaker activation of defence-related genes occurs in rice plants over-accumulating Pi in leaves, which is in agreement with the phenotype of blast susceptibility observed in these plants. These data support that Pi, when in excess, compromises defence mechanisms in rice while demonstrating that miR399 functions as a negative regulator of rice immunity. The two signalling pathways, Pi signalling and defence signalling, must operate in a coordinated manner in controlling disease resistance. This information provides a basis to understand the molecular mechanisms involved in immunity in rice plants under high Pi fertilization, an aspect that should be considered in management of the rice blast disease.

Metabolomics as an Emerging Tool for the Study of Plant-Pathogen Interactions

Plants defend themselves from most microbial attacks via mechanisms including cell wall fortification, production of antimicrobial compounds, and generation of reactive oxygen species. Successful pathogens overcome these host defenses, as well as obtain nutrients from the host. Perturbations of plant metabolism play a central role in determining the outcome of attempted infections. Metabolomic analyses, for example between healthy, newly infected and diseased or resistant plants, have the potential to reveal perturbations to signaling or output pathways with key roles in determining the outcome of a plant-microbe interaction. However, application of this -omic and its tools in plant pathology studies is lagging relative to genomic and transcriptomic methods. Thus, it is imperative to bring the power of metabolomics to bear on the study of plant resistance/susceptibility. This review discusses metabolomics studies that link changes in primary or specialized metabolism to the defense responses of plants against bacterial, fungal, nematode, and viral pathogens. Also examined are cases where metabolomics unveils virulence mechanisms used by pathogens. Finally, how integrating metabolomics with other -omics can advance plant pathology research is discussed.

iTRAQ proteomics reveals the regulatory response to Magnaporthe oryzae in durable resistant vs. susceptible rice genotypes

Rice blast disease caused by Magnaporthe oryzae (M. oryzae) is one of the most serious diseases. Although previous research using two-dimensional gel-based proteomics to assess the proteins related to the rice blast resistance had been done, few proteins were identified. Here, we used the iTRAQ method to detect the differentially expressed proteins (DEPs) in the durable resistant rice variety Gangyuan8 (GY8) and the susceptible rice variety Lijiangxintuanheigu (LTH) in response to M. oryzae invasion, and then transcriptome sequencing was used to assist analysis A total of 193 and 672 DEPs were specifically identified in GY8 and LTH, respectively, with only 46 similarly expressed DEPs being shared by GY8 and LTH.39 DEPs involved in plant-pathogen interaction, plant hormone signal transduction, fatty acid metabolism and peroxisome biosynthesis were significantly different between compatible interaction (LTH) and incompatible interaction (GY8). Some proteins participated in peroxide signal transduction and biosynthesis was down-regulated in GY8 but up-regulated in LTH. A lot of genes encoding pathogenesis-related gene (PR), such as chitinase and glucanase, were significantly up-regulated at both the transcriptome and proteome levels at 24 hours post-inoculation in GY8, but up-regulated at the transcriptome level and down-regulated at the proteome level in LTH. Our study reveals that the pathogen-associated molecular pattern (PAMP)-triggered immunity defense system may be activated at the transcriptome level but was inhibited at the protein level in susceptible rice varieties after inoculation. The results may facilitate future studies of the molecular mechanisms of rice blast resistance.

Identification and characterization of genes frequently responsive to Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae infections in rice

Background

Disease resistance is an important factor that impacts rice production. However, the mechanisms underlying rice disease resistance remain to be elucidated.

Results

Here, we show that a robust set of genes has been defined in rice response to the infections of Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae (Mor). We conducted a comprehensive analysis of the available microarray data from a variety of rice samples with inoculation of Xoo and Mor. A set of 12,932 genes was identified to be regulated by Xoo and another set of 2709 Mor-regulated genes was determined. GO enrichment analysis of the regulated genes by Xoo or Mor suggested mitochondrion may be an arena for the up-regulated genes and chloroplast be another for the down-regulated genes by Xoo or Mor. Cytokinin-related processes were most frequently repressed by Xoo, while processes relevant to jasmonic acid and abscisic acid were most frequently activated by Xoo and Mor. Among genes responsive to Xoo and Mor, defense responses and diverse signaling pathways were the most frequently enriched resistance mechanisms. InterPro annotation showed the zinc finger domain family, WRKY proteins, and Myb domain proteins were the most significant transcription factors regulated by Xoo and Mor. KEGG analysis demonstrated pathways including ‘phenylpropanoid biosynthesis’, ‘biosynthesis of antibiotics’, ‘phenylalanine metabolism’, and ‘biosynthesis of secondary metabolites’ were most frequently triggered by Xoo and Mor, whereas ‘circadian rhythm-plant’ was the most frequent pathway repressed by Xoo and Mor.

Conclusions

The genes identified here represent a robust set of genes responsive to the infections of Xoo and Mor, which provides an overview of transcriptional reprogramming during rice defense against Xoo and Mor infections. Our study would be helpful in understanding the mechanisms of rice disease resistance.

Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

BACKGROUND

MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the post-transcriptional level in eukaryotes. In rice, MIR7695 expression is regulated by infection with the rice blast fungus Magnaporthe oryzae with subsequent down-regulation of an alternatively spliced transcript of natural resistance-associated macrophage protein 6 (OsNramp6). NRAMP6 functions as an iron transporter in rice.

RESULTS

Rice plants grown under high iron supply showed blast resistance, which supports that iron is a factor in controlling blast resistance. During pathogen infection, iron accumulated in the vicinity of M. oryzae appressoria, the sites of pathogen entry, and in cells surrounding infected regions of the rice leaf. Activation-tagged MIR7695 rice plants (MIR7695-Ac) exhibited enhanced iron accumulation and resistance to M. oryzae infection. RNA-seq analysis revealed that blast resistance in MIR7695-Ac plants was associated with strong induction of defense-related genes, including pathogenesis-related and diterpenoid biosynthetic genes. Levels of phytoalexins during pathogen infection were higher in MIR7695-Ac than wild-type plants. Early phytoalexin biosynthetic genes, OsCPS2 and OsCPS4, were also highly upregulated in wild-type rice plants grown under high iron supply.

CONCLUSIONS

Our data support a positive role of miR7695 in regulating rice immunity that further underpin links between defense and iron signaling in rice. These findings provides a basis to better understand regulatory mechanisms involved in rice immunity in which miR7695 participates which has a great potential for the development of strategies to improve blast resistance in rice.

Transcriptomic Insights into Innate Immunity Responding to Red Rot Disease in Red Alga Pyropia yezoensis

Pyropia yezoensis, one of the most economically important marine algae, suffers from the biotic stress of the oomycete necrotrophic pathogen Pythium porphyrae. However, little is known about the molecular defensive mechanisms employed by Pyr. yezoensis during the infection process. In the present study, we defined three stages of red rot disease based on histopathological features and photosynthetic physiology. Transcriptomic analysis was carried out at different stages of infection to identify the genes related to the innate immune system in Pyr. yezoensis. In total, 2139 up-regulated genes and 1672 down-regulated genes were identified from all the infected groups. Pathogen receptor genes, including three lectin genes (pattern recognition receptors (PRRs)) and five genes encoding typical plant R protein domains (leucine rich repeat (LRR), nucleotide binding site (NBS), or Toll/interleukin-1 receptor (TIR)), were found to be up-regulated after infection. Several defense mechanisms that were typically regarded as PAMP-triggered immunity (PTI) in plants were induced during the infection. These included defensive and protective enzymes, heat shock proteins, secondary metabolites, cellulase, and protease inhibitors. As a part of the effector-triggered immunity (ETI), the expression of genes related to the ubiquitin-proteasome system (UPS) and hypersensitive cell death response (HR) increased significantly during the infection. The current study suggests that, similar to plants, Pyr. yezoensis possesses a conserved innate immune system that counters the invasion of necrotrophic pathogen Pyt. porphyrae. However, the innate immunity genes of Pyr. yezoensis appear to be more ancient in origin compared to those in higher plants.

Deciphering signalling network in broad spectrum Near Isogenic Lines of rice resistant to Magnaporthe oryzae

Disease resistance (R) genes like Pi9, Pita, Pi21, Pi54 are playing important role for broad spectrum blast resistance in rice. Development of near isogenic lines (NILs) using these type of broad spectrum genes and understanding their signalling networks is essential to cope up with highly evolving Magnaporthe oryzae strains for longer duration. Here, transcriptional-level changes were studied in three near-isogenic lines (PB1 + Pi1, PB1 + Pi9 and PB1 + Pi54) of rice resistant to blast infection, to find the loci that are unique to resistant lines developed in the background of Pusa Basmati 1 (PB1). The pathway analysis of loci, unique to resistant NILs compared to susceptible control revealed that plant secondary metabolite synthesis was the common mechanism among all NILs to counter against M. oryzae infection. Comparative transcriptome analysis helped to find out common clusters of co-expressed significant differentially expressed loci (SDEL) in both PB1 + Pi9 and PB1 + Pi54 NILs. SDELs from these clusters were involved in the synthesis and degradation of starch; synthesis and elongation of fatty acids; hydrolysis of phospholipids; synthesis of phenylpropanoid; and metabolism of ethylene and jasmonic acid. Through detailed analysis of loci specific to each resistant NIL, we identified a network of signalling pathways mediated by each blast resistance gene. The study also offers insights into transcriptomic dynamics, points to a set of important candidate genes that serve as module to regulate the changes in resistant NILs. We suggest that pyramiding of the blast resistance gene Pi9 with Pi54 will lead to maximum broad spectrum resistance to M. oryzae.

Transcriptome analysis of a rice cultivar reveals the differentially expressed genes in response to wild and mutant strains of Xanthomonas oryzae pv. oryzae

Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating disease in most of the rice growing regions worldwide. Among the 42 BB resistance (R) genes, Xa23 is an executor R gene, conferring broad-spectrum disease resistance to all naturally occurring biotypes of Xoo. In this study, CBB23, a rice line carrying Xa23 gene, was inoculated with wild PXO99^A and its mutant, P99M2, to retrieve the differentially expressed genes (DEGs). RNA-Seq analysis retrieved 1,235 DEGs (p-value ≤ 0.05) at 12, 24, 36, and 48 hours of post inoculation (hpi). Gene ontology (GO) analysis classified the DEGs functionally into biological process, cellular component and molecular function. KEGG pathway analysis categorized the DEGs into 11 different pathways, and the ribosome is a prominent pathway followed by biosynthesis of phenylpropanoids. Gene co-expression network analysis identified the clusters of transcription factors (TFs) which may be involved in PXO99^A resistance. Additionally, we retrieved 67 differentially expressed TFs and 26 peroxidase responsive genes which may be involved in disease resistance mechanism. DEGs involved in the host-pathogen interaction, e.g., signaling mechanism, cell wall and plant hormones were identified. This data would be a valuable resource for researchers to identify the candidate genes associated with Xoo resistance.

OsDCL1a activation impairs phytoalexin biosynthesis and compromises disease resistance in rice

BACKGROUND AND AIMS

MicroRNAs (miRNAs) are small non-coding RNAs that act as post-transcriptional regulators of gene expression via sequence-specific cleavage or translational repression of target transcripts. They are transcribed as long single-stranded RNA precursors with unique stem-loop structures that are processed by a DICER-Like (DCL) ribonuclease, typically DCL1, to produce mature miRNAs. Although a plethora of miRNAs have been found to be regulated by pathogen infection in plants, the biological function of most miRNAs remains largely unknown. Here, the contribution of OsDCL1 to rice immunity was investigated.

METHODS

Activation-tagged Osdcl1a (Osdcl1a-Ac) rice mutants were examined for resistance to pathogen infection. mRNA and small RNA deep sequencing, quantitative real-time PCR (RT-qPCR) and stem-loop reverse tanscripion-PCR (RT-PCR) were used to examine DCL1a-mediated alterations in the rice transcriptome. Rice diterpene phytoalexins were quantified by liquid chromatography-tandem mass spectrometry (LC-MSMS). Accumulation of O2·- was determined by nitroblue tetrazolium (NBT) staining.

KEY RESULTS

dcl1a-Ac mutants exhibit enhanced susceptibility to infection by fungal pathogens which was associated with a weaker induction of defence gene expression. Comparison of the mRNA and miRNA transcriptomes of dcl1a-Ac and wild-type plants revealed misregulation of genes involved in detoxification of reactive oxygen species. Consequently, dcl1a-Ac plants accumulated O2·- in their leaves and were more sensitive to methyl viologen-induced oxidative stress. Furthermore, dcl1a-Ac plants showed downregulation of diterpenoid phytoalexin biosynthetic genes, these genes also being weakly induced during pathogen infection. Upon pathogen challenge, dcl1a-Ac plants failed to accumulate major diterpenoid phytoalexins. OsDCL1a activation resulted in marked alterations in the rice miRNAome, including both upregulation and downregulation of miRNAs.

CONCLUSIONS

OsDCL1a activation enhances susceptibility to infection by fungal pathogens in rice. Activation of OsDCL1a represses the pathogen-inducible host defence response and negatively regulates diterpenoid phytoalexin production. These findings provide a basis to understand the molecular mechanisms through which OsDCL1a mediates rice immunity.

RiceMetaSysB: a database of blast and bacterial blight responsive genes in rice and its utilization in identifying key blast-resistant WRKY genes

Nearly two decades of revolution in the area of genomics serves as the basis of present-day molecular breeding in major food crops such as rice. Here we report an open source database on two major biotic stresses of rice, named RiceMetaSysB, which provides detailed information about rice blast and bacterial blight (BB) responsive genes (RGs). Meta-analysis of microarray data from different blast- and BB-related experiments across 241 and 186 samples identified 15135 unique genes for blast and 7475 for BB. A total of 9365 and 5375 simple sequence repeats (SSRs) in blast and BB RGs were identified for marker development. Retrieval of candidate genes using different search options like genotypes, tissue, developmental stage of the host, strain, hours/days post-inoculation, physical position and SSR marker information is facilitated in the database. Search options like 'common genes among varieties' and 'strains' have been enabled to identify robust candidate genes. A 2D representation of the data can be used to compare expression profiles across genes, genotypes and strains. To demonstrate the utility of this database, we queried for blast-responsive WRKY genes (fold change ≥5) using their gene IDs. The structural variations in the 12 WRKY genes so identified and their promoter regions were explored in two rice genotypes contrasting for their reaction to blast infection. Expression analysis of these genes in panicle tissue infected with a virulent and an avirulent strain of Magnaporthe oryzae could identify WRKY7, WRKY58, WRKY62, WRKY64 and WRKY76 as potential candidate genes for resistance to panicle blast, as they showed higher expression only in the resistant genotype against the virulent strain. Thus, we demonstrated that RiceMetaSysB can play an important role in providing robust candidate genes for rice blast and BB.

Comparative Transcriptome Analysis Between Resistant and Susceptible Rice Cultivars Responding to Striped Stem Borer (SSB), Chilo suppressalis (Walker) Infestation

The striped stem borer, Chilo suppressalis (Walker), is a notorious pest of rice that causes large losses in China. Breeding and screening of resistance rice cultivars are effective strategies for C. suppressalis management. In this study, insect-resistant traits of 47 rice cultivars were investigated by C. suppressalis artificial infestation (AI) both in field and greenhouse experiments, using the susceptible (S) cultivar 1665 as a control. Results suggest that two rice cultivars, namely 1688 and 1654, are resistant (R) and moderately resistant (MR) to C. suppressalis, respectively. Then, a comparative transcriptome (RNA-Seq) was de novo assembled and differentially expressed genes (DEGs) with altered expression levels were investigated among cultivars 1688, 1654, and 1665, with or without C. suppressalis infestation for 24 h. A total of 2569 and 1861 genes were up-regulated, and 3852 and 1861 genes were down-regulated in cultivars 1688 and 1654, respectively after artificial infestation with C. suppressalis compared to the non-infested control (CK). For the susceptible cultivar 1665, a total of 882 genes were up-regulated and 3863 genes were down-regulated after artificial infestation with C. suppressalis compared to the CK. Twenty four DEGs belong to proteinase inhibitor, lectin and chitinase gene families; plant hormone signal transduction and plant-pathogen interaction pathways were selected as candidate genes to test their possible role in C. suppressalis resistance. RT-qPCR results revealed that 13 genes were significantly up-regulated and 8 were significantly down-regulated in the resistant cultivar 1688 with C. suppressalis artificial infestation (1688AI) compared to the CK. Three genes, LTPL164, LTPL151, and LOC Os11g32100, showed more than a 10-fold higher expression in 1688AI than in 1688CK, suggesting their potential role in insect resistance. Overall, our results provide an important foundation for further understanding the insect resistance mechanisms of selected resistant varieties that will help us to breed C. suppressalis resistant rice varieties.

A Pelota-like gene regulates root development and defence responses in rice

BACKGROUND AND AIMS

Pelota (Pelo) are evolutionarily conserved genes reported to be involved in ribosome rescue, cell cycle control and meiotic cell division. However, there is little known about their function in plants. The aim of this study was to elucidate the function of an ethylmethane sulphonate (EMS)-derived mutation of a Pelo-like gene in rice (named Ospelo).

METHODS

A dysfunctional mutant was used to characterize the function of OsPelo. Analyses of its expression and sub-cellular localization were performed. The whole-genome transcriptomic change in leaves of Ospelo was also investigated by RNA sequencing.

KEY RESULTS

The Ospelo mutant showed defects in root system development and spotted leaves at early seedling stages. Map-based cloning revealed that the mutation occurred in the putative Pelo gene. OsPelo was found to be expressed in various tissues throughout the plant, and the protein was located in mitochondria. Defence responses were induced in the Ospelo mutant, as shown by enhanced resistance to the bacterial pathogen Xanthomonas oryzae pv. oryzae, coupled with upregulation of three pathogenesis-related marker genes. In addition, whole-genome transcriptome analysis showed that OsPelo was significantly associated with a number of biological processes, including translation, metabolism and biotic stress response. Detailed analysis showed that activation of a number of innate immunity-related genes might be responsible for the enhanced disease resistance in the Ospelo mutant.

CONCLUSIONS

These results demonstrate that OsPelo positively regulates root development while its loss of function enhances pathogen resistance by pre-activation of defence responses in rice.

Transcriptomic Analysis of Oryza sativa Leaves Reveals Key Changes in Response to Magnaporthe oryzae MSP1

Rice blast disease, caused by Magnaporthe oryzae, results in an extensive loss of rice productivity. Previously, we identified a novel M. oryzae secreted protein, termed MSP1 which causes cell death and pathogen-associated molecular pattern (PAMP)-triggered immune (PTI) responses in rice. Here, we report the transcriptome profile of MSP1-induced response in rice, which led to the identification of 21,619 genes, among which 4,386 showed significant changes (P < 0.05 and fold change > 2 or < 1/2) in response to exogenous MSP1 treatment. Functional annotation of differentially regulated genes showed that the suppressed genes were deeply associated with photosynthesis, secondary metabolism, lipid synthesis, and protein synthesis, while the induced genes were involved in lipid degradation, protein degradation, and signaling. Moreover, expression of genes encoding receptor-like kinases, MAPKs, WRKYs, hormone signaling proteins and pathogenesis-related (PR) proteins were also induced by MSP1. Mapping these differentially expressed genes onto various pathways revealed critical information about the MSP1-triggered responses, providing new insights into the molecular mechanism and components of MSP1-triggered PTI responses in rice.

Expression Profile of Defense Genes in Rice Lines Pyramided with Resistance Genes Against Bacterial Blight, Fungal Blast and Insect Gall Midge

BACKGROUND

Rice, a major food crop of the world, endures many major biotic stresses like bacterial blight (BB), fungal blast (BL) and the insect Asian rice gall midge (GM) that cause significant yield losses. Progress in tagging, mapping and cloning of several resistance (R) genes against aforesaid stresses has led to marker assisted multigene introgression into elite cultivars for multiple and durable resistance. However, no detailed study has been made on possible interactions among these genes when expressed simultaneously under combined stresses.

RESULTS

Our studies monitored expression profiles of 14 defense related genes in 11 rice breeding lines derived from an elite cultivar with different combination of R genes against BB, BL and GM under single and multiple challenge. Four of the genes found implicated earlier under combined GM and BB stress were confirmed to be induced (≥ 2 fold) in stem tissue following GM infestation; while one of these, cytochrome P450 family protein, was also induced in leaf in plants challenged by either BB or BL but not together. Three of the genes highlighted earlier in plants challenged by both BB and BL were also found induced in stem under GM challenge. Pi54 the target R gene against BL was also found induced when challenged by GM. Though expression of some genes was noted to be inhibited under combined pest challenge, such effects did not result in compromise in resistance against any of the target pests.

CONCLUSION

While R genes generally tended to respond to specific pest challenge, several of the downstream defense genes responded to multiple pest challenge either single, sequential or simultaneous, without any distinct antagonism in expression of resistance to the target pests in two of the pyramided lines RPNF05 and RPNF08.

CaWRKY22 Acts as a Positive Regulator in Pepper Response to RalstoniaSolanacearum by Constituting Networks with CaWRKY6, CaWRKY27, CaWRKY40, and CaWRKY58

The WRKY web, which is comprised of a subset of WRKY transcription factors (TFs), plays a crucial role in the regulation of plant immunity, however, the mode of organization and operation of this network remains obscure, especially in non-model plants such as pepper (Capsicum annuum). Herein, CaWRKY22, a member of a subgroup of IIe WRKY proteins from pepper, was functionally characterized in pepper immunity against Ralstonia Solanacearum. CaWRKY22 was found to target the nuclei, and its transcript level was significantly upregulated by Ralstonia Solanacearum inoculation (RSI) and exogenously applied salicylic acid (SA), Methyl jasmonate (MeJA), or ethephon (ETH). Loss-of-function CaWRKY22, caused by virus-induced gene silencing (VIGS), enhanced pepper’s susceptibility to RSI. In addition, the silencing of CaWRKY22 perturbed the hypersensitive response (HR)-like cell death elicited by RSI and downregulated defense-related genes including CaPO2, CaPR4, CaACC, CaBPR1, CaDEF1, CaHIR1, and CaWRKY40. CaWRKY22 was found to directly bind to the promoters of CaPR1, CaDEF1, and CaWRKY40 by chromatin immuno-precipitation (ChIP) analysis. Contrastingly, transient overexpression of CaWRKY22 in pepper leaves triggered significant HR-like cell death and upregulated the tested immunity associated maker genes. Moreover, the transient overexpression of CaWRKY22 upregulated the expression of CaWRKY6 and CaWRKY27 while it downregulated of the expression of CaWRKY58. Conversely, the transient overexpression of CaWRKY6, CaWRKY27, and CaWRKY40 upregulated the expression of CaWRKY22, while transient overexpression of CaWRKY58 downregulated the transcript levels of CaWRKY22. These data collectively recommend the role of CaWRKY22 as a positive regulator of pepper immunity against R. Solanacearum, which is regulated by signaling synergistically mediated by SA, jasmonic acid (JA), and ethylene (ET), integrating into WRKY networks with WRKY TFs including CaWRKY6, CaWRKY27, CaWRKY40, and CaWRKY58.

Current understanding of pattern-triggered immunity and hormone-mediated defense in rice (Oryza sativa) in response to Magnaporthe oryzae infection

Plant pathogens represent a huge threat to world food security, affecting both crop production and quality. Although significant progress has been made in improving plant immunity by expressing key, defense-related genes and proteins from different species in transgenic crops, a challenge remains for molecular breeders and biotechnologists to successfully engineer elite, transgenic crop varieties with improved resistance against critical plant pathogens. Upon pathogen attack, including infection of rice (Oryza sativa) by Magnaporthe oryzae, host plants initiate a complex defense response at molecular, biochemical and physiological levels. Plants perceive the presence of pathogens by detecting microbe-associated molecular patterns via pattern recognition receptors, and initiate a first line of innate immunity, the so-called pattern-triggered immunity (PTI). This results in a series of downstream defense responses, including the production of hormones, which collectively function to fend off pathogen attacks. A variety of studies have demonstrated that many genes are involved in the defense response of rice to M. oryzae. In this review, the current understanding of mechanisms that improve rice defense response to M. oryzae will be discussed, with special focus on PTI and the phytohormones ethylene, jasmonic acid, salicylic acid, and abscisic acid; as well as on the mediation of defense signaling mechanisms by PTI and these hormones. Potential target genes that may serve as promising candidates for improving rice immunity against M. oryzae will also be discussed.

Genome-Wide Expression Profiling of OsWRKY Superfamily Genes during Infection with Xanthomonas oryzae pv. oryzae Using Real-Time PCR

WRKY transcription factors (TFs) are involved in regulating a range of biological processes such as growth, development, and the responses to biotic and abiotic stresses. Genome-wide expression profiling of OsWRKY TF superfamily genes in rice after infection with Xanthomonas oryzae pv. oryzae (Xoo) was performed to elucidate the function of OsWRKY TFs in the interaction between rice and Xoo. Of the 111 OsWRKY TF genes tested, the transcription of 94 genes changed after Xoo infection. The OsWRKY TF genes were classified into eight types according to their expression profiles. Eighty-two genes in Groups I, II, III, IV, VII were up-regulated after exposure to a compatible or an incompatible race of Xoo. Examination of salicylic acid (SA)-deficient rice lines revealed that SA was involved in Xa1-mediated resistance to Xoo infection. OsWRKY TF genes involved in Xa1-mediated resistance were classified according to their SA-dependent or -independent expression. In SA-deficient rice, the expression of 12 of 57 OsWRKY TF genes involved in Xa1-mediated resistance was compromised. Of these six OsWRKY TF genes were induced by SA. OsWRKY88, an example of a gene possibly involved in SA-dependent Xa1-mediated resistance, activated defense related genes and increased resistance to Xoo. Thus, expression profiling of OsWRKY TF genes may help predict the functions of OsWRKY TF genes involved in Xa1-mediated resistance.

Common Stress Transcriptome Analysis Reveals Functional and Genomic Architecture Differences Between Early and Delayed Response Genes

To identify the similarities among responses to diverse environmental stresses, we analyzed the transcriptome response of rice roots to three rhizotoxic perturbations (chromium, ferulic acid and mercury) and identified common early-transient, early-constant and delayed gene inductions. Common early response genes were mostly associated with signal transduction and hormones, and delayed response genes with lipid metabolism. Network component analysis revealed complicated interactions among common genes, the most highly connected signaling hubs being PP2C68, MPK5, LRR-RLK and NPR1. Gene architecture studies revealed different conserved promoter motifs and a different ratio of CpG island distribution between early and delayed genes. In addition, early-transient genes had more exons and a shorter first exon. IMEter was used to calculate the transcription regulation effects of introns, with greater effects for the first introns of early-transient than delayed genes. The higher Ka/Ks (non-synonymous/synonymous mutation) ratio of early-constant genes than early-transient, delayed and the genome median demonstrates the rapid evolution of early-constant genes. Our results suggest that finely tuned transcriptional control in response to environmental stress in rice depends on genomic architecture and signal intensity and duration.

Understanding Host-Pathogen Interactions with Expression Profiling of NILs Carrying Rice-Blast Resistance Pi9 Gene

Magnaporthe oryzae infection causes rice blast, a destructive disease that is responsible for considerable decrease in rice yield. Development of resistant varieties via introgressing resistance genes with marker-assisted breeding can eliminate pesticide use and minimize crop losses. Here, resistant near-isogenic line (NIL) of Pusa Basmati-1(PB1) carrying broad spectrum rice blast resistance gene Pi9 was used to investigate Pi9-mediated resistance response. Infected and uninfected resistant NIL and susceptible control line were subjected to RNA-Seq. With the exception of one gene (Pi9), transcriptional signatures between the two lines were alike, reflecting basal similarities in their profiles. Resistant and susceptible lines possessed 1043 (727 up-regulated and 316 down-regulated) and 568 (341 up-regulated and 227 down-regulated) unique and significant differentially expressed loci (SDEL), respectively. Pathway analysis revealed higher transcriptional activation of kinases, WRKY, MYB, and ERF transcription factors, JA-ET hormones, chitinases, glycosyl hydrolases, lipid biosynthesis, pathogenesis and secondary metabolism related genes in resistant NIL than susceptible line. Singular enrichment analysis demonstrated that blast resistant NIL is significantly enriched with genes for primary and secondary metabolism, response to biotic stimulus and transcriptional regulation. The co-expression network showed proteins of genes in response to biotic stimulus interacted in a manner unique to resistant NIL upon M. oryzae infection. These data suggest that Pi9 modulates genome-wide transcriptional regulation in resistant NIL but not in susceptible PB1. We successfully used transcriptome profiling to understand the molecular basis of Pi9-mediated resistance mechanisms, identified potential candidate genes involved in early pathogen response and revealed the sophisticated transcriptional reprogramming during rice-M. oryzae interactions.

Characterization of the cytokinin-responsive transcriptome in rice

BACKGROUND

Cytokinin activates transcriptional cascades important for development and the responses to biotic and abiotic stresses. Most of what is known regarding cytokinin-regulated gene expression comes from studies of the dicotyledonous plant Arabidopsis thaliana. To expand the understanding of the cytokinin-regulated transcriptome, we employed RNA-Seq to analyze gene expression in response to cytokinin in roots and shoots of the monocotyledonous plant rice.

RESULTS

We identified over 4,600 and approximately 2,400 genes differentially expressed in response to cytokinin in roots and shoots respectively. There were some similarities in the sets of cytokinin-regulated genes identified in rice and Arabidopsis, including an up-regulation of genes that act to reduce cytokinin function. Consistent with this, we found that the preferred DNA-binding motif of a rice type-B response regulator is similar to those from Arabidopsis. Analysis of the genes regulated by cytokinin in rice revealed a large number of transcription factors, receptor-like kinases, and genes involved in protein degradation, as well as genes involved in development and the response to biotic stress. Consistent with the over-representation of genes involved in biotic stress, there is a substantial overlap in the genes regulated by cytokinin and those differentially expressed in response to pathogen infection, suggesting that cytokinin plays an integral role in the transcriptional response to pathogens in rice, including the induction of a large number of WRKY transcription factors.

CONCLUSIONS

These results begin to unravel the complex gene regulation after cytokinin perception in a crop of agricultural importance and provide insight into the processes and responses modulated by cytokinin in monocots.

Transcriptional Profiling of Rice Treated with MoHrip1 Reveal the Function of Protein Elicitor in Enhancement of Disease Resistance and Plant Growth

MoHrip1 is a protein elicitor isolated from Magnaporthe oryzae and was found to induce blast-resistance in rice. To investigate the comprehensive functions of MoHrip1, next-generation sequencing (NGS)-based digital gene expression (DGE) profiling was performed to collect the transcriptional data of differentially expressed genes (DEGs) induced by MoHrip1. A total of 308 genes were identified with differential expression, and 80 genes were predicted to be induced specifically by MoHrip1. Among these 308 genes, a series of genes associated with the salicylic acid (SA) pathway, phytoalexin, transcription factors, and pathogen-related proteins were identified. Both the SA signaling pathway and the gibberellin (GA) pathway were activated, while the jasmonic acid (JA) signaling pathway was repressed. The contents of endogenous SA and GA and the morphological characteristics of the rice after treatment were measured to provide evidence supporting the predictions made based on the DGE data. The 80 genes mentioned above might be candidate genes for studying interactions with MoHrip1. The transcriptional data provided global effect information in rice induced by MoHrip1, and all the results demonstrated that MoHrip1 could induce pathogen resistance and promote plant growth by regulating the contents of SA and GA directly or indirectly.

OsWRKY80-OsWRKY4 Module as a Positive Regulatory Circuit in Rice Resistance Against Rhizoctonia solani

BACKGROUND

Plant WRKY transcription factors play pivotal roles in diverse biological processes but most notably in plant defense response to pathogens. Sheath blight represents one of the predominant diseases in rice. However, our knowledge about the functions of WRKY proteins in rice defense against sheath blight is rather limited.

RESULTS

Here we demonstrate that the expression of Oryza sativa WRKY80 gene (OsWRKY80) is rapidly and strongly induced upon infection of Rhizoctonia solani, the causal agent of rice sheath blight disease. OsWRKY80 expression is also induced by exogenous jasmonic acid (JA) and ethylene (ET), but not by salicylic acid (SA). OsWRKY80-GFP is localized in the nuclei of onion epidermal cells in a transient expression assay. Consistently, OsWRKY80 exhibits transcriptional activation activity in a GAL4 assay in yeast cells. Overexpression of OsWRKY80 in rice plants significantly enhanced disease resistance to R. solani, concomitant with elevated expression of OsWRKY4, another positive regulator in rice defense against R. solani. Suppression of OsWRKY80 by RNA interference (RNAi), on the other hand, compromised disease resistance to R. solani. Results of yeast one-hybrid assay and transient expression assay in tobacco cells have revealed that OsWRKY80 specifically binds to the promoter regions of OsWRKY4, which contain W-box (TTGAC[C/T]) or W-box like (TGAC[C/T]) cis-elements.

CONCLUSIONS

We propose that OsWRKY80 functions upstream of OsWRKY4 as an important positive regulatory circuit that is implicated in rice defense response to sheath blight pathogen R. solani.

Fungal Elicitor MoHrip2 Induces Disease Resistance in Rice Leaves, Triggering Stress-Related Pathways

MoHrip2 Magnaporthe oryzae hypersensitive protein 2 is an elicitor protein of rice blast fungus M. oryzae. Rice seedlings treated with MoHrip2 have shown an induced resistance to rice blast. To elucidate the mechanism underlying this MoHrip2 elicitation in rice, we used differential-display 2-D gel electrophoresis and qRT-PCR to assess the differential expression among the total proteins extracted from rice leaves at 24 h after treatment with MoHrip2 and buffer as a control. Among ~1000 protein spots detected on each gel, 10 proteins were newly induced, 4 were up-regulated, and 3 were down-regulated in MoHrip2-treated samples compared with the buffer control. Seventeen differentially expressed proteins were detected using MS/MS analysis and categorized into six groups according to their putative function: defense-related transcriptional factors, signal transduction-related proteins, reactive oxygen species (ROS) production, programmed cell death (PCD), defense-related proteins, and photosynthesis and energy-related proteins. The qPCR results (relative expression level of genes) further supported the differential expression of proteins in MoHrip2-treated rice leaves identified with 2D-gel, suggesting that MoHrip2 triggers an early defense response in rice leaves via stress-related pathways, and the results provide evidence for elicitor-induced resistance at the protein level.

Magnaporthe oryzae Effector AVR-Pii Helps to Establish Compatibility by Inhibition of the Rice NADP-Malic Enzyme Resulting in Disruption of Oxidative Burst and Host Innate Immunity

Plant disease resistance occurs as a hypersensitive response (HR) at the site of attempted pathogen invasion. This specific event is initiated in response to recognition of pathogen-associated molecular pattern (PAMP) and subsequent PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI). Both PTI and ETI mechanisms are tightly connected with reactive oxygen species (ROS) production and disease resistance that involves distinct biphasic ROS production as one of its pivotal plant immune responses. This unique oxidative burst is strongly dependent on the resistant cultivars because a monophasic ROS burst is a hallmark of the susceptible cultivars. However, the cause of the differential ROS burst remains unknown. In the study here, we revealed the plausible underlying mechanism of the differential ROS burst through functional understanding of the Magnaporthe oryzae (M. oryzae) AVR effector, AVR-Pii. We performed yeast two-hybrid (Y2H) screening using AVR-Pii as bait and isolated rice NADP-malic enzyme2 (Os-NADP-ME2) as the rice target protein. To our surprise, deletion of the rice Os-NADP-ME2 gene in a resistant rice cultivar disrupted innate immunity against the rice blast fungus. Malic enzyme activity and inhibition studies demonstrated that AVR-Pii proteins specifically inhibit in vitro NADP-ME activity. Overall, we demonstrate that rice blast fungus, M. oryzae attenuates the host ROS burst via AVR-Pii-mediated inhibition of Os-NADP-ME2, which is indispensable in ROS metabolism for the innate immunity of rice. This characterization of the regulation of the host oxidative burst will help to elucidate how the products of AVR genes function associated with virulence of the pathogen.

The durably resistant rice cultivar Digu activates defence gene expression before the full maturation of Magnaporthe oryzae appressorium

Rice blast caused by the fungal pathogen Magnaporthe oryzae is one of the most destructive diseases worldwide. Although the rice-M. oryzae interaction has been studied extensively, the early molecular events that occur in rice before full maturation of the appressorium during M. oryzae invasion are unknown. Here, we report a comparative transcriptomics analysis of the durably resistant rice variety Digu and the susceptible rice variety Lijiangxintuanheigu (LTH) in response to infection by M. oryzae (5, 10 and 20 h post-inoculation, prior to full development of the appressorium). We found that the transcriptional responses differed significantly between these two rice varieties. Gene ontology and pathway analyses revealed that many biological processes, including extracellular recognition and biosynthesis of antioxidants, terpenes and hormones, were specifically activated in Digu shortly after infection. Forty-eight genes encoding receptor kinases (RKs) were significantly differentially regulated by M. oryzae infection in Digu. One of these genes, LOC_Os08g10300, encoding a leucine-rich repeat RK from the LRR VIII-2 subfamily, conferred enhanced resistance to M. oryzae when overexpressed in rice. Our study reveals that a multitude of molecular events occur in the durably resistant rice Digu before the full maturation of the appressorium after M. oryzae infection and that membrane-associated RKs play important roles in the early response.

Overexpression of Rice Wall-Associated Kinase 25 (OsWAK25) Alters Resistance to Bacterial and Fungal Pathogens

Wall-associated kinases comprise a sub-family of receptor-like kinases that function in plant growth and stress responses. Previous studies have shown that the rice wall-associated kinase, OsWAK25, interacts with a diverse set of proteins associated with both biotic and abiotic stress responses. Here, we show that wounding and BTH treatments induce OsWAK25 transcript expression in rice. We generated OsWAK25 overexpression lines and show that these lines exhibit a lesion mimic phenotype and enhanced expression of rice NH1 (NPR1 homolog 1), OsPAL2, PBZ1 and PR10. Furthermore, these lines show resistance to the hemibiotrophic pathogens, Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae, yet display increased susceptibility to necrotrophic fungal pathogens, Rhizoctonia solani and Cochliobolus miyabeanus.

Trait Specific Expression Profiling of Salt Stress Responsive Genes in Diverse Rice Genotypes as Determined by Modified Significance Analysis of Microarrays

Stress responsive gene expression is commonly profiled in a comparative manner involving different stress conditions or genotypes with contrasting reputation of tolerance/resistance. In contrast, this research exploited a wide natural variation in terms of taxonomy, origin and salt sensitivity in eight genotypes of rice to identify the trait specific patterns of gene expression under salt stress. Genome wide transcptomic responses were interrogated by the weighted continuous morpho-physiological trait responses using modified Significance Analysis of Microarrays. More number of genes was found to be differentially expressed under salt stressed compared to that of under unstressed conditions. Higher numbers of genes were observed to be differentially expressed for the traits shoot Na(+)/K(+), shoot Na(+), root K(+), biomass and shoot Cl(-), respectively. The results identified around 60 genes to be involved in Na(+), K(+), and anion homeostasis, transport, and transmembrane activity under stressed conditions. Gene Ontology (GO) enrichment analysis identified 1.36% (578 genes) of the entire transcriptome to be involved in the major molecular functions such as signal transduction (>150 genes), transcription factor (81 genes), and translation factor activity (62 genes) etc., under salt stress. Chromosomal mapping of the genes suggests that majority of the genes are located on chromosomes 1, 2, 3, 6, and 7. The gene network analysis showed that the transcription factors and translation initiation factors formed the major gene networks and are mostly active in nucleus, cytoplasm and mitochondria whereas the membrane and vesicle bound proteins formed a secondary network active in plasma membrane and vacuoles. The novel genes and the genes with unknown functions thus identified provide picture of a synergistic salinity response representing the potentially fundamental mechanisms that are active in the wide natural genetic background of rice and will be of greater use once their roles are functionally verified.