The B-3 ethylene response factor MtERF1-1 mediates resistance to a subset of root pathogens in Medicago truncatula without adversely affecting symbiosis with rhizobia

Defense and senescence interplay in legume nodules

Immunity and senescence play a crucial role in the functioning of the legume symbiotic nodules. The miss-regulation of one of these processes compromises the symbiosis leading to death of the endosymbiont and the arrest of the nodule functioning. The relationship between immunity and senescence has been extensively studied in plant organs where a synergistic response can be observed. However, the interplay between immunity and senescence in the symbiotic organ is poorly discussed in the literature and these phenomena are often mixed up. Recent studies revealed that the cooperation between immunity and senescence is not always observed in the nodule, suggesting complex interactions between these two processes within the symbiotic organ. Here, we discuss recent results on the interplay between immunity and senescence in the nodule and the specificities of this relationship during legume-rhizobium symbiosis.

Ethylene-MPK8-ERF.C1-PR module confers resistance against Botrytis cinerea in tomato fruit without compromising ripening

The plant hormone ethylene plays a critical role in fruit defense against Botrytis cinerea attack, but the underlying mechanisms remain poorly understood. Here, we showed that ethylene response factor SlERF.C1 acts as a key regulator to trigger the ethylene-mediated defense against B. cinerea in tomato fruits without compromising ripening. Knockout of SlERF.C1 increased fruit susceptibility to B. cinerea with no effect on ripening process, while overexpression enhanced resistance. RNA-Seq, transactivation assays, EMSA and ChIP-qPCR results indicated that SlERF.C1 activated the transcription of PR genes by binding to their promoters. Moreover, SlERF.C1 interacted with the mitogen-activated protein kinase SlMPK8 which allowed SlMPK8 to phosphorylate SlERF.C1 at the Ser174 residue and increases its transcriptional activity. Knocking out of SlMPK8 increased fruit susceptibility to B. cinerea, whereas overexpression enhanced resistance without affecting ripening. Furthermore, genetic crosses between SlMPK8-KO and SlERF.C1-OE lines reduced the resistance to B. cinerea attack in SlERF.C1-OE fruits. In addition, B. cinerea infection induced ethylene production which in turn triggered SlMPK8 transcription and enhanced the phosphorylation of SlERF.C1. Overall, our findings reveal the regulatory mechanism of the 'Ethylene-MPK8-ERF.C1-PR' module in resistance against B. cinerea and provide new insight into the manipulation of gray mold disease in fruits.

Genetic Analysis of Partially Resistant and Susceptible Chickpea Cultivars in Response to Ascochyta rabiei Infection

The molecular mechanism involved in chickpea (Cicer arietinum L.) resistance to the necrotrophic fungal pathogen Ascochyta rabiei is not well documented. A. rabiei infection can cause severe damage in chickpea, resulting in significant economic losses. Understanding the resistance mechanism against ascochyta blight can help to define strategies to develop resistant cultivars. In this study, differentially expressed genes from two partially resistant cultivars (CDC Corinne and CDC Luna) and a susceptible cultivar (ICCV 96029) to ascochyta blight were identified in the early stages (24, 48 and 72 h) of A. rabiei infection using RNA-seq. Altogether, 3073 genes were differentially expressed in response to A. rabiei infection across different time points and cultivars. A larger number of differentially expressed genes (DEGs) were found in CDC Corinne and CDC Luna than in ICCV 96029. Various transcription factors including ERF, WRKY, bHLH and MYB were differentially expressed in response to A. rabiei infection. Genes involved in pathogen detection and immune signalings such as receptor-like kinases (RLKs), Leucine-Rich Repeat (LRR)-RLKs, and genes associated with the post-infection defence response were differentially expressed among the cultivars. GO functional enrichment and pathway analysis of the DEGs suggested that the biological processes such as metabolic process, response to stimulus and catalytic activity were overrepresented in both resistant and susceptible chickpea cultivars. The expression patterns of eight randomly selected genes revealed by RNA-seq were confirmed by quantitative PCR (qPCR) analysis. The results provide insights into the complex molecular mechanism of the chickpea defence in response to the A. rabiei infection.

Comprehensive transcriptome analyses of Fusarium-infected root xylem tissues to decipher genes involved in chickpea wilt resistance

Fusarium wilt is the most destructive soil-borne disease that poses a major threat to chickpea production. To comprehensively understand the interaction between chickpea and Fusarium oxysporum, the xylem-specific transcriptome analysis of wilt-resistant (WR315) and wilt-susceptible (JG62) genotypes at an early timepoint (4DPI) was investigated. Differential expression analysis showed that 1368 and 348 DEGs responded to pathogen infection in resistant and susceptible genotypes, respectively. Both genotypes showed transcriptional reprogramming in response to Foc2, but the responses in WR315 were more severe than in JG62. Results of the KEGG pathway analysis revealed that most of the DEGS in both genotypes with enrichment in metabolic pathways, secondary metabolite biosynthesis, plant hormone signal transduction, and carbon metabolism. Genes associated with defense-related metabolites synthesis such as thaumatin-like protein 1b, cysteine-rich receptor-like protein kinases, MLP-like proteins, polygalacturonase inhibitor 2-like, ethylene-responsive transcription factors, glycine-rich cell wall structural protein-like, beta-galactosidase-like, subtilisin-like protease, thioredoxin-like protein, chitin elicitor receptor kinase-like, proline transporter-like, non-specific lipid transfer protein and sugar transporter were mostly up-regulated in resistant as compared to susceptible genotypes. The results of this study provide disease resistance genes, which would be helpful in understanding the Foc resistance mechanism in chickpea.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03803-9.

The saponin bomb: a nucleolar-localized β-glucosidase hydrolyzes triterpene saponins in Medicago truncatula

Plants often protect themselves from their own bioactive defense metabolites by storing them in less active forms. Consequently, plants also need systems allowing correct spatiotemporal reactivation of such metabolites, for instance under pathogen or herbivore attack. Via co-expression analysis with public transcriptomes, we determined that the model legume Medicago truncatula has evolved a two-component system composed of a β-glucosidase, denominated G1, and triterpene saponins, which are physically separated from each other in intact cells. G1 expression is root-specific, stress-inducible, and coregulated with that of the genes encoding the triterpene saponin biosynthetic enzymes. However, the G1 protein is stored in the nucleolus and is released and united with its typically vacuolar-stored substrates only upon tissue damage, partly mediated by the surfactant action of the saponins themselves. Subsequently, enzymatic removal of carbohydrate groups from the saponins creates a pool of metabolites with an increased broad-spectrum antimicrobial activity. The evolution of this defense system benefited from both the intrinsic condensation abilities of the enzyme and the bioactivity properties of its substrates. We dub this two-component system the saponin bomb, in analogy with the mustard oil and cyanide bombs, commonly used to describe the renowned β-glucosidase-dependent defense systems for glucosinolates and cyanogenic glucosides.

Enhancing the Expression of the OsF3H Gene in Oryza sativa Leads to the Regulation of Multiple Biosynthetic Pathways and Transcriptomic Changes That Influence Insect Resistance

The white-backed planthopper (WBPH) is a major pest of rice crops and causes severe loss of yield. We previously developed the WBPH-resistant rice cultivar "OxF3H" by overexpressing the OsF3H gene. Although there was a higher accumulation of the flavonoids kaempferol (Kr) and quercetin (Qu) as well as salicylic acid (SA) in OxF3H transgenic (OsF3H or Trans) plants compared to the wild type (WT), it is still unclear how OsF3H overexpression affects these WBPH resistant-related changes in gene expression in OxF3H plants. In this study, we analyze RNA-seq data from OxF3H and WT at several points (0 h, 3 h, 12 h, and 24 h) after WBPH infection to explain how overall changes in gene expression happen in these two cultivars. RT-qPCR further validated a number of the genes. Results revealed that the highest number of DEGs (4735) between the two genotypes was detected after 24 h of infection. Interestingly, it was found that several of the DEGs between the WT and OsF3H under control conditions were also differentially expressed in OsF3H in response to WBPH infestation. These results indicate that significant differences in gene expression between the "OxF3H" and "WT" exist as the infection time increases. Many of these DEGs were related to oxidoreductase activity, response to stress, salicylic acid biosynthesis, metabolic process, defense response to pathogen, cellular response to toxic substance, and regulation of hormone levels. Moreover, genes involved in salicylic acid (SA) and ethylene (Et) biosynthesis were upregulated in OxF3H plants, while jasmonic acid (JA), brassinosteroid (Br), and abscisic acid (ABA) signaling pathways were found downregulated in OxF3H plants during WBPH infestation. Interestingly, many DEGs related to pathogenesis, such as OsPR1, OsPR1b, OsNPR1, OsNPR3, and OsNPR5, were found to be significantly upregulated in OxF3H plants. Additionally, genes related to the MAPKs pathway and about 30 WRKY genes involved in different pathways were upregulated in OxF3H plants after WBPH infestation. This suggests that overexpression of the OxF3H gene leads to multiple transcriptomic changes and impacts plant hormones and pathogenic-related and secondary-metabolites-related genes, enhancing the plant's resistance to WBPH infestation.

Genome-Wide Identification of ERF Transcription Factor Family and Functional Analysis of the Drought Stress-Responsive Genes in Melilotus albus

As an important forage legume with high values in feed and medicine, Melilotus albus has been widely cultivated. The AP2/ERF transcription factor has been shown to play an important regulatory role in plant drought resistance, but it has not been reported in the legume forage crop M. albus. To digger the genes of M. albus in response to drought stress, we identified and analyzed the ERF gene family of M. albus at the genome-wide level. A total of 100 MaERF genes containing a single AP2 domain sequence were identified in this study, named MaERF001 to MaERF100, and bioinformatics analysis was performed. Collinearity analysis indicated that segmental duplication may play a key role in the expansion of the M. albus ERF gene family. Cis-acting element predictions suggest that MaERF genes are involved in various hormonal responses and abiotic stresses. The expression patterns indicated that MaERFs responded to drought stress to varying degrees. Furthermore, four up-regulated ERFs (MaERF008, MaERF037, MaERF054 and MaERF058) under drought stress were overexpressed in yeast and indicated their biological functions to confer the tolerance to drought. This work will advance the understanding of the molecular mechanisms underlying the drought response in M. albus. Further study of the promising potential candidate genes identified in this study will provide a valuable resource as the next step in functional genomics studies and improve the possibility of improving drought tolerance in M. albus by transgenic approaches.

Research Progress and Prospect of Alfalfa Resistance to Pathogens and Pests

Alfalfa is one of the most important legume forages in the world and contributes greatly to the improvement of ecosystems, nutrition, and food security. Diseases caused by pathogens and pests severely restrict the production of alfalfa. Breeding resistant varieties is the most economical and effective strategy for the control of alfalfa diseases and pests, and the key to breeding resistant varieties is to identify important resistance genes. Plant innate immunity is the theoretical basis for identifying resistant genes and breeding resistant varieties. In recent years, the framework of plant immunity theory has been gradually formed and improved, and considerable progress has been made in the identification of alfalfa resistance genes and the revelation of the related mechanisms. In this review, we summarize the basic theory of plant immunity and identify alfalfa resistance genes to different pathogens and insects and resistance mechanisms. The current situation, problems, and future prospects of alfalfa resistance research are also discussed. Breeding resistant cultivars with effective resistance genes, together with other novel plant protection technologies, will greatly improve alfalfa production.

GmMKK4-activated GmMPK6 stimulates GmERF113 to trigger resistance to Phytophthora sojae in soybean

Phytophthora root and stem rot is a worldwide soybean (Glycine max) disease caused by the soil-borne pathogen Phytophthora sojae. This disease is devastating to soybean production, so improvement of resistance to P. sojae is a major target in soybean breeding. Mitogen-activated protein kinase (MAPK) cascades are important signaling modules that convert environmental stimuli into cellular responses. Compared with extensive studies in Arabidopsis, the molecular mechanism of MAPK cascades in soybean disease resistance is barely elucidated. In this work, we found that the gene expression of mitogen-activated protein kinase 6 (GmMPK6) was potently induced by P. sojae infection in the disease-resistant soybean cultivar 'Suinong 10'. Overexpression of GmMPK6 in soybean resulted in enhanced resistance to P. sojae and silencing of GmMPK6 led to the opposite phenotype. In our attempt to dissect the role of GmMPK6 in soybean resistance to phytophthora disease, we found that MAPK kinase 4 (GmMKK4) and the ERF transcription factor GmERF113 physically interact with GmMPK6, and we determined that GmMKK4 could phosphorylate and activate GmMPK6, which could subsequently phosphorylate GmERF113 upon P. sojae infection, suggesting that P. sojae can stimulate the GmMKK4-GmMPK6-GmERF113 signaling pathway in soybean. Moreover, phosphorylation of GmERF113 by the GmMKK4-GmMPK6 module promoted GmERF113 stability, nuclear localization and transcriptional activity, which significantly enhanced expression of the defense-related genes GmPR1 and GmPR10-1 and hence improved disease resistance of the transgenic soybean seedlings. In all, our data reveal that the GmMKK4-GmMPK6-GmERF113 cascade triggers resistance to P. sojae in soybean and shed light on functions of MAPK kinases in plant disease resistance.

Time-course transcriptome analysis identifies rewiring patterns of transcriptional regulatory networks in rice under Rhizoctonia solani infection

Sheath Blight (SB) disease in rice is caused by the infection from the fungal pathogen Rhizoctonia solani (R. solani). SB is one of the most severe rice diseases that can cause up to 50% yield losses in rice. Naturally occurring rice varieties resistant to SB have not been reported yet. We have performed a Time-Series RNA-Seq analysis on a widely cultivated rice variety BPT-5204 for identifying transcriptome level response signatures during R. solani infection at 1st, 2nd and 5th day post infection (dpi). In total, 428, 3225 and 1225 genes were differentially expressed in the treated rice plants on 1, 2 and 5 dpi, respectively. GO and KEGG enrichment analysis identified significant processes and pathways differentially altered in the rice plants during the fungal infection. Machine learning and network based integrative approach was used to construct rice Transcriptional Regulatory Networks (TRNs) for the three time points. TRN analysis identified SUB1B, MYB30 and CCA1 as important regulatory hub transcription factors in rice during R. solani infection. Jasmonic acid, salicylic acid, ethylene biogenesis and signaling were induced on infection. SAR was up regulated, while photosynthesis and carbon fixation processes were significantly down regulated. Involvement of MAPK, CYPs, peroxidase, PAL, chitinase genes were also observed in response to the fungal infection. The integrative analysis identified seven putative SB resistance genes differentially regulated in rice during R. solani infection.

Transcriptional Profiling of Resistant and Susceptible Cultivars of Grapevine (Vitis L.) Reveals Hypersensitive Responses to Plasmopara viticola

Grapevine downy mildew is the most serious disease of grapevine cultivars that affects the rate of resistance/susceptibility to Plasmopara viticola. In this study, we used the susceptible cultivar "Zitian Seedless" and the resistant cultivar "Kober 5BB" as materials to determine the transcriptome differences and phenotypes of the leaves after inoculation with downy mildew. The differences in microstructures and molecular levels were compared and analyzed. Fluorescence staining and microscopic observations confirmed that hypersensitive cell death occurred around the stomata in "Kober 5BB" infected by downy mildew zoospores. Meanwhile, transcriptomic profiling indicated that there were 11,713 and 6,997 gene expression differences between the resistant and susceptible cultivars at 72 h after inoculation when compared to control (0 h), respectively. The differentially expressed genes of the two cultivars are significantly enriched in different pathways, including response to plant-pathogen interaction, mitogen-activated protein kinase (MAPK) signaling pathway, plant hormone signal transduction, phenylpropanoid, and flavonoid biosynthesis. Furthermore, the results of functional enrichment analysis showed that H₂O₂ metabolism, cell death, reactive oxygen response, and carbohydrate metabolism are also involved in the defense response of "Kober 5BB," wherein a total of 322 key genes have been identified. The protein interaction network showed that metacaspases (MCAs), vacuolar processing enzymes (VPEs), and Papain-like cysteine proteases (PLCPs) play an important role in the execution of hypersensitive responses (HR). In conclusion, we demonstrated that HR cell death is the key strategy in the process of grape defense against downy mildew, which may be mediated or activated by Caspase-like proteases.

KIN3 impacts arbuscular mycorrhizal symbiosis and promotes fungal colonisation in Medicago truncatula

Arbuscular mycorrhizal fungi help their host plant in the acquisition of nutrients, and this association is itself impacted by soil nutrient levels. High phosphorus levels inhibit the symbiosis, whereas high nitrogen levels enhance it. The genetic mechanisms regulating the symbiosis in response to soil nutrients are poorly understood. Here, we characterised the symbiotic phenotypes in four Medicago truncatula Tnt1-insertion mutants affected in arbuscular mycorrhizal colonisation. We located their Tnt1 insertions and identified alleles for two genes known to be involved in mycorrhization, RAM1 and KIN3. We compared the effects of the kin3-2 and ram1-4 mutations on gene expression, revealing that the two genes alter the expression of overlapping but not identical gene sets, suggesting that RAM1 acts upstream of KIN3. Additionally, KIN3 appears to be involved in the suppression of plant defences in response to the fungal symbiont. KIN3 is located on the endoplasmic reticulum of arbuscule-containing cortical cells, and kin3-2 mutants plants hosted significantly fewer arbuscules than the wild type. KIN3 plays an essential role in the symbiotic response to soil nitrogen levels, as, contrary to wild-type plants, the kin3-2 mutant did not exhibit increased root colonisation under high nitrogen.

Overexpression of MtRAV3 enhances osmotic and salt tolerance and inhibits growth of Medicago truncatula

Related to ABI3/VP1 (RAV) transcription factors play important roles in regulating plant growth and stress tolerance, which have been studied in many plant species, but have remained largely unidentified in legumes. To functionally characterize RAV in legumes, MtRAV3 from legume model plant Medicago truncatula was isolated and its function was investigated by overexpressing MtRAV3 in M. truncatula. Expression analysis demonstrated that MtRAV3 was markedly induced by NaCl and polyethylene glycol (PEG). MtRAV3 overexpression enhanced tolerance of transgenic M. truncatula to mannitol, drought and salt stresses, and induced the expression of adversity-related genes, including MtWRKY76, MtMYB61, cold-acclimation specific protein 31 (MtCAS31), alternative oxidase 1 (MtAOX1) and ethylene response factor 1 (MtERF1). There were lower relative electrolyte leakage and higher chlorophyll content of leaves in the MtRAV3 overexpression plants than in wild type plants under both salt and drought stress. MtRAV3 overexpression M. truncatula were featured by some phenotypes of dwarfing, late flowering, more branches, smaller flower and leaf organs. Further investigations showed that the expression levels of DWARF14 (MtD14), CAROTENOID CLEAVAGE DIOXYGENASES 7 (MtCCD7) and GA3-oxidase1 (MtGA3ox1), which related to dwarf and branch phenotype, were obviously reduced, as well as MtGA3ox1' (MTR_1g011580), GA20-oxidase1 (MtGA20ox1), MtGA20ox1' (MTR_1g102070) and GA20-oxidase2 (MtGA20ox2) involved in gibberellins (GAs) pathway. Overall, our results revealed that MtRAV3 exerted an important role in adversity response and plant growth, was a multifunctional gene in M. truncatula, which provided reference for genetic improvement of alfalfa (Medicago sativa).

Strategies to Manage Rice Sheath Blight: Lessons from Interactions between Rice and Rhizoctonia solani

Rhizoctonia solani is an important phytopathogenic fungus with a wide host range and worldwide distribution. The anastomosis group AG1 IA of R. solani has been identified as the predominant causal agent of rice sheath blight, one of the most devastating diseases of crop plants. As a necrotrophic pathogen, R. solani exhibits many characteristics different from biotrophic and hemi-biotrophic pathogens during co-evolutionary interaction with host plants. Various types of secondary metabolites, carbohydrate-active enzymes, secreted proteins and effectors have been revealed to be essential pathogenicity factors in R. solani. Meanwhile, reactive oxygen species, phytohormone signaling, transcription factors and many other defense-associated genes have been identified to contribute to sheath blight resistance in rice. Here, we summarize the recent advances in studies on molecular interactions between rice and R. solani. Based on knowledge of rice-R. solani interactions and sheath blight resistance QTLs, multiple effective strategies have been developed to generate rice cultivars with enhanced sheath blight resistance.

A functional genomics approach to dissect spotted alfalfa aphid resistance in Medicago truncatula

Aphids are virus-spreading insect pests affecting crops worldwide and their fast population build-up and insecticide resistance make them problematic to control. Here, we aim to understand the molecular basis of spotted alfalfa aphid (SAA) or Therioaphis trifolii f. maculata resistance in Medicago truncatula, a model organism for legume species. We compared susceptible and resistant near isogenic Medicago lines upon SAA feeding via transcriptome sequencing. Expression of genes involved in defense and stress responses, protein kinase activity and DNA binding were enriched in the resistant line. Potentially underlying some of these changes in gene expression was the finding that members of the MYB, NAC, AP2 domain and ERF transcription factor gene families were differentially expressed in the resistant versus susceptible lines. A TILLING population created in the resistant cultivar was screened using exome capture sequencing and served as a reverse genetics tool to functionally characterise genes involved in the aphid resistance response. This screening revealed three transcription factors (a NAC, AP2 domain and ERF) as important regulators in the defence response, as a premature stop-codon in the resistant background led to a delay in aphid mortality and enhanced plant susceptibility. This combined functional genomics approach will facilitate the future development of pest resistant crops by uncovering candidate target genes that can convey enhanced aphid resistance.

Hemoglobins in the legume-Rhizobium symbiosis

Legume nodules have two types of hemoglobins: symbiotic or leghemoglobins (Lbs) and nonsymbiotic or phytoglobins (Glbs). The latter are categorized into three phylogenetic classes differing in heme coordination and O₂ affinity. This review is focused on the roles of Lbs and Glbs in the symbiosis of rhizobia with crop legumes and the model legumes for indeterminate (Medicago truncatula) and determinate (Lotus japonicus) nodulation. Only two hemoglobin functions are well established in nodules: Lbs deliver O₂ to the bacteroids and act as O₂ buffers, preventing nitrogenase inactivation; and Glb1-1 modulates nitric oxide concentration during symbiosis, from the early stage, avoiding the plant's defense response, to nodule senescence. Here, we critically examine early and recent results, update and correct the information on Lbs and Glbs with the latest genome versions, provide novel expression data and identify targets for future research. Crucial unresolved questions include the expression of multiple Lbs in nodules, their presence in the nuclei and in uninfected nodule cells, and, intriguingly, their expression in nonsymbiotic tissues. RNA-sequencing data analysis shows that Lbs are expressed as early as a few hours after inoculation and that their mRNAs are also detectable in roots and pods, which clearly suggests that these heme proteins play additional roles unrelated to nitrogen fixation. Likewise, issues awaiting investigation are the functions of other Glbs in nodules, the spatiotemporal expression profiles of Lbs and Glbs at the mRNA and protein levels, and the molecular mechanisms underlying their regulation during nodule development and in response to stress and hormones.

Ethylene Is Not Essential for R-Gene Mediated Resistance but Negatively Regulates Moderate Resistance to Some Aphids in Medicago truncatula

Ethylene is important for plant responses to environmental factors. However, little is known about its role in aphid resistance. Several types of genetic resistance against multiple aphid species, including both moderate and strong resistance mediated by R genes, have been identified in Medicago truncatula. To investigate the potential role of ethylene, a M. truncatula ethylene- insensitive mutant, sickle, was analysed. The sickle mutant occurs in the accession A17 that has moderate resistance to Acyrthosiphon kondoi, A. pisum and Therioaphis trifolii. The sickle mutant resulted in increased antibiosis-mediated resistance against A. kondoi and T. trifolii but had no effect on A. pisum. When sickle was introduced into a genetic background carrying resistance genes, AKR (A. kondoi resistance), APR (A. pisum resistance) and TTR (T. trifolii resistance), it had no effect on the strong aphid resistance mediated by these genes, suggesting that ethylene signaling is not essential for their function. Interestingly, for the moderate aphid resistant accession, the sickle mutant delayed leaf senescence following aphid infestation and reduced the plant biomass losses caused by both A. kondoi and T. trifolii. These results suggest manipulation of the ethylene signaling pathway could provide aphid resistance and enhance plant tolerance against aphid feeding.

Understanding sheath blight resistance in rice: the road behind and the road ahead

Rice sheath blight disease, caused by the basidiomycetous necrotroph Rhizoctonia solani, became one of the major threats to the rice cultivation worldwide, especially after the adoption of high-yielding varieties. The pathogen is challenging to manage because of its extensively broad host range and high genetic variability and also due to the inability to find any satisfactory level of natural resistance from the available rice germplasm. It is high time to find remedies to combat the pathogen for reducing rice yield losses and subsequently to minimize the threat to global food security. The development of genetic resistance is one of the alternative means to avoid the use of hazardous chemical fungicides. This review mainly focuses on the effort of better understanding the host-pathogen relationship, finding the gene loci/markers imparting resistance response and modifying the host genome through transgenic development. The latest development and trend in the R. solani-rice pathosystem research with gap analysis are provided.

Isolation, sequencing, and expression analysis of 30 AP2/ERF transcription factors in apple

BACKGROUND

AP2/ERF transcription factors are involved in the regulation of plant growth, development, and stress responses. Our research objective was to characterize novel apple (Malus × domestica Borkh.) genes encoding AP2/ERF transcription factors involved in regulation of plant growth, development, and stress response. The transcriptional level of apple AP2/ERF genes in different tissues and under various biotic and abiotic stress was determined to provide valuable insights into the function of AP2/ERF transcription factors in apple.

METHODS

Thirty full-length cDNA sequences of apple AP2/ERF genes were isolated from 'Zihong Fuji' apple (Malus × domestica cv. Zihong Fuji) via homologous comparison and RT-PCR confirmation, and the obtained cDNA sequences and the deduced amino acid sequences were analyzed with bioinformatics methods. Expression levels of apple AP2/ERF genes were detected in 16 different tissues using a known array. Expression patterns of apple AP2/ERF genes were detected in response to Alternaria alternata apple pathotype (AAAP) infection using RNA-seq with existing data, and the expression of apple AP2/ERF genes was analyzed under NaCl and mannitol treatments using qRT-PCR.

RESULTS

The sequencing results produced 30 cDNAs (designated as MdERF3-8, MdERF11, MdERF16-19, MdERF22-28, MdERF31-35, MdERF39, MdAP2D60, MdAP2D62-65, and MdRAV2). Phylogenetic analysis revealed that MdERF11/16, MdERF33/35, MdERF34/39, and MdERF18/23 belonged to groups A-2, A-4, A-5, and A-6 of the DREB subfamily, respectively; MdERF31, MdERF19, MdERF4/25/28/32, MdERF24, MdERF5/6/27, and MdERF3/7/8/17/22/26 belonged to groups B-1, B-2, B-3, B-4, B-5, and B-6 of the ERF subfamily, respectively; MdAP2D60 and MdAP2D62/63/64/65 belonged to the AP2 subfamily; and MdRAV2 belonged to the RAV subfamily. Array results indicated that 30 apple AP2/ERF genes were expressed in all examined tissues to different degrees. RNA-seq results using previously reported data showed that many members of the apple ERF and DREB subfamilies were induced by Alternaria alternate apple pathotype (AAAP) infection. Under salt treatment, many members in the apple ERF and DREB subfamilies were transcriptionally up or down-regulated. Under mannitol treatment, many members of the apple ERF, DREB, and AP2 subfamilies were induced at the transcriptional level. Taken together, the results indicated that the cloned apple AP2/ERF genes were expressed in all examined tissues. These genes were up-regulated or down-regulated in response to AAAP infection and to salt or mannitol treatment, which suggested they may be involved in regulating growth, development, and stress response in apple.

RAVL1 Activates Brassinosteroids and Ethylene Signaling to Modulate Response to Sheath Blight Disease in Rice

Rhizoctonia solani causes sheath blight disease in rice; however, the defense mechanism of rice plants against R. solani remains elusive. To analyze the roles of brassinosteroid (BR) and ethylene signaling on rice defense to R. solani, wild-type (WT) rice and several mutants and overexpressing (OX) lines were inoculated with R. solani. Mutants d61-1 and d2 were less susceptible to sheath blight disease, bri1-D was more susceptible, and ravl1 and d61-1/EIL1 Ri5 were similarly susceptible compared with WT. The double mutant ravl1/d61-1 was phenotypically similar to the ravl1 mutant. Transcriptome analysis, chromatin immunoprecipitation assay, electrophoretic mobility shift assay, and transient assays indicted that RAVL1 might directly activate Ethylene insensitive 3-like 1 (EIL1), a master regulator of ethylene signaling. Mutants ers1 and d61-1/RAVL1 OX were resistant to sheath blight disease, whereas EIL1 RNAi mutants and RAVL1 OX were more susceptible than WT. BRI1 and D2 expression in EIL1 Ri5/RAVL1 OX and EIL1 expression in d61-1/RAVL1 OX indicated that RAVL1 activates BRI1/D2 and EIL1, respectively, independent of BR and ethylene signaling. Our analyses provide information on how BR and ethylene signaling regulate sheath blight disease and on the regulatory function of RAVL1 in rice sheath blight disease.

Defence signalling marker gene responses to hormonal elicitation differ between roots and shoots

Phytohormones such as jasmonic acid (JA), salicylic acid (SA), ethylene (ET) and abscisic acid (ABA) play a key role in regulation of plant immune responses to different attackers. Extensive research over recent years has led to the identification of molecular markers for specific hormonal-regulated defence pathways. However, most of our current knowledge on the regulation of plant immunity derives from studies focused on above-ground organs, mainly on the model plant Arabidopsis thaliana. Therefore, it is unclear whether the paradigms based on experiments on above-ground organs are entirely transferable to roots. Here, we used the non-model plant Brassica rapa to study the regulation dynamics of hormonal-related marker genes in both roots and shoots. These markers were identified in Arabidopsis shoots after elicitation of the JA-, SA-, ET- or ABA-signalling pathways, and are commonly used to study induced responses. We assessed whether the regulation of those genes by hormonal elicitation differs between roots and shoots. To discern whether the differences in marker gene expression between roots and shoots are related to differences in hormone production or to differential responsiveness, we also measured actual hormone content in the treated tissue after elicitation. Our results show that some of the widely used markers did not show specific responsiveness to single hormone applications in B. rapa. We further found that hormonal elicitation led to different response patterns of the molecular markers in shoots and roots. Our results suggest that the regulation of some hormonal-related marker genes in B. rapa is organ specific and differs from the Arabidopsis-derived paradigms.

Effective enhancement of resistance to Phytophthora infestans by overexpression of miR172a and b in Solanum lycopersicum

Overexpression of miR172a and b in tomato ( Solanum lycopersicum ) Zaofen No. 2 increased resistance to Phytophthora infestans infection by suppressing of an AP2/ERF transcription factor. The miR172 family has been shown to participate in the growth phase transition, flowering time control, abiotic and biotic stresses by regulating the expression of a small group of AP2/ERF transcription factors. In this study, the precursors of miR172a and b were cloned from tomato, Solanum pimpinellifolium L3708. We used the degradome sequencing to determine the cleavage site of miR172 to a member of the AP2/ERF transcription factor family (Solyc11g072600.1.1). qRT-PCR results showed that the expression of AP2/ERF was negatively correlated with the expression of miR172 in S. pimpinellifolium L3708 infected with Phytophthora infestans. Overexpression of miR172a and b in S. lycopersicum Zaofen No. 2 conferred greater resistance to P. infestans infection, as evidenced by decreased disease index, lesion sizes, and P. infestans abundance. The SOD and POD play important roles in scavenging late massive ROS in plant-pathogen interaction. Malonaldehyde (MDA) is widely recognized as an indicator of lipid peroxidation. Membrane damage in plants can be estimated by measuring leakage of electrolytes, which is evaluated by determining relative electrolyte leakage (REL). Less H₂O₂ and O₂^-, higher activities of POD and SOD, less MDA content and REL, and higher chlorophyll content and photosynthetic rate were also shown in transgenic plants after inoculation with P. infestans. Our results constitute the first step towards further investigations into the biological function and molecular mechanism of miR172-mediated silencing of AP2/ERF transcription factors in S. lycopersicum-P. infestans interaction and provide a candidate gene for breeding to enhance biotic stress-resistance in S. lycopersicum.

Multiple regulatory roles of AP2/ERF transcription factor in angiosperm

APETALA2/ethylene response factor (AP2/ERF) transcription factor (TF) is a superfamily in plant kingdom, which has been reported to be involved in regulation of plant growth and development, fruit ripening, defense response, and metabolism. As the final response gene in ethylene signaling pathway, AP2/ERF TF could feedback modulate phytohormone biosynthesis, including ethylene, cytokinin, gibberellin, and abscisic acid. Moreover, AP2/ERF TF also participates in response to the signals of auxin, cytokinin, abscisic acid, and jasmonate. Thus, this superfamily is key regulator for connecting the phytohormonal signals. In this review, based on the evidence of structural and functional studies, we discussed the multiple regulator roles of AP2/ERF TF in angiosperm, and then constructed the network model of AP2/ERF TF in response to various phytohormonal signals and regulatory mechanism of the cross-talk.

Ethylene Signaling Is Important for Isoflavonoid-Mediated Resistance to Rhizoctonia solani in Roots of Medicago truncatula

The root-infecting necrotrophic fungal pathogen Rhizoctoniasolani causes significant disease to all the world's major food crops. As a model for pathogenesis of legumes, we have examined the interaction of R. solani AG8 with Medicago truncatula. RNAseq analysis of the moderately resistant M. truncatula accession A17 and highly susceptible sickle (skl) mutant (defective in ethylene sensing) identified major early transcriptional reprogramming in A17. Responses specific to A17 included components of ethylene signaling, reactive oxygen species metabolism, and consistent upregulation of the isoflavonoid biosynthesis pathway. Mass spectrometry revealed accumulation of the isoflavonoid-related compounds liquiritigenin, formononetin, medicarpin, and biochanin A in A17. Overexpression of an isoflavone synthase in M. truncatula roots increased isoflavonoid accumulation and resistance to R. solani. Addition of exogenous medicarpin suggested this phytoalexin may be one of several isoflavonoids required to contribute to resistance to R. solani. Together, these results provide evidence for the role of ethylene-mediated accumulation of isoflavonoids during defense against root pathogens in legumes. The involvement of ethylene signaling and isoflavonoids in the regulation of both symbiont-legume and pathogen-legume interactions in the same tissue may suggest tight regulation of these responses are required in the root tissue.

Fungal Plant Pathogenesis Mediated by Effectors

The interactions between fungi and plants encompass a spectrum of ecologies ranging from saprotrophy (growth on dead plant material) through pathogenesis (growth of the fungus accompanied by disease on the plant) to symbiosis (growth of the fungus with growth enhancement of the plant). We consider pathogenesis in this article and the key roles played by a range of pathogen-encoded molecules that have collectively become known as effectors.

Ethylene response factors in Arabidopsis immunity

Pathogen attack leads to transcriptional changes and metabolic modifications allowing the establishment of appropriate plant defences. Transcription factors (TFs) are key players in plant innate immunity. Notably, ethylene response factor (ERF) TFs are integrators of hormonal pathways and are directly responsible for the transcriptional regulation of several jasmonate (JA)/ethylene (ET)-responsive defence genes. Transcriptional activation or repression by ERFs is achieved through the binding to JA/ET-responsive gene promoters. In this review, we describe the regulation and mode of action at a molecular level of ERFs involved in Arabidopsis thaliana immunity. In particular, we focus on defence activators such as ERF1, ORA59, ERF6, and the recently described ERF96.

Proteomic Analysis of Rhizoctonia solani Identifies Infection-specific, Redox Associated Proteins and Insight into Adaptation to Different Plant Hosts

Rhizoctonia solani is an important root infecting pathogen of a range of food staples worldwide including wheat, rice, maize, soybean, potato and others. Conventional resistance breeding strategies are hindered by the absence of tractable genetic resistance in any crop host. Understanding the biology and pathogenicity mechanisms of this fungus is important for addressing these disease issues, however, little is known about how R. solani causes disease. This study capitalizes on recent genomic studies by applying mass spectrometry based proteomics to identify soluble, membrane-bound and culture filtrate proteins produced under wheat infection and vegetative growth conditions. Many of the proteins found in the culture filtrate had predicted functions relating to modification of the plant cell wall, a major activity required for pathogenesis on the plant host, including a number found only under infection conditions. Other infection related proteins included a high proportion of proteins with redox associated functions and many novel proteins without functional classification. The majority of infection only proteins tested were confirmed to show transcript up-regulation during infection including a thaumatin which increased susceptibility to R. solani when expressed in Nicotiana benthamiana. In addition, analysis of expression during infection of different plant hosts highlighted how the infection strategy of this broad host range pathogen can be adapted to the particular host being encountered. Data are available via ProteomeXchange with identifier PXD002806.

Tomato SlERF.A1, SlERF.B4, SlERF.C3 and SlERF.A3, Members of B3 Group of ERF Family, Are Required for Resistance to Botrytis cinerea

The Ethylene-Responsive Factors (ERFs) comprise a large family of transcriptional factors that play critical roles in plant immunity. Gray mold disease caused by Botrytis cinerea, a typical necrotrophic fungal pathogen, is the serious disease that threatens tomato production worldwide. However, littler is known about the molecular mechanism regulating the immunity to B. cinerea in tomato. In the present study, virus-induced gene silencing (VIGS)-based functional analyses of 18 members of B3 group (also called Group IX) in tomato ERF family were performed to identify putative ERFs that are involved in disease resistance against B. cinerea. VIGS-based silencing of either SlERF.B1 or SlERF.C2 had lethal effect while silencing of SlERF.A3 (Pit4) significantly suppressed vegetative growth of tomato plants. Importantly, silencing of SlERF.A1, SlERF.A3, SlERF.B4, or SlERF.C3 resulted in increased susceptibility to B. cinerea, attenuated the B. cinerea-induced expression of jasmonic acid/ethylene-mediated signaling responsive defense genes and promoted the B. cinerea-induced H₂O₂ accumulation. However, silencing of SlERF.A3 also decreased the resistance against Pseudomonas syringae pv. tomato (Pst) DC3000 but silencing of SlERF.A1, SlERF.B4 or SlERF.C3 did not affect the resistance to this bacterial pathogen. Expression of SlERF.A1, SlERF.A3, SlERF.B4, or SlERF.C3 was induced by B. cinerea and by defense signaling hormones such as salicylic acid, methyl jasmonate, and 1-aminocyclopropane-1-carboxylic acid (an ethylene precursor). SlERF.A1, SlERF.B4, SlERF.C3, and SlERF.A3 proteins were found to localize in nucleus of cells and possess transactivation activity in yeasts. These data suggest that SlERF.A1, SlERF.B4, and SlERF.C3, three previously uncharacterized ERFs in B3 group, and SlERF.A3, a previously identified ERF with function in immunity to Pst DC3000, play important roles in resistance against B. cinerea in tomato.

Ethylene: Traffic Controller on Hormonal Crossroads to Defense

Ethylene (ET) is an important hormone in plant responses to microbial pathogens and herbivorous insects, and in the interaction of plants with beneficial microbes and insects. Early ET signaling events during these biotic interactions involve activities of mitogen-activated protein kinases and ETHYLENE RESPONSE FACTOR transcription factors. Rather than being the principal regulator, ET often modulates defense signaling pathways, including those regulated by jasmonic acid and salicylic acid. Hormonal signal integrations with ET steer the defense signaling network to activate specific defenses that can have direct effects on attackers, or systemically prime distant plant parts for enhanced defense against future attack. ET also regulates volatile signals that attract carnivorous enemies of herbivores or warn neighboring plants. Conversely, ET signaling can also be exploited by attackers to hijack the defense signaling network to suppress effective defenses. In this review, we summarize recent findings on the significant role of ET in the plants' battle against their enemies.

A rapid method for profiling of volatile and semi-volatile phytohormones using methyl chloroformate derivatisation and GC-MS

Phytohormones are central components of complex signalling networks in plants. The interplay between these metabolites, which include abscisic acid (ABA), auxin (IAA), ethylene, jasmonic acid (JA) and salicylic acid (SA), regulate plant growth and development and modulate responses to biotic and abiotic stress. Few methods of phytohormone profiling can adequately quantify a large range of plant hormones simultaneously and without the requirement for laborious or highly specialised extraction protocols. Here we describe the development and validation of a phytohormone profiling protocol, based on methyl-chloroformate derivatisation of the plant metabolites and analysis by gas chromatography/mass spectrometry (GC-MS). We describe the analysis of 11 metabolites, either plant phytohormones or intermediates of phytohormone metabolism; ABA, azelaic acid, IAA, JA and SA, and the phytohormone precursors 1-aminocyclopropane 1-carboxylic acid, benzoic acid, cinnamic acid, 13-epi-12-oxophytodienoic acid (13-epi-OPDA), linoleic acid and linolenic acid, and validate the isolation from foliar tissue of the model legume Medicago truncatula. The preparation is insensitive to the presence of water, facilitating measurement of the volatile metabolites. Quantitation was linear over four orders of magnitude, and the limits of detection between two and 10 ng/mL for all measured metabolites using a single quadrupole GC-MS.

Deep Sequencing of the Medicago truncatula Root Transcriptome Reveals a Massive and Early Interaction between Nodulation Factor and Ethylene Signals

The legume-rhizobium symbiosis is initiated through the activation of the Nodulation (Nod) factor-signaling cascade, leading to a rapid reprogramming of host cell developmental pathways. In this work, we combine transcriptome sequencing with molecular genetics and network analysis to quantify and categorize the transcriptional changes occurring in roots of Medicago truncatula from minutes to days after inoculation with Sinorhizobium medicae. To identify the nature of the inductive and regulatory cues, we employed mutants with absent or decreased Nod factor sensitivities (i.e. Nodulation factor perception and Lysine motif domain-containing receptor-like kinase3, respectively) and an ethylene (ET)-insensitive, Nod factor-hypersensitive mutant (sickle). This unique data set encompasses nine time points, allowing observation of the symbiotic regulation of diverse biological processes with high temporal resolution. Among the many outputs of the study is the early Nod factor-induced, ET-regulated expression of ET signaling and biosynthesis genes. Coupled with the observation of massive transcriptional derepression in the ET-insensitive background, these results suggest that Nod factor signaling activates ET production to attenuate its own signal. Promoter:β-glucuronidase fusions report ET biosynthesis both in root hairs responding to rhizobium as well as in meristematic tissue during nodule organogenesis and growth, indicating that ET signaling functions at multiple developmental stages during symbiosis. In addition, we identified thousands of novel candidate genes undergoing Nod factor-dependent, ET-regulated expression. We leveraged the power of this large data set to model Nod factor- and ET-regulated signaling networks using MERLIN, a regulatory network inference algorithm. These analyses predict key nodes regulating the biological process impacted by Nod factor perception. We have made these results available to the research community through a searchable online resource.

Characterization of Brachypodium distachyon as a nonhost model against switchgrass rust pathogen Puccinia emaculata

BACKGROUND

Switchgrass rust, caused by Puccinia emaculata, is an important disease of switchgrass, a potential biofuel crop in the United States. In severe cases, switchgrass rust has the potential to significantly affect biomass yield. In an effort to identify novel sources of resistance against switchgrass rust, we explored nonhost resistance against P. emaculata by characterizing its interactions with six monocot nonhost plant species. We also studied the genetic variations for resistance among Brachypodium inbred accessions and the involvement of various defense pathways in nonhost resistance of Brachypodium.

RESULTS

We characterized P. emaculata interactions with six monocot nonhost species and identified Brachypodium distachyon (Bd21) as a suitable nonhost model to study switchgrass rust. Interestingly, screening of Brachypodium accessions identified natural variations in resistance to switchgrass rust. Brachypodium inbred accessions Bd3-1 and Bd30-1 were identified as most and least resistant to switchgrass rust, respectively, when compared to tested accessions. Transcript profiling of defense-related genes indicated that the genes which were induced in Bd21after P. emaculata inoculation also had higher basal transcript abundance in Bd3-1 when compared to Bd30-1 and Bd21 indicating their potential involvement in nonhost resistance against switchgrass rust.

CONCLUSION

In the present study, we identified Brachypodium as a suitable nonhost model to study switchgrass rust which exhibit type I nonhost resistance. Variations in resistance response were also observed among tested Brachypodium accessions. Brachypodium nonhost resistance against P. emaculata may involve various defense pathways as indicated by transcript profiling of defense related genes. Overall, this study provides a new avenue to utilize novel sources of nonhost resistance in Brachypodium against switchgrass rust.

What lies beneath: belowground defense strategies in plants

Diseases caused by soil-borne pathogens result worldwide in significant yield losses in economically important crops. In contrast to foliar diseases, relatively little is known about the nature of root defenses against these pathogens. This review summarizes the current knowledge on root infection strategies, root-specific preformed barriers, pathogen recognition, and defense signaling. Studies reviewed here suggest that many commonalities as well as differences exist in defense strategies employed by roots and foliar tissues during pathogen attack. Importantly, in addition to pathogens, plant roots interact with a plethora of non-pathogenic and symbiotic microorganisms. Therefore, a good understanding of how plant roots interact with the microbiome would be particularly important to engineer resistance to root pathogens without negatively altering root-beneficial microbe interactions.

Genome-Wide Analysis of the AP2/ERF Superfamily Genes and their Responses to Abiotic Stress in Medicago truncatula

The AP2/ERF superfamily is a large, plant-specific transcription factor family that is involved in many important processes, including plant growth, development, and stress responses. Using Medicago truncatula genome information, we identified and characterized 123 putative AP2/ERF genes, which were named as MtERF1-123. These genes were classified into four families based on phylogenetic analysis, which is consistent with the results of other plant species. MtERF genes are distributed throughout all chromosomes but are clustered on various chromosomes due to genomic tandem and segmental duplication. Using transcriptome, high-throughput sequencing data, and qRT-PCR analysis, we assessed the expression patterns of the MtERF genes in tissues during development and under abiotic stresses. In total, 87 MtERF genes were expressed in plant tissues, most of which were expressed in specific tissues during development or under specific abiotic stress treatments. These results support the notion that MtERF genes are involved in developmental regulation and environmental responses in M. truncatula. Furthermore, a cluster of DREB subfamily members on chromosome 6 was induced by both cold and freezing stress, representing a positive gene regulatory response under low temperature stress, which suggests that these genes might contribute to freezing tolerance to M. truncatula. In summary, our genome-wide characterization, evolutionary analysis, and expression pattern analysis of MtERF genes in M. truncatula provides valuable information for characterizing the molecular functions of these genes and utilizing them to improve stress tolerance in plants.

The induction of Ethylene response factor 3 (ERF3) in potato as a result of co-inoculation with Pseudomonas sp. R41805 and Rhizophagus irregularis MUCL 41833 - a possible role in plant defense

Colonization of plant rhizosphere/roots by beneficial microorganisms (e.g. plant growth promoting rhizobacteria - PGPR, arbuscular mycorrhizal fungi - AMF) confers broad-spectrum resistance to virulent pathogens and is known as induced systemic resistance (ISR) and mycorrhizal-induced resistance (MIR). ISR or MIR, an indirect mechanism for biocontrol, involves complex signaling networks that are regulated by several plant hormones, the most important of which are salicylic acid (SA), jasmonic acid (JA) and ethylene (ET). In the present study, we investigated if inoculation of potato plantlets with an AMF (Rhizophagus irregularis MUCL 41833) and a PGPR (Pseudomonas sp R41805) either alone or in combination, could elicit host defense response genes in the presence or absence of Rhizoctonia Solani EC-1, a major potato pathogen. RT-qPCR revealed the significant expression of ethylene response factor 3 (EFR3) in mycorrhized potato plantlets inoculated with Pseudomonas sp R41805 and also in mycorrhized potato plantlets inoculated with Pseudomonas sp R41805 and challenged with R. solani. The significance of ethylene response factors (ERFs) in pathogen defense has been well documented in the literature. The results of the present study suggest that the dual inoculation of potato with PGPR and AMF may play a part in the activation of plant systemic defense systems via ERF3.

Cold acclimation-induced freezing tolerance of Medicago truncatula seedlings is negatively regulated by ethylene

To evaluate the role of ethylene in cold acclimation and cold stress, freezing tolerance and characteristics associated with cold acclimation were investigated using legume model plant Medicago truncatula Gaertn Jemalong A17. There was a rapid suppression of ethylene production during cold acclimation in A17 plants. Ethylene level was negatively correlated with freezing tolerance as inhibition of ethylene biosynthesis by inhibitors of ethylene biosynthesis enhanced freezing tolerance, while exogenous application of ethylene reduced cold acclimation-induced freezing tolerance. The involvement of ethylene signaling in modulation of freezing tolerance and cold acclimation was further studied using ethylene-insensitive mutant sickle skl. Although skl mutant was more tolerant to freezing than its wild-type counterpart A17 plants, cold acclimation enhanced freezing tolerance in 17 plants, but not in skl mutant. Expression of several ethylene response genes including EIN3, EIN3/EIL and ERFs was suppressed in skl mutant compared to A17 plants under non-cold-acclimated conditions. Cold acclimation downregulated expression of EIN3, EIN3/EIL and ERFs in A17 plants, while expression patterns of these genes were relatively constant in skl mutant during cold acclimation. Cold acclimation-induced increases in transcription of MtCBFs and MtCAS15 were suppressed in skl mutant compared with A17 plants. These results suggest that MtSKL1 is required for perception of the change of ethylene level in M. truncatula plants for the full development of the cold acclimation response by suppressing expression of MtEIN3 and MtEIN3/EIL1, which in turn downregulates expression of MtERFs, leading to the enhanced tolerance of M. truncatula to freezing by upregulating MtCBFs and MtCAS15.

Intervention of Phytohormone Pathways by Pathogen Effectors

The constant struggle between plants and microbes has driven the evolution of multiple defense strategies in the host as well as offense strategies in the pathogen. To defend themselves from pathogen attack, plants often rely on elaborate signaling networks regulated by phytohormones. In turn, pathogens have adopted innovative strategies to manipulate phytohormone-regulated defenses. Tactics frequently employed by plant pathogens involve hijacking, evading, or disrupting hormone signaling pathways and/or crosstalk. As reviewed here, this is achieved mechanistically via pathogen-derived molecules known as effectors, which target phytohormone receptors, transcriptional activators and repressors, and other components of phytohormone signaling in the host plant. Herbivores and sap-sucking insects employ obligate pathogens such as viruses, phytoplasma, or symbiotic bacteria to intervene with phytohormone-regulated defenses. Overall, an improved understanding of phytohormone intervention strategies employed by pests and pathogens during their interactions with plants will ultimately lead to the development of new crop protection strategies.

Genome sequencing and comparative genomics of the broad host-range pathogen Rhizoctonia solani AG8

Rhizoctonia solani is a soil-borne basidiomycete fungus with a necrotrophic lifestyle which is classified into fourteen reproductively incompatible anastomosis groups (AGs). One of these, AG8, is a devastating pathogen causing bare patch of cereals, brassicas and legumes. R. solani is a multinucleate heterokaryon containing significant heterozygosity within a single cell. This complexity posed significant challenges for the assembly of its genome. We present a high quality genome assembly of R. solani AG8 and a manually curated set of 13,964 genes supported by RNA-seq. The AG8 genome assembly used novel methods to produce a haploid representation of its heterokaryotic state. The whole-genomes of AG8, the rice pathogen AG1-IA and the potato pathogen AG3 were observed to be syntenic and co-linear. Genes and functions putatively relevant to pathogenicity were highlighted by comparing AG8 to known pathogenicity genes, orthology databases spanning 197 phytopathogenic taxa and AG1-IA. We also observed SNP-level "hypermutation" of CpG dinucleotides to TpG between AG8 nuclei, with similarities to repeat-induced point mutation (RIP). Interestingly, gene-coding regions were widely affected along with repetitive DNA, which has not been previously observed for RIP in mononuclear fungi of the Pezizomycotina. The rate of heterozygous SNP mutations within this single isolate of AG8 was observed to be higher than SNP mutation rates observed across populations of most fungal species compared. Comparative analyses were combined to predict biological processes relevant to AG8 and 308 proteins with effector-like characteristics, forming a valuable resource for further study of this pathosystem. Predicted effector-like proteins had elevated levels of non-synonymous point mutations relative to synonymous mutations (dN/dS), suggesting that they may be under diversifying selection pressures. In addition, the distant relationship to sequenced necrotrophs of the Ascomycota suggests the R. solani genome sequence may prove to be a useful resource in future comparative analysis of plant pathogens.

The symbiotic transcription factor MtEFD and cytokinins are positively acting in the Medicago truncatula and Ralstonia solanacearum pathogenic interaction

• A plant-microbe dual biological system was set up involving the model legume Medicago truncatula and two bacteria, the soil-borne root pathogen Ralstonia solanacearum and the beneficial symbiont Sinorhizobium meliloti. • Comparison of transcriptomes under symbiotic and pathogenic conditions highlighted the transcription factor MtEFD (Ethylene response Factor required for nodule Differentiation) as being upregulated in both interactions, together with a set of cytokinin-related transcripts involved in metabolism, signaling and response. MtRR4 (Response Regulator), a cytokinin primary response gene negatively regulating cytokinin signaling and known as a target of MtEFD in nodulation processes, was retrieved in this set of transcripts. • Refined studies of MtEFD and MtRR4 expression during M. truncatula and R. solanacearum interaction indicated differential kinetics of induction and requirement of central regulators of bacterial pathogenicity, HrpG and HrpB. Similar to MtRR4, MtEFD upregulation during the pathogenic interaction was dependent on cytokinin perception mediated by the MtCRE1 (Cytokinin REsponse 1) receptor. • The use of M. truncatula efd-1 and cre1-1 mutants evidenced MtEFD and cytokinin perception as positive factors for bacterial wilt development. These factors therefore play an important role in both root nodulation and root disease development.

In silico identification of transcription factors in Medicago sativa using available transcriptomic resources

Transcription factors (TFs) are proteins that govern organismal development and response to the environment by regulating gene expression. Information on the amount and diversity of TFs within individual plant species is critical for understanding of their biological roles and evolutionary history across the plant kingdom. Currently, only scattered information on separate TFs is available for alfalfa, the most extensively cultivated forage legume in the world. In the meantime, several large transcriptomic resources that can be used to identify and characterize alfalfa TF genes are freely accessible online. In this study, we have performed an in silico analysis of transcriptome data generated in our laboratory and publicly acquirable from other sources to reveal and systematize alfalfa transcription factors. Transcriptome-wide mining enabled prediction of 983 TFs along with their sequence features and putative phylogenies of the largest families. All data were assembled into a simple open-access database named AlfalfaTFDB ( http://plantpathology.ba.ars.usda.gov/alfalfatfdb.html ). Transcriptomic analysis used in this work represents an effective approach for the identification of TF genes in plants with incomplete genomes, such as alfalfa. Integrated TF repertoires of Medicago sativa will provide an important tool for studying regulation of gene expression in other complex non-model species of agricultural significance.

MtQRRS1, an R-locus required for Medicago truncatula quantitative resistance to Ralstonia solanacearum

Ralstonia solanacearum is a major soilborne pathogen that attacks > 200 plant species, including major crops. To characterize MtQRRS1, a major quantitative trait locus (QTL) for resistance towards this bacterium in the model legume Medicago truncatula, genetic and functional approaches were combined. QTL analyses together with disease scoring of heterogeneous inbred families were used to define the locus. The candidate region was studied by physical mapping using a bacterial artificial chromosome (BAC) library of the resistant line, and sequencing. In planta bacterial growth measurements, grafting experiments and gene expression analysis were performed to investigate the mechanisms by which this locus confers resistance to R. solanacearum. The MtQRRS1 locus was localized to the same position in two recombinant inbred line populations and was narrowed down to a 64 kb region. Comparison of parental line sequences revealed 15 candidate genes with sequence polymorphisms, but no evidence of differential gene expression upon infection. A role for the hypocotyl in resistance establishment was shown. These data indicate that the quantitative resistance to bacterial wilt conferred by MtQRRS1, which contains a cluster of seven R genes, is shared by different accessions and may act through intralocus interactions to promote resistance.

Bioactive molecules in soil ecosystems: masters of the underground

Complex biological and ecological processes occur in the rhizosphere through ecosystem-level interactions between roots, microorganisms and soil fauna. Over the past decade, studies of the rhizosphere have revealed that when roots, microorganisms and soil fauna physically contact one another, bioactive molecular exchanges often mediate these interactions as intercellular signal, which prepare the partners for successful interactions. Despite the importance of bioactive molecules in sustainable agriculture, little is known of their numerous functions, and improving plant health and productivity by altering ecological processes remains difficult. In this review, we describe the major bioactive molecules present in below-ground ecosystems (i.e., flavonoids, exopolysaccharides, antibiotics and quorum-sensing signals), and we discuss how these molecules affect microbial communities, nutrient availability and plant defense responses.

Genetic and genomic analysis of Rhizoctonia solani interactions with Arabidopsis; evidence of resistance mediated through NADPH oxidases

Rhizoctonia solani is an important soil-borne necrotrophic fungal pathogen, with a broad host range and little effective resistance in crop plants. Arabidopsis is resistant to R. solani AG8 but susceptible to R. solani AG2-1. A screen of 36 Arabidopsis ecotypes and mutants affected in the auxin, camalexin, salicylic acid, abscisic acid and ethylene/jasmonic acid pathways did not reveal any variation in response to R. solani and demonstrated that resistance to AG8 was independent of these defense pathways. The Arabidopsis Affymetrix ATH1 Genome array was used to assess global gene expression changes in plants infected with AG8 and AG2-1 at seven days post-infection. While there was considerable overlap in the response, some gene families were differentially affected by AG8 or AG2-1 and included those involved in oxidative stress, cell wall associated proteins, transcription factors and heat shock protein genes. Since a substantial proportion of the gene expression changes were associated with oxidative stress responses, we analysed the role of NADPH oxidases in resistance. While single NADPH oxidase mutants had no effect, a NADPH oxidase double mutant atrbohf atrbohd resulted in an almost complete loss of resistance to AG8, suggesting that reactive oxidative species play an important role in Arabidopsis's resistance to R. solani.

A Medicago truncatula ABC transporter belonging to subfamily G modulates the level of isoflavonoids

Full-sized ATP-binding cassette (ABC) transporters of the G subfamily (ABCG) are considered to be essential components of the plant immune system. These proteins have been proposed to be implicated in the active transmembrane transport of various secondary metabolites. Despite the importance of ABCG-based transport for plant-microbe interactions, these proteins are still poorly recognized in legumes. The experiments described here demonstrated that the level of Medicago truncatula ABCG10 (MtABCG10) mRNA was elevated following application of fungal oligosaccharides to plant roots. Spatial expression pattern analysis with a reporter gene revealed that the MtABCG10 promoter was active in various organs, mostly within their vascular tissues. The corresponding protein was located in the plasma membrane. Silencing of MtABCG10 in hairy roots resulted in lower accumulation of the phenylpropanoid pathway-derived medicarpin and its precursors. PCR-based experiments indicated that infection with Fusarium oxysporum, a root-infecting pathogen, progressed faster in MtABCG10-silenced composite plants (consisting of wild-type shoots on transgenic roots) than in the corresponding controls. Based on the presented data, it is proposed that in Medicago, full-sized ABCG transporters might modulate isoflavonoid levels during the defence response associated with de novo synthesis of phytoalexins.

Transgenic rice with inducible ethylene production exhibits broad-spectrum disease resistance to the fungal pathogens Magnaporthe oryzae and Rhizoctonia solani

Rice blast (Magnaporthe oryzae) and sheath blight (Rhizoctonia solani) are the two most devastating diseases of rice (Oryza sativa), and have severe impacts on crop yield and grain quality. Recent evidence suggests that ethylene (ET) may play a more prominent role than salicylic acid and jasmonic acid in mediating rice disease resistance. In this study, we attempt to genetically manipulate endogenous ET levels in rice for enhancing resistance to rice blast and sheath blight diseases. Transgenic lines with inducible production of ET were generated by expressing the rice ACS2 (1-aminocyclopropane-1-carboxylic acid synthase, a key enzyme of ET biosynthesis) transgene under control of a strong pathogen-inducible promoter. In comparison with the wild-type plant, the OsACS2-overexpression lines showed significantly increased levels of the OsACS2 transcripts, endogenous ET and defence gene expression, especially in response to pathogen infection. More importantly, the transgenic lines exhibited increased resistance to a field isolate of R. solani, as well as different races of M. oryzae. Assessment of the growth rate, generational time and seed production revealed little or no differences between wild type and transgenic lines. These results suggest that pathogen-inducible production of ET in transgenic rice can enhance resistance to necrotrophic and hemibiotrophic fungal pathogens without negatively impacting crop productivity.

An alfalfa (Medicago sativa L.) ethylene response factor gene, MsERF11, enhances salt tolerance in transgenic Arabidopsis

A novel orthologue of ethylene response factor gene, MsERF11, was isolated from alfalfa in this study. It has an open reading frame of 807 bp, encoding a predicted polypeptide of 268 amino acids. Sequence similarity analysis clearly suggested that MsERF11 encoded an ethylene response factor protein. The results of transient expression of MsERF11 in onion epidermal cells indicated that MsERF11 is a nuclear protein. The expression pattern of MsERF11 gene was analyzed by real-time quantitative PCR and a higher level of expression was observed in leaves than was observed in roots, stems, flower buds and flowers. Furthermore, the expression was induced by PEG6000, NaCl, Al2(SO4)3 and six different hormones. Over-expressing MsERF11 resulted in enhanced tolerances to salt stress in transgenic Arabidopsis plants. This research indicates that MsERF11 has the potential to be used for improving crop's salt tolerance in areas where salinity is a limiting factor for agricultural productivity.

KEY MESSAGE

MsERF11 was isolated from alfalfa. Its expression was induced by different abiotic stresses and hormones. Over-expressing MsERF11 resulted in enhanced salt tolerance in transgenic Arabidopsis plants.

Repeated leaf wounding alters the colonization of Medicago truncatula roots by beneficial and pathogenic microorganisms

In nature, plants are subject to various stresses that are often accompanied by wounding of the aboveground tissues. As wounding affects plants locally and systemically, we investigated the impact of leaf wounding on interactions of Medicago truncatula with root-colonizing microorganisms, such as the arbuscular mycorrhizal (AM) fungus Glomus intraradices, the pathogenic oomycete Aphanomyces euteiches and the nitrogen-fixing bacterium Sinorhizobium meliloti. To obtain a long-lasting wound response, repeated wounding was performed and resulted in locally and systemically increased jasmonic acid (JA) levels accompanied by the expression of jasmonate-induced genes, among them the genes encoding allene oxide cyclase 1 (MtAOC1) and a putative cell wall-bound invertase (cwINV). After repeated wounding, colonization with the AM fungus was increased, suggesting a role of jasmonates as positive regulators of mycorrhization, whereas the interaction with the rhizobacterium was not affected. In contrast, wounded plants appeared to be less susceptible to pathogens which might be caused by JA-induced defence mechanisms. The effects of wounding on mycorrhization and pathogen infection could be partially mimicked by foliar application of JA. In addition to JA itself, the positive effect on mycorrhization might be mediated by systemically induced cwINV, which was previously shown to exhibit a regulatory function on interaction with AM fungi.

Differential expression of peach ERF transcriptional activators in response to signaling molecules and inoculation with Xanthomonas campestris pv. pruni

Ethylene response factors (ERFs) are a large family of transcription factors (TFs) that have diverse functions in plant development and immunity. However, very little is known about the molecular regulation of these TFs in stone fruits during disease incidence. In the present study, we describe the identification of five peach ERFs (Pp-ERFs), aiming to elucidate their potential roles in defense against Xanthomonas campestris pv. pruni (Xcp), the causal agent of bacterial spot disease. The phylogenetic analysis along with sequence comparisons indicated that all Pp-ERFs are transcriptional activators belonging to groups IX and IIV ERFs. The transactivation capacity of these proteins was verified in vivo where they all induced the expression of the GUS reporter gene and in a GCC-dependent manner. The nuclear localization was also confirmed for two of these proteins, Pp-ERF2.b and Pp-ERF2.c, after their transient expression in onion epidermal cells. The induction kinetics of Pp-ERFs after inoculation with Xcp was determined by qRT-PCR. Except for Pp-ERF2.b, transcript levels of Pp-ERFs increased strongly and rapidly in the resistant 'Venture' compared to the susceptible 'BabyGold 5' cultivar after infection with Xcp. In contrast, the expression of Pp-ERF2.b was several-fold higher in the susceptible cultivar after bacterial infection. The expression of Pp-ERFs was also monitored after treating with signaling compounds; salicylic acid (SA) (1 mM), ethephon (1 mM) and methyl jasmonate (MeJA) (50 μM). Although the results generally emphasize the role of ethylene/jasmonic acid (ET/JA) signaling pathways in regulating the expression of Pp-ERFs, there was a coordination of the timing of ET/JA responses, suggesting compensatory rather than synergistic interactions between these pathways during defense against Xcp.

Interactions of Arabidopsis and M. truncatula with the same pathogens differ in dependence on ethylene and ethylene response factors

Microbial pathogens inflict large losses to agriculture annually and thus mechanisms of plant resistance and how to deploy them to enhance disease resistance in crops are foci of much research interest. We recently described the important role of ethylene and Ethylene Response transcription Factors (ERFs), particularly MtERF1-1, in mediating resistance to the fungal pathogen Rhizoctonia solani in the model legume, Medicago truncatula. Previous studies on the closely related AtERF14, a master regulator of ethylene dependent defenses including other ERFs, suggested that in Arabidopsis these defenses were not essential for resistance to the same R. solani isolate but were required for resistance to another fungal pathogen, Fusarium oxysporum. Medicago plants with roots over-expressing MtERF1-1 were challenged with F. oxysporum but showed no altered resistance. These results further support a potential for divergent roles of ethylene associated defenses in different plant hosts responding to the same pathogen.