Regulation of basal resistance by a powdery mildew-induced cysteine-rich receptor-like protein kinase in barley

All Roads Lead to Rome: Pathways to Engineering Disease Resistance in Plants

Unlike animals, plants are unable to move and lack specialized immune cells and circulating antibodies. As a result, they are always threatened by a large number of microbial pathogens and harmful pests that can significantly reduce crop yield worldwide. Therefore, the development of new strategies to control them is essential to mitigate the increasing risk of crops lost to plant diseases. Recent developments in genetic engineering, including efficient gene manipulation and transformation methods, gene editing and synthetic biology, coupled with the understanding of microbial pathogenicity and plant immunity, both at molecular and genomic levels, have enhanced the capabilities to develop disease resistance in plants. This review comprehensively explains the fundamental mechanisms underlying the tug-of-war between pathogens and hosts, and provides a detailed overview of different strategies for developing disease resistance in plants. Additionally, it provides a summary of the potential genes that can be employed in resistance breeding for key crops to combat a wide range of potential pathogens and pests, including fungi, oomycetes, bacteria, viruses, nematodes, and insects. Furthermore, this review addresses the limitations associated with these strategies and their possible solutions. Finally, it discusses the future perspectives for producing plants with durable and broad-spectrum disease resistance.

The cysteine-rich receptor-like kinase CRK10 targeted by Coniella diplodiella effector CdE1 contributes to white rot resistance in grapevine

Grape white rot is a devastating fungal disease caused by Coniella diplodiella. The pathogen delivers effectors into the host cell that target crucial immune components to facilitate its infection. Here, we examined a secreted effector of C. diplodiella, known as CdE1, which has been found to inhibit Bax-triggered cell death in Nicotiana benthamiana plants. The expression of CdE1 was induced at 12-48 h after inoculation with C. diplodiella, and the transient overexpression of CdE1 led to increased susceptibility of grapevine to the fungus. Subsequent experiments revealed an interaction between CdE1 and Vitis davidii cysteine-rich receptor-like kinase 10 (VdCRK10) and suppression of VdCRK10-mediated immunity against C. diplodiella, partially by decreasing the accumulation of VdCRK10 protein. Furthermore, our investigation revealed that CRK10 expression was significantly higher and was up-regulated in the resistant wild grapevine V. davidii during C. diplodiella infection. The activity of the VdCRK10 promoter is induced by C. diplodiella and is higher than that of Vitis vitifera VvCRK10, indicating the involvement of transcriptional regulation in CRK10 gene expression. Taken together, our results highlight the potential of VdCRK10 as a resistant gene for enhancing white rot resistance in grapevine.

Genome-wide association mapping for seedling and adult resistance to powdery mildew in barley

KEY MESSAGE

Two new major QTL were identified for powdery mildew resistance. We confirmed that the QTL on 7HS contributed mainly to the adult-plant resistance, while another one on chromosome arm 1HS made a significant contribution to the seedling resistance. Powdery mildew (PM), caused by Blumeria hordei, can occur at all post emergent stages of barley and constantly threatens crop production. To identify more genes for effective resistance to powdery mildew for use in breeding programs, 696 barley accessions collected from different regions of the world were evaluated for PM resistance at seedling and adult growth stages in three different states of Australia. These barley accessions were genotyped using DArTSeq with over 18,000 markers for a genome-wide association study (GWAS). Using the FarmCPU model, 54 markers showed significant associations with PM resistance scored at the seedling and adult-plant stages in different states of Australia. Another 40 markers showed tentative associations (LOD > 4.0) with resistance. These markers are distributed across all seven barley chromosomes. Most of them were grouped into eleven QTL regions, coinciding with the locations of most of the reported resistance genes. Two major MTAs were identified on chromosome arms 3HS and 5HL, with one on 3HS contributing to adult plant resistance and the one on 5HL to both seedling and adult plant resistance. An MTA on 7HS contributed mainly to the adult-plant resistance, while another one on chromosome arm 1HS made a significant contribution to the seedling resistance.

An update on evolutionary, structural, and functional studies of receptor-like kinases in plants

All living organisms must develop mechanisms to cope with and adapt to new environments. The transition of plants from aquatic to terrestrial environment provided new opportunities for them to exploit additional resources but made them vulnerable to harsh and ever-changing conditions. As such, the transmembrane receptor-like kinases (RLKs) have been extensively duplicated and expanded in land plants, increasing the number of RLKs in the advanced angiosperms, thus becoming one of the largest protein families in eukaryotes. The basic structure of the RLKs consists of a variable extracellular domain (ECD), a transmembrane domain (TM), and a conserved kinase domain (KD). Their variable ECDs can perceive various kinds of ligands that activate the conserved KD through a series of auto- and trans-phosphorylation events, allowing the KDs to keep the conserved kinase activities as a molecular switch that stabilizes their intracellular signaling cascades, possibly maintaining cellular homeostasis as their advantages in different environmental conditions. The RLK signaling mechanisms may require a coreceptor and other interactors, which ultimately leads to the control of various functions of growth and development, fertilization, and immunity. Therefore, the identification of new signaling mechanisms might offer a unique insight into the regulatory mechanism of RLKs in plant development and adaptations. Here, we give an overview update of recent advances in RLKs and their signaling mechanisms.

Exploring Aegilops caudata: A Comprehensive Study of the CslF6 Gene and β-Glucan

In the quest for sustainable and nutritious food sources, exploration of ancient grains and wild relatives of cultivated cereals has gained attention. Aegilops caudata, a wild wheatgrass species, stands out as a promising genetic resource due to its potential for crop enhancement and intriguing nutritional properties. This manuscript investigates the CslF6 gene sequence and protein structure of Aegilops caudata, employing comparative analysis with other grass species to identify potential differences impacting β-glucan content. The study involves comprehensive isolation and characterization of the CslF6 gene in Ae. caudata, utilizing genomic sequence analysis, protein structure prediction, and comparative genomics. Comparisons with sequences from diverse monocots reveal evolutionary relationships, highlighting high identities with wheat genomes. Specific amino acid motifs in the CslF6 enzyme sequence, particularly those proximal to key catalytic motifs, exhibit variations among monocot species. These differences likely contribute to alterations in β-glucan composition, notably impacting the DP3:DP4 ratio, which is crucial for understanding and modulating the final β-glucan content. The study positions Ae. caudata uniquely within the evolutionary landscape of CslF6 among monocots, suggesting potential genetic divergence or unique functional adaptations within this species. Overall, this investigation enriches our understanding of β-glucan biosynthesis, shedding light on the role of specific amino acid residues in modulating enzymatic activity and polysaccharide composition.

Integrated omics and machine learning-assisted profiling of cysteine-rich-receptor-like kinases from three peanut spp. revealed their role in multiple stresses

Arachis hypogaea (peanut) is a leading oil and protein-providing crop with a major food source in many countries. It is mostly grown in tropical regions and is largely affected by abiotic and biotic stresses. Cysteine-rich receptor-like kinases (CRKs) is a family of transmembrane proteins that play important roles in regulating stress-signaling and defense mechanisms, enabling plants to tolerate stress conditions. However, almost no information is available regarding this gene family in Arachis hypogaea and its progenitors. This study conducts a pangenome-wide investigation of A. hypogaea and its two progenitors, A. duranensis and A. ipaensis CRK genes (AhCRKs, AdCRKs, and AiCRKs). The gene structure, conserved motif patterns, phylogenetic history, chromosomal distribution, and duplication were studied in detail, showing the intraspecies structural conservation and evolutionary patterns. Promoter cis-elements, protein-protein interactions, GO enrichment, and miRNA targets were also predicted, showing their potential functional conservation. Their expression in salt and drought stresses was also comprehensively studied. The CRKs identified were divided into three groups, phylogenetically. The expansion of this gene family in peanuts was caused by both types of duplication: tandem and segmental. Furthermore, positive as well as negative selection pressure directed the duplication process. The peanut CRK genes were also enriched in hormones, light, development, and stress-related elements. MicroRNA (miRNA) also targeted the AhCRK genes, which suggests the regulatory association of miRNAs in the expression of these genes. Transcriptome datasets showed that AhCRKs have varying expression levels under different abiotic stress conditions. Furthermore, the multi-stress responsiveness of the AhCRK genes was evaluated using a machine learning-based method, Random Forest (RF) classifier. The 3D structures of AhCRKs were also predicted. Our study can be utilized in developing a detailed understanding of the stress regulatory mechanisms of the CRK gene family in peanuts and its further studies to improve the genetic makeup of peanuts to thrive better under stress conditions.

Cysteine-rich receptor-like protein kinases: emerging regulators of plant stress responses

Cysteine-rich receptor-like kinases (CRKs) belong to a large DUF26-containing receptor-like kinase (RLK) family. They play key roles in immunity, abiotic stress response, and growth and development. How CRKs regulate diverse processes is a long-standing question. Recent studies have advanced our understanding of the molecular mechanisms underlying CRK functions in Ca2+ influx, reactive oxygen species (ROS) production, mitogen-activated protein kinase (MAPK) cascade activation, callose deposition, stomatal immunity, and programmed cell death (PCD). We review the CRK structure-function relationship with a focus on the roles of CRKs in immunity, the abiotic stress response, and the growth-stress tolerance tradeoff. We provide a critical analysis and synthesis of how CRKs control sophisticated regulatory networks that determine diverse plant phenotypic outputs.

CRK41 Modulates Microtubule Depolymerization in Response to Salt Stress in Arabidopsis

The pivotal role of cysteine-rich receptor-like kinases (CRKs) in modulating growth, development, and responses to stress has been widely acknowledged in Arabidopsis. However, the function and regulation of CRK41 has remained unclear. In this study, we demonstrate that CRK41 is critical for modulating microtubule depolymerization in response to salt stress. The crk41 mutant exhibited increased tolerance, while overexpression of CRK41 led to hypersensitivity to salt. Further analysis revealed that CRK41 interacts directly with the MAP kinase3 (MPK3), but not with MPK6. Inactivation of either MPK3 or MPK6 could abrogate the salt tolerance of the crk41 mutant. Upon NaCl treatment, microtubule depolymerization was heightened in the crk41 mutant, yet alleviated in the crk41mpk3 and crk41mpk6 double mutants, indicating that CRK41 suppresses MAPK-mediated microtubule depolymerizations. Collectively, these results reveal that CRK41 plays a crucial role in regulating microtubule depolymerization triggered by salt stress through coordination with MPK3/MPK6 signalling pathways, which are key factors in maintaining microtubule stability and conferring salt stress resistance in plants.

Engineering plant immune circuit: walking to the bright future with a novel toolbox

Plant pathogens destroy crops and cause severe yield losses, leading to an insufficient food supply to sustain the human population. Apart from relying on natural plant immune systems to combat biological agents or waiting for the appropriate evolutionary steps to occur over time, researchers are currently seeking new breakthrough methods to boost disease resistance in plants through genetic engineering. Here, we summarize the past two decades of research in disease resistance engineering against an assortment of pathogens through modifying the plant immune components (internal and external) with several biotechnological techniques. We also discuss potential strategies and provide perspectives on engineering plant immune systems for enhanced pathogen resistance and plant fitness.

Functional Characterization of the Cystine-Rich-Receptor-like Kinases (CRKs) and Their Expression Response to Sclerotinia sclerotiorum and Abiotic Stresses in Brassica napus

Cysteine-rich receptor-like kinases (CRKs) are transmembrane proteins that bind to the calcium ion to regulate stress-signaling and plant development-related pathways, as indicated by several pieces of evidence. However, the CRK gene family hasn’t been inadequately examined in Brassica napus. In our study, 27 members of the CRK gene family were identified in Brassica napus, which are categorized into three phylogenetic groups and display synteny relationship to the Arabidopsis thaliana orthologs. All the CRK genes contain highly conserved N-terminal PKINASE domain; however, the distribution of motifs and gene structure were variable conserved. The functional divergence analysis between BnaCRK groups indicates a shift in evolutionary rate after duplication events, demonstrating that BnaCRKs might direct a specific function. RNA-Seq datasets and quantitative real-time PCR (qRT-PCR) exhibit the complex expression profile of the BnaCRKs in plant tissues under multiple stresses. Nevertheless, BnaA06CRK6-1 and BnaA08CRK8 from group B were perceived to play a predominant role in the Brassica napus stress signaling pathway in response to drought, salinity, and Sclerotinia sclerotiorum infection. Insights gained from this study improve our knowledge about the Brassica napus CRK gene family and provide a basis for enhancing the quality of rapeseed.

Molecular Interactions Between Leptosphaeria maculans and Brassica Species

Canola is an important oilseed crop, providing food, feed, and fuel around the world. However, blackleg disease, caused by the ascomycete Leptosphaeria maculans, causes significant yield losses annually. With the recent advances in genomic technologies, the understanding of the Brassica napus-L. maculans interaction has rapidly increased, with numerous Avr and R genes cloned, setting this system up as a model organism for studying plant-pathogen associations. Although the B. napus-L. maculans interaction follows Flor's gene-for-gene hypothesis for qualitative resistance, it also puts some unique spins on the interaction. This review discusses the current status of the host-pathogen interaction and highlights some of the future gaps that need addressing moving forward.

GBS-Based SNP Map Pinpoints the QTL Associated With Sorghum Downy Mildew Resistance in Maize (Zea mays L.)

Sorghum downy mildew (SDM), caused by the biotrophic fungi Peronosclerospora sorghi, threatens maize production worldwide, including India. To identify quantitative trait loci (QTL) associated with resistance to SDM, we used a recombinant inbred line (RIL) population derived from a cross between resistant inbred line UMI936 (w) and susceptible inbred line UMI79. The RIL population was phenotyped for SDM resistance in three environments [E1-field (Coimbatore), E2-greenhouse (Coimbatore), and E3-field (Mandya)] and also utilized to construct the genetic linkage map by genotyping by sequencing (GBS) approach. The map comprises 1516 SNP markers in 10 linkage groups (LGs) with a total length of 6924.7 cM and an average marker distance of 4.57 cM. The QTL analysis with the phenotype and marker data detected nine QTL on chromosome 1, 2, 3, 5, 6, and 7 across three environments. Of these, QTL namely qDMR1.2, qDMR3.1, qDMR5.1, and qDMR6.1 were notable due to their high phenotypic variance. qDMR3.1 from chromosome 3 was detected in more than one environment (E1 and E2), explaining the 10.3% and 13.1% phenotypic variance. Three QTL, qDMR1.2, qDMR5.1, and qDMR6.1 from chromosomes 1, 5, and 6 were identified in either E1 or E3, explaining 15.2%–18% phenotypic variance. Moreover, genome mining on three QTL (qDMR3.1, qDMR5.1, and qDMR6.1) reveals the putative candidate genes related to SDM resistance. The information generated in this study will be helpful for map-based cloning and marker-assisted selection in maize breeding programs.

Insights into the mechanism of Huanglongbing tolerance in the Australian finger lime (Citrus australasica)

The Australian finger lime (Citrus australasica) is tolerant to Huanglongbing (HLB; Citrus greening). This species can be utilized to develop HLB tolerant citrus cultivars through conventional breeding and biotechnological approaches. In this report, we conducted a comprehensive analysis of transcriptomic data following a non-choice infection assay to understand the CaLas tolerance mechanisms in the finger lime. After filtering 3,768 differentially expressed genes (DEGs), 2,396 were downregulated and 1,372 were upregulated in CaLas-infected finger lime compared to CaLas-infected HLB-susceptible 'Valencia' sweet orange. Comparative analyses revealed several DEGs belonging to cell wall, β-glucanase, proteolysis, R genes, signaling, redox state, peroxidases, glutathione-S-transferase, secondary metabolites, and pathogenesis-related (PR) proteins categories. Our results indicate that the finger lime has evolved specific redox control systems to mitigate the reactive oxygen species and modulate the plant defense response. We also identified candidate genes responsible for the production of Cys-rich secretory proteins and Pathogenesis-related 1 (PR1-like) proteins that are highly upregulated in infected finger lime relative to noninfected and infected 'Valencia' sweet orange. Additionally, the anatomical analysis of phloem and stem tissues in finger lime and 'Valencia' suggested better regeneration of phloem tissues in finger lime in response to HLB infection. Analysis of callose formation following infection revealed a significant difference in the production of callose plugs between the stem phloem of CaLas+ 'Valencia' sweet orange and finger lime. Understanding the mechanism of resistance will help the scientific community design strategies to protect trees from CaLas infection and assist citrus breeders in developing durable HLB tolerant citrus varieties.

The RLK protein TaCRK10 activates wheat high-temperature seedling-plant resistance to stripe rust through interacting with TaH2A.1

Plants sense various pathogens and activate immunity responses through receptor-like kinases (RLKs). Cysteine-rich receptor-like kinases (CRKs) are involved in massive transduction pathways upon perception of a pathogen. However, the roles of CRKs in response to stripe rust are unclear. In the present study, we identified a CRK gene (designated TaCRK10) from wheat variety Xiaoyan 6 (XY6) that harbors high-temperature seedling-plant (HTSP) resistance to stripe rust caused by fungal pathogen Puccinia striiformis f. sp. tritici (Pst). The expression level of TaCRK10 was induced by Pst inoculation and high temperature treatment. Knockdown of TaCRK10 by virus-induced gene silencing resulted in attenuated wheat HTSP resistance to Pst, whereas there is no effect on Pst development and host responses under normal temperatures. Notably, overexpression of TaCRK10 in susceptible variety Fielder provided resistance only under normal temperatures at 14 days with reactive oxygen species accumulation and defense-related gene expression of the salicylic acid pathway. Moreover, TaCRK10 physically interacted with and phosphorylated a histone variant TaH2A.1, which belongs to the H2A.W group. Silencing of TaH2A.1 suppressed wheat resistance to Pst, indicating that TaH2A.1 plays a positive role in wheat resistance to Pst. Thus, TaCRK10 serves as an important sensor of Pst infection and high temperatures, and it activates wheat resistance to Pst through regulating nuclear processes. This knowledge helps elucidate the molecular mechanism of wheat HTSP resistance to Pst and promotes efforts in developing wheat varieties with resistance to stripe rust.

The cysteine-rich receptor-like kinase TaCRK3 contributes to defense against Rhizoctonia cerealis in wheat

Sharp eyespot, caused by the necrotrophic fungal pathogen Rhizoctonia cerealis, is a devastating disease of bread wheat (Triticum aestivum). However, the molecular mechanisms underlying wheat defense against R. cerealis are still largely unknown. In this study, by comparative transcriptomic analysis we identified a novel cysteine-rich receptor-like kinase (CRK)-encoding gene, designated as TaCRK3, and investigated its role in defense against R. cerealis. TaCRK3 transcript abundance was significantly elevated by R. cerealis and exogenous ethylene treatments. Silencing of TaCRK3 significantly compromised resistance to R. cerealis and repressed expression of an ethylene biosynthesis enzyme-encoding gene, ACO2, and a subset of defense-associated genes in wheat, whose transcript levels are up-regulated by ethylene stimulus. TaCRK3 protein was localized at the plasma membrane in wheat. Noticeably, both the heterologously expressed TaCRK3 protein and its partial peptide harboring two DUF26 (DOMAIN OF UNKNOWN FUNCTION 26) domains could inhibit growth of R. cerealis mycelia. These results suggest that TaCRK3 mediates wheat resistance to R. cerealis through direct antifungal activity and heightening the expression of defense-associated genes in the ethylene signaling pathway. Moreover, its DUF26 domains are required for the antifungal activity of TaCRK3. Our results reveal that TaCRK3 is a promising gene for breeding wheat varieties with resistance to R. cerealis.

A cysteine-rich receptor-like protein kinase CaCKR5 modulates immune response against Ralstonia solanacearum infection in pepper

BACKGROUND

Cysteine-rich receptor-like kinases (CRKs) represent a large subfamily of receptor-like kinases and play vital roles in diverse physiological processes in regulating plant growth and development.

RESULTS

CaCRK5 transcripts were induced in pepper upon the infection of Ralstonia solanacearum and treatment with salicylic acid. The fusions between CaCRK5 and green fluorescence protein were targeted to the plasma membrane. Suppression of CaCRK5 via virus-induced gene silencing (VIGS) made pepper plants significantly susceptible to R. solanacearum infection, which was accompanied with decreased expression of defense related genes CaPR1, CaSAR8.2, CaDEF1 and CaACO1. Overexpression of CaCRK5 increased resistance against R. solanacearum in Nicotiana benthamiana. Furthermore, electrophoretic mobility shift assay and chromatin immunoprecipitation coupled with quantitative real-time PCR analysis revealed that a homeodomain zipper I protein CaHDZ27 can active the expression of CaCRK5 through directly binding to its promoter. Yeast two-hybrid and bimolecular fluorescence complementation (BiFC) analyses suggested that CaCRK5 heterodimerized with the homologous member CaCRK6 on the plasma membrane.

CONCLUSIONS

Our data revealed that CaCRK5 played a positive role in regulating immune responses against R. solanacearum infection in pepper.

Wheat Pm4 resistance to powdery mildew is controlled by alternative splice variants encoding chimeric proteins

Crop breeding for resistance to pathogens largely relies on genes encoding receptors that confer race-specific immunity. Here, we report the identification of the wheat Pm4 race-specific resistance gene to powdery mildew. Pm4 encodes a putative chimeric protein of a serine/threonine kinase and multiple C2 domains and transmembrane regions, a unique domain architecture among known resistance proteins. Pm4 undergoes constitutive alternative splicing, generating two isoforms with different protein domain topologies that are both essential for resistance function. Both isoforms interact and localize to the endoplasmatic reticulum when co-expressed. Pm4 reveals additional diversity of immune receptor architecture to be explored for breeding and suggests an endoplasmatic reticulum-based molecular mechanism of Pm4-mediated race-specific resistance.

Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25

BACKGROUND

Barley scald, caused by the fungus Rhynchosporium commune, is distributed worldwide to all barley growing areas especially in cool and humid climates. Scald is an economically important leaf disease resulting in yield losses of up to 40%. To breed resistant cultivars the identification of quantitative trait loci (QTLs) conferring resistance to scald is necessary. Introgressing promising resistance alleles of wild barley is a way to broaden the genetic basis of scald resistance in cultivated barley. Here, we apply nested association mapping (NAM) to map resistance QTLs in the barley NAM population HEB-25, comprising 1420 lines in BC1S3 generation, derived from crosses of 25 wild barley accessions with cv. Barke.

RESULTS

In scald infection trials in the greenhouse variability of resistance across and within HEB-25 families was found. NAM based on 33,005 informative SNPs resulted in the identification of eight reliable QTLs for resistance against scald with most wild alleles increasing resistance as compared to cv. Barke. Three of them are located in the region of known resistance genes and two in the regions of QTLs, respectively. The most promising wild allele was found at Rrs17 in one specific wild donor. Also, novel QTLs with beneficial wild allele effects on scald resistance were detected.

CONCLUSIONS

To sum up, wild barley represents a rich resource for scald resistance. As the QTLs were linked to the physical map the identified candidate genes will facilitate cloning of the scald resistance genes. The closely linked flanking molecular markers can be used for marker-assisted selection of the respective resistance genes to integrate them in elite cultivars.

A novel cysteine-rich receptor-like kinase gene, TaCRK2, contributes to leaf rust resistance in wheat

Leaf rust, caused by Puccinia triticina, is one of the most destructive fungal diseases in wheat production worldwide. The hypersensitive reaction (HR) is an important defence response against P. triticina infection. In this study, the physiological races 165 and 260 of P. triticina were combined with a line derived from the bread wheat cultivar Thatcher with the leaf rust resistance locus Lr26 to form compatible and incompatible combinations, respectively. Based on an RNA-Seq database of the interaction systems, a new wheat cysteine-rich receptor-like kinase gene, TaCRK2, is specifically induced and up-regulated in the incompatible combination. We identified that TaCRK2 was regulated in a Ca²⁺ -dependent manner. Knockdown of TaCRK2 by virus-induced gene silencing and RNAi leads to a dramatic increase in HR area and the number of haustorial mother cells at the single infection site. In addition, urediniospores, a P. triticina-specific pathogenic marker in compatible combinations, were observed on leaf surfaces of silenced plants at approximately 15 days after inoculation in the incompatible combination. Moreover, transcription levels of TaPR1, TaPR2, and TaPR5 were obviously reduced in TaCRK2-silenced plants. TaCRK2 overexpression in Nicotiana benthamiana induced strong HR-like cell death. Finally, transient expression of green fluorescent protein fused with TaCRK2 in N. benthamiana indicated that TaCRK2 localizes in the endoplasmic reticulum. Thus, TaCRK2 plays an important role in the resistance to P. triticina infection and has a positive regulation effect on the HR cell death process induced by P. triticina.

The genetics of exapted resistance to two exotic pathogens in pedunculate oak

Exotic pathogens cause severe damage in natural populations in the absence of coevolutionary dynamics with their hosts. However, some resistance to such pathogens may occur in naive populations. The objective of this study was to investigate the genetics of this so-called 'exapted' resistance to two pathogens of Asian origin (Erysiphe alphitoides and Phytophthora cinnamomi) in European oak. Host-pathogen compatibility was assessed by recording infection success and pathogen growth in a full-sib family of Quercus robur under controlled and natural conditions. Two high-resolution genetic maps anchored on the reference genome were used to study the genetic architecture of resistance and to identify positional candidate genes. Two genomic regions, each containing six strong and stable quantitative trait loci (QTLs) accounting for 12-19% of the phenotypic variation, were mainly associated with E. alphitoides infection. Candidate genes, especially genes encoding receptor-like-kinases and galactinol synthases, were identified in these regions. The three QTLs associated with P. cinnamomi infection did not colocate with QTLs found for E. alphitoides. These findings provide evidence that exapted resistance to E. alphitoides and P. cinnamomi is present in Q. robur and suggest that the underlying molecular mechanisms involve genes encoding proteins with extracellular signaling functions.

iTRAQ-Based Proteomic Analysis of Watermelon Fruits in Response to Cucumber green mottle mosaic virus Infection

Cucumber green mottle mosaic virus (CGMMV) is an important viral pathogen on cucurbit plants worldwide, which can cause severe fruit decay symptoms on infected watermelon (usually called “watermelon blood flesh”). However, the molecular mechanism of this disease has not been well understood. In this study, we employed the isobaric tags for relative and absolute quantitation (iTRAQ) technique to analyze the proteomic profiles of watermelon fruits in response to CGMMV infection. A total of 595 differentially accumulated proteins (DAPs) were identified, of which 404 were upregulated and 191 were downregulated. Functional annotation analysis showed that these DAPs were mainly involved in photosynthesis, carbohydrate metabolism, secondary metabolite biosynthesis, plant–pathogen interaction, and protein synthesis and turnover. The accumulation levels of several proteins related to chlorophyll metabolism, pyruvate metabolism, TCA cycle, heat shock proteins, thioredoxins, ribosomal proteins, translation initiation factors, and elongation factors were strongly affected by CGMMV infection. Furthermore, a correlation analysis was performed between CGMMV-responsive proteome and transcriptome data of watermelon fruits obtained in our previous study, which could contribute to comprehensively elucidating the molecular mechanism of “watermelon blood flesh”. To confirm the iTRAQ-based proteome data, the corresponding transcripts of ten DAPs were validated by determining their abundance via quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). These results could provide a scientific basis for in-depth understanding of the pathogenic mechanisms underlying CGMMV-induced “watermelon blood flesh”, and lay the foundation for further functional exploration and verification of related genes and proteins.

Proteomics of PTI and Two ETI Immune Reactions in Potato Leaves

Plants have a variety of ways to defend themselves against pathogens. A commonly used model of the plant immune system is divided into a general response triggered by pathogen-associated molecular patterns (PAMPs), and a specific response triggered by effectors. The first type of response is known as PAMP triggered immunity (PTI), and the second is known as effector-triggered immunity (ETI). To obtain better insight into changes of protein abundance in immunity reactions, we performed a comparative proteomic analysis of a PTI and two different ETI models (relating to Phytophthora infestans) in potato. Several proteins showed higher abundance in all immune reactions, such as a protein annotated as sterol carrier protein 2 that could be interesting since Phytophthora species are sterol auxotrophs. RNA binding proteins also showed altered abundance in the different immune reactions. Furthermore, we identified some PTI-specific changes of protein abundance, such as for example, a glyoxysomal fatty acid beta-oxidation multifunctional protein and a MAR-binding protein. Interestingly, a lysine histone demethylase was decreased in PTI, and that prompted us to also analyze protein methylation in our datasets. The proteins upregulated explicitly in ETI included several catalases. Few proteins were regulated in only one of the ETI interactions. For example, histones were only downregulated in the ETI-Avr2 interaction, and a putative multiprotein bridging factor was only upregulated in the ETI-IpiO interaction. One example of a methylated protein that increased in the ETI interactions was a serine hydroxymethyltransferase.

Genomic dissection and transcriptional profiling of Cysteine-rich receptor-like kinases in five cereals and functional characterization of TaCRK68-A

Cysteine-rich receptor-like kinases (CRK) constitute one of the largest subfamily of receptor-like kinases, which play crucial roles in plant development and stress response. In total, 43, 37, 36, 38 and 170 CRK genes including duplicated genes were identified in the genome of Brachypodium distachyon, Hordeum vulgare, Oryza sativa, Sorghum bicolor and Triticum aestivum, respectively. These CRK proteins were tightly clustered into four phylogenetic groups and exhibited close syntenic relationship among orthologous genes. Majority of CRK proteins contain a transmembrane domain for plasma membrane localization. The organization of exon/intron, domains and motifs were variably conserved. Tissue-specific expression suggested the involvement of certain CRK genes in plant development. Modulated expression revealed their specific stress-responsive functions. Co-expression and interaction analysis indicated their role in signaling. Ks value and divergence time analysis suggested duplication of TaCRK genes before the hybridization of T. aestivum sub-genomes. Expression comparison of duplicated TaCRK genes revealed functional retention, neofunctionalization or pseudo-functionalization. Recombinant expression of a stress-responsive gene TaCRK68-A in Escherichia coli and Saccharomyces cerevisiae displayed enhanced tolerance against heat, drought, cold and salinity stresses. The study suggested vital functions of CRKs during development and stresses, and provides the basis for functional characterization of each gene in future studies.

Small RNA discovery in the interaction between barley and the powdery mildew pathogen

Background

Plants encounter pathogenic and non-pathogenic microorganisms on a nearly constant basis. Small RNAs such as siRNAs and miRNAs/milRNAs influence pathogen virulence and host defense responses. We exploited the biotrophic interaction between the powdery mildew fungus, Blumeria graminis f. sp. hordei (Bgh), and its diploid host plant, barley (Hordeum vulgare) to explore fungal and plant sRNAs expressed during Bgh infection of barley leaf epidermal cells.

Results

RNA was isolated from four fast-neutron immune-signaling mutants and their progenitor over a time course representing key stages of Bgh infection, including appressorium formation, penetration of epidermal cells, and development of haustorial feeding structures. The Cereal Introduction (CI) 16151 progenitor carries the resistance allele Mla6, while Bgh isolate 5874 harbors the AVR_a6 avirulence effector, resulting in an incompatible interaction. Parallel Analysis of RNA Ends (PARE) was used to verify sRNAs with likely transcript targets in both barley and Bgh. Bgh sRNAs are predicted to regulate effectors, metabolic genes, and translation-related genes. Barley sRNAs are predicted to influence the accumulation of transcripts that encode auxin response factors, NAC transcription factors, homeodomain transcription factors, and several splicing factors. We also identified phasing small interfering RNAs (phasiRNAs) in barley that overlap transcripts that encode receptor-like kinases (RLKs) and nucleotide-binding, leucine-rich domain proteins (NLRs).

Conclusions

These data suggest that Bgh sRNAs regulate gene expression in metabolism, translation-related, and pathogen effectors. PARE-validated targets of predicted Bgh milRNAs include both EKA (effectors homologous to AVR_k1 and AVR_a10) and CSEP (candidate secreted effector protein) families. We also identified barley phasiRNAs and miRNAs in response to Bgh infection. These include phasiRNA loci that overlap with a significant proportion of receptor-like kinases, suggesting an additional sRNA control mechanism may be active in barley leaves as opposed to predominant R-gene phasiRNA overlap in many eudicots. In addition, we identified conserved miRNAs, novel miRNA candidates, and barley genome mapped sRNAs that have PARE validated transcript targets in barley. The miRNA target transcripts are enriched in transcription factors, signaling-related proteins, and photosynthesis-related proteins. Together these results suggest both barley and Bgh control metabolism and infection-related responses via the specific accumulation and targeting of genes via sRNAs.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5947-z) contains supplementary material, which is available to authorized users.

Semi-dominant mutation in the cysteine-rich receptor-like kinase gene, ALS1, conducts constitutive defence response in rice

Plants have evolved a sophisticated two-branch defence system to prevent the growth and spread of pathogen infection. The novel Cys-rich repeat (CRR) containing receptor-like kinases, known as CRKs, were reported to mediate defence resistance in plants. For rice, there are only two reports of CRKs. A semi-dominant lesion mimic mutant als1 (apoptosis leaf and sheath 1) in rice was identified to demonstrate spontaneous lesions on the leaf blade and sheath. A map-based cloning strategy was used for fine mapping and cloning of ALS1, which was confirmed to be a typical CRK in rice. Functional studies of ALS1 were conducted, including phylogenetic analysis, expression analysis, subcellular location and blast resistance identification. Most pathogenesis-related (PR) genes and other defence-related genes were activated and up-regulated to a high degree. ALS1 was expressed mainly in the leaf blade and sheath, in which further study revealed that ALS1 was present in the vascular bundles. ALS1 was located in the cell membrane of rice protoplasts, and its mutation did not change its subcellular location. Jasmonic acid (JA) and salicylic acid (SA) accumulation were observed in als1, and enhanced blast resistance was also observed. The mutation of ALS1 caused a constitutively activated defence response in als1. The results of our study imply that ALS1 participates in a defence response resembling the common SA-, JA- and NH1-mediated defence responses in rice.

Genome-wide analysis of the soybean CRK-family and transcriptional regulation by biotic stress signals triggering plant immunity

Cysteine-rich receptor-like kinases (CRKs) are transmembrane proteins that exhibit ectodomains containing the domain of unknown function 26 (DUF26). The CRKs form a large subfamily of receptor-like kinases in plants, and their possible functions remain to be elucidated. Several lines of evidence suggest that CRKs play important roles in plant defense responses to environmental stress, including plant immunity. We performed a genome-wide analysis of CRK encoding genes in soybean (Glycine max). We found 91 GmCRKs distributed in 16 chromosomes, and identified several tandem and segmental duplications, which influenced the expansion of this gene family. According to our phylogenetic analysis, GmCRKs are grouped in four clades. Furthermore, 12% of the members exhibited GmCRKs with a duplicated bi-modular organization of the ectodomains, containing four DUF26 domains. Expression analysis of GmCRKs was performed by exploring publicly available databases, and by RT-qPCR analysis of selected genes in soybean leaves responding to biotic stress signals. GmCRKs exhibited diverse expression patterns in leaves, stems, roots, and other tissues. Some of them were highly expressed in only one type of tissue, suggesting predominant roles in specific tissues. Furthermore, several GmCRKs were induced with PAMPs, DAMPs and the pathogens Phakopsora pachyrhizi and Phytophthora sojae. Expression profiles of several GmCRKs encoding highly similar proteins exhibited antagonist modes of regulation. The results suggest a fine-tuning control of GmCRKs transcriptional regulation in response to external stimuli, including PAMPs and DAMPs. This study offers a comprehensive view of the GmCRKs family in soybean, and provides a foundation for evolutionary and functional analysis of this family of plant proteins involved in the perception of pathogens and activation of plant immunity.

Comparative RNA-Seq analysis reveals a critical role for brassinosteroids in rose (Rosa hybrida) petal defense against Botrytis cinerea infection

Background

One of the most popular ornamental plants worldwide, roses (Rosa sp.), are very susceptible to Botrytis gray mold disease. The necrotrophic infection of rose petals by B. cinerea causes the collapse and death of these tissues in both the growth and post-harvest stages, resulting in serious economic losses. To understand the molecular basis of rose resistance against B. cinerea, we profiled the petal transcriptome using RNA-Seq technology.

Results

We identified differentially transcribed genes (DTGs) in petals during B. cinerea infection at 30 h post inoculation (hpi) and/or 48 hpi. Gene ontology term enrichment and pathway analyses revealed that metabolic, secondary metabolite biosynthesis, plant-pathogen interaction, and plant hormone signal transduction pathways were involved. The expression of 370 cell-surface immune receptors was upregulated during infection. In addition, 188 genes encoding transcription factors were upregulated, particularly in the ERF, WRKY, bHLH, MYB, and NAC families, implying their involvement in resistance against B. cinerea. We further identified 325 upregulated DTGs in the hormone signal transduction pathways. Among them, the brassinosteroid (BR)-related genes were the most significantly enriched. To confirm the role of BR in Botrytis resistance, exogenous BR was applied to rose flowers before the inoculation of B. cinerea, which enhanced the defense response in these petals.

Conclusions

Our global transcriptome profiling provides insights into the complex gene regulatory networks mediating the rose petal response to B. cinerea. We further demonstrated the role of the phytohormone BR in the resistance of petals to necrotrophic fungal pathogens.

Electronic supplementary material

The online version of this article (10.1186/s12863-018-0668-x) contains supplementary material, which is available to authorized users.

Barley susceptibility factor RACB modulates transcript levels of signalling protein genes in compatible interaction with Blumeria graminis f.sp. hordei

RHO (rat sarcoma homologue) GTPases (guanosine triphosphatases) are regulators of downstream transcriptional responses of eukaryotes to intracellular and extracellular stimuli. For plants, little is known about the function of Rho-like GTPases [called RACs (rat sarcoma-related C botulinum substrate) or ROPs (RHO of plants)] in transcriptional reprogramming of cells. However, in plant hormone response and innate immunity, RAC/ROP proteins influence gene expression patterns. The barley RAC/ROP RACB is required for full susceptibility of barley to the powdery mildew fungus Blumeria graminis f.sp. hordei (Bgh). We compared the transcriptomes of barley plants either silenced for RACB or over-expressing constitutively activated RACB with and without inoculation with Bgh. This revealed a large overlap of the barley transcriptome during the early response to Bgh and during the over-expression of constitutively activated RACB. Global pathway analyses and stringent analyses of differentially expressed genes suggested that RACB influences, amongst others, the expression of signalling receptor kinases. Transient induced gene silencing of RACB-regulated signalling genes (a leucine-rich repeat protein, a leucine-rich repeat receptor-like kinase and an S-domain SD1-receptor-like kinase) suggested that they might be involved in RACB-modulated susceptibility to powdery mildew. We discuss the function of RACB in regulating the transcriptional responses of susceptible barley to Bgh.

Genome-Wide Identification and Functional Analyses of the CRK Gene Family in Cotton Reveals GbCRK18 Confers Verticillium Wilt Resistance in Gossypium barbadense

Cysteine-rich receptor-like kinases (CRKs) are a large subfamily of plant receptor-like kinases that play a critical role in disease resistance in plants. However, knowledge about the CRK gene family in cotton and its function against Verticillium wilt (VW), a destructive disease caused by Verticillium dahliae that significantly reduces cotton yields is lacking. In this study, we identified a total of 30 typical CRKs in a Gossypium barbadense genome (GbCRKs). Eleven of these (>30%) are located on the A06 and D06 chromosomes, and 18 consisted of 9 paralogous pairs encoded in the A and D subgenomes. Phylogenetic analysis showed that the GbCRKs could be classified into four broad groups, the expansion of which has probably been driven by tandem duplication. Gene expression profiling of the GbCRKs in resistant and susceptible cotton cultivars revealed that a phylogenetic cluster of nine of the GbCRK genes were up-regulated in response to V. dahliae infection. Virus-induced gene silencing of each of these nine GbCRKs independently revealed that the silencing of GbCRK18 was sufficient to compromise VW resistance in G. barbadense. GbCRK18 expression could be induced by V. dahliae infection or jasmonic acid, and displayed plasma membrane localization. Therefore, our expression analyses indicated that the CRK gene family is differentially regulated in response to Verticillium infection, while gene silencing experiments revealed that GbCRK18 in particular confers VW resistance in G. barbadense.

Multi-environment QTL studies suggest a role for cysteine-rich protein kinase genes in quantitative resistance to blackleg disease in Brassica napus

BACKGROUND

Resistance to the blackleg disease of Brassica napus (canola/oilseed rape), caused by the hemibiotrophic fungal pathogen Leptosphaeria maculans, is determined by both race-specific resistance (R) genes and quantitative resistance loci (QTL), or adult-plant resistance (APR). While the introgression of R genes into breeding material is relatively simple, QTL are often detected sporadically, making them harder to capture in breeding programs. For the effective deployment of APR in crop varieties, resistance QTL need to have a reliable influence on phenotype in multiple environments and be well defined genetically to enable marker-assisted selection (MAS).

RESULTS

Doubled-haploid populations produced from the susceptible B. napus variety Topas and APR varieties AG-Castle and AV-Sapphire were analysed for resistance to blackleg in two locations over 3 and 4 years, respectively. Three stable QTL were detected in each population, with two loci appearing to be common to both APR varieties. Physical delineation of three QTL regions was sufficient to identify candidate defense-related genes, including a cluster of cysteine-rich receptor-like kinases contained within a 49 gene QTL interval on chromosome A01. Individual L. maculans isolates were used to define the physical intervals for the race-specific R genes Rlm3 and Rlm4 and to identify QTL common to both field studies and the cotyledon resistance response.

CONCLUSION

Through multi-environment QTL analysis we have identified and delineated four significant and stable QTL suitable for MAS of quantitative blackleg resistance in B. napus, and identified candidate genes which potentially play a role in quantitative defense responses to L. maculans.

Fine mapping of a dominantly inherited powdery mildew resistance major-effect QTL, Pm1.1, in cucumber identifies a 41.1 kb region containing two tandemly arrayed cysteine-rich receptor-like protein kinase genes

A dominantly inherited major-effect QTL for powdery mildew resistance in cucumber was fine mapped. Two tandemly arrayed cysteine-rich receptor-like protein kinase genes were identified as the most possible candidates. Powdery mildew (PM) is one of the most severe fungal diseases of cucumber (Cucumis sativus L.) and other cucurbit crops, but the molecular genetic mechanisms of powdery mildew resistance in cucurbits are still poorly understood. In this study, through marker-assisted backcrossing with an elite cucumber inbred line, D8 (PM susceptible), we developed a single-segment substitution line, SSSL0.7, carrying 95 kb fragment from PM resistance donor, Jin5-508, that was defined by two microsatellite markers, SSR16472 and SSR16881. A segregating population with 3600 F2 plants was developed from the SSSL0.7 × D8 mating; segregation analysis confirmed a dominantly inherited major-effect QTL, Pm1.1 in cucumber chromosome 1 underlying PM resistance in SSSL0.7. New molecular markers were developed through exploring the next generation resequenced genomes of Jin5-508 and D8. Linkage analysis and QTL mapping in a subset of the F2 plants delimited the Pm1.1 locus into a 41.1 kb region, in which eight genes were predicted. Comparative gene expression analysis revealed that two concatenated genes, Csa1M064780 and Csa1M064790 encoding the same function of a cysteine-rich receptor-like protein kinase, were the most likely candidate genes. GFP fusion protein-aided subcellular localization indicated that both candidate genes were located in the plasma membrane, but Csa1M064780 was also found in the nucleus. This is the first report of dominantly inherited PM resistance in cucumber. Results of this study will provide new insights into understanding the phenotypic and genetic mechanisms of PM resistance in cucumber. This work should also facilitate marker-assisted selection in cucumber breeding for PM resistance.

Comparative Temporal Transcriptome Profiling of Wheat near Isogenic Line Carrying Lr57 under Compatible and Incompatible Interactions

Leaf rust caused by Puccinia triticina (Pt) is one of the most important diseases of bread wheat globally. Recent advances in sequencing technologies have provided opportunities to analyse the complete transcriptomes of the host as well as pathogen for studying differential gene expression during infection. Pathogen induced differential gene expression was characterized in a near isogenic line carrying leaf rust resistance gene Lr57 and susceptible recipient genotype WL711. RNA samples were collected at five different time points 0, 12, 24, 48, and 72 h post inoculation (HPI) with Pt 77-5. A total of 3020 transcripts were differentially expressed with 1458 and 2692 transcripts in WL711 and WL711+Lr57, respectively. The highest number of differentially expressed transcripts was detected at 12 HPI. Functional categorization using Blast2GO classified the genes into biological processes, molecular function and cellular components. WL711+Lr57 showed much higher number of differentially expressed nucleotide binding and leucine rich repeat genes and expressed more protein kinases and pathogenesis related proteins such as chitinases, glucanases and other PR proteins as compared to susceptible genotype. Pathway annotation with KEGG categorized genes into 13 major classes with carbohydrate metabolism being the most prominent followed by amino acid, secondary metabolites, and nucleotide metabolism. Gene co-expression network analysis identified four and eight clusters of highly correlated genes in WL711 and WL711+Lr57, respectively. Comparative analysis of the differentially expressed transcripts led to the identification of some transcripts which were specifically expressed only in WL711+Lr57. It was apparent from the whole transcriptome sequencing that the resistance gene Lr57 directed the expression of different genes involved in building the resistance response in the host to combat invading pathogen. The RNAseq data and differentially expressed transcripts identified in present study is a genomic resource which can be used for further studying the host pathogen interaction for Lr57 and wheat transcriptome in general.

Large-Scale Phenomics Identifies Primary and Fine-Tuning Roles for CRKs in Responses Related to Oxidative Stress

Cysteine-rich receptor-like kinases (CRKs) are transmembrane proteins characterized by the presence of two domains of unknown function 26 (DUF26) in their ectodomain. The CRKs form one of the largest groups of receptor-like protein kinases in plants, but their biological functions have so far remained largely uncharacterized. We conducted a large-scale phenotyping approach of a nearly complete crk T-DNA insertion line collection showing that CRKs control important aspects of plant development and stress adaptation in response to biotic and abiotic stimuli in a non-redundant fashion. In particular, the analysis of reactive oxygen species (ROS)-related stress responses, such as regulation of the stomatal aperture, suggests that CRKs participate in ROS/redox signalling and sensing. CRKs play general and fine-tuning roles in the regulation of stomatal closure induced by microbial and abiotic cues. Despite their great number and high similarity, large-scale phenotyping identified specific functions in diverse processes for many CRKs and indicated that CRK2 and CRK5 play predominant roles in growth regulation and stress adaptation, respectively. As a whole, the CRKs contribute to specificity in ROS signalling. Individual CRKs control distinct responses in an antagonistic fashion suggesting future potential for using CRKs in genetic approaches to improve plant performance and stress tolerance.

Comparative transcriptome profiling of a rice line carrying Xa39 and its parents triggered by Xanthomonas oryzae pv. oryzae provides novel insights into the broad-spectrum hypersensitive response

BACKGROUND

Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating rice disease worldwide. Xa39 is a resistance (R) gene with a broad-spectrum hypersensitive response (BSHR) to Xoo. Nevertheless, the molecular mechanisms of resistance mediated by Xa39 remain unclear. In this study, the transcriptome profiling of a rice line carrying Xa39 and its parents at the early stage of Xoo infection were investigated.

RESULTS

A rice introgression line H471 carrying Xa39 exhibited a typical local hypersensitive response phenotype, accompanied by programmed cell death after inoculation with the Xoo Philippines' race 9b. Transcriptome profiling of H471 and its parents at 1 and 2 days post-inoculation was performed using RNA sequencing. In total, 306 differentially expressed genes (DEGs) were identified in H471 compared with its recurrent parent Huang-Hua-Zhan after inoculation with Xoo. Among them, 121 (39.5%) genes, with functional enrichments that were related to defense response, protein amino acid phosphorylation, and apoptosis, were found to be constitutively expressed. The other 185 (60.5%) genes, with GO terms that belonged to defense response, were significantly responsive to Xoo infection in H471. Ten up-regulated and 12 down-regulated genes encoding intracellular immune receptors were identified in H471 compared with Huang-Hua-Zhan. LOC_Os11g37759, which was located in the fine-mapping region harboring Xa39, is a Xa39 candidate gene. The putative BSHR-related co-regulatory networks were constructed using 33 DEGs from four functional groups, including gibberellic acid receptors and brassinosteroid regulators, which were differentially co-expressed with LOC_Os11g37759 in infected H471. Our results indicated that there might be cross-talk between the Xa39-mediated signal transduction cascades and the GA/BR signaling pathway, and that the defense mechanism was related to diverse kinases, transcription factors, post-translational regulation, and R genes.

CONCLUSIONS

The present study provides the comprehensive transcriptome profile of a rice introgression line carrying Xa39 and its parents, and identifies a set of DEGs involved in BSHR mediated by Xa39. These data provide novel insights into the regulatory networks of plant disease resistance mediated by R genes, and the identified DEGs will serve as candidates for Xa39 cloning and for further understanding the molecular mechanism of BSHR.

Exploration of microRNAs and their targets engaging in the resistance interaction between wheat and stripe rust

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat worldwide. miRNAs are important regulators, they play very central roles in plant organ development, vegetable phase change and defense responses. In this study, two miRNA libraries from wheat cultivar Xingzi 9104 (XZ) challenged with the avirulent Pst race CYR32 and sterile water were constructed, respectively. A total of 596 miRNA candidates were obtained. 420 wheat-specific candidate miRNAs were screened in adult plants challenged with Pst using microarray-based analyses. We analyzed the abundance of candidate miRNAs, and the levels of a subset of candidate miRNAs were determined by quantitative real time PCR (qRT-PCR). The qRT-PCR results indicated that some miRNAs were involved in the incompatible interaction between wheat and Pst. In addition, we identified some miRNAs differentially expressed in different leaves. Additionally, the target genes of wheat miRNAs were confirmed by using degradome sequencing technology. Most of the annotated target genes are related to signal transduction, energy metabolism, and other functions. We selected some target genes for relative expression analysis using qRT-PCR, and found that RabGAP/TBC domain-containing protein, zinc finger protein and Cysteine-rich receptor-like protein kinase 41 may play important role in the incompatible interaction between XZ and CYR32. Intriguingly, miRNAs and target gene seem to form a complicated regulation network that regulates the wheat-Pst interaction. Our data provide the foundation for evaluating the important regulatory roles of miRNAs in the wheat-Pst interaction.

A secreted protein with plant-specific cysteine-rich motif functions as a mannose-binding lectin that exhibits antifungal activity

Plants have a variety of mechanisms for defending against plant pathogens and tolerating environmental stresses such as drought and high salinity. Ginkbilobin2 (Gnk2) is a seed storage protein in gymnosperm that possesses antifungal activity and a plant-specific cysteine-rich motif (domain of unknown function26 [DUF26]). The Gnk2-homologous sequence is also observed in an extracellular region of cysteine-rich repeat receptor-like kinases that function in response to biotic and abiotic stresses. Here, we report the lectin-like molecular function of Gnk2 and the structural basis of its monosaccharide recognition. Nuclear magnetic resonance experiments showed that mannan was the only yeast (Saccharomyces cerevisiae) cell wall polysaccharide that interacted with Gnk2. Gnk2 also interacted with mannose, a building block of mannan, with a specificity that was similar to those of mannose-binding legume lectins, by strictly recognizing the configuration of the hydroxy group at the C4 position of the monosaccharide. The crystal structure of Gnk2 in complex with mannose revealed that three residues (asparagine-11, arginine-93, and glutamate-104) recognized mannose by hydrogen bonds, which defined the carbohydrate-binding specificity. These interactions were directly related to the ability of Gnk2 to inhibit the growth of fungi, including the plant pathogenic Fusarium spp., which were disrupted by mutation of arginine-93 or the presence of yeast mannan in the assay system. In addition, Gnk2 did not inhibit the growth of a yeast mutant strain lacking the α1,2-linked mannose moiety. These results provide insights into the molecular basis of the DUF26 protein family.

A nonRD receptor-like kinase prevents nodule early senescence and defense-like reactions during symbiosis

Rhizobia and legumes establish symbiotic interactions leading to the production of root nodules, in which bacteria fix atmospheric nitrogen for the plant's benefit. This symbiosis is efficient because of the high rhizobia population within nodules. Here, we investigated how legumes accommodate such bacterial colonization. We used a reverse genetic approach to identify a Medicago truncatula gene, SymCRK, which encodes a cysteine-rich receptor-like kinase that is required for rhizobia maintenance within the plant cells, and performed detailed phenotypic analyses of the corresponding mutant. The Medicago truncatula symCRK mutant developed nonfunctional and necrotic nodules. A nonarginine asparate (nonRD) motif, typical of receptors involved in innate immunity, is present in the SymCRK kinase domain. Similar to the dnf2 mutant, bacteroid differentiation defect, defense-like reactions and early senescence were observed in the symCRK nodules. However, the dnf2 and symCRK nodules differ by their degree of colonization, which is higher in symCRK. Furthermore, in contrast to dnf2, symCRK is not a conditional mutant. These results suggest that in M. truncatula at least two genes are involved in the symbiotic control of immunity. Furthermore, phenotype differences between the two mutants suggest that two distinct molecular mechanisms control suppression of plant immunity during nodulation.

Ethylene and jasmonic acid act as negative modulators during mutualistic symbiosis between Laccaria bicolor and Populus roots

The plant hormones ethylene, jasmonic acid and salicylic acid have interconnecting roles during the response of plant tissues to mutualistic and pathogenic symbionts. We used morphological studies of transgenic- or hormone-treated Populus roots as well as whole-genome oligoarrays to examine how these hormones affect root colonization by the mutualistic ectomycorrhizal fungus Laccaria bicolor S238N. We found that genes regulated by ethylene, jasmonic acid and salicylic acid were regulated in the late stages of the interaction between L. bicolor and poplar. Both ethylene and jasmonic acid treatments were found to impede fungal colonization of roots, and this effect was correlated to an increase in the expression of certain transcription factors (e.g. ETHYLENE RESPONSE FACTOR1) and a decrease in the expression of genes associated with microbial perception and cell wall modification. Further, we found that ethylene and jasmonic acid showed extensive transcriptional cross-talk, cross-talk that was opposed by salicylic acid signaling. We conclude that ethylene and jasmonic acid pathways are induced late in the colonization of root tissues in order to limit fungal growth within roots. This induction is probably an adaptive response by the plant such that its growth and vigor are not compromised by the fungus.

The barley HvNAC6 transcription factor affects ABA accumulation and promotes basal resistance against powdery mildew

Barley HvNAC6 is a member of the plant-specific NAC (NAM, ATAF1,2, CUC2) transcription factor family and we have shown previously that it acts as a positive regulator of basal resistance in barley against the biotrophic pathogen Blumeria graminis f. sp. hordei (Bgh). In this study, we use a transgenic approach to constitutively silence HvNAC6 expression, using RNA interference (RNAi), to investigate the in vivo functions of HvNAC6 in basal resistance responses in barley in relation to the phytohormone ABA. The HvNAC6 RNAi plants displayed reduced HvNAC6 transcript levels and were more susceptible to Bgh than wild-type plants. Application of exogenous ABA increased basal resistance against Bgh in wild-type plants, but not in HvNAC6 RNAi plants, suggesting that ABA is a positive regulator of basal resistance which depends on HvNAC6. Silencing of HvNAC6 expression altered the light/dark rhythm of ABA levels which were, however, not influenced by Bgh inoculation. The expression of the two ABA biosynthetic genes HvNCED1 and HvNCED2 was compromised, and transcript levels of the ABA conjugating HvBG7 enzyme were elevated in the HvNAC6 RNAi lines, but this effect was not clearly associated with transgene-mediated resistance. Together, these data support a function of HvNAC6 as a regulator of ABA-mediated defence responses for maintenance of effective basal resistance against Bgh.

The conserved oligomeric Golgi complex is involved in penetration resistance of barley to the barley powdery mildew fungus

Membrane trafficking is vital to plant development and adaptation to the environment. It is suggested that post-Golgi vesicles and multivesicular bodies are essential for plant defence against directly penetrating fungal parasites at the cell wall. However, the actual plant proteins involved in membrane transport for defence are largely unidentified. We applied a candidate gene approach and single cell transient-induced gene silencing for the identification of membrane trafficking proteins of barley involved in the response to the fungal pathogen Blumeria graminis f.sp. hordei. This revealed potential components of vesicle tethering complexes [putative exocyst subunit HvEXO70F-like and subunits of the conserved oligomeric Golgi (COG) complex] and Golgi membrane trafficking (COPIγ coatomer and HvYPT1-like RAB GTPase) as essential for resistance to fungal penetration into the host cell.

Comparative proteomic analysis of rice seedlings in response to inoculation with Bacillus cereus

Reports suggest that Bacillus spp. can be used to increase plant growth and resistance to disease, but the molecular mechanisms underlying the interaction between Bacillus spp. and plant is not completely understood. In the present study, to clarify these underlying mechanisms, the interaction between Bacillus cereus and rice was investigated using two-dimensional gel electrophoresis. Through comparative analysis, a total of 31 differentially expressed proteins were obtained upon B. cereus NMSL88 treatment, including 22 proteins that were up-regulated and nine that were down-regulated. These data indicated that certain proteins involved in plant growth and development were up-regulated, such as xyloglucan endotransglycosylase. Interestingly, proteins involved in defence were also up-regulated, including peroxidases, glutathione S-transferases and kinases. Thus, proteins associated with disease resistance characteristics were induced in the plants after exposure to B. cereus NMSL88. In addition, several proteins involved in protein and lipid metabolism showed significant changes in expression.

SIGNIFICANCE AND IMPACT OF THE STUDY

The present study is the first report to reveal the molecular mechanisms involved in rice seedlings in response to inoculation with Bacillus cereus at the level of proteome. The results demonstrated that B. cereus NMSL88 can up-regulate the expression of proteins related to plant growth and defence, and lead to enhanced plant growth and disease resistance.

Plant innate immunity: perception of conserved microbial signatures

Plants and animals sense conserved microbial signatures through receptors localized to the plasma membrane and cytoplasm. These receptors typically carry or associate with non-arginine-aspartate (non-RD) kinases that initiate complex signaling networks cumulating in robust defense responses. In plants, coregulatory receptor kinases have been identified that not only are critical for the innate immune response but also serve an essential function in other regulatory signaling pathways.