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Biological control is a promising approach to enhance pathogen and pest control to ensure high productivity in cash crop production. Therefore, PGPR biofertilizers are very suitable for application in the cultivation of tea plants (Camellia sinensis) and tobacco, but it is rarely reported so far. In this study, production of a consortium of three strains of PGPR were applied to tobacco and tea plants. The results demonstrated that plants treated with PGPR exhibited enhanced resistance against the bacterial pathogen Pseudomonas syringae (PstDC3000). The significant effect in improving the plant's ability to resist pathogen invasion was verified through measurements of oxygen activity, bacterial colony counts, and expression levels of resistance-related genes (NPR1, PR1, JAZ1, POD etc.). Moreover, the application of PGPR in the tea plantation showed significantly reduced population occurrences of tea green leafhoppers (Empoasca onukii Matsuda), tea thrips (Thysanoptera:Thripidae), Aleurocanthus spiniferus (Quaintanca) and alleviated anthracnose disease in tea seedlings. Therefore, PGPR biofertilizers may serve as a viable biological control method to improve tobacco and tea plant yield and quality. Our findings revealed part of the mechanism by which PGPR helped improve plant biostresses resistance, enabling better application in agricultural production. [ABSTRACT FROM AUTHOR]

Plant activators have emerged as promising alternatives to conventional crop protection chemicals for managing crop diseases due to their unique mode of action. By priming the plant's innate immune system, these compounds can induce disease resistance against a broad spectrum of pathogens without directly inhibiting their proliferation. Key advantages of plant activators include prolonged defense activity, lower effective dosages, and negligible risk of pathogen resistance development. Among the various defensive pathways targeted, the salicylic acid (SA) signaling cascade has been extensively explored, leading to the successful development of commercial activators of systemic acquired resistance, such as benzothiadiazole, for widespread application in crop protection. While the action sites of many SA-targeting activators have been preliminarily mapped to different steps along the pathway, a comprehensive understanding of their precise mechanisms remains elusive. This review provides a historical perspective on plant activator development and outlines diverse screening strategies employed, from whole-plant bioassays to molecular and transgenic approaches. We elaborate on the various components, biological significance, and regulatory circuits governing the SA pathway while critically examining the structural features, bioactivities, and proposed modes of action of classical activators such as benzothiadiazole derivatives, salicylic acid analogs, and other small molecules. Insights from field trials assessing the practical applicability of such activators are also discussed. Furthermore, we highlight the current status, challenges, and future prospects in the realm of SA-targeting activator development globally, with a focus on recent endeavors in China. Collectively, this comprehensive review aims to describe existing knowledge and provide a roadmap for future research toward developing more potent plant activators that enhance crop health. [ABSTRACT FROM AUTHOR]

Mycorrhizal fungi, a category of fungi that form symbiotic relationships with plant roots, can participate in the induction of plant disease resistance by secreting phosphatase enzymes. While extensive research exists on the mechanisms by which mycorrhizal fungi induce resistance, the specific contributions of phosphatases to these processes require further elucidation. This article reviews the spectrum of mycorrhizal fungi-induced resistance mechanisms and synthesizes a current understanding of how phosphatases mediate these effects, such as the induction of defense structures in plants, the negative regulation of plant immune responses, and the limitation of pathogen invasion and spread. It explores the role of phosphatases in the resistance induced by mycorrhizal fungi and provides prospective future research directions in this field. [ABSTRACT FROM AUTHOR]

Pectobacterium is a major bacterial causal agent leading to soft rot disease in host plants. With the Arabidopsis-Pectobacterium pathosystem, we investigated the function of an Arabidopsis thaliana WRKY55 during defense responses to Pectobacterium carotovorum ssp. carotovorum (Pcc). Pcc-infection specifically induced WRKY55 gene expression. The overexpression of WRKY55 was resistant to the Pcc infection, while wrky55 knock-out plants compromised the defense responses against Pcc. WRKY55 expression was mediated via Arabidopsis COI1-dependent signaling pathway showing that WRKY55 can contribute to the gene expression of jasmonic acid-mediated defense marker genes such as PDF1.2 and LOX2. WRKY55 physically interacts with Arabidopsis ORA59 facilitating the expression of PDF1.2. Our results suggest that WRKY55 can function as a positive regulator for resistance against Pcc in Arabidopsis.

The pattern‐triggered immunity (PTI) response is triggered at the plant cell surface by the recognition of microbe‐derived molecules known as microbe‐ or pathogen‐associated molecular patterns or molecules derived from compromised host cells called damage‐associated molecular patterns. Membrane‐localized receptor proteins, known as pattern recognition receptors, are responsible for this recognition. Although much of the machinery of PTI is conserved, natural variation for the PTI response exists within and across species with respect to the components responsible for pattern recognition, activation of the response, and the strength of the response induced. This review describes what is known about this variation. We discuss how variation in the PTI response can be measured and how this knowledge might be utilized in the control of plant disease and in developing plant varieties with enhanced disease resistance. [ABSTRACT FROM AUTHOR]

Banana is one of the most important fruits in the world due to its status as a major food source for more than 400 million people. Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) causes substantial losses of banana crops every year, and molecular host resistance mechanisms are currently unknown. We here performed a genomewide analysis of the autophagy-related protein 8 (ATG8) family in a wild banana species. The banana genome was found to contain 10 MaATG8 genes. Four MaATG8s formed a gene cluster in the distal part of chromosome 4. Phylogenetic analysis of ATG8 families in banana, Arabidopsis thaliana, citrus, rice, and ginger revealed five major phylogenetic clades shared by all of these plant species, demonstrating evolutionary conservation of the MaATG8 families. The transcriptomic analysis of plants infected with Foc TR4 showed that nine of the MaATG8 genes were more highly induced in resistant cultivars than in susceptible cultivars. Finally, MaATG8F was found to interact with MaATG4B in vitro (with yeast two-hybrid assays), and MaATG8F and MaATG4B all positively regulated banana resistance to Foc TR4. Our study provides novel insights into the structure, distribution, evolution, and expression of the MaATG8 family in bananas. Furthermore, the discovery of interactions between MaATG8F and MaATG4B could facilitate future research of disease resistance genes for the genetic improvement of bananas. [ABSTRACT FROM AUTHOR]

Introduction: Aspergillus nomiae is known as a pathogenic fungus that infects humans and plants but has never been reported as an entomophagous fungus (EPF) that can provide other functions as an endotype. Methods: A strain of EPF was isolated and identified from diseased larvae of Spodoptera litura in a soybean field and designated AnS1Gzl-1. Pathogenicity of the strain toward various insect pests was evaluated, especially the ability to colonize plants and induce resistance against phytopathogens and insect pests. Results: The isolated EPF strain AnS1Gzl-1 was identified as A. nomiae; it showed strong pathogenicity toward five insect pests belonging to Lepidoptera and Hemiptera. Furthermore, the strain inhibited the growth of Sclerotinia sclerotiorum in vitro, a causal agent of soil-borne plant disease. It colonized plants as an endophyte via root irrigation with a high colonization rate of 90%, thereby inducing plant resistance against phytopathogen infection, and disrupting the feeding selectivity of S. litura larvae. Discussion: This is the first record of a natural infection of A. nomiae on insects. A. nomiae has the potential to be used as a dual biocontrol EPF because of its ability to not only kill a broad spectrum of insect pests directly but also induce resistance against phytopathogens via plant colonization. [ABSTRACT FROM AUTHOR]

Mycorrhizal fungi, a category of fungi that form symbiotic relationships with plant roots, can participate in the induction of plant disease resistance by secreting phosphatase enzymes. While extensive research exists on the mechanisms by which mycorrhizal fungi induce resistance, the specific contributions of phosphatases to these processes require further elucidation. This article reviews the spectrum of mycorrhizal fungi-induced resistance mechanisms and synthesizes a current understanding of how phosphatases mediate these effects, such as the induction of defense structures in plants, the negative regulation of plant immune responses, and the limitation of pathogen invasion and spread. It explores the role of phosphatases in the resistance induced by mycorrhizal fungi and provides prospective future research directions in this field.

Plant viruses cause crop losses in agronomically and economically important crops, making global food security a challenge. Although traditional plant breeding has been effective in controlling plant viral diseases, it is unlikely to solve the problems associated with the frequent emergence of new and more virulent virus species or strains. As a result, there is an urgent need to develop alternative virus control strategies that can be used to more easily contain viral diseases. A better understanding of plant defence mechanisms will open up new avenues for research into plant- pathogen interactions and the development of broad-spectrum virus resistance. The scientific literature was evaluated and structured in this review, and the results of the reliability of the methods of analysis used were filtered. As a result, we described the molecular mechanisms by which viruses interact with host plant cells. To develop an effective strategy for the control of plant pathogens with a significant intensity on the agricultural market, clear and standardised recommendations are required. The current review will provide key insights into the molecular underpinnings underlying the coordination of plant disease resistance, such as main classes of resistance genes, RNA interference, and the RNA-mediated adaptive immune system of bacteria and archaea – clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated Cas proteins – CRISPR/Cas. Future issues related to resistance to plant viral diseases will largely depend on integrated research to transfer fundamental knowledge to applied problems, bridging the gap between laboratory and field work.

Microbial volatile organic compounds (MVOCs) are a diverse group of volatile organic compounds that microorganisms may produce and release into the environment. These compounds have both positive and negative effects on plants, as they have been shown to be effective at mitigating stresses and functioning as immune stimulants. Furthermore, MVOCs modulate plant growth and systemic plant resistance, while also serving as attractants or repellents for insects and other stressors that pose threats to plants. Considering the economic value of strawberries as one of the most popular and consumed fruits worldwide, harnessing the benefits of MVOCs becomes particularly significant. MVOCs offer cost-effective and efficient solutions for disease control and pest management in horticultural production, as they can be utilized at low concentrations. This paper provides a comprehensive review of the current knowledge on microorganisms that contribute to the production of beneficial volatile organic compounds for enhancing disease resistance in fruit products, with a specific emphasis on broad horticultural production. The review also identifies research gaps and highlights the functions of MVOCs in horticulture, along with the different types of MVOCs that impact plant disease resistance in strawberry production. By offering a novel perspective on the application and utilization of volatile organic compounds in sustainable horticulture, this review presents an innovative approach to maximizing the efficiency of horticultural production through the use of natural products.

Key message: We analyzed the evolutionary pattern of cysteine-rich peptides (CRPs) to infer the relationship between CRP copy number and plant ecotype, and the origin of bi-domains CRPs. Plants produce cysteine-rich peptides (CRPs) that have long-lasting broad-spectrum antimicrobial activity to protect themselves from various groups of pathogens. We analyzed 240 plant genomes, ranging from algae to eudicots, and discovered that CRPs are widely distributed in plants. Our comparative genomics results revealed that CRP genes have been amplified through both whole genome and local tandem duplication. The copy number of these genes varied significantly across lineages and was associated with the plant ecotype. This may be due to their resistance to changing pathogenic environments. The conserved and lineage-specific CRP families contribute to diverse antimicrobial activities. Furthermore, we investigated the unique bi-domain CRPs that result from unequal crossover events. Our findings provide a unique evolutionary perspective on CRPs and insights into their antimicrobial and symbiosis characteristics. [ABSTRACT FROM AUTHOR]

Leaf sheath blight disease (SB) of rice caused by the soil-borne fungus Rhizoctonia solani results in 10–30% global yield loss annually and can reach 50% under severe outbreaks. Many disease resistance genes and receptor-like kinases (RLKs) are recruited early on by the host plant to respond to pathogens. Wall-associated receptor kinases (WAKs), a subfamily of receptor-like kinases, have been shown to play a role in fungal defense. The rice gene WAK91 (OsWAK91), co-located in the major SB resistance QTL region on chromosome 9, was identified by us as a candidate in defense against rice sheath blight. An SNP mutation T/C in the WAK91 gene was identified in the susceptible rice variety Cocodrie (CCDR) and the resistant line MCR010277 (MCR). The consequence of the resistant allele C is a stop codon loss, resulting in an open reading frame with extra 62 amino acid carrying a longer protein kinase domain and additional phosphorylation sites. Our genotype and phenotype analysis of the parents CCDR and MCR and the top 20 individuals of the double haploid SB population strongly correlate with the SNP. The susceptible allele T is present in the japonica subspecies and most tropical and temperate japonica lines. Multiple US commercial rice varieties with a japonica background carry the susceptible allele and are known for SB susceptibility. This discovery opens the possibility of introducing resistance alleles into high-yielding commercial varieties to reduce yield losses incurred by the sheath blight disease. [ABSTRACT FROM AUTHOR]

Abstract Background In the ten years since the initial publication of the RenSeq protocol, the method has proved to be a powerful tool for studying disease resistance in plants and providing target genes for breeding programmes. Since the initial publication of the methodology, it has continued to be developed as new technologies have become available and the increased availability of computing power has made new bioinformatic approaches possible. Most recently, this has included the development of a k-mer based association genetics approach, the use of PacBio HiFi data, and graphical genotyping with diagnostic RenSeq. However, there is not yet a unified workflow available and researchers must instead configure approaches from various sources themselves. This makes reproducibility and version control a challenge and limits the ability to perform these analyses to those with bioinformatics expertise. Results Here we present HISS, consisting of three workflows which take a user from raw RenSeq reads to the identification of candidates for disease resistance genes. These workflows conduct the assembly of enriched HiFi reads from an accession with the resistance phenotype of interest. A panel of accessions both possessing and lacking the resistance are then used in an association genetics approach (AgRenSeq) to identify contigs positively associated with the resistance phenotype. Candidate genes are then identified on these contigs and assessed for their presence or absence in the panel with a graphical genotyping approach that uses dRenSeq. These workflows are implemented via Snakemake, a python-based workflow manager. Software dependencies are either shipped with the release or handled with conda. All code is freely available and is distributed under the GNU GPL-3.0 license. Conclusions HISS provides a user-friendly, portable, and easily customised approach for identifying novel disease resistance genes in plants. It is easily installed with all dependencies handled internally or shipped with the release and represents a significant improvement in the ease of use of these bioinformatics analyses.

The rust diseases, including leaf rust caused by Puccinia triticina (Pt), stem rust caused by P. graminis f. sp. tritici (Pgt), and stripe rust caused by P. striiformis f. sp. tritici (Pst), are major limiting factors in wheat production worldwide. Identification of novel sources of rust resistance genes is key to developing cultivars resistant to rapidly evolving pathogen populations. Aegilops longissima is a diploid wild grass native to the Levant and closely related to the modern bread wheat D subgenome. To explore resistance genes in the species, we evaluated a large panel of Ae. longissima for resistance to several races of Pt, Pgt, and Pst, and conducted a genome-wide association study (GWAS) to map rust resistance loci in the species. A panel of 404 Ae. longissima accessions, mostly collected from Israel, were screened for seedling-stage resistance to four races of Pt, four races of Pgt, and three races of Pst. Out of the 404 accessions screened, two were found that were resistant to all 11 races of the three rust pathogens screened. The percentage of all accessions screened that were resistant to a given rust pathogen race ranged from 18.5% to 99.7%. Genotyping-by-sequencing (GBS) was performed on 381 accessions of the Ae. longissima panel, wherein 125,343 single nucleotide polymorphisms (SNPs) were obtained after alignment to the Ae. longissima reference genome assembly and quality control filtering. Genetic diversity analysis revealed the presence of two distinct subpopulations, which followed a geographic pattern of a northern and a southern subpopulation. Association mapping was performed in the genotyped portion of the collection (n = 381) and in each subpopulation (n = 204 and 174) independently via a single-locus mixed-linear model, and two multi-locus models, FarmCPU, and BLINK. A large number (195) of markers were significantly associated with resistance to at least one of 10 rust pathogen races evaluated, nine of which are key candidate markers for further investigation due to their detection via multiple models and/or their association with resistance to more than one pathogen race. The novel resistance loci identified will provide additional diversity available for use in wheat breeding. [ABSTRACT FROM AUTHOR]

Tobacco black shank (TBS), caused by Phytophthora nicotianae, is one of the most harmful diseases of tobacco. There are many studies have examined the mechanism underlying the induction of disease resistance by arbuscular mycorrhizal fungi (AMF) and Ɓ-aminobutyric acid (BABA) alone, but the synergistic effects of AMF and BABA on disease resistance have not yet been studied. This study examined the synergistic effects of BABA application and AMF inoculation on the immune response to TBS in tobacco. The results showed that spraying BABA on leaves could increase the colonization rate of AMF, the disease index of tobacco infected by P.nicotianae treated with AMF and BABA was lower than that of P.nicotianae alone. The control effect of AMF and BABA on tobacco infected by P.nicotianae was higher than that of AMF or BABA and P.nicotianae alone. Joint application of AMF and BABA significantly increased the content of N, P, and K in the leaves and roots, in the joint AMF and BABA treatment than in the sole P. nicotianae treatment. The dry weight of plants treated with AMF and BABA was 22.3% higher than that treated with P.nicotianae alone. In comparison to P. nicotianae alone, the combination treatment with AMF and BABA had increased Pn, Gs, Tr, and root activity, while P. nicotianae alone had reduced Ci, H2O2 content, and MDA levels. SOD, POD, CAT, APX, and Ph activity and expression levels were increased under the combined treatment of AMF and BABA than in P.nicotianae alone. In comparison to the treatment of P.nicotianae alone, the combined use of AMF and BABA increased the accumulation of GSH, proline, total phenols, and flavonoids. Therefore, the joint application of AMF and BABA can enhance the TBS resistance of tobacco plants to a greater degree than the application of either AMF or BABA alone. In summary, the application of defense-related amino acids, combined with inoculation with AMF, significantly promoted immune responses in tobacco. Our findings provide new insights that will aid the development and use of green disease control agents. [ABSTRACT FROM AUTHOR]

Lychee downy blight (LDB) is an oomycete pathogen (Peronophythora litchi) disease, which affects the fruits and leaves of lychee, resulting in economic losses. Chemical fungicides are commonly used for disease control, while for eco-safety measures, the study of molecular mechanisms involved in lychee resistance against LDB is necessary. Non-coding RNAs (ncRNAs), including long ncRNAs (lncRNAs), circular (circRNAs), and microRNAs (miRNAs), play a crucial role in plant disease resistance. To examine lychee response (fruits and leaves) to LDB, we studied the expression patterns of ncRNAs and mRNAs under LDB treatment. By whole transcriptome sequencing analyses, a total of 36,885 mRNAs, 2627 lncRNAs, 4682 circRNAs, and 525 miRNAs were identified in lychee. A differential expression (DE) analysis revealed that there were 1095 DEmRNAs, 89 DElncRNAs, 28 DEcircRNAs, and 28 DEmiRNAs in the LDB-treated fruits, as well as 1158 DEmRNAs, 132 DElncRNAs, 13 DEcircRNAs, and 197 DEmiRNAs in the LDB-treated leaves. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the potential function of DEmRNAs and the targets of ncRNAs were involved in plant defense. Furthermore, co-expression networks of putative interacting ncRNAs and mRNAs were developed, in which mRNAs encoded some receptor proteins, pointing to potential ncRNAs associated with LDB infection. Our study provided a new, brief insight to the putative role of ncRNAs in lychee response to LDB. [ABSTRACT FROM AUTHOR]

Background: In the ten years since the initial publication of the RenSeq protocol, the method has proved to be a powerful tool for studying disease resistance in plants and providing target genes for breeding programmes. Since the initial publication of the methodology, it has continued to be developed as new technologies have become available and the increased availability of computing power has made new bioinformatic approaches possible. Most recently, this has included the development of a k-mer based association genetics approach, the use of PacBio HiFi data, and graphical genotyping with diagnostic RenSeq. However, there is not yet a unified workflow available and researchers must instead configure approaches from various sources themselves. This makes reproducibility and version control a challenge and limits the ability to perform these analyses to those with bioinformatics expertise. Results: Here we present HISS, consisting of three workflows which take a user from raw RenSeq reads to the identification of candidates for disease resistance genes. These workflows conduct the assembly of enriched HiFi reads from an accession with the resistance phenotype of interest. A panel of accessions both possessing and lacking the resistance are then used in an association genetics approach (AgRenSeq) to identify contigs positively associated with the resistance phenotype. Candidate genes are then identified on these contigs and assessed for their presence or absence in the panel with a graphical genotyping approach that uses dRenSeq. These workflows are implemented via Snakemake, a python-based workflow manager. Software dependencies are either shipped with the release or handled with conda. All code is freely available and is distributed under the GNU GPL-3.0 license. Conclusions: HISS provides a user-friendly, portable, and easily customised approach for identifying novel disease resistance genes in plants. It is easily installed with all dependencies handled internally or shipped with the release and represents a significant improvement in the ease of use of these bioinformatics analyses. [ABSTRACT FROM AUTHOR]

Plant viruses cause crop losses in agronomically and economically important crops, making global food security a challenge. Although traditional plant breeding has been effective in controlling plant viral diseases, it is unlikely to solve the problems associated with the frequent emergence of new and more virulent virus species or strains. As a result, there is an urgent need to develop alternative virus control strategies that can be used to more easily contain viral diseases. A better understanding of plant defence mechanisms will open up new avenues for research into plantpathogen interactions and the development of broad-spectrum virus resistance. The scientific literature was evaluated and structured in this review, and the results of the reliability of the methods of analysis used were filtered. As a result, we described the molecular mechanisms by which viruses interact with host plant cells. To develop an effective strategy for the control of plant pathogens with a significant intensity on the agricultural market, clear and standardised recommendations are required. The current review will provide key insights into the molecular underpinnings underlying the coordination of plant disease resistance, such as main classes of resistance genes, RNA interference, and the RNA-mediated adaptive immune system of bacteria and archaea -- clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated Cas proteins -- CRISPR/Cas. Future issues related to resistance to plant viral diseases will largely depend on integrated research to transfer fundamental knowledge to applied problems, bridging the gap between laboratory and field work. [ABSTRACT FROM AUTHOR]

Long noncoding RNAs (lncRNAs) participate in a wide range of biological processes, but lncRNAs in plants remain largely unknown; in particular, we lack a systematic identification of plant lncRNAs involved in hormone responses. To explore the molecular mechanism of the response of poplar to salicylic acid (SA), the changes in protective enzymes, which are closely related to plant resistance induced by exogenous SA, were studied, and the expression of mRNA and lncRNA were determined by high-throughput RNA sequencing. The results showed that the activities of phenylalanine ammonia lyase (PAL) and polyphenol oxidase (PPO), in the leaves of Populus × euramericana, were significantly increased by exogenous SA application. High-throughput RNA sequencing showed that 26,366 genes and 5690 lncRNAs were detected under the different treatment conditions: SA and H2O application. Among these, 606 genes and 49 lncRNAs were differentially expressed. According to target prediction, lncRNAs and target genes involved in light response, stress response, plant disease resistance, and growth and development, were differentially expressed in SA-treated leaves. Interaction analysis showed that lncRNA–mRNA interactions, following exogenous SA, were involved in the response of poplar leaves to the external environment. Our study provides a comprehensive view of Populus × euramericana lncRNAs and offers insights into the potential functions and regulatory interactions of SA-responsive lncRNAs, thus forming the foundation for future functional analysis of SA-responsive lncRNAs in Populus × euramericana. [ABSTRACT FROM AUTHOR]

SUMMARY: The soybean Rpp1 locus confers resistance to Phakopsora pachyrhizi, causal agent of rust, and resistance is usually dominant over susceptibility. However, dominance of Rpp1‐mediated resistance is lost when a resistant genotype (Rpp1 or Rpp1b) is crossed with susceptible line TMG06_0011, and the mechanism of this dominant susceptibility (DS) is unknown. Sequencing the Rpp1 region reveals that the TMG06_0011 Rpp1 locus has a single nucleotide‐binding site leucine‐rich repeat (NBS‐LRR) gene (DS‐R), whereas resistant PI 594760B (Rpp1b) is similar to PI 200492 (Rpp1) and has three NBS‐LRR resistance gene candidates. Evidence that DS‐R is the cause of DS was reflected in virus‐induced gene silencing of DS‐R in Rpp1b/DS‐R or Rpp1/DS‐R heterozygous plants with resistance partially restored. In heterozygous Rpp1b/DS‐R plants, expression of Rpp1b candidate genes was not significantly altered, indicating no effect of DS‐R on transcription. Physical interaction of the DS‐R protein with candidate Rpp1b resistance proteins was supported by yeast two‐hybrid studies and in silico modeling. Thus, we conclude that suppression of resistance most likely does not occur at the transcript level, but instead probably at the protein level, possibly with Rpp1 function inhibited by binding to the DS‐R protein. The DS‐R gene was found in other soybean lines, with an estimated allele frequency of 6% in a diverse population, and also found in wild soybean (Glycine soja). The identification of a dominant susceptible NBS‐LRR gene provides insight into the behavior of NBS‐LRR proteins and serves as a reminder to breeders that the dominance of an R gene can be influenced by a susceptibility allele. Significance Statement: Most resistance genes are inherited dominantly, although the present study serves as a reminder to breeders that the dominance of an R gene can be influenced by a susceptibility allele. The study identified a susceptible NBS‐LRR allele that can negate the dominance of the Rpp1‐mediated resistance to Asian soybean rust. The results support suppression of resistance occurring at the protein level, possibly through the interaction between the susceptible protein and the resistance protein. [ABSTRACT FROM AUTHOR]

Introduction: Nucleotide-binding leucine-rich repeat (NLR) genes play a crucial role in green plants' responding to various pathogens. Genome-scale evolutionary studies of NLR genes are important for discovering and applying functional NLR genes. However, little is known about the evolution of NLR genes in the Apiaceae family including agricultural and medical plants. Methods: In this study, comparative genomic analysis was performed in four Apiaceae species to trace the dynamic evolutionary patterns of NLR genes during speciation in this family. Results: The results revealed different number of NLR genes in these four Apiaceae species, namely, Angelica sinensis (95), Coriandrum sativum (183), Apium graveolens (153) and Daucus carota (149). Phylogenetic analysis demonstrated that NLR genes in these four species were derived from 183 ancestral NLR lineages and experienced different levels of gene-loss and gain events. The contraction pattern of the ancestral NLR lineages was discovered during the evolution of D. carota, whereas a different pattern of contraction after first expansion of NLR genes was observed for A. sinensis, C. sativum and A. graveolens. Discussion: Taken together, rapid and dynamic gene content variation has shaped evolutionary history of NLR genes in Apiaceae species. [ABSTRACT FROM AUTHOR]

The rust diseases, including leaf rust caused by Puccinia triticina (Pt), stem rust caused by P. graminis f. sp. tritici (Pgt), and stripe rust caused by P. striiformis f. sp. tritici (Pst), are major limiting factors in wheat production worldwide. Identification of novel sources of rust resistance genes is key to developing cultivars resistant to rapidly evolving pathogen populations. Aegilops longissima is a diploid wild grass native to the Levant and closely related to the modern bread wheat D subgenome. To explore resistance genes in the species, we evaluated a large panel of Ae. longissima for resistance to several races of Pt, Pgt, and Pst, and conducted a genome-wide association study (GWAS) to map rust resistance loci in the species. A panel of 404 Ae. longissima accessions, mostly collected from Israel, were screened for seedling-stage resistance to four races of Pt, four races of Pgt, and three races of Pst. Out of the 404 accessions screened, two were found that were resistant to all 11 races of the three rust pathogens screened. The percentage of all accessions screened that were resistant to a given rust pathogen race ranged from 18.5% to 99.7%. Genotyping-by-sequencing (GBS) was performed on 381 accessions of the Ae. longissima panel, wherein 125,343 single nucleotide polymorphisms (SNPs) were obtained after alignment to the Ae. longissima reference genome assembly and quality control filtering. Genetic diversity analysis revealed the presence of two distinct subpopulations, which followed a geographic pattern of a northern and a southern subpopulation. Association mapping was performed in the genotyped portion of the collection (n = 381) and in each subpopulation (n = 204 and 174) independently via a single-locus mixed-linear model, and two multi-locus models, FarmCPU, and BLINK. A large number (195) of markers were significantly associated with resistance to at least one of 10 rust pathogen races evaluated, nine of which are key candidate markers for further investigation due to their detection via multiple models and/or their association with resistance to more than one pathogen race. The novel resistance loci identified will provide additional diversity available for use in wheat breeding.

Tobacco black shank (TBS), caused by Phytophthora nicotianae, is one of the most harmful diseases of tobacco. There are many studies have examined the mechanism underlying the induction of disease resistance by arbuscular mycorrhizal fungi (AMF) and β-aminobutyric acid (BABA) alone, but the synergistic effects of AMF and BABA on disease resistance have not yet been studied. This study examined the synergistic effects of BABA application and AMF inoculation on the immune response to TBS in tobacco. The results showed that spraying BABA on leaves could increase the colonization rate of AMF, the disease index of tobacco infected by P.nicotianae treated with AMF and BABA was lower than that of P.nicotianae alone. The control effect of AMF and BABA on tobacco infected by P.nicotianae was higher than that of AMF or BABA and P.nicotianae alone. Joint application of AMF and BABA significantly increased the content of N, P, and K in the leaves and roots, in the joint AMF and BABA treatment than in the sole P. nicotianae treatment. The dry weight of plants treated with AMF and BABA was 22.3% higher than that treated with P.nicotianae alone. In comparison to P. nicotianae alone, the combination treatment with AMF and BABA had increased Pn, Gs, Tr, and root activity, while P. nicotianae alone had reduced Ci, H2O2 content, and MDA levels. SOD, POD, CAT, APX, and Ph activity and expression levels were increased under the combined treatment of AMF and BABA than in P.nicotianae alone. In comparison to the treatment of P.nicotianae alone, the combined use of AMF and BABA increased the accumulation of GSH, proline, total phenols, and flavonoids. Therefore, the joint application of AMF and BABA can enhance the TBS resistance of tobacco plants to a greater degree than the application of either AMF or BABA alone. In summary, the application of defense-related amino acids, combined with inoculation with AMF, significantly promoted immune responses in tobacco. Our findings provide new insights that will aid the development and use of green disease control agents.

Botrytis cinerea, a plant pathogenic fungus with a wide host range, has reduced sensitivity to fungicides as well as phytoalexins, threatening cultivation of economically important fruits and vegetable crops worldwide. B. cinerea tolerates a wide array of phytoalexins, through efflux and/or enzymatic detoxification. Previously, we provided evidence that a distinctive set of genes were induced in B. cinerea when treated with different phytoalexins such as rishitin (produced by tomato and potato), capsidiol (tobacco and bell pepper) and resveratrol (grape and blueberry). In this study, we focused on the functional analyses of B. cinerea genes implicated in rishitin tolerance. LC/MS profiling revealed that B. cinerea can metabolize/detoxify rishitin into at least 4 oxidized forms. Heterologous expression of Bcin08g04910 and Bcin16g01490, two B. cinerea oxidoreductases upregulated by rishitin, in a plant symbiotic fungus Epichloë festucae revealed that these rishitin-induced enzymes are involved in the oxidation of rishitin. Expression of BcatrB, encoding an exporter of structurally unrelated phytoalexins and fungicides, was significantly upregulated by rishitin but not by capsidiol and was thus expected to be involved in the rishitin tolerance. Conidia of BcatrB KO (ΔbcatrB) showed enhanced sensitivity to rishitin, but not to capsidiol, despite their structural similarity. ΔbcatrB showed reduced virulence on tomato, but maintained full virulence on bell pepper, indicating that B. cinerea activates BcatrB by recognizing appropriate phytoalexins to utilize it in tolerance. Surveying 26 plant species across 13 families revealed that the BcatrB promoter is mainly activated during the infection of B. cinerea in plants belonging to the Solanaceae, Fabaceae and Brassicaceae. The BcatrB promoter was also activated by in vitro treatments of phytoalexins produced by members of these plant families, namely rishitin (Solanaceae), medicarpin and glyceollin (Fabaceae), as well as camalexin and brassinin (Brassicaceae). Consistently, ΔbcatrB showed reduced virulence on red clover, which produces medicarpin. These results suggest that B. cinerea distinguishes phytoalexins and induces differential expression of appropriate genes during the infection. Likewise, BcatrB plays a critical role in the strategy employed by B. cinerea to bypass the plant innate immune responses in a wide variety of important crops belonging to the Solanaceae, Brassicaceae and Fabaceae.

Banana is one of the most important fruits in the world due to its status as a major food source for more than 400 million people. Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) causes substantial losses of banana crops every year, and molecular host resistance mechanisms are currently unknown. We here performed a genomewide analysis of the autophagy-related protein 8 (ATG8) family in a wild banana species. The banana genome was found to contain 10 MaATG8 genes. Four MaATG8s formed a gene cluster in the distal part of chromosome 4. Phylogenetic analysis of ATG8 families in banana, Arabidopsis thaliana, citrus, rice, and ginger revealed five major phylogenetic clades shared by all of these plant species, demonstrating evolutionary conservation of the MaATG8 families. The transcriptomic analysis of plants infected with Foc TR4 showed that nine of the MaATG8 genes were more highly induced in resistant cultivars than in susceptible cultivars. Finally, MaATG8F was found to interact with MaATG4B in vitro (with yeast two-hybrid assays), and MaATG8F and MaATG4B all positively regulated banana resistance to Foc TR4. Our study provides novel insights into the structure, distribution, evolution, and expression of the MaATG8 family in bananas. Furthermore, the discovery of interactions between MaATG8F and MaATG4B could facilitate future research of disease resistance genes for the genetic improvement of bananas.

Rabproteins are the largest members of the small G protein family and are widely distributed in eukaryotes. It comprises eight subfamilies and is responsible for regulating vesicle transport, plant growth and development, and biotic and abiotic stress responses. In this study, the small G protein gene StRab5b was cloned from potato, and its biological information, expression profile and induced expression level, overexpression and gene silencing were examined on regulating potato resistance to Phytophthora infestans using PCR, qPCR and Virus-induced gene silencing (VIGS). Our results indicate that the amino acid of StRab5b shows the highest and lowest homology with NbRab5b in N. benthamiana and StRab in potato respectively. StRab5b expression varied among different potato tissues and varieties, and was induced by P. infestans infection. Transiently ectopic expression of StRab5b in N. benthamiana enhanced its resistance to P. infestans, whereas, silencing of StRab5b and its homologous gene facilitated pathogen infection in potato and N. benthamiana respectively. Furthermore, stable expression of the StRab5b gene in potatoes enhanced its redox-stress response capacity, as manifested by the accumulation of H2O2 in infected leaves and subsequent increase in the activity and expression of ROS scavenging enzymes, thereby attenuating the development of P. infestans and ultimately reducing the lesions on infected potato leaves. In addition, the LOX gene transcripts and JA level were upregulated rapidly after inoculation with P. infestans. Collectively, our results suggest that StRab5b positively regulates the resistance against potato late blight (PLB) via JA-mediated defense signaling pathway. [ABSTRACT FROM AUTHOR]

(1) Corn is the most widely planted food crop, feed crop, and economic crop in the world, and plays an important role in agricultural production and national economy development. The copine gene, also known as the BONZAI gene, encodes a Ca2+-dependent phospholipid membrane binding protein that is widely present in eukaryotes. It has been found that the copine protein is a negative regulator of disease resistance regulation and plays a key role in plants' disease resistance response. In this study, the Agrobacterium-tumefacien-mediated method was used to successfully obtain T2 generation ZmBON3-gene-overexpressing plants and gene-edited plants. Related phenotypes and molecular identification showed that the disease resistance of overexpression plants was significantly reduced, and the disease resistance of gene-edited plants was significantly increased, which verified that the ZmBON3 gene was a negative regulatory gene. By detecting the physiological indexes related to defense, it was found that the content of H2O2 and the enzyme active water of CAT, POD, SOD, and PAL in ZmBON3-gene-edited plants was higher than those in the control plants and ZmBON3-gene-overexpressing plants, and the content of H2O2 and CAT, POD, and SOD in ZmBON3-gene-overexpressing plants was significantly higher than that in the control plants and ZmBON3-gene-overexpressing plants. The enzyme activity of PAL was the lowest. By detecting the expression of key genes of defense-related signaling pathways, it was found that ZmBON3 may be involved in the related defense processes mediated by the R gene, SA pathway, JA pathway, and ABA pathway. In addition, ZmBON3-geneedited plants showed obvious dwarf phenomenon at the seedling stage, but this did not affect the ear length, axis diameter, ear row number, and grain color. [ABSTRACT FROM AUTHOR]

Horticultural plants, in particular fruit trees, berry crops, and ornamentals, are valuable objects for studying their genetic and biochemical properties. Along with traditional methods of studying these plants, modern molecular genetic technologies are emerging, in particular genome editing using CRISPR/Cas9 nucleases. In this review, we have analyzed modern advances in genome editing of horticultural plants. To date, it has become possible to improve many plant characteristics using this technology, e.g., making plants resistant to biotic and abiotic stress factors, changing the time of flowering and fruit ripening, changing the growth characteristics of plants, as well as the taste properties of their fruits. CRISPR/Cas9 genome editing has been successfully carried out for many horticultural plants. Dozens of genes from these plants have been modified by means of genome editing technology. We have considered the main ways of delivering genetic constructs to plants as well as limitations that complicate the editing of target genes. The article reviews the prospects of using genome editing to improve the valuable properties of plants important to humans. [ABSTRACT FROM AUTHOR]

The GDSL esterase/lipase family contains many functional genes that perform important biological functions in growth and development, morphogenesis, seed oil synthesis, and defense responses in plants. The expression of GDSL esterase/lipase genes can respond to biotic and abiotic stresses. Although GDSL esterase/lipase family genes have been identified and studied in other plants, they have not been identified and their functions remain unclear in tomato. This study is the first to identify 80 GDSL esterase/lipase family genes in tomato, which were named SlGELP1–80. These genes were mapped to their positions on the chromosomes and their physical and chemical properties, gene structure, phylogenetic relationships, collinear relationships, and cis-acting elements were analyzed. The spatiotemporal expression characteristics of the SlGELP genes in tomato were diverse. In addition, RNA-seq analysis indicated that the expression patterns of the SlGELP genes in tomato differed before and after inoculation with Stemphylium lycopersici. qRT-PCR was used to analyze the expression of five SlGELP genes after treatments with S. lycopersici, salicylic acid and jasmonic acid. Finally, this study was the first to identify and analyze GDSL esterase/lipase family genes in tomato via bioinformatics approaches, and these findings provide new insights for improving the study of plant disease resistance.

Plants are engaged in a coevolutionary arms race with their pathogens that drives rapid diversification and specialization of genes involved in resistance and virulence. However, some major innovations in plant–pathogen interactions, such as molecular decoys, trans -kingdom RNA interference, two-speed genomes, and receptor networks, evolved through the expansion of the functional landscape of genes. This is a typical outcome of genetic co-option, the evolutionary process by which available genes are recruited into new biological functions. Co-option into plant–pathogen interactions emerges generally from (i) cis -regulatory variation, (ii) horizontal gene transfer (HGT), (iii) mutations altering molecular promiscuity, and (iv) rewiring of gene networks and protein complexes. Understanding these molecular mechanisms is key for the functional and predictive biology of plant–pathogen interactions. The coevolution of plants and their filamentous pathogens shapes elaborate molecular mechanisms for survival and manipulation. Recent studies have revealed that the evolution of several key innovations, both in plant defense and pathogen virulence, involved the co-option of pre-existing genetic components, adding new functions to old ones. Co-option by regulatory and mobile genetic elements has recruited new genes for defense and virulence, enabling concerted gene activation and trans -kingdom manipulation of gene expression. The diversification of plant disease resistance and pathogen effector proteins involves the reshuffling and repurposing of existing protein domains and protein family members. [ABSTRACT FROM AUTHOR]

Asexual Epichloë are endophytic fungi that form mutualistic symbioses with cool-season grasses, conferring to their hosts protection against biotic and abiotic stresses. Symbioses are maintained between grass generations as hyphae are vertically transmitted from parent to progeny plants through seed. However, endophyte transmission to the seed is an imperfect process where not all seeds become infected. The mechanisms underpinning the varying efficiencies of seed transmission are poorly understood. Host gene expression in response to Epichloë sp. LpTG-3 strain AR37 was examined within inflorescence primordia and ovaries of high and low endophyte transmission genotypes within a single population of perennial ryegrass. A genome-wide association study was conducted to identify population-level single nucleotide polymorphisms (SNPs) and associated genes correlated with vertical transmission efficiency. For low transmitters of AR37, upregulation of perennial ryegrass receptor-like kinases and resistance genes, typically associated with phytopathogen detection, comprised the largest group of differentially expressed genes (DEGs) in both inflorescence primordia and ovaries. DEGs involved in signaling and plant defense responses, such as cell wall modification, secondary metabolism, and reactive oxygen activities were also abundant. Transmission-associated SNPs were associated with genes for which gene ontology analysis identified "response to fungus" as the most significantly enriched term. Moreover, endophyte biomass as measured by quantitative PCR of Epichloë non-ribosomal peptide synthetase genes, was significantly lower in reproductive tissues of low-transmission hosts compared to high-transmission hosts. Endophyte seed-transmission efficiency appears to be influenced primarily by plant defense responses which reduce endophyte colonization of host reproductive tissues. [ABSTRACT FROM AUTHOR]

Black rot of crucifers caused by Xanthomonas campestris pv. campestris (Xcc) is one of the most destructive diseases affecting vegetable Brassica crops, as well as the model plant Arabidopsis thaliana. Although the interaction between both model organisms has been studied, there is still a gap in knowledge regarding the characterization of the response of different races of Xcc. The objective of this study was to screen out the pathogenicity of Xcc Brazilian isolates, representing different races and collected from different Brassica fields, in the model plant A. thaliana. Six Xcc isolates comprising five different races were pressure infiltrated on A. thaliana leaves. Plants were phenotyped for the percentage of lesion area and in planta bacterial population growth. We report a great variation in the pathogen aggressiveness at race and isolate levels, characterized mostly by trade-offs between disease severity and in planta survival rate. Our data provide a valuable piece of knowledge about Xcc phenotypic responses at race and isolate levels. These results contribute for further functional studies in the model plant A. thaliana, besides providing a better understanding of Xcc race structure complexity. [ABSTRACT FROM AUTHOR]

Plant cell walls delimit plant cells from their environment and provide mechanical stability to withstand internal turgor pressure as well as external influences. Environmental factors can be beneficial or harmful for the plants and vary substantially depending on prevailing combinations of climate conditions and stress exposure. Consequently, the physicochemical properties of plant cell walls need to be adaptive, and their functional integrity needs to be monitored by the plant. One major threat to plants is posed by phytopathogens, which employ a diversity of infection strategies and lifestyles to colonise host tissues. During these interactions, the plant cell wall represents a barrier that impedes the colonisation of host tissues and pathogen spread. In a tussle over maintenance and breakdown, plant cell walls can be rapidly and efficiently remodelled by enzymatic activities of plant and pathogen origin, heavily influencing the outcome of plant-pathogen interactions. We review the role of locally and systemically induced cell wall remodelling and the importance of tissue-dependent cell wall properties for the interaction with pathogens. Furthermore, we discuss the importance of cell wall-dependent signalling for defence response induction and the influence of abiotic factors on cell wall integrity and cell wall-associated pathogen resistance mechanisms., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Pectobacterium is a major bacterial causal agent leading to soft rot disease in host plants. With the Arabidopsis-Pectobacterium pathosystem, we investigated the function of an Arabidopsis thaliana WRKY55 during defense responses to Pectobacterium carotovorum ssp. carotovorum (Pcc). Pcc-infection specifically induced WRKY55 gene expression. The overexpression of WRKY55 was resistant to the Pcc infection, while wrky55 knockout plants compromised the defense responses against Pcc. WRKY55 expression was mediated via Arabidopsis COI1-dependent signaling pathway showing that WRKY55 can contribute to the gene expression of jasmonic acid-mediated defense marker genes such as PDF1.2 and LOX2. WRKY55 physically interacts with Arabidopsis ORA59 facilitating the expression of PDF1.2</i. Our results suggest that WRKY55 can function as a positive regulator for resistance against Pcc in Arabidopsis.

Lychee downy blight (LDB) is an oomycete pathogen (Peronophythora litchi) disease, which affects the fruits and leaves of lychee, resulting in economic losses. Chemical fungicides are commonly used for disease control, while for eco-safety measures, the study of molecular mechanisms involved in lychee resistance against LDB is necessary. Non-coding RNAs (ncRNAs), including long ncRNAs (lncRNAs), circular (circRNAs), and microRNAs (miRNAs), play a crucial role in plant disease resistance. To examine lychee response (fruits and leaves) to LDB, we studied the expression patterns of ncRNAs and mRNAs under LDB treatment. By whole transcriptome sequencing analyses, a total of 36,885 mRNAs, 2627 lncRNAs, 4682 circRNAs, and 525 miRNAs were identified in lychee. A differential expression (DE) analysis revealed that there were 1095 DEmRNAs, 89 DElncRNAs, 28 DEcircRNAs, and 28 DEmiRNAs in the LDB-treated fruits, as well as 1158 DEmRNAs, 132 DElncRNAs, 13 DEcircRNAs, and 197 DEmiRNAs in the LDB-treated leaves. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the potential function of DEmRNAs and the targets of ncRNAs were involved in plant defense. Furthermore, co-expression networks of putative interacting ncRNAs and mRNAs were developed, in which mRNAs encoded some receptor proteins, pointing to potential ncRNAs associated with LDB infection. Our study provided a new, brief insight to the putative role of ncRNAs in lychee response to LDB.

Resistance to the soybean cyst nematode (SCN) is a topic incorporating multiple mechanisms and multiple types of science. It is also a topic of substantial agricultural importance, as SCN is estimated to cause more yield damage than any other pathogen of soybean, one of the world's main food crops. Both soybean and SCN have experienced jumps in experimental tractability in the past decade, and significant advances have been made. The rhg1-b locus, deployed on millions of farm acres, has been durable and will remain important, but local SCN populations are gradually evolving to overcome rhg1-b. Multiple other SCN resistance quantitative trait loci (QTL) of proven value are now in play with soybean breeders. QTL causal gene discovery and mechanistic insights into SCN resistance are contributing to both basic and applied disciplines. Additional understanding of SCN and other cyst nematodes will also grow in importance and lead to novel disease control strategies. [ABSTRACT FROM AUTHOR]

The entomopathogenic fungus Beauveria bassiana is widely used for insect pest control and can produce three distinct infective unit types under different nutritional and environmental conditions: aerial conidia, blastospores, and submerged conidia. Here, we identified endophytic colonization ability and existing forms of the three types of B. bassiana infective units after inoculating Arabidopsis plants via soil drenching, and tested their effects on their presence mold disease caused by Botrytis cinerea. We found that all B. bassiana infective unit types colonized Arabidopsis leaves, with germinating and producing hyphae by hydrophilic blastopores and submerged conidia; further, we showed that blastospores were more effective in defending against B. cinerea , compared with aerial conidia. These findings suggest that in addition to aerial conidia, the colonization of other two types of entomopathogenic fungal infective units could also have important impacts on plant resistance. This study contributes to better understanding on the function of B. bassiana as fungal endophytes, which could lead to a new paradigm for how to successfully use these organisms in biological control against plant diseases. [Display omitted] • All three distinct Beauveria bassiana spore types can colonize/establish in plants. • Its blastospores and submerged conidia can germinate/produce hyphae in leaves. • Its aerial conidia, however, cannot produce hyphae inside the leaves. • Endophytic colonization by aerial conidia or blastospores helps plants resist mold. • B. bassiana blastospores confer greater disease resistance than aerial conidia. [ABSTRACT FROM AUTHOR]

This article is a Commentary on Meile et al. (2023), 238: 1562–1577. [ABSTRACT FROM AUTHOR]

The self-association of Toll/interleukin-1 receptor/resistance protein (TIR) domains has been implicated in signaling in plant and animal immunity receptors. Structure-based studies identified different TIR-domain dimerization interfaces required for signaling of the plant nucleotide-binding oligomerization domain-like receptors (NLRs) L6 from flax and disease resistance protein RPS4 from Arabidopsis Here we show that the crystal structure of the TIR domain from the Arabidopsis NLR suppressor of npr1-1, constitutive 1 (SNC1) contains both an L6-like interface involving helices αD and αE (DE interface) and an RPS4-like interface involving helices αA and αE (AE interface). Mutations in either the AE- or DE-interface region disrupt cell-death signaling activity of SNC1, L6, and RPS4 TIR domains and full-length L6 and RPS4. Self-association of L6 and RPS4 TIR domains is affected by mutations in either region, whereas only AE-interface mutations affect SNC1 TIR-domain self-association. We further show two similar interfaces in the crystal structure of the TIR domain from the Arabidopsis NLR recognition of Peronospora parasitica 1 (RPP1). These data demonstrate that both the AE and DE self-association interfaces are simultaneously required for self-association and cell-death signaling in diverse plant NLRs.

Long noncoding RNAs (lncRNAs) participate in a wide range of biological processes, but lncRNAs in plants remain largely unknown; in particular, we lack a systematic identification of plant lncRNAs involved in hormone responses. To explore the molecular mechanism of the response of poplar to salicylic acid (SA), the changes in protective enzymes, which are closely related to plant resistance induced by exogenous SA, were studied, and the expression of mRNA and lncRNA were determined by high-throughput RNA sequencing. The results showed that the activities of phenylalanine ammonia lyase (PAL) and polyphenol oxidase (PPO), in the leaves of Populus × euramericana, were significantly increased by exogenous SA application. High-throughput RNA sequencing showed that 26,366 genes and 5690 lncRNAs were detected under the different treatment conditions: SA and H2O application. Among these, 606 genes and 49 lncRNAs were differentially expressed. According to target prediction, lncRNAs and target genes involved in light response, stress response, plant disease resistance, and growth and development, were differentially expressed in SA-treated leaves. Interaction analysis showed that lncRNA–mRNA interactions, following exogenous SA, were involved in the response of poplar leaves to the external environment. Our study provides a comprehensive view of Populus × euramericana lncRNAs and offers insights into the potential functions and regulatory interactions of SA-responsive lncRNAs, thus forming the foundation for future functional analysis of SA-responsive lncRNAs in Populus × euramericana.

Nucleotide-binding leucine-rich-repeat (NLR) genes comprise the largest family of plant disease-resistance genes. Angiosperm NLR genes are phylogenetically divided into the TNL, CNL, and RNL subclasses. NLR copy numbers and subclass composition vary tremendously across angiosperm genomes. However, the evolutionary associations between genomic NLR content and ecological adaptation, or between NLR content and signal transduction components, are poorly characterized because of limited genome availability. In this study, we established an angiosperm NLR atlas (ANNA, https://biobigdata.nju.edu.cn/ANNA/) that includes NLR genes from over 300 angiosperm genomes. Using ANNA, we revealed that NLR copy numbers differ up to 66-fold among closely related species owing to rapid gene loss and gain. Interestingly, NLR contraction was associated with adaptations to aquatic, parasitic, and carnivorous lifestyles. The convergent NLR reduction in aquatic plants resembles the lack of NLR expansion during the long-term evolution of green algae before the colonization of land. A co-evolutionary pattern between NLR subclasses and plant immune pathway components was also identified, suggesting that immune pathway deficiencies may drive TNL loss. Finally, we identified a conserved TNL lineage that may function independently of the EDS1–SAG101–NRG1 module. Collectively, these findings provide new insights into the evolution of NLR genes in the context of ecological adaptation and genome content variation. Nucleotide-binding leucine-rich-repeat (NLR) genes comprise the largest family of plant disease-resistance genes. An angiosperm NLR atlas (ANNA) was established in this study, which includes more than 90 000 NLR genes from over 300 angiosperm genomes. Analysis of NLR genes in ANNA revealed that NLR gene reduction is associated with ecological specialization and the deletion of signal transduction components. [ABSTRACT FROM AUTHOR]

(1) Corn is the most widely planted food crop, feed crop, and economic crop in the world, and plays an important role in agricultural production and national economy development. The copine gene, also known as the BONZAI gene, encodes a Ca2+-dependent phospholipid membrane binding protein that is widely present in eukaryotes. It has been found that the copine protein is a negative regulator of disease resistance regulation and plays a key role in plants’ disease resistance response. In this study, the Agrobacterium-tumefacien-mediated method was used to successfully obtain T2 generation ZmBON3-gene-overexpressing plants and gene-edited plants. Related phenotypes and molecular identification showed that the disease resistance of overexpression plants was significantly reduced, and the disease resistance of gene-edited plants was significantly increased, which verified that the ZmBON3 gene was a negative regulatory gene. By detecting the physiological indexes related to defense, it was found that the content of H2O2 and the enzyme active water of CAT, POD, SOD, and PAL in ZmBON3-gene-edited plants was higher than those in the control plants and ZmBON3-gene-overexpressing plants, and the content of H2O2 and CAT, POD, and SOD in ZmBON3-gene-overexpressing plants was significantly higher than that in the control plants and ZmBON3-gene-overexpressing plants. The enzyme activity of PAL was the lowest. By detecting the expression of key genes of defense-related signaling pathways, it was found that ZmBON3 may be involved in the related defense processes mediated by the R gene, SA pathway, JA pathway, and ABA pathway. In addition, ZmBON3-geneedited plants showed obvious dwarf phenomenon at the seedling stage, but this did not affect the ear length, axis diameter, ear row number, and grain color.

Horticultural plants, in particular fruit trees, berry crops, and ornamentals, are valuable objects for studying their genetic and biochemical properties. Along with traditional methods of studying these plants, modern molecular genetic technologies are emerging, in particular genome editing using CRISPR/Cas9 nucleases. In this review, we have analyzed modern advances in genome editing of horticultural plants. To date, it has become possible to improve many plant characteristics using this technology, e.g., making plants resistant to biotic and abiotic stress factors, changing the time of flowering and fruit ripening, changing the growth characteristics of plants, as well as the taste properties of their fruits. CRISPR/Cas9 genome editing has been successfully carried out for many horticultural plants. Dozens of genes from these plants have been modified by means of genome editing technology. We have considered the main ways of delivering genetic constructs to plants as well as limitations that complicate the editing of target genes. The article reviews the prospects of using genome editing to improve the valuable properties of plants important to humans.

TIR (Toll/interleukin-1 receptor/resistance protein) domains are cytoplasmic domains widely found in animals and plants, where they are essential components of the innate immune system. A key feature of TIR-domain function in signaling is weak and transient self-association and association with other TIR domains. An additional new role of TIR domains as catalytic enzymes has been established with the recent discovery of NAD+-nucleosidase activity by several TIR domains, mostly involved in cell-death pathways. Although self-association of TIR domains is necessary in both cases, the functional specificity of TIR domains is related in part to the nature of the TIR : TIR interactions in the respective signalosomes. Here, we review the well-studied TIR domain-containing proteins involved in eukaryotic immunity, focusing on the structures, interactions and their corresponding functional roles. Structurally, the signalosomes fall into two separate groups, the scaffold and enzyme TIR-domain assemblies, both of which feature open-ended complexes with two strands of TIR domains, but differ in the orientation of the two strands. We compare and contrast how TIR domains assemble and signal through distinct scaffolding and enzymatic roles, ultimately leading to distinct cellular innate-immunity and cell-death outcomes. [ABSTRACT FROM AUTHOR]

Plants employ sensor-helper pairs of NLR immune receptors to recognize pathogen effectors and activate immune responses. Yet, the subcellular localization of NLRs pre- and postactivation during pathogen infection remains poorly understood. Here, we show that NRC4, from the "NRC" solanaceous helper NLR family, undergoes dynamic changes in subcellular localization by shuttling to and fromthe plant-pathogen haustorium interface established during infection by the Irish potato famine pathogen Phytophthora infestans. Specifically, prior to activation, NRC4 accumulates at the extrahaustorial membrane (EHM), presumably to mediate response to perihaustorial effectors that are recognized by NRC4-dependent sensor NLRs. However, not all NLRs accumulate at the EHM, as the closely related helper NRC2 and the distantly related ZAR1 did not accumulate at the EHM. NRC4 required an intact N-terminal coiled-coil domain to accumulate at the EHM, whereas the functionally conserved MADA motif implicated in cell death activation and membrane insertion was dispensable for this process. Strikingly, a constitutively autoactive NRC4 mutant did not accumulate at the EHM and showed punctate distribution that mainly associated with the plasmamembrane, suggesting that postactivation, NRC4may undergo a conformation switch to formclusters that do not preferentially associate with the EHM. When NRC4 is activated by a sensor NLR during infection, however, NRC4 forms puncta mainly at the EHM and, to a lesser extent, at the plasma membrane. We conclude that following activation at the EHM, NRC4 may spread to other cellular membranes from its primary site of activation to trigger immune responses. [ABSTRACT FROM AUTHOR]

Nucleotide-binding leucine-rich repeat receptors (NLRs) are the largest class of immune receptors in plants. They play a key role in the plant surveillance system by monitoring pathogen effectors that are delivered into the plant cell. Recent structural biology and biochemical analyses have uncovered how NLRs are activated to form oligomeric resistosomes upon the recognition of pathogen effectors. In the resistosome, the signaling domain of the NLR is brought to the center of a ringed structure to initiate immune signaling and regulated cell death (RCD). The N terminus of the coiled-coil (CC) domain of the NLR protein HOPZ-ACTIVATED RESISTANCE 1 likely forms a pore in the plasma membrane to trigger RCD in a way analogous to animal pore-forming proteins that trigger necroptosis or pyroptosis. NLRs that carry TOLL-INTERLEUKIN1-RECEPTOR as a signaling domain may also employ pore-forming resistosomes for RCD execution. In addition, increasing evidence supports intimate connections between NLRs and surface receptors in immune signaling. These new findings are rapidly advancing our understanding of the plant immune system. [ABSTRACT FROM AUTHOR]