Plant diseases can cause severe damages to agricultural production. Timely and accurate identification of plant diseases is the basis and prerequisite for effective disease management. With the rapid development of information technology, the research and applications of plant disease identification by using image processing technology are increasing, which improves the levels of the monitoring and management of plant diseases and provides powerful supports for ensuring agricultural safety production. In this comprehensive review, the problems and challenges in the research and applications of plant disease image recognition were systematically discussed from the aspects of plant disease image recognition, disease image acquisition, disease image preprocessing, disease image segmentation, disease image feature extraction, disease image feature selection, disease image recognition models, and their practical applications. Simultaneously, the relevant solutions were proposed. Furthermore, the research and applications of plant disease image recognition in the future were prospected from the aspects including acquisition and management of plant disease images, key techniques for plant disease image recognition, and multi-platform plant disease image recognition. The aim of this review is to provide references for the research and applications of plant disease image recognition and to promote the development of plant protection informatization and smart phytoprotection.

Potato common scab is caused by Streptomyces spp. Potato common scab disease is widely distributed in potato producing areas of the world. For many years, common scab has hampered the potato industry, especially the developing of seed potatoes industry. In this paper, the occurrence of common scab, pathogen distribution, disease detection, pathogenic mechanism, cultivar resistance research and green prevention and control technology were reviewed, and the urgent problems in potato common scab research were put forward in order to provide new ideas for in-depth research and green prevention and control of potato common scab.

To clarify the pathogen species and isolation frequency inside and outside of soybean seeds in Inner Mongolia, and to make clear whether soybean seeds carry quarantine pathogen Phytophthora sojae, a total of 218 isolates were obtained from the inside of seeds and 196 isolates were obtained from the outside of seeds using washing assay and medial culture method, respectively. P. sojae was not isolated from the soybean seeds tested. Combined with colony morphology observation and ITS-rDNA sequence analysis, the above isolates were preliminarily identified. The internal isolates of seeds belonged to 16 genera, and the external isolates of seeds belonged to 17 genera. In combination with literature reports, 24 candidate fungal strains belonging to 9 genera were selected and tested for virulence, it showed that they all could cause lesions on etiolated soybean seedlings. Finally, the tested soybean seeds were confirmed to be free of P. sojae by specific primer amplification. These results provide an important reference for the scientific control of soybean diseases caused by seed borne pathogens.

To identify the pathogens causing root rot on Lonicera japonica, we collected diseased root samples and conducted microbe isolation. The causal agents of the disease were identified as Fusarium solani and Fusarium incarnatum through pathogenicity test, and based on morphological characteristics and phylogenetic analysis results, and combined infection by these two species of fungi led to more severe symptoms. The optimal tempera-ture for mycelial growth of the two pathogens is 28 ℃, and the growth was suppressed when the temperature was lower than 4 ℃ and above 50 ℃; The optimal temperature for spore germination of F. incarnatum is 28 ℃, and 25-28℃ for F. solani; The two pathogens are insensitive to pH and can grow at pH 5-11; A light/dark cycle of 12 h light/12 h dark is suitable for mycelial growth of F. incarnatum, while total darkness is suitable for F. solani; The lethal temperatures for mycelial growth of F. incarnatum and F. solani are 50 ℃ and 55 ℃ for 10 min respectively, and are 50 ℃ for 10 min for spore germination of both the pathogens; The most suitable carbon source for both fungal pathogens is pectin, and the most suitable nitrogen source is tryptone for F. incarnatum but peptone for F. solani. In addition, the utilization efficiency of F. incarnatum is low to the other tested nitrogen sources, whereas F. solani showed a broad-spectrum adaptability to carbon and nitrogen sources. To explore biocontrol agents against F. incarnatum and F. solani, bacterial strains were isolated from rhizosphere soil of healthy L. japonica. By confronting incubation test, enzyme activity test and pot experiment in greenhouse, two strains BG1 and BS37, which showed good performance in promoting the growth of L. japonica and controlling root rot, were obtained. BG1 and BS37 were identified as Paenibacillus polymyxa and Bacillus subtilis, with a control efficacy of 59.41% and 52.47%, respectively. The results provide good potential biocontrol resources for the control of L. japonica root rot.

Diseases caused by oomycetes pose a substantial risk to agricultural production, establishing this pathogen as a principal research and control focus within agroforestry. To explore the status quo and future direction of the field of oomycetes, we used the Web of Science as our data source and conducted a bibliometric analysis of oomycete-related literature from 1985 to 2023. Additionally, CiteSpace was employed to create a knowledge graph, providing a visual representation of the findings. The publication volume analysis indicates a predominant research presence in countries such as the United States, China and Germany. Notably, China has demonstrated remarkable growth over the last five years, ascending to global prominence in this field by 2022. In terms of institutional contributions, the US Department of Agriculture, Nanjing Agricultural University, and the University of California system emerge as leading entities, both in publication volume and the impactful nature of their research. The hotspot analysis delineates that the field predominantly investigates ten specific types, including the Pythium spp., Phytophthora infestans, Ph. capsici and so on. Key research themes include systemic acquired resistance, climate change impact, and antibacterial activities. Furthermore, cluster analysis of literature co-citation unveils several evolving significant research directions within the oomycete fields, represented by RXLR effectors, convergent evolution, and virulence factors. Moreover, a detailed examination of highly cited literature underscores the raising interest in factor pathogenic mechanisms of effector, prevention and control of disease, biological control and immune signal regulation . These works are beneficial for new researchers of oomycetes to quickly understand the current research status and cutting-edge hotspots in this field, and provide some reference for predicting potential research directions of oomycetes.

In order to clarify the the population structure types, pathogenicity and the potential risks to different crops of Verticillium wilt of watermelon, the physiological type, physiological races, mating types and pathogenicity differentiation of Verticillium dahliae from watermelon were measured and the pathogenicity of 20 strains was studied by using root-drenching method. At the same time, the pathogenicity to watermelon of V. dahliae from six crops and the pathogenicity to four crops of V. dahliae from watermelon were determined. The results showed that all the 20 strains were identified as nondefoliated stains, physiological race 2 and MAT1-2-1 mating type. There were significant differences in the pathogenicity among the tested strains, the AUDPC values were from 238.92 to 606.81, the AUDPC values of WM05 and WM14 strains were 606.81 and 514.72, respectively, which were significantly higher than those of the other 18 strains. The pathogenicity of WM05 and WM14 strains was relatively strong. However, the AUDPC values of WM01, WM20, WM24 and WM19 strains were only 238.92, 249.15, 256.11 and 257.45, which showed relatively weak pathogenicity. V. dahliae from cotton, eggplant, potato, sunflower, tomato and honeysuckle could infect watermelon, and there were significant differences in pathogenicity. V. dahliae from watermelon could infect cotton, eggplant, potato and sunflower. The pathogenicity was the strongest on eggplant and was the weakest on cotton, and was comparable to that of watermelon on potato and sunflower.

Potato Early Blight (PEB) is an important disease of the foliage of potatoes during the growing season and is widespread in all major potato producing areas worldwide. At present, there are no specific agents and potato varieties resistant to the disease completely. In this study, we identified the main cultivar ‘Cooperation-88’ (C88) in Yunnan Province was resistant to the potato early blight caused by Alternaria solani inoculated on leaves in comparison with the susceptible variety ‘Désirée’ by AUDPC. High-throughput RNA-seq in ‘Cooperation-88’ after infection at the early (A. so_e, 0-72 h), middle (A. so_m, 73-120 h) and late (A. so_l, >120 h) stages was performed on Illumina HiSeq PE150 platform. Transcriptome analysis revealed a total of 13 083 genes expressed differentially at A. so_e, of which 7 438 were up-regulated and 5 645 were down-regulated. At A. so_m, a total of 12 121 genes was differentially expressed, of which 3 299 were up-regulated and 8 822 were down-regulated. At A. so_l, a total of 10 530 genes was differentially expressed, of which 1 686 were up-regulated and 8 844 were down-regulated. A set of 2 720 identical genes was found in all the three periods, while 4 997 genes specific to A. so_e, 3 975 genes specific to A. so_m and 3 230 genes specific to A. so_l. Based on gene ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and qRT-PCR validation along with the results of electron microscopic observations, it was speculated that the increased synthesis of pectin lyase and cellulose synthetase was involved in cell wall remodeling of ‘C88’ in the early stage of A. solani infection. The expression levels of glutathione S-transferase and cytochrome P450 were significantly up-regulated in ‘C88’ at mid-infestation, which were involved in the detoxification pathway. Late synthesis of large amounts of antioxidants to stimulate defence mechanisms. In the three periods, high expression levels of transcription factors, such as bHLH, ZIP, MYB, ERF, etc, associated with disease resistance and extensive involvement in the ubiquitination pathway. Overall, our findings could provide a theoretical basis for research on the early blight resistance in potato and accelerate the resistance breeding.

Utilizing disease resistance genes, particularly those encoding NLR (Nucleotide-binding, leucine-rich repeat receptor) proteins, offers the most cost-effective strategy for crop disease management. These genes have become a major research focus in plant pathology due to their frequent identification and broad application potential in breeding disease-resistant crops. Key advances in NLR research include: 1) the efficient cloning of NLR genes and their corresponding pathogen avirulence (Avr) genes; 2) mechanistic insights into NLR activation pathways, such as resistosome-mediated calcium signaling and TNL (TIR-NB-LRR)-dependent production of NAD⁺-derived signaling molecules; and 3) innovative applications in molecular engineering, including chimeric protein engineering, cross-species resistance transfer, and co-transfer of helper NLRs. This review summarizes these advances and highlights future research directions by integrating high-throughput sequencing, artificial intelligence-based structural prediction, and gene editing to decode calcium signaling mechanisms and immune homeostasis regulation in NLR networks, thereby facilitating the development of durable and broad-spectrum disease-resistant crop varieties.

Viruses in the genus Polerovirus of the family Solemoviridae exhibit a broad host range and can infect plants from many families, including Fabaceae, Solanaceae, Cucurbitaceae, Brassicaceae and others. They are responsible for significant economic losses globally and frequently co-infect with umbraviruses, which are members of the family Tombusviridae, leading to severe plant diseases. In order to explore the occurrence and distribution of poleroviruses in Yunnan, along with the potential outbreak risk associated with co-infection involving umbraviruses, a comprehensive disease survey was conducted in commercial crops including vegetables and fruits, as well as in the weeds surrounding these crops in Yunnan. Additionally, virus species were also detected and identified by RT-PCR. A total of 669 samples of 5 families, comprising 25 species of commercial crops and surrounding weeds, including vegetables, tobacco, potatoes, passion fruit and others, were collected from 7 states and cities in Yunnan Province, including Kunming, Yuxi, Baoshan, Dali, Chuxiong, Xishuangbanna and Honghe. Among the 11 commercial crops, 6 species of poleroviruses were found, which were the species potato leafroll virus, the species cucurbit aphid-borne yellows virus, the species suakwa aphid-borne yellows virus, the species pepper vein yellows virus 1, the species pepper vein yellows virus 3, and the species brassica yellows virus, respectively. Among them, PeVYV-3 had the highest average detection rate of 6.73% and was the dominant virus species in vegetables and fruits in Yunnan province. It was the first report in domestic and abroad that BrYV infected pea, PeVYV-3 infected eggplant, PeVYV-1 infected pea and broad bean, CABYV infected tobacco and pea. Moreover, the occurrence of SABYV in Yunnan Province was first reported. The host range of poleroviruses is gradually expanding, especially in various parts of Yunnan, indicating that the harm of poleroviruses to crops is gradually increasing. In addition, there is a risk of disease outbreaks with umbravirus co-infection. The research results contribute to a deeper understanding of the main types, distribution, and occurrence trends of poleroviruses in Yunnan, providing reference for comprehensive prevention and control of plant diseases caused by poleroviruses and their combined infection with umbraviruses.

Leucine-rich repeat receptor-like protein kinases (LRR-RLKs), a typical type of receptor-like kinase in plant, play important roles in response to pathogen infection. To clarify basic characteristics of the LRR-RLK family members in foxtail millet and their roles in resistance to infection by Sclerospora graminicola, members of this gene family in foxtail millet were identified, and their evolutionary pattern, sequence characteristics, gene structure, promoter sequence and expression pattern were analyzed by bioinformatics method. Meanwhile, the transcriptome data of resistant and susceptible foxtail millet varieties infected with S. graminicola were obtained at 3 different growth stages, and the co-expression modules of resistance gene and the core genes were identified via the weighted gene co-expression network analysis (WGCNA). The results showed that the LRR-RLK genes were distributed on overall 9 chromosomes of foxtail millet. A phylogenetic analysis was conducted on LRR-RLK genes from foxtail millet and Arabidopsis, and the result indicated that they were mainly divided into 4 categories. Structural analysis displayed that their kinase domains were relatively conservative. The promoter regions of these LRR-RLK genes contained multiple cis-acting elements related to defense and stress responses as well as meristem expression, indicating their involvement in multiple biological processes. A co-expression network of resistance-related genes was developed by using WGCNA. Of 44 gene co-expression modules that were identified, 3 (Turquoise, Blue and Yellow) were specific modules associated with resistance to S. graminicola, from which 12 core genes were identified. Functional annotation showed that these genes were involved in plant disease resistance. Further RT-qPCR analysis of the 6 core genes (Seita.9G413000, Seita.9G296000, Seita.9G557200, Seita.9G493600, Seita.3G241700 and Seita.9G163200) confirmed that they were induced in response to S. graminicola infection, indicating that these core genes may play important roles in resistance to the pathogen infection. The results provide a valuable reference for further revealing the molecular mechanism underlying the resistance of foxtail millet to S. graminicola.

Fusarium crown rot, mainly caused by Fusarium pseudograminearum, is a destructive disease in wheat production. To establish a rapid and reliable detection method for F. peasudeograminearum, the specific PCR primer pair (Fpg-F1/R2) was designed based on the RPB sequence, and real-time fluorescence quantitative PCR (qPCR) was used to validate the efficiency of the primer. The results showed that the primer pair had high specificity and sensitivity of 100 pg of DNA. Furthermore, the qPCR system for early and rapid detection of F. peasudeograminearum had an amplification efficiency of 87.5% and correlation coefficient of 0.99, and the pathologic threshold of F. pseudograminearum in soil was determined by using this detection system. It was found that F. pseudograminearum could cause Fusarium crown rot when the DNA concentration of F. pseudograminearum in field soil exceeded 213 pg·g-1. Hence, the qPCR-based method we developed for F. pseudograminearum detection has the advantages of high specificity and sensitivity, and can be used for rapid and early detection of F. pseudograminearum even in field soils.

Rhodococcus fascians is a gram-positive actinomycete that can cause plant diseases with a very wide host range. The pathogenic strains of Rhodococcus fascians make abnormal plant tissues form, such as leaf gall, cluster, flat stem, which affects plant growth and causes serious economic losses. As the identification and classification of the genus Rhodococcus were complex and is often confused with other plant diseases with similar symptoms, resulting in few studies being carried out. This review outlines the classification status, biological characteristics, pathogenic mechanisms, disease symptoms, isolation and identification methods, transmission routes of infection and prevention and control measures of R. fascians. It is expected to provide a reference for related research and precise prevention and control of leafy gall disease caused by R. fascians.

Viral diseases in cucumber in Qudi are more and more serious in recent years. To detect and identify the main viruses, the plant samples of cucumber were collected from Qudi town, Jiyang district, and next-gene-ration sequencing technology (NGS), RT-PCR amplification and analysis of viral genome sequences were carried out. The results showed that the viruses infecting cucumber in the spring were cucumber green mottle mosaic virus (CGMMV) and watermelon silver mottle virus (WSMoV). Besides CGMMV and WSMoV, cucumber plants in the autumn were also infected with zucchini yellow mosaic virus (ZYMV). The detection rates of CGMMV, WSMoV and ZYMV by RT-PCR were 68.2%, 45.5% and 50.0%, respectively, and the detection rate of complex infection was 50%. Genetic sequence analysis revealed that the coat protein (CP) gene sequence of CGMMV [JY2-6 (GenBank accession number: OR591512) isolated in this study was similar to the sequence of CGMMV [SDRZ (GenBank accession number: KX185151)] isolated from cucumber in Rizhao, and the identity was 100%. The nucleocapsid (N) gene sequence of WSMoV [JY2-4 (GenBank accession number: OR591517) isolated in this study was similar to the sequence of WSMoV [W6412 (GenBank accession number: AM113765)] isolated from watermelon in Thailand, and the identity was 99.1%. The CP gene sequence of ZYMV [JY2-7 (GenBank accession number: OR591522) isolated in this study was similar to the sequence of ZYMV [Yaz.Ashk.S.Z (GenBank accession number: KX495623)] isolated from cucumber in Iran, and the identity was 97%. This study demonstrated that the cucumber in Qudi was mainly infected by CGMMV, WSMoV and ZYMV, and complex infection was also common. This study provided a basis for virus prevention of cucumber in Qudi.

In recent years, apple diaporthe neck and root rot has become one of the most important limiting factors for the development of apple production in Yunnan Province. In this study, the typical disease samples were collected and the fungal isolate M2g7-1 was obtained by tissue separation approach. The purified culture M2g7-1 was preliminary determined belonging to Diaporthe spp. based on the morphological features of colony, pycnidia, cirrus, two forms of conidia. The pathogenicity of M2g7-1 was further validated on apple young branches to fulfill the Koch's law. The taxonomic of pathogen M2g7-1 has been further determined with combining molecular phylogenetics. The phylogenetic tree was created with the data set of sequences from the internal transcribed spacer (ITS) of ribosomal DNA, the histone H3 (HIS) gene, the translation elongation factor 1-alpha (TEF) gene, and the beta-tubulin (TUB) gene. Based on morphological and molecular biology analysis, the pathogen M2g7-1 was finally identified as Diaporthe eres. This is the first report of D. eres as the pathogen of apple diaporthe neck and root rot. The research results provide a theoretical basis for the epidemic research and comprehensive control of this disease.

Fusarium sacchari is one of the major pathogenic fungus that cause sugarcane pokkah boeng. In order to explore the function of metalloproteinase effector proteins in F. sacchari, we used the genomic data of F. sacchari to predict the secretory metalloproteinase proteins, and successfully amplified a zinc-type metalloproteinase effector protein gene Fs03538. The results showed that Fs03538 contained a typical ZnMc super family domain, and the 1-18 amino acid sequences at the N-terminal of the protein contain specific signal sequences. Subcellular localization showed that Fs03538 could be localized in the nucleus of Nicotiana benthamiana; qRT-PCR analysis showed that the expression level of Fs03538 was induced and reached the highest peak at 12 h post F. sacchari infection. Agrobacterium tumefaciens mediated transient expression system confirmed that Fs03538 could inhibit the necrosis of tobacco cells induced by mouse Bcl-2-associated X protein (BAX). As compared with the wild type F. sacchari strain CNO-1, the Fs03538 knock-out mutant showed no significant difference on mycelial growth and conidia production, but the pathogenicity on sugarcane was significantly decreased. Taken together, the results of the study suggest that Fs03538 is an important virulence factor of F. sacchari, which highly expressed at the time of infection and could inhibit the host immune responses by entering the host cell nucleus.

To identify the pathogen causing anthracnose disease on quinoa plants and investigate its biological characteristics, we collected diseased quinoa plants with typical anthracnose symptoms and conducted pathogen isolation and purification experiments. A representative strain LMTJ was obtained and determined as the pathogen of quinoa anthracnose by completing Koch′s postulates. Combined with morphological characteristics and the result of multi-gene phylogenetic analyses (ACT, CHS-1, GAPDH, ITS and TUB2), the pathogen was identified as Colletotrichum spinaciae. The suitable culture condition for mycelial growth of C. spinaciae LMTJ strain is that with starch as carbon source, peptone as nitrogen source, temperature at 20~25 ℃ and pH value of 6.0~7.0, while for sporulation is with sucrose as carbon source, sodium nitrate as nitrogen source, temperature at 20~25 ℃ and pH value of 6.0. To screen effective fungicides for the prevention and control of quinoa anthracnose, the toxicity of 5 fungicides to C. spinaciae LMTJ strain was tested. The results showed that all the tested fungicides could inhibit mycelial growth of LMTJ, of which 92.8% iprodione exhibited the strongest inhibitory effect, with EC₅₀ of 2.7654 mg·L^-1. The results provide scientific basis for the diagnosis and control of quinoa anthracnose.

In this study, the fungal strain LD-11 was isolated from the infected plant of Lonicera caerulea (cv Lanjingling) collected in the horticulture experimental station of Northeast Agricultural University, Harbin, Heilongjiang Province. The strain was identified as Epicoccum nigrum by morphology, rDNA-ITS, LSU, TUB, RPB2 gene sequence amplification and phylogenetic tree construction. The experimental results showed that E. nigrum LD-11 could grow on PDA, OA and MEA medium. The optimal culture medium was OA, and the optimal culture conditions were growth temperature of 25 ℃, pH 6, carbon source is starch and nitrogen source is yeast extract, and full light conditions were conducive to mycelial growth. This study is the first time to isolate and identify E. nigrum, the pathogen of leaf spot disease in L. caerulea, which will provide an important source of pathogenic fungi for future research on control of plant disease.

Peach shoot blight caused by Diaporthe amygdali (anamorph Phomosis amygdali) is a significant fungal disease in major peach-producing regions of southern China, which has severely hindered the development of peach industry and resulted in substantial economic losses for peach farmers. This paper presents a comprehensive review on its historical occurrence, distribution, damage, as well as biological characteristics of the causing pathogen, pathogen detection, disease cycle, and integrated prevention and control strategies for the disease. Furthermore, potential issues are analyzed and directions for future research are proposed. The review provides a reference for further studies on peach shoot blight.

The occurrence of Fusarium crown rot (FCR) caused by Fusarium pseudograminearum has been becoming increasingly serious in China, which has posed a severe threat to wheat yield and quality. The SEY1 belongs to the RHD3 (Root Hair Defective 3) family and encodes a dynamin-like GTPase protein participating in endoplasmic reticulum (ER) fusion. The ER is involved in the synthesis of deoxynivalenol (DON) in different pathogenic fungi, while its function in F. pseudograminearum has not been reported. In this study, subcellular localization of GFP-tagged Sey1 (FpSey1) protein in F. pseudograminearum was observed, and the results showed that FpSey1 was localized in the ER. The FpSEY1 deletion mutant (ΔFpSey1) was generated through PEG-mediated protoplast transformation and verified by Southern blot analysis, and complemented strains were obtained as well. Compared with the wild-type strain, the ΔFpSey1 mutant exhibited significant reduction in vegetative growth, conidiation, relative expression of DON biosynthesis related genes (TRI1, TRI5, TRI10) , and the virulence on wheat coleoptiles and barley leaves. In addition, the ΔFpSey1 mutant is more sensitive to salt stress, hydrogen peroxide (H₂O₂), but more tolerant to dithiothreitol (DTT) than the wild-type and complemented strains. These results indicate that FpSey1 localized in the ER plays important roles in the growth and infection of F. pseudograminearum.

Purpureocillium lilacinum exhibits excellent biocontrol potential against various plant pathogenic nematodes. However, its field application is currently limited to conventional methods, such as root irrigation, broadcasting, and hole application, highlighting an urgent need to develop more efficient delivery systems. This study evaluated the compatibility of P. lilacinum strain 36-1 with 10 commercial water-soluble fertilizers (WSFs) through in vitro plate assays, pot experiments, and field trials, by examining fungal growth rate, conidiation capacity, spore viability, root colonization efficiency, and biocontrol efficacy against tomato root-knot nematode disease in an integrated water-fertilizer-biocontrol agent system. The results demonstrated that the four WSFs (Stanley, Lai Lv Shi, Alfam, and Miracle-Gro) exhibited relatively good compatibility with strain 36-1 within their commercially recommended concentration ranges. When these four WSFs were individually mixed with the fermentation filtrate of strain 36-1, they all enhanced the conidial survival rate and egg parasitism rate on Meloidogyne incognita of strain 36-1, without compromising its nematicidal activity. In tomato fields where root-knot nematode disease was severe (induced by artificial inoculation of M. incognita), the combined application of P. lilacinum strain 36-1 with Miracle-Gro (2.5 g·L^-1) or Lai Lv Shi (0.5 g·L^-1) under the integrated water-fertilizer-biocontrol agent system achieved control efficacies of 39.41% and 37.47% against root-knot nematodes, respectively. Although these values showed no significant difference (P<0.05) compared with the control efficacy of strain 36-1 applied alone, the tomato yield was increased by 34.64% and 28.44%, respectively. Therefore, integrating P. lilacinum into water-fertilizer systems can establish a simplified, eco-friendly water-fertilizer-biocontrol agent system to control crop nematode diseases.

Bacteria from the genus of Pectobacterium are the important plant pathogens causing significant economic losses worldwide, and the emergence of antibiotic-resistant strains further exacerbates the challenges in Pectobacterium-caused disease prevention and control.This study used Pectobacteriums isolated from different host plants as materials and used plate analysis to obtain streptomycin-resistant strains formed in the wild. Clarify its taxonomic status through genome sequencing and comparative genome research, and streptomycin resistance genes were predicted. The results shown that among the eight strains isolated from different hosts, NJAU2 obtained from Yunnan yellow-flowered calla lily disease strains is highly resistant to streptomycin. NJAU2 genome was 5 062 459 bp in length, with G+C content of 51.83% and N50 length of 306 378 bp, containing 4 568 protein-coding genes. NJAU2 clusters on the same branch as the type strain P. aroidearum SCRI 109^T and the reported strain P. aroidearum PC1 based on the Multi-Locus Sequence Analysis results of 8 housekeeping genes (fliA, fusA, glyA, gyrB, purA, rpoA, rpoS, secY). This result is consistent with the phylogenetic relationship constructed based on the 16S rRNA gene sequence. Furthermore, the Average Nucleotide Identity (ANI) and DNA-DNA Hybridization (isDDH) analysis with various Pectobacterium strains also support this classification. Therefore, the naturally occurring streptomycin-resistant strain NJAU2 is classified as a new species within the Pectobacterium genus: Pectobacterium aroidearum, and named Pectobacterium aroidearum NJAU2. P. aroidearum NJAU2 carrying sets of genes encoding proteins for streptomycin-resistanc in its genome. Comparison with the Comprehensive Antibiotic Resistance Database (CARD) identified 328 genes belonging seven types of drug resistance mechanisms. Moreover, in NJAU2 genome, 15 genes were annotated encoding aminoglycoside antibiotic resistance, including rpsL and gidB that are related to streptomycin resistance. The discovery of P. aroidearum NJAU2 provides new material for research in the direction of streptomycin resistance in Pectobacterium spp..

Meloidogyne enterolobii, which is highly pathogenic to a wide range of host plants and spreads rapidly, can cause devastating damage to many crops. To deeply analyze the pathogenic mechanism of this nematode, here we take T106, a gene specifically induced in tomato roots in response to M. enterolobii infection based on previous transcriptome data, as our target. We silenced T106 in tomato plants via TRV virus-induced gene silencing technology, and then inoculated tomato seedlings with M. enterolobii to observe the difference in nematode and giant cell development in root system between T106-silenced and T106-unsilenced plants. The results showed that the silencing vector we constructed could effectively silence T106 gene in tomato plants, with a silencing efficiency of 85%; compared with T106-unsilenced control plants, there was no significant decrease in the percentage of root knots in T106-silenced plants, but the development of M. enterolobii in root knots was inhibited, and the number of eggs produced by M. enterolobii was reduced by 79.3%; meanwhile, the area occupied by giant cells was also decreased. In summary, T106 might be a susceptible gene targeted by M. enterolobii. Exploration of such susceptible genes in plants is vital for finding new ways to control root-knot nematodes including M. enterolobii.

Rice is an important grain crop in the world. Although some genes that confer resistance to rice blast and bacterial blight, two important diseases threatening rice production, have been identified in rice plants, the corresponding resistance gene resources remain scarce. In this study, we found that the transcription factor OsEIL4 is involved in regulating rice resistance to these two rice diseases. Quantitative real-time PCR (qPCR) assays showed that the expression of OsEIL4 was markedly induced upon Magnaporthe oryzae (M. oryzae) or Xanthomonas oryzae pv. oryzae (Xoo) infection. Moreover, compared with wild-type rice plants, Oseil4 (CRISPR/Cas9-based OsEIL4 knockout) and OsEIL4-RNAi rice lines were more susceptible, while OsEIL4-OX (overexpression) plants were more resistant to M. oryzae and Xoo. Further qPCR analysis of the transcript levels of the marker genes of ethylene pathway and defense-related genes OsPR1a and OsPR5 exhibited that they were downregulated in Oseil4 lines but upregulated in OsEIL4-OX lines, suggesting that OsEIL4, which functions as a positive regulator in ethylene pathway, mediates rice resistance by modulating PR genes expression. Subcellular localization and yeast-one-hybrid assay results confirmed that OsEIL4 has transcriptional activity, indicating that it may regulate rice disease resistance by exercising transcriptional regulatory function. This study explores a gene resource with broad-spectrum resistance, providing a new possibility for molecular breeding of rice disease resistance.

In order to investigate the occurrence and population genetic structure of tobacco vein banding mosaic virus on tobacco in Xingyi City, Guizhou Qianxinan Prefecture, and understand the genetic variation mechanism of tobacco vein banding mosaic viruses on tobacco isolates in Guizhou, Detection and identification of tobacco samples with typical TVBMV symptoms collected from Xingyi City, Qianxinan Prefecture, Guizhou Province were performed using electron microscopy negative staining, ultra-thin section preparation observation and molecular biology methods. Phylogenetic analysis and population genetic structure analysis of Guizhou tobacco samples was based on CP gene sequence of virus isolates using bioinformatics software. The results showed that among the 22 tobacco samples collected, the detection rate of TVBMV was 13.64%. The consistencies of nucleotide and amino acid sequences between the obtained TVBMV Guizhou tobacco isolate and the other 42 isolates published in GenBank were 94.1%-99.6% and 93.4%-100%, respectively. Phylogenetic analysis based on the amino acid sequence of the CP gene divides the isolates into four groups corresponding to the geographical distribution. The clustering results have obvious geographical distribution characteristics. Genetic diversity analysis shows that each group of TVBMV isolates exhibits a high level of genetic diversity due to the influence of geographical distribution. The analysis of population genetic structure shows that negative selection, genetic drift and ecological environment are the important effoectors for the genetic variation of TVBMV population. The research results provide theoretical support for the prevention and control of tobacco virus diseases and disease resistance breeding in Guizhou.

Anthracnose is a common worldwide fungal disease in soybean production, seriously affecting the commercial value of soybean pods as well as seed yield and vigour. In this study, four fungal strains (XZ-1-XZ-4) were isolated from the stalk of a diseased soybean plant within soybean-producing regions of Xuzhou City, Jiangsu Province, using tissue isolation and single spore purification methods. According to morphological chara-cteristics and ITS-TUB2-based phylogenetic analysis results, XZ-1 and XZ-2 were identified as Colletotrichum truncatum, XZ-3 and XZ-4 were identified as Fusarium proliferatum and Fusarium equiseti, respectively. Pathogenicity test results showed that all the four fungi were pathogenic, indicating a complex infection of soybean plants by Colletotrichum and Fusarium phytopathogens in the field. Furthermore, the resistance of 56 soybean varieties/lines to C. truncatum strain XZ-1 was evaluated by using two different inoculation methods (i.e., inoculation of fresh soybean pod with mycelial suspension, inoculation of etiolated hypocotyl with mycelial plug). It was showed that disease indexes obtained by the two inoculation methods were slightly different, but the resistance grades were almost the same, with a match rate of 92.9%. Of these 56 soybean varieties/lines tested, 3 were identified as resistant and 19 moderately resistant; No highly resistant varieties were found, and only 39.3% of the varieties were resistant to soybean anthracnose. This study combines the results of the above two inoculation methods to rapidly and accurately identify the resistance level of soybean varieties (lines) to anthracnose, laying a foundation for screening and utilizing resistant soybean germplasms, and for identifying anthracnose-resistant genes in soybean.

Fusarium solani, known for its extensive host range, is the causal agent of the destructive root rot disease in agriculture production. Secreted proteins play important roles in the infection of host plants by phytopathogenic fungi. To identify the secreted proteins and effectors in F. solani, we performed an in-depth analysis of the F. solani genome in this study. Among the total 17654 genomic proteins, 1032 proteins were predicted to be the candidate secreted proteins by using SignalP, TMHMM, WoLF PSORT and PredGPI softwares, accounting for 5.85% of the total proteins in F. solani. Among them, 258 proteins were predicated to be carbohydrate-active enzymes (CAZymes) by using the dbCAN3 software, with the glycoside hydrolase family being the most abundant. Furthermore, 185 secreted proteins were predicated to be candidate effectors, with 183 sequences being annotated in the PHI database. By employing a virus-based transient expression system, we investigated the effect of the 5 candidate effectors annotated for increased virulence on BAX-triggered programmed cell death, and the result showed that the two effectors (XP_046140852.1 and XP_046131041.1) could suppress BAX-triggered programmed cell death in N. benthamiana. These findings provide not only an important reference for further analysis of the pathogenic molecular mechanism of F. solani but also a theoretical basis for understanding the interactions between F. solani and host plants.

Tomato brown rugose fruit virus (ToBRFV) has been spreading rapidly in tomato-producing areas around the world in recent years, causing severe economic losses. Symptoms of suspected ToBRFV infection appeared on tomatoes in Jianshui, Yunnan Province, and caused harm to the surrounding tomato production areas. In this study, the tomato samples suspected of being infected with ToBRFV in the Yunnan Jianshui field were identified by electron microscopy and RT-PCR. RT-PCR amplified the whole genome sequence of the virus, and the phylogenetic tree was constructed to analyze the evolutionary relationship of the viruses. The results showed that the rod-shaped virions, about 18 nm × 300 nm, with the typical structural characteristics of Tobamovirus, were found in the diseased tomato fruits.The target segment of 591 bp was amplified by RT-PCR using ToBRFV-specific detection primers.The Blast result in NCBI showed that this segment shared the highest identity (more than 99.00%) with the ToBRFV. We named this ToBRFV isolate as ToBRFV-2022-JS (GenBank accession number:OR593752). Sequencing result revealed that the complete sequence of ToBRFV-2022-JS was 6 386 nt, with four ORFs encoding the 126 kDa and 183 kDa replicates, the 30 kDa movement protein (MP), and the 17.5 kDa capsid protein (CP), respectively. Phylogenetic tree analysis showed that this isolate was the closest relative to ToBRFV Yinchuan isolate (GenBank accession number: OR500698.1), with 99.73% nucleotide sequence identity. The above results indicated that tomato fruits in Jianshui, Yunnan were infected with ToBRFV. The results provide a basis for the monitoring, prevention, and control of ToBRFV in tomato production areas in Yunnan.

Citrus is one of the most important fruits in China and is cultivated extensively in southern China. Fusarium fujikuroi has been reported to cause diseases on various plants excluding citrus worldwide. In this study, by using tissue separation method, 23 Fusarium-like isolates were isolated from diseased citrus leaves from eight different citrus planting areas in Hubei province. STJ-4 was selected as a representative isolate for further analysis, which included analyses of morphological characteristics, partial sequences of ITS, EF-1α, and RPB1 genes, phylogenetic trees based on the three genes and pathogenicity. Results showed that the STJ-4 isolate was identified as F. fujikuroi, which is the first report of F. fujikuroi causing leaf rot disease on citrus. Our study is important for developing the prevention strategies against F. fujikuroi in the future.

To study the species and genetic variation of yam viruses in Henan province, 188 yam samples suspected of viral diseases were analyzed by high-throughput sequencing and RT-PCR. The results showed that five viruses were detected from yam samples: Japanese yam mosaic virus (JYMV), youcai mosaic virus (YoMV), yam latent virus (YLV), broad bean wilt virus 2 (BBWV 2) and yam yellow spot mosaic virus (YYSMV). The detection rates of JYMV, YoMV, YYSMV, BBWV 2 and YLV were 94.15 %, 87.23 %, 68.09 %, 42.02% and 29.79 %, respectively. 98.94% of the yam samples had complex infection. In this study, there were 20 complex infection types in 188 samples, among which JYMV + YYSMV + YoMV was the main complex infection type, and the detection rate was 26.60 %. Molecular variation analysis showed that YoMV and JYMV were more highly conserved, followed by YYSMV, YLV and BBWV 2, which showed more variation. Phylogenetic tree analyses indicated that the isolates obtained in this study were closely related to those from the same region. At the same time, HTS analysis results showed that other unclassified virus species were detected on yam, so it is necessary to conduct a comprehensive and systematic study on the types of yam viruses in Henan Province.

Plants and pathogens have developed a highly complex interactive relationship through long-term co-evolution, fundamentally driven by a molecular arms race between pathogen effectors and the plant immune system. Plants activate multilayered defense responses through their innate immune system to combat pathogen infection, while pathogens in turn have evolved diverse effectors that precisely target critical immune signaling nodes. These effectors not only interfere with fundamental immune pathways including PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI) but also modulate defense networks like plant hormone signaling and reactive oxygen species metabolism. More critically, pathogen effectors achieve systemic reprogramming of the host transcriptional network through strategies such as directly regulating host gene expression, targeting key transcriptional regulatory elements, manipulating epigenetic modifications, and post-transcriptional modifications, thereby facilitating immune evasion and pathogenic infection. Recently, there have been significant advances in understanding the pathogenic mechanisms of pathogen-mediated manipulation of plant immune responses. This review systematically examines the molecular mechanisms by which pathogen effectors regulate host immune responses through interfering with defense signaling pathways and reprogramming the host transcriptome. We also explore the application of these findings in developing disease-resistant materials, providing a theoretical foundation for elucidating plant-pathogen interactions and advancing disease-resistant crop breeding.

Colletotrichum higginsianum is the major pathogen of anthracnose in cruciferous plants, which can severely damage the production of Chinese flowering cabbage (Brassica parachinensis) in south China. Scytalone dehydratase (Scd) is a key enzyme in the biosynthesis of DHN-melanin that can affect pathogenicity by mediated DHN-melanin biosynthesis in many plant pathogenic fungi. In this study, we identified a conserved scytalone dehydratase ChScd in C. higginsianum. The expression of gene ChSCD was analysed by using RT-qPCR technology, and it was found that the expression level of this gene was significantly up-regulated during the melanization of the hyphae and appressoria of C. higginsianum. Meanwhile, in order to analyse the biological function of the gene ChSCD, the Agrobacterium tumefaciens-mediated transformation technology was used to construct knockout and complementation mutant strains of the gene ChSCD. The results showed that the knockout of gene ChSCD blocked the biosynthesis of DHN-melanin in C. higginsianum, resulting in the loss of the melanization ability in both hyphae and appressoria, and leading to the significantly reduced in tolerance to cell wall interfering substances and oxidative stresses, the appressorium formation rate, turgor pressure, and pathogenicity of the ChscdΔ mutants. In summary, ChScd plays a crucial role in the biosynthesis of DHN melanin in C. higginsianum, which in turn affects the stress resistance, the formation rate of appressorium, turgor pressure, and the pathogenicity of the pathogen.

Cucumber seedling damping-off caused by Pythium aphidermatum is one of the main soil-borne diseases seriously affecting the survival of cucumber seedlings. With the expansion of eggplant cultivation area in greenhouse, the occurrence and damages of the disease are increasing year by year. In this study, a bacterial strain ZF514, capable of producing volatile substance with antagonistic effect against P. aphidermatum, was isolated from rhizosphere soil of healthy cucumber plants in Hangzhou, China. According to morphological cha-racteristics, physiological and biochemical properties, and multi-gene (16S rDNA-gyrA-rpoB) phylogenetic analysis, strain ZF514 was identified as Bacillus velezensis. Strain ZF514 also exhibited significant antagonistic effects on the 5 common phytopathogenic fungi by dual culture on two-section of a Petri dish. The results of pot experiments showed that simulated fumigation treatment of soil with strain ZF514 significantly reduced disease incidence of cucumber seedling damping-off, and the control effect reached 63.69%. In summary, the volatile substance-producing B. velezensis strain ZF514 has potential to be explored as an environment-friendly microbial fumigant against soil-borne diseases.

Brown rot, caused by Monilinia spp., is a serious threat to both stone fruit and pome fruit, greatly affecting the long-distance transportation and exportation of fruits. Based on genomic and transcriptomic analysis of infection of Monilinia fructicola on peach fruit, it was detected that the expression patterns of MfHMG5 and MfHMG6 genes in early stages of infection were similar, and both down-regulated significantly at 1 h after inoculation and then gradually increased. In order to investigate the biological functions of these two genes, the knockout and overexpression transformants of MfHMG5, and knockout and complemented transformants of MfHMG6 were obtained and the corresponding phenotypes were investigated. It was found that the knockout and overexpression of MfHMG5 gene decreased the growth rate and sporulation ability, but did not affect the pathogenicity of M. fructicola. Knock out of MfHMG6 gene reduced the growth rate, virulence and sporulation ability of M. fructicola, and led to the increased expression of MfHMG5 gene. These results indicated that HMG-box family genes MfHMG5 and MfHMG6 were involved in regulating the growth and pathogenesis of M. fructicola.

In the autumn of 2019, a new leaf spot disease was discovered on Zizania latifolia plants in two locations, Langya in Jinhua, and Daji in Lishui, Zhejiang Province. We isolated the pathogen using tissue separation method, and identified it as Epicoccum sorghinum through multiple methods, including morphological observation, biological identification and pathogenicity test. Besides, to prevent the effect of E. sorghinum on the yield and quality of Z. latifolia, 12 chemical fungicides were screened. Among these, prochloraz showed the best inhibitory effect on the pathogen. Additionally it had the least side effect on the growth of Ustilago esculenta, another mutually beneficial organism associated with Z. latifolia. So prochloraz can be used as an effective fungicide for the disease management. This study provides a scientific basis for the identification and understanding the leaf spot disease in Z. latifolia. It offers insights into the selection of chemical fungicides for its control, which is valuable for agricultural and disease management.

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is a typical airborne disease that poses a serious threat to wheat production. Understanding the inoculum sources and migration pathways of stripe rust is of great significance for formulating effective disease management strategies. This review systematically summarizes the progress made over the past 70 years by 4 generations of rust researchers in identifying the sources and migration pathways through field surveys, population genetic analyses, and air trajectory simulations. An integrated research framework is proposed, emphasizing field investigation as the foundation, population genetics as the core, and air trajectory simulations as a means of validation. The review also discusses the potential to refine and adjust these routes through the integration of emerging technologies, and proposes a shift from qualitative to quantitative research, thereby contributing to the development of sustainable disease management strategies.

Anthracnose is one of the most important fungal diseases that pose significant threat to the production of Yunnan red pear cultivar ‘Caiyunhong’. The disease mainly causes fruit rot, resulting in a disease incidence of more than 35% in normal conditions. The causal agent was identified as Colletotrichum fructicola based on the morphological characteristics, phylogenetic relationship inferred from ITS, ACT, TUB and CHS sequences, and the result of pathogenicity test. This is the first report of C. Fructicola causing anthracnose on ‘Caiyunhong’ fruit in China, which provides a theoretical basis for effective prevention and control of the disease.

To investigate the occurrence of gummy stem blight (GSB) on Trichosanthes kirilowii and the causing pathogen of the disease, and to screen effective plant-derived antimicrobial agents, we collected the plants with symptoms of GSB at T. kirilowii-planting regions in Qianshan City, Anhui Province, and conducted pathogen isolation and purification experiments. Based on morphological characteristics and the result of molecular identification, the isolates were identified as Stagonosporopsis caricae. Meanwhile, the inhibitory effects of 20 Chinese herbal medicine extracts against S. caricae were determined, and over 90% inhibition rate was obtained when ethanol extract from Cnidii Fructus (CF) or Macleaya Fructus (MF) was used at a concentration of 15 mg·mL^-1, while over 80% inhibition rate for Sophorae Flavescentis Radix (SFR) or Polygoni Cuspidati Rhizoma et Radix (PCRR) extract. Further tests showed that both CF and SFR extracts showed significant inhibitory effect on mycelial growth of S. caricae, with EC₅₀ values of 0.1648-0.5289 and 0.7347-0.8332 mg·mL^-1, respectively. This study provides a theoretical basis for the environment-friendly control of GSB on T. kirilowii.

Colletotrichum fructicola, belonging to the C. gloeosporioides species complex, is the dominant pathogenic species causing anthracnose on plum trees. In this study, multiple alignment of ApMat sequences of 36 strains in the C. gloeosporioides complex was performed, a pair of C. fructicola-specific primers: F2(5′-CGTGACCCAGGAGGCGACCACGCATCTGT-3′ ) and R2(5′-GGTGATCTCTCCTAGCGTTCGTACGTCTAAT-3′) was designed based on the specific sequences of the pathogen, and a PCR detection method was develo-ped accordingly. The results showed that a specific target amplicon of 132 bp could only be produced by C. fructicola with the primer pair F2/R2, with a detection sensitivity of 100 fg·μL^-1. Using this PCR detection system, the target pathogen C. fructicola can be quickly detected from the leaves of plum trees artificially inoculated with C. fructicola HN47-2 strain and the leaves of plum trees naturally infected with C. fructicola. The C. fructicola-specific PCR detection method established in this study provides an important technical support for early diagnosis, dynamic monitoring and accurate prevention and control of plum anthracnose caused by C. fructicola in the field.

Beet necrotic yellow vein virus (BNYVV)-caused sugar beet rhizomania is the most important viral disease in sugar beet, severely affecting beet yield and sugar content. BNYVV is persistently transmitted by Polymyxa betae, a root-specific parasitic plasmodiophorid. The resting spores of Polymyxa betae can survive in soil for long periods of time. Thus, the viral disease is difficult to be eradicated once it occurs. Currently, plan-ting resistant varieties is the only way to reduce losses caused by the disease. In recent years, the large-scale planting of single resistant varieties leads to emergence of resistance-breaking BNYVV isolates in sugar beet producing areas worldwide, including Xinjiang and Heilongjiang in China. These virus strains have broken the antiviral activity of the resistance varieties, leading to more severe rhizomania. This paper reviews the research overview of sugar beet rhizomania, focuses on recent research progress on BNYVV-plant-vector interactions, and prospects future research directions for urgent breakthroughs.