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.

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.

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.

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.

Plant secondary metabolites are a class of small-molecule compounds non-essential for fundamental plant growth and development, including phenolic, terpenoids, and nitrogen-containing compounds. As integral components of the plant defense system, these metabolites play a core regulatory role in plant-microbe interactions. Microorganisms can modulate the accumulation of plant secondary metabolites through various strategies, such as activating the plant immune system or secreting plant hormones. Meanwhile, secondary metabolites can inhibit pathogen infection through diverse mechanisms: on the one hand, they can promote the synthesis of compounds like methyl salicylate to activate systemic acquired resistance against pathogens; on the other hand, secondary metabolites act as phytoalexins to directly inhibit microbial pathogens by disrupting pathogen membrane integrity, interfering with microbial metabolism, or inducing oxidative stress. Some metabolites additionally inhibit the synthesis and secretion of pathogen virulence factors. Furthermore, developing novel green pesticides based on plant secondary metabolites has become a highly promising research direction in the field of plant protection. This review systematically summarizes the multifunctional roles of plant secondary metabolites in plant-microbe interactions, detailing their involvement in activating plant immunity and outlining the molecular regulatory networks underpinning pathogen defense.

The development of plant diseases is not solely driven by plant-pathogen interactions but also arises from complex networks involving plants, pathogens, and microbiota, with microbe-microbe interactions playing a critical role. Recent advances in high-throughput sequencing and microbe-microbe interaction studies have highlighted the capacity of pathogens to reshape plant microbiome composition, influencing microbial diversity and revealing the function of the core microbiota under diseased conditions. During disease progression, microbial interactions, such as resource competition, contact-dependent interaction, and chemical signal interference, can either facilitate or suppress pathogen colonization and virulence. This review synthesizes current knowledge on microbiome structural dynamics during plant disease, examines the competitive and cooperative interactions between microbiota members and pathogens, and outlines promising future directions such as the strategic use of biocontrol agents and the exploration of biocontrol agent-pathogen and biocontrol agent-microbiome interactions. These insights provide a conceptual framework for improving plant disease management and designing microbiomes that promote plant health.

Fusarium head blight (FHB), caused by the Fusarium graminearum species complex (FGSC), is a globally significant fungal disease that poses a severe threat to wheat yield and quality. Due to the lack of resis-tant cultivars, chemical control has long been the primary strategy for managing FHB. However, with the growing demand for green and sustainable agriculture, biological control has become an increasingly important component of integrated disease management systems. In recent years, numerous biocontrol microorganisms have been identified and applied for FHB control, demonstrating considerable practical potential. This review summarizes microbial resources available for managing wheat FHB, outlines the underlying biocontrol mechanisms, evaluates the current status of biocontrol formulations development, and discusses the challenges associated with their application. Finally, we propose strategies to improve the development and utilization of biocontrol agents, aiming to provide theoretical and technological support for the sustainable management of FHB in wheat.

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.

Rice blast, caused by Pyricularia oryzae, is a major biological constraint to rice production in China. It frequently causes outbreaks and epidemics across all rice-growing regions, posing a serious threat to high and stable yields. This study reviews the following aspects concerning rice blast: its occurrence and damage, the biology of P. oryzae and sources of infection, chemical agents for blast control, pathogenesis of P. oryzae and development of targets for green fungicides, avirulence genes of P. oryzae and major blast resistance genes in rice, mechanisms underlying rice blast resistance, and challenges in evaluating blast resistance in rice varieties. Furthermore, it outlines future research priorities for the green prevention and control of rice blast, aimed at enhancing sustainable management strategies for this disease in China.

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.

Gene editing enables precise modification of specific genomic loci and has been widely used in plant disease resistance engineering. This technology is built upon programmable nucleases that have evolved through successive generations: zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins (CRISPR-Cas) systems. The latter now dominates as the mainstream platform owing to its high efficiency and ease of programming. In addition to conventional targeted knockout mutagenesis, precision tools such as base editing, prime editing, and targeted integration have been progressively optimized and implemented in plant systems. In plant disease research, these technologies not only facilitate functional genomics studies but also accelerate the discovery of novel disease resistance genes through high-throughput functional gene screening and saturation mutagenesis libraries construction. Furthermore, they provide multidimensional strategies for creating disease-resistant germplasms. This review synthesizes the evolution of gene editing technologies and highlights their applications in crop disease resistance research, including the development of edited materials for wheat powdery mildew resistance, rice blast and bacterial blight resistance, as well as other critical pathosystems. This establishes actionable frameworks for mechanistically dissecting plant immunity and advancing precision breeding for sustainable crop protection.

Tobacco black shank, caused by Phytophthora parasitica var. nicotianae, is a devastating soil-borne disease that severely impacts tobacco production. In this study, over 16 000 microbial strains were isolated from tobacco rhizosphere soils collected across eight counties (districts) in Yuxi City, Yunnan Province using the dilution plate method. Through the plate confrontation assay, seven strains exhibiting significant antagonistic activity against P. parasitica var. nicotianae were selected. Pot experiments demonstrated that all seven antagonistic strains could effectively control tobacco black shank, with strain CJ-S-5292 showing the highest control efficacy of 75.79% and exhibiting excellent root colonization capability. Based on morphological characteristics, Physiological and biochemical properties, and phylogenetic analysis of 16S rRNA and gyrB gene sequences, CJ-S-5292 was identified as Bacillus amyloliquefaciens. Further investigations revealed that CJ-S-5292 not only significantly inhibited mycelial growth of P. parasitica var. nicotianae but also induced morphological abnormalities including increased branching and fragmentation of hyphae. The cell-free fermentation supernatant of CJ-S-5292 also showed remarkable inhibitory effects on pathogen growth. Comparative studies of application methods indicated that root irrigation (72.22% control efficiency) and combined treatment (75.91%) were significantly more effective than foliar spraying (42.59%). Field trials further confirmed that root irrigation with CJ-S-5292 achieved 66.62% disease control efficiency, comparable to conventional chemical fungicides. This study demonstrates that B. amyloliquefaciens CJ-S-5292 possesses outstanding biocontrol potential, providing a high-quality microbial resource for the green control of tobacco black shank disease.

Rice viruses pose a significant threat to global rice production, and their pathogenic mechanisms involve intricate interactions between the viruses and host plants. During pathogenesis, rice viruses employ diverse strategies to manipulate host cellular processes and promote viral infection and replication. Emerging research has uncovered common mechanisms underlying the pathogenicity of different rice viruses, suggesting the existence of potentially conserved targets for antiviral interference. This review summarizes recent global advances in rice virus research, systematically elucidating the distinct pathogenic mechanisms among various rice viruses while highlighting conserved molecular strategies shared by viral pathogenicity factors. The insights presented aim to facilitate the development of broad-spectrum antiviral rice breeding and effective disease management strategies. In addition, future research directions for elucidating the molecular mechanisms of rice virus pathogenesis are outlined.

A wide variety of microorganisms inhabit the surfaces and interiors of the plants. These microorganisms and their functional substances are collectively referred to as the plant microbiome, which has an impact on a series of basic life activities of plants, such as nutrient acquisition, immune regulation, and stress tolerance. This article focuses on the latest research progress of the plant microbiome, elaborating on the formation rules of the plant microbiota and its regulatory mechanisms on host phenotypes, and deeply exploring the applications of the plant microbiome in disease control. Moreover, in view of the controversial points regarding the role of the plant microbiota in triggering or exacerbating diseases, this article further discusses the emerging research paradigm of the pathobiome, as well as its action mechanisms and driving factors. In the future, through the cross integration of artificial intelligence, multi-omics technologies, and classical plant pathology research techniques, the formation mechanisms of the symbiotic state and pathogenic state of the plant microbiome will be deeply revealed. This will lay an important theoretical foundation for accurately exploring and utilizing the beneficial traits of the plant microbiome, establishing an efficient, safe, and environmentally friendly plant disease control system, and promoting sustainable agricultural development.

The growth, development, environmental adaptation, and infection processes of plant pathogenic fungi are dynamically orchestrated through multi-layered molecular networks, with post-translational modifications (PTMs) functioning as critical "molecular hubs" coordinating these biological and pathogenic programs. This paper reviews several important types of PTMs in plant pathogenic fungi, including phosphorylation, glycosylation, ubiquitination, lipidation, novel acylation, redox modifications, and ADP-ribosylation. It explores their regulatory mechanisms in the biological and pathogenic processes of plant pathogenic fungi, summarizes the main strategies and methods for studying PTMs, analyzes the relationship between PTMs and plant disease control, and proposes future perspectives in the study of PTMs governing the pathogenesis of plant pathogenic fungi. The aim is to provide a theoretical foundation for deciphering the pathogenic mechanisms of plant pathogenic fungi and innovating sustainable disease management approaches.

The bacterial pathogen Xanthomonas delivers type III effector proteins (T3Es) into plant cells via its type III secretion system (T3SS), subverting host immunity, metabolism, and phytohormone signaling networks, ultimately causing devastating diseases such as bacterial wilt and leaf blight. This review systematically summarizes the functional diversity of Xanthomonas T3Es and their molecular mechanisms: Transcription activator-like (TAL) effectors activate host gene expression by binding to specific promoter elements, while non-TAL effectors suppress plant immune responses via post-translational modifications (e.g., ubiquitination, phosphorylation) or protein-protein interactions. To counter pathogen infection, plants have evolved multiple defense strategies, including NLR (nucleotide-binding leucine-rich repeat) receptor-mediated effector-triggered immunity (ETI), "executor" genes that hijack TAL effectors via EBE (effector-binding element) traps to induce hypersensitive responses, and mutations in susceptible gene promoters conferring resistance. By deciphering these molecular interactions between Xanthomonas T3Es and host plants, this review provides critical insights and technical strategies for developing eco-friendly plant disease management strategies.

Peanut (Arachis hypogaea), which is widely cultivated across the world, provides high-quality vegetable oil, protein, dietary fiber, minerals, and vitamins for humans. However, in field conditions, the peanut is easily affected by various biotic and abiotic stresses. Diplodia gossypina is the dominant pathogen causing severe collar rot on peanuts. To dissect the pathogenic mechanism of D. gossypina, genome sequencing analysis was performed by using the D. gossypina strain A20_4. The sequencing data showed that the genome assembly size of D. gossypina A20_4 is 43.03 Mb with a GC content of 54.91%. The de novo assembly identified a total of 10,745 genes, containing 41,526 coding sequences and 2.20% of repeat sequences, of which 6,461 genes (60.13%) were annotated using BlastP from GO annotation, 3,245 genes (30.20%) and 3,093 genes (28.79%) were annotated from KOG and KEGG annotations, respectively. Meanwhile, the secreted proteins and effectors in 10,745 protein sequences encoded by the whole genome of D. gossypina A20_4 were analyzed, and the results showed that there are 790 secreted protein genes including 220 carbohydrate-active enzymes and 224 potential effector proteins. The functions of 222 potential effector proteins can be annotated by PHI-base. According to the annotation results, 12 key pathogenic factors were identified in D. gossypina A20_4. Moreover, a serine/threonine protein kinase SNF1 gene required for autophagy process was identified and analyzed. Deciphering the whole genome of D. gossypina A20_4 provides us with novel insights into understanding evolution, pathogenic molecular mechanism, host-pathogen interaction, and many other complexities of the pathogen.

Plants are subject to attack and infection by a variety of pests and pathogens as they grow, and have evolved sophisticated and complex defense systems in response to pathogen invasions, which can trigger specific transcription factors for effective immune responses through multiple signaling pathways. The AP2/ERF (APETALA2/ethylene response factor) family members play important roles as plant-specific transcription factors in plant growth, development and biotic and abiotic stress responses. In this review, we summarized the classification, structural features, sequence recognition and functions of AP2/ERF transcription factors by referring to the relevant research progress in recent years at home and abroad, and focused on those of AP2/ERF transcription factors involved in plant disease resistance in the areas of transcriptional regulation, post-translational modification-phosphorylation regulation, secondary metabolite synthesis and hormone signaling. It provides a theoretical reference for the in-depth study of the regulation mechanism of AP2/ERF involved in plant disease resistance. Finally, the research and application prospects of AP2/ERF were discussed and prospected.

Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), is a devastating soil-borne disease threatening global banana production. The conidia and chlamydospores in the soil are the primary inoculum for this disease. The C2H2-type zinc-finger transcription factor FlbC in Aspergillus nidulans is a key regulator of conidial development. In this study, the FlbC homolog gene FocFlbC was identified in Foc TR4, and its knockout mutant (ΔFocFlbC) and complemented strain were constructed using protoplast-mediated genetic transformation technology. The subcellular localization and biological functions of this protein were analyzed. The results showed that the FocFlbC protein was localized to the nucleus in both hyphae and conidia. Compared to the wild-type (WT) strain, the ΔFocFlbC mutant exhibited significantly reduced mycelial growth rate on maltose medium, while growth on other carbon sources showed no significant difference; conidiation of the ΔFocFlbC mutant was significantly reduced on all tested carbon sources. Furthermore, the ratio of conidiation between the WT and mutant was highest on maltose medium, differing significantly from other carbon sources. Although the FocFlbC deletion mutation showed no significant effect on biomass accumulation or conidial germination, the mutant exhibited the following phenotypic defects compared to the wild-type strain: reduced tolerance to cell wall and salt stresses; decreased enzymatic activities of α-amylase, filter paper cellulase, and β-1,4-D-glucanase, accompanied by downregulated expression of corresponding hydrolase genes; significantly reduced virulence. These phenotypic defects were restored in the complemented strain. In conclusion, FocFlbC not only regulates hyphal growth on maltose and conidial development of Foc TR4, but also participates in regulating cell wall integrity, salt stress response, hydrolase synthesis, and virulence. The results provide a theoretical basis for further elucidating the molecular mechanism underlying the growth, development, and pathogenicity of Foc TR4.

Banana Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense (Foc), is a devastating soil-borne disease that poses a severe threat to global banana production. Biological control constitutes an essential component in the integrated management system of the disease. This study characterized the diversity of root endophytic bacterial communities in two diploid (Musa acuminata ‘Siam Ruby’, Musa balbisiana) and two triploid (Musa acuminata ‘Tianbao’, Musa × paradisiaca ‘Dwarf Plantain’) banana cultivars cultivated under the same ecological conditions through 16S rRNA gene high-throughput sequencing (V5-V7 regions). The results demonstrated higher diversity in diploid root bacterial endophytes compared to triploid plants; distinct differences in bacterial community structure were observed between ploidy types, with diploid roots showing notably greater relative abundance of biocontrol-associated genera, such as Bacillus and Bradyrhizobium. Fourteen endophytic bacterial strains with antagonistic activity against Foc were isolated from diploid cultivars Musa ornata and Musa acuminata ‘Siam Ruby’. Among these, two Bacillus velezensis strains (ZB-1 and Z-7) significantly reduced the severity of banana Fusarium wilt caused by Foc in pot experiments. The lipopeptide extracts from both strains disrupted the morphology of Foc conidia and hyphae, resulting in a 99.02% and 98.67% reduction in sporulation capacity, respectively. Meanwhile, the lipopeptide extracts caused damage to the hyphal biomembrane system and inhibited lipid metabolism. This study demonstrates that diploid banana plants harbor abundant beneficial and antagonistic bacterial communities, providing both a crucial theoretical foundation and a microbial repository for developing microbiota-driven sustainable biocontrol strategies against Fusarium wilt.

The occurrence of potyviruses and poleroviruses in vegetable crops is common, and seriously affects quality and yield. In order to develop environmental friendly and efficient plant virus inhibitors, potyviruses and poleroviruses were detected and analyzed using RT-PCR in suspected virus disease samples of vegetable crops such as Capsicum annuum, Solanum lycopersicum, Cucurbita moschata, Cucurbita pepo, Phaseolus vulgaris and Vigna unguiculata in Luoyang city. The results showed that the main viruses were pepper vein yellows virus (PeVYV) in pepper, potato virus Y (PVY) in tomato, and zucchini yellow mosaic virus (ZYMV) and cucurbit aphid-borne yellows virus (CABYV) in pumpkin and zucchini. Co-infection with ZYMV and CABYV was common. In kidney beans, melon aphid-borne yellows virus (MABYV) was detected, while no virus was detected in cowpea samples. Among them, the occurrence of ZYMV in pumpkin and zucchini was more serious, and kidney bean was found as a new natural host of MABYV for the first time. The phylogenetic analysis showed that the PVY-LYFQ isolate obtained in this study had a relatively distant relationship with other PVY isolates, and the genetic variability of PVY isolates was not closely related to their geographic locations or hosts, as well as the genetic variability of PeVYV isolates was not directly related to their geographic locations, but was related to their hosts to some extent; the genetic variability of ZYMV isolates were related to both their geographic locations and hosts to some extent; the genetic variability of CABYV and MABYV genome sequences was all related to their geographic locations. This study provides an important theoretical basis for the prevention and monitoring of potyviruse and poleroviruse diseases, the implementation of control measures, and the development of control drugs in vegetable crops in the Luoyang area.

Soil-borne pathogens are responsible for a variety of crop diseases, leading to substantial economic losses and posing a significant threat to global agricultural productivity. Due to the distinct infection cycle characteristics of soil-borne diseases, accurate quantification of pathogen load in pre-sowing soil is crucial for effective disease management. This review systematically evaluates the development of quantitative detection methods for soil-borne plant pathogens, with a focus on qPCR technology, which is distinguished by its high sensitivity, specificity, and absolute quantification capabilities. We outline standardized protocols and key factors for large-volume soil processing and qPCR-based detection systems. Furthermore, we analyze the correlation between soil pathogen abundance and disease occurrence, as well as its implications in disease risk warning systems. We assess recent advancements in pathogen detection technologies both domestically and internationally, along with emerging trends. This comprehensive review aims to provide researchers, agronomic service providers, and policymakers with a scientific foundation and technical guidance for improving soil-borne disease surveillance and control strategies.

Tomato leaf curl New Delhi virus (ToLCNDV) is a newly discovered begomovirus in China, which transmitted by whitefly (Bemisia tabaci). It was first discovered in Zhejiang and Shanghai, and then discovered in Jiangsu. It seriously affected the local production of cucurbitaceae crops. In this study, a watermelon isolate collected from Nantong, Jiangsu Province was detected by PCR, and rubbed onto Nicotiana benthamiana, tomato, watermelon, melon and cucumber. The inoculated plants exhibited symptoms such as curling and chlorosis, indicating that this virus strain could be mechanically transmitted. The whole genome amplification and sequence analysis of this isolate showed that it had the closest genetic relationship with the isolate previously reported in China and clustered into the same branch of the phylogenetic tree. Systematic evolution also showed a correlation between the evolution of the virus and its geographic location, which indicated that ToLCNDV in China might originate from Indian. There was no evidence of recombination in any of the Chinese isolates. This study will serve as a reference to study the origin, evolution, mutation, and control of the virus.

Soil-borne wheat virus diseases, transmitted by the obligate parasite Polymyxa graminis, are caused by wheat yellow mosaic virus (WYMV) and Chinese wheat mosaic virus (CWMV) in China. The complete genomic sequences, molecular evolution, virus characteristics, and infection mechanisms of these two viruses have been intensively characterized. This article systematically reviews the pathogen biology, epidemiological distribution, transmission mechanisms, and molecular pathogenesis mediated by viral proteins, along with host resistance mechanisms involving functionally validated quantitative trait loci (QTLs) and cloned resistance genes. Meanwhile, disease-suppressive mechanisms mediated by the rhizosphere microbiota and current eco-friendly management strategies were examined. Finally, we propose that future efforts should be focused on identifying and utilizing key resistance genes in breeding resistant varieties and developing soil microecology-based disease control technologies, thereby establishing technical support systems for sustainable management of soil-borne wheat virus disease.

Wheat Fusarium crown rot (FCR) is mainly caused by Fusarium pseudograminearum. Influenced by straw returning to the field and conservation tillage practices, this disease has been exacerbated annually in the Huang-Huai-Hai wheat-maize double cropping region of China. The disease causes browning and rot at the base of the stem, leading to "white heads," withered stems, and shriveled grains, which seriously affects yield. The pathogen primarily infects through subterranean stems or the crown-root junction. After wheat harvest, the pathogen continues to reproduce on wheat stubble and spreads in fields via chopped straw, accumulating throughout the year. Infected seeds or harvesters are suspected to contribute to long-distance dissemination of the pathogen. Seedling resistance identification utilizes seed soaking or grain inoculation methods, while adult plant resistance identification prioritizes rapid investigation of white head incidence, combined with precise assessment of stem base rot severity. Comprehensive disease management adopts a tiered strategy emphasizing ecological regulation, supplemented by biological and chemical controls. Selecting crown rot-resistant wheat varieties such as ‘Hengguan 35’, and implementing integrated measures in severely affected fields - including deep soil plowing, chemical seed dressing, optimized fertilizer/water management, jointing-stage prevention, and delayed sowing - can effectively curb disease occurrence and mitigate yield losses, ensuring wheat yield stability and food security.

Heterotrimeric G proteins, conserved signaling components in eukaryotes, consist of three subunits (Gα, Gβ, and Gγ) and serve as core elements in transmembrane signal transduction. In animals, G protein signaling is mediated through a G protein-coupled receptor (GPCR)-dependent pathway involving guanine nucleotide exchange factors (GEFs). In contrast, plants possess a significantly reduced number of heterotrimeric G protein subunits compared to animals, yet these proteins participate in a remarkably broad range of biological processes and play a central role, particularly in plant immune defense. This review systematically summarizes the molecular characteristics and structure-function relationships of plant heterotrimeric G protein subunits. It focuses on elucidating their regulatory networks and mechanistic roles in plant immune signaling and proposes future research directions for key scientific questions in this field, aiming to provide valuable references for related research.

In the long-term co-evolution between plants and pathogens, plants have developed a sophisticated immune system to restrict pathogen invasion and damage. Among these, plasma membrane-tethered receptor-like kinases (RLKs) and receptor-like proteins (RLPs) are key components of the plant innate immune system. As pattern recognition receptors (PRRs), they activate pattern-triggered immunity (PTI) by sensing pathogen-associated molecular patterns (PAMPs) or host-derived damage-associated molecular patterns (DAMPs). Although the core signaling pathways of PTI are highly conserved in plants, genetic variation in PRRs within and across species significantly influences their ligand recognition capability, signal transduction efficiency, and immune response intensity. This review summarizes the strategies for identifying PRRs, the biological significance of genetic variation, and their application potential in disease resistance breeding. It also discusses factors affecting the disease resistance spectrum conferred by PRRs and the future directions for high-throughput identification of PRR resistance genotypes.

Plants emit a large variety of volatile organic compounds (VOCs) during infection by the pathogenic microbes. These compounds can be classified into different types based on their chemical structures and biosynthetic pathways, primarily including volatile terpenoids (VTPs), volatile fatty acid derivatives (VAAs), volatile phenylpropanoids/benzenoids (VPBs) and nitrogen-containing volatiles. Given the general antimicrobial activity of plant VOCs and the large amount of emission following infection, these compounds have often been assumed to function in defence against pathogens. This review summarizes the recent advances in the field of plant VOCs and pathogens, focusing on the main components of plant VOCs, their direct antimicrobial effects, and their regulatory roles in plant self-resistance, while also provides an outlook on further investigations of plant VOCs in botanical pathogen resistance.

As one of the major vegetable crops in Shanxi Province, tomato plants are constantly suffering from various virus infections, which severely limit tomato yield and quality. To determine the virus species and infection types on tomato plants, 154 samples exhibiting virus-like symptoms were collected from 7 cities and subjected to small RNA sequencing combined with PCR/RT-PCR for virus detection and identification. A total of six viruses were identified from these tomato samples. According to the detection rate from high to low, they were cucumber mosaic virus (CMV) (85.71%), tomato yellow leaf curl virus (TYLCV) (45.45%), southern tomato virus (STV) (41.56%), and tomato mosaic virus (ToMV) (27.27%), potato virus Y (PVY) (25.97%) and tomato chlorosis virus (ToCV) (18.18%). Among them, CMV was the dominant virus infecting tomato plants in Shanxi Province. Analysis of infection types showed that a total of 32 types were classified from the above samples, including 4 types of single virus infection and 28 types of mixed infection. Among them, CMV, CMV+ToMV, CMV+STV+TYLCV, CMV+PVY+STV, CMV+TYLCV, CMV+STV+ToCV+TYLCV and CMV+PVY were the most common types, with detection rates of 16.23%, 10.39%, 9.09%, 8.44%, 5.84%, 5.84%, and 5.19%, respectively and mainly exhibited mosaic, narrowing, chlorosis and leaf curling symptoms. Analysis of CMV satellite RNA (satCMV) association revealed that 66.23% of samples in 22 viral infection types were associated with satCMV, and samples in 10 infection types were partially associated with satCMV. Combined with the field symptoms, we found that CMV, CMV+ToMV and CMV+PVY+STV-infected samples showed severer symptoms, and CMV+STV showed milder symptoms in the presence of satCMV, and samples of other infection types exhibited no obvious symptom changes when associated with satCMV. Phylogenetic analysis showed that the pairwise identity of the 10 satCMV isolates from Shanxi was 93.4%-100%, and clustered with isolates from China and Greece. In this study, we identified 6 viruses and 1 satellite RNA in tomato plants in Shanxi Province, among which PVY and STV were reported in Shanxi tomato plants for the first time. And we comprehensively analyzed the relationship between virus infection types and field symptoms, providing an important reference for the rapid diagnosis and control of tomato virus diseases.

In 2021, a tea plant leaf spot disease was found in the Jin Xuan tea plants( Camellia sinensis cv.Jinxuan). A representative strain was isolated from the diseased leaves according to Koch’s postulates. The isolates were further identified as Cladosporium cladosporioides based on morphological characteristics and phylogenetic analysis with internal transcribed spacer region (ITS) and β-Actin gene. The results showed that the pathogen causing the disease was Cladosporium cladosporioides. This is the first report of Cladosporium cladosporioides in tea plants in China

The tomato leaves and fruits suspected to be infected with tomato brown rugose fruit virus (ToBRFV) were collected from the tomato planting area in Chifeng City, Inner Mongolia, in March 2024. RT-PCR technology was employed to amplify approximately 798 bp sequence with degenerate primers ToBRFV-MP-F/R to detect the presence of TOBRFV in this study. Furthermore, based on the sequencing results, the complete genome sequence of ToBRFV-NMG was obtained using four pairs of specifically designed primers. BLAST comparison showed that the cloned ToBRFV-NMG complete genomic nucleotide sequence shared the highest identity (99.86%) with the Shandong isolate of ToBRFV (ToBRFV-SD, GenBank accession number: MT018320). Phylogenetic trees showed that the genome sequence of the newly isolated ToBRFV-NMG was most closely related to the ToBRFV-SD isolate reported in Shandong in 2020. Both of them were clustered in the same branch, and they were also closely related to other isolates of Tobamovirus as well. Pathogenicity analysis showed that the virus infected tomato leaf was able to infect Nicotiana benthamiana, Capsicum annuum L., and Solanum lycopersium resulting in symptoms such as wrinkling, mosaic and necrosis that are consistent with those observed in the field. The viral sequence was determined by RT-PCR and was identical to the sequence of ToBRFV-NMG. These results confirm that the tomato fruits and leaves were infected by a ToBRFV isolate. This is the first report of tomato infected by ToBRFV in Inner Mongolia, which sheds light on the identification, prevention and control of local viral diseases.

Root rot was found in main durian-planting areas in Hainan Province. The symptoms include root and root crown rot, which resulted in reduced tree vigor (leaf yellowing, leaf drop), branch wilt, even the death of entire tree. This causes serious economic losses to durian production. To identify the causal agent of this disease, diseased root samples of durian trees were collected from Sanya, Ledong, Lingshui and Baoting in Hainan Province from 2023 to 2024, and tissue isolation method was used to obtain potential pathogens. Based on morphological characteristics, phylogenetic relationship inferred from rDNA-ITS, Ypt1, β-Tubulin and EF-1α, and the result of pathogenicity test, the pathogen was identified as Phytophthora palmivora. This is the first report of durian root rot caused by P. palmivora in China.

Plant diseases, caused by diverse pathogenic agents, are key constraints limiting crop yield and quality improvement. Among these, diseases caused by bacterial pathogens are characterized by rapid spread, challenging control, and severe damage. Through sustained co-evolution with pathogens, plants have evolved multi-layered defense systems. Pattern-triggered immunity (PTI) constitutes plants′ primary defense layer, mediated by pattern recognition receptors (PRRs) that recognize conserved pathogen-associated molecular patterns (PAMPs). This surveillance mechanism effectively restricts infection by non-adapted pathogens. However, pathogens continuously evolve evasion strategies to subvert host recognition. Consequently, the uncovering of new PAMPs is critical for countering pathogen virulence adaptation and enhancing plant immunity. This paper comprehensively reviews the typical characteristics and identification methods of PAMPs from phytopathogenic bacteria, collates the reported bacterial PAMPs along with their recognition mechanisms and research progress on downstream signaling pathways. It aims to provide theoretical frameworks for discovering and functionally characterizing new PAMPs while establishing scientific groundwork for developing sustainable crop protection strategies.

To investigate the causal agent of leaf blight occurred on Picea asperata Mast, diseased samples were collected in Dalian, Liaoning Province, and tissue isolation was performed. The pathogenicity of the representative isolates was verified by Koch′s postulates. The pathogen was identified as Nothophoma quercina according to morphological characteristics and multi-gene (ITS, RPB2, TUB2, and LSU)-based phylogenetic analysis result. The growth of N. quercina on different culture media, carbon sources, nitrogen sources, tempera-tures, light conditions, and pH values was determined. The results showed that N. quercina grew best on SDA culture medium, with soluble starch as carbon source and urea as nitrogen source, at 25°C, pH 7.0, and a 12 h light/12 h dark cycle. Ten pesticides were tested for their in vitro antifungal activity against N. quercina, and 98% pyraclostrobin TC showed the best inhibitory effect, with an EC₅₀ value of 0.0196 μg·mL^-1. Five pesticides with higher inhibitory effects were selected for further field efficacy trials. It was showed that the best control effect was achieved by using 250 g·L^-1 pyraclostrobin EC, with an efficacy of over 65% in July and September. The results lay a basis for further investigating the occurrence regularity and chemical control of the disease.

As a major biological disaster threatening China′s food security, Rice viral diseases have shown an increasing prevalence in recent years. Among them the compound epidemic of Southern rice black-streaked dwarf virus and rice stripe mosaic virus in South China′s Rice-growing Regions is particularly serious. Addressing issues in traditional control technologies such as delayed monitoring, excessive pesticide application, and low prevention efficiency, this study innovatively integrates a three-pronged green, simplified, and lightweight prevention and control technology system encompassing ‘monitoring and early warning-source interception-precision pesticide application’. Through systematic verification in epidemic areas of Yunfu City, Guangdong Province, the technical system comprises three core measures: 1) Establishment of an early warning system based on virus-carrying rate monitoring; 2) Seedling-stage control combining insect-proof net-covered nursery with pesticide-treated transplanting; 3) Development of precision pesticide application protocols based on pest dynamics in paddy fields. Application results demonstrate over 96.7% control efficacy against viral diseases, with 30.0% reduction in pesticide usage compared to conventional control areas, achieving dual objectives of enhanced disease control efficiency and reduced chemical input with improved efficacy. This technical system has developed into a replicable standardized operational protocol, not only providing key technical support for viral disease control in South China′s rice regions but also offering significant reference value for integrated disease management in China′s major rice-growing areas through its ‘prevention-first, green control’ philosophy.

Rice dwarf disease, caused by rice dwarf virus (RDV), poses a significant threat to rice production. Establishing a RDV monitoring system is critical for early field surveillance and disease control. In this study, a 1 056 bp fragment of the P9 gene of RDV was amplified via reverse transcription-PCR (RT-PCR) from RDV-infected rice plant and expressed in Escherichia coli BL21 (DE3). Purified P9 protein was used to immunize New Zealand white rabbits, generating P9 polyclonal antiserum. Enzyme-linked immunosorbent assay (ELISA) revealed an antiserum titer of 1∶32 000. Western blot analysis confirmed that the antigen-affinity-purified polyclonal antibody specifically recognized RDV P9 protein in both infected rice plants and viruliferous insect vectors. The antibody was further applied in indirect ELISA and dot-ELISA assays, combined with RT-PCR, to analyze 223 field samples (rice, barnyard grass, and three insect vectors: Nephotettix cincticeps, Recilia dorsalis, and Nilaparvata lugens) collected from Xianyou County, Putian City, Fujian Province. The results showed RDV infection rates of 29.03% in rice and 19.05% in barnyard grass, with viral carrier rates of 12.28% in N. cincticeps, 2.56% in R. dorsalis, and 0 in N. lugens. The RDV P9 polyclonal antibody exhibited high titer and specificity. This study successfully developed high-titer, high-specificity polyclonal antibodies against RDV P9. The established serological methods not only enhance diagnostic reliability for rice dwarf disease but also provide critical technical support for future investigations into P9 protein function and field-based RDV detection.

The antifungal activity of dark segmented endophytes (DSE) in blueberry roots against Fusarium oxysporum was investigated through the plate confrontation assay, double plate technique, and control effect experiment. The results showed that all the 8 DSE strains could successfully colonize in blueberry roots, leading to the inhibition of F. oxysporum with a maximum inhibition rate of 74.03%. Both volatile substances and fermentation filtrate produced by these 8 DSE strains exhibited certain inhibitory effect on mycelial growth of F. oxysporum, with the highest inhibitory rate of 37.25% for volatile substances and 66.13% for 50% concentration of fermentation filtrate. In the control efficacy test, sterile blueberry tissue seedlings were firstly treated with a certain DSE strain before inoculation with F. oxysporum. The strains FL1 (Thozetella neonive), MJY26 (Phalocephala fortinii), and MF4 (Phalocephala fortinii) showed good biocontrol effects on root rot caused by F. oxysporum, with control effects of 72.76%, 75.86%, and 77.93%, respectively. Inoculation with FL1, MJY26, and MF4 strains significantly increased the activities of phenylalanine ammonia lyase, polyphenol oxidase, and peroxidase antioxidant in blueberry, and also root vigor of these blueberry seedlings, thereby reducing stress caused by F. oxysporum. The DSE strain MF4 showing best inhibitory effect against F. oxysporum was selected for further test. This strain showed a prevention and control effect of 79.27% on Fusarium root rot of blueberry seedlings in pot experiment. The results lay an important foundation for developing DSE microbial agents against blueberry root rot caused by F. oxysporum.

Phenylpyrrole(PPs)fungicides have emerged as a critical class of agrochemicals for plant disease management in modern agriculture due to their unique mode of action. However, the emergence and spread of field-resistant fungal strains pose a significant threat to their long-term efficacy. This review comprehensively summarizes the development history, representative compounds, modes of action, and resistance evolution of phenylpyrrole fungicides. It elaborates on the molecular resistance mechanisms in plant pathogenic fungi, focusing on mutations in key components of the Hog1-MAPK signaling pathway, including the histidine kinase gene Os1 (HHK3) and its downstream genes OS2, OS4, and OS5, as well as mutations in the transcription factor Mrr1 that lead to overexpression of the efflux pump AtrB. The review aims to provide a scientific basis for optimizing the application strategies and resistance management of phenylpyrrole fungicides.

Soft rot of konjac was found in main konjac-planting areas in Shangluo region of Shaanxi Province, China. The symptoms include petiole and corm rot, which result in leaf yellowing and wilt, even the death of entire plant. This has caused serious economic losses to konjac production. To identify the causal agent of this disease, petiole and corm samples of konjac with typical symptoms of soft rot were collected from Shanyang, Danfeng and Shangnan counties in Shangluo region from 2023 to 2024, and tissue isolation method was used to obtain potential pathogens. Based on morphological and biochemical characteristics, phylogenetic relationship inferred from full genome and the 16S rRNA sequence, and the result of pathogenicity test, the pathogen was identified as Raoultella ornithinolytica. This is the first report of konjac soft rot caused by R. ornithinolytica in the world.

Rice sheath blight, caused by Rhizoctonia solani, is one of the three major diseases of rice, posing a serious threat to rice production. Currently, the sustainable management of rice sheath blight remains constrained by both the limited availability of resistant germplasm and the incomplete understanding of molecular defense mechanisms, representing critical barriers to effective disease control. Although sugar transport proteins (STPs) have been implicated in plant immunity, their functions in rice resistance against R. solani remain unclear. This study demonstrated that R. solani inoculation significantly induced the expression of rice STP genes. Through integrated bioinformatics analysis, protein structure prediction, subcellular localization, and functional validation, we revealed that: OsSTP4 and OsSTP14, as stably expressed alkaline transmembrane proteins, exhibited broad substrate specificity for hexose transport (including glucose, fructose, and galactose), while OsSTP26 specifically transported glucose due to its structural instability; three-dimensional structure modeling identified a unique acidic amino acid cluster in the extracellular domain of STP4, suggesting its potential role in substrate recognition via electrostatic interactions; functional validation showed that OsSTP4-silenced plants exhibited enhanced susceptibility to sheath blight, while OsSTP26 knockout mutants displayed less susceptible to sheath blight compared to wild-type control. These findings unveil the functional antagonism between OsSTP4 and OsSTP26 in sheath blight resistance, elucidating their molecular basis in this regulatory process and providing theoretical insights into the functional heterogeneity of the STP family members.

In the study, a metacaspases gene was islated from the cDNA library of the interaction between the wheat cultivar ‘Suwon 11’ and Puccinia striiformis West. f. sp. tritic Eriks.＆ Henn.(Pst). The gene was designed as TaMCA3. Through transient overexpression experiments, it was found that the TaMCA3 gene can effectively inhibit cell necrosis induced by the cell necrosis inducer BAX. The protoplast subcellular localization experiment showed that the TaMCA3 protein is mainly distributed in the cytoplasm. During the compatible interaction between wheat and Pst, it is shown that TaMCA3 participates in the susceptibility process of wheat to Pst. After using VIGS (virus-induced gene silence) technology to transiently silence TaMCA3, in comparison to the control plants, the silenced plants exhibited obvious necrotic spots on their leaves, and the number of urediniospore pustules of Pst CYR31 was significantly reduced. This indicates that silencing TaMCA3 can significantly enhance wheat′s resistance to Pst CYR31. Furthermore, by using yeast two-hybrid screening identified TaASP, a left-handed aspartate protease, was identified as the interacting target of TaMCA3. In vitro and in vito protein interaction experiments confirmed the interaction between TaASP and TaMCA3. This discovery provides new insights for a deeper understanding of the specific functions and mechanisms of TaMCA3 in the interaction between wheat and Pst.

Carya illinoensis is an important non-timber forest species in China, and one of the most serious diseases caused by Colletotrichum spp. dangerously threaten the development of the pecan industry. In order to investigate the pathological mechanism of Colletotrichum spp. in pecan, C. fructicola B-5 was used to establish and applied the genetic transformation system. The results showed that mycelium was cultured in CM medium for 20 h, 1% lysing enzyme was lysed at 30 °C for 3 h. The production of protoplasts was up to 8.92×10⁶ cells·mL^-1. Using PEG-mediated protoplast transformation, the plasmid with the resistance gene and GFP gene can be transferred into B-5 protoplasts, and the biological characteristics of the positive transformant B-5(GFP) did not change significantly. The B-5(GFP) strain was used to analyze the infection dynamics of Colletotrichum spp. on the host leaves. The results showed that the conidia began to germinate on the surface of the host after 9 h, began to infect the host mesophyll tissue after 48 h, and a large number of primary hyphae were produced after 96 h, and the infected part showed cell death. The genetic transformation system of C. fructicola in pecan was successfully established in this study, and the infection dynamics of C. fructicola B-5(GFP) on pecan were preliminarily clarified, which laid a foundation for subsequent pathogenic mechanism analysis and prevention and control.

In this study, an infectious clone of zucchini yellow mosaic virus (ZYMV) was constructed, and the differentially expressed genes (DEGs) of ZYMV-infected Cucumis melon were analyzed via RNA-Seq technology. The RNA was extracted from the leaves of ZYMV-infected C. melon, the 3 segments divided from the full genome of CGMMV were cloned separately by using RT-PCR, and then the ZYMV infectious clone was constructed through homologous recombination. Healthy C. melon was inoculated with pCB-ZYMV, typical mosaic symptoms were observed in the C. melon at 7 days post inoculation (dpi), and ZYMV CP protein could be detected by Western blot. The total RNAs extracted from the ZYMV-infected and healthy C. melon leaves, respectively, were sent to the biotech company for high-throughput transcriptome sequencing analysis. A total of 3 108 differentially expressed genes (DEGs) were screened, of which 1 558 were up-regulated and 1 550 were down-regulated. GO, COG annotation and KEGG pathway analysis revealed the involvement of many DEGs in host plant carbohydrate transport and metabolism, plant signal transduction, plant-pathogen interactions, starch and sucrose metabolism, and MAPK cascade response and other physiological metabolic pathways related to disease resistance. To validate the RNA-seq results, the differential expression of eight genes were examined by qRT-PCR, which was basically consistent with the transcriptome results. This study is of great significance for elucidating the molecular mechanism of ZYMV resistance in melon and breeding selection of ZYMV resistant melon varieties.

Plant disease specimens are important for the research and teaching of plant pathology. However, plant disease specimens made by conventional methods are prone to discoloration, being damaged, making it difficult to preserve for long periods. In this study, we used a combined method of vacuum lyophilized technology and crystal resin dripping technology to prepare specimens of a telial horn and jelly-like state of a telium of the apple rust fungus. This method is low-cost, and effective, by which plant disease specimens that are made can be preserved for a long term, being maintained the original morphological characteristic and color of plant tissue and the pathogens. It also provides a plant disease preparation method being used in teaching courses or related aspects to plant pathology.

Cotton Verticillium wilt is a major soil borne disease in cotton production, which seriously endangers the yield and quality of cotton. There are two pathotypes of pathogens, defoliating and non-defoliating. The defoliating strains cause cotton leaves to be yellowing, wilting, and defoliating, while the non-defoliating strains only exhibit yellowing and wilting, but without defoliating. The threatening to cotton industry caused by the defoliating Verticillium dahliae strains has been increasing year by year in China. Multiple plant hormones are involved in the physiological defoliation process of cotton, but the function of plant hormones in the pathological defoliation process of cotton is not yet clear. This study analyzed hormone levels, the tissue-specific expression patterns and levels of key genes in hormone pathways, in cotton plants infected with defoliating strain XJ592 and non-defoliating strain XJ511. The functions and variation patterns of plant hormones in the defoliation process were also clarified. Results showed that salicylic acid and ethylene play a positive regulatory role in the process of cotton defoliation induced by V. dahliae, while jasmonic acid, auxin, and cytokinin play a negative regulatory role. Multiple plant hormones co-regulate cotton defoliation.

High-throughput sequencing has become a crucial tool for advancing our understanding of fungal genomics and transcriptomics. However, accurately assessing gene expression levels from RNA sequencing (RNA-Seq) data necessitates the precise mapping of short sequence reads back to their correct locations in the reference genome. Sequenced strains often exhibit sequence variations from the reference genome strains, and due to the reference genome containing only one type of nucleotide information at any given locus, reads carrying alternative nucleotide information will have at least one mismatch with the reference genome, leading to mapping biases during the read alignment. To address this bias, researchers have developed various software and algorithms. Nevertheless, the applicability of these methods for fungal RNA-Seq data remains unclear. In this study, we took Fusarium graminearum, an important plant pathogenic fungus, as an example. Utilizing both simulated and real RNA-Seq data of this fungus, we comprehensively assessed the mapping biases and mapping rates of various mapping methods when dealing with single nucleotide polymorphisms (SNPs), RNA editing, and sequencing errors in reads. The results indicate that the graph-based genomic approach using the vg software outperforms others, demonstrating optimal performance. This method requires lower sequencing depth and significantly reduces mapping biases caused by polymorphic sites while improving reads mapping rates. These findings provide a reference for the analysis of complex fungal RNA-Seq data.