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PubMed2026

Rapid transcriptional reprogramming underlies Fusarium wilt resistance in strawberry: insights from comparative physiological and transcriptomic analyses.

INTRODUCTION: Fusarium wilt caused by Fusarium oxysporum f. sp. fragariae (Fof) severely constrains strawberry production, yet the underlying resistance mechanisms remain unclear. METHODS: A total of 64 strawberry germplasm accessions were evaluated for Fusarium wilt resistance. Integrated physiological and transcriptomic analyses were subsequently performed using the highly resistant cultivar 'Akihime' (ZJ) and the highly susceptible cultivar 'Ning Yu' (NY). RESULTS: Resistant resources were abundant, particularly among wild strawberry accessions. Compared with NY, ZJ exhibited higher soluble sugar accumulation, reduced oxidative damage, and increased peroxidase (POD) and phenylalanine ammonia-lyase (PAL) activities. Transcriptomic analyses revealed distinct temporal response patterns: ZJ underwent rapid and extensive transcriptional reprogramming at 24 h post-inoculation, whereas NY showed limited early responses but pronounced changes at 120 h. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that the early response of ZJ was mainly associated with stress-related processes, jasmonic acid-mediated signaling, transmembrane transport, plant-pathogen interaction, mitogen-activated protein kinase (MAPK) signaling, glutathione metabolism, plant hormone signal transduction, and secondary metabolism. Quantitative real-time polymerase chain reaction (qRT-PCR) validation supported the RNA-seq results and identified candidate genes associated with pathogen recognition, signaling, redox regulation, and protein homeostasis. DISCUSSION: These results indicate that rapid early immune activation and coordinated physiological and metabolic reprogramming are closely associated with strawberry resistance to Fof and provide useful germplasm and candidate genes for future functional validation and resistance breeding.

Fusarium oxysporum f. sp. fragariae↗
PubMed2024

Transcriptome analysis under pecan scab infection reveals the molecular mechanisms of the defense response in pecans.

Pecan scab, caused by the fungal pathogen Venturia effusa, is the most devastating disease of pecan (Carya illinoinensis) in the southeastern United States. Resistance to this pathogen is determined by a complex interaction between host genetics and disease pathotype with even field-susceptible cultivars being resistant to most scab isolates. To understand the underlying molecular mechanisms of scab resistance in pecan, we performed a transcriptome analysis of the pecan cultivar, 'Desirable', in response to inoculation with a pathogenic and a non-pathogenic scab isolate at three different time points (24, 48, and 96 hrs. post-inoculation). Differential gene expression and gene ontology enrichment analyses showed contrasting gene expression patterns and pathway enrichment in response to the contrasting isolates with varying pathogenicity. The weighted gene co-expression network analysis of differentially expressed genes detected 11 gene modules. Among them, two modules had significant enrichment of genes involved with defense responses. These genes were particularly upregulated in the resistant reaction at the early stage of fungal infection (24 h) compared to the susceptible reaction. Hub genes in these modules were predominantly related to receptor-like protein kinase activity, signal reception, signal transduction, biosynthesis and transport of plant secondary metabolites, and oxidoreductase activity. Results of this study suggest that the early response of pathogen-related signal transduction and development of cellular barriers against the invading fungus are likely defense mechanisms employed by pecan cultivars against non-virulent scab isolates. The transcriptomic data generated here provide the foundation for identifying candidate resistance genes in pecan against V. effusa and for exploring the molecular mechanisms of disease resistance.

Carya↗
PubMed2026

Genome-wide AP2/ERF analysis identifies HmaERF87 as a positive regulator of Hydrangea macrophylla leaf spot resistance.

A total of 164 APETALA2/ethylene-responsive factor (AP2/ERF) genes were identified in Hydrangea macrophylla, and HmaERF87 positively contributes to leaf spot resistance. The APETALA2/ethylene-responsive factor (AP2/ERF) transcription factor family plays important roles in plant stress responses, but its contribution to disease resistance in Hydrangea macrophylla (hydrangea) remains poorly understood. In this study, 164 AP2/ERF genes were identified in the H. macrophylla genome and classified into APETALA2 (AP2), ethylene-responsive factor (ERF), dehydration-responsive element-binding (DREB), and related to ABI3/VP1 (RAV) subfamilies. Their chromosomal distribution, conserved motifs, gene structures, and duplication patterns were analyzed. A total of 46 pathogen-responsive H. macrophylla AP2/ERF (HmaERF) genes were identified from the RNA sequencing (RNA-seq) dataset of resistant and susceptible cultivar leaves collected before and after Corynespora cassiicola inoculation. Promoter analysis revealed that the HmaERF genes with upregulated expression post-C. cassiicola infection showed a higher frequency and copy number of jasmonate-responsive cis-regulatory elements, suggesting their possible involvement in hormone-mediated defense responses. Three infection-induced candidate genes, including HmaERF56, HmaERF87, and HmaERF129, were selected for functional validation using virus-induced gene silencing (VIGS) in hydrangea leaf discs. Silencing of HmaERF87 expression via VIGS significantly increased lesion development after C. cassiicola inoculation, whereas the transient overexpression of HmaERF87 reduced the area of leaf disc lesions. Subcellular localization showed that the HmaERF87 protein was localized in the nucleus, and yeast assays indicated that its transcriptional activation activity was mainly associated with the C-terminal region of the protein. These results support a role for HmaERF87 as a positive regulator of H. macrophylla resistance to leaf spot disease and provide a candidate gene for further studies of disease resistance in hydrangea.

Plant Proteins↗
PubMed2026

Strain Diversity and Resistance to Cucumber Green Mottle Mosaic Virus (CGMMV) in Cucumber.

Cucumber green mottle mosaic virus (CGMMV) is a tobamovirus that causes disease in cucumber crops worldwide, leading to significant economic losses. To study the variability of CGMMV in southeastern Spain, partial genome sequences were obtained from isolates collected in 2017 and 2020 from cucumber crops. Phylogenetic analyses revealed that isolates clustered into two major groups, Asian (AS)-like and European (EU)-like CGMMV isolates. These two groups coexisted in the same area, crops, and even individual plants, although the AS type predominated. The accumulation and symptom expression of molecularly cloned isolates from these two groups were assessed in two cucumber cultivars (resistant and susceptible) under both summer and winter conditions. An in planta antagonistic interaction was detected between the AS and EU isolates, in which the accumulation of CGMMV-EU was suppressed during mixed infections. A multivariate analysis did not identify statistically significant differences because of variations in environmental conditions. Unlike CGMMV-EU, CGMMV-AS did not show significant differences in accumulation based on the plant genotype. To further investigate this, the response to CGMMV-AS infection was analyzed in additional susceptible and resistant cultivars. All cultivars appeared to be similarly susceptible to CGMMV-AS, in contrast to CGMMV-EU, which accumulated to a much lower extent in resistant compared with susceptible plants. These results reinforce the need to continue epidemiological surveillance, identify new sources of resistance, and implement strict control of infected seed trade, given the growing threat that CGMMV-AS isolates pose to cucumber cultivation.

agroinfectious clone↗
PubMed2026

Emergence of Fusarium oxysporum f. sp. fragariae in the Eastern United States.

Historically, Fusarium oxysporum f. sp. fragariae (Fof), the causal agent of Fusarium wilt in strawberry, has been a major problem for strawberry production in California but has been largely absent in the rest of the United States. During the growing seasons of 2023 to 2025, independent detections of Fof were made on strawberry plants exhibiting symptoms of Fusarium wilt in the eastern U.S. states of Florida, North Carolina, New York, Connecticut, and Virginia. Sixteen isolates were obtained from symptomatic plants across this region, and a subset (n = 14) were confirmed to be Fof by pathogenicity testing, morphological characterization, PCR diagnostics, and whole-genome sequencing. Specifically, these tests demonstrated that all tested isolates were virulent on susceptible (fw1) strawberry cultivars but not on resistant (FW1) cultivars, classifying them as race 1. Although all isolates tested positive with the more recently developed Fof-specific PCR assay by Burkhardt et al. (2019), many (43.75%) failed detection with the commonly used Suga et al. (2013) assay. Comparative genomics revealed that these isolates represent at least three distinct phylogenetic clades (Y1, Y2, and the putative Y10), suggesting multiple independent introductions rather than a single dissemination event. The genetic diversity of the eastern U.S. Fof populations and their likely origin from nursery stock highlight the need for more robust diagnostics, certified clean planting stock, and region-specific resistance trials to manage Fusarium wilt beyond California.

Fusarium↗
PubMed2026

The curious case of sporadic nematode susceptibility in "Tifguard" peanut (Arachis hypogaea): seed mixture or genetic instability?

The Runner-type peanut (Arachis hypogaea L.) cultivar "Tifguard" carries an introgressed chromosomal segment on chromosome A09 from A. cardenasii that confers resistance to root-knot nematode (RKN). Despite this, a proportion of "Tifguard" plants show RKN symptoms, which could plausibly be attributed to seed mixture or outcrossing. However, recent work has shown that cultivated peanut exhibits surprisingly frequent large-scale chromosomal instability (1% to 5%); suggesting that resistance loss could arise from spontaneous structural genomic change. To test these possibilities, we grew foundation seed in an RKN-infested field and collected symptomatic and asymptomatic plants. Lineages derived by single-seed descent were genotyped using the Axiom Arachis 48K SNP array v2 and whole-genome sequencing. Symptomatic lineages lacked the A. cardenasii introgression on chromosome A09 and instead carried the complete endogenous A. hypogaea A09 region at the expected dosage. There was no evidence of large-scale homoeologous exchange, deletion, or other genomic instability affecting this chromosome. Most susceptible plants were closely related to resistant "Tifguard" but lacked the A09 introgression, with a smaller proportion assignable to known nematode-susceptible cultivars, implicating seed mixture with a possible contribution from cross-pollination rather than genomic instability. Because resistance depends on a single major-effect segment, rare events have disproportionate phenotypic impact, placing high demands on genetic purity. For important traits conferred by major loci, marker-based testing across seed-increase stages could verify trait retention directly, and is increasingly practical as marker costs decline.

Arachis↗
PubMed2026

Comparative analysis of DDR-related genes and microRNA expression during rice germination: Implications for salinity susceptibility screening.

Soil salinity poses a significant threat to the agri-food sector and particularly to rice cultivation. High salinity during germination induces overproduction of reactive oxygen species (ROS) that cause lesions in the DNA resulting in reduced vigor. MicroRNAs (miRNAs) are known to modulate stress response in plants, however, studies focusing on its relation with the expression of the DNA damage response (DDR)-related genes are not thoroughly explored. In this regard, the aim of this work was to investigate the link between the expression of miRNAs and putative targeted DDR-related genes in response to salinity stress during germination. Eight varieties representative of indica and japonica rice subspecies were categorized into clusters through a principal component analysis (PCA) based on their germination performance and stress tolerance index under varying concentrations of NaCl. Subsequently, the expression patterns of six miRNAs and their putative targeted DDR genes were measured in two contrastive cultivars through quantitative real-time PCR (qRT-PCR) while correlations were examined through Pearson's analysis. Results showed distinct expression profiles between halotolerant and sensitive cultivars. Two miRNAs were further investigated in mature dry seeds of all the cultivars to verify their earliest, seed-specific discriminative potential. The distinct miR414 expression pattern may represent a potential biomarker for identifying salinity-susceptible cultivars during early-stage breeding screening.

Oryza↗
PubMed2026

Correlative analysis of endogenous miRNA expression profiles underlying brown planthopper adaptation to resistant rice.

The brown planthopper (Nilaparvata lugens Stål, BPH) is a major insect pest threatening global rice production. However, the molecular mechanisms underlying the adaptation of BPH populations with different virulence levels to resistant rice cultivars remain poorly understood. MicroRNAs (miRNAs), as key post-transcriptional regulators, play critical roles in host adaptation in herbivorous insects. In this study, we analyzed the miRNA expression profiles of a high-virulent population (IR56p) and a low-virulence population (TN1p) after feeding on susceptible (TN1) and resistant (IR56) rice cultivars. Our findings reveal distinct miRNA-mediated regulatory strategies employed by the two populations. The IR56p population showed downregulation of miRNAs including miR-10, miR-124, and miR-316, showing an inverse correlation with increased expression of predicted target genes involved in detoxification (carboxylesterase, UDP-glycosyltransferase) and effector function (calmodulin). In contrast, several miRNAs highly expressed in IR56p, including miR-307, miR-317, and miR-275, were predicted to target rice genes associated with hormone signaling, cell wall biosynthesis, and oxidative homeostasis, suggesting a possible but unproven inter-species regulatory role that requires functional validation. Collectively, these descriptive and correlative findings provide hypothesis generating insights into insect-plant coevolution and identifies candidate molecular targets for future functional validation and RNA interference-based pest management strategies.

Animals↗
PubMed2026

Identification of Novel Sources and Genetic Mapping for Bacterial Leaf Streak Resistance in a Geographically Diverse Panel of Wheat.

Bacterial leaf streak (BLS), caused by Xanthomonas translucens pv. undulosa (Xtu), has recently emerged as a significant threat to wheat production in the Northern Great Plains region of the United States. Deploying resistant cultivars is an economical and practical method of controlling BLS. To identify novel sources of BLS resistance, we screened a set of 355 bread wheat landraces and cultivars representing global diversity for their response to BLS. A wide distribution of seedling responses against BLS was observed, with most genotypes displaying a moderately to highly susceptible response. Notably, we identified 5 resistant and 33 moderately resistant responses. A high-resolution genome-wide association study using 302,524 high-quality single-nucleotide polymorphisms (SNPs) identified 10 significant marker-trait associations (MTAs) on chromosomes 1A, 1D, 3B, 4A, and 5A corresponding to unique genomic regions associated with BLS resistance. Compared with previous studies, four of these genomic regions are likely novel. Of these, MTA 'scaffold15531_2782724' associated with q5A.1 was highly significant (-log10P = 9.39) and exhibited the highest SNP effect (0.35). An association on chromosome 3B validated a previously identified 3B quantitative trait locus (QTL) mapped at approximately 6 Mbp in the hard red spring wheat cultivar 'Boost', and the high-resolution mapping from our study further refined the interval for this QTL. Furthermore, the narrow haplotype blocks reported in this study could be valuable for fine mapping of important regions. The novel resistant sources, along with identified genomic loci and corresponding SNP markers from this study, would be helpful for wheat-breeding programs to enhance BLS resistance.[Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

BLS↗
PubMed2026

First genomic insights into the introgression of almond PPV-Marcus resistance into peach.

AIM: Sharka, caused by Plum pox virus (PPV), is one of the most damaging viral diseases of stone fruit crops, with peach among the most susceptible cultivated Prunus species. Almond is a promising source of resistance, but its genetic architecture and expression in a peach genetic background remain largely unknown. This study aimed to construct parental genetic linkage maps and identify genomic regions associated with PPV response in almond × peach interspecific populations. METHODS: Progenies derived from the almond cultivars 'Del Cid', 'Garrigues', and 'Mono' were evaluated by RT-PCR after graft inoculation with the PPV-Marcus (PPV-M) strain over consecutive infection cycles. Phenotypic data were summarized for each genotype using best linear unbiased estimates (BLUEs). High-density SNP almond and peach arrays were used to construct parental maps for 'Garrigues' and 'Mono' and perform quantitative trait locus (QTL) analysis. RESULTS: Phenotypic variation was observed among and within families. 'Del Cid'-derived progenies showed the greatest resistance, 'Garrigues'-derived progenies displayed intermediate responses, and 'Mono'-derived progenies showed greater susceptibility and variability. The parental maps covered 546.69 cM in 'Mono' and 521.72 cM in 'Garrigues', with average intervals of 0.61 and 1.26 cM per unique marker position, respectively, and showed strong collinearity with the reference genome. QTL associated with PPV-M response were detected on linkage groups (LG) 1 and 6 in 'Garrigues' and LG2 in 'Mono'. The main QTL in 'Garrigues' peaked near 22.39 Mb on LG1, whereas the 'Mono' QTL was located at 22.27-22.62 Mb on LG2; a weaker QTL was detected near 25.38 Mb on LG6 in 'Garrigues'. The results support a quantitative and genetic-background-dependent architecture of PPV resistance. CONCLUSION: This study provides the first evidence of genomic regions associated with PPV-Marcus response in almond × peach populations. The detected QTLs provide an initial basis to support the introgression of almond-derived resistance into peach breeding material.

Prunus↗
PubMed2026

Genome-wide identification of CHY zinc finger and RING finger (CHYR) genes in pepper and functional characterization of CaCHYR5 in response to Phytophthora capsici infection.

CHY zinc finger and RING finger (CHYR) proteins play crucial roles in the growth and development, as well as stress response. To date, no systematic or comprehensive analysis of the CHYR gene family has been performed in pepper (Capsicum annuum L.). In this study, we identified 8 CaCHYR genes (CaCHYR1-CaCHYR8), which were classified into 3 groups based on phylogenetic relationships. CaCHYR members within the same group exhibited similar distributions of conserved motifs and exon-intron structures. Chromosomal localization analysis showed that 8 CaCHYR genes were unevenly distributed on 6 chromosomes. Segmental duplication, rather than tandem duplication, was found to be the major contributor to the expansion of this gene family. CaCHYR genes feature a variety of cis-elements involved in developmental processes, phytohormone responses, and stress adaptation. Expression analysis based on RNA-seq data revealed that CaCHYR genes exhibited distinct spatial expression patterns across different tissues and in response to Phytophthora capsici infection (PCI), and quantitative real-time PCR (qRT-PCR) further confirmed that three of them (CaCHYR2, CaCHYR3, and CaCHYR5) exhibited altered expression under PCI. Furthermore, transient overexpression of CaCHYR5 in pepper leaves increased susceptibility to PCI, suggesting its potential negative regulatory role in pepper defense against P. capsici. Collectively, these findings reveal the expression patterns and regulatory functions of pepper CHYR genes in growth and development, laying a groundwork for breeding pepper cultivars tolerant to PCI.

Phytophthora capsici infection (PCI)↗
PubMed2026

Leaf Rust in Rye: From Pathogen Biology to Host Defense and Resistance Breeding.

Leaf rust (LR), caused by Puccinia recondita f. sp. secalis (Prs), is considered one of the most dangerous rye (Secale cereale L.) diseases, causing yield losses exceeding 35%. This review summarizes all currently available data about this disease: pathogen characteristics (including its life cycle, natural variation, and disease symptoms), resistance resources, and the background of the plant immune response at the genome, transcriptome, and metabolome levels. The research conducted so far has allowed for the identification of dozens of genes that play a significant role in the rye immune response to Prs infection. Among them, genes encoding NBS-LRR proteins (including SECCE1Rv1G0014220, the most likely Pr3 candidate), glycosyltransferase, β-1,3-glucanase, 1-deoxy-D-xylulose 5-phosphate synthase, β-1,3-glucanase, UDP-glycosyltransferase, pathogenesis-related protein 1, ammonium transporter, and cytochrome P450 enzymes are candidates for seedling and all-stage resistance, whereas ScLr_ABC25 currently represents the most promising candidate associated with adult-plant resistance. Among the metabolites differentially accumulated in response to Prs, those related to phenylpropanoids, diterpenoids, and thiamine branches seem to play the most important role in the immune response. Finally, we suggest how the knowledge acquired so far about the rye-Prs interaction can be used in modern breeding programs aimed at obtaining cultivars with enhanced resistance to LR, such as through the use of functional gene markers and/or metabolic biomarker-assisted selection and, in the more distant future, by developing and applying new genomic techniques for precise editing of resistance and susceptibility genes, engineering synthetic immune receptors and decoys, and pan-genomic exploration for identification of rare or lineage-specific resistance alleles. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Plant Diseases↗
PubMed2025

Candidate genes at the Rmi1 locus for resistance to Meloidogyne incognita in soybean.

The RKN resistance locus Rmi1 was fine-mapped to two genes on chromosome 10, a glycosyl hydrolase family 9 β-1,4-endoglucanase gene and a type I pectin methylesterase gene. Root-knot nematodes (Meloidogyne spp.) are a serious threat to soybean production in the southeast USA, with yield losses of more than $165 million in 2023. Development and deployment of resistant soybean cultivars is the most effective strategy for managing these nematode pests; however, the identity of the resistance genes and underlying mechanism of resistance remains obscure. An additive resistance gene, Resistance to M. incognita-1 (Rmi1), to the predominant species, was first identified in soybean cultivar Forrest but never mapped to a genomic region. Multiple mapping studies have identified a major quantitative trait locus (QTL) with additive action on chromosome 10. In this study, a population consisting of 170 F2:3 families derived from a cross of Bossier (susceptible) × Forrest (resistant) was initially used to confirm that Rmi1 is in the chromosome 10 QTL. Subsequently, 884 F5:6 recombinant inbred lines (RILs) derived from the same cross were used to fine-map the Rmi1 causal gene(s) to two genes - a β-1,4-endoglucanase (Glyma.10G017000, EG) and a pectin methylesterase/methylesterase inhibitor (Glyma.10G017100, PME1). Both gene candidates have the potential to play a role in the resistance response to M. incognita. Both gene promoters harbor SNPs and indels and the encoded proteins exhibit amino acid polymorphisms, including a premature stop in PME1 of resistant soybeans. Additionally, both genes show a higher expression level in susceptible roots compared to resistant roots in the absence of infection. This suggests that Rmi1 may confer one or more pre-existing differences related to cell wall modification in soybean roots, ultimately leading to a decrease in susceptibility.

Tylenchoidea↗
PubMed2026

Quantitative trait loci associated with improved fruit yield under heat-stress conditions in fresh-market tomato.

Rising temperatures and more frequent heat stress events pose a major challenge to global tomato production, particularly in tropical and subtropical regions such as the southern United States. High temperatures during flowering and fruit set lead to poor fruit set and reduced yield. Although several commercial cultivars and breeding lines are described as heat-tolerant, the genetic basis of yield performance under heat stress conditions in fresh-market tomato remains poorly understood. This study aimed to identify genomic regions associated with fruit yield under natural heat stress. A biparental recombinant inbred line (RIL) population developed by the UF/IFAS tomato breeding program was evaluated under natural field heat stress in the fall seasons of 2016, 2017, and 2018, with fruit yield recorded as the primary trait. Genotyping of RILs was performed with the AgriPlex commercial tomato panel. Multi-environment QTL analysis was conducted to identify loci associated with fruit yield under heat stress. A major locus on chromosome 12 was selected for validation. Backcross populations segregating for this region were evaluated in a randomized block design during the fall of 2020 at the Gulf Coast Research and Education Center (GCREC), Balm, Florida. Multi-environment QTL analysis identified several loci on chromosome 4, 5, 6, and 12 associated with fruit yield under natural heat stress conditions. Among these, a locus on chromosome 12 showed consistent effects across multiple harvests and environments and explained a relatively larger proportion of phenotypic variance. Validation using backcross populations confirmed that genotype carrying the chromosome 12 QTL produced significantly higher yield under natural heat stress than susceptible genotypes. Overall, this study identified an agronomically important region on chromosome 12 that can be targeted to improve tomato yield under heat stress. The results also highlight multiple genomic regions contributing to higher yield under heat stress. These findings provide a foundation for developing breeding strategies for developing heat-tolerant fresh-market tomato cultivars.

QTL analysis↗
PubMed2025

Polyploidy-mediated variations in glutamate receptor proteins linked to Fusarium wilt resistance in upland cotton.

Cotton production in the US faces a serious threat from Fusarium oxysporum f. sp. vasinfectum race 4 (FOV4), a soil-borne fungus causing Fusarium wilt by infecting the roots and vascular system of susceptible cotton, leading to rapid wilting and death. Here, we investigate genetic mechanisms of resistance to FOV4 in the highly resistant upland cotton genotype "U1" using an early-generation segregating biparental population ("U1" × "CSX8308") with comprehensive genomic resources. Reference-grade genomic assemblies of the parents revealed minor structural variations between "U1" haplotypes, a high degree of collinearity at chromosome synteny and micro-synteny levels, and significant divergence from "CSX8308" with 8.9 million SNPs. QTL analysis identified significant markers on chromosomes D03 and A02 linked to reduced Fusarium wilt severity. Within these regions, two glutamate-receptor-like (GLR) genes showed structural variation and overlapped between translocated segments on A02 and D03, suggesting a rare but important reinforcing effect of parallel evolution between susceptible and resistant genotypes. Transcriptome profiles of "U1" under FOV4 infection reveal activation of calcium-binding proteins and transcription factors regulating plant hormones (ethylene, abscisic acid, jasmonic acid, and salicylic acid), along with enzymes involved in cell wall remodeling and phytoalexin production. Advancing cotton improvement depends on incorporating durable genetic disease resistance into high-yielding, high-quality cultivars.

Fusarium↗
PubMed2026

Identification and characterization of PsFwC9 conferring Fusarium wilt resistance in pea.

Pea (Pisum sativum L.) is one of the most important edible legumes in China, with both planting area and total yield ranking among the highest in the world. Fusarium wilt, caused by Fusarium oxysporum f. sp. pisi (Fop), is a severe factor limiting pea production. The deployment of resistant pea cultivars is the most effective and sustainable strategy for controlling this disease. In the present study, a novel resistance gene PsFwC9, conferring resistance to Fop race 5, was identified in the resistant pure line Chengwan 9-8 (CW9-8), and its candidate gene Psat4g213640 was characterized and functionally validated to be associated with disease resistance. Genetic analysis of the F₂ population derived from the cross between the resistant parent CW9-8 and the susceptible parent Chengwan 9-1 (CW9-1) revealed that PsFwC9 was controlled by a single dominant gene. Based on whole-genome resequencing, bulked segregant analysis sequencing (BSA-seq) and fine mapping, PsFwC9 was localized to an 817.06-kb region on chromosome 4 (i.e. linkage group IV, chr4LG4), flanked by KASP markers A016508 and A016511, and co-segregated with four markers. Haplotype analysis revealed that only the marker A016615 was significantly associated with Fusarium wilt resistance, and this marker was designated as a diagnostic marker for PsFwC9. Marker A016615 was located at 425 699 725 bp on chr4LG4, corresponding to the 277 bp within Psat4g213640, where a 'A/G' single-nucleotide polymorphism caused an amino acid substitution leading to an alteration in protein structure; therefore, Psat4g213640 was identified as the PsFwC9 candidate gene. Quantitative real-time PCR analysis showed no significant difference in the expression levels of Psat4g213640 between CW9-8 and CW9-1. Overexpression of the candidate gene Psat4g213640CW9-8 in the hairy root system significantly enhanced the resistance of CW9-1 to Fusarium wilt, whereas RNA interference-mediated silencing of Psat4g213640CW9-8 reduced the resistance of CW9-8, indicating that Psat4g213640CW9-8 played a crucial role in pea resistance to Fusarium wilt. In addition, subcellular localization showed that the protein encoded by Psat4g213640 was targeted to the endoplasmic reticulum. Collectively, these findings not only enriched the gene resources for disease resistance in pea and provided an important foundation for elucidating the molecular mechanism of PsFwC9-mediated resistance, but also provided important technical support for the practical application of molecular breeding for disease resistance in pea.

Journal Article↗
PubMed2026

Tobamoviruses: Advances in Molecular Biology, Host Interactions and Integrated Disease Management.

Tobamoviruses (viruses in the genus Tobamovirus, family Virgaviridae) lead to major yield losses in economically important crops around the world. In this review, we go beyond the canonical gene expression framework by integrating recent discoveries of reverse open reading frames (rORFs) on the negative-strand RNA. These rORFs have only been experimentally validated in cucumber green mottle mosaic virus (CGMMV), with predicted sequence-conserved homologs across a subset of the genus, including TMV, ToBRFV, and PMMoV. However, they are not universally present in all tobamoviruses. We systematically dissect the infection cycle-from disassembly and replication to cell-to-cell and systemic movement-with an emphasis on the host factors hijacked at each stage. We synthesize current understanding of plant antiviral immunity, focusing on RNA silencing and NLR receptor-mediated resistance as two pillars of defense, along with the transcription factors and microRNAs that orchestrate these responses. We critically evaluate the experimental evidence for both plant defenses and viral counter-strategies, noting that many mechanistic models derive from limited model systems. We further characterize host genetic resistance and susceptibility factors applicable to crop breeding. These resources include dominant NLR and non-NLR resistance, as well as recessive resistance derived from modified host susceptibility genes. We address how viral mutations, recombination and fitness trade-offs undermine resistance durability. We then evaluate their practical deployment through conventional breeding, the exploitation of quantitative resistance, and genome editing, and outline associated agronomic drawbacks and regulatory constraints. Using ToBRFV as a case study, we analyze its epidemiological traits and assess the current arsenal of surveillance tools, from field diagnostics to remote sensing. Finally, we survey management strategies across a spectrum of maturity. Some approaches, including sanitation protocols and conventionally bred resistant cultivars, have proven effective under field conditions. The first dsRNA-based biopesticide has recently been registered in China, while other biological control agents and low-risk chemical approaches remain largely at the experimental stage. We also discuss the bottlenecks that impede lab-to-field transition and highlight promising solutions such as precision breeding and evolution-oriented cultivar deployment. By bridging molecular virology, epidemiology, and integrated disease management, this review provides a critical, bench-to-field framework for the sustainable control of tobamoviruses.

TMV↗
PubMed2025

Quantitative trait loci for Globodera pallida resistance derived from wild potato species Solanum gourlayi.

Globodera pallida is a major pest that is responsible for huge losses in potato yields worldwide. Expanding the gene pool of cultivated potatoes with clones resistant to this pest is made possible by searching for resistance genes in wild Solanum species. The aim of this study was to identify quantitative trait loci (QTLs) for potato resistance to Globodera pallida derived from Solanum gourlayi. A resistant diploid potato clone, Sg 2/7 (Solanum gourlayi, accession CGN17592), was crossed with a susceptible potato hybrid clone, DW 94-4235, to generate an F1 mapping population. All clones were tested for nematode resistance using G. pallida, pathotypes Pa2 and Pa3, in 2 or 3 years (2017-2019), respectively. Diversity Array Technology (DArTseq) was used for genotyping and genetic map construction. QTLs for nematode resistance were identified on potato chromosomes II, IV, V, VI, VII, X, XI, and XII, explaining from 10.1 to 21.5% of phenotypic variance. The most significant QTL for resistance to G. pallida pathotype Pa2 was identified on chromosome XII, explaining 20.9% of the phenotypic variance in the dataset from 2017. The most significant QTL for resistance to the G. pallida Pa3 pathotype was identified on chromosome VI, with a CAPS marker Exp928 in its peak, explaining 21.5% of the phenotypic variance in the dataset from 2017. The novel QTLs for resistance to S. gourlayi may be useful for breeding resistant potato cultivars, further studies of candidate genes, and host responses of potato to G. pallida infection.

Quantitative Trait Loci↗