Nitric oxide interplay with hydrogen sulfide modulates gene expression and photosystem II function through enhanced antioxidant defense under PEG-induced osmotic stress in common bean (Phaseolus vulgaris L.).

Plants activate induced defences through the recognition of molecular patterns. Like pathogen-associated molecular patterns, herbivore-associated molecular patterns (HAMPs) can be recognised by cell surface pattern recognition receptors, leading to defensive transcriptional changes in host plants. Herbivore-induced defensive outputs are regulated by the circadian clock, but the underlying molecular mechanisms remain unknown. To investigate how the plant circadian clock regulates transcriptional reprogramming of a specific HAMP-induced pathway, we characterised the daytime and nighttime transcriptional response to the caterpillar-derived HAMP peptide In11 in the legume crop cowpea (Vigna unguiculata). Using diel and free-running conditions, we found that daytime In11 elicitation resulted in stronger late-induced gene expression than nighttime. Plants with a conditional arrhythmic phenotype in constant light conditions lost time-of-day gated responses to In11 treatment, and this was associated with arrhythmic expression of circadian clock core transcription factor Late Elongated Hypocotyl VuLHY1 and VuLHY2. Reporter assays with VuLHY homologues indicated that they interact with the promoter of daytime In11-induced Kunitz Trypsin Inhibitor (VuKTI) via a canonical and a polymorphic CCA1/LHY binding site (CBS), consistent with a mechanism of direct regulation by circadian clock transcription factors. This study improves our understanding of the time-dependent mechanisms that regulate herbivore-induced gene expression.

Chickpea (Cicer arietinum) is a nutritionally valuable legume crops; however, its productivity is significantly constrained by drought stress. This study aimed to evaluate morpho-physiological traits and molecular response of chickpea genotypes under well-watered (control) and drought conditions to identify drought-tolerant lines. Plants of 83 chickpea genotypes (55-60days old) were subjected to drought by withholding irrigation until soil moisture dropped 20-40%. Key physiological and agronomic traits such as relative water content (RWC), membrane stability index (MSI), chlorophyll content, yield parameters, drought tolerance efficiency (DTE),and drought susceptibility index (DSI) were measured. Data analysis was performed using R software for pairwise distance, correlation, Principal Component Aanalysis (PCA), and heat mapping. PCA explained 53.8% of the total variability, effectively separating genotypes based on stress response. Additionally, simple sequence repeat (SSR) markers were used to evaluate genetic variability. Genotypes SAGL19008 and SAGL162380 showed higher RWC, MSI,and chlorophyll content under drought, while genotypeICC4958 exhibited the highest DTE (101.19%) and the lowest DSI (60.54%), indicating strong drought tolerance. The identified genotypes hold potential for incorporation into breeding programs aimed at improving drought resilience in chickpea, thereby contributing to food security and sustainable agriculture.

Adzuki bean (Vigna angularis [Willd.] Ohwi & H. Ohashi) is a high-value legume crop widely cultivated globally, primarily in Asia, for its nutritional benefits and economic importance. In 2023, an epidemic outbreak of stem rot disease was observed in commercial adzuki bean fields in Shangzhi City, Heilongjiang Province, China. Through tissue isolation and fulfillment of Koch's postulates, nine pathogenic fungal isolates were obtained from diseased stems. Morphological, molecular, and phylogenetic analyses identified Fusarium graminearum Schwabe and F. oxysporum f. sp. glycines as the causal agents, representing the first report of these fungi causing stem rot on adzuki bean in China. Pathogenicity testing of nine plant species (seven legumes and two cereals: corn and wheat) revealed that all tested crops commonly cultivated in Northeast China were susceptible to infection by F. graminearum and F. oxysporum. In vitro screening identified high sensitivity of F. graminearum to tebuconazole, with 80.0% mycelial growth inhibition at 4.3 × 10-4 g·ml-1, and high sensitivity of F. oxysporum to ethylicin, with 82.7% inhibition at 8.0 × 10-4 g·ml-1. This study provides a comprehensive characterization of the pathogens, defines their host range, and identifies tebuconazole and ethylicin as effective candidates for field control, offering management strategies to protect adzuki bean production in Heilongjiang Province.

Winter oilseed rape (WOSR, Brassica napus) is a major food, feed and fuel crop that heavily relies on pesticides and fertilisers to obtain maximum yield. We tested the potential of intercropping WOSR with legumes (frost-sensitive spring faba bean, frost-sensitive berseem clover or winter hardy pea) to reduce the abundance of and damage caused by the WOSR insect pest complex, enhance biocontrol and replace synthetic inputs with ecosystem functions. Each intercrop was tested under varying crop management practices (full or reduced fertilizer and pesticide input, WOSR row spacing and sowing time of legume crop relative to WOSR). WOSR - spring faba bean intercropping reduced the abundance of cabbage stem flea beetle larvae on average from 6.87 to 3.48 per plant compared to WOSR sole cropping, but a 10-day sowing delay of the clover or spring faba bean intercrop increased cabbage stem flea beetle larvae per plant from 3.17 to 5.52 compared to when the crops were sown simultaneously. WOSR - spring faba bean intercropping also reduced pollen beetle bud damage by 34% (95% CI: 16%, 48%) compared to WOSR sole cropping. Parasitism rates of pollen beetle and cabbage seed weevil were not affected by intercropping or crop management. WOSR seed yield (kg ha-1) was 35% (95% CI: 13%, 51%) lower in WOSR-spring faba bean intercropping compared to WOSR sole cropping, and 38% (95% CI: 26%, 47%) lower in low input compared to high input systems. Our results confirmed that intercropping WOSR with frost-sensitive legumes can reduce insect pest pressure, but also highlighted a trade-off with WOSR yield and the importance of legume sowing time in relation to WOSR. © 2026 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Abstract Sainfoin ( Onobrychis viciifolia ) is a forage legume crop with resurgent popularity due to its anti-bloating and anthelmintic properties attributed to its relatively high content of condensed tannins. Although this property of sainfoin is desirable, sainfoin lags behind other popular forage crops in attributes, such as biomass yield, waterlogging tolerance, and stand persistence. Traditional breeding efforts to improve sainfoin have been constrained by its tetraploid genome and obligatory outcrossing nature. To accelerate the development of competitive cultivars using molecular-based approaches, a method for stable genetic transformation was needed. Here we describe a method for Agrobacterium tumefaciens -mediated transformation of sainfoin ‘AAC Mountainview’ cotyledons using A. tumefaciens strain GV3101 that produces an average transformation efficiency of 10%. We used the FB_35S::RUBY binary vector for transformation which harbors the RUBY reporter gene to enable quick and easy identification of transformation events early in the tissue culturing process. This research establishes the foundation for future advances in sainfoin through molecular-based improvement.

The spotted or legume pod borer, Maruca vitrata (Lepidoptera: Crambidae), is a global insect pest of many economically important grain and vegetable legume crops. Although the species is believed to have originated in the Indo-Malayan region, populations in India have shown evidence of genetic divergence, potentially representing distinct cryptic species or host-associated races. A comprehensive understanding of the evolutionary relationships and functional divergence within M. vitrata is currently limited by the absence of detailed genomic resources. Integrating karyotype data with high-resolution genomic information is therefore essential to elucidate the genetic architecture and evolutionary dynamics of the Indian lineage of M. vitrata and to inform effective pest management strategies. PacBio HiFi sequencing and proximity ligation technique (Hi-C), we provide here an improved genome assembly of M. vitrata. The 459.3Mb genome was assembled into 45 scaffolds with a scaffold N50 of 15.6Mb. The 31 pseudochromosomes (size range from 9.48 to 20.42Mb) accounted for 458Mb, representing 99.73% of the genome assembly. The genome has a repeat content of 36.67% and 21,586 protein-coding genes. The genome completeness analysis using BUSCO with the Insecta lineage((Insecta_odb10) captured 99.5% of the complete BUSCOs. The karyotype analysis revealed the presence of 31 chromosomes (1n). This genome-scale data helps by identifying target genes for the development pest management strategies in the future. The 31 pseudochromosomes correspond to the 31 chromosomes identified through karyotype analysis, thereby confirming the chromosomal-level completeness and structural accuracy of the assembly.

Dolichos bean is a nutritionally rich yet underutilized orphan legume crop. Conventional phenotype-based genetic improvement has been slow; therefore, integrating genomic selection (GS) into breeding programs is essential to accelerate genetic gain. Our objective in this study was to optimize the factors influencing GS success in dolichos bean by identifying: (i) the most effective GS model, (ii) an appropriate training population (TP), and (iii) the ideal selection generation for fresh pod yield. Four populations with distinct genetic structures were evaluated for fresh pod yield and genotyped using 413 SSR markers distributed across 11 linkage groups. The TPs were evaluated across five environments (locations and/or years), whereas the breeding populations (BPs) were evaluated over two seasons. Four GS models were trained on two differentially structured TPs and validated on two breeding populations. The optimal generation for genomic prediction was assessed by comparing an early-generation segregating population (F2:3) with an advanced-generation population (F5:6). Our results indicate that the RKHS model showed the highest predictive ability (i.e. correlation between observed and predicted fresh pod yield) compared to the other three models. We found that a closely structured Recombinant Inbred Line (RIL) population is the most effective for training genomic prediction models. Furthermore, predictive abilities were comparable between the F2:3 and F5:6 generations. We conclude that predicting fresh pod yield in early segregating generations using an RKHS model trained on a RIL population is highly effective strategy for implementing GS in dolichos bean improvement programs.

Mitogen-activated protein kinases (MAPKs) modulate the organization of the plant cytoskeleton. The spatial organization of microtubules is critical for cell division, polarity, shape control, and elongation during plant growth and morphogenesis. Here, we analyzed the impact of the stress-induced MAPK (SIMK) abundance on the tubulin cytoskeleton in different plant organs and tissues of an important legume crop species, alfalfa (Medicago sativa L.). For this purpose, we have established unique transgenic double lines with genetically manipulated SIMK, possessing microtubular molecular fluorescent marker, the tag RED FLUORESCENT PROTEIN-TUBULIN ALPHA 6 (tagRFP-TUA6). We show that lower or higher SIMK abundance can change cell division planes (CDPs) and phragmoplast orientations in roots. In addition, the transgenic line with downregulated SIMK shows disordered and disorganized microtubules, and a reduced degree of microtubule bundling mainly in leaves and stems. This may be linked to smaller habitus, shorter stems, and smaller leaves. Obtained results indicate that the genetic manipulation of SIMK abundance has effect on microtubule organization and plant development in alfalfa. This study also paves the way for testing anti-microtubular drugs on alfalfa and for biotechnological use of the newly-developed lines.

Legume nodulation is initiated when soil bacteria rhizobia infect root hairs and is tightly regulated by host-derived mechanisms that restrict nodule numbers to balance the benefits of symbiotic nitrogen fixation with the plant's growth and metabolic demands. However, how plants actively promote the initiation of nodulation to counterbalance these restrictive mechanisms and maintain an optimal level of nodulation remains largely unknown. Here, we report a systemic regulatory mechanism through which soybean (Glycine max) promotes rhizobial infection. We show that inoculation of soybean roots with rhizobia suppresses the biogenesis of microRNA miR4416-5p in shoots, a mobile microRNA that is transported from shoots to roots. The resulting reduction of miR4416-5p levels in roots enhances the expression of a vegetative lectin gene Lectin 3 (GmLe3), which promotes rhizobial infection, thereby enhancing nodule formation and improving plant productivity under low nitrogen conditions. We further demonstrate that suppression of miR4416-5p biogenesis in shoots is triggered by the root-derived C-TERMINALLY ENCODED PEPTIDE 7 (GmCEP7), establishing a long-distance GmCEP7-miR4416-5p-GmLe3 regulatory loop that is critical for desirable symbiotic synergy and plant productivity. Comparative genomic analysis reveals that this miR4416-5p-mediated regulatory module is absent in the model legumes Medicago truncatula and Lotus japonicus but appears to be conserved in economically important legume crops common bean (Phaseolus vulgaris) and pigeonpea (Cajanus cajan), suggesting an evolutionary innovation in nodulation control. These findings uncover a systemic mechanism that promotes rhizobial infection and highlight an evolutionary innovation in regulation of nodulation with potential implications for improving legume crop productivity under nitrogen-limited conditions.

Chickpea is one of the most important grain legume crops of India. Chickpea production is constantly under threat from various biotic and abiotic stresses. Dry root rot (DRR) caused by the necrotic fungus Macrophomina phaseolina is an important threat to chickpea productivity. Identifying resistant sources is the first step in breeding resilient varieties. In the present study, 56 genotypes from different chickpea regions of India were evaluated for their response to DRR using different screening methods, including paper towel, pot inoculation, and mycelium suspension drenching, followed by screening promising lines in the sick plot. This multi-method approach is crucial as genotypes’ responses to disease can vary depending on the screening technique used. Among the tested genotypes, RVSSG 64, demonstrated consistent resistance across all screening methods. Additionally, genotypes RVSSG 58, JSC 37, H14-04, and H14-21 with varying degrees of resistance were also identified.

Mungbean is an important legume crop native to India. In this study, 500 indigenous mungbean accessions collected from diverse eco-geographical regions of India were evaluated for agronomic trait genetic variability and core collection development. The accessions were grown in an augmented design during 2019 and 2020, and data were recorded for seven quantitative and 13 qualitative traits. Analysis of variance (ANOVA), frequency distribution, and box-plot analyses revealed substantial phenotypic variation among the accessions. Traits including plant height (PHT), number of pods per plant (NPP), hundred-seed weight (HSW), and single-plant yield (SPY) exhibited high heritability coupled with high genetic advance, indicating the predominance of additive genetic effects. Principal component analysis showed that the first three principal components explained 70% of the total phenotypic variation. The Shannon–Weaver diversity index further indicated high levels of genetic diversity within the population. Based on quantitative traits, the accessions were grouped into six major clusters and 42 sub-clusters, with SPY, NPP, HSW, PHT, and days to 50% flowering (DFF) contributing substantially to genetic divergence. Correlation analysis suggested that direct selection for SPY and indirect selection through associated traits, including NPP, HSW, PHT, NSP, and pod length (POL), may enhance yield improvement. The germplasm collection also possessed desirable traits such as high yield potential, contrasting maturity groups, and plant types suitable for mechanical harvesting and bold-seeded type. A representative core set comprising 50 accessions was developed using the PowerCore program, providing valuable genetic resources for mungbean breeding and genetic improvement programs.

Soybean (Glycine max) is an important legume crop worldwide. An emerging leaf spot was observed in soybean plants with obvious black necrotic spot symptoms during the disease survey in Changping District, Beijing, China. To confirm the causal agent, the pathogen was isolated from the diseased leaves. Three isolates were obtained and showed a morphology extremely similar to Paramyrothecium vignicola. The isolates were identified by morphological and molecular characteristics. Phylogenetic analyses were performed using multiple gene regions (ITS, cmdA, rpb2, and tub2). The result indicated that the three isolates showed a high similarity (100%) with the known P. vignicola strains. Pathogenicity and host range tests of the isolates were performed on soybean and other legume crops. Three isolates were strongly pathogenic to soybean, hyacinth bean, common bean, faba bean, pea, mung bean, and lentil; moderate pathogenicity on adzuki bean; mild pathogenicity on cowpea and peanut. To screen resistant germplasms for disease control, the screening experiment of inoculum concentration of P. vignicola were performed. The result showed the most suitable concentration of P. vignicola isolate is 1 × 105 spores/mL for evaluation of germplasms resistance. Paramyrothecium species have been frequently identified to cause leaf spot and blight disease on a wide range of vegetables, ornamental plants, and economic crops. To our knowledge, this is the first report of P. vignicola inducing leaf spot on soybean worldwide. This study indicates P. vignicola might pose a potential risk to legume crops in the future.

Protein informatics: Development and validation of a universal NIR spectroscopy-based deep learning and chemometric models for protein quantification in legume crops—A high-throughput approach for large germplasm screening

Thrips (Order: Thysanoptera) are significant agricultural pests that cause severe economic losses globally through direct feeding damage and their role as vectors of orthotospoviruses. South Florida's warm climate and diverse cropping systems, particularly legume crops such as snap bean (Phaseolus vulgaris L.) and lablab (Lablab purpureus), provide favorable environment for thrips infestations. Three thrips species, Megalurothrips usitatus (Bagnall), Thrips palmi Karny, and Frankliniella insularis (Franklin) (Thysanoptera: Thripidae), are prevalent in the region, with M. usitatus being an invasive pest that poses a significant threat to leguminous crops. Accurate species identification is critical for effective integrated pest management strategies. However, morphological identification is challenging due to the small size, subtle diagnostic traits, and high phenotypic similarity among thrips species, particularly in immature stages. This study aimed to develop a rapid, reliable molecular identification tool for these thrips species using high-resolution melting (HRM) analysis, a post-polymerase chain reaction (PCR) technique that differentiates DNA sequences based on their unique melting profiles. HRM analysis enables species-specific identification by detecting genetic variations and single nucleotide polymorphisms in PCR amplicons. We optimized and validated an HRM-based assay for the precise identification of M. usitatus, T. palmi, and F. insularis using both adult and larval stages collected from leguminous crops in South Florida. The assay demonstrated high specificity, sensitivity, and reproducibility, providing a robust molecular diagnostic tool for species identification. This method has the potential to enhance pest management efforts by facilitating early detection and targeted management, reducing the economic impact of thrips on legume production in the region.

Salt stress is a major challengeto the production of legumes as it affects their germination, growth, yield, and general physiology. Further, it also impairs their nitrogen fixation by causing osmotic stress and sodium-induced nutrient imbalances. Treatment with melatonin, a potent antioxidant and growth regulator, leads to the metabolic reprogramming of the plants to improve the stress tolerance capabilities of plants, and therefore, could be useful for improving resilience to salt stress. Horsegram, a nutraceutical legume, shows genotype-dependent variability toward salt stress tolerance; however, how the contrasting genotypes (salt-tolerant and susceptible) respond to melatonin treatment is relatively unclear. Based on our previous findings, two salt-tolerant (DH-22 and DH-29) and two salt-sensitive (DH-11 and DH-12) genotypes of horsegram were selected to investigate the effects of melatonin on salt-stressed seedlings. All four horsegram accessions were subjected to exogenous melatonin treatment at concentrations of 50, 100, and 150µM under 100mM NaCl. Results suggested that the melatonin treatment significantly improved growth and biochemical profiles in all horsegram genotypes under salt stress. The tolerant genotypes showed superior root and shoot growth, higher relative water content, chlorophyll, carotenoids, proline, phenolic, and flavonoid compounds, and increased antioxidant enzyme activity. They also exhibited lower levels of oxidative stress markers like malondialdehyde, hydrogen peroxide, and ion leakage compared with sensitive genotypes. The histochemical staining methods involving 3,3'-diaminobenzidine, nitro blue tetrazolium, and trypan blue stains further indicated the melatonin-induced reduction in cell death and reactive oxygen species accumulation in salt-affected horsegram seedlings. Overall, the tolerant genotypes were recorded to respond better to melatonin-mediated stress amelioration than the sensitive genotypes. Further, the present study also underlines the melatonin's potential to improve stress tolerance in legume crops like horsegram to improve salt stress resilience. Future research should concentrate on identifying the molecular processes that explain horsegram's melatonin-mediated salt tolerance. Furthermore, field-based assessments are required to confirm its usefulness for crop development programs.

The productivity and sustainability of legume crops are highly dependent on their tripartite symbiotic system with rhizobia and arbuscular mycorrhizal fungi (AMF), a system currently facing significant pressure from long-term excessive nitrogen (N) fertilization. However, how long-term N input and host niche selection jointly regulate the structure and function of this tripartite symbiotic system remains poorly understood. Using a soybean pot experiment with soils collected in 2022 from a 24-year field experiment (winter wheat-summer maize rotation, receiving annual urea at 0, 200, 400, 600 kg N ha-1 year-1 since 1998), we systematically elucidated these mechanisms. The results demonstrate that host niche selection is the dominant driver structuring the core symbiotic network. This manifests as a progressive, stringent homogeneous selection for rhizobia from soil to nodules, and as dispersal limitation for AMF, imposed by strong physical filtration at the root epidermis. Long-term N input nonlinearly disrupted this host-dominated framework. Specifically, excessive N fertilization shifted rhizobial community assembly from deterministic to stochastic dominance, weakened their cross-kingdom synergy with AMF, and triggered a transition in the systemic N-cycling pathway. This transition moved from an efficient, low-loss internal symbiotic N-fixation mode to a high-loss-risk external N metabolism mode. This functional trade-off ultimately compromised the system's nutrient accumulation and retention capacity, offering a mechanistic explanation for how excessive N fertilization drives agroecosystems from symbiosis-dependence to fertilizer-dependence. These findings demonstrate that optimizing N management sustains nutrient retention and productivity by preserving the host-shaped symbiotic network, offering a reference for reducing fertilizer dependence and improving the sustainability of legume production.

The legume pod borer, Helicoverpa armigera (Hübner), is one of the pervasive and destructive pests of legume crops, causing significant yield losses. In this study, we evaluated the nutritional performance and digestive enzyme activities of H. armigera when fed on ten mung bean varieties, including Baghmalek, India, Veys, Omrani, Parto, Simite1, Simite2, VC6371, VC3960, and VC6368. Additionally, biochemical profiling of these mung bean varieties, assessing starch, protein, anthocyanin, total phenolic and flavonoid content, was conducted to explore potential correlations with the nutritional physiology of H. armigera. The findings indicated that the larvae fed on Parto had lowest approximate digestibility, efficiency of conversion of ingested food, and relative growth rate, while those fed on VC6371 had the highest values. The values of efficiency of conversion of digested food were lower on Baghmalek and Parto and higher on VC6368 and VC6371. The lowest value of larval gain weight was on Parto. The highest proteolytic and amylolytic activities of larvae were observed on Veys and India, respectively; while the lowest enzyme activities were recorded on Parto. Our findings indicate that the low protein content combined with high levels of anthocyanin, total phenolics, and flavonoids may contribute to the potential tolerance of mung bean varieties against H. armigera. Cluster analysis revealed that VC6368 and VC6371 were the most suitablevarieties for H. armigera development, whereas Baghmalek and Parto were nutritionally less suitableand may severe as promising candidates for breeding or cultivation to minimise damage caused by this pest.

Lentil (Lens culinaris Medik.) is an important legume crop cultivated predominantly under dryland conditions where water deficit stress frequently limits yield. Understanding key yield-related and physiological traits that influence grain production under drought is essential for developing effective mitigation strategies. This study aimed to identify these traits and to evaluate the potential of growth regulators and bacterial inoculation to alleviate the effects of water stress in lentils. Field studies were conducted as a factorial experiment over two consecutive years using combinations of Pseudomonas fluorescens seed inoculation and foliar application of spermidine (0, 0.5, and 1 mM) and melatonin (0, 50, and 100 μM). Analysis of variance revealed significant effects for all treatments and their interactions on agronomic traits, yield components, and physiological parameters. Stepwise regression analysis showed that 100-seed weight, number of seeds per plant, and stem dry weight had the greatest direct positive effects on seed yield, whereas leaf dry weight had a negative effect. Among physiological traits, soluble sugars, photosynthetic pigments, and antioxidant enzyme activity were positively associated with yield, whereas total phenols, flavonoids, and malondialdehyde were major negative contributors. The combined application of 100 μM melatonin and 1 mM spermidine significantly improved sugar accumulation, photosynthetic pigment content, and antioxidant enzyme activity while reducing oxidative damage indicators. The integration of biochemical and statistical analyses effectively identified key traits driving lentil yield under drought stress. Foliar application of melatonin and spermidine also shows promise as an agronomic practice to improve lentil tolerance and productivity in water-limited environments. © 2026 Society of Chemical Industry.

Pea (Pisum sativum L.) is an essential legume crop cultivated globally as food and feed. However, its production is greatly constrained by Fusarium oxysporum f. sp. pisi (Fop). Breeding for resistance is the most efficient management strategy, but the genetic foundation of Fop resistance remains unclear. Previous quantitative trait loci mapping has located several genomic regions associated with resistance to Fop. However, the large marker-trait distances hampered the implementation of marker-assisted selection. To unravel candidate genes for Fop races 1 and 2, diversity array technology (DArT) markers were applied to 324 pea core collections for a genome-wide association study (GWAS). Phenotyping of the collections were performed under controlled growth chamber conditions with three independent experiments in a 324×3×7 factorial design. The collections were inoculated, and disease incidence was quantified over time using the area under the disease progress curve as the primary phenotypic measure for analyses. Phenotypic results revealed quantitative response and implicated wild accessions and landraces as favorable reservoirs of Fop resistance. GWAS using 26,045 DArT markers with three different models detected 15 marker-trait associations (MTAs) for Fop race 1 and 27 MTAs for Fop race 2 resistance. MTAs were scattered across six pea chromosomes, with several of them located within the confidence interval of four previous Fop resistance loci-thereby refining their location. In addition, 28 potential candidate genes were identified near associated markers involved in Fop resistance, including genes encoding a reverse transcriptase, exocyst and conserved oligomeric Golgi complex subunits, a FERONIA-like receptor kinase, homoserine kinase, a heat shock 70 protein, adenosine triphosphate transporters, and multiple transcription factors and plant defense-related proteins. These putative genes and molecular pathways provide a foundation for the sustainable management of Fop.