Early Blight Disease Research Articles

Preliminary Insights into Sustainable Control of Solanum lycopersicum Early Blight: Harnessing Arbuscular Mycorrhizal Fungi and Reducing Fungicide Dose

Tomato (Solanum lycopersicum L.) production is constantly threatened by several fungal pathogens, such as Alternaria solani, the causal agent of early blight disease. In this study, a greenhouse experiment was set up to evaluate the biocontrol ability of arbuscular mycorrhizal fungi (AMF) against A. solani in the presence of reduced doses of fungicides (i.e., captan and copper oxychloride). Disease severity, plant growth traits, chlorophyll and phosphorus content, phenolic compounds, and antioxidant activity were assessed. The effects of fungicide dose on AMF were investigated by root colonization, spore density, and mycorrhizal dependence evaluation. AMF-inoculated and fungicide-treated plants reduced disease severity compared to fungicide-treated and non-mycorrhizal plants, in most cases, regardless of the fungicide dose. AMF improved plant growth, especially when combined with copper oxychloride. However, plant fresh weight decreased in plants treated with the lowest dose of captan (25 g 100 L−1). Overall, AMF colonization decreased in plants with high fungicide doses, while the leaf color parameters did not show differences between treatments. The results suggest reducing the fungicide dose using AMF is possible, particularly for copper oxychloride. Further studies will be required to confirm these data. This integrated approach could offer a sustainable alternative to decrease the use of chemical control.

Early Blight Disease Management of Potato

Early Blight Disease Management of Potato

Assessment of Early Blight Disease Resistant Tomato F1 Hybrid Arka Abhed in Karimnagar District of Telangana, India

Tomato is the major Solanaceous vegetable crop grown in Karimnagar District of Telangana. Alternaria tomatophila and Alternaria solani cause early blight disease and severe yield losses to the tomato growers in Karimnagar District. Early blight is the major problem in Karimnagar from June to September months causing severe crop losses to the tomato farmers. Usually farmers are spraying different fungicides based on Copper to control early blight disease for private hybrids. It controls 25-35% of the disease and increased cost of cultivation. Hence, early blight disease resistant hybrid Arka Abhed was tested against private hybrid in KVK, Karimnagar operational area. Data on disease incidence was collected at 15, 30, 60, 90,120 DAP in all the hybrids. The data revealed that Arka abhed recorded significantly very lower incidence of early blight disease than private hybrid during all crop growth stages. It recorded 1.5% early blight incidence whereas private hybrid recorded 32.4%. Reduced number of sprayings to control early blight disease were also significantly low i.e. two sprays were carried out whereas in private hybrid seven sprays were done during in rainy period. According to yield Arka Abhed recorded 68.3t/ha whereas it was 58.6t/ha in private hybrid. The peduncle in green in colour for long days and taste also same for all the days in storage period for 8-12 days in Arka Abhed. Average fruit weight is 86 gr to 112 grams were recorded.

Eco-friendly synthesis of tin oxide nanoparticles: A novel strategy for managing early blight and soft rot in tomato crops

Tomato, a globally cultivated crop, is susceptible to early blight (Alternaria solani) and soft rot disease (Pectobacterium carotovorum), resulting in significant yield reductions. In this study, we report the biosynthesis of tin oxide nanoparticles (SnO2 NPs) via a novel, eco-friendly route and evaluate their efficacy against these phytopathogens. Characterization of SnO2 NPs revealed a mean particle size of 11.5 nm, uniform distribution, and pure and high crystallinity, as confirmed by TEM, SAED pattern, and P-XRD analysis. The green-synthesized SnO2 NPs achieved 100 % inhibition of fungal growth at 500 μg/mL and displayed a larger zone of inhibition against Pectobacterium carotovorum than the conventional antibiotic streptomycin. A notable decrease in the exponential phase of the OD600 curve and CFU/mL was further observed with increasing concentrations of NPs. They also demonstrated superior antioxidant properties compared to the standard, achieving over 90 % inhibition at a concentration of 300 μg/mL. The Terminalia chebula seed extract not only acts as a stabilizing agent but also exhibit antimicrobial activity. The synergy between the intrinsic antimicrobial properties of the SnO2 NPs and the bioactive compounds from the seed extract enhance the overall effectiveness of the nanoparticles against these pathogens. Our findings suggest that green-synthesized SnO2 NPs offer a promising and sustainable solution for managing early blight and soft rot disease in tomato crops.

ASSESSMENT OF EARLY BLIGHT RESISTANCE IN INDIAN POTATO CULTIVARS AND ASSOCIATED BIOCHEMICAL CHANGES DURING DISEASE DEVELOPMENT

Among the twenty-three varieties of potato screened against early blight disease under field conditions during Rabi 2020-21 and Rabi 2021-22 in Gujarat at Anand agricultural University, Anand, varieties were categorized into resistant (R), moderately resistant (MR), moderately susceptible (MS), susceptible (S) and highly susceptible (HS). For biochemical analysis some varieties disease reaction revealed Kufri Lima as resistant, Kufri Himalini and Kufri Nilkanth as moderately resistant, Kufri Mohan and Kufri Chadramukhi as moderately susceptible Kufri Pukhraj and Kufri Kesar as susceptible and Kufri Lalit as highly susceptible varieties to early blight disease. These varieties biochemical analysis revealed that healthy leaves of resistant, moderately resistant, moderately susceptible, susceptible and highly susceptible varieties showed higher content of moisture, total soluble sugar and total chlorophyll as compared to diseased leaves. While diseased leaves of resistant, moderately resistant, moderately susceptible, susceptible and highly susceptible varieties contained higher content of phenol and true protein compared to healthy leaves.

Antifungal Efficacy of Kappaphycus alvarezii and Other Macro-algae against Alternaria solani Induced Early Blight in Tomato (Solanum lycopersicum L.)

Aims: To evaluate the antifungal activity of various seaweed extracts against A. solani under in vitro conditions. Methodology: The pathogen A.solani was isolated and its pathogenicity confirmed through inoculation on tomato plants. Molecular characterization was performed using PCR amplification and sequencing of the Internal Transcribed Spacer (ITS) region. Seaweed species, including Sargassum wightii, Kappaphycus alvarezii, Gracilaria edulis, Caulerpa racemosa, and Ulva lactuca, were collected, processed, and extracted using various solvents. The antifungal activity of these seaweed extracts was assessed using the Poisoned Food Technique, measuring the inhibition of A. solani growth. Results: Among the seaweed extracts tested, Kappaphycus alvarezii demonstrated the highest antifungal activity, with a maximum mycelial growth inhibition of 76% at a 5% concentration. Sargassum wightii also showed significant antifungal properties, with a 71.10% reduction in mycelial growth. Conclusion: The study reveals the promising potential of seaweed extracts, particularly Kappaphycus alvarezii and Sargassum wightii, as natural antifungal agents against A. solani. These findings suggest that seaweed-based bio-stimulants could serve as effective, eco-friendly alternatives to chemical fungicides in managing early blight disease in tomatoes are in tomato crops and highlights the potential of seaweed extracts as a natural antifungal agent.

Effects of application methods of microbial mixture on early blight disease (Alternaria solani) and growth of potato

Early blight (Alternaria solani) is one of important diseases in potato in Indonesia. In previous study, a microbial consortium (Trichoderma harzianum, Bacillus subtilis and Pseudomonas sp.) suppressed the bacterial wilt disease in potato. For application, the microbial consortium was mixed with compost (10%). As the microbial consortium is originally intended for controlling soil-borne diseases, this study examined the ability of the microbial consortium to suppress early blight disease and the effects of application methods on its efficacy. The application methods examined were the methods that targeted for soil-borne as well as airborne diseases. The experiment was conducted in a greenhouse at the Department of Plants and Diseases, Faculty of Agriculture, Universitas Padjadjaran, Sumedang, West Java, Indonesia. The experiment used Randomized Complete Block Design with 10 treatments and three replications. The treatments included application of microbes mixed with compost in planting hole solely or in combination with soaking the potato tubers in suspension of the microbes, drenching water extract of the mixture at 2, 4, 6 weeks after planting (WAP) with or without foliar application of the water extract. The result showed that application method influenced the abilities of the microbial mixture in suppressing early blight disease and supporting the potato growth. Even though the application of microbe-compost in planting medium inhibited the development of early blight disease by 37.8-39.5%, the regular foliar spray of the water extract of the mixture enhanced the disease suppression. Combination between application of the microbe-compost in the planting hole, drenching its water extract at 2, 4, 6 WAP and weekly foliar spray of the water extract suppressed early blight disease by 80.8%. This combination of application methods also supported better plant height, numbers of potato leaflets, roots fresh weight and production of potato tuber.

Influence of Temperature and Relative Humidity on Spore Germination and Early Blight Disease Development of Tomato Caused by Alternaria solani

Early blight of tomato caused by Alternaria solani is one of the most important and devastating disease of tomato which causing extensive yield losses to the crop. Environmental factors play an important role in the development of disease. To investigate the congenial conditions to develop the disease and germination of fungal spores an experiment was conducted in the year 2019 and 2020 at vegetable pathology laboratory of Dr Yashwant Singh Parmar University of Horticulture and Forestry Nauni Solan, Himachal Pradesh, India. Under investigations effect of temperature and relative humidity (RH) on conidial germination and early blight diseases development of tomato caused by Alternaria solani was studied under in vitro and in vivo conditions. Under in vitro conditions, maximum germination of conidia (75.54%) was recorded at 30°C after 24 hours and minimum (23.24%) was recorded at 15°C. length of germ tube (129.55 µm) was maximum at 25°C, whereas, minimum (67.09 µm) was observed at 15°C. In case of relative humidity maximum conidial germination (95.18%) and germ tube length of 238.95 µm was observed at 100% level. Under in vivo conditions disease severity was maximum (81.48%) at 30°C followed by 25°C (78.21%), whereas, minimum (18.88%) was recorded at 40°C. Similarly, the maximum (88.09%) disease severity was observed at 100% RH level while, it was minimum at 38% level of humidity. Overall, the relative humidity of more than 90% and temperature range of 25–30°C was found most congenial for the development of disease.

Exploring the Antifungal Efficacy of Essential Oils against Alternaria solani, the Causative Pathogen of Early Leaf Blight in Tomato Plants

Alternaria solani is an important necrotrophic fungus that is responsible for the early blight disease which is a common disease in tomato fields. In this research, the antifungal activity of essential oils extracted from Satureja hortensis, Thymbra spicata, Thymus sipyleus, Origanum majorana, O. syriacium, O. onites, O. vulgar, Artemisia absinthium, A. santonicum and A. spicigera were tested against Alternaria solani the causative agent of Tomato early blight disease. The study was carried out in two different ways, in vitro and in vivo. In vitro studies were conducted on media mixed with essential oils, and different concentrations of oils were examined on fungal growth in petri dishes. In in vivo studies, the effects of essential oils on the development of disease lesions were evaluated by infecting healthy tomato fruits. The concentrations used in the study were 140, 280, 560 and 1000 µl/L in the in vitro and 2.5, 5, 10 and 20 µl/fruit under in vivo conditions. Among the in vitro trials, the essential oils extracted from Thymus sipyleus and O. onites exhibited the most pronounced antifungal efficacy, achieving complete growth inhibition of the fungal pathogen across all concentrations whereas the essential oils from Artemisia spicigera and A. santonicum displayed relatively lower efficacy compared to the other oils. Conversely, under in vivo conditions, the essential oils derived from O. majorana and A. absinthium demonstrated the greatest capacity to impede the development of disease lesions on the fruit, yielding inhibition rates of 84% and 64% at 2.5 µl per fruit concentrations, respectively. In contrast the essential oils from Artemisia spicigera and A. santonicum had the least effect on the development of the disease, as there was disease lesions appeared even on the fruits that were applied at 20µl/fruit doses. Although most of the essential oils had some degree of antifungal action, still much effort is needed to put on both in vitro and in vivo trials to strength the reliability and consistency of the future related researches.

Network analyses predict major regulators of resistance to early blight disease complex in tomato

BackgroundEarly blight and brown leaf spot are often cited as the most problematic pathogens of tomato in many agricultural regions. Their causal agents are Alternaria spp., a genus of Ascomycota containing numerous necrotrophic pathogens. Breeding programs have yielded quantitatively resistant commercial cultivars, but fungicide application remains necessary to mitigate the yield losses. A major hindrance to resistance breeding is the complexity of the genetic determinants of resistance and susceptibility. In the absence of sufficiently resistant germplasm, we sequenced the transcriptomes of Heinz 1706 tomatoes treated with strongly virulent and weakly virulent isolates of Alternaria spp. 3 h post infection. We expanded existing functional gene annotations in tomato and using network statistics, we analyzed the transcriptional modules associated with defense and susceptibility.ResultsThe induced responses are very distinct. The weakly virulent isolate induced a defense response of calcium-signaling, hormone responses, and transcription factors. These defense-associated processes were found in a single transcriptional module alongside secondary metabolite biosynthesis genes, and other defense responses. Co-expression and gene regulatory networks independently predicted several D clade ethylene response factors to be early regulators of the defense transcriptional module, as well as other transcription factors both known and novel in pathogen defense, including several JA-associated genes. In contrast, the strongly virulent isolate elicited a much weaker response, and a separate transcriptional module bereft of hormone signaling.ConclusionsOur findings have predicted major defense regulators and several targets for downstream functional analyses. Combined with our improved gene functional annotation, they suggest that defense is achieved through induction of Alternaria-specific immune pathways, and susceptibility is mediated by modulating hormone responses. The implication of multiple specific clade D ethylene response factors and upregulation of JA-associated genes suggests that host defense in this pathosystem involves ethylene response factors to modulate jasmonic acid signaling.

Early and late blight disease identification in tomato plants using a neural network-based model to augmenting agricultural productivity.

Computer-advanced technologies have a significant impact across various fields. It is widely recognized that diseases have a detrimental effect on crop productivity and can significantly impact the economy, particularly in agricultural countries. Tomatoes hold great economic importance among cash crops, second only to potatoes. Globally, tomato production reaches a staggering 160 million tons annually, making it even more crucial for agricultural development. Unfortunately, the tomato crop is susceptible to several diseases, with early blight and late blight as two prominent culprits responsible for a production decrease of around 79%. Traditional disease detection and identification methods are time-consuming, expensive, and destructive, often requiring pathologists' expertise. Thus, the primary research objective is to enhance disease identification accuracy by leveraging deep learning techniques. A model based on the inception-V3 architecture has been devised to classify diseases affecting tomato plant leaves. The model was trained and tested using the PlantVillage dataset, which comprises 6000 sample images of tomato leaves. The training and testing process utilized an 80 : 20 ratio, resulting in an impressive classification accuracy of 97.44% for the proposed model. The proposed solution aims to enable the tomato industry to thrive in the global market by mitigating the impact of tomato leaf diseases. By reducing the prevalence of these diseases, the solution can increase demand and contribute to the industry's growth.

Optimizing Tomato Health: Holistic Approach to Early Blight Disease Management

An experiment was conducted to evaluate the effect of fungicide (mancozeb) and botanicals against early blight of tomato caused by Alternaria solani at the experimental field and glasshouse of Plant Pathology department, College of Agriculture, Pune, Maharashtra, during Kharif season (2019-2020). Six treatments including control with four replications were taken up using Randomized Block Design RBD. Growth inhibition of fungus Alternaria solani causing early leaf blight of tomato was studied in vivo for determining the efficacy of one fungicide and eight botanicals. Exploring possibility of managing A. solani by use of botanicals revealed that the clove extract of garlic was the best followed by neem leaf and ginger rhizome extract showing highest growth inhibition of the fungus. Among the plant leaf extracts, garlic clove extract @10% was found effective to inhibit the growth of pathogen i.e. 64.60% Per cent disease control PDC (glasshouse trial) and 51.85% PDC (open Field trial). The contact fungicide Mancozeb@0.25% showed disease control of 75.52% (Glasshouse trial) and PDC of 70.34% (Field trial) in in vivo condition. Presently many farmers are using chemicals for control of early blight of tomato however, they cause health hazards. Therefore, this investigation provides valuable insights for farmers in selecting suitable plant extracts to control early blight of tomatoes.

Early Blight and Late Blight Disease Detection in Potato Using Efficientnetb0

Potatoes are an important crop heavily consumed by Indian food products. It is produced on a massive scale, with China, India, Russia, Poland, and the USA being the main producers. Numerous leaf diseases harm the crop during its production. A typical Indian farmer lacks the tools necessary to detect Leaf Disease before damage is done. On a dataset of potato leaf images retrieved from Kaggle, we employed the EfficientNetB0 of Deep Learning to address this problem. This model uses width scaling and resolution scaling apart from depth scaling to perform the classification. Our work mainly focuses on the diseases Early Blight and Late Blight, two serious potato diseases. Early blight Spots start off as tiny, dry, dark, and papery specks that develop into brown to black, circular to oval-shaped regions. Veins that round the spots frequently give them an angular appearance. Late blight syntoms appear as small, light to dark green and round to irregularly shaped. Water-soaked patches are the first signs of late blight. The Data Collection has 2152 pictures in total, 2000 of which are diseased and 152 of which are healthy. The deep learning model provides a testing accuracy of 99.05%, which is higher than several widely used techniques available to provide farmers with knowledge about correct diseases well in time.

Leveraging Inception V3 for Precise Early and Late Blight Disease Classification in Potato Crops

Leveraging Inception V3 for Precise Early and Late Blight Disease Classification in Potato Crops

Bacillus velezensis YXDHD1-7 Prevents Early Blight Disease by Promoting Growth and Enhancing Defense Enzyme Activities in Tomato Plants.

Bacillus velezensis is well known as a plant growth-promoting rhizobacteria (PGPR) and biocontrol agent. Nevertheless, there are very few reports on the study of B. velezensis on tomato early blight, especially the biocontrol effects among different inoculation concentrations. In this study, an IAA-producing strain, Bacillus velezensis YXDHD1-7 was isolated from the tomato rhizosphere soil, which had the strongest inhibitory effect against Alternaria solani. Inoculation with bacterial suspensions of this strain promoted the growth of tomato seedlings effectively. Furthermore, inoculations at 106, 107, and 108 cfu/mL resulted in control efficacies of 100%, 83.15%, and 69.90%, respectively. Genome sequencing showed that it possesses 22 gene clusters associated with the synthesis of antimicrobial metabolites and genes that are involved in the production of IAA. Furthermore, it may be able to produce spermidine and volatile compounds that also enhance plant growth and defense responses. Our results suggest that strain YXDHD1-7 prevents early blight disease by promoting growth and enhancing the defense enzyme activities in tomato plants. This strain is a promising candidate for an excellent microbial inoculant that can be used to enhance tomato production.

Green-fabricated silver nanoparticles from Quercus incana leaf extract to control the early blight of tomatoes caused by Alternaria solani.

Early blight (EB) of Tomatoes, caused by Alternaria solani, is a serious fungal disease that adversely affects tomato production. Infection is characterized by dark lesions on leaves, stems, and fruits. Several agrochemicals can be used to control infection, these chemicals may disrupt environmental equilibrium. An alternative technology is needed to address this significant fungal threat. This study was designed to control the growth of EB in tomatoes caused by A. solani, using green-fabricated silver nanoparticles (Ag-NPs). Ag-NPs were synthesized through an environmentally friendly and cost-effective approach using leaf extract of Quercus incana Roxb. (Fagaceae). The physico-chemical characterization of the Ag-NPs was conducted through UV-visible spectroscopy, scanning electron microscopy, X-ray diffraction analysis, and Fourier transform infrared spectrometry. The Ag-NPs produced were round with a mean diameter of 27nm. The antifungal activity of these Ag-NPs was assessed through in vitro Petri plate and in vitro leaflet assays against A. solani. The green fabricated Ag-NPs exhibited excellent antifungal activity in vitro at a concentration of 100mg/l against A. solani, inhibiting growth by 98.27 ± 1.58% and 92.79 ± 1.33% during Petri plate and leaflet assays, respectively. In conclusion, this study suggests the practical application of green-fabricated Ag-NPs from Q. incana leaf extract against A. solani to effectively control EB disease in tomatoes.

A new technique for using gamma irradiation to enhance silver nanoparticles synthesized by chemical reduction and their effect on tomato early blight disease under field conditions

Early blight disease causes a significant loss in tomato production. This study focuses on the effective suppression of Alternaria solani, which causes huge losses in tomato yield. This research was conducted at the Egyptian Atomic Energy Authority Nuclear Research Centre. Infected plants were treated with silver nanoparticles (AgNPs). Two chemical materials, sodium borohydride and trisodium phosphate, were used for the synthesized silver nanoparticles. 1% polyvinylpyridine (PVP) was used as a stabilizer agent. AgNPs were exposed to several doses of gamma irradiation (0, 1.5, 3, 6, 12, and 24) kilo Gray (kGy) in order to enhance and maximize the effect of AgNPs on Alternaria solani. UV–Vis spectroscopy (UV), Fourier-transform infrared spectroscopy (FTIR), and transmission electron microscopy (TEM) were used to characterize AgNPs; sodium borohydride and trisodium citrate were used for the chemical reduction. AgNPs and AgNPs + gamma irradiation led to increases in shoot fresh weight and shoot dry weight; they also elevated the antioxidant enzymes, as well as peroxides and catalase, when compared with control (untreated) plants. AgNPs and AgNPs + gamma irradiation decreased the disease severity compared with the control untreated. Our study not only corroborates established trends in nano-agriculture but also introduces novel insights into the specific effects of gamma irradiation on AgNP that led to a decrease in this size in the quantum dot range (3–10) nm, as shown in Tem. By drawing parallels with the work of esteemed researchers in the field.

Evaluation of different fungicides against Alternaria solani causing early blight disease of potato under in vitro conditions

Potato (Solanum tuberosum) is a widely cultivated starch crop known for its edible underground storage organ, providing essential nutrients globally. Early blight, caused by the fungal pathogen Alternaria solani can lead to significant yield losses in potato crop, reports indicated that average annual yield losses due to early blight range from approximately 50 per cent to 75 per cent of production. Chemical protection have been a prominent approach in controlling early blight. Under in vitro evaluation fungicides, among non-systemic fungicides, mancozeb 75% WP exhibited the highest mean mycelial growth inhibition at 96.25 per cent, followed by thiram 75% WP with a mean mycelial growth inhibition of 92.51 per cent. Among six systemic fungicides evaluated, hexaconazole 5% EC and tebuconazole 25.9% EC recorded cent per cent mycelial growth inhibition at all four concentrations (0.025, 0.05, 0.1, 0.15%) tested which were significantly superior over rest of fungicides followed by difenconazole 25% EC. Among seven combi product fungicide tested, (captan 70% + hexaconazole 5%) 75% WP showed the mycelial growth inhibition of 100 per cent at all three concentrations tested, significantly over other combi-product fungicides.

Multi-omics approaches to understand pathogenicity during potato early blight disease caused by Alternaria solani.

Potato early blight (PEB), a foliar disease of potato during the growing period, caused by Alternaria sp., is common in major potato-producing areas worldwide. Effective agents to control this disease or completely resistant potato varieties are absent. Large-scale use of fungicides is limited due to possibility of increase in pathogen resistance and the requirements of ecological agriculture. In this study, we focused on the composition and infection characteristics of early blight pathogens in Yunnan Province and screened candidate pathogenesis-related pathways and genes. We isolated 85 strains of Alternaria sp. fungi from typical early blight spots in three potato-growing regions in Yunnan Province from 2018 to 2022, and identified 35 strains of Alternaria solani and 50 strains of Alternaria alternata by morphological characterization and ITS sequence comparison, which were identified as the main and conditional pathogens causing early blight in potato, respectively. Scanning electron microscope analysis confirmed only A. solani producing appressorium at 4 h after inoculation successfully infected the leaf cells. Via genome assembly and annotation, combine transcriptome and proteomic analysis, the following pathogenicity-related unit, transcription factors and metabolic pathway were identified: (1) cell wall-degrading enzymes, such as pectinase, keratinase, and cellulase; (2) genes and pathways related to conidia germination and pathogenicity, such as ubiquitination and peroxisomes; and (3) transcription factors, such as Zn-clus, C2H2, bZIP, and bHLH. These elements were responsible for PEB epidemic in Yunnan.

Genotyping-by-Sequencing Reveals Population Differentiation and Linkage Disequilibrium in Alternaria linariae from Tomato.

Alternaria linariae is an economically important foliar pathogen that causes early blight disease in tomatoes. Understanding genetic diversity, population genetic structure, and evolutionary potential is crucial to contemplating effective disease management strategies. We leveraged genotyping-by-sequencing (GBS) technology to compare genome-wide variation in 124 isolates of Alternaria spp. (A. alternata, A. linariae, and A. solani) for comparative genome analysis and to test the hypotheses of genetic differentiation and linkage disequilibrium (LD) in A. linariae collected from tomatoes in western North Carolina. We performed a pangenome-aware variant calling and filtering with GBSapp and identified 53,238 variants conserved across the reference genomes of three Alternaria spp. The highest marker density was observed on chromosome 1 (7 Mb). Both discriminant analysis of principal components and Bayesian model-based STRUCTURE analysis of A. linariae isolates revealed three subpopulations with minimal admixture. The genetic differentiation coefficients (FST) within A. linariae subpopulations were similar and high (0.86), indicating that alleles in the subpopulationsarefixed and the genetic structure is likely due to restricted recombination. Analysis of molecular variance indicated higher variation among populations (89%) than within the population (11%). We found long-range LD between pairs of loci in A. linariae, supporting the hypothesis of low recombination expected for a fungal pathogen with limited sexual reproduction. Our findings provide evidence of a high level of population genetic differentiation in A. linariae, which reinforces the importance of developing tomato varieties with broad-spectrum resistance to various isolates of A. linariae.