Recent advances in generative artificial intelligence (GenAI) have enabled the creation of high-resolution synthetic images, offering an alternative to traditional data collection for training computer vision models in agriculture. In crop disease diagnosis, synthetic images can supplement datasets when real image acquisition is limited, potentially reducing resource-intensive field collection. Therefore, this study evaluated how different ratios of real-field to Gen-AI-based synthetic watermelon (Citrullus lanatus) disease images (including an additional unknown class) affect EfficientNetV2-L classification performance and feature-space separability. The training dataset was divided into five treatments: H0 (real images only), H1 (synthetic images only), H2 (equal real-to-synthetic ratio), H3 (one real image to ten synthetic images, 1:10), and H4 (H3 plus random images to enhance variability). Models were trained using a custom EfficientNetV2-L architecture with fine-tuning and transfer learning approaches. Treatments H2, H3, and H4 demonstrated strong and consistent performance across all classes, with H2 achieving overall accuracy of 0.80, followed by H3 (0.98) and H4 (0.98). H3 achieved near-perfect precision and recall (0.95-0.99) across all classes, resulting in F1-scores of 0.98. H4 also maintained high precision and recall scores (0.94-1.00), including accurate detection of the additional unknown class (F1 = 0.98). Overall weighted F1-scores increased substantially from 0.72 (H0) to 0.81 (H2) and reached 0.98 in H3-H4, indicating the benefit of hybrid synthetic-real data fusion. These findings show that real-synthetic data fusion enhances model performance and generalization, while synthetic images alone were not effective under the tested conditions.

Abstract Bacterial spot of tomato and pepper (BST/P) is an economically devastating disease caused by four distinct Xanthomonas pathogens: X. euvesicatoria pv. euvesicatoria ( Xe ), X. euvesicatoria pv. perforans ( Xp ), X. hortorum pv. gardneri ( Xg ), and X. vesicatoria ( Xv ). A key component of virulence in these pathogens is the type III secretion system (T3SS), which delivers type III effector (T3E) proteins into host plant cells. To comprehensively characterize T3E repertoires and assess the stability of core effectors at a population scale, we evaluated a global dataset comprising 1,037 quality-filtered genomes, including 585 Xp , 350 Xe , 69 Xg , and 33 Xv strains. Across this collection, genes for six effectors were present in 100% of the examined genomes (XopK, XopL, XopM, XopN, XopX, and XopZ1) and an additional four effectors in ≥95% of genomes (XopK, XopL, XopM, XopN, XopX, and XopZ1). Xp and Xe populations maintained large total effector repertoires with extensive allelic variation, displaying exceptional polymorphism within XopD and XopAD. In contrast, Xg and Xv exhibited highly stable effector profiles with markedly reduced allelic diversification across geographic regions and decades. Disruptive mutations, including early stop codons and frameshifts mutations, in genes for XopAZ, XopAF, and XopAR were prevalent across specific pathogens pointing to ongoing pseudogenization and targeted gene loss. These findings provide a high-resolution characterization of the conserved and variable components of the BST/P pathogen effector arsenal and serve as a foundation for monitoring population evolution and breeding durable disease resistance to multiple pathogens.

Florida is a leading watermelon producer. During the unusually wet spring of 2018, when Florida watermelon fields received twice the 15-year average rainfall, severely diseased plants with atypical symptoms were observed across production areas. Bacterial strains were consistently isolated from tissue and characterized using phenotypic and molecular tests. Seventeen strains were isolated, and phenotypic characterization along with 16S rRNA gene sequence analysis identified all as Xanthomonas spp. Multilocus sequence analysis (MLSA) of eleven strains identified one, three and seven strains as X. cucurbitae, X. melonis, and X. arboricola, respectively. X. arboricola strains exhibited high intra-genetic diversity in the population and cluster most closely with the type strain of X. arboricola CFBP 2528T. The three X. melonis sequences were identical to each other but differed from the type strain LMG 8670T, whereas the X. cucurbitae strain was identical to the type strain CFBP 2542T. Pathogenicity assays conducted across five cucurbit hosts found that only X. cucurbitae consistently caused pathogenic reactions on all cucurbit hosts, whereas X. melonis caused mild symptoms and X. arboricola only caused disease under conditions of prolonged leaf wetness. These findings represent the first documented outbreak in Florida involving three distinct Xanthomonas species on watermelon. The emergence of X. cucurbitae on watermelon and host range shift of X. melonis and X. arboricola are discussed in this study. Further studies are needed to understand the impact and co-existence of pathogenic and opportunistic strains during disease outbreaks and their effect on driving pathogen evolution and host adaptation.

As sessile organisms, plants are constantly exposed to various abiotic and biotic factors in their environment. Among the biotic factors, beneficial microorganisms, pathogens, and insects cause metabolic changes that affect growth and productivity. In response to these interactions and stress conditions, plants have developed sophisticated metabolic plasticity, adjusting their primary and secondary metabolic pathways. Secondary metabolites are specialized compounds that serve various ecological functions, such as defense against herbivores and pathogens, allelopathy, interaction with beneficial microorganisms, and attraction of pollinators and seed dispersers. These metabolites also act as signaling molecules in plant-microbe interactions, regulating the relationship between plants and microbes. Recent genetic and chemical research has revealed that secondary metabolites have multiple functions, acting as powerful regulators of both plant growth and defense beyond their roles in primary metabolism. This review explored the microbiome's complexity and emerging trends in understanding how microbiome composition and/or synthetic microbial community (SynCom) influence microbial and plant metabolic activities. Addressing the correlation between the varieties of microorganisms or SynCom and their metabolic profiles is crucial for elucidating the biological mechanisms that induce alterations in microbial communities and their metabolic functions within the rhizosphere and plant microbiomes. This knowledge will contribute to developing strategies to enhance beneficial interactions and mitigate the effects of pathogens that can reduce plant growth and productivity.

The hop plant (Humulus lupulus) is an economically important perennial species of plant because of its role in beer production. Although most hop production occurs in central Washington State, local production in regions around the United States is gaining popularity owing to local microbreweries wanting to use locally grown hops in their production. In Florida, production has recently increased, and although most hop plants are grown from tissue culture, the development of a cost-effective diagnostic assay for hop viruses is critical to ensure planting material is clean. In this study, a tetraplex reverse transcription digital PCR (RT-dPCR) assay was developed for the detection of four common hop viruses; Apple mosaic virus (ApMV), Hop mosaic virus (HMV), Hop latent virus (HLV), and American hop latent virus (AHLV). A synthetic control was generated with corresponding viral sequences inserted in tandem for optimization. Stem, petiole, and leaf tissue sampled from each of three different cultivars with different viral profiles were screened with the tetraplex RT-dPCR assay. Across all tissue types and cultivars, HLV had the highest titer level followed by HMV, and ApMV had the lowest levels. Additionally, there were significant levels of variation among tissue types across cultivars. These data highlight the utility of this assay for detecting viruses in hop tissue and provide a useful diagnostic tool for screening hop plants to confirm they are healthy. This assay will be used in vector studies but also integrated into diagnostic services.

Emerging and re-emerging plant diseases continue to present multifarious threats to global food security. Considerable recent efforts are therefore being channeled towards understanding the nature of pathogen emergence, their spread and evolution. Xanthomonas euvesicatoria pv. perforans (Xep), one of the causal agents of bacterial spot of tomato, rapidly emerged and displaced other bacterial spot xanthomonads in many tomato production regions around the world. In less than three decades, it has become a dominant xanthomonad pathogen in tomato production systems across the world and presents a compelling example for understanding diversification of recently emerged bacterial plant pathogens. Although Xep has been continuously monitored in Florida since its discovery, the global population structure and evolution at the genome-scale is yet to be fully explored. The objectives of this work were to determine genetic diversity globally to ascertain if different tomato production regions contain genetically distinct Xep populations, to examine genetic relatedness of strains collected in tomato seed production areas in East Asia and other production regions, and to evaluate variation in type III secretion effectors, which are critical pathogenicity and virulence factors, in relationship to population structure. We used genome data from 270 strains from 13 countries for phylogenetic analysis and characterization of type III effector gene diversity among strains. Our results showed notable genetic diversity in the pathogen. We found genetically similar strains in distant tomato production regions, including seed production regions, and diversification over the past 100 years, which is consistent with intercontinental dissemination of the pathogen in hybrid tomato production chains. Evolution of the Xep pangenome, including the acquisition and loss of type III secreted effectors, is apparent within and among phylogenetic lineages. The apparent long-distance movement of the pathogen, together with variants that may not yet be widely distributed, poses risks of emergence of new variants in tomato production.

The current advancements in generative artificial intelligence (GenAI) models have paved the way for new possibilities for generating high-resolution synthetic images, thereby offering a promising alternative to traditional image acquisition for training computer vision models in agriculture. In the context of crop disease diagnosis, GenAI models are being used to create synthetic images of various diseases, potentially facilitating model creation and reducing the dependency on resource-intensive in-field data collection. However, limited research has been conducted on evaluating the effectiveness of integrating real with synthetic images to improve disease classification performance. Therefore, this study aims to investigate whether combining a limited number of real images with synthetic images can enhance the prediction accuracy of an EfficientNetV2-L model for classifying watermelon (Citrullus lanatus) diseases. The training dataset was divided into five treatments: H0 (only real images), H1 (only synthetic images), H2 (1:1 real-to-synthetic), H3 (1:10 real-to-synthetic), and H4 (H3 + random images to improve variability and model generalization). All treatments were trained using a custom EfficientNetV2-L architecture with enhanced fine-tuning and transfer learning techniques. Models trained on H2, H3, and H4 treatments demonstrated high precision, recall, and F1-score metrics. Additionally, the weighted F1-score increased from 0.65 (on H0) to 1.00 (on H3-H4) signifying that the addition of a small number of real images with a considerable volume of synthetic images improved model performance and generalizability. Overall, this validates the findings that synthetic images alone cannot adequately substitute for real images; instead, both must be used in a hybrid manner to maximize model performance for crop disease classification.

Megalurothrips usitatus (Bagnall) (Thysanoptera: Thripidae), an economically important pest of leguminous crops, is native to the Asian tropics. M. usitatus was recorded for the first time in 2020 in southern Florida (USA), where it has significantly impacted production of snap bean ( Phaseolus vulgaris L.; Fabaceae). Surveys were conducted in five fields between October 2021 and April 2022 to determine the abundance of M . usitatus in relation to other thrips species. From crop establishment until harvest, whole plant samples were collected from each field at weekly intervals. During each phenological stage (vegetative, flowering, fruiting), plant parts present at the time of sampling (foliage, flowers, pods) were partitioned and processed separately to determine the relative abundance of thrips species as affected by phenological stages and plant parts. To analyze the effect of plant part, only the fruiting stage, when all plant parts were present, was used. Thrips palmi Karny, the primary pest of snap bean prior to the establishment of M . usitatus , was the most abundant thrips species. M. usitatus was the second most abundant thrips species, and mostly found in flowers during the fruiting stage. Frankliniella occidentalis (Pergande), not previously reported as a pest of snap bean in south Florida, was the third most abundant, followed by Frankliniella bispinosa Morgan and Frankliniella insularis (Franklin). Overall abundance of thrips species was the lowest during the vegetative stage when only foliage was present and highest during the fruiting stage when all plant parts were present and most abundant in flowers. Sex ratios were female-biased for each species. Contrary to our hypothesis, the study did not produce evidence that M. usitatus establishes earlier in commercial snap bean fields or reaches higher levels of abundance than T. palmi .

AbstractEmerging and re-emerging plant diseases continue to present multifarious threats to global food security. Considerable recent efforts are therefore being channeled towards understanding the nature of pathogen emergence, their spread and evolution.Xanthomonas euvesicatoriapv.perforans (Xep), one of the causal agents of bacterial spot of tomato, rapidly emerged and displaced other bacterial spot xanthomonads in tomato production regions around the world. In less than three decades, it has become a dominant xanthomonad pathogen in tomato production systems across the world and presents a model for understanding diversification of recently emerged bacterial plant pathogens. AlthoughXephas been continuously monitored in Florida since its discovery, the global population structure and evolution at the genome-scale is yet to be fully explored. The objectives of this work were to determine genetic diversity globally to ascertain if different tomato production regions contain genetically distinctXeppopulations, to examine genetic relatedness of strains collected in tomato seed production areas in East Asia and other production regions, and to evaluate variation in type III effectors, which are critical pathogenicity and virulence factors, in relationship to population structure. We used genome data from 270 strains from 13 countries for phylogenetic analysis and characterization ofXopeffector gene diversity among strains. Our results showed notable genetic diversity in the pathogen. We found genetically similar strains in distant tomato production regions, including seed production regions, and diversification over the past 100 years, which is consistent with intercontinental dissemination of the pathogen in hybrid tomato production chains. Evolution of theXeppangenome, including the acquisition and loss of type III secreted effectors, is apparent within and among phylogenetic lineages. The apparent long-distance movement of the pathogen, together with variants that may not yet be widely distributed, poses risks of emergence of new variants in tomato production.

The emergence of plant pathogens is often associated with waves of unique evolutionary and epidemiological events. Xanthomonas hortorum pv. gardneri is one of the major pathogens causing bacterial spot disease of tomatoes. After its first report in the 1950s, there were no formal reports on this pathogen until the 1990s, despite active global research on the pathogens that cause tomato and pepper bacterial spot disease. Given the recently documented global distribution of X. hortorum pv. gardneri, our objective was to examine genomic diversification associated with its emergence. We sequenced the genomes of X. hortorum pv. gardneri strains collected in eight countries to examine global population structure and pathways of emergence using phylodynamic analysis. We found that strains isolated post-1990 group by region of collection and show minimal impact of recombination on genetic variation. A period of rapid geographic expansion in X. hortorum pv. gardneri is associated with acquisition of a large plasmid conferring copper tolerance by horizontal transfer and coincides with the burgeoning hybrid tomato seed industry through the 1980s. The ancestry of X. hortorum pv. gardneri is consistent with introduction to hybrid tomato seed production and dissemination during the rapid increase in trade of hybrid seeds.

Type III effectors (T3Es) are major determinants of Xanthomonas virulence and targets for resistance breeding. XopJ2 (synonym AvrBsT) is a highly conserved YopJ-family T3E acquired by X. perforans, the pathogen responsible for bacterial spot disease of tomato. In this study, we characterized a new variant (XopJ2b) of XopJ2, which is predicted to have a similar three-dimensional (3D) structure as the canonical XopJ2 (XopJ2a) despite sharing only 70% sequence identity. XopJ2b carries an acetyltransferase domain and the critical residues required for its activity, and the positions of these residues are predicted to be conserved in the 3D structure of the proteins. We demonstrated that XopJ2b is a functional T3E and triggers a hypersensitive response (HR) when translocated into pepper cells. Like XopJ2a, XopJ2b triggers HR in Arabidopsis that is suppressed by the deacetylase, SOBER1. We found xopJ2b in genome sequences of X. euvesicatoria, X. citri, X. guizotiae, and X. vasicola strains, suggesting widespread horizontal transfer. In X. perforans, xopJ2b was present in strains collected in North America, Africa, Asia, Australia, and Europe, whereas xopJ2a had a narrower geographic distribution. This study expands the Xanthomonas T3E repertoire, demonstrates functional conservation in T3E evolution, and further supports the importance of XopJ2 in X. perforans fitness on tomato. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

The bacterium Xanthomonas campestris pv. campestris causes black rot, one of the most important diseases affecting brassica production worldwide. Typically, the foliar application of copper-based bactericides is used to manage the disease. However, reports of copper tolerance among xanthomonads, expanded production of diverse brassica crops, and inherent climate challenges have motivated the brassica industry in Florida to evaluate alternatives to copper for improved black rot management. Across nine cabbage trials conducted in 2021 and 2022 in Florida, twelve alternatives were evaluated individually or as tank mixtures within a program. Each trial included a copper hydroxide standard (Kocide 3000) and a nontreated control. Based on the area under disease progress curve (AUDPC), solo applications of the plant defense activators Actigard (acibenzolar-S-methyl), Howler (Pseudomonas chlororaphis), Regalia (Reynoutria sachalinensis extract), ReyZox (Reynoutria sachalinensis extract + azoxystrobin), Theia (Bacillus subtilis), and Vacciplant (laminarin) reduced disease severity compared to the nontreated control and performed equivalent to or better than the Kocide 3000 standard across trials. Howler, Regalia, and Kocide 3000 increased cabbage yields compared to the non-treated control in at least one trial, while Actigard failed to improve yield in any trial. Applications of Microthiol (sulfur), either alone or as a tank mixture, failed to reduce disease severity or improve yield. Regardless of the program, maximum disease control at the final rating was limited to 8% compared to the nontreated control, indicating a need to improve integrated approaches for black rot management.

In this review, we highlight studies in which whole-genome sequencing, comparative genomics, and population genomics have provided unprecedented insights into past and ongoing pathogen evolution. These include new understandings of the adaptive evolution of secretion systems and their effectors. We focus on Xanthomonas pathosystems that have seen intensive study and improved our understanding of pathogen emergence and evolution, particularly in the context of host specialization: citrus canker, bacterial blight of rice, and bacterial spot of tomato and pepper. Across pathosystems, pathogens appear to follow a pattern of bursts of evolution and diversification that impact host adaptation. There remains a need for studies on the mechanisms of host range evolution and genetic exchange among closely related but differentially host-specialized species and to start moving beyond the study of specific strain and host cultivar pairwise interactions to thinking about these pathosystems in a community context.

. Tomato (Solanum lycopersicum) is an important vegetable crop and a valuable source of nutrients for the human diet. The southeast is the main fresh market tomato producer of the United States, with much of the production concentrated in Florida. However, production in this region is threatened by plant diseases such as target spot of tomato (TS) caused by Corynespora cassiicola, a multitrophic fungus widely distributed in tropical and subtropical areas. TS can infect foliage and fruit, often resulting in significant yield losses in conductive environments. There are no known TS-resistant cultivars, and control relies entirely on fungicidal sprays. However, several studies have demonstrated that the fungus is developing resistance to commonly used fungicides which further complicates disease management. The objective of this work was to identify sources of resistance to TS from wild Solanum accessions. Initial screens of 83 accessions informed the selection of 24 accessions for a more robust screening in which six diverse C. cassiicola isolates were used for single-isolate inoculation experiments. The results from a broad-sense mixed-model analysis including data from all six experiments demonstrated that all 24 accessions had significantly lower disease severities compared with the susceptible controls, suggesting that all accessions potentially harbor resistance quantitative trait loci (QTLs). Solanum cheesmaniae accession LA0524, S. galapagense accessions LA0483 and LA0532, and S. pimpinellifolium accession LA2093 were among the most resistant accessions tested and may be particularly useful for introgression of resistance into cultivated germplasm and for mapping of TS resistance QTLs.

Pomegranate (Punica granatum L.) has primarily been cultivated at home in Florida and other southeastern states. Over the past 15 years, growers, nurseries, researchers, and Extension agents have explored the potential of pomegranate as an alternative fruit crop. Early field trials revealed that pomegranates are highly susceptible to Colletotrichum gloeosporioides, causing severe anthracnose fruit rot and premature fruit drop. The development and use of disease-resistant cultivars are considered some of the best methods to manage this disease. This publication presents our findings from evaluating 35 pomegranate cultivars under natural disease pressure in central Florida and by artificial inoculation. The susceptibility of such pomegranate cultivars varied widely, with six exhibiting resistance to anthracnose fruit rot. More comprehensive research is warranted to further develop anthracnose-resistant cultivars and to enhance our understanding of disease resistance in this crop.

Pseudoperonospora cubensis, the causal agent of Cucurbit downy mildew (CDM), is one of the most important diseases affecting cucurbit production in the United States. This disease is especially damaging to Florida production areas, as the state is a top producer of many cucurbit species. In addition, winter production in central and south Florida likely serves as a likely source of P. cubensis inoculum for spring and summer cucurbit production throughout the eastern United States, where CDM is unable to overwinter in the absence of a living host. Over 2 years (2017 and 2018) and four seasons (spring 2017, spring 2018, fall 2017, and fall 2018), 274 P. cubensis isolates were collected from cucurbit hosts at production sites in south, central, and north Florida. The isolates were analyzed with 10 simple sequence repeat (SSR) markers to establish population structure and genetic diversity and further assigned to a clade based on a qPCR assay. Results of population structure and genetic diversity analyses differentiated isolates based on cucurbit host and clade (1 or 2). Of the isolates assigned to clade by qPCR, butternut squash, watermelon, and zucchini were dominated by clade 1 isolates, whereas cucumber isolates were split 34 and 59% between clades 1 and 2, respectively. Clade assignments agreed with isolate clustering observed within discriminant analysis of principal components (DAPC) based on SSR markers, although watermelon isolates formed a group distinct from the other clade 1 isolates. For seasonal collections from cucumber at each location, isolates were typically skewed to one clade or the other and varied across locations and seasons within each year of the study. This variable population structure of cucumber isolates could have consequences for regional disease management. This is the first study to characterize P. cubensis populations in Florida and evaluate the effect of cucurbit host and clade-type on isolate diversity and population structure, with implications for CDM management in Florida and other United States cucurbit production areas.

Pomegranate, a pivotal fruit that is well recognized globally and a rapidly emerging crop in the southeastern United States and other subtropical regions, faces a formidable challenge from Colletotrichum spp., a fungal pathogen causing anthracnose fruit rot, which leads to severe to complete premature fruit drop. The development and use of disease-resistant cultivars are considered the most cost-effective and sustainable approach to managing this disease. Identifying sources of resistance is essential for developing new cultivars with improved resistance to this disease. This project aimed to expand the scope of evaluation through a 2-year field study in central Florida, examining fruit from 35 cultivars from diverse origins using both artificial inoculation at the petal dehiscent stage and natural infection. Lesion size on the fruit was measured during the growing season in a field setting. Subsequently, seven cultivars were selected for further testing by inoculating detached mature fruit and measuring lesion size to confirm observed resistance and determine the correlation between resistance observed in planta in the field and on detached fruit in the laboratory. The field study revealed significant genetic differences among pomegranate cultivars in susceptibility to naturally occurring and induced anthracnose fruit rot and classified cultivars into five resistance or susceptibility classes. Five cultivars that originated from different regions of the world, including ‘Azadi’, showed consistent resistance to anthracnose fruit rot in the field. Resistance remained strong on detached mature fruit. A strong positive correlation existed between resistance levels on in-planta fruit and on detached mature fruit, suggesting a possible simple, efficient approach to screening breeding populations for anthracnose fruit rot resistance in pomegranate. These findings represent an important step toward developing new anthracnose-resistant cultivars and understanding and improving disease resistance in this increasingly important fruit crop in the world.

Bacterial spot of tomato (BST) is a disease that severely afflicts tomato crops, especially in geographic areas such as the Southeastern U.S., where the environmental conditions favor rapid disease development. Farmers usually use chemical treatments such as copper–mancozeb mixtures and acibenzolar-S-methyl, among other methods, to manage BST. However, these chemical treatments generally fail to improve marketable yields, thus raising the question of whether the BST treatments are economical. We evaluated the efficacy and profitability of bactericide treatments consisting of copper-mancozeb, acibenzolar-S-methyl, and streptomycin, as well as three inoculation levels of Xanthomonas euvesicatoria pv. perforans, on the management of BST in Florida. Across three separate field trials, BST severity was inversely correlated with marketable tomato yields; however, bactericide treatments provided no statistical improvement in marketable yields. By accounting for yield and the BST treatment costs, our profitability analysis showed that the BST treatments did not pay off economically; the net returns of these treatments were statistically equivalent to the untreated controls.