Phenotypic and Genetic Diversity of Xanthomonas perforans Populations from Tomato in North Carolina

Exploring the genetic makeup of Xanthomonas species causing bacterial spot in Taiwan: evidence of population shift and local adaptation

The introduction of plant pathogens can quickly reshape disease dynamics in island agro-ecologies, representing a continuous challenge for local crop management strategies. Xanthomonas pathogens causing tomato bacterial spot were probably introduced in Taiwan several decades ago, creating a unique opportunity to study the genetic makeup and adaptive response of this alien population. We examined the phenotypic and genotypic identity of 669 pathogen entries collected across different regions of Taiwan in the last three decades. The analysis detected a major population shift, where X. euvesicatoria and X. vesicatoria races T1 and T2 were replaced by new races of X. perforans. After its introduction, race T4 quickly became dominant in all tomato-growing areas of the island. The genomic analysis of 317 global genomes indicates that the Xanthomonas population in Taiwan has a narrow genetic background, most likely resulting from a small number of colonization events. However, despite the apparent genetic uniformity, X. perforans race T4 shows multiple phenotypic responses in tomato lines. Additionally, an in-depth analysis of effector composition suggests diversification in response to local adaptation. These include unique mutations on avrXv3 which might allow the pathogen to overcome Xv3/Rx4 resistance gene. The findings underscore the dynamic evolution of a pathogen when introduced in a semi-isolated environment and provide insights into the potential management strategies for this important disease of tomato.

Identification of quantitative trait loci associated with bacterial spot race T4 resistance in intra-specific populations of tomato (Solanum lycopersicum L.)

Bacterial spot of tomato is a serious disease caused by at least four species and four races of Xanthomonas- X. euvesicatoria (race T1), X. vesicatoria (race T2), X. perforans (race T3 and T4), and X. gardneri, with X. perforans race T4 being predominant in the southeast USA. Practical management of this disease is challenging because of the need for more effective chemicals and commercially resistant cultivars. Identification of genetic resistance is the first step to developing a disease-resistant variety. The objective of this study was to identify quantitative trait loci (QTL) conferring resistance to race T4 in two independent recombinant inbred lines (RILs) populations NC 10204 (intra-specific) and NC 13666 (interspecific) developed by crossing NC 30P x NC22L-1(2008) and NC 1CELBR x PI 270443, respectively. Seven QTLs on chromosomes 2, 6, 7, 11, and 12 were identified in NC 10204. The QTL on chromosome 6 explained the highest percentage of phenotypic variance (up to 21.3%), followed by the QTL on chromosome 12 (up to 8.2%). On the other hand, the QTLs on chromosomes 1, 3, 4, 6, 7, 8, 9, and 11 were detected in NC 13666. The QTLs on chromosomes 6, 7, and 11 were co-located in NC 10204 and NC 13666 populations. The donor of the resistance associated with these QTL in NC 10204 is a released breeding line with superior horticultural traits. Therefore, both the donor parent and the QTL information will be useful in tomato breeding programs as there will be minimal linkage drag associated with the bacterial spot resistance.

Exploring Diversity of Bacterial Spot Associated Xanthomonas Population of Pepper in Southwest Florida

Bacterial spot caused by Xanthomonas spp. is a significant disease that challenges pepper growers worldwide and is particularly severe in a hot and humid environment. Understanding the pathogen's population biology is critical for sustainable disease management. The goal of this study was to characterize the species, race, and bactericide sensitivity of bacterial spot-associated Xanthomonas collected from pepper in Florida. A survey of pepper production fields in southwest Florida between 2019 and 2021-covering two counties, eight farms, and two transplant facilities-resulted in the isolation of 542 Xanthomonas euvesicatoria and 35 Xanthomonas perforans strains. Four races were identified on pepper, of which most strains were race P1 (42%), race P6 (26%), race P3 (24%), and less common was race P4 (8%). All X. perforans strains were characterized as race P1 and showed a compatible reaction on tomato. Sixty-two and 96% of strains were sensitive to copper sulfate and streptomycin, respectively. One farm that did not use copper to manage the disease contained only copper-sensitive strains and was the only farm with race P3 strains. Strains were assayed for starch hydrolysis activity of which a third of X. euvesicatoria strains were strongly amylolytic, a characteristic not typically observed in X. euvesicatoria. All X. perforans strains produced bacteriocins against X. euvesicatoria in vitro. The Xanthomonas population causing bacterial spot on pepper in southwest Florida is diverse and dynamic; thus, regular monitoring provides pertinent information to plant breeders and growers for designing disease management strategies.

Migration Drives the Replacement of Xanthomonas perforans Races in the Absence of Widely Deployed Resistance

Changes in Xanthomonas race and species composition causing bacterial spot of tomato have occurred throughout the world and are often associated with epidemics. Knowledge of bacterial population structure is key for resistance discovery and deployment. We surveyed Xanthomonas spp. composition from processing tomato fields in the Midwestern United States over a 4-year period between 2017 and 2020, compared these to strains collected previously, and found that X. perforans is currently the most prevalent species. We characterized 564 X. perforans isolates for sequence variation in avrXv3 to distinguish between race T3 and T4 and validated race designation using hypersensitive response (HR) assays for 106 isolates. Race T4 accounted for over 95% of X. perforans isolates collected in the Midwest between 2017 and 2020. Whole genome sequencing, Average Nucleotide Identity (ANI) analysis, core genome alignment and single nucleotide polymorphism (SNP) detection relative to a reference strain, and phylogenomic analysis suggest that the majority of Midwestern X. perforans strains collected between 2017 and 2020 were nearly identical, with greater than 99.99% ANI to X. perforans isolates collected from Collier County, Florida in 2012. These isolates shared a common SNP variant resulting an a premature stop codon in avrXv3. One sequenced isolate was identified with a deletion of avrXv3 and shared 99.99% ANI with a strain collected in Collier Co., Florida in 2006. A population shift to X. perforans T4 occurred in the absence of widely deployed resistance, with only 7% of tomato varieties tested having the resistant allele at the Xv3/Rx-4 locus. The persistence of nearly identical strains over multiple years suggests that migration led to the establishment of an endemic population. Our findings validate a genomics-based framework to track shifts in X. perforans populations due to migration, mutation, drift, or selection based on comparisons to 146 genomes.

Epidemiology, diversity, and management of bacterial spot of tomato caused by Xanthomonas perforans

Tomato is an important crop grown worldwide. Various plant diseases cause massive losses in tomato plants due to diverse biotic agents. Bacterial spot of tomato (BST) is a worldwide disease that results in high losses in processed and fresh tomato. Xanthomonas perforans, an aerobic, single-flagellated, rod-shaped, Gram-negative plant pathogenic bacterium, is one of the leading causes of BST. Over the past three decades, X. perforans has increasingly been reported from tomato-growing regions and became a major bacterial disease. X. perforans thrives under high humidity and high temperature, which is commonplace in tropical and subtropical climates. Distinguishing symptoms of BST are necrotic lesions that can coalesce and cause a shot-hole appearance. X. perforans can occasionally cause fruit symptoms depending on disease pressure during fruit development. Short-distance movement in the field is mainly dependent on wind-driven rain, whereas long distance movement occurs through contaminated seed or plant material. X. perforans harbors a suite of effectors that increase pathogen virulence, fitness, and dissemination. BST management mainly relies on copper-based compounds; however, resistance is widespread. Alternative compounds, such as nanomaterials, are currently being evaluated and show high potential for BST management. Resistance breeding remains difficult to attain due to limited resistant germplasm. While the increased genetic diversity and gain and loss of effectors in X. perforans limits the success of single-gene resistance, the adoption of effector-specific transgenes and quantitative resistance may lead to durable host resistance. However, further research that aims to more effectively implement novel management tools is required to curb disease spread. KEY POINTS: • Xanthomonas perforans causes bacterial spot on tomato epidemics through infected seedlings and movement of plant material. • Genetic diversity plays a major role in shaping populations which is evident in loss and gain of effectors. • Management relies on copper sprays, but nanoparticles are a promising alternative to reduce copper toxicity.

Dynamics and Spread of Bacterial Spot Epidemics in Tomato Transplants Grown for Field Production

Tomato transplants are the primary means of establishing commercial tomato production fields in the eastern United States. Transplants are often suspected as the source of inoculum for major outbreaks in production fields of bacterial spot of tomato (BST) caused by Xanthomonas perforans (Xp). A combination of high plant densities with overhead irrigation, high humidity, and high temperatures are conducive to BST outbreaks during transplant production. In addition to chemical control, transplant growers use roguing to remove diseased transplants, as a primary way to manage BST during transplant production. The value of roguing is often questioned, because information about the rate of pathogen spread and the incubation period between infection and symptom development is limited. In this study, we evaluated the extent of X. perforans spread on tomato transplants relative to symptom development by using a rifampicin-resistant X. perforans strain and conducting experiments in an environmentally controlled greenhouse simulating grower practices and also at a commercial transplant facility in Florida. BST symptom development typically lagged behind X. perforans dispersal by at least 5 to 7 days depending on environmental conditions. Furthermore, X. perforans was capable of aerosolization, which resulted in long-distance dispersal of ≤2 m under highly favorable conditions. Growers should rogue diseased plants and surrounding nonsymptomatic plants by >1 and ≤3 m, depending on outbreak severity, to limit disease spread. As a result, proper disease management should reduce introduction of nonsymptomatic transplants into the field and subsequently reduce pesticide applications.

Advances and Challenges in Bacterial Spot Resistance Breeding in Tomato (Solanum lycopersicum L.)

Bacterial spot is a serious disease of tomato caused by at least four species of Xanthomonas. These include X. euvesicatoria (race T1), X. vesicatoria (race T2), X. perforans (races T3 and T4), and X. gardneri, with the distinct geographical distribution of each group. Currently, X. gardneri and X. perforans are two major bacterial pathogens of tomato in North America, with X. perforans (race T4) dominating in east-coast while X. gardneri dominating in the Midwest. The disease causes up to 66% yield loss. Management of this disease is challenging due to the lack of useful chemical control measures and commercial resistant cultivars. Although major genes for resistance (R) and quantitative resistance have been identified, breeding tomato for resistance to bacterial spot has been impeded by multiple factors including the emergence of new races of the pathogen that overcome the resistance, multigenic control of the resistance, linkage drag, non-additive components of the resistance and a low correlation between seedling assays and field resistance. Transgenic tomato with Bs2 and EFR genes was effective against multiple races of Xanthomonas. However, it has not been commercialized because of public concerns and complex regulatory processes. The genomics-assisted breeding, effectors-based genomics breeding, and genome editing technology could be novel approaches to achieve durable resistance to bacterial spot in tomato. The main goal of this paper is to understand the current status of bacterial spot of tomato including its distribution and pathogen diversity, challenges in disease management, disease resistance sources, resistance genetics and breeding, and future prospectives with novel breeding approaches.