Molecular epidemiology of Xanthomonas perforans outbreaks in tomato from transplant to field by single-nucleotide polymorphism analysis

Outbreaks of bacterial spot on tomato (BST) caused by Xanthomonas perforans (Xp) are a major concern for sustainable crop production. BST is a common occurrence in tomato transplants grown for field production. We hypothesized that BST outbreaks in commercial fields originate from Xp strains inadvertently introduced from commercial transplant facilities. To test this hypothesis, we used a genome-wide single nucleotide polymorphism (SNP) analysis to characterize Xp strains recovered from tomato transplant facilities and fields in commercial production areas. Xp strains were isolated from symptomatic transplants prior to rogueing at two commercial transplant growers. Then the same group of transplants were tracked to commercial fields to recover Xp strains from diseased plants prior to harvest. Whole-genome sequencing was carried out on 84 strains isolated from transplant and field plants from Florida and South Carolina. SNPs were called using three reference strains that represented the genetic variation of the sampled strains. Field strains showing genetic similarity to transplant strains had a difference of 2 to 210 SNPs. Transplant and field strains clustered together by grower within each phylogenomic group, consistent with expectations. The range of genetic divergence among strains isolated from field plants was similar to the range obtained from strains on transplants. Using the range of genetic variation observed in transplants, we estimate that at least 60% to 100% of field strains were an extension of the transplant strain population. Our results stress the importance of BST management to reduce Xp movement from transplant to field and minimize subsequent disease outbreaks. Importance Current management of X. perforans (Xp) on tomato mainly relies on the frequent application of pesticides. However, the lack of effective pesticides and development of strain tolerance to certain bactericides limits the ability to control outbreaks in production fields. Better knowledge of probable sources of Xp inoculum during tomato production is required to refine management strategies. Tomato plants are typically established in the field using transplants. This study aimed to determine if strains from field epidemics could be coming from transplant facilities or resulted from local field outbreaks. The overall goal was to identify potential sources of inoculum and subsequently develop strategies to reduce carryover from transplant production to the field. Our results indicate that tomato producers should shift disease management efforts to transplant facilities to reduce disease in the field. Improved transplant health should reduce the likelihood of bacterial spot outbreaks and subsequently reduce pesticide usage in the field.