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Characterizing the epidemiological link between transplant and field outbreaks of bacterial spot on tomato with whole genome sequencing

Peter Abrahamian: Gulf Coast Research and Education Center, University of Florida

<div>Bacterial leaf spot (BLS), caused by <em>Xanthomonas perforans</em> (<em>Xp</em>), is a major tomato disease. During transplant production, environmental conditions, grower practices and lack of efficient disease control measures contribute to severe BLS outbreaks. In Florida, growers primarily rely on transplant seedlings for field production. Therefore, we hypothesized that disease outbreaks in the field are caused by using contaminated transplant seedlings. Our objective was to monitor and characterize <em>Xp</em> outbreaks associated with tomato seedlings in transplant houses and in production fields. We surveyed <em>Xp</em> strains from two commercial transplant growers (A and B) and tracked the same seedlings of different cultivars into corresponding fields. A total of 67 strains were sequenced on the Illumina MiSeq2000 platform. The pairwise average nucleotide identity between strains was higher than 99%. Transplant and field strains clustered together by grower, irrespective of cultivar or time. Single nucleotide polymorphism (SNP)-based analysis showed that 90% and 80% of field strains showed high genetic similarity to at least one or more transplant strains from grower A and B, respectively. Our SNP-based analysis demonstrated that contaminated seedlings are a major source of introducing <em>Xp</em> strains into fields. As a result, BLS management during tomato transplant production is critical to reduce <em>Xp</em> levels prior to field planting.</div>