The Distribution of Onion Virulence Gene Clusters Among Pantoea spp

is a gram-negative bacterium and the primary causal agent of center rot of onions in Georgia. Previous genomic studies identified two virulence gene clusters, HiVir and , associated with center rot. The HiVir gene cluster is required to induce necrosis on onion tissues via synthesis of pantaphos, (2-hydroxy[phosphono-methyl)maleate), a phosphonate phytotoxin. The gene cluster aids in tolerance to thiosulfinates generated during onion tissue damage. Whole genome sequencing of other species suggests that these gene clusters are present outside of . To assess the distribution of these gene clusters, two PCR primer sets were designed to detect the presence of HiVir and . Two hundred fifty-two strains of spp. were phenotyped using the red onion scale necrosis (RSN) assay and were genotyped using PCR for the presence of these virulence genes. A diverse panel of strains from three distinct culture collections comprised of 24 species, 41 isolation sources, and 23 countries, collected from 1946-2019, was tested. There is a significant association between the PCR assay and strains recovered from symptomatic onion ( < 0.001). There is also a significant association of a positive HiVir PCR and RSN assay among strains but not among spp., congeners. This may indicate a divergent HiVir cluster or different pathogenicity and virulence mechanisms. Last, we describe natural positive [RSN /HiVir / ] strains, which cause extensive bulb necrosis in a neck-to-bulb infection assay compared to negative [RSN /HiVir / ] strains. A combination of assays that include PCR of virulence genes [HiVir and ] and an RSN assay can potentially aid in identification of onion-bulb-rotting pathogenic strains.