Pantoea ananatis 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 alt, associated with center rot. The HiVir gene cluster is required to
induce necrosis on onion tissues via synthesis of pantaphos, (2-hydroxy[phosphonomethyl)
maleate), a phosphonate phytotoxin. The alt gene cluster aids in tolerance
to thiosulfinates generated during onion tissue damage. Whole genome sequencing
of other Pantoea species suggests that these gene clusters are present outside of
P. ananatis. To assess the distribution of these gene clusters, two PCR primer sets
were designed to detect the presence of HiVir and alt. Two hundred fifty-two strains
of Pantoea 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 Pantoea species, 41
isolation sources, and 23 countries, collected from 1946–2019, was tested. There is a
significant association between the alt PCR assay and Pantoea strains recovered from
symptomatic onion (P < 0.001). There is also a significant association of a positive
HiVir PCR and RSN assay among P. ananatis strains but not among Pantoea spp.,
congeners. This may indicate a divergent HiVir cluster or different pathogenicity and
virulence mechanisms. Last, we describe natural alt positive [RSN C /HiVir C /alt C ]
P. ananatis strains, which cause extensive bulb necrosis in a neck-to-bulb infection
assay compared to alt negative [RSN C /HiVir C /alt] P. ananatis strains. A combination
of assays that include PCR of virulence genes [HiVir and alt] and an RSN assay can
potentially aid in identification of onion-bulb-rotting pathogenic P. ananatis strains.The Vidalia Onion Committee, United States Department of Agriculture (USDA), ANII, Uruguay), CSIC Grupos de Investigación I + D 2000 (CSIC, Udelar, Uruguay), Specialty Crops Research Initiative Award from the USDA, and National Institute of Food and Agriculture.http://www.frontiersin.org/Plant_Scienceam2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog
