P-164 - A TaqMan qPCR-based detection assay for Pseudomonas syringae pv. aptata causing bacterial leaf spot of Table beet and Swiss Chard

Bacterial leaf spot caused by Pseudomonas syringae pv. aptata affects Table beet (Beta vulgaris ssp. vulgaris) and Swiss chard (Beta vulgaris ssp. cicla). We are working with a worldwide collection of P. syringae pv. aptata strains, previously assembled from infested seeds and symptomatic leaves of beet and chard, including both pathogenic and non-pathogenic strains.This collection was used to generate a phylogenetic tree based on 19 housekeeping genes, revealing 78 distinct phylogroups, with most pathogenic strains clustering in MLST1 and MLST3 within phylogroup 2b. Given their strong association with pathogenicity, we aimed to identify a genetic marker specific to MLST1 and MLST3. Using the K-mer Exclusion by Cross-reference approach, we identified loci unique to pathogenic strains, which were further screened against genomes, confirming specificity in silico. A unique gene specific to MLST3 was identified. A TaqMan qPCR assay was developed using primers and probes targeting this MLST3-specific locus. Initial testing of the primer/probe pair on 47 MLST3 strains confirmed specificity for MLST3, with no cross-reactivity to closely related strains from phylogroups 2a, 2b, 2c, 2d, or non-pathogenic and MLST1 strains. This qPCR method demonstrates high analytical specificity, detecting the target pathogen while excluding non-target organisms. After validation it should offer rapid and precise pathogen detection in seed lots, environmental samples, and epidemiological studies, supporting targeted disease management strategies. We are evaluating this tool for seed health assays.