Population Structure of Alternaria brassicicola Suggests Genetic Diversity in Organic Broccoli Farms in Connecticut Is Driven by Multiple Introductions

Alternaria brassicicola is the predominant causal agent of Alternaria leaf blight and head rot (ABHR) in organic broccoli production in the Northeastern United States. A prior regional study indicated a high level of genetic diversity within individual fields, which we sought to investigate here to understand important routes of spread and mechanisms of reproduction. We genotyped 171 isolates collected from three certified organic farms in Connecticut across two growing seasons (2022 and 2023) using microsatellite markers. Results revealed high genotypic diversity and significant linkage disequilibrium, indicating a clonal population structure. Discriminant analysis of principal components (DAPC) and hierarchical analysis of molecular variance (AMOVA) showed low but significant genetic differentiation among fields and years, with most variation occurring within populations. Shared multilocus genotypes (MLGs) across fields and years suggest that diversity is primarily driven by multiple introductions, likely via contaminated seed, rather than recombination. These findings underscore the importance of seed source in pathogen dispersal and highlight the need for improved seed testing and cultural management practices to mitigate ABHR in organic broccoli systems.