High Genetic Diversity of Phytophthora palmivora in Colombian Cacao: Evidence Against Geographic Barriers

Phytophthora palmivora causes significant economic losses in Colombian cacao crops, yet its population structure and pathogenicity remain poorly characterized. This study tested the hypothesis that the Colombian Andes mountain complex acts as a geographic barrier limiting gene flow among P. palmivora populations. We analyzed 73 isolates from western, central, and eastern cacao-growing regions using DArTseq genotyping and standardized pathogenicity assays. High genotypic diversity was observed (Simpson's index = 0.99), with corrected association index analysis indicating predominantly clonal reproduction, consistent with all isolates being the A2 mating type. Discriminant analysis of principal components identified seven genetic clusters, but these showed no correlation with geographic distribution, contradicting our geographic barrier hypothesis. Mantel tests confirmed no isolation-by-distance ( r = 0.004, P = 0.650). Pathogenicity tests on detached CCN51 leaves revealed extensive virulence variation that was independent of genetic clustering or geography. These findings suggest that observed genetic diversity results from multiple pathogen introductions and anthropogenic dispersal rather than geographic barrier. The lack of correlation between genotype and virulence indicates that pathogenicity determinants are independent of neutral molecular markers used for population structure analysis. Management recommendations include stringent phytosanitary measures to prevent further introductions and consideration of pathogen diversity in resistance breeding programs.