Molecular Diversity of Phytophthora megakarya Isolates Causing Black Pod Disease of Cocoa in Cross River and Edo States, Nigeria

Black pod disease of cocoa (Theobroma cacao), caused primarily by Phytophthora megakarya in West Africa, is responsible for annual yield losses estimated at 20 to 30 percent in Nigerian cocoa producing states. Despite its economic significance, the molecular diversity of P. megakarya isolates across Nigeria's two main cocoa belts remains inadequately characterised, limiting the design of durable resistance strategies. This study investigated the molecular diversity of 68 P. megakarya isolates collected from symptomatic cocoa pods in Cross River and Edo States using microsatellite markers and internal transcribed spacer sequencing. Isolates were collected from 12 farms across both states during the 2022 and 2023 main crop seasons. Population genetic analyses including AMOVA, cluster analysis, and haplotype network construction were performed using established bioinformatics pipelines. Results revealed significant genetic differentiation between Cross River and Edo State populations, with FST values of 0.31 indicating moderate population structure across the two zones. Cross River State isolates showed higher genotypic diversity, consistent with a longer history of P. megakarya establishment in that region. Several unique haplotypes were identified in recently affected farms in Edo State, suggesting ongoing range expansion accompanied by genetic drift. Virulence assays on detached pods of four cocoa genotypes confirmed aggressiveness variation linked to specific molecular clusters. These findings provide critical baseline data for tracking pathogen dispersal and informing targeted breeding for durable resistance. Keywords: Phytophthora megakarya, black pod, molecular diversity, cocoa, Cross River State.