|Three clonal lineages of the cocoa pathogen Phytophthora megakarya in Nigeria|
O. O. Kolawole (1), E. M. GOSS (2). (1) University of Ibadan and Cocoa Research Institute of Nigeria, Ibadan, Nigeria; (2) University of Florida, Gainesville, FL, U.S.A.
Black pod disease of cocoa caused by <i>Phytophthora megakarya </i>is the most destructive disease affecting cocoa production in Central and West Africa. <i>P. megakarya</i> is an aggressive and highly virulent pathogen that can cause 60 to 100% loss of cocoa pods. To reduce use of fungicides currently used to control the disease, breeding for resistant cultivars is a research priority. However, there is little knowledge of the population structure and diversity of the pathogen, which is critical for breeding resistance that will be effective and durable. We used genotyping-by-sequencing to obtain SNPs from 95 isolates of <i>P. megakarya</i> collected from cocoa pods in southern Nigeria. We found two genetically diverged groups of 80 and 15 isolates. The larger group was found in all states sampled, whereas the minor group was found only in the southeast cocoa-growing areas near the border with Cameroon. The dominant group comprised a single clonal group containing limited genetic variation. The minor group included two closely related clonal lineages. We found no evidence of recent sexual reproduction. These data will be used to examine the evolution of the pathogen in Central Africa and to inform breeding efforts.