Magnaporthe oryzae populations in Sub-Saharan Africa are diverse and show signs of local adaptation

Abstract Rice blast caused by Magnaporthe oryzae is one of the most economically damaging diseases of rice worldwide. The disease originated in Asia but was detected for the first time in Sub-Saharan Africa (SSA) around 100 years ago. Despite its importance, the evolutionary processes involved in shaping the population structure of M. oryzae in SSA remain unclear. In this study, we investigate the population history of M. oryzae using a combined dataset of 180 genomes. Our results show that SSA populations are more diverse than earlier perceived, and harbor all genetic groups previously reported in Asia. While M. oryzae populations in SSA and Asia draw from the same genetic pools, both are experiencing different evolutionary trajectories resulting from unknown selection pressures or demographic processes. The distribution of rare alleles, measured as Tajima’s D values, show significant differences at the substructure level. Genome-wide analysis indicates potential events of population contraction strongly affecting M. oryzae in SSA. In addition, the distribution and haplotype diversity of effectors might suggest a process of local adaptation to SSA conditions. These findings provide additional clues about the evolutionary history of M. oryzae outside the center of origin and help to build customized disease management strategies.