Genomic profiles of Pyricularia oryzae in Sub-Saharan Africa: exploring population differences and their evolutionary implications in the region

Geoffrey Onaga^1*Worrawit Suktrakul²Margaret Wanjiku³Quibod Lorenzo Ian⁴Jean-Baka Kodjo Domelevo Entfellner³Joseph Bigirimana⁵George Habarugira⁵Rosemary Murori⁵Godfrey Asea⁶Tella Hamidatou Euridice¹Aubin Gbènakpon AMAGNIDE¹Zenna Negussie¹Abdelbagi M. Ismail⁵Chatchawan Jantasuriyarat²Ricardo Oliva⁷

• ¹Africa Rice Center, Abidjan, Côte d'Ivoire
• ²Kasetsart University, Bangkok, Thailand
• ³International Livestock Research Institute Biosciences Eastern and Central Africa, Nairobi, Kenya
• ⁴International Rice Research Institute, Manila, Philippines
• ⁵International Rice Research Institute Kenya, Nairobi, Kenya
• ⁶National Crops Resources Research Institute, Kampala, Uganda
• ⁷Alliance of Bioversity International and International Center for Tropical Agriculture, Bogotá, Colombia

Rice blast, caused by Pyricularia oryzae (teleomorph: Magnaporthe oryzae), is one of the most economically damaging diseases affecting rice worldwide. The evolutionary history of African rice blast isolates remains underexplored relative to that of their Asian and European counterparts, accounting for knowledge gaps that hinder its control. Here, using 180 genome sequences (45 from SSA and 135 from other regions), we characterized the genetic origins, population structure, admixture, demographic history, and effector diversity of Sub-Saharan Africa (SSA) isolates. Our findings provide new dates for the divergence of SSA populations from Asian populations. The introduction of P. oryzae into Africa occurred mainly from China in the late 19th century, initially in West Africa (WA; Mali and Burkina Faso), and subsequently in Uganda and Madagascar during the early 20th century, before extending to the wider African region, with subsequent repeated introductions. Tajima's D and demographic modeling suggested complex population dynamics shaped by migration and asymmetric Rice blast Genomic Profiles in SSA founder events, highlighting considerably shared genetic ancestry between Asia and East Africa (EA), in contrast with that between Asia and WA. Genome-wide association analysis identified a specific set of single nucleotide polymorphism markers, along with several candidate genes linked to adaptation. Effector repertoire analysis revealed that SSA isolates harbor fewer effectors and exhibit lower genetic diversity than Asian populations, with some effectors under positive selection, particularly in WA. Overall, this study improves the existing knowledge on P. oryzae populations in SSA and provides avenues for future management strategies.