Population genetics of the maize foliar pathogen cercospora zeina crous & U. braun in five countries of Sub-Saharan Africa

Abstract

Cercospora zeina, a causal pathogen of gray leaf spot (GLS) of maize, is responsible for up to 1 % of global yield losses. Previous small-scale population genetics studies have revealed that C. zeina is a highly diverse pathogen. Using microsatellite markers, we set out to determine the genetic diversity and population structure of 835 C. zeina isolates from five countries in Sub-Saharan Africa: Kenya, South Africa, Uganda, Zambia, and Zimbabwe, and to establish their evolutionary potential. Our findings revealed that populations from different farming systems exhibited partial, but significant population differentiation. Also, smallholder populations had a higher genetic diversity, number of private alleles and lower clonality than commercial populations. Country-level populations were highly diverse and structured, with migration occurring among populations. Interestingly, Zambia came out as a distinct population, with a lower genetic diversity, higher clonality and private alleles, indicative of a more recently introduced population. Our findings rejected the existing hypothesis of Durban harbor being the entry point of C. zeina into Africa, thus suggesting that the pathogen has other point(s) of entry. Additionally, signatures of cryptic sexual recombination were observed even though an attempt to induce the sexual stage in laboratory conditions was unsuccessful. We found no evidence for C. zeae-maydis, C. zeina’s sibling species in more than 1000 isolates collected from around Africa, thus confirming that C. zeina is the predominant species in Africa. Overall, this pathogen is a genetically well-established pathogen in Africa with its population structure being influenced by sexual recombination, migration and human activities. This study, therefore, provides a basis for effective monitoring of C. zeina’s dispersal and is a tool for designing more effective regional-specific management strategies to reduce the acquisition and movement of highly virulent strains that overcome host resistance or fungicide control.