Comparative population genetics of Exserohilum turcicum in smallholder farms of Kenya and Uganda

Abstract

Exserohilum turcicum, the causal agent of northern leaf blight (NLB), poses a major threat to maize production in sub-Saharan Africa. Effective disease management depends on understanding the biology and population genetic structure of the pathogen, yet studies from Africa remain limited. Here, we investigated the genetic diversity and evolutionary forces shaping E. turcicum populations in Kenya and Uganda. A total of 494 strains were genotyped using 12 microsatellite markers. Gene diversity was relatively low in Kenya (He = 0.45) and Uganda (He = 0.42) compared with previous reports. Analysis of molecular variance revealed weak but significant differentiation between countries (ΦPT = 0.178, p = 0.001), with more variation occurring within countries (82%) than among them (18%). Cluster analyses showed high levels of gene flow within each country but limited admixture between countries, suggesting geographical barriers to dispersal. Grouping populations according to shared agroecological zones did not result in distinct genetic clustering, indicating that population structure was not driven by agroecological similarity. This interpretation was supported by a weak isolation-by-distance correlation (R2 = 0.077), consistent with restricted long-distance gene flow. Most populations deviated from the expected 1:1 mating-type ratio, highlighting the importance of clonal reproduction in shaping population structure. Collectively, these findings suggest that E. turcicum populations are largely panmictic within countries but exhibit restricted cross-country movement. These results provide a valuable foundation for developing sustainable, regionally targeted strategies to manage NLB in East Africa.