Variability of Phytophthora Infestans in Uganda and Kenya and its implications to late blight management in potato and tomato

Abstract

Phytopthora infestans (Mont.) de Bary the pathogen responsible for causing late blight in potato is a rapidly evolving and highly adaptable pathogen. The pathogen has both asexual and sexual reproduction systems but the asexual method of reproduction is dominant in most parts of the world including Sub-Sahara Africa (SSA). The asexual clone, which has been dominant in SSA, is the US-1 genotype identified by an A1 mating type and Ib mitochondrial (mt) DNA haplotype. In Kenya and Uganda, findings from studies conducted until early 2000 indicated that the US-1 clonal lineage had been the dominant genotype for more than half a century. In a subsequent study conducted in 2007, a new clonal lineage named KE-1 was found in two fields in Kenya but the US-1 genotype was still dominant. The KE-1 genotype is of the A1 mating type but has a Ia mtDNA haplotype. The results presented in this thesis show that four years after the discovery of the KE-1, the old US-1 lineage has been completely displaced in Kenya on potato. Subsequently, the new lineage has migrated into Uganda through the eastern part of the country that borders western Kenya. All potato samples from eastern Uganda contained the KE-1 genotype. Moreover, samples from eight fields in western Uganda were also of the KE-1 genotype, which is in agreement with an on-going displacement. However, the new lineage does not displace the old lineage on tomato – only on potato. In a study of the variation in AVr4 effector genes from the two clonal lineages, it was observed that the US-1 genotype is undeniably an old lineage, which has been undergoing population expansion over the years. The KE-1 genotype was found to possess few generations indicating it is indeed a new genotype in the region. However, despite the differences observed between the new and the old lineages, the KE-1 genotype of P. infestans is more aggressive than the US-1 genotype since it has displaced this older population. Consequently, the appearance of a new pathogenically fit clonal lineage means that late blight will be more acute in east African region and its control difficult. However, despite all the setbacks that come with fighting potato and tomato late blight, future breakthrough is still possible if continued research on population dynamics of P. infestans in the region continues. Keywords: Late blight, population structure, SSR, Effectors, Kenya, Uganda