MOLECULAR CHARACTERIZATION OF POTATO VIRUS Y AND EVALUATION OF NOVEL POTATO CLONES FOR EARLINESS AND RESISTANCE IN KENYA.

Abstract

The potato (Solanum tuberosum), is the second most important food crop in Kenya after maize and the fourth most important crop in the world after rice, wheat, and maize. Numerous pests and a broad spectrum of bacterial, viral, and fungal diseases can affect the potato crop. Potato virus Y (PVY) is one such disease that can result in up to 100% crop loss and substantial production reductions. New variations with distinct biological characteristics that affect potato production worldwide are produced as a result of PVY strain evolution. There is still little and inadequate documentation regarding its phylogeography in East Africa in comparison to the global distribution of PVY. To investigate this, a survey was conducted to assess the distribution of PVY infection in Kenya's major potato-growing areas: Kiambu, Nyandarua, Meru, Nakuru, Bomet, West Pokot, Kisii, and Bungoma. Positively identified PVY samples were subjected to sequencing to unveil the level of genetic diversity within the Kenyan potato gene pool. A randomized complete block design was used in four trial sites for potato populations from Scotland to test for earliness and PVY resistance in KALRO-Kakamega, Alupe, and Sang’alo. Seed bulking was done in Kapsokwony. Data was recorded at 40, 70, and, 90 days post-emergence to capture data for earliness and test for PVY infection in the potato cultivars. Bioinformatics tools were used for the De novo assembly and mapping, genome alignment, recombination, and phylogenetic analysis. The overall prevalence of the strains in the eight counties stood at 36.62%. PVY was more prevalent in Meru (100% affected), followed by Kiambu (61%), Bomet (40%), and Nyandarua (26.7%). Bungoma, Nakuru, Kisii, and Elgeyo Marakwet recorded 0% of PVY infection. Molecular characterization of seven potato virus Y-positive strains and a whole genome sequencing of the PVY Kenyan isolate revealed the molecular footprint of PVY in Kenya. The N-type (PVYN) and recombinant PVY strain type (PVY N:O) were prevalent in the areas of study sampled. Partial sequences of the seven potato virus Y strains identified from farmer fields deposited in the NCBI database were OR571473, OR571477, OR571474, OR571476, OR571478, OR571479, OR571475, and a complete genome of Kenyan PVY isolate, accession number PP069009. The evolutionary relationship of the Kenyan isolate PP069009 was unveiled, demonstrating a strong 92% probability of clustering with a sequence from the United States of America [JQ924287]. Population genetics analysis revealed a calculated nucleotide diversity (π) of 0.00354881, while Analysis of Molecular Variance (AMOVA) had an øST value of 0.45224. The extensive haplotype network depicted diverse PVY strains across continents. Potato population screening from Scotland was accessed at 40, 70, and 90 days post-emergence. Tests of Between-Subjects Effects combining genotypes and three field sites were significant (F = 54.43.435, DF= (61-2), P <0.05) with Sang'alo displaying the best mean phenotype of 2.6675. 12 of the 60 genotypes were selected for further processing in KEPHIS and KALRO. I, therefore, present the first molecular footprint of the Kenyan PVY whole genome (PP069009), illustratively describing its’ phylogenetic positioning, historical transmission patterns across continents, and the adaptive selection pressures, emphasizing its potential role in PVY's adaptive evolutionary process. However, I stress the need for further investigations into the specific evolutionary dynamics shaping PVY populations in distinct geographical regions, especially Africa, as the virus is continually evolving. Upon adoption, climate smart cultivars will support potato productivity among small-scale farmers. Information obtained from this study will help in policy development on managing PVY infections in Kenya.