| dc.description.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. | en_US |
