Detection, distribution and genetic diversity of sweet potato leaf curl virus (SPLCV) from western, coastal and central regions of Kenya

Abstract

Leaf curling in sweet potato has been reported throughout the world. One of the causal agents is Sweet potato leaf curl virus (SPLCV) which belongs to the genus Begomovirus (family Geminiviridaey. Since SPLCV could become an important constraint for sweet potato production in Kenya; detection, distribution and genetic diversity of sweet potato leaf curl virus from Western, Coastal, and Central regions of Kenya is important. Polymerase chain reaction (PCR) was done in 512 collected sweet potato samples, using degenerate and specific primers. Specific primers SPB, PW were used to amplify the coat protein (AVI), and the ORFs ACI and AC4 fragments. Western region had infected samples with cumulative positive of 78% followed by Coast with 69.4% and Central 3.9%. To evaluate genetic diversity and variability among begomoviruses obtained from 45 sweet potato genotypes; analysis of the nucleotide sequence of a fragment of the protein gene (ACl), (AVl) and (AC2) was carried out. Phylogenetic analysis using the obtained nucleotide sequences of the AC l, the full length nucleotide sequences of the coat protein gene (AVI) and (AC2) clustered all sweet potato begomoviruses together. However in AC 1, 3 were closely related to SPLCV with nucleotide sequence identities that varied from nearly 61 to 96 % and closely related to Asia samples. AVI protein from Central samples was closely related with an over 92% nucleotide sequence identity. The diversity within the coat protein (AVI) was available but distributed in all regions. Results indicated that these isolates were closely related to SPLCV coat protein with amino sequence identities that ranged from 90 to 100 %. AC2 fragments from Western and Coast had a close relationship of 95 % nucleotide sequence identity and amino acid sequence identity of 96% showing that the AC2 protein may have the same ancestor. Samples from Western and Coast with 95% sequence identity and 96% amino acid sequence identity supports that the AC2 protein fragment was from the same ancestor. Several isolates from western clustered as subgroups with 86-85% nucleotide sequence identity. The research study reports the first PCR detection of begomovirus infecting sweet potato and the first genetic diversity and variability of begomovirus infecting sweet potato in Western, Central and coastal regions of Kenya. The study indicates that future development of sweet potato begomovirus management such as genomics strategies should focus on SPLCV as a threat in Kenya sweet potato growing regions.