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NextRAD sequencing unravels the genetic diversity of cassava-colonizing Bemisia tabaci

Everlyne Wosula: International Institute of Tropical Agriculture

<div><em>Bemisia tabaci</em> is a vector of cassava mosaic begomoviruses and cassava brown streak ipomoviruses which cause significant cassava yield losses in Africa. Cassava-colonizing <em>B. tabaci</em> comprise several cryptic species that cannot be distinguished morphologically and so are separated by sequencing the mitochondrial DNA cytochrome oxidase I (mtCOI). The objectives of this study were to (i) determine the effectiveness of the mtCOI marker for delineating cassava <em>B. tabaci</em> haplogroups and (ii) determine if there is gene flow among these haplogroups. Ninety-five whitefly specimens collected from cassava in eight African countries were genotyped using NextRAD sequencing, and their phylogeny and population genetics were investigated using the resultant single nucleotide polymorphism (SNP) markers. SNP marker and mtCOI data obtained from the same insect were compared. Eight genetically distinct groups were identified based on mtCOI, while phylogenetic analysis using SNPs identified six major groups. STRUCTURE analysis identified four ancestral <em>B. tabaci</em> populations that have contributed alleles to the six SNP-based groups. Significant gene flows were detected between several of the six SNP-based groups. This study reveals that mtCOI is not an effective marker for phylogenetic classification of cassava-colonizing <em>B. tabaci</em>, and that more robust SNP-based multilocus markers should be developed. Significant gene flows between populations could lead to the emergence of haplogroups that might alter the dynamics of cassava virus spread and disease severity in Africa. Continuous monitoring of the genetic composition of whitefly populations should be an essential component in efforts to combat cassava viruses in Africa.</div>