insects Article Distribution and Molecular Diversity of Whitefly Species Colonizing Cassava in Kenya Florence M. Munguti 1,2, * , Dora C. Kilalo 1 , Evans N. Nyaboga 3 , Everlyne N. Wosula 4 , Isaac Macharia 2 and Agnes W. Mwango’mbe 1   Citation: Munguti, F.M.; Kilalo, D.C.; Nyaboga, E.N.; Wosula, E.N.; Macharia, I.; Mwango’mbe, A.W. Distribution and Molecular Diversity of Whitefly Species Colonizing Cassava in Kenya. Insects 2021, 12, 875. https://doi.org/10.3390/ insects12100875 Academic Editor: Dorith Rotenberg Received: 30 July 2021 Accepted: 4 September 2021 Published: 27 September 2021 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). 1 Department of Plant Science and Crop Protection, University Nairobi, Kangemi, Nairobi P.O. Box 29053-00625, Kenya; dchao@uonbi.ac.ke (D.C.K.); wakesho123@gmail.com (A.W.M.) 2 Kenya Plant Health Inspectorate Service, GPO, Nairobi P.O. Box 49592-00100, Kenya; macharia.isaac@kephis.org 3 Department of Biochemistry, University Nairobi, GPO, Nairobi P.O. Box 30197-00100, Kenya; nyaboga@uonbi.ac.ke 4 International Institute of Tropical Agriculture, Dar es Salaam P.O. Box 34441, Tanzania; E.Wosula@cgiar.org * Correspondence: fmunguti@kephis.org Simple Summary: The whitefly, Bemisia tabaci (Gennadium, Hemiptera) is a crop pest and plant- virus vector known to transmit more than 300 plant viruses. Among other plant viruses, the vector transmits viruses that cause the two major devastating viral diseases of cassava in sub-Saharan Africa namely cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). In order to achieve effective implementation of whitefly management programs including prevention of spread of the species, accurate species identification is vital. Morphological identification approaches toward whitefly species limits the capacity to accurately identify new species, especially the presence of cryptic species such as the numerous B. tabaci genetic groups. Using the mitochondrial DNA cytochrome oxidase 1 (mtCO1) sequences, four distinct whitefly species namely Bemisia tabaci, Bemisia afer, Aleurodicus dispersus and Paraleyrodes bondari were identified in samples collected from major cassava growing regions in Kenya. The study presents the first report of P. bondari (Bondar’s nesting whitefly) on cassava in Kenya. We found three B. tabaci genetic groups of SSA1, SSA2 and Indian Ocean (IO) putative species colonizing cassava in Kenya. The information is useful to inform better management strategies of the whitefly vectors to reduce the impact of cassava viral diseases, which continue to be a threat to food security in major cassava growing regions. Abstract: The whitefly, Bemisia tabaci (Gennadium, Hemiptera) has been reported to transmit viruses that cause cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) in many parts of sub-Saharan Africa (SSA). Currently, there is limited information on the distribution, species and haplotype composition of the whitefly populations colonizing cassava in Kenya. A study was conducted in the major cassava growing regions of Kenya to address this gap. Analyses of mitochondrial DNA cytochrome oxidase 1 (mtCO1) sequences revealed the presence of four distinct whitefly species: Bemisia tabaci, Bemisia afer, Aleurodicus dispersus and Paraleyrodes bondari in Kenya. The B. tabaci haplotypes were further resolved into SSA1, SSA2 and Indian Ocean (IO) putative species. The SSA1 population had three haplogroups of SSA1-SG1, SSA-SG2 and SSA1-SG3. Application of KASP genotyping grouped the Bemisia tabaci into two haplogroups namely sub-Saharan Africa East and Southern Africa (SSA-ESA) and sub-Saharan Africa East and Central Africa (SSA-ECA). The study presents the first report of P. bondari (Bondar’s nesting whitefly) on cassava in Kenya. Bemisia tabaci was widely distributed in all the major cassava growing regions in Kenya. The increased detection of different whitefly species on cassava and genetically diverse B. tabaci mitotypes indicates a significant influence on the dynamics of cassava virus epidemics in the field. The study highlights the need for continuous monitoring of invasive whitefly species population on cassava for timely application of management practices to reduce the impact of cassava viral diseases and prevent potential yield losses. Keywords: Bemisia tabaci; mtCOI gene; P. bondari; KASP genotyping; haplotype Insects 2021, 12, 875. https://doi.org/10.3390/insects12100875 https://www.mdpi.com/journal/insects