IITA scientist develops a cheaper and faster tool for identifying whiteflies

27 May 2020

A CGIAR-IITA scientist has developed a more cost and time effective molecular diagnostic tool that can accurately identify different subgroups of cassava whiteflies, Bemisia tabaci. The tool can be used in local laboratories in Africa that often lack expensive sequencing technologies.

This innovation marks a major milestone in efforts to accurately characterize whiteflies, which transmit viruses that cause cassava mosaic disease (CMD) and cassava brown streak disease (CBSD), major diseases that have wreaked havoc with Africa’s cassava crop over several decades. The combined damage resulting from infection with these two diseases is estimated to cause annual yield losses amounting to 50% in East and Central Africa, equivalent to more than US$1 billion.

IITA scientist develops a cheaper and faster tool for identifying whiteflies

Efforts to control pests and diseases are founded on proper identification. However, the whitefly is a complex species that requires the use of genetic tools to make accurate identifications. The most widely used method has been partial sequencing of the mitochondrial DNA cytochrome oxidase I gene (COI).

This was recently found to be much less effective in identifying cassava whiteflies compared to the more robust single nucleotide polymorphism (SNP)-based genotyping method using NextRAD sequencing.

Dr Everlyne Wosula, a Vector Entomologist based at IITA–Tanzania, has made use of the SNP data to develop a cheaper and more rapid diagnostic method using the Kompetitive Allele-Specific (KASP) PCR. This breakthrough has been published in a paper “KASP genotyping as a molecular tool for diagnosis of cassava-colonizing Bemisia tabaci” in the ‘Insects’ journal. This is the first time that this method has been used for insect identification.

The KASP assay method gives reliable results in a day and at a fraction of the cost of sequencing-based methods. One hundred fifty one of 152 whitefly specimens (99.3%) collected from cassava from 12 countries across sub-Saharan Africa and tested with KASP, gave the correct identity obtained from the SNP genotyping.

“Therefore, using this method to keep track of potentially dangerous whitefly populations as part of their early warning systems for pests and diseases will be very straightforward for many national laboratories in Africa with limited resources,” Wosula said.

Wosula previously analyzed over 7,453 SNPs occurring across the genomes of cassava-colonizing B. tabaci from Africa NextRAD sequencing. This research revealed the existence of six haplogroups of whitefly species in Africa, designated as sub-Saharan Africa (SSA) 2, SSA4, SSA-Central Africa, SSA-East and Southern Africa, SSA-West Africa, and SSA-East and Central Africa.

The findings were published in the paper “Unravelling the genetic diversity among cassava Bemisia tabaci whiteflies using NextRAD sequencing” in the Genome, Biology and Evolution journal.

The new KASP diagnostic that has been based on this earlier research is already being used in new research programs to monitor cassava whiteflies in several African countries. Although most of the work is currently being done in the IITA-Tanzania lab, Wosula has plans to provide training so that the technique can also be added to the toolkits of national research systems and universities across Africa.

Wosula collaborated with researchers from Boyce Thompson Institute at Ithaca, New York and the United States Department of Agriculture – Agriculture Research Services (USDA-ARS) and was supported by members of the Virus Vector Ecology Group at IITA-Tanzania. The research was funded by USAID and the Roots, Tubers and Bananas Program (RTB) of CGIAR.