A scientist with the International Institute of Tropical Agriculture (IITA) 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 characterise 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 $1.00 billion.
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-colonising Bemisia tabaci in the Insects journal. This is the first time that this method has been used for insect identification.
Wosula’s research work focuses on population genetic diversity, biology and behaviour of whiteflies, and exploring novel techniques for management of whiteflies in cassava.
She holds a BSc and an MSc in Horticulture from Jomo Kenyatta University of Agriculture and Technology, and PhD in Plant Pathology with a minor in Entomology (2012) from Louisiana State University (LSU).
Prior to joining IITA, she worked as a Postdoctoral Research Associate at the University of Nebraska –Lincoln, Department of Entomology (2013 -2015), Graduate Assistant at the Department of Plant Pathology and Crop Physiology – LSU (2008 – 2012), Technical Assistant at the International Centre of Insect Physiology and Ecology (2004 – 2007), Field Officer Cereal Grower Association (2003) and Tea Extension Assistant (2001-2002) with Kenya Tea Development Agency.
She has over 10 years of experience working on virus-vector interaction complexes that include aphids and sweet potato potyviruses, wheat curl mites and wheat viruses and currently on whiteflies and cassava viruses.
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 says.
Wosula previously analysed 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.
RTB is a partnership collaboration of five research centres, led by the International Potato Center, with decades of experience in these crops on different continents, including four CGIAR research centres (Bioversity International, the International Center for Tropical Agriculture, IITA and the International Potato Center) and the French Agricultural Research Centre for International Development (CIRAD).
By working with more than 360 other partners, these five centres mobilize complementary expertise and resources; avoid duplication of efforts; and create synergies to increase the benefits of their research for smallholder farmers, consumers and other stakeholders.
Root, tuber and banana crops – cassava, potatoes, sweet potatoes, yams, bananas, plantains, and tropical and Andean roots and tubers– are some of the most important staple crops in the world’s poorest regions.
They provide around 15% or more of the daily per capita calorie intake for the 763 million people living in the least developed countries.
Often rich in key nutrients such as provitamin A, RTB crops can significantly improve nutrition and food security. Many RTB crops can be grown with few inputs and often under harsh conditions. Yet they respond very well to intensification and are high yielders in terms of calories produced per hectare.
As important cash crops, they can help boost family incomes and are frequently grown or marketed by women. But RTB crops present several common challenges.
They are propagated clonally rather than with seeds, which allows yield-reducing pathogens to build up over time. This calls for a strong design of private-public seed systems. The crops’ bulk and perishability put pressure on postharvest innovation. High genetic complexity in any variety.