Cassava improvement in the era of “agrigenomics”

Ismail Yusuf Rabbi (i.rabbi@cgiar.org), Melaku Gedil, Morag Ferguson, and Peter Kulakow
I. Rabbi, Postdoctoral Fellow (Molecular Genetics); M. Gedil, Head, Bioscience Center, IITA, Ibadan, Nigeria; M. Ferguson, Molecular Geneticist, IITA, Nairobi, Kenya; and P. Kulakow, Cassava Breeder, IITA, Ibadan, Nigeria

Pro-vitamin A 'yellow root' cassava developed by the IITA cassava breeding program. Photo by IITA.
Pro-vitamin A 'yellow root' cassava developed by the IITA cassava breeding program. Photo by IITA.

In the last 45 years, IITA has played a pivotal role in the genetic improvement of cassava for resource-poor farmers in sub-Saharan Africa (SSA). More than 400 cassava varieties have been developed that are not only high yielding but also resistant to diseases and pests. Many of these improved varieties have been extensively deployed in SSA and have helped to avert humanitarian crises caused by the viral disease pandemics that devastated local landraces in East and Central Africa. The cassava breeding program in Ibadan has a collection of more than 750 elite cassava clones representing current and historical materials accumulated over the last 45 years. These materials, referred to as the genetic gain collection (GGC), are accompanied by extensive field evaluation (phenotypic) data. In addition, the active breeding collection contains over 1000 African landraces and more than 400 new advanced breeding clones that are also accompanied by phenotypic data, including observations of disease and pest resistance, plant architecture, flowering ability, and performance in storage root yield. The most recent success of the conventional cassava breeding program culminated in the release of three vitamin A cassava varieties by the Government of Nigeria. These varieties (IITA TMS I011368, IITA TMS I011371, and IITA TMS I011412) were first cloned from seedlings in Ibadan in 2001 and have been subjected to extensive field testing throughout Nigeria. While almost all cassava in Nigeria are currently white fleshed, vitamin A cassava produces yellow-fleshed roots with nutritionally significant concentrations of carotenoids that produce vitamin A in the human body when consumed as yellow gari or fufu. In cooperation with HarvestPlus, IITA and partners will distribute vitamin A cassava planting materials to more than 25,000 farmers in 2013. New yellow-fleshed genotypes in the pipeline promise continued improvement in pro-vitamin A content, yield, and dry matter in the coming years.

Preparation of cassava DNA for genotyping by sequencing. Photo by IITA.
Preparation of cassava DNA for genotyping by sequencing. Photo by IITA.

As the vitamin A cassava illustrates, the genetic improvement of cassava has mostly been achieved through conventional breeding methods based on phenotypic selection. The only known direct application of molecular markers in cassava breeding is selection for resistance to cassava mosaic disease and cassava green mite. Recent advances and a reduction in the cost of the next-generation sequencing technologies now promise to usher in a new era for cassava breeding that will combine the success of conventional hybridization, selection, and multilocational yield trials with the latest advances in genomic resources.

Setting the stage for “next-generation cassava breeding”
Cognizant of the potential of marker technologies to improve the efficiency and effectiveness of cassava breeding, IITA, in collaboration with partners, embarked on the development and deployment of molecular markers1. With the recent accumulation of genomic resources in cassava research, including the first full cassava genome sequence2, our emphasis at IITA has shifted towards the application of these resources in molecular breeding3. One recent achievement is the identification and validation of nearly 1500 single nucleotide polymorphism (SNP) markers through an international collaboration led by IITA’s geneticist, Morag Ferguson4. These SNPs have been converted to a highly parallel hybridization-based genotyping system that has been shared with the international cassava research community through partnership with the Generation Challenge Program (GCP).

An example of an SNP genotyping data plotted with KBioscience’s SNPviewer software. Inset: raw SNP genotyping data from Illumina’s GoldenGate®assay.
An example of an SNP genotyping data plotted with KBioscience’s SNPviewer software. Inset: raw SNP genotyping data from Illumina’s GoldenGate®assay.

In addition, the first SNP-based genetic linkage map of cassava has been developed by IITA in collaboration with Heneriko Kulembeka of the Agricultural Research Institute (ARI), Ukiriguru, Tanzania. A linkage map is analogous to landmarks (SNP markers in this case) placed along chromosomes that guide researchers to genes or genomic regions controlling traits of interest. Such a linkage map is an indispensable tool for marker-assisted selection (MAS). SNP and SSR markers have also been applied to uncover quantitative trait loci (QTL) associated with resistance to cassava brown streak disease (CBSD)―which is ravaging cassava production in Eastern and Southern Africa―in a collaboration between IITA, CIAT, and ARI-Tanzania. Another dramatic development in cassava genomics is the recently completed sequencing of the cassava genome through the partnership of the US Department of Energy’s Joint Genome Institute and 454 Life Sciences2.

Genotyping-by-sequencing
The progress in next- generation technologies has drastically reduced the costs of DNA sequencing so that genotyping-by-sequencing (GBS) is now feasible for species such as cassava, ushering in a new era of agricultural genomics5. This will revolutionize the application of genomic tools for cassava improvement. GBS involves the cutting of genomic DNA into short pieces at specific locations using a restriction enzyme. The ends of these pieces are sequenced using techniques that allow sequencing of many samples at the same time. The beauty of this method is the use of adaptors containing barcodes (unique tags) that are enzymatically joined to the digested DNA fragments, enabling simultaneous sequencing or multiplexing of up to 384 samples in one sequencing reaction. This economy of scale greatly reduces the cost of processing each individual DNA to less than $10/sample. Approximately 200,000 markers can be identified and mapped in a very short time. With this powerful tool, breeders may conduct genomics-based research that was inconceivable a couple of years ago. Some of the exciting new research applications include polymorphism discovery, high-density genotyping for QTL detection and fine mapping, genome-wide association studies, genomic selection, improving reference genome assembly, and kinship estimation.

High-density QTL mapping and fine mapping
In the past, a limitation for QTL mapping was the number of markers on a genetic linkage map. With new SNP-based technologies this is no longer a limitation. This allows for fine mapping of QTLs so long as a sufficient number of individuals in the mapping population can be developed. IITA, in collaboration with national partners [ARI-Tanzania and National Crops Resources Research Institute (NaCRRI), Uganda], is using SNPs to discover QTLs associated with sources of tolerance for CBSD.

Preparation of gari, the most popular food product from cassava. Photo by IITA.
Preparation of gari, the most popular food product from cassava. Photo by IITA.

The next frontier for cassava genomics
Using the genotyping by sequencing approach, scientists from IITA and Cornell University, USA, are currently genotyping more than 2000 accessions of cassava, including released varieties, advanced breeding lines, and landraces from Africa. This is a pilot study of genomic selection funded by the Bill & Melinda Gates Foundation to explore the potential for using the IITA breeding collection, including genetic gain, local germplasm, and current advanced breeding lines, as the base population to begin genomic selection for West Africa. The IITA breeding collection has been extensively characterized in many locations and over many years. The convergence of high-density SNP data and extensive phenotypic data in IITA’s cassava collection sets the stage for the implementation of genome-wide association studies (GWAS) and genomic selection (GS) in breeding. The aim of GWAS is to pinpoint the genetic polymorphisms underlying agriculturally important traits. In GWAS, the whole genome is scanned for significant marker-trait associations, using a sample of individuals from the germplasm collections, such as a breeder’s collection. This approach of “allele mining” overcomes the limitations of traditional gene mapping by (a) providing higher resolution, (b) uncovering more genetic variants from broad germplasm, and most importantly, (c) creating the possibility of exploiting historical phenotypic data for future advances in breeding cassava.

A schema of genomic selection (GS) processes, starting from phenotyping and genotyping of the training population and selection of parental candidates via genomic estimated breeding value (GEBV)–based selection. Note that selection model improvement can be performed iteratively as new penotype and marker data accumulate.
A schema of genomic selection (GS) processes, starting from phenotyping and genotyping of the training population and selection of parental candidates via genomic estimated breeding value (GEBV)–based selection. Note that selection model improvement can be performed iteratively as new penotype and marker data accumulate.

GS is a breeding strategy that seeks to predict phenotypes from high-density genotypic data alone, using a statistical model based on both phenotypic and genotypic information from a “training population”. For cassava, phenotyping is the slowest and most expensive phase of the crop’s breeding cycle because of the crop’s low multiplication ratio of between 5 and 10 cuttings/plant. Thus, it takes several cycles of propagation (up to 6 years) to carry out a proper multilocational field trial evaluation. The implementation of GS at the seedling stage should: (a) dramatically reduce the length of the breeding cycle, (b) increase the number/unit time of crosses and selections, and (c) increase the number of seedlings that could be accurately evaluated. The reduced breeding cycle means that the ”engine of evolution,” i.e., recombination and selection, can proceed at a rate that is three times as fast as phenotypic-based selection, while saving resources. In conclusion, cassava breeding in IITA is being redefined, thanks to the increasing availability and deployment of genomic resources. Combining these resources with IITA’s long-standing conventional breeding pipeline means that the best days of cassava improvement lie ahead. These efforts will ultimately satisfy the increasing need for more healthy and nutritious food produced in environmentally sustainable ways.

References
1 Lokko et al. 2007. Cassava. In: Kole et al (ed). Genome mapping and molecular breeding in plants, Vol. 3. Pulses, Sugar and Tuber Crops. Springer-Verlag Berlin Heidelberg.
2 Prochnik S., P.R. Marri,B. Desany, P.D. Rabinowicz, et al. 2011. Tropical Plant Biol. doi:10.1007/s12042-011-9088-z. 3 Ferguson M., I.Y. Rabbi, D-J.Kim, M. Gedil, L.A.B. Lopez-Lavalle, and E. Okogbenin. 2011a. Tropical Plant Biol. DOI 10.1007/s12042-011-9087-0.
4 Ferguson M.E., S.J. Hearne, T.J. Close, S. Wanamaker, W.A. Moskal, C.D. Town, J. de Young, P.R. Marri, I.Y. Rabbi, and E.P. de Villiers. 2011b. Theor Appl Genet. DOI: 10.1007/s00122-011-1739-9.
5 Elshire R., J. Glaubitz, Q. Sun, J. Poland, and K. Kawamoto. 2011. PLoS ONE 6:e19379.

A tale of an African farmer

Farmer Baba Alphonse, northern Benin
Farmer Baba Alphonse, northern Benin

Sixty-year old farmer Alphonse Ogoule-Okpe of Ogoukpate Village, about 40 km from Porto Novo in northern Bénin, had all but abandoned cassava and maize farming.

Many years ago, insects (mealybug and cassava green mite) and diseases (such as blight) had attacked his cassava crops and “Baba” Alphonse and many like him in his village were hit hard because of the low yields and loss of a food and cash crop. The problem was compounded by the poor soil conditions in the fields.

During a visit to the small village by IITA scientists who distributed planting materials of improved IITA cassava varieties, Baba Alphonse said, “I would be happy if the problem with these insects and diseases will be over. Thanks to IITA, I can plant a new variety that is resistant to the problem pests.”

Unknown to farmer Alphonse, a few kilometers away from his farm was where the predator of the cassava green mite, T. aripo, was first released in Benin by IITA—way back in 1993. That—and his use of the new varieties from IITA would help ensure better cassava harvests for his family and the community.

The power of biocontrol

Farmers and scientists have, time and time again, turned back to nature to find solutions to pest problems in crop fields.

Variegated grasshopper (<em srcset=Zonocerus variegatus). Photo from Wikimedia commons ” width=”250″ height=”188″ />
Variegated grasshopper (Zonocerus variegatus). Photo from Wikimedia commons

When several exotic pests were accidentally introduced into Africa from South America through infected planting materials in the early 1970s, ravaging economically important crops, such as cassava, scientists turned to the origins of the pests to solve the problem.

A lot has been said about the benefits of biological control or biocontrol. It is natural and safe to the environment and humans, and rigorous tests ensure that it is effective only on the target pests.

And almost three decades of research and development at IITA have shown the continuing effectiveness and sustainability of biological control in combination with other approaches for managing insect pests.

These biocontrol practices and technologies provide the subsistence farmers in sub-Saharan Africa with solutions that are sometimes their only safety net.

This issue on biocontrol celebrates the success of solutions to problems in tropical agriculture that IITA and its partners have developed for millions of African farmers.

PROSAB ends

Farmer tending cowpea crops in Borno. Photo by IITA
Farmer tending cowpea crops in Borno. Photo by IITA

An 81% increase in farmers’ incomes over the past 5 years from improved yields, better access to farm inputs, and social empowerment are the key results of the US$6.33 million PROSAB project in northern Nigeria.

PROSAB is Promoting Sustainable Agriculture in Borno State, a project started in 2004 by IITA with Canadian International Development Agency (CIDA) funding.

In a conference held last September in the state capital of Maiduguri, government officials, farmers, participants, local partners, and other stakeholders said that PROSAB has “helped significantly increase agricultural productivity and build the capacity of thousands of farmers and farmers’ associations in the northern Nigerian state.”

Key project interventions included the introduction of improved crop varieties from IITA, training of farmers on improved agronomic practices, and promotion of gender equality, especially empowerment of women, in agricultural development.

The local government plans to upscale the project to further reduce poverty by promoting greater farmer education on best agricultural practices through the Agricultural Development Program; and encouraging more women to participate in the program.

Amare Tegbaru, PROSAB Manager, says the program has also improved the nutrition of farmers, especially children. “Farmers who adopted improved technologies and management practices experienced increased food availability and improved livelihood. Also, considerable progress has been made in addressing the problems of declining soil fertility and witchweed (Striga hermonthica),” he says.

Enhanced knowledge availability

IITA is promoting greater access to R4D knowledge by making use of knowledge resource access, video-sharing, and online social networking services.

google books

Last year, in partnership with Google Books, IITA started digitizing and uploading more than 200 publications, which are now available via Google Book Search (GBS). It also uploaded videos in SciVee and YouTube. Now, IITA has accounts with Twitter and Facebook too.

Increasing its online presence is an initiative aimed at “getting the word out” to a wider audience and driving more traffic to the Institute’s Web sites. With these free and popular online services, IITA is potentially tapping into a 300 million-plus combined user-base. Even with just a 1% bite, potentially some 3 million people will get to know more about IITA and what we do.

Rust-resistant soybean

TGX1835-10e, a rust-resistant soybean. Photo by IITA
TGX1835-10e, a rust-resistant soybean. Photo by IITA
A new soybean variety that is resistant to the deadly Asian soybean rust—a fungal disease that could wipe out as much as 80% of infested crops—has been released. The rust-resistant soybean is the first of its kind to be made available for cultivation in West and Central Africa and has the potential of increasing soybean production in rust-prone areas of the region.

Tagged TGx 1835-10E, the variety was bred by scientists at IITA and further developed in collaboration with Nigeria’s National Cereal Research Institute (NCRI).

“The variety is high yielding, averaging 1.6 t/ha grain and 2.2 t/ha fodder in field trials in Nigeria,” says Olumide Shokalu, NCRI pathologist who conducted the trials. It is also early maturing, has good promiscuous nodulation, and resists pod shattering and other prevalent diseases.

“The variety can be used for direct cultivation in tropical Africa or as a source of resistance genes. It was previously released in Uganda through Makerere University, and has already shown excellent performance in trials carried out in Southern Africa, suggesting that it is a well-adapted variety,” says Hailu Tefera, IITA soybean breeder.

Drought-tolerant maize

Drought-tolerant maize developed and disseminated by IITA, other international agricultural research centers, and national partners are helping farmers make a profit despite droughts in northern Nigeria. Drought remains one of the major limiting factors to profitable maize production in Africa.

“The drought-tolerant maize varieties have mitigated the effects of drought on maize production and farmers are having better incomes,” says Olumide Ibikunle, Research and Development Manager, Premier Seeds. “The seed industry is also better off because demand for maize has actually increased.”

Over the years IITA, CIMMYT, and partners have released several drought-tolerant varieties including Samaz 16, ZM309, and ZM523, in sub-Saharan Africa to cushion the effects of drought on the crop and, ultimately, on farmers and their households.

Researchers and other stakeholders said that developing such varieties will boost maize production, enhancing not only incomes but more importantly food security.

Dual-resistance cassava

IITA scientists are a step closer to making a breakthrough in developing cassava that is resistant to both the cassava brown streak disease (CBSD) and the cassava mosaic disease (CMD) in Eastern and Central Africa. The two diseases are the biggest threats to cassava production in the region putting at risk the food security and livelihoods of over 200 million people.

According to Edward Kanju, IITA cassava breeder, 14 types of the crop under research are very promising. Kanju’s team had just harvested an advanced trial of such cassava in Uganda.

This is the fourth year of trials for dual-resistance cassava for the mid-altitudes in Uganda. The trials are being conducted at Mukono, near Kampala, an area regarded as a hot spot for CBSD and CMD. The breeding work started with over 5,000 true seeds of parents with tolerance to CBSD from Tanzania for crossing with IITA varieties that are resistant to CMD.

Farmers have also been involved in the selection process to ensure that the varieties meet their preferences on cooking, taste, texture, and yield. Breeding for dual-resistance cassava is also being conducted in Tanzania and DR Congo.

The cassava scourge

James Legg, j.legg@cgiar.org

Close up of Bemisia tabaci adults. Photo by CIAT
Close up of Bemisia tabaci adults. Photo by CIAT

Who would think that delicate and exquisite little insects such as whiteflies could pose an ongoing and global challenge to humankind’s need to meet its food requirements?

Whiteflies are one of the top 10 most serious pest threats to agriculture. Although whiteflies, in the taxonomic family Aleyrodidae, are a diverse group of insects of more than 1,200 species, only a few of these are economically important. Among this small group, Bemisia tabaci (Genn.) is by far the most important single species.

B. tabaci was first described from tobacco in Greece, towards the end of the 19th century. Its progress has closely matched developments seen in agriculture in subsequent years, and it now occurs virtually throughout the crop-growing parts of the globe. Its preference for warm weather means that it is particularly prevalent in the tropics, although it has also been able to exploit protected agricultural environments in temperate regions.

Deadly partnerships
If B. tabaci contented itself with doing its own thing and sucking small quantities of sap from the plants that it feeds on, it would probably have fallen under the radar of those whose job it is to protect crops. But it did not. Over time, it evolved a relationship with plant viruses, a relationship that allowed the whitefly to pick up viruses when feeding on plants, harbor them for some time, before introducing them to another plant during feeding, thereby giving rise to a new infection. This enabled the viruses transmitted to expand their ranges as B. tabaci populations grew and spread. These deadly partnerships thus gave rise to plant disease epidemics that had devastating impacts on the crops affected, and on the people growing them.

Large population of B. tabaci adults feeding on the underside of a young cassava leaf
Large population of B. tabaci adults feeding on the underside of a young cassava leaf. Photo by IITA

B. tabaci transmits many hundreds of virus species, a number that keep rising as more viruses are described and research efforts on the B. tabaci vector are also broadened. The viruses transmitted fall into four virus genera: Begomovirus (family Geminiviridae), Ipomovirus (Potyviridae), Crinivirus, and Carlavirus (Closteroviridae). More than 90% of the more than 100 species transmitted, however, are in the Begomovirus group. One of Africa’s most economically destructive diseases, cassava mosaic disease (CMD), is caused by a group of viruses in the Begomovirus genus. Collectively, these are usually referred to as the cassava mosaic geminiviruses. Evidence also points to B. tabaci being the vector of cassava’s other major expanding disease threat, cassava brown streak disease (CBSD) caused by the Ipomovirus, cassava brown streak virus.

Cassava has always been at the heart of IITA’s research-for-development agenda. Thus, diseases such as CMD and CBSD, and the agents that promote their spread, have long been the focus of research efforts. From its earliest beginnings, IITA was fortunate to receive cassava germplasm, developed in East Africa through the Amani breeding program that most importantly was endowed with resistance to CMD.

It may have been an unfortunate spin-off of the tremendous success of the CMD-resistant varieties, but B. tabaci, the humble vector of the CMGs, received very little research attention before the 1990s. Things were to change abruptly in the mid-1990s, however. It became increasingly clear that unusually large whitefly populations were propelling the expansion of a new, highly virulent form of CMD in Uganda.

Studying the pandemic
IITA initiated a wide-ranging research program with the dual aims of enhancing scientific understanding of the deadly virus-vector combination as well as working with national partners to manage the pandemic.

The genetics and epidemiology of CMGs associated with the pandemic were extensively documented over the decade following the initial explosion of interest. Although less research attention was focused on the whitefly vector, a number of important advances were made in understanding the nature and role of B. tabaci. Perhaps most significantly, it was demonstrated that superabundance of B. tabaci was a key factor driving the pandemic’s so-called ”front”, and, furthermore, that the front could be pushed forwards by up to 100 km/year in this way. Although whiteflies are weak fliers, single B. tabaci individuals have been shown elsewhere to fly for up to 7 km, assisted by the wind, and given a generation time of slightly less than one month, it is easy to see how such a long distance spread could be achieved.

Superabundant <em srcset=B. tabaci and the CMD pandemic (Yellow shaded area is the approximate region affected by the CMD pandemic by 2009. Arrows indicate the direction of pandemic expansion. White explosions indicate areas in which B. tabaci superabundance has been most prominent, together with associated physical damage to cassava crops.)” width=”250″ height=”181″ />
Superabundant B. tabaci and the CMD pandemic (Yellow shaded area is the approximate region affected by the CMD pandemic by 2009. Arrows indicate the direction of pandemic expansion. White explosions indicate areas in which B. tabaci superabundance has been most prominent, together with associated physical damage to cassava crops.). by IITA

Extensive and regular disease surveys conducted by IITA and its NARS partners from 1997 up to the present have helped build up a comprehensive picture of the pandemic’s expansion into 11 countries of East and Central Africa and the interrelationships with vector populations. Moreover, these data have been used to provide risk assessments of future patterns of spread which have supported disease management initiatives.

Superabundant B. tabaci populations are typically 100-fold greater than those outside the pandemic zone. As well as delivering a sharply increased level of virus transmission, these cause physical damage to cassava plants. Experimental studies conducted at IITA-Uganda showed that yield losses from whitefly damage alone can be as much as 50%, and that these losses are particularly severe for some of the recent releases of CMD-resistant varieties. A gray-black sooty mold covering the lower leaves that develops on the sugary excreta produced by whitefly nymphs is a characteristic symptom of heavy whitefly infestation. These symptoms have been observed in various parts of East and Central Africa, and always occur in areas affected by the CMD pandemic.

Research priority
The obvious research question that has been thrown up from these sets of circumstances is: ”what causes superabundance in B. tabaci?” There are two principal hypotheses. One suggests that superabundance is a result of the spread of a novel ‘fitter’ B. tabaci biotype, and the second, that superabundance is the consequence of a synergistic interaction between B. tabaci and CMD-infected cassava plants.

To examine the first hypothesis, IITA has been working with the University of Arizona, USA, to develop molecular markers to allow discrimination between cassava-colonizing B. tabaci populations. The earliest work made use of sequence portions of the cytochrome oxidase 1 gene of mitochondrial DNA (mtCO1). MtC01 sequences were obtained from whiteflies collected along transects straddling the pandemic ”front” in Uganda. Analysis of sequence homologies showed that there were two major genotype clusters, and that one of these, the so-called “invader” was strongly associated with the pandemic-affected zone. Subsequent collections made after the pandemic had covered the whole of the cassava-growing area of Uganda, however, provided an apparently contradictory outcome, as the ”invader” genotype cluster appeared only infrequently. This is not altogether surprising, however, as B. tabaci cassava biotypes from different countries, and even different continents, have been shown to be able to interbreed successfully.

Finding novel solutions
Current efforts are therefore focusing on developing microsatellite markers that provide a much wider coverage of the B. tabaci genome and will make it more likely that we can discriminate between putative superabundant and normal B. tabaci biotypes. To investigate the intrinsic biological characteristics of different cassava B. tabaci populations, their associated genetics and the biology of offspring produced through inter- and intra-population mating, core funds are currently being used to run a PhD program in Tanzania. This study will also be used to examine the hypothesis of B. tabaci-CMD infected cassava synergism. Preliminary results from cage trials conducted at NRI using a single variety have shown increased B. tabaci abundance on CMD-infected plants, when compared with uninfected material.

Chlorosis on shoot tip and sooty mold on lower leaves caused by heavy <em srcset=B. tabaci infestation” width=”250″ height=”188″ />
Chlorosis on shoot tip and sooty mold on lower leaves caused by heavy B. tabaci infestation. Photo by IITA

The idea that diseased cassava makes for a better food source for B. tabaci has parallels in studies conducted with B. tabaci on other host plants, where virus infection has led to increased whitefly populations. In the cassava system there are some contradictions, however. It is significant that the greatest abundances of B. tabaci in pandemic-affected areas are actually observed on CMD-free resistant varieties. Further research is clearly required before a clear-cut explanation can be given for the superabundance enigma.

With whitefly numbers at record levels, and physical damage exacerbating the already grave problems posed by CMD, it has been increasingly recognized that effective measures for whitefly control need to be identified. Two main options appeared to offer greatest potential: resistance and biocontrol. Pesticides, although widely used in northern commercial agricultural systems, are easily dismissed for use on cassava in SSA, because of the extreme cost and the environmental hazard that they pose.

Is biocontrol the answer?
IITA had great success in its classical biological control programs for managing cassava mealybug and cassava green mite. Why not do a similar thing for whiteflies? Sadly, B. tabaci poses a greater challenge since it is considered to be African in origin, and therefore should already be benefiting from the presence of indigenous natural enemies. Significant work was nevertheless undertaken at IITA-Uganda to characterize the natural enemies of B. tabaci on cassava and to investigate the potential for augmentation.

A combination of surveys, life table studies, mortality measurements, and behavioral assessments conducted over a 10-year period—from 1999 to 2008—revealed that although natural enemies accounted for significant mortality in B. tabaci populations, under normal circumstances this was not sufficient to keep B. tabaci populations at levels below those causing significant economic damage.

To change this balance, it was concluded that complementary B. tabaci control measures would be required, such as the introduction of climate-matched exotic B. tabaci parasitoids or the use of cassava varieties either less favorable to whiteflies or more favorable to parasitoids. Although no attempt has yet been made to introduce exotic B. tabaci parasitoids to East Africa, a significant amount of effort has been made to enhance whitefly resistance in cassava germplasm. IITA partnered with CIAT, NRI, and NARO (Uganda), under the SP-IPM’s Tropical Whitefly Project, to pioneer efforts to introduce to East Africa strong sources of whitefly resistance developed in Latin America by CIAT (albeit to different whitefly species).

The NARO team have had some success in identifying Latin American germplasm that appears to have partial resistance to African B. tabaci, but the challenge still remains to combine these sources of resistance with the other key traits that are required by cassava in the East African farming environment. To achieve this, whitefly resistance markers will need to be built in to marker-assisted selection approaches. Much untapped potential may yet exist, however, in African germplasm, and beyond that, within wild relatives. These are important areas of future research.

Women bringing cassava to market
Women bringing cassava to market. Photo by IITA

Need more studies on whitefly
The recent upsurge in the importance of CBSV in the Great Lakes region of East/Central Africa poses yet more challenges to the cassava research community. Although published reports identify B. tabaci as the vector, researchers remain divided on the accuracy of this claim. As such, IITA, working closely with NRI, is actively addressing this question systematically, by combining field epidemiological studies with cage-based transmission experiments, both of which are being facilitated by newly improved virus diagnostic techniques.

Preliminary results seem to support the earlier claim that B. tabaci is the vector, as the level of CBSV infection in whitefly-protected experimental plots was approximately half that in whitefly-infested plots. These preliminary data will need to be confirmed by repeat trial plantings and cage trial results before any more definitive outcome can be claimed.

Whiteflies have been recognized as an important threat to cassava production for more than a century, but at the outset of the 21st century, that threat appears to be greater than ever. It appears likely that B. tabaci is driving a dual pandemic of CMD and CBSD through the cassava-growing heartlands of Africa.

Recognition of the importance of the twin threats to cassava is at an all-time high, with record levels of funding available to tackle them. By contrast, the role of the vector in the cassava crisis has received much less recognition. This fact will need to be addressed by IITA and its partners in developing future cassava-oriented R4D projects and programs.