Cassava improvement in the era of “agrigenomics”

Ismail Yusuf Rabbi (, 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.

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.

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.

Banana 2008 media coverage

Continuing follow-up media coverage and reports by various news services on the Banana 2008 Conference are now available.

These include the five-part series from the Voice of America: Banana mooted as top crop in Africa, Disease threatens African banana industry, Top trade lawyer doubts feasibility of East African banana exports to Europe, Governments and global businesses urged to help African banana sector, and Sweeping reforms needed to improve African banana industry,

New African: Ripe for the picking

African Agriculture: Sweeping reforkms needed to improve African banana industry

The audio of reports (in MP3) could be streamed or downloaded directly from within the story webpage.

Banana 2008 [update!]

Banana2008 logo

Representatives from the banana research and industry from all over Africa had an excellent meeting in Kenya in October 2008. The ambition to develop a 10-year strategic roadmap that would harmonize and guide efforts to promote the marketing and trade of the crop in the continent has been kick-started with contributions of key players in the banana world and critical reviewers. The prospects look promising and further details will be released post-conference.

The conference on “Banana and plantain in Africa: Harnessing international partnerships to increase research impact” took place at the Leisure Lodge Resort in Mombasa, Kenya on 5-9 October. This was the first Pan-African banana conference that links research to markets within the African context.

The event was organized and coordinated by IITA in cooperation with Bioversity International, Forum for Agricultural Research in Africa (FARA), Kenya Agricultural Research Institute (KARI), and the International Society for Horticultural Science (ISHS), and supported by the International Service for the Acquisition of Agri-Biotech Applications, the National Agricultural Research Organization of Uganda, Du Roi, and Bill and Melinda Gates Foundation.

The conference had three major themes: markets and trade, production, and innovation systems. The role of research and the importance of public-private sector partnerships were also highlighted.

The strategy document shapes and changes the way bananas are produced and marketed in Africa, linking state-of-the-art research to new markets and stimulating trade. In the long term, the impact will be to change commercial banana production from a donor aid-supported system to one which is sustained by an invigorated private sector that actively seeks technological interventions.

Banana facts

In terms of production, bananas are the world’s 4th most important food crop, mostly grown and consumed in the tropical and subtropical zones. The crop is grown in more than 120 countries, with an annual world production of around 104 million tons; around a third each is produced in the African, Asia-Pacific, and Latin American and Caribbean regions.

About 87% of all the bananas grown worldwide is produced by small-scale farmers for local consumption as a food security crop, and for local markets than for international trade. They provide a staple food for millions of people, particularly in Africa.

Approximately 13% of worldwide banana production is destined for the export market. The banana fruit is extremely important as an export commodity especially in Latin America and Caribbean, which contribute over 83% of the total banana in the international market. The banana export industry is also the backbone of the economies of many Caribbean countries, and the crop plays a vital role in the social and political fabrics of the islands.

In Africa, only five countries namely, Côte d’Ivoire, Cameroon, Somalia, Ghana, and Cape Verde, export approximately 427,000 tons of banana and plantain. There are more than 500 banana varieties in the world, but the Cavendish is the most exported banana cultivar.
The banana’s ability to produce fruits all year round makes it an important food security crop and cash crop in the tropics.

Bananas and plantains supply more than 25% of the carbohydrate requirements for over 70 million people in Africa. East Africa is the largest banana-producing and consuming region in Africa with Uganda being the world’s second leading producer after India, with a total production of about 10.5 million tons. In some African countries such as Uganda the daily consumption of banana may exceed 1.6 kilogram per person, which is the highest in the world.

Nutritionally, fresh bananas contain 35% carbohydrates, 6-7% fiber, 1-2% protein and fat, and major elements such as potassium, magnesium, phosphorus, calcium, iron, and vitamins A, B6, and C. Bananas are also used to manufacture beer, wine, and other products and form an important part of the cultural life of many people.

FAO Agriculture Data. 2002.
FAOSTAT Agriculture Data. 2001 and 2004.
Robinson, J.C. 1996. Bananas and Plantains, CABI Publishing, Wallingford, UK, 238 pp.
Tripathi, L., J.N. Tripathi, and Irie V.B. 2007. Bananas and plantains (Musa spp.): Transgenics and Biotechnology. Transgenic Plant Journal 1(1). pp 185-2001.

Thomas Dubois: Young scientist on the rise

Thomas Dubois, IITA
Thomas Dubois, IITA

Thomas Dubois joined IITA in 2003 to manage the German Federal Ministry for Economic Cooperation and Development (BMZ)-funded regional biocontrol project for banana, based in Uganda. This project has now made significant progress: banana infected with certain strains of endophytic fungi grow more vigorously and are better protected against pests and diseases. The development of this novel “bioprotection” is an exciting research theme that has the potential to revolutionize current thinking on biocontrol. Current focus of this project is to optimize inoculation techniques and scale up activities with commercial producers of tissue-cultured (TC) plants as part of a recently funded Eastern African Programme and Research Network for Biotechnology, Biosafety and Biotechnology Policy Development (BIO-EARN) project in Kenya and Uganda.

In 2006, Thomas received the prestigious CGIAR Young Scientist Award. At present he is heading a BMZ project on improving market pathways for TC banana centered on commercial TC producers and nursery distribution centers. He is also spearheading the 2008 International Banana Conference in Mombasa, Kenya, as Chair of the Organizing Committee.

How did you come to IITA?
I studied bio-engineering first and then some foreign exchanges spurred my international ambitions. After my studies, in 1998, I was placed with IITA in Onne, southeast Nigeria. I absolutely fell in love with the then cowboy attitudes: nothing beats eating goat head, listening to Afropop in between oilrigs and blown up tankers! I liked the applied work, screening banana plants for nematode resistance, working under the supervision of Abdou Tenkouano and the late Paul Speijer. While I was at Onne, I was accepted at Cornell University to do my PhD studies in Insect Pathology. As I told Lukas Brader, the DG at that time, “I will be back.” After my PhD studies I was quickly involved in a fairly high-profile project with the United States Department of Agriculture, combating a devastating invasive insect species in the northern US; I traveled to China every year for prolonged periods of time. I toyed with the idea of entering Business School and tried to get into private industry. I settled with management consulting firms, using the Ivy League degree as leverage. I tried to get back into the CGIAR system and landed an 8-month stint with IITA in Uganda in 2003. This was a short project related to the use of endophytes, with no job security but ideal to get my foot in the door. I have been at IITA ever since.

What are some of your memorable experiences in research in the field or in the lab?
I like the applied and hands-on work. You can get much more done with a large dedicated team of staff, sometimes with less access to good infrastructure and facilities. I had to play farm manager for more than a year, doing activities from supplying water, fuel, and satellite dishes to keep the station running, to chasing away cows from encroaching the research fields in my spare time.

What are your realizations on the job?
I have come to appreciate several important realizations. First of all comes focus. It is easy to be carried away and drift into the development aspect of things. We are first and foremost scientists, on the applied side of science, publishing our work through peer-reviewed journals. It should be up to partner organizations to feed high-tech science upstream or to implement the work downstream. So choosing the right partners is essential. Secondly, teamwork is important. I started to fully appreciate this fairly late. Competition is natural in low quantities but, by definition, has no place in an institution that aims to do Research to nourish Africa. By working synergistically as a team and sometimes reaching out to other “competitor” organizations you would be surprised at what can be achieved in a short time and how the relationship can be swiftly turned into fruitful collaboration. Thirdly, at IITA, the sky seems to be the limit but sometimes you have to let go. One person simply cannot run two large international projects, write some more, fly to DR Congo to help with restructuring the agricultural sector, correct PhD theses, be a webmaster, and run a massive conference at the same time. My workload is insane but it is partly my fault.

What are your future plans?
In the immediate future, I would focus on my project on improving market pathways for TC banana centered on commercial TC producers and nursery distribution centers. Also, commercialization of the technology with private enterprises—this is what the BIO-EARN project is trying to do. At some point later, I hope to leave science and secure a managerial position with more job security as well. Deep down I know I am not a scientist “pure sang”. Moving on to the bigger scheme of things can be anything, ranging from research management, policy, advocacy, consultancy to donor relations.

Dubois examining a banana plant. Photo by IITA
Dubois examining a banana plant. Photo by IITA

Any advice for colleagues?
I am among the youngest at IITA so I should be receiving advice from others! A strong focus has been on mentoring students and I would hope that some colleagues would train more students. I have been supervising over 25 students in the last 5 years, both those from within Africa and European-based MSc students who do their research at IITA-Uganda. Benefits are manifold for them and IITA. Secondly, I think IITA folk could benefit if they “sell” themselves a bit more, through radio, TV, websites, and the popular press. Benefits include changing donor conceptions and misconceptions, putting science in the forefront, and ultimately benefiting farmers. Thirdly, it has helped me to think a lot out of the box and be a generalist. I came as an entomologist with a title of “biocontrol specialist”. Now I am running a socioeconomic project entirely focused on market pathways for banana seed systems. One could look out of the box for good private sector players or partners. This is essential, in my opinion, for long-term sustainability.

What is your dream for Africa?
I hope Africa will, at some point, be weaned off the many donor agencies, volunteering organizations, and NGOs that seem to be becoming a sustainable big-bucket business rather than a means to an end. A conducive climate for private sector development, together with good governance, is what I wish for sub-Saharan Africa.

Leena Tripathi: Looking after the welfare of smallholder banana growers

Leena Tripathi was born and grew up in India. She gained a PhD in Plant Molecular Biology from the National Botanical Institute, Lucknow, after completing an MSc in Molecular Biology and Biotechnology at G.B. Pant University of Agriculture and Technology, Pantnagar, India.

She joined IITA in 2000 and worked first in Nigeria and currently in Uganda where her primary research focuses on the development of transgenic Musa spp. with disease and pest resistance. She has established strong links with national and regional partners, and advanced labs. She is also Guest Faculty at the United Nations Industrial Development Organization (UNIDO) for biosafety courses.

Please describe your research work.
Since 2000, I have been developing transgenic banana and plantain resistant to pests and diseases. Currently, I am leading projects on producing bananas resistant to Xanthomonas wilt using the transgenic approach. I am also involved in capacity building in biotechnology and biosafety. I have trained several African scientists in genetic transformation and tissue culture. I have assisted in building capacity on genetically modified organism (GMO) detection and biosafety in East Africa by training students and national scientists on banana transformation and molecular biology. And I would like to acknowledge the strong financial support from donors such as Gatsby Charitable Foundation, African Agricultural Technology Foundation (AATF), US Agency for International Development, and the UK Department for International Development (DFID); and IITA of course.

Why did you choose to work in Africa?
Africa has missed the Green Revolution but should not miss the Gene Revolution. For this it needs human capacity in biotechnology that will help to accomplish things that conventional plant breeding could never do. The public needs to be better informed about the importance of biotechnology in food production.

What is the importance of transgenic technologies in banana improvement?
Many pests and diseases significantly affect banana cultivation and cause crop losses worldwide. Development of disease-resistant banana by conventional breeding remains difficult for various technical reasons. Transgenic technologies are the most cost-effective approach. There are enormous potentials for genetic manipulation using appropriate transgenes from other plants to achieve objectives in a far shorter time. It may also be possible to incorporate other characteristics such as drought tolerance, thus extending the geographical spread of production.

How do you demystify or explain a concept like biotechnology to lay audiences?
People think that biotechnology is just genetic modification (GM) technology. Contrary to its name, biotechnology is not a single technology; it is a group of technologies that uses biological systems, living organisms, or their derivatives, to make or modify products or processes for specific use. This includes recombinant DNA technology, genetic engineering, GM foods, biopharmaceuticals, bioremediation, and more.

Biotechnology is not new; it has flourished since prehistoric times. When the first human beings realized that they could plant their own crops and breed their own animals, they learned to use biotechnology. The discovery that fruit juices fermented into wine, or that milk could be converted into cheese or yogurt, or that beer could be made by fermenting solutions of malt and hops, started the study of biotechnology. When the first bakers found that they could make soft, spongy bread rather than a firm, thin cracker, they were acting as fledgling biotechnologists.

“Modern” biotechnology derives from techniques discovered only in the last 20 years. These include the ability to cut and stitch DNA, to move DNA and genes from one organism to another, and to persuade the new gene in this new organism, that is to make new proteins. Genetic engineering technology is a branch of modern biotechnology and involves the transfer of gene(s) from one organism to another to create a new species of crops, animals, or microorganism. Modern biotechnology has offered opportunities to produce more nutritious and better tasting foods, higher crop yields, and plants that are naturally protected from disease and insects.

What have you learned on the job?
I joined IITA as a biotechnologist with plenty of experience in research but not in the field. Working at IITA has been overwhelmingly positive. I have gained experience in both research and administration. I have learned to appreciate the benefits of working in multidisciplinary and multicultural teams and of linking research to farmers in the field. I can now write successful project proposals, get funding, lead projects, and disseminate results to national partners and finally to farmers. Good communication skills are essential for successful research. One needs to be a good team worker and establish strong and successful partnerships as we are doing at IITA-Uganda. When I was relocated here, I realized the situation was very different. IITA in Ibadan has facilities but in Uganda, IITA facilities are based within a national partner, the National Agricultural Research Organization. I wanted to learn quickly from the experiences of others so I talked to colleagues about their work and successes and to national scientists about their expectations. I learned quickly.

Any advice for IITA colleagues?
IITA scientists should be committed to provide strong leadership in the key research areas to ensure scientific excellence and the quality of products. They should work applying “new science” to enhance food security and income generation for resource-poor farmers.

What are your future research plans?
I want to evaluate the disease resistance of banana varieties in the field, evaluate transgenic plants in the confined field for efficacy against Xanthomonas wilt disease, with the University of Leeds develop nematode-resistant plantains, and develop varieties with multiple disease resistance by integrating several genes with different targets or modes of action into the plant genome. I also want to train more national staff/students to build capacity in the region.

What is your formula for success?
The addition and sometimes multiplication of five key elements: vision, strategy, confidence, hard work, and learning. I am focused and have a clear vision for my research, based on project outputs. I frame strategy with clear goals. I follow the strategy with my group members and work hard to achieve the goals. At each step I identify problems and learn to solve or avoid them so that the group moves smoothly and fast to achieve the goals. I set the goals for my group at the start of each year. Everyone works extra hours to achieve group goals. I do not hesitate to seek advice and suggestions from experts, superiors, and collaborators to move things efficiently. Support is very important. I have benefited from support and encouragement from my superiors, higher IITA management, donors, collaborators, and from family. IITA nominated me for the CGIAR Young Scientist award in 2005 and gave me their Top Scientist award, based on my research achievements.

Increasing capacity for plant healthcare

Plants, like people, need healthcare. But in Africa, where agriculture is dominated by smallholders, farmers do not have access to reliable plant health advice and management services.

Many farmers rely on extension workers and researchers from national and international organizations for such needs. And such help is not always readily or quickly available.

Bunchy top virus-affected banana in Rusizi Valley, DRC, Rwanda, and Burundi. Photo by IITA
Bunchy top virus-affected banana in Rusizi Valley, DRC, Rwanda, and Burundi. Photo by IITA

This is why IITA and its partners are developing the capacity of national agricultural research and extension systems (NARES) in research, disease surveillance, diagnostics, and deployment of control options. A good example is in banana: when national partners at the L’Institut des Sciences Agronomiques du Burundi (ISABU) in Central Africa needed help in diagnosing and culturing the pathogen that was attacking banana, they turned to IITA for assistance. ISABU wanted to develop local capacity to independently make diagnoses, culture Banana Xanthomonas Wilt (BXW) from diseased banana plant samples, and provide treatment advice.

At that time, IITA was already working on BXW in Burundi under the Crop Crisis Control Project (C3P), managed by the Catholic Relief Services (CRS). IITA and CRS liaised closely to develop a regional training course, for national partners from Burundi, Rwanda, and Democratic Republic of Congo (DRC) to learn new techniques, while encouraging greater collaboration among scientists.

Thus, IITA and partners that include CABI UK, Central Science Laboratory (CSL), CRS, and the Consortium for Improving Agriculture-based Livelihoods in Central Africa (CIALCA) conducted a Training Course on Surveillance and Vigilance for Plant Diseases in Burundi early this year. It is a pilot effort to kick-start a series of capacity building initiatives in the banana-growing countries in the region.

The training was attended by participants from extension and research, universities, and a regional organization. Trainers came from IITA, CABI and Global Plant Clinic (GPC, see box), and Central Science Laboratory (CSL).

Training covered new methods for surveillance and vigilance of all banana diseases. Feedback from the participants highlighted the need for sustained training and the importance of introducing a system of mobile plant clinics to effectively link farmers and transfer knowledge.

The mobile plant clinics initiative was developed by CABI UK as part of GPC, led by Eric Boa and has been tried and tested across the world. Under the umbrella of Mobile Plant Clinics and GPC, IITA had collaborated on initiating clinics in Rwanda, Cameroon, Sierra Leone, and Benin and providing training in diagnostics and surveillance in Uganda, DRC, and Burundi.

“Training, however, is just the tip of the iceberg. It is important to consolidate capacity building in diagnostic techniques and to ensure that people adopt new methods with confidence and then use them regularly,” said Fen Beed, IITA’s plant pathologist based in Uganda. “Isolating and identifying plant bacteria require practice as does the conduct of participatory disease surveys. When such methods are reliably deployed, the national programs could significantly improve the reliable detection of BXW and other disease outbreaks.”

Training participants look at Banana Xanthomonas Wilt chart. Photo by IITA

Knowing where a disease occurs allows extension staff to target particular areas and plan control programs. This requires careful organization and marshalling of resources. Although IITA already has effective recommendations for managing BXW, it lacks mechanisms for presenting them to farmers and monitoring their uptake. Further effort is needed to implement training that emphasizes direct action to help farmers.

In their after-training report, Beed and colleagues said that “Effective extension depends on sound intelligence about disease distribution and the damage it causes. National governments need to understand the risks posed to new areas and the actions required to control disease through sound research planning and identification of best management strategies.”

Beed and colleagues forwarded this blueprint for managing risk and reducing banana disease losses to ensure success of a plant healthcare service managed by national programs.

It is important to undertake systematic and comprehensive surveys of banana growing areas to get an update on the distribution of BXW and control strategies being used by growers. The surveys provide the opportunity to determine spread and identify reasons why control strategies may not have been adopted. Where control methods have been deployed their socioeconomic impact can be quantified.

The extensive surveys will assess incidence and severity of BXW and other banana pests and diseases.
Systematic and quantitative surveillance of banana-growing areas begin with participatory surveys, a promising technique for assessing large numbers of growers quickly. Survey results can identify sites where permanent sample plots (PSP) would be established for more intensive assessments. PSP sites should be regularly monitored for disease incidence, severity, and efficacy of control methods. Data produced can determine disease spread and help to evaluate socioeconomic impact and deployment of control options.

The C3P project made huge strides towards developing databases on the spread of BXW and the influence of farmers’ practices to control this disease. These databases can be further updated with information from the surveys and with data generated from pilot sites.

The databases could be linked to regional databases of climate, growing conditions, topography, farmer demographics, and agricultural practices (e.g., produced by the CIALCA project and many others). This allows use of the databases for predicting spread and risk due to disease at various geographic scales.

The next step is to establish and operate an extensive system of mobile plant clinics in targeted areas. Training courses for plant doctors are available and both DR Congo and Rwanda already have some experience in running clinics. The clinics concentrate on giving advice and gathering “intelligence” about banana problems, providing information on disease control, and offering services for other crops and diseases. This is important since farmers rarely grow bananas in isolation of other crops.

Once clinics are established and their benefits realized they can be self-sustaining and can provide a routine service to farmers and extension officers.

Upgrading facilities
There is a need to ensure that participating laboratories can isolate and confirm the presence of pathogens that cause BXW and other diseases of banana. Field staff should learn how to collect diseased plant samples for sending to diagnostic centers. Diagnostic centers will be established in the region and linkages developed with advanced research institutes (ARI) to provide technical backstopping for disease diagnostics using, for example, molecular techniques.

Banana field trials in Rwanda. Photo by IITA
Banana field trials in Rwanda. Photo by IITA

In addition, for BXW, rapid diagnostic field-based kits will be fully tested for accuracy to confirm the presence of the disease. Standard operating procedures for laboratory methods should be introduced to ensure consistent results and interpretation of results. The responsibilities of staff from national, regional, and ARI laboratories should be identified and links among them strengthened to create and nurture a network of expertise available to all.

Awareness raising
Data produced from the three activities can be used to publish new disease reports and develop pest risk analysis (PRA) documents for each banana disease in the region. PRA documents are crucial as they summarize all current information and increase awareness of disease recognition, distribution, control and risks. They must be routinely updated with new information and shared across the region to alert stakeholders of potential risks. This can lead to the deployment of preemptive disease control strategies before a disease epidemic breaks out.

Monitoring and evaluation
Detailed assessment of the progress and linkages should be undertaken. The increased capacity in laboratory and field techniques should be shared by project members through training. The support of IITA and the GPC in diagnostics, surveillance, and vigilance techniques encourages national and regional cooperation and use of new methodologies. Empowering scientists and extension staff and making them accountable for their actions is a powerful way to encourage sustainable development and to promote trade.

The benefit of creating a knowledge network for banana diseases in the region is clear. This network can be expanded through linkages with scientists and the private sector and key extension, research, and government staff from Burundi, DRC, Rwanda, and regional organizations.

The International Plant Diagnostic Network (IPDN) was set up in response to NARES’ surveys that highlighted the lack of diagnostic capacity in much of Africa and in recognition that this directly hindered the adoption of appropriate and effective integrated pest management programs and therefore international trade. IPDN has been established in collaboration with IITA in East and West Africa to increase communication and data sharing. Software for digital imaging and diagnosis, information management, and access to disease management recommendations provides a platform for enhanced diagnosis and communication between laboratory staff and experts across the world. Improved diagnostics tools and protocols have been developed and tested. This has been combined with training programs to enhance technical capacity and increase networking among diagnosticians in East and West Africa.

Initiatives such as IPDN can benefit by collaboration with similar internet-based initiatives in Africa such as the East Africa Phytosanitary Information Committee (EAPIC). EAPIC is linked to FAO’s International Plant Portal to provide posting of plant pests for each respective country, which now includes Kenya, Tanzania, Uganda, and Zambia. The plant pest list helps in developing harmonized border inspection protocols, which support capacity building efforts in plant pest survey, identification, and communication systems, such as IPDN.

A follow-on project with these components that combines good science, effective surveillance, and proven advisory services could strengthen the contribution of extension and research to increase food security, income generation, and improved trade in Africa. It also highlights support required from national and regional organizations, governments, and donors. These include local training for diagnostic techniques and expansion of participatory disease surveys and strengthening of disease vigilance through the establishment of mobile plant clinics.

Figure 1. Disease management scenario (fire fighting vs. preemptive control)
Figure 1. Disease management scenario (fire fighting vs. preemptive control)

”Addressing all these considerations will contribute significantly towards providing a service to support farmers and trade that would move away from the current scenario of ‘fire-fighting’ diseases to providing preemptive control (see Figure 1),” concluded Beed.

Global Plant Clinics

The CABI Bioscience Global Plant Clinic (GPC) provides a comprehensive diagnostic and advisory service for disease problems on all tropical crops. The Service is unique in its global operation and the range of plant diseases it handles. CABI Bioscience has been identifying plant diseases for over 90 years and other key partners in GPC include Rothamstead Research and Central Science Laboratories. The Global Plant Clinic gives expert advice on the interpretation and application of diagnostic results drawing on extensive international experience in a wide range of crops and information from CAB International’s award-winning Crop Protection Compendium.

Mobile plant clinic in Butembo, DR Congo. Photo by IITA

The GPC has initiated a series of mobile plant health clinics that offer regular and reliable advice on all plant health problems affecting any crop. These clinics are run by plant “doctors”, many of whom are agronomists or extension workers, who work for existing, grassroots organizations.

The clinics are not a technology but an advisory service. They link diagnostic labs with extension workers (plant doctors) and provide regulatory bodies in plant health with up-to-date information on current priorities by clinic ‘area of influence’. Such clinics have little direct expense. In the long term they need public investment and private support (from farmers or input suppliers such as those responsible for improved varieties or even fertilizer).

According to GPC head Dr Eric Boa, “Farmers benefit from advice at clinics: they preempt new problems and avert losses by quick action; reduce pesticide use; and reduce losses and save money by giving good or better recommendations for managing a problem. On vigilance/surveillance, clinics identify current problems affecting priority problems in an area.”

In banana, the most recent disease outbreak due to banana Xanthomonas wilt (BXW) was first reported to move from Ethiopia to Uganda by regional scientists and was subsequently confirmed by the GPC in Uganda in 2001. As the disease spread within Uganda and relentlessly across the region research programs led by CRS, IITA, and other national scientists tracked its movement into Burundi, DRC, Rwanda, Tanzania, Kenya, and the causal agent was confirmed by GPC.

BXW is one of several damaging diseases in East Africa and the demand for better surveillance and vigilance through mobile plant clinics has been widely expressed. The deployment of control options through clinics was based upon methods used to control a similar disease of banana caused by another bacterium. These primarily consist of the use of disease-free planting material and farmers tools and the removal of male flower buds to prevent infection from insect vectors.

Growing banana from “seeds”

Bananas are an important crop for global trade and nutrition where they are intensively cultivated, but few efforts exist to breed superior bananas. One of the reasons for this is that humans have intensively “selected” against seeded bananas and it is difficult or impossible to pollinate many banana varieties and successfully produce seeds.

Finding seeds in breeding plots in Namulonge, Uganda. Photo by IITA

Many of the most important banana varieties are triploid, which means that they carry an extra copy of each chromosome compared to the normal diploid. Being a triploid means that it is difficult for normal chromosome pairing and segregation to make fertile eggs or pollen, which results in most triploids being nearly sterile. Sterile bananas are great for people who don’t like to crack their teeth on banana seeds, but mean that bananas have to be multiplied via vegetative propagation, similar to propagation of potatoes, sweet potatoes, cassava, and selected varieties of other fruit trees or ornamental species.

Gardeners are familiar with “seed potatoes,” small potato tubers that are planted to produce a potato crop. Bananas do not form tubers; new plants derive from “suckers” that emerge from the lower banana stem (corm). These suckers can be uprooted and used to plant new banana plants. Similar to potato tubers, these suckers were a part of the original mother plant, which means that they potentially carry whatever disease pathogens or pests had infested the mother plant. Therefore, banana suckers are one of the main means of transport and spread of certain disease-causing agents, including important fungi, bacteria, and viruses.

Nematodes and pests can also hitchhike on banana suckers to infest the new crop. Not only does such hitchhiking result in early infection/infestation of new banana plants in a farmer’s field, but transporting long distances may help introduce a new disease or pest problem in a new location. This dual hazard of reduced yield potential of already infected planting material that may introduce new pests and diseases emphasizes the need for superior disease-free planting material produced through a “seed system” designed to minimize the risks of spreading pathogens and pests.

Banana bicycle transport, Burundi
Banana bicycle transport, Burundi. Photo by IITA

The traditional means of obtaining banana planting material (“seed”) is to acquire suckers from one’s own banana garden, from a neighbor, or from a more distant source. This method served to spread common varieties around the world and to multiply them in their new locations. This system can be modified to produce more banana suckers or shoots by manipulating banana corms to allow more buds to sprout. One such method that is described here is called macropropagation. A higher tech procedure to rapidly produce many plants in just a few generations of propagation is called tissue culture. In tissue culture, plants are first surface sterilized and then grown in aseptic culture in test tubes using an artificial growth medium based on a gelling agent like agar. The tender tissue-cultured plants can then be planted in the field after rooting and hardening under protected conditions.

Seed systems for producing clean planting material can be operated at various levels of technology and efficiency. In some cases, plant health could be improved by merely raising the awareness of the negative impact of planting “sick” suckers. Where infected plants look visibly different from healthy plants, either because of reduced vigor or visual disease symptoms in infected plants, the propagator could practice negative selection against “sick” plants or positive selection for “healthy” plants (or both). Such plants could be multiplied faster by applying a rapid propagation method such as macropropagation. However, while low-tech and affordable for farmers, such a system does not eliminate problems that cannot be detected by visual observation. Unfortunately, many diseases and pests fall into this category for at least part of their infection cycle.

For crops such as cereals, seed certification systems were developed to assure varietal purity, and later expanded to include freedom from weed seeds and seed-transmitted pathogens. Since most pathogens are seed-transmissible for vegetatively-propagated crops like potato or banana, disease management is the major focus of most seed potato certification programs and banana multiplication programs. Modern technology has provided diagnostic tests to detect significant pathogens. These tests are similar to those used in modern laboratories to diagnose human diseases, and can be expensive. For this reason, it is more efficient to test a small number of plants and multiply those that were negative for all pathogens tested in the battery of diagnostic tests.

It is possible to use tissue culture to efficiently and rapidly multiply plants that tested “clean” in the pathogen testing. Most potatoes eaten in the Western world are just a few field generations removed from tissue-cultured plants used to produce “seed potatoes” in screened glasshouses to start the seed production cycle. Similarly, most dessert bananas in the global export trade are from plants originally propagated in tissue culture from plants that tested clean for known banana diseases. A modified form of tissue culture can also be used to eliminate pathogens from plants that did not test clean, after which they can be propagated to produce “seed” planting material. There is great potential to improve the health of banana plantations in the developing world through increased use of this technology.

Tissue culture is the process of growing plants that have been surface sterilized and planted in test tubes or similar containers in sterile medium that contains all the nutrients they need to grow. This is almost always done in indoor laboratory facilities and the medium also contains the sugars needed to grow, since there isn’t enough light for photosynthesis.

Sanitation is extremely important, since a single mold spore is enough to contaminate a test tube. Tissue-cultured plants are generally tested for pathogens before commencing the multiplication cycle so that infected plants are not multiplied. The small banana plantlets produce small suckers that can be detached and planted as new plants, or an experienced technician can cut sections that contain buds that will grow. Extra shoots can sometimes be induced by cutting through the growing points so that multiple plants develop from single buds. This process can be repeated every 5-8 weeks so that a single plant can produce many new plantlets in a relatively short period of time.Bananas are sometimes unstable in tissue culture and mutant versions can develop. For this reason, most multiplication labs try to limit the number of multiplication cycles before renewing their cultures from field plants observed to have all the correct traits for that variety.

When tissue-cultured plants are rooted in soil, hardened, and then planted back in the field, they can be more susceptible to some pests and diseases than the original plant was. To restore natural levels of resistance, these plants can be reinfected with the endophyte microorganisms that normally coexist with bananas, similar to the gut bacteria that are important for human intestinal health (see related article on endophytes).

Macropropagated banana plant in chamber. Photo by IITA

Macropropagation falls somewhere between tissue culture and traditional systems of distributing suckers. In macropropagation, large suckers from healthy banana plants are removed and the roots and soft stem portion (pseudostem) of the sucker are cut away to expose the buds of the corm (the hard stem portion at the base of the sucker). The bare corms are briefly dipped in boiling water to kill any nematodes (micro-worms) that were not removed when cutting off roots. Small cuts are made through the buds to encourage development of multiple sprouts from each bud. The apical (top) bud is often removed because it can suppress development of lower buds. The corm is then covered with moist wood shavings and incubated in a small plastic-covered chamber for a few weeks to encourage shoot development.

Primary shoots can be rooted and used as planting material, or cut off and the growing point again cut to promote additional shooting. Shoots that develop are broken off with a bit of hard stem and roots attached, placed in small nursery bags in a similar high humidity chamber for a few days to allow root development, and finally moved to a nursery for hardening. Hardened plants can be planted in the field, similar to suckers or hardened plants from tissue culture.

Banana roadside market in rural southwest Uganda. Photo by IITA
Banana roadside market in rural southwest Uganda. Photo by IITA

A major drawback of macropropagation is that rustic or low-tech methods of detecting pathogens have not been developed, so this method can propagate infected plants if they were chosen as mother plants. Both macropropagated plants and tissue-cultured plants have less food reserves than suckers and require more care (compost/manure, watering) after planting than suckers. Careful siting of “mother gardens” established from tissue-cultured plants in clean areas may be the best way to produce suckers for macropropagation.

Traditional seed systems have produced most of the nearly 6 billion banana and plantain plants in Africa currently spread over nearly 4 million hectares of farm and gardens. Many of these are in excellent condition; others have become infected with one or more banana diseases and need to be replaced. Since new banana diseases have been introduced to Africa in the last century, and many diseases have increased in distribution and prevalence, greater care needs to be practiced to multiply “healthy seed”.

Breeding programs are nearly ready to release new varieties with resistance to some of the disease problems.

A combination of new and old seed systems can improve the overall health of new plantings by providing healthy plants of both preferred older varieties and resistant new varieties.

IITA’s research on macropropagation is supported by the Directorate General for Development Cooperation (Belgium) and Agricultural Productivity Enhancement Program (APEP-USAID) Uganda Agricultural Productivity Enhancement Project.

Ticket out of poverty

Market in Nigeria. Photo by IITA
A market in Nigeria. photo by IITA

The world’s food supply has for the last few decades worked well but now new dynamics, as reflected by the recent food crisis, call for change. The current system, based on large-scale production in the developed world, is efficient and responsive to market dictates though distorted by subsidies. It could be stabilized when complemented with a more significant system from the developing world. Such a two-tiered system would also protect poor regions of the world from extreme food scenarios.

Today’s world food situation has been well aired in the media. But what is not fully appreciated is the opportunity it also brings for Africa. As the most food-deprived region of the world, Africa needs a more robust agricultural growth. This food crisis, albeit temporary, could be used to trigger an agricultural turn-around. African countries are food importers and thus affected by international prices of traded food commodities, but have untapped assets to exploit for the immediate and longer term.

The African food basket is, in many countries, complex and its commodities are affected differently by international food prices. For example, while maize prices in Tanzania were dragged up with the world prices, the effect on sorghum, cassava, and plantain was much less. This allows some immediate substitution and underscores the need for focusing on local production, helps reduce foreign currency needs that limit a country’s purchasing power, and stimulates rural economies to benefit both the rural and urban poor.1

Food commodities also allow for substitution in agroprocessing. If rice is used to produce starch, it can be replaced with other crops such as millet/sorghum or roots and tubers. Bread does not have to be 100% wheat. Tef, banana, sweetpotato, millet, sorghum, and a mix can be used that includes cassava, and yam. This richness needs to be more appreciated and encouraged.2

For the less immediate term Africa just needs to produce more (see Figure 1). Its food output is extremely low. But its diversity of ecologies, altitudes, and cultures, is a powerful asset. Africa can produce more food by expanding acreage, unlike Asia. But other things need to happen before the potential of ample arable lands can be realized. Immediate needs would be rural feeder roads, access to credit and inputs, and a stimulated processing sector. The latter is increasingly important as the growing urban migration means more consumers are far from production zones and food shelf-life and convenience are major concerns.

Figure 1. Index of total agricultural output per capita by region (index 1961-2005). Adapted from FAOSTAT 2006. Source: Hazel and Woods.
Figure 1. Index of total agricultural output per capita by region (index 1961-2005). Adapted from FAOSTAT 2006. Source: Hazel and Woods.

For the medium term, Africa has to increase yields. For most food crops of sub-Saharan Africa3 yields can be increased by 150-300% immediately, because varieties already exist with this potential4.

To benefit more from what it grows, Africa also needs a parallel effort to reduce huge (postharvest) losses, ranging from 18 to 40% depending on the crop. Investments in food processing and transformation, energy, and roads are needed.

This processing and transformation capacity is also critical to address the rural-to-urban migration, which is itself a major challenge. Not long ago, 80-90% of Africans were rural; today most are urban. Wars have accelerated rural-to-urban migration. Africa must increase production even more, because it is not one to one in feeding the urban versus the rural poor. As production systems function today there is tremendous waste at all levels, rural and urban.

A holistic approach to the sector is essential and includes the now well-rehearsed list of needs and problems—infrastructure, finance, taxation, corruption, communication, soils, inputs, productivity, and numerous postharvest technologies and processes. As these elements are developed and constraints cleared away, the approach has to adjust. Underinvestment in infrastructure is costly in many ways. Transport difficulties, for example, give Malawi’s (2007/8) maize surpluses few outlets so that farmers do not fully gain from favorable global prices.

Family eating banana
Family eating banana

It is not uncommon to have food shortages in one part of a country, when another has food surpluses. Poor information and transport systems, plus the short shelf-life of many commodities prevent Africa from benefiting fully from its harvest. In Ethiopia, widespread drought (2003) in some parts of the country put at risk over 12 million people, while in other parts, prices collapsed due to a bumper crop of cereals (Borlaug and Natios). Zambians (2004) were suffering from a shortage of cassava, when Nigeria had abundant surpluses.

Small producers are one group that needs special attention. While they are the key to Africa’s food self-sufficiency, it is hard for them to respond effectively to increased food needs on their own. One way to support them is to encourage the movement of their produce into alternative uses within the food chain.1 Again, this means investments in the agroprocessing sectors and a slew of processed food products. Farmers take all the risks but rarely benefit long from any gains.

Conclusion: The full use of Africa’s assets—arable land, different ecologies, altitudes, cultural differences, and eating habits—gives Africa resources more powerful than oil. Emphasizing and then benefiting from the agricultural sector has positive repercussions that reach far into all segments of an economy, in particular in increasing employment at all levels and with it, purchasing power.

1 Hartmann. 2004. An Approach to Hunger and Poverty. IITA.
2 Cereal imports in the last couple of years have increased by a factor of three to five times.
3 Rice is the exception where the yield gap is around 67%.
4 For example, IITA varieties of these crops already have this potential built into their genetic codes.

Science meets industry

In Uganda, the local word for food is matooke, which is what the Ugandans call the green banana, their staple food. Nowhere is banana eaten in such a scale as in this East African nation of 31 million.

Ugandans reportedly eat, on average, more than a quarter of a kilogram of banana in a day, or in some areas, 450 kilograms per year! That’s a lot of bananas.

Bananas are as important to the Great Lakes region as rice is to East or Southeast Asia. They are a valuable source of vitamins, minerals, and carbohydrates or calories; they are the primary source of income for 16 million smallholder farmers in Uganda; and they play a central role in the sociocultural fabric of the country.

About one-third of the total global banana production comes from sub-Saharan Africa where millions of subsistence farmers and consumers depend on the crop as a staple food. Bananas are easy to grow especially in the Great Lakes region where growing conditions for the crop are ideal.

Enhancing small tissue culture plants with endophytes. Photo by IITA

But banana production in the region is being threatened by a complex of pest and disease problems, including Fusarium wilt (Fusarium oxysporum f.sp cubense), black leaf streak or sigatoka (Mycosphaerella fijiensis), viruses, banana weevils (Cosmopolites sordidus), and nematodes (e.g., Radopholus similis). The most serious threat at the moment is banana Xanthomonas wilt (BXW, Xanthomonas vasicola pv. musacearum), which could devastate the banana industry in East Africa. These pests and diseases damage the banana plants, cause yield loss, and eventually food insecurity and loss of livelihoods.

With the food security and livelihood of millions of farmers at stake, science and industry meet to save the crop and develop technologies to make production more sustainable. One technology involves the rapid, mass propagation of more robust bananas using endophyte-enhanced tissue culture,” said Thomas Dubois, biocontrol specialist and nematologist based in Uganda, who leads the team of IITA scientists that helped develop the technology.

“Old” technology
Tissue culture is not a new technology. Tissue-cultured banana is the norm in the rest of the world. Commercial tissue culture laboratories are beginning to emerge across East Africa to satisfy the rapidly rising demand for healthy planting material.

Tissue culture banana plants made in specialized private-sector laboratories are healthy and can grow faster than traditional plants. They are also ideal for establishing large plantations, which are then uniform, enabling better planning for harvests and marketing.

Tissue culture banana plantlets. Photo by IITA

Tissue culture produces clean plantlets without disease but also without a natural defense system. They are quite sensitive to the relatively harsh conditions in the East African fields, including attack by pests and diseases, and low soil fertility. The smallholder fields are burdened with biotic pest pressures and abiotic constraints, and the small-scale farmers do not practice essential high-input field maintenance. Thus, tissue culture adoption in Africa faces a “barrier”.

This is where IITA came to the rescue. “Endophytes” is a general term for naturally occurring microorganisms inside the plant that protect it from pests and diseases, and that enhance plant growth. Every single individual plant species, including banana, contains endophytes. They can be used as a natural form of control. Introducing endophytes in plants during propagation is like immunizing them. Plants inoculated or “vaccinated” with endophytes become resistant to pests or diseases.

Army against pests and diseases
The endophytes become part of the planting material before the young tissue culture plants are sold to farmers. Once inside, the endophytes go to work, boosting the plant’s immune system—so long as they get there first, before the pathogen.

Thus, farmers are provided with a weapon to fight the banana weevils and nematodes, which abound in the soil and which are transferred by farmer-to-farmer contact through exchange of infected planting material.

IITA, through its station in Kampala, Uganda, developed the endophyte technology to produce robust pest- and disease-free banana planting material, in collaboration with various national and international partners. Research on this technology started in 1997 with funding from the German Federal Ministry for Economic Cooperation and Development (BMZ).

IITA isolated nonpathogenic strains of endophytes belonging to the Fusarium family from healthy plants growing under high levels of pest and disease pressure. Institute scientists developed a rapid, easy, and low-cost laboratory screening protocol for testing the numerous endophyte strains obtained against the banana weevil and the burrowing nematode. They also devised a more efficient technique to mass produce the best strains, and introduce them into the tissue-cultured plantlets. The endophyte-enhanced plants are then grown in screenhouses and in farmers’ fields to assess their performance against target pests.

Genetically modified endophyte strains with genes for fluorescent colors. Photos by IITA
Genetically modified endophyte strains with genes for fluorescent colors. Photos by IITA

Using endophytes as biological control agents offers several advantages. When endophytes enter the plants first, they get a head start over the other microorganisms, and once they are established, other microorganisms would offer less competition. Because the endophytes are already in the plantlets when they are transplanted, control can be targeted using low levels or doses, and performance is consistent. Using endophytes also makes it easier to control cryptic pests such as the banana weevil and the burrowing nematode, which are embedded within plant tissues.

As an off-shoot of work on endophytes, IITA-Uganda scientists realized that endophytes circumvent many of the barriers associated with conventional biopesticides. This has spurred novel research in using conventional biopesticides, such as Beauveria bassiana, as artifical endophytes in seed systems. B. bassiana worldwide is the most researched and commercialized fungal biopesticide against a variety of insect pests.

Laboratory and screenhouse studies have revealed the great potential of this entomopathogenic fungus for use against the banana weevil. However, impractical field delivery methods and high costs associated with its application prevent its use and commercialization in banana fields.

IITA’s research also showed that B. bassiana can “colonize” the internal banana tissues for at least four months and that B. bassiana-enhanced plants reduced larval damage by more than 50%. It kills the damaging insect stages inside the plant; it is protected from adverse biotic and abiotic factors; little inoculum is required, greatly reducing cost. Farmers do not need to apply the biological control organism themselves, as the technology is easily transferable to a commercial tissue culture producer.

But IITA’s research-for-development work does not end there. How does IITA make endophyte-treated plantlets available to farmers, the ultimate users of the technology, as a ready-to-plant product at low cost?

Confluence of science and industry
The Institute has established strategic alliances with several private and public sector entities to develop international public goods. It leads the research effort on endophyte-enhanced tissue culture technology, and a commercial tissue culture entity and a private biocontrol company handle the formulation, distribution, application, and storage of the plantlets. In the process, IITA and its partners are helping commercialize the banana industry in East Africa.

Endophyte-enhanced banana tissue culture research is undertaken with research partners that include the University of Bonn, Germany; the National Agricultural Research Organization (NARO), Uganda; the University of Pretoria, South Africa; Makerere University, Uganda; Wageningen University, the Netherlands; the Catholic University of Leuven, Belgium; and the Biologische Bundesanstalt fur Land-und Forstwirtschaft, Germany.
The work though is not confined to banana production in Africa. Bioversity International, in collaboration with IITA’s German partners, is testing endophyte-enhanced tissue culture with large-scale banana producers in Costa Rica, using Latin American endophyte strains.

Since IITA does not have the in-house capability to undertake large-scale endophyte-based research in its facilities, the Institute partnered with several private and public organizations involved in tissue culture: Agro-Genetic Technologies (AGT), a commercial tissue culture laboratory in Uganda; Jomo Kenyatta University of Agriculture and Technology (JKUAT) and RealIPM, a biopesticide company in Kenya.

An exploratory and collaborative effort to produce more robust tissue culture plantlets as research material has developed into a synergistic partnership that bridged upstream research and downstream application. On the other hand, linking up with large-scale tissue culture producers in Uganda and Kenya have helped refine and move the technology from the lab to the farmers themselves.

Researcher inspecting banana plantlets in greenhouse, DRC. Photo by IITA
Researcher inspecting banana plantlets in greenhouse, DRC. Photo by IITA

Through collaboration, endophyte-enhanced technology is now being tested in farmers’ fields in East and Central Africa. The technology enables the farmers to switch from subsistence to income generation, and more importantly to reach and create markets.

Following the research-for-development model, IITA and its partners realized that engaging and mobilizing the community of farmers is essential for the technology to succeed and gain wider adoption.

IITA saw the value of harmonizing public-private sector collaboration at the early stages of the project. It has adopted this approach in its R4D work in Africa, and is promoting its application in technology transfer work in other areas of research, mandate crops, and commodities.