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The Integrated Breeding Platform: one-stop crop-breeding shop for developing countries

Africa, Asia, Capacity building, Crop breeding, Crop information and data management, Integrated Breeding Platform, Themes No Responses »

Oct 192015

By 2050, the global demand for food will nearly double, numbers of farmers are predicted to decrease and the amount of suitable farmland is not expected to expand. To meet these challenges, farmers will rely on plant breeders becoming more efficient at producing crop varieties that are higher yielding and more resilient.

The Integrated Breeding Platform (IBP), established by the CGIAR Generation Challenge Programme (GCP), provides plant breeders with state-of-the-art, modern breeding tools and management techniques to increase agricultural productivity and breeding efficiency. Its work democratises and facilitates the adoption of these tools and techniques across world regions and economies, from emerging national programmes to well-established companies. In particular, it is helping to bridge the technological and scientific gap prevailing in developing countries by providing purpose-built informatics, capacity-building opportunities and crop-specific expertise to support the adoption of best practice by breeders, including the use of molecular technologies. This will help reduce the time and resources required to develop improved varieties for farmers.

IBP is certainly a winner for maize breeder Thanda Dhliwayo of the International Maize and Wheat Improvement Center (CIMMYT): “IBP is the only publicly available integrated breeding data-management system. I see a lot of potential in increasing efficiency and genetic gain of public breeding programmes,” he says.

For Graham McLaren, who was GCP’s Bioinformatics and Crop Information Sub-Programme Leader, an informatics system is vital for advancing the adoption of modern breeding strategies and the use of molecular technologies.

“One of the biggest constraints to the successful deployment of molecular technologies in public plant breeding, especially in the developing world, is a lack of access to informatics tools to track samples, manage breeding logistics and data, and analyse and support breeding decisions,” says Graham, who is now IBP Deployment Manager for Eastern and Southern Africa.

This is why IBP was set up, explains Graham: “We want to put informatics tools in the hands of breeders – be they in the public or private sector, including small- and medium-scale enterprises – because we know they can make a huge difference.”

Breeders access IBP’s services through its Web Portal.

Handling big data

Knowledge is power, making data are almost a crucial a raw material for plant breeding as seeds. To make good choices about which plants to use, breeders need information from thousands of plant lines about a wide range plant of characteristics, usually collected during field trials or greenhouse experiments, in a process known as phenotyping. Effective information management is therefore critical in the success of a breeding programme. IBP tackles these crucial information management issues, and many of its current users are finding it invaluable for handling their phenotypic data. IBP also aims to facilitate the use of molecular-breeding techniques, which require genetic as well as phenotypic information (see box), and support users in integrating these into their breeding process.

The advent and implementation of molecular breeding has increased breeders’ efficiency and capacity to generate new varieties – although the inclusion of genetic data has also added to the amount of information that breeders need to handle.

An abundant harvest of nutrient-enriched cassava in Nigeria.

“Prior to molecular breeding, we would record our observations of how plants performed in the field [phenotypic data] in a paper field book; we would either file the book away or re-enter the data into an Excel spreadsheet,” says Adeyemi (Yemi) Olojede, Assistant Director and Coordinator in charge of the Cassava Research Programme at the National Root Crops Research Institute (NRCRI) in Nigeria and Crop Database Manager for NRCRI’s GCP-funded projects.

“We still need to phenotype, but molecular-breeding techniques allow us to select for plant characteristics early in the breeding process by analysing the plant’s genotype to see if it has genes associated with desirable traits,” says Yemi. Groundwork is needed in order to make this possible: “This means we need to analyse the data of each plant’s genetic make-up as well as the phenotypic data so we can verify whether certain genes are responsible for the traits we observe.”

By using molecular markers to make certain which plants have useful genes right from the start – simply by testing a tiny bit of seed or seedling tissue – breeders and agronomists like Yemi can carefully select which ‘parent’ plants to use. These are then crossed in just the same way as in conventional breeding, but using only the most promising parents makes each generation is a much bigger step forward. Another advantage for breeders is that they do not necessarily have to grow all of the progeny from each set of crosses – usually thousands – all the way to maturity to see which plants have inherited the traits they are interested in.

The IBP Breeding Management System makes it much easier for breeders to manage their data and make good use of both phenotypic and genotypic information. The Crossing Manager function facilitates the planning and tracking of crosses.

All of this makes breeding more efficient, reducing the time and cost associated with field trials and cutting the cumulative time it takes to breed new varieties by half or more. The end result is that farmers get the new crop varieties they need more quickly.

Keeping track of masses of information has always been a headache for breeders. However, the increased burden of data management that molecular breeding brings – together with the need to be able to carry out specialised genotypic analysis (study of the genetic make-up of an organism) – has proved to be a limitation for many public national breeding programmes such as NRCRI. These have consequently struggled to adopt molecular-breeding techniques as readily as the private sector.

Wanting to overcome this limitation as part of its mission to advance plant science and improve crops for greater food security in the developing world, in 2009 GCP gave Graham McLaren the momentous task of overseeing the development of the Integrated Breeding Platform.

Clearing the bottleneck

The IBP Web Portal provides information and access to services and crop-specific community spaces. These help breeders design and carry out integrated breeding projects, using conventional breeding methods combined with and enhanced by marker-assisted selection methods. The Portal also provides access to downloadable informatics tools, particularly the Breeding Management System (BMS).

While there are multiple analytical and data-management systems on the market for plant breeders, what sets the BMS apart is its availability to breeders in developing countries and its integrated approach. Within a single software suite, breeders are able to manage all their activities, from choosing which plants to cross to setting up field trials.

Graham explains that IBP has brought together all the basic tools that a breeder needs to carry out day-to-day logistics, data management and analysis, and decision support. “We’ve worked with different breeders to develop a whole suite of tools – the BMS – that can be configured to support their various needs,” explains Graham. “Having all the tools in one place allows breeders to move from one tool to the next during their breeding activities, without complex data manipulation. We’ve also set up the system for others to develop and share their tools, so that it can continue to grow with new innovative ideas.”

The IBP Breeding Management System has a complete range of interconnected tools. The Germplasm Lists Manager supports breeders in managing their sets of breeding materials.

Another feature of the Platform is that it provides breeders with access to genotyping services to allow them to do marker-assisted breeding. This is particularly useful for breeders in developing countries, who often don’t have the capacity to do this work. “It’s about giving all breeders the opportunity to enhance the way they do their job, without breaking the budget,” says Graham.

A unique and holistic component of IBP is the Platform’s community-focused tools. “IBP is as much about sharing knowledge as it is about managing data,” says Graham. “We’ve integrated social media to allow anybody with an interest in breeding, say, cowpeas, to join the cowpea community. They needn’t necessarily be a collaborator; they just have to have an interest in breeding cowpeas. They could read about what’s going on, contact people in the community and say ‘I’ve seen results for your trial. Could you send me some seed because I think it will do well in my region?’ or ‘Could you please further explain the breeding method you used?’ That’s what we hope to inspire with those communities.”

Graham concedes that this aspiration for the Platform has not yet been fully realised. However, he is hopeful that by providing training, coupled with the support from several key institutes and breeders, these communities will help to increase adoption of IBP and its tools.

“We are well aware that this Platform will be a big step for a lot of breeders out there, and they will need to invest time and patience into learning how to adapt it to their circumstances,” says Graham. “However, this short-term investment will save them time and money in the long term by making their process a lot more efficient.”

For Guoyou Ye, a senior scientist with the International Rice Research Institute (IRRI), participating in IBP meant that he has gained a lot more understanding about the needs of breeders in developing countries for user-friendly tools.

“I started to spend time doing something for the resource-poor breeders. This has resulted in many invitations by breeding programmes in different countries to conduct training, and has given me a chance to establish a network for future work. I also had the chance to work with internationally well-known scientists and informatics specialists,” he says.

Freshly threshed rice in India.

Providing help where it is needed

Yemi Olojede is another person who has been championing IBP, and his focus has been in Nigeria and other African countries. He spent time at GCP’s headquarters in Mexico in 2012 to sharpen his data-management skills and provide user insights on the cassava database. “I enjoy working with the IBP team,” says Yemi. “They pay attention to what we [agronomists and breeders] want and are determined to resolve the issues we raise.”

Yemi has also helped the IBP team run workshops for plant breeders throughout Africa.

He recounts that attendees were always fascinated by IBP and the BMS, but cautious about the effort required to learn how to use it. They were pleased, though, when they received step-by-step ‘how to’ manuals to help them train other breeders in their institutes, with additional support to be provided by IBP or Yemi’s team in Nigeria.

“We told them if they had any challenges, they could call us and we would help them,” says Yemi. “I feel this extra support is a good thing for the future of this project, as it will build confidence in the people we teach. They can then go back to their research institutes and train their colleagues, who are more likely to listen and learn from them than from someone else.”

IBP is continuing to run these training courses, through newly established regional hubs in Africa and Asia.

Mark Sawkins, IBP Deployment Manager for West and Central Africa, is helping to coordinate the formation and integration of the regional hubs within key agricultural institutes, including the Africa Rice Center in Benin, Biosciences Eastern and Central Africa (BecA) in Kenya, Centre d’étude régional pour l’amélioration de l’adaptation à la sécheresse (CERAAS) in Senegal, the Chinese Academy of Agricultural Sciences (CAAS) in China, the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in India, the International Institute of Tropical Agriculture (IITA) in Nigeria, and the National Center for Genetic Engineering and Biotechnology (BIOTEC) in Thailand. Several further hubs are planned in additional countries, including in Latin America.

He says the hubs provide localised support in the use of IBP tools: “Their role is to champion IBP in their region,” says Mark. “They can take advantage of their established relationships and skills to help new users adopt the Platform. This includes providing education and training, technical support for IBP tools, and encouraging users to build their networks through the crop communities.”

IBP Regional Hubs worldwide.

Breeding rice and maize more efficiently using IBP

For Mounirou El-Hassimi Sow, a rice breeder from the Africa Rice Center, IBP is more than just a tool that helps him manage his data: “I’m seeing the whole world of rice breeders as a small village where I can talk to everyone,” he says.

“Through IBP, I have access to this great network of people, who I would never have met, who I can refer to when I have some challenges.”

Social networking tools are a novel feature incorporated into IBP to further develop the capacity of breeders like Mounirou. IBP hosts a number of crop-based and technical Communities of Practice that were established by GCP. These have nurtured relationships between breeders across different countries and organisations, encouraging knowledge sharing and support for young scientists.

Another way GCP has promoted and developed capacity to use IBP and molecular-breeding techniques is through training. Starting in April 2012, the Integrated Breeding Multiyear Course (IB–MYC) trained 150 plant breeders and technicians from Africa and Asia. The participants attended three two-week intensive face-to-face training workshops spread over three years, with assignments and ongoing support between sessions.

Roland Bocco (Africa Rice center, Benin), Dinesh K. Agarwal (ICAR, India) and Susheel K. Sarkar (ICAR, India) work together on a statistics assignment during their final workshop of the Integrated Breeding Multiyear Course (IB–MYC).

Mounirou participated in the course and says it provided him with the opportunity to learn more about molecular breeding and practice using the associated management and data analysis tools. “I had learnt about the tools in university and seen them on the Internet, but I did not know how to use them,” says Mounirou. “During the first year, we learnt about the theory and how the tools work. During the second and third years, we were comfortable enough with the tools to use our own data and troubleshoot this with the tutors. This was great and provided me with confirmation that these tools were applicable and useful for my work.”

Mounirou says he is now sharing what he learnt during the course with his co-workers and other plant breeders in Africa. “Since the Africa Rice Center became a regional hub for IBP, I’ve volunteered to help train rice breeders. It’s great to be able to share what I learnt and help them realise how this tool will help make their work so much easier.”

A maize farmer and community-based seed producer in Kenya.

Another IB–MYC trainee, Murenga Geoffrey Mwimali, a maize breeder from the Kenya Agriculture and Livestock Research Organisation (KALRO), is also helping his networks to benefit from IBP. “When I returned from the training, I took the initiative to demonstrate the Platform to the management of my organisation, to show them that it is what we need to implement at the institute level. They were overwhelmingly positive, and we are working on running a training course for other researchers in the organisation to learn how to use the Platform.”

Jean-Marcel Ribaut, GCP and IBP Director, says these championing efforts are exactly what GCP and IBP were hoping IB–MYC would initiate. “By providing this initial intensive training to these selected participants, we felt this groundswell of capacity would slowly grow once they built their confidence,” says Jean-Marcel. “That young researchers like these feel they are competent and obligated to share what they learnt is a true credit to the product and the participants.”

From the GCP nest to world-scale deployment

IBP has been the single largest GCP investment. From 2009 to 2014, GCP allocated USD 22 million to the initiative, with financial support from the Bill & Melinda Gates Foundation, the European Commission, the UK Department for International Development, CGIAR and the Swiss Agency for Development and Cooperation. This represented 15 percent of GCP’s entire budget.

Following GCP’s close in December 2014, IBP will continue to develop and improve over the next five years, with funding primarily originating from the Bill & Melinda Gates Foundation. While the priority has been on informatics and service development in Phase I, the main focus of Phase II will be to concentrate on deployment and adoption. In the long term, the Platform is seeking further ongoing funding, and also looking into implementing some form of user-contribution for specialised or consulting services.

“We wanted to develop a tool to provide developing countries with access to modern breeding technologies, breeding materials and related information in a centralised and practical manner, which would help them adopt molecular-breeding approaches and improve their plant-breeding efficiency,” says Jean-Marcel. “I believe we have achieved this and at the same time built a tool that will prove very useful for commercial companies too. If we want the tool to continue to be affordable and sustainable for developing countries, then we have to look at ways of finding new sources of funding and of making revenue to offset the costs.”

Stewart Andrews, IBP Business Manager, is helping to make this happen.

“What we are looking at is a tiered membership system in the private sector, where enterprises would pay more the larger they are,” explains Stewart. “This would also be dependent on where in the world they are, with enterprises in Europe and North America contributing proportionately more financially than those in developing countries. This will help us to continue investing in our solutions while keeping them accessible to national programmes and universities in developing countries at little to no fee.”

For Jean-Marcel, creating a commercial stream for IBP services is a win for all parties. “If we are able to generate revenue we can not only provide sustainable support and offset the cost for poorer institutes, we can also continue to develop and improve the BMS software suite so that it becomes the tool of choice all over the world. In terms of social responsibility, the corporate world can play an essential role in this not only as donors but even more effectively as clients and users – adopting the BMS makes good business sense.”

Stewart says a sustainable income is vital for providing training and assistance. “We currently have about 7,000 researchers in the developing world who get this software for free, and each week we get 20–25 requests for help, assistance and training. This support costs money but is indispensable, particularly for those in the developing world who are trying to implement molecular breeding for the first time. You have to remember that this software is all part of a revolution in terms of plant breeding, so we need to provide as much assistance as we can if these breeders are going to buy into molecular breeding and all of its benefits.”

The IBP team is convinced that rolling out IBP will have a significant impact on plant breeding in developing countries.

Indeed, so far there have been more than 1,300 unique downloads of the BMS, with at least 250 early adopters worldwide using the software suite across their day-to-day breeding activities. The Platform’s strategy now builds on three regional teams (West and Central Africa, Eastern and Southern Africa, and South and South East Asia), each including experienced breeders and data managers. With the help of local representatives at seven well-established Regional Hubs to date (with more Hubs in development), this strategy has thus far yielded commitments from six African countries at the national level; from 24 Institutes spanning 58 breeding programmes at different stages of the adoption process; from 14 Universities where faculty members are using and/or teaching the BMS, partially or entirely; and from 134 “champions” engaged in the deployment plans and in supporting their peers.

“Because IBP has a very wide application, it will speed up crop improvement in many parts of the world and in many different environments. What this means is that new crop varieties will be developed in a more rapid and therefore more efficient manner,” concludes Graham.

Chiedozie Egesi: cassava champion for poor African farmers

Africa, Capacity building, Cassava, Researchers No Responses »

Oct 182015

“You can use any technology in the world, you can develop any product, but you need the products that farmers are willing to grow in their field.”

So says Chiedozie Egesi, a plant breeder and geneticist who has been one of the inspirational leaders and Principal Investigators for the CGIAR Generation Challenge Programme’s (GCP) Cassava Research Initiative in Africa.

It was his commitment to helping farmers that led Chiedozie to forsake his dream of becoming a surgeon, and instead to train as a plant breeder and help smallholder farmers in Nigeria. Having grown up in a small town in south-eastern Nigeria where poverty was a daily reality, he was particularly concerned about food security and nutrition for the people. He dreamt of developing cassava varieties that could beat the pests and diseases that often devastate such crops.

Peeling cassava roots.

“The food people grow should be nutritious, resistant and high-yielding enough to allow them to sell some of it and make money for other things in life, such as building a house, getting a motorbike or sending their kids to school,” Chiedozie says.

Nigeria is the most populous African country, with a population of more than 174 million. The main staple food is cassava, making Nigeria the world’s largest producer and consumer of the crop. But cassava is also important in other African countries. It is grown by nearly every farming family in sub-Saharan Africa. Africa produced nearly 140 million metric tonnes of cassava in 2012 – but most of the production is low-yielding subsistence farming for food by small-scale farmers for food for their own households alone.

After almost eight years working on GCP-supported cassava projects, Chiedozie is proud of what they have managed to accomplish: “That we’ve been able to give African farmers the varieties that they will love to grow is my biggest achievement”.

Meet Chiedozie and hear all about his research and the importance of cassava in the video series below (or watch on YouTube):

Transformation for Chiedozie – and for cassava

Chiedozie’s journey with GCP began after he had gained his PhD in yam breeding from the University of Ibadan, Nigeria. He undertook further studies and training at Cornell University and the University of Washington, both in the USA. He then returned home to Nigeria to lead the cassava breeding team at the National Root Crops Research Institute (NRCRI) and, following a promotion in 2010, was made Assistant Director of NRCRI’s Biotechnology Department. In 2004, a chance find on the Internet of a molecular breeding training programme in South Africa first led to Chiedozie’s involvement in GCP.

In 2010, work by Chiedozie and the NRCRI team, in collaboration with a transnational network of partners, resulted in the official release to Nigerian farmers of Africa’s first cassava variety developed using molecular-breeding techniques. Known as UMUCASS33 (or CR 41-10), it was resistant to cassava mosaic disease (CMD) – a devastating plant disease that can wipe out entire cassava crops – and also highly nutritious. In addition to a stream of further disease-resistant varieties, in 2012 they followed this accomplishment with the release of a high-starch variety bred using molecular techniques.

Nigerian women at work processing cassava.

In 2011, the cassava team together with the International Institute of Tropical Agriculture (IITA) and HarvestPlus (another CGIAR Challenge Programme focussed on the nutritional enrichment of crops), released three cassava varieties rich in pro-vitamin A, which hold the potential to provide children under five and women of reproductive age with up to 25 percent of their daily vitamin A requirement – a figure Chiedozie and his team are now ambitiously striving to increase to 50 percent. In 2014, they released three more pro-vitamin A varieties with higher concentrations of beta-carotene.

These new and improved varieties – all generated as a direct or indirect result of his engagement in GCP projects – are, Chiedozie says, worth their weight in gold for the people of Africa.

Research that delivers benefits to poor farmers is what drives Chiedozie. In addition to the direct rewards of new varieties there are other highlights from his involvement with GCP, indicating a long term change in breeding science: “People are now using improved or modern techniques in breeding; people think about database management in cassava breeding across Africa; and African breeders are getting PhDs in molecular breeding.”

Cassava leaves.

Building African capacity

Chiedozie believes a crucial element of GCP’s success in breeding better cassava varieties for smallholder African farmers lies in the capacity building and infrastructure support provided by GCP.

After his initial GCP training at the University of Pretoria, South Africa, Chiedozie engaged in other capacity-building opportunities, including a one-year visiting scientist fellowship at the International Center for Tropical Agriculture (CIAT) in Colombia. The significance of these early GCP opportunities was, Chiedozie says, momentous: “Prior to my GCP work, I was more or less a plant breeder, and a conventional one at that. Whilst I’d been exposed to molecular tools during my early work on yam and other crops, I was not applying them in my work back then.”

Chiedozie emphasises that such training opportunities are vital for the future food security of Africa. “We raised up a new crop of cassava breeders in Africa – people who were bold enough to take up a molecular breeding project and pursue it with support from the international centres. And today we are seeing the results of that. Cassava breeding programmes are standing today because of our quality of seeds sown in the past.”

The networking opportunities offered by the Cassava Community of Practice – founded by GCP and now hosted by the Integrated Breeding Platform (IBP) – have meant that Chiedozie and his colleagues could expand their collaboration at the local, national and regional levels: “We now have a network of cassava breeders that you can count on and relate with in different countries. This has really widened our horizons and also made our work more visible,” he says, citing effective links formed with Côte d’Ivoire, Ethiopia, Ghana, Liberia, Malawi, Mozambique, Sierra Leone and South Sudan.

Selling fufu, a staple food made with cassava flour, at a market in Nigeria.

A paradigm shift

These opportunities have led to what Chiedozie calls a ‘paradigm shift’ in how national research agencies are viewed by donors and research investors: “GCP helped us to build an image for ourselves in Nigeria and in Africa, and this created a confidence in other global actors, who, on seeing our ability to deliver results, are choosing to invest in us.

“Our work with GCP helped us to gain that capacity that we needed to be able to negotiate or even make a request for funding. And people are able to trust that you can deliver if you have delivered in the past for an organisation like GCP. So it gave us credibility; it gives us a platform to be able to speak to donors directly, and donors can now approach us, which never used to happen in pre GCP days.”

This newly found confidence and profile sees the NRCRI cassava team currently engaging with the Bill & Melinda Gates Foundation and the CGIAR Research Program on Roots, Tubers and Bananas (RTB) on research that will expand on and follow through on what GCP started.

Hear from Chiedozie on the beneficial outcomes of GCP – in terms not only of variety releases but also of attracting further projects, prestige, and enthusiastic young breeders – in the video below (or on YouTube):

For Chiedozie, his dream of helping his country’s struggling farmers and people is coming true. He has no regrets about dropping his dream of becoming a surgeon for one of helping his country as a plant breeder: “Coming from Umuahia, a small town in the southeast of the country, I grew up in an environment where you see people who are struggling, weak from disease, poor, and with no opportunities to send their children to school.

“Despite the social injustice around me, I always thought there was opportunity to improve people’s lives. This is what the GCP-supported research has helped me to do, even faster than I would have believed possible.”

Ghana’s plant researchers blossom in their own fields

Africa, Capacity building, Cassava, Maize, Partnerships No Responses »

Oct 132015

The vibrant colours of a cassava leaf.

Little did some of Ghana’s crop researchers know back in 2007 that they would be cultivating not just their plants but also themselves over the following seven years.

“When you see one person being trained and then another person being trained, it doesn’t mean much. But when you put all the numbers together and they see themselves as a force, as a team, I think that’s where new strength lies for our African researchers,” reflects Elizabeth Parkes on the impacts of the CGIAR Generation Challenge Programme (GCP).

Elizabeth is a cassava breeder in Ghana. She works for the Crops Research Institute (CRI) of Ghana’s Council for Scientific and Industrial Research (CSIR) and is currently on a leave of absence working at the International Institute of Tropical Agriculture (IITA).

“Wherever I go, whatever opportunity I have, I refer back to GCP and its capacity-building work. You see, it’s good to release new plant varieties, but it’s also good to release people,” she says.

The internationally funded GCP set out to enhance the local plant-breeding capabilities of people like Elizabeth, and so help developing nations meet ever-growing demands for food in the face of climate change and worsening drought conditions, the threat of crop disease, and other pressures.

Scientists at the Crops Research Institute (CRI) work to improve crop production in Ghana and so ensure national food security and decent livelihoods for people like this Ghanaian cassava farmer.

This has meant empowering scientists with cutting-edge tools and knowledge, as well as overcoming some surprisingly down-to-earth obstacles.

“One thing that really energises me,” enthuses GCP Consultant Hannibal Muhtar, “is seeing people understand why they need to do the work and being given the chance to do the how.”

Hannibal, under his GCP remit, was asked to visit the research sites of GCP-funded projects at research centres and stations across Africa, to identify those where effective research might be hindered by significant gaps in three fundamental areas: infrastructure, equipment and support services. He selected 19 target research sites, in Burkina Faso, Ethiopia, Ghana, Kenya, Mali, Niger, Nigeria and Tanzania. Two of these were in Ghana, namely the CRI research sites at Kumasi and Tamale.

The mission of CRI is to ensure high and sustainable crop productivity and food security in Ghana through the development and dissemination of environmentally sound technologies. Its research areas are broad and include maize, rice, cowpeas, soybeans, groundnuts, cassava, yams, cocoyams, sweetpotatoes, plantains and bananas.

In developing countries like Ghana that the obstacles to achieving research objectives are often quite mundane in nature: a faulty weather station, a lack of irrigation systems, or fields ravaged by weeds or drainage problems and in dire need of rehabilitation. Yet such factors compromise brilliant research.

Even a simple lack of fencing commonly results not only in equipment being stolen, but also in precious experimental crops being stomped on by roaming cattle and wild animals such as boars, monkeys, hippopotamuses and hyenas; this also poses a serious threat to the safety of field staff.

“The real challenge lies not in the science, but rather in the real nuts and bolts of getting the work done in local field conditions,” Hannibal explains.

He says: “If GCP had not invested in research support infrastructure and services, then their investment in research would have been in vain. Tools and services must be in place as and when needed, and in good working order. Tractors must be able to plough when they should plough.”

Cassava chips on sale in a Ghanaian market.

Ghana gains a new centre of excellence

Elizabeth is one of more than 10 researchers from Ghana who gained their PhDs via GCP-funded research projects. They were given the opportunity to travel to international research laboratories to learn the latest research methods, train in genotyping and establish contacts with leading scientific minds.

“They [GCP] have made us attractive for others to collaborate with,” says Elizabeth.

“GCP gave you the keys to solving your own problems; it put structures in place so that knowledge learnt abroad could be transferred and applied at home.

“Before GCP we really struggled, but now everybody wants to have training in Ghana. Everybody wants to have something to do with us, and I will always say thank you to GCP for that, for making us attractive as researchers,” Elizabeth says.

At the outset of the Programme, Elizabeth was learning how to breed new cassava varieties suitable for African soils. She worked with scientists from IITA in Nigeria to use genetic resources (germplasm) from South America, where cassava originates, to integrate the CMD2 gene into local germplasm using molecular breeding. CMD2 gives cassava resistance to the devastating cassava mosaic disease, which slowly shrivels and yellows leaves and roots, destroying crop yields.

Elizabeth Parkes poses with a sturdy and nutritious harvest of cassava roots.

Cassava is a lifeline for African people, and is a particularly important staple food for poorer farmers. More cassava is produced in Africa than any other crop, according to 2012 figures from the Food and Agriculture Organization of the United Nations. It is grown by nearly every farming family in sub-Saharan Africa, supplying about a third of people’s daily energy intake in the region. This makes cassava mosaic disease a potential disaster, and makes effectively breeding improved varieties an activity with real impact.

“We started out doing low-cost marker-assisted selection, for which we had some grants. Someway, somehow, the government got interested and brought in more resources. So together we started a small biotech lab. Now this lab has become the Centre of Excellence for West African productivity,” says Elizabeth.

“I have attended three GCP Annual Research Meetings, and I have won awards for my posters. This greatly boosted my confidence,” says Elizabeth. She also continues to be an active member of the Cassava Community of Practice – founded by GCP and now hosted by the Integrated Breeding Platform (IBP) – which facilitates and supports the integration of marker-assisted selection into cassava breeding. All this has accelerated Elizabeth’s quest to produce and disseminate farmer-preferred cassava varieties that are resistant to pests and diseases.

“We are all forever grateful to GCP and its funders. GCP has had a huge impact on research in Ghana, especially for cassava, rice, maize and yam. All the agricultural research institutes and individual scientists who came into contact with GCP have been fundamentally transformed.”

Capacity building à la carte a real ‘life changer’

For Allen Oppong, a maize pathologist at CRI, GCP was a life changer too: “Indeed, I am very grateful to GCP for making me what I am today.”

Allen’s first experience of GCP was in 2007, when he won a Capacity building à la carte grant for research into characterising locally adapted maize varieties. During the project he travelled to international research meetings and received training in marker-assisted selection in advanced laboratories.

Infrastructure improvements funded by GCP also came at a critical time for Allen. There was a drought, which, without the irrigation systems provided through the Programme, would have meant a much longer research process.

Even without drought, these kinds of improvements can dramatically speed up breeding, as Hannibal explains: “By providing glasshouses or the capacity to irrigate in the dry season, we are enabling breeders to accelerate their breeding cycles, so that they can work all year round rather than having to wait until the rain comes.”

“Through the support of GCP,” Allen recalls, “I was able to characterise maize varieties found in Ghana using the bulk fingerprinting technique. This work has been published and I think it’s useful information for maize breeding in Ghana – and possibly other parts of the world.”

One of the biggest challenges that Allen experienced during his GCP work was getting farmers to try the new varieties that are being developed.

“Most people don’t like change. The new varieties are higher yielding, disease resistant, nutritious – all good qualities. But the challenge is demonstrating to farmers that these materials are better than what they have.

A Ghanaian farmer holds a just-harvested maize ear.

“You can have very good material that has all these attributes, but if the farmer doesn’t have access to it, then how can he know the attributes that you are talking about? How can he see it when it is in your research station?”

Ghanaian farmers generally select maize varieties for their adaptation to specific local environments. But as Allen explains, average maize yields in Ghana, at 1–1.5 tonnes per hectare, are well below the global average of 5.2 tonnes per hectare.

Allen is looking forward optimistically to this next stage. “We have the capacity to more than double what we are producing now. The possibility is there, as long as farmers adopt the good materials.”

A ‘kick-start’ for plant science and for people

The catalytic effect of international funding programmes like GCP on small research laboratories in developing countries is often underestimated.

“We got GCP support to kick-start molecular biology research activities,” says Marian Quain, a senior research scientist at CRI. “It provided us with laboratory chemicals, reagent and equipment. My lab also received funding under the Genotyping Support Service initiative to characterise hundreds of sweetpotato, yam and cassava accessions.

“This support from GCP contributed immensely to transforming the lab.”

Ruth Prempeh – CRI researcher who was able to achieve her PhD with GCP support – hard at work collecting data in the field.

Funding injections can kick-start careers for young scientists too. In 2009, Ruth Prempeh received funding for her PhD, Genetic analysis of postharvest physiological deterioration in cassava (Manihot esculenta Crantz) storage roots, which was completed in 2013.

“From my thesis, l have prepared three manuscripts for publication. I have also had the opportunity to attend the three-year Integrated Breeding Multiyear Course, during which l acquired knowledge and skills in data analysis, interpretation and management and also in using modern technologies for crop improvement,” says Ruth.

“This has been very useful and has really had an impact on my career, making me what l am today. With this, l know l have a great future and I believe l will achieve great things. I am really proud to have been associated with GCP and very grateful for the opportunity.”

Elizabeth Parkes: Cassava’s ‘woman of destiny’ in Ghana

Africa, Capacity building, Cassava, Researchers, Women in science No Responses »

Oct 092015

Elizabeth Parkes

Elizabeth Parkes grew up in Ghana as the youngest child and only girl in a middle-class family of nine children. Through visiting poor communities with her family, she began from an early age to build her understanding of the lives of resource-poor families in this part of West Africa and their need for reliable and nutritious food.

She also knows first-hand the important role women play on a farm and in a family. “Rural families are held together by women, so if you are able to change their lot, you can make a real mark,” says Elizabeth.

It was this sense of social conscience that drew her to a career in agricultural research: “My father, a Regional Education Officer, was not very amused; he thought agricultural research was a man’s job!” she recalls.

But Elizabeth was on a mission. “I see African communities where poverty and hunger are seemingly huge problems with no way out,” she says. “If I put in enough effort, I can bring some solutions. My primary target group is the less privileged, and women in particular have been my friends throughout. This sometimes means subtly getting the men to consider some changes in roles.”

This sense of destiny led to Elizabeth gaining a Bachelor’s degree in Agriculture, a Diploma in Education and a Master’s in Crop Science.

Meet Elizabeth in the complete podcast below (or see a playlist on PodOmatic) – and be inspired by her warmth and passion!

A worker in a Ghanaian cooperative producing garri, or gari, a kind of granular cassava flour used to prepare a range of foods.

Turning point: cassava to help the vulnerable

During a stint of national service between academic degrees, she was based in the tiny poor village of Aworowa in the Brong Ahafo Region. There was no electricity in her room, and the street lights came on once a week.

In a poor Ghanaian community everyone has to pitch in to the heavy daily round of chores.

“We all fetched water from the stream to drink and cook,” Elizabeth recalls. The plight of the villagers inspired Elizabeth to approach a scientist engaged in root and tuber projects at the Crops Research Institute (CRI) of Ghana’s Council for Scientific and Industrial Research (CSIR). She offered to carry out some research on cassava, hoping this might help the local people.

“I saw the struggle for households,” says Elizabeth. “I lived with them for one year, which transformed my interest and focus onto the vulnerable and less privileged.”

As a result, Elizabeth established CRI cassava trials in the region, and these trials continue today with Elizabeth still in touch with the villagers.

When her year of national service finished, Elizabeth was appointed as Assistant Research Officer at CRI – their first woman to be assigned to a research project. Already, she was beginning to fulfil her destiny.

Healthy cassava plants.

Challenges and opportunities

Unlike most crops, cassava is propagated, not by seed, but using cut sections of stem like these – just one of the many challenges this previously neglected crop offers breeders.

But cassava is not the easiest crop for a young researcher to cut their teeth on. It has long been regarded as an ‘orphan’ crop – one that researchers and funders have forgotten in their drive to work with the higher profile crops of wheat, rice and maize.

Cassava is a challenging crop for breeders to work with. “In addition to factors such as pests and disease, cassava is a long-season and very labour-intensive crop. It can take a whole year before you can expect to reap any rewards, and if you don’t have a strong team who can step in at different points throughout the breeding process, you can often find unexpected results at the end of it, and then you have to start all over again,” Elizabeth says.

But while many other young researchers gave up on with cassava, Elizabeth stuck with it, knowing the importance of this crop to farmers, especially women. And this is where Elizabeth’s involvement with the CGIAR Generation Challenge Programme (GCP) really started to make a difference to her future.

During GCP’s first research phase, Elizabeth’s path crossed with GCP scientist Martin Fregene, who encouraged Elizabeth to lead the Ghana partners involved in GCP’s cassava projects. She soon climbed the GCP research ranks, receiving multiple study grants, managing projects, and mixing and mingling with elite scientists. Along the way, Elizabeth also learnt new molecular breeding techniques. More recently, she was appointed Ghana’s lead researcher for GCP’s Phase II Cassava Research Initiative.

A place at the table, and sharing joy

Elizabeth Parkes examines a healthy crop of monster roots from an improved cassava variety.

Elizabeth believes the support GCP gave her to develop her skills and capacity is what has made a difference to her own and others’ destinies as research scientists: “GCP has made us visible and attractive to others; we are now setting the pace and doing science in a more refined and effective manner. I see GCP as the pace setters.

“GCP gave you the keys to solving your own problems and put structures in place so that knowledge learnt abroad could be transferred and applied at home.

“When I first joined GCP,” Elizabeth recalls, “I saw myself as somebody from a national research programme being given a place at the table; my inputs were recognised and what I said carried weight in decision-making.”

Elizabeth has attended three GCP Annual (later General) Research Meetings and won awards for her posters. “This greatly boosted my confidence,” she says. She is an active member of the Cassava Community of Practice – founded by GCP and now hosted by the Integrated Breeding Platform (IBP) – which facilitates and supports the integration of marker-assisted selection into cassava breeding. All this has accelerated Elizabeth’s quest to produce and disseminate farmer-preferred cassava varieties that are resistant to pests and diseases.

“With the Community of Practice you can call on other scientists; you share talk, you share ideas, you share joy. We share everything together,” Elizabeth enthuses. ‘Joy’ is a word that is often on Elizabeth’s lips when she describes the help that GCP has given her and others.

A farmer in Benin transforms cassava into garri, or gari, used as the basis of many different dishes.

In less than a decade, Elizabeth has become a valued researcher at CRI (currently on secondment at the International Institute of Tropical Agriculture, IITA) as well as Ghana’s leading GCP-supported scientist working on cassava. But in fulfilling her own destiny, she’s also passionate about helping others to achieve their potential.

“Building human capacity is my greatest joy,” she says. Farmers, breeders and a Ghanaian private-sector company are just a few of the fortunate beneficiaries of her expertise over recent years.

Nurturing women

Angelique Ipanga tends her cassava plants in the Democratic Republic of Congo. Cassava is often seen as a “women’s crop,” and the work of cultivating and preparing it falls largely on women’s shoulders.

Elizabeth talks about one of her favourite people, a farmer called Bea: “She’s very serious. She wants to learn more and she keeps expanding her farm.”

Bea hadn’t planted cassava before, so she pestered Elizabeth to find out more about how to do it properly. With Elizabeth’s guidance, Bea’s cassava-growing skills flourished, and she became so successful that she was recognised as the best farmer in her community.

“These are things that make me glad… that at least I have impacted somebody who hadn’t planted cassava before, and it’s amazing,” says Elizabeth. “There are people out there who need us, and when we give them our best, they will give the world their best as well.”

Elizabeth is also passionate about helping other women researchers: “I’ve pushed to make people recognise that women can do advanced agricultural science, and do it well. To see a talented woman researcher firmly established in her career and with her kids around her is thrilling.”

And so Elizabeth is now herself firmly established in world-class agricultural research, and further interesting stories are sure to follow.

“I’ve stuck with cassava because that’s my destiny! I may add other root and tuber crops, but cassava is my pivot.”

Nigeria’s cassava researchers leading the march

Africa, Capacity building, Cassava, Partnerships No Responses »

Oct 072015

Young Nigerian scientists often leave Africa and look for jobs with international research agencies overseas. But with the CGIAR Generation Challenge Programme (GCP)-funded Cassava Research Initiative (RI), two young nationals have been leading the international collaboration and injecting confidence into Africa’s research capacity.

Leadership is a quality admired and consistently sought after, particularly when overcoming a challenge. Some leaders direct from afar; others rise through the ranks and work with their peers on the ground – winning respect from the people they lead as they get their hands dirty.

Dream team: Emmanuel Okogbenin (left) and Chiedozie Egesi (right), both of Nigeria’s National Root Crops Research Institute.

“If you want to work for the people, you have to walk with the people – that’s an African concept,” says Emmanuel Okogbenin, a plant breeder and geneticist at Nigeria’s National Root Crops Research Institute (NRCRI). “Then when you work with the people, you really understand what they want. When you speak, they know they can trust you.”

This powerful sentiment is one reason why GCP sought the collaboration of NRCRI in overcoming the challenge of sustaining Africa’s, and indeed the world’s, cassava production.

Having started as a small farm in 1923, NRCRI has taken giant strides to become one of Nigeria’s best research institutes, contributing immensely to the country’s economic development and making it the leading producer of cassava in the world. NRCRI Executive Director Julius Chukwuma Okonkwo says, “This would not have been attainable if not for the trust and support that GCP had in us when they made two of our young cassava researchers the leaders of an international collaboration.”

The two researchers to whom Julius refers are Emmanuel and his colleague Chiedozie Egesi, also a plant breeder and geneticist at NRCRI. Their combined 36 years’ of cassava research experience is matched by their passion to get the best out of Nigeria’s main staple crop.

And they are happy to get some dirt under their fingernails. “It’s just as important to work with the farmers in the field and understand what they want, as it is to do the research in the lab,” says Emmanuel. “At the end of the day we need to please the farmers, as they are the ones who will be using the new varieties that we are developing to sustain their livelihoods.”

Nigerian farmers display their cassava harvest.

Developing and leading Africa’s cassava research

Between 2010 and 2014, both Emmanuel and Chiedozie led three different projects within GCP’s Cassava RI, working with other colleagues in national breeding programmes in Ghana, Tanzania and Uganda, as well as the International Institute of Tropical Agriculture (IITA), the International Center for Tropical Agriculture (CIAT), the Brazilian Corporation of Agricultural Research (EMBRAPA) and Cornell University in the USA. The aim of the initiative was to use molecular-breeding techniques to accelerate the development of high-starch cassava varieties with resistance to diseases and tolerance to drought – and so ensure both food supplies and income for farmers.

Meet Chiedozie and Emmanuel in the video playlist below, learn more about cassava in Africa, and hear all about their research (or watch on Youtube):

Emmanuel explains that before GCP, “most African national programmes didn’t really have established crop-breeding programmes, and didn’t have the resources” to do the scale of research GCP assisted with. Nor did they have the capacity to use molecular-breeding techniques, which can potentially halve the time it takes to develop new varieties.

With help from GCP and CIAT, NRCRI was able to equip a new molecular-breeding laboratory, and staff were trained to incorporate molecular-breeding techniques into their breeding programme. “GCP was there not only to provide technology, but also to guide us in how to operate that technology,” explains Chiedozie.

Julius points out that both Chiedozie and Emmanuel were also influential in disseminating this knowledge and, in turn, building and sustaining NRCRI’s human capacity. “They both mentored many young scientists who have chosen a career in cassava and molecular breeding because of this.”

Transporting a bountiful cassava harvest from farm to market in Nigeria.

With training and infrastructure in place, NRCRI led an international collaboration that in 2010 released Africa’s first cassava variety developed using molecular-breeding techniques. Known as UMUCASS33 (or CR 41-10), it was resistant to cassava mosaic disease (CMD) – a devastating plant disease that can wipe out farmers’ entire cassava crops – and also highly nutritious. This was swiftly followed by a second similar variety, CR 36-5, and supplied to farmers.

Between this landmark release and GCP’s close in 2014, the cassava team had already released nearly 20 higher yielding, more nutritious varieties resistant to diseases and pests, and had begun working on developing drought-tolerant varieties.

These new and improved varieties – all generated as a direct or indirect result of his engagement in GCP projects – are, Chiedozie says, worth their weight in gold: “Through these materials, people’s livelihoods can be improved. The food people grow should be nutritious, resistant and high-yielding enough to allow them to sell some of it and make money for other things in life, such as building a house, getting a motorbike or sending their kids to school.” This social aspect is particularly pertinent in Nigeria, where these cassava varieties will have the greatest impact.

Feeding a giant

Nigerian farmer with his bountiful cassava harvest.

Nigeria is often referred to as the ‘Giant of Africa’. It is the most populous African country, with over 174 million inhabitants. The population’s main staple food is cassava, making Nigeria the world’s largest producer and consumer of the crop. At the same time, the country imports almost USD 4 billion of wheat every year – a figure that is expected to quadruple by 2030 if wheat consumption continues to grow at the same rate it is today.

The government is wary of this ‘overreliance’ on imported grain and is working towards making the country less reliant on wheat by imposing a wheat tariff. It also hopes to boost cassava production and commercialisation by promoting 20 percent substitution of cassava flour for wheat in breadmaking.

“The government feels that to quickly change the fortunes of farmers, cassava is the way to go,” explains Emmanuel, who liaises with the Nigerian Government to promote to farmers the benefit of cassava varieties with high starch concentrations. It is the flour from these varieties that is being used to partially replace wheat flour to make bread. GCP support has been crucial here too, in providing vital scientific information to the government. Emmanuel explains: “The tariff from wheat is expected to be ploughed back to support agricultural development – especially in the cassava sector – as the government seeks to increase cassava production to support flour mills.”

Cassava offers a huge opportunity to transform the agricultural economy, stimulate rural development and further improve Nigeria’s gross domestic product. In 2014, Nigeria’s economy surpassed that of South Africa’s to become the largest on the continent. By 2050, Nigeria is expected to rise further and become one of the world’s top 20 economies.

Unfortunately, however, like many growing economies worldwide, Nigeria is still working to address severe inequality, including in the distribution of wealth and in feeding the country’s expanding population.

A woman with her children at work in a cassava processing centre in Nigeria.

It’s a problem Chiedozie understands well: “Nigeria is an oil-producing country, but you still see grinding poverty in some cases,” he says. “Coming from a small town in the southeast of the country, I grew up in an environment where you see people who are struggling, weak from disease, poor, and with no opportunities to send their children to school,” he reveals. The poverty challenge, he explains, hits smallholder farmers particularly hard: “Urban development caught up with them in the end: some of them don’t even have access to the land that they inherited, so they’re forced to farm along the street.”

For Chiedozie, the seemingly bleak picture only served to ignite a fierce determination and motivation to act: “Despite the social injustice around me, I always thought there was opportunity to improve people’s lives.” And thus galvanised by the plight of Nigerian farmers, Chiedozie promptly shelved his plans for a career in medical surgery and pursued biological sciences and a PhD in crop genetics, a course he interspersed with training stints in the USA at Cornell University and the University of Washington, before returning to his homeland to accept a job as head of the cassava breeding team, and – following a promotion in 2010 – to become Assistant Director of the Biotechnology Department at NRCRI.

Empowering African researchers

Carrying cassava at a processing centre in Nigeria.

Emmanuel, who followed a similar educational route to Chiedozie, says both he and his colleague are exceptions to the norm in Africa, where African researchers tend to look for opportunities at international or private institutes rather than in national breeding programmes.

“It is difficult being a researcher in Africa,” says Emmanuel. “We don’t get paid as much as breeders in more developed countries, and funding is very hard to obtain.”

Emmanuel says his proudest moment was when GCP was looking for Africans to take up leadership roles. “They felt we could change things around and set a precedent to bring people back to the continent,” he says. “They appreciated our values and the need to install African leaders on the ground in Africa rather than in Europe, Asia or the Americas.”

Jean-Marcel Ribaut, GCP’s Director, says that seeking this local leadership was a novel approach for a transnational programme like GCP at the time, and proved to be an imperative feature for all GCP Research Initiatives. “The reasoning behind the approach is two-fold: Firstly, it’s important that our national partners share in feeling ownership of the projects and outcomes; secondly, they are gaining experience in the role so they can continue to do so after the close of the Programme in 2014,” he says. “We feel that most of our leading institutes, NRCRI included, are in a better position now than when they joined the project, and that this, along with their experience, has already gained them more exposure and funding opportunities.”

This is indeed true of the NRCRI cassava team, which is engaging with the Bill & Melinda Gates Foundation, Cornell University, IITA and Uganda’s National Crop Resources Research Institute in an initiative that Chiedozie promises will be at the front of cutting-edge technology. “We are still working out specifics, but it will see us continuing to use marker-assisted breeding techniques to develop higher yielding, stress-tolerant cassava varieties.”

Chiedozie adds this would not have been possible without GCP, which helped them to develop their capacity in Nigeria and in Africa, and this has “created a confidence in other global actors, who, on seeing our ability to deliver results, are choosing to invest in us.”

Before GCP came along, cassava was something of an orphan crop in agricultural research. Among the challenges to efficient breeding of cassava are that it is slow to grow and is propagated, not by seed, but using cut sections of stem like those shown. But with investment and capacity building from GCP, particularly in molecular breeding tools, African cassava scientists have gained a new confidence and prestige.

Continuing the momentum

One organisation that has been impressed by the work done at NRCRI is the CGIAR Research Program on Roots, Tubers and Bananas (RTB). RTB Director Graham Thiele has been following the work done at NRCRI since 2010 with great interest. “We have been really impressed to see a national programme like NRCRI playing a leading role in these successful GCP projects, and grow as a result of this,” he says.

One area of research that has particularly impressed Graham is Chiedozie and Emmanuel’s pre-emptive breeding for cassava brown streak disease (CBSD) resistance. “CBSD isn’t currently an issue in Nigeria but it has the potential to wipe out all crops, as it has in Uganda and Tanzania, if it continues to spread west from these countries,” he explains.

“What Chiedozie and Emmanuel are doing is using molecular markers, developed in collaboration with IITA, to search for genes in their varieties that confer resistance to brown streak virus. They can then use these when breeding for CBSD resistance without exposing cassava to the virus. It’s very exciting and forward thinking, as normally people breed for resistance only when the disasters happen.”

As GCP approached its sunset in December 2014, Chiedozie and Emmanuel were reaching out to RTB to seek funding to continue this and other projects they are currently working on. “They’ve already created some great varieties but have plenty more in the pipeline, so we want to help them finish this work and, most importantly, keep the momentum going,” says Graham.

Chiedozie looks forward to the next steps with optimism, confirming that the new collaboration will continue in the quest to “give African farmers varieties of cassava that they will love to grow.”

Tanzania’s researchers turn high-end science into real food

Africa, Capacity building, Cassava, Groundnuts, Partnerships No Responses »

Oct 012015

A farmer from Dodoma, Tanzania, an area where climate change is causing increasing heat and drought. Groundnut is an important crop for local famers, forming the basis of their livelihood together with maize and livestock.

If you don’t live with poor people, then your science is of no use to poor people. This is the very clear sentiment of Omari Mponda, one of Tanzania’s top groundnut researchers.

“Sometimes people do rocket science. But that’s not going to help the poor,” says Omari. “Scientists in labs are very good at molecular markers, but markers by themselves will not address the productivity on the ground. You cannot remove poverty through that alone.”

Omari is the Zonal Research Coordinator and plant breeder at Tanzania’s Agricultural Research Institute at Naliendele (ARI–Naliendele).

The passion and dedication of Omari and his colleagues at this East African research centre were the reason why, between 2008 and 2014, the CGIAR Generation Challenge Programme (GCP) provided funding for legumes research at ARI–Naliendele that especially targeted drought, as part of the Tropical Legumes I project. This project supplied national institutes across Africa, Asia and Latin America with training and infrastructure improvements that enabled local researchers to do more advanced plant science that could make a real difference to farmers.

Researchers like Omari, who are working on the ground in developing countries, are a crucial part of the global quest to develop solutions for future food security and improved livelihoods in these countries.

GCP set out to enhance the plant-breeding skills and capacity of researchers in developing nations, such as Tanzania, so that they can develop their own crop varieties that will cope with increasingly extreme drought conditions.

A farmer in dryland Tanzania shows off his groundnut crop.

“One thing that really energises me,” enthuses GCP Consultant Hannibal Muhtar, “is seeing people understand why they need to do the work and being given the chance to do the how.”

Hannibal, under his GCP remit, was asked to visit the research sites of GCP-funded projects at research centres and stations across Africa, to identify those where effective research might be hindered by significant gaps in three fundamental areas: infrastructure, equipment and support services. He selected 19 target research sites – in Burkina Faso, Ethiopia, Ghana, Kenya, Mali, Niger, Nigeria and Tanzania.

Hannibal Muhtar (left) and Omari Mponda at ARI–Naliendele.

Two of the locations chosen for some practical empowerment were in Tanzania, namely the ARI research sites at Naliendele and Mtwara, where simple infrastructure improvements like irrigation tubing and portable weather stations have made a surprising difference to the capacity of local researchers.

In developing countries like Tanzania, the obstacles to achieving research objectives are often quite mundane in nature: a faulty weather station, the lack of irrigation systems, or fields ravaged by weeds and in dire need of rehabilitation. Yet such factors compromise brilliant research.

“The real challenge lies not in the science, but rather in the real nuts and bolts of getting the work done in local field conditions,” Hannibal explains.

Bridging the gap between the lab and farmers

Since 2008, researchers at ARI–Naliendele in Tanzania have been working together with the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) to identify suitable groundnut breeding materials to help the country’s farmers improve crop yields. Currently, yields are at less than one-third of their potential.

“We are bridging the big science to the poor people, to see the real issues we should be addressing. You can have a very good resistant variety, but maybe that variety is not liked by farmers,” Omari says.

He recalls a case where one farmer who helped with variety selection for international research had identified a groundnut variety that was resistant to disease, but the shells were too difficult to crack.

“So that variety won’t help the poor, because he [the farmer] is not able to open the shell. So the breeder had to rethink, what trait could loosen, or make it easier to shell?” recounts Omari.

Shelled groundnuts on sale in Ghana.

The mission of the 10-year GCP was to use genetic diversity and advanced plant science to improve crops in developing countries. More than 200 partners were involved in the programme, including members of the international CGIAR group plus academia and regional and national research programmes.

National institutes like Tanzania’s ARI–Naliendele, established in 1970, are essential linchpins between advanced research centres in developed countries and poor farmers around the world facing the day-to-day realities of climate change and plant pests and diseases.

“If each organisation works in isolation, they will spend a lot of money developing new varieties but nothing will change on the ground. So in actually working together through programmes like the GCP, we can see some change happening,” says Omari.

Through the GCP project, Tanzania’s groundnut researchers received 300 reference-set lines from ICRISAT, which were then phenotyped over three years (2008–2010) for both drought tolerance and disease resistance in order to select the most useful lines under local conditions. To help with this process, Tanzanian scientists and technicians travelled to ICRISAT headquarters in India, where they were trained in phenotyping: that is, how to identify and measure observable characteristics – in this case, traits relating to the plants’ abilities to cope with drought and disease.

After the researchers identified the best varieties, these were provided to participating farmers so they could trial them in their fields for selection in 2011–2012. Five new varieties have since been released to Tanzanian farmers based on this collaboration between ARI and ICRISAT.

A young groundnut plant.

Things are speeding up in Tanzania

For ARI–Naliendele, the laboratory and field infrastructure provided by GCP funding has helped accelerate the work of local researchers and breeders. It has been transformative for Tanzanian scientists, according to Omari.

“For example, irrigation is very costly, but with the GCP support for an irrigation system, we can fast track our work – we can come up with new varieties in a much shorter period. That is something that will change our lives,” says Omari.

“Groundnut has a very low multiplication ratio, so if you plant one kilogram, you will get only 10 kilograms next year,” he explains. “Ten kilograms in 12 months is not enough. With irrigation, it means that we can have at least two or three crops within a season. Some of the varieties we are developing can be fast tracked to the end users. The speed of getting varieties from the research to the farmers has increased by maybe three times.”

Washing harvested groundnuts, Zimbabwe.

GCP also funded computers, measuring scales, laboratory equipment and a portable weather station, which all help to assure good, reliable information on phenotyping.

Scientists too have become quicker and better at their work from having more advanced skills, according to Omari: “We now have more competent groundnut breeders in Tanzania.

“Initially, we depended on germplasm being brought over by ICRISAT and somebody selecting varieties for us. But they have been training us to do our own crosses, so we can now decide what grows in our breeding programme,” he says.

“For us, it is a big achievement to be able to do national crosses. We are advancing toward being a functional breeding programme in Tanzania.

“These gains made are not only sustainable, but also give us independence and autonomy to operate. We developing-country scientists are used to conventional breeding, but we now see the value and the need for adjusting ourselves to understand the use of molecular markers in groundnut breeding.”

Tanzania’s new zest for advanced plant breeding

A farmer at work in her cassava field in northern Tanzania.

According to cassava breeder Geoffrey Mkamilo, a Principal Agricultural Research Officer at ARI: “There are some things that you just cannot do by conventional breeding.”

Usually researchers looking to breed better drought-tolerant and disease- and pest-resistant crops would use conventional breeding methods. This means researchers would be trying to pick out resilient plants by phenotyping alone, looking at how they are growing in the field under different conditions, which can take considerable time to deliver results – especially for crops that are slow to mature, like cassava.

Molecular breeding, on the other hand, involves using molecular markers to make the breeding process faster and more effective. These markers are genetic sequences known to be linked to useful genes that confer plant traits such as drought tolerance or disease resistance. Breeders can easily test small amounts of plant material for these markers, so they act like genetic ‘tags’, flagging up whether or not particular genes are present.

This knowledge helps breeders to efficiently select the best parent plants to use in their crosses, and accurately identify which of the progeny have inherited the gene or genes in question without having to grow them all to maturity. Phenotyping is still needed in discovering markers, linking genetic information with physical traits, and in testing the performance of materials in the field, but overall the time taken produce a new variety can be reduced by years.

“Before I started working with GCP, molecular breeding for me was very, very difficult… I wasn’t trained to become a molecular breeder. Now, with GCP, I can speak the same language,” Geoffrey says.

A farmer carefully packs harvested cassava tubers for transportation to the market in Bungu, Tanzania.

Via GCP, Geoffrey had the opportunity to work with scientists based in Colombia at the International Center for Tropical Agriculture (CIAT) and in Nigeria at the International Institute of Tropical Agriculture (IITA), among other experts in research institutes across the world.

The team first began to release new cassava varieties developed using marker-assisted selection in 2011, with four varieties for two different Tanzanian environments. These varieties had manifold benefits: dual resistance to cassava mosaic disease (CMD) and cassava brown streak disease (CBSD), and productivity potential of up to double the yield of existing commercial varieties.

The research continues to produce ever better cassava varieties, and in this endeavour Geoffrey cannot overemphasise the power of integrating conventional breeding practices with molecular breeding.

“I have received so many phone calls from farmers; they even call in the night. They say, ‘Geoffrey, we have heard that you have very good materials. Where do we get these materials?’ So many, many farmers are calling,” says Geoffrey. “Many, many organisations – even NGOs, they also call. They want these materials. And even the private sector calls. GCP has contributed tremendously to this.”

Groundnut boom may help crack poverty in Africa

Africa, Capacity building, Crop breeding, Genetics, Genomics, Groundnuts, Legumes No Responses »

Jun 222015

Photo: Joseph Hill/Flickr (Creative Commons)

Groundnut plants growing in Senegal.

Across Africa, governments and scientists alike are heralding groundnuts’ potential to lead resource-poor farmers out of poverty.

Around 5,000 years ago in the north of Argentina, two species of wild groundnuts got together to produce a natural hybrid. The result of this pairing is the groundnut grown today across the globe, particularly in Africa and Asia. Now, scientists are discovering the treasures hidden in the genes of these ancient ancestors.

Nearly half of the world’s groundnut growing area lies within the African continent, yet Africa’s production of the legume has, until recently, accounted for only 25 percent of global yield. Drought, pests, diseases and contamination are all culprits in reducing yields and quality. But through the CGIAR Generation Challenge Programme (GCP), scientists have been developing improved varieties using genes from the plant’s ancient ancestors. These new varieties are destined to make great strides towards alleviating poverty in some of the world’s most resource-poor countries.

A Ugandan farmer at work weeding her groundnut field.

A grounding in the history of Africa’s groundnuts

From simple bar snack in the west to staple food in developing countries, groundnuts – also commonly known as peanuts – have a place in the lives of many peoples across the world. First domesticated in the lush valleys of Paraguay, groundnuts have been successfully bred and cultivated for millennia. Today they form a billion-dollar industry in China, India and the USA, while also sustaining the livelihoods of millions of farming families across Africa and Asia.

“The groundnut is one of the most important income-generating crops for my country and other countries in East Africa,” says Malawian groundnut breeder Patrick Okori, Principal Scientist at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), who was also GCP’s Product Delivery Coordinator for groundnuts.

“It’s like a small bank for many smallholder farmers, one that can be easily converted into cash, fetching the highest prices,” he says.

The situation is similar in West Africa, according to groundnut breeder Issa Faye from the Institut Sénégalais de Recherches Agricoles (ISRA; Senegalese Agricultural Research Institute), who has been involved in GCP since 2008. “It’s very important for Senegal,” he says. “It’s the most important cash crop here – a big source of revenue for farmers around the country. Senegal is one of the largest exporters of peanut in West Africa.”

Groundnuts have good potential for sustaining a strong African export industry in future, while providing a great source of nutrition for Africa’s regional farming families.

“We believe that by using what we have learnt through GCP, we will be able to boost the production and exportation of groundnuts from Senegal to European countries, and even to Asian countries,” says Issa. “So it’s very, very important for us.”

Harvested groundnuts in Senegal.

How Africa lost its groundnut export market

Groundnuts in distress under drought conditions.

In Africa, groundnuts have mostly been grown by impoverished smallholder farmers, in infertile soils and dryland areas where rainfall is both low and erratic. Drought and disease cause about USD 500 million worth of losses to groundnut production in Africa every year.

“Because groundnut is self-pollinating, most of the time poor farmers can recycle the seed and keep growing it over and over,” Patrick says. “But for such a crop you need to refresh the seed frequently, and after a certain period you should cull it. So the absence of, or limited access to, improved seed for farmers is one of the big challenges we have. Because of this, productivity is generally less than 50 percent of what would be expected.”

Rosette virus damage to groundnut above and below ground.

Diseases such as the devastating groundnut rosette virus – which is only found in Africa and has been known to completely wipe out crops in some areas – as well as pests and preharvest seed contamination have all limited crop yields and quality and have subsequently shut out Africa’s groundnuts from export markets.

The biggest blow for Africa came in the 1980s from a carcinogenic fungal toxin known as aflatoxin, explains Patrick.

Aflatoxin-contaminated groundnut kernels from Mozambique.

Aflatoxin is produced by mould species of the genus Aspergillus, which can naturally occur in the soil in which groundnuts are grown. When the fungus infects the legume it produces a toxin which, if consumed in high enough quantities, can be fatal or cause cancer. Groundnut crops the world over are menaced by aflatoxin, but Africa lost its export market because of high contamination levels.

“That’s why a substantial focus of the GCP research programme has been to develop varieties of groundnuts with resistance to the fungus,” says Patrick.

After a decade of GCP support, a suite of new groundnut varieties representing a broad diversity of characteristics is expected to be rolled out in the next two or three years. This suite will provide a solid genetic base of resistance from which today’s best commercial varieties can be improved, so the levels of aflatoxin contamination in the field can ultimately be reduced.

Ancestral genes could hold the key to drought tolerance and disease resistance

In April 2014, the genomes of the groundnut’s two wild ancestral parents were successfully sequenced by the International Peanut Genome Initiative – a multinational group of crop geneticists, who had been working in collaboration for several years.

The sequencing work has given breeders access to 96 percent of all groundnut genes and provided the molecular map needed to breed drought-tolerant and disease-resistant higher-yielding varieties, faster.

“The wild relatives of a number of crops contain genetic stocks that hold the most promise to overcome drought and disease,” says Vincent Vadez, ICRISAT Principal Scientist and groundnut research leader for GCP’s Legumes Research Initiative. And for groundnut, these stocks have already had a major impact in generating the genetic tools that are key to making more rapid and efficient progress in crop breeding.

“Genetically, the groundnut has always been a really tough nut to crack,” says GCP collaborator David Bertioli, from the University of Brasilia in Brazil. “It has a complex genetic structure, narrow genetic diversity and a reputation for being slow and difficult to breed. Until its genome was sequenced, the groundnut was bred relatively blindly compared to other crops, so it has remained among the less studied crops,” he says.

With the successful genome sequencing, however, researchers can now understand groundnut breeding in ways they could only dream of before.

Groundnut cracked.

“Working with a wild species allows you to bring in new versions of genes that are valuable for the crop, like disease resistance, and also other unexpected things, like improved yield under drought,” David says. “Even things like seed size can be altered this way, which you don’t really expect.”

The sequencing of the groundnut genome was funded by The Peanut Foundation, Mars Inc. and three Chinese academies (the Chinese Academy of Agricultural Sciences, the Henan Academy of Agricultural Sciences, and the Shandong Academy of Agricultural Sciences), but David credits GCP work for paving the way. “GCP research built up the populations and genetic maps that laid the groundwork for the material that then went on to be sequenced.”

Chair of GCP’s Consortium Committee, David Hoisington – formerly ICRISAT’s Director of Research and now Senior Research Scientist and Program Director at the University of Georgia – says the sequencing could be a huge step forward for boosting agriculture in developing countries.

“Researchers and plant breeders now have much better tools available to breed more productive and more resilient groundnut varieties, with improved yields and better nutrition,” he says.

These resilient varieties should be available to farmers across Africa within a few years.

Genetics alone will not lift productivity – farmers’ local knowledge is vital

Improvements in the yield, quality and share of the global market of groundnuts produced by developing countries are already being seen as a result of GCP support, says Vincent Vadez. “But for this trend to continue, the crop’s ability to tolerate drought and resist diseases must be improved without increasing the use of costly chemicals that most resource-poor farmers simply cannot afford,” he says.

While genetic improvements are fundamental to developing the disease resistance and drought tolerance so desperately needed by African farmers, there are other important factors that can influence the overall outcome of a breeding programme, he explains. Understanding the plant itself, the soil and the climate of a region are all vital in creating the kinds of varieties farmers need and can grow in their fields.

Photo: Y Wachira/Bioversity International

Kenyan groundnut farmer Patrick Odima with some of his crop.

“I have grown increasingly convinced that overlooking these aspects in our genetic improvements would be to our peril,” Vincent warns. “There are big gains to be made from looking at very simple sorts of agronomic management changes, like sowing density – the number of seeds you plant per square metre. Groundnuts are often cultivated at seeding rates that are unlikely to achieve the best possible yields, especially when they’re grown in infertile soils.”

For Omari Mponda, now Director of Tanzania’s Agricultural Research Institute at Naliendele (ARI–Naliendele), previously Zonal Research Coordinator and plant breeder, and country groundnut research leader for GCP’s Tropical Legumes I project (TLI; see box below), combining good genetics with sound agronomic management is a matter of success or failure for any crop-breeding programme, especially in poverty-stricken countries.

“Molecular markers by themselves will not address the productivity on the ground,” he says, agreeing with Vincent. “A new variety of groundnut may have very good resistance, but its pods may be too hard, making shelling very difficult. This does not help the poor people, because they can’t open the shells with their bare hands.”

And helping the poor of Africa is the real issue, Omari says. “We must remind ourselves of that.”

This means listening to the farmers: “It means finding out what they think and experience, and using that local knowledge. Only then should the genetics come in. We need to focus on the connections between local knowledge and scientific knowledge. This is vital.”

Participants at a farmer field day in Mali interact with ICRISAT staff and examine different groundnut varieties and books on aflatoxin control and management options.

Local knowledge and high-end genetics working together in Tanzania

Like Malawi, Tanzania has also experienced the full spectrum of constraints to groundnut production – from drought, aflatoxin contamination, poor soil and limited access to new seed, to a lack of government extension officers visiting farmers to ensure they have the knowledge and skills needed to improve their farming practices and productivity.

Although more than one million hectares of Tanzania is groundnut cropping land, the resources supplied by the government have until now been minimal, says Omari, compared to those received for traditional cash crops such as cashews and coffee.

A farmer and her children near Dodoma, Tanzania, an area where climate change is causing increasing heat and drought. Groundnut is an important crop for local famers, forming the basis of their livelihood together with maize and livestock.

“But the groundnut is now viewed differently by the government in my country as a result of GCP’s catalytic efforts,” Omari says. “More resources are being put into groundnut research.”

In the realm of infrastructure, for instance, the use of GCP funds to build a new irrigation system at Naliendele has since prompted Tanzania’s government to invest further in irrigation for breeder seed production.

“They saw it was impossible for us to irrigate our crops with only one borehole, for instance, so they injected new funds into our irrigation system. We now have two boreholes and a whole new system, which has helped expand the seed production flow. Without GCP, this probably wouldn’t have happened.”

Irrigation, for Omari, ultimately means being able to get varieties to the farmers much faster: “maybe three times as fast,” he says. “This means we’ll be able to speed up the multiplication of seeds – in the past we were relying on rainfed seed, which took longer to bulk and get to farmers.”

With such practical outcomes from GCP’s research and funding efforts and the new genetic resources becoming available, breeders like Omari see a bright future for groundnut research in Tanzania.

Groundnut farmer near Dodoma, Tanzania.

The gains being made at Naliendele are not only sustainable, Omari explains, but have given the researchers independence and autonomy. “Before we were only learning – now we have become experts in what we do.”

Prior to GCP, Omari and his colleagues were used to conventional breeding and lacked access to cutting-edge science.

“We used to depend on germplasm supplied to us by ICRISAT, but now we see the value in learning to use molecular markers in groundnut breeding to grow our own crosses, and we are rapidly advancing to a functional breeding programme in Tanzania.”

Omari says he and his team now look forward to the next phase of their research, when they expect to make impact by practically applying their knowledge to groundnut production in Tanzania.

Similar breeding success in Senegal

Harvesting groundnuts in Senegal.

Issa Faye became involved in GCP in 2008 when the programme partly funded his PhD in fresh seed dormancy in groundnuts. “I was an example of a young scientist who was trained and helped by GCP in groundnut research,” he says.

“I remember when I was just starting my thesis, my supervisor would say, ‘You are very lucky because you will not be limited to using conventional breeding. You are starting at a time when GCP funding is allowing us to use marker-assisted selection [MAS] in our breeding programme’.”

The importance of MAS in groundnut breeding, Issa says, cannot be overstated.

“It is very difficult to distinguish varieties of cultivated groundnut because most of them are morphologically very similar. But if you use molecular markers you can easily distinguish them and know the diversity of the matter you are using, which makes your programme more efficient. It makes it easier to develop varieties, compared to the conventional breeding programme we were using before we started working with GCP.”

By using markers that are known to be linked to useful genes for traits such as drought tolerance, disease resistance, or resistance to aflatoxin-producing fungi, breeders can test plant materials to see whether or not they are present. This helps them to select the best parent plants to use in their crosses, and accurately identify which of the progeny have inherited the gene or genes in question without having to grow them all to maturity, saving time and money.

These women in Salima District, Malawi, boil groundnuts at home and carry their tubs to the Siyasiya roadside market.

Senegal, like other developing countries, does not have enough of its own resources for funding research activities, explains Issa. “We can say we are quite lucky here because we have a well-developed and well-equipped lab, which is a good platform for doing molecular MAS. But we need to keep improving it if we want to be on the top. We need more human resources and more equipment for boosting all the breeding programmes in Senegal and across other regions of West Africa.”

Recently, Issa says, the Senegalese government has demonstrated awareness of the importance of supporting these activities. “We think that we will be receiving more funds from the government because they have seen that it’s a kind of investment. If you want to develop agriculture, you need to support research. Funding from the government will be more important in the coming years,” he says.

“Now that we have resources developed through GCP, we hope that some drought-tolerant varieties will come and will be very useful for farmers in Senegal and even for other countries in West Africa that are facing drought.”

It’s all about poverty

“The achievements of GCP in groundnut research are just the beginning,” says Vincent. The legacy of the new breeding material GCP has provided, he says, is that it is destined to form the basis of new and ongoing research programmes, putting research well ahead of where it would otherwise have been.

“There wasn’t time within the scope of GCP to develop finished varieties because that takes such a long time, but these products will come,” he says.

For Vincent, diverse partnerships facilitated by GCP have been essential for this to happen. “The groundnut work led by ICRISAT and collaborators in the target countries – Malawi, Senegal, and Tanzania – has been continuously moving forward.”

Groundnut harvesting at Chitedze Agriculture Research Station, Malawi.

Issa agrees: “It was fantastic to be involved in this programme. We know each other now and this will ease our collaborations. We hope to keep working with all the community, and that will obviously have a positive impact on our work.”

For Omari, a lack of such community and collaboration can only mean failure when it comes to addressing poverty.

“If we all worked in isolation, a lot of money would be spent developing new varieties but nothing would change on the ground,” he says. “Our work in Tanzania is all about the problem of poverty, and as scientists we want to make sure the new varieties are highly productive for the farmers around our area. This means we need to work closely with members of the agricultural industry, as a team.”

Omari says he and his colleagues see themselves as facilitators between the farmers of Tanzania and the ‘upstream end’ of science represented by ICRISAT and GCP. “We are responsible for bringing these two ends together and making the collaboration work,” he says.

Only from there can we come up with improved technologies that will really succeed at helping to reduce poverty in Africa.”

As climate change threatens to aggravate poverty more and more in the future, the highly nutritious, drought-tolerant groundnut may well be essential to sustain a rapidly expanding global population.

By developing new, robust varieties with improved adaptation to drought, GCP researchers are well on the way to increasing the productivity and profitability of the groundnut in some of the poorest regions of Africa, shifting the identity of the humble nut to potential crop champion for future generations.

Superior bean pods boost yields in face of drought

Africa, Beans, Capacity building, Crop breeding, Legumes No Responses »

Jun 192015

Bean Market in Kampala, Uganda.

Common beans are the world’s most important food legume, particularly for subsistence and smallholder farmers in East and Southern Africa. They are a crucial source of protein, are easy to grow, are very adaptable to different cropping systems, and mature quickly.

To some, beans are ‘a near-perfect food’ because of their high protein and fibre content plus their complex carbohydrates and other nutrients. One cup of beans provides at least half the recommended daily allowance of folate, or folic acid – a B vitamin that is especially important for pregnant women to prevent birth defects. One cup also supplies 25–30 percent of the daily requirement of iron, 25 percent of that of magnesium and copper, and 15 percent of the potassium and zinc requirement.

Unfortunately, yields in Africa are well below their potential – between 20 and 30 percent below. The main culprit is drought, which affects 70 percent of Africa’s major bean-producing regions. Drought is especially severe in the mid-altitudes of Ethiopia, Kenya, Malawi and Zimbabwe, as well as across Southern Africa.

“For the past seven or eight years, rains have been very unreliable in central and northern Malawi,” says Virginia Chisale, a bean breeder with Malawi’s Department of Agricultural Research and Technical Services.

“In the past, rains used to be very reliable and people were able to know the right time to plant to meet the rains in critical conditions,” she says. “Now these primary agriculture regions are either not receiving rain for long periods of time, or rains are not falling at the right time.”

Virginia recounts that during the 2011/12 cropping season there were no rains soon after planting, when it is important that beans receive moisture. Such instances can cut bean yields by half.

Steve Beebe in the field.

“Drought is a recurrent problem of rainfed agriculture throughout the world,” says Steve Beebe, a leading bean breeder with the International Center for Tropical Agriculture (CIAT). “Since over 80 percent of the world’s cultivated lands are rainfed, drought stress has major implications for global economy and trade.”

Steve was the Product Delivery Coordinator for the beans component of the Legumes Research Initiative (RI), part of Phase II of the CGIAR Generation Challenge Programme (GCP). The RI incorporated several projects, the biggest of which was Tropical Legumes I (TLI) (see box). The main objective of the work on beans within TLI was to identify and develop drought-tolerant varieties using marker-assisted breeding techniques. The resulting new varieties were then evaluated for their performance in Ethiopia, Kenya, Malawi and Zimbabwe.

“It’s vital that we develop high-yielding drought-tolerant varieties so as to help farmers, particularly in developing countries, adapt to drought and produce sustained yields for their families and local economies,” says Steve.

For an overview of the work on beans from the perspectives of four different partners, watch our video below, “The ABCs of bean breeding”.

What makes a plant drought tolerant?

The question of what makes a plant drought tolerant is one that breeders have debated for centuries. No single plant characteristic or trait can be fully responsible for protecting the plant from the stress of intense heat and reduced access to water.

“It’s a difficult question to answer for any plant, including beans,” says Steve. “Once you do isolate a trait genetically, it can often be difficult to identify this trait in a plant in the field, for example, identifying the architecture and length of a plant’s roots.”

Phenotyping is an important process in conventional plant breeding. It involves identifying and measuring the presence of physical traits such as seed colour, pod size, stem thickness or root length. Gathering data about a range of such characteristics across a number of different plant lines helps breeders decide which plants to use as parents in crosses and which of the progeny have inherited useful traits.

Root length has long been thought of as a drought-tolerance trait: the longer the root, the more chance it has of tapping into moisture stored deeper in the soil profile.

Given, however, that it is difficult to inspect root length in the field, researchers at CIAT have been exploring other more accessible drought-tolerance traits they can more easily identify and measure. One of these is measuring the weight of the plants’ seeds.

Comparison between varieties in trials of drought tolerant beans at CIAT’s headquarters in Colombia.

Fat beans indicate plants coping with drought stress

“We measure seed weight because we are discovering that under drought stress, drought-tolerant bean varieties will divert sugars from their leaves, stems and pods to their seed,” says Steve. “We call this trait ‘pod filling’, and for us it is the most important drought-tolerance trait to be found over the last several years.”

Finding bean plants with larger, heavier seeds when growing under drought conditions indicates that the plants are coping well, and means farmers’ yields are maintained.

As part of GCP’s Legumes RI, African partners like Virginia have been measuring the seed weight of several advanced breeding lines, which can be used as parents to develop new varieties. These breeding lines have been bred by CIAT and demonstrate this pod-filling process and consequent tolerance of drought.

Although this measurement is relatively cheap and easy for breeders all over the world to do, Steve and his team are interested in finding an even more efficient way to spot plants that maintain full pods under drought.

“We are trying to understand which genes control this trait so we can use molecular-assisted breeding techniques to determine when the trait is present,” says Steve. Having identified several regions of genes related to pod filling, he and his team have developed molecular markers to help breeders identify which plants have these desired genes. “The use of molecular markers in selection significantly reduces the time and cost of the breeding process, making it more efficient. This means that we get improved varieties out to farmers more quickly.”

Bean farmer in Rwanda.

Molecular markers (also known as DNA markers) are used by researchers as ‘flags’ to identify particular genes within a plant’s genome (DNA) that control desired traits, such as drought tolerance. These markers are themselves fragments of DNA that highlight particular genes or regions of genes by binding near them.

To use an analogy, think of a story as the plant’s genome: its words are the plant’s genes, and a molecular marker works like a text highlighter. Molecular markers are not precise enough to highlight specific words (genes), but they can highlight sentences (genomic regions) that contain these words (genes), making it easier and quicker to identify whether or not they are present.

Beans from Rwanda.

Plant breeders can use molecular markers from early on in the breeding process to choose parents for their crosses and determine whether progeny they have produced have the desired trait, based on testing only a small amount of seed or seedling tissue.

“If the genes are present, we grow the progeny and conduct the appropriate phenotyping; if not, we throw the progeny away,” explains Steve. “This saves us resources and time because we need to grow and phenotype only the few hundred progeny which we know have the desired genes, instead of a few thousand progeny, most of which would not possess the gene.”

GCP has supported this foundation work, building on the extensive bean research already done by CIAT dating back to the 1970s, to develop molecular markers not only for drought-tolerance traits such as pod filling, but also for traits associated with resistance to important insect and disease menaces.

“Under drought conditions, plants become more susceptible to pests and diseases, so it was important that we also try to identify and include resistance traits in the drought-tolerant progeny,” says Steve.

Drought is but one plant stressor – diseases and pests wreak havoc too

Common bacterial blight on bean.

The bean diseases that farmers in Ethiopia, Kenya, Malawi and Zimbabwe continually confront are angular leaf spot, bean common mosaic virus, common bacterial blight and rust. Key insect pests are bean stem maggot and aphids.

“We’ve had reports of bean stem maggot and bean common mosaic virus wiping out a whole field of beans,” says Virginia. “Although angular leaf spot and common bacterial blight are not as damaging, they can still reduce yields by over 50 percent.”

Virginia says this is devastating for farmers in Malawi, many of whom only have enough land and money to grow beans to feed their families and sell what little excess there is at market to purchase other necessities.

“This is why we are excited by the prospect of developing not just drought-tolerant varieties, but drought-tolerant varieties with disease and pest resistance as well,” says Virginia.

Virginia’s team in Malawi – along with other breeders in Ethiopia, Kenya and Zimbabwe – are currently using over 200 Mesoamerican and Andean bean breeding lines supplied by CIAT to help breed for drought tolerance and disease and pest resistance. Although many do not yet have the capacity to do molecular breeding in their countries, thanks to advances in plant science it is becoming more feasible and cheaper to outsource molecular breeding stages of the process (see box above).

“With help from GCP and CIAT, we have successfully crossed a line from CIAT with some local varieties to produce plants that are high yielding and resistant to most common bean diseases,” Virginia says.

Malawian farmer Jinny Lemson grows beans to feed her livestock.

Ethiopia’s new bean breeders

Young women sorting beans after a harvest in Ethiopia.

One man who has been helping build this new breeding capacity is Bodo Raatz, a molecular geneticist who joined CIAT and GCP’s Legumes RI in late 2011.

“We’ve [CIAT] hosted several African PhD students here in Colombia and have conducted several workshops in Colombia and Africa too,” says Bodo.

“At the workshops we teach local breeders and technicians how to use genetic tools and markers for advanced breeding methods, phenotyping and data management. The more people there are who can do this work, the quicker new varieties will filter through to farmers.”

Bodo says he has found delivering the training both personally and professionally rewarding, especially “seeing the participants understand the concepts and start using the tools and techniques to develop new lines [of bean varieties] and contribute to the project.”

One national breeder whom Bodo has seen advance from the training is Daniel Ambachew, then a bean breeder at the Southern Agricultural Research Institute (SARI) in Ethiopia.

Daniel started as a GCP-funded Master’s student enrolled at Haramaya University, Ethiopia, evaluating bean varieties with both tolerance to drought and resistance to bean stem maggot. He eventually became the Ethiopian project leader for beans within GCP’s Legumes RI.

“Daniel is currently one of only a handful of bean breeders in Ethiopia who are using molecular-assisted breeding techniques to breed new varieties,” says Bodo. “It’s quite an achievement, especially now that he has taken on the lead role in Ethiopia.”

Buying and selling at a bean market in Kampala, Uganda.

For Daniel, learning about and using the new molecular-breeding techniques has been an exciting new challenge. “The most interesting part of the technology is that it helps us understand what is going on in the plant at a molecular level and lets us know if the crosses we are making are successful and the genes we want are present,” says Daniel. “All this helps improve our efficiency and speeds up the time it takes us to breed and release new varieties for farmers.”

By the end of 2014, Daniel and his team had finished the third year of trials and had several drought-tolerant lines ready for national trials in 2015 and eventual release in 2016.

Between 2012 and 2014, Daniel, and two other breeders from SARI, attended GCP’s three-year Integrated Breeding Multiyear Course, learning how to design molecular-assisted breeding trials; collect, analyse and interpret genotypic and phenotypic data from the trials; and manage data using the GCP’s Integrated Breeding Platform (IBP), particularly its Breeding Management System (BMS).

“The IBP is a really fantastic tool,” says Daniel. “During the course we learnt about the importance of recording clear and consistent phenotypic data, and the IBP helps us to do this as well as store it in a database. It makes it easier to refer to and learn from the past. I’m now trying to pass on the knowledge I’ve learnt as well as create and implement a data-management policy for all plant breeders and technicians in our institute.”

Bodo agrees with Daniel about the importance of IBP and believes it will be a true legacy of GCP beyond the Programme’s end in 2014. “The Platform has been designed to be the main data-management platform for plant breeders. It allows breeders to talk the same language and will reduce the need for learning new systems.”

Daniel says the challenge for his institute now is to build further capacity among staff – and to retain it. “At the moment we only have two bean breeders,” says Daniel. “It’s hard to retain research staff in Ethiopia as salaries are very low, so people move on to new, higher paying positions when they get the chance. It’s not unique to Ethiopia, but true of all Africa.”

Bean trials at KALRO in Kenya.

Kenya chasing higher bean yields

Across the border, Kenya has also been facing staffing issues.

“We are behind Ethiopia, Malawi and Zimbabwe in terms of our capacity and our trials,” says David Karanja, a bean breeder and project leader at the Kenya Agricultural and Livestock Research Organisation (KALRO, formerly the Kenya Agricultural Research Institute, or KARI). “At the start of the project, we didn’t have a breeder to lead the project for almost two years. However, we are now rapidly catching up with the others.”

And it’s a good thing too, as the country is in need of higher yielding beans to accommodate its population’s insatiable appetite for the crop. Out of the four target African countries, Kenya is the largest bean producer and consumer. As such, the country relies on beans imports from Ethiopia, Malawi, Tanzania and Uganda.

“A lot of families eat beans every day,” says David. “On average, the population eats 14–16 kilograms per person each year, but in western Kenya the average is over 60 kilograms.”

Githeri, a Kenyan staple food made with maize and beans.

Kenyans consume an average total of 400,000 tonnes of beans each year, consistently more than the country produces. Projected trends in population growth indicate that this demand for beans will continue to increase by three to four percent annually.

Even though the area planted to beans has been increasing, David says farmers and breeders need to work together to improve productivity, which is well below where it should be. “The national average yield is 100 kilograms per hectare, which can range from 50 kilograms up to 700 kilograms, depending on whether we experience a drought, or a pest or disease epidemic,” explains David. “The minimum target we should be aiming for is 1,200 kilograms per hectare.”

Such a figure may seem impossible, but David believes that new breeding techniques and the varieties KALRO are producing with the help of CIAT are providing hope that farmers can reach these lofty goals.

“We have several bean lines that are showing good potential to produce higher yields under drought conditions and also have resistance to diseases like rust and mosaic virus,” says David. “They are currently under national trials, and we are confident these will be released to farmers in 2015.”

Varieties fare differently in KALRO bean trials in Kenya.

Commercialising beans

Maturing bean pods.

“Many subsistence farmers have limited access to good quality bean seeds; they lack knowledge of good crop, pest and disease management; and they have poor post-harvest storage facilities,” says Godwill Makunde, who was previously a breeder at Zimbabwe’s Crop Breeding Institute (CBI) and leader of GCP’s Legumes RI bean project in Zimbabwe.

TLI’s sister project, Tropical Legumes II (TLII, see box above), led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), provided the route by which the upstream work of TLI would have impact in helping these farmers, seeking to deliver the new varieties developed under TLI into their hands. As part of TLII, Godwill, his successor Bruce Mutari, and other African partners worked on developing sustainable seed systems.

“Because beans are self-pollinating, which means each crop is capable of producing seed exactly as it was sown, farmers tend to propagate seed on farm,” says Godwill. “While this can be cost effective, it can reduce farmers’ access to higher yielding, tolerant lines, like the ones we are currently producing.”

In none of the partner countries of TLI and TLII are there formal systems for producing and disseminating bean seeds. Godwill and other partners are working with seed companies on developing a sustainable model where both farmers and seed companies can benefit.

Success built on a solid foundation

Field workers tend beans in Rwanda.

A key to the success of the beans component of GCP’s Legumes RI, according to Ndeye Ndack Diop, GCP’s Capacity Building Theme Leader and TLI Project Manager, has been partners’ existing relationships with each other.

“Many of the partners are part of a very strong network of bean breeders: the Bean Coordinated Agricultural Project [BeanCAP],” explains Ndeye Ndack, adding that the TLI and BeanCAP networks benefited each other.

BeanCAP released more than 1,500 molecular markers to TLI researchers, which have helped broaden the genetic tools available to developing-country bean breeders.

TLI was also able to leverage and advance previous BeanCAP work and networks. For example, it was through this collaboration that GCP was introduced to LGC Genomics, a company it then worked with on many other crop projects.

To sustain integrated breeding practices beyond the Programme’s close in 2014, GCP established Communities of Practice (CoPs) that are discipline- and commodity-oriented.

“GCP’s CoP for beans has also helped to broaden both the TLI and BeanCAP networks too,” says Ndeye Ndack. “The ultimate goal of the CoPs is to provide a platform for community problem solving, idea generation and information sharing.”

Developing physical capacity

Besides developing human capacity, GCP has also invested in developing infrastructure in Ethiopia, Kenya and Zimbabwe.

SARI now has an irrigation system to enable them to conduct drought trials year round. “We have 12.5 hectares of irrigation now, which we use to increase our efficiency and secure our research,” says Daniel. “We can also increase seed with this irrigation during the off-season and develop early generation seeds for seed producers.”

In Zimbabwe, CBI received specialised equipment that enables them to extract DNA and send it for genotyping in the UK.

Both SARI and CBI also received automatic weather stations from GCP for high-precision climatic data capture, with automated data loading and sharing with other partners in the network.

Delivering the right beans to farmers

Back in Malawi, Virginia says another important facet of the TLII project is that researchers understand what qualities farmers want in their beans. “It’s no use developing higher yielding beans if the farmer doesn’t like the colour, or they don’t taste nice,” she says. “For example, consumers in central Malawi prefer khaki or ‘sugar beans’, which are tan with brown, black or red speckles. While those in southern Malawi tend to prefer red beans. Farmers know this and will grow beans that they know consumers will want.”

Diversity at bean market in Masaka, Uganda.

Breeders in all four countries have been conducting workshops and small trials with farmers to find out this information. In Kenya, David finds farmer participation a great way to promote the work they are doing and show the impact the new drought-tolerant and disease-resistant lines can have.

“Farmers are excited and want to grow these varieties immediately when they see for themselves the difference in yield these new varieties can produce compared to their regular varieties,” says David. “They understand the pressure on them to produce more yields and are grateful that these varieties are becoming more readily available as well as tailored to their needs.”

For Steve, such anecdotes provide him and his collaborators with incentives to continue their quest to discover more molecular markers associated with drought tolerance, post-GCP.

“It’s a testament to everyone involved that we have been able to develop these advanced lines with pod-filling traits using molecular techniques, and make them available to farmers in six years instead of ten,” says Steve.

Cowpea research helps secure food supply during the ‘hungry months’ in Africa

Africa, Capacity building, Cowpeas, Crop breeding, Genetics, Genomics, Legumes No Responses »

Jun 122015

Growing cowpea pods.

Each year, millions of people in Senegal go hungry for several months, many surviving on no more than one meal a day. Locals call this time soudure – the hungry period. It typically lasts from June through to September, when previous winter and spring cereal supplies are exhausted and people wait anxiously for a bountiful autumn cereal harvest.

During this period, a bowl of fresh green cowpea pods once a day is the best that many people can hope for. Cowpeas are the first summer crop to mature, with some varieties ready to harvest in as little as 60 days.

While cowpeas provide valued food security in Africa, yields remain low. In Senegal, average cowpea yields are 450 kilograms per hectare, a mere 10–30 percent of their potential. This poor productivity is primarily because of losses due to insects and diseases, but is sometimes further compounded by chronic drought.

In 2007, the CGIAR Generation Challenge Programme (GCP) brought together a team of plant breeders and geneticists from Burkina Faso, Mozambique, Nigeria, Senegal and the USA to collaborate on cowpea. Their goal was to breed varieties that would be higher yielding, drought tolerant and resistant to pests and diseases, and so help secure and improve local cowpea production in sub-Saharan African countries.

A trader selling cowpea at Bodija market, Ibadan, Nigeria.

Cowpea production – almost all of it comes from Africa

A type of legume originating in West Africa, cowpeas are also known as niébé in francophone Africa and as black-eyed peas in the USA. They are well adapted to drier, warmer regions and grow well in poor soils. In Africa, they are mostly grown in the hot, drought-prone savannas and very arid sub-Saharan regions, often together with pearl millet and sorghum.

Nutritionally, cowpeas are a major source of dietary protein in many developing countries. Young leaves, unripe pods and peas are used as vegetables, and the mature grain is processed for various snacks and main meal dishes. As a cash crop, both for grain and animal fodder, cowpea is highly valued in sub-Saharan Africa.

Worldwide, an estimated 14.5 million hectares of land is planted with cowpea each year. Global production of dried cowpeas in 2010 was 5.5 million tonnes, 94 percent of which was grown in Africa.

“In Senegal, cowpeas cover more than 200,000 hectares,” says Ndiaga Cissé, cowpea breeder at L’institut sénégalais de recherches agricoles (ISRA; Senegalese Agricultural Research Institute). “This makes it the second most grown legume in Senegal, after groundnuts.”

In 2011, Senegal experienced its third drought within a decade. Low and erratic rainfall led to poor harvests in 2011 and 2012: yields of cereal crops (wheat, barley and maize) fell by 36 percent compared to 2010. Consequently, the hungry period in 2012 started three months earlier than usual, making gap-fillers like cowpea even more important. In fact, cereal production in sub-Saharan African countries has not seen substantial growth over the last two decades – total area, yield and production grew by only 4.3 percent, 1.5 percent and 5.8 percent, respectively.

Climate change is expected to further compound this situation across sub-Saharan Africa. Droughts are forecast to occur more frequently, weakening plants and making them more vulnerable to pests and diseases.

“Improved varieties of cowpeas are urgently needed to narrow the gap between actual and potential yields,” says Ndiaga. “They will not only provide security to farmers in the face of climate change, but will also help with food security and overall livelihoods.”

Farmers in Northern Nigeria transport their cowpea harvest.

Mapping the cowpea genome

For over 30 years, Phil Roberts, a professor in the Department of Nematology at the University of California, Riverside (UCR), has been breeding new varieties of cowpea. “UCR has a long history of research in cowpea breeding that goes back to the mid-seventies,” explains Phil. “One of the reasons we were commissioned by GCP in 2007 was to use our experience, particularly in using molecular breeding, to help African cowpea-breeding programmes produce higher yielding cowpeas.”

For seven years, Phil and his team at UCR coordinated the cowpea component of the Tropical Legumes I (TLI) project led by GCP (see box below). The objective of this work was to advance cowpea breeding by applying modern, molecular breeding techniques, tools and knowledge to develop lines and varieties with drought tolerance and resistance to pests and diseases in the sub-Saharan African countries Burkina Faso, Mozambique, Nigeria and Senegal.

The molecular breeding technology that UCR uses for cowpeas is based on finding genes that help cowpea plants tolerate insects and diseases, identifying markers that can indicate the presence of known genes, and using these to incorporate valuable genes into higher yielding varieties.

“Using molecular breeding techniques is a lot easier and quicker, and certainly less hit-or-miss, than conventional breeding techniques,” says Phil. “We can shorten the time needed to breed better adapted cowpea varieties preferred by farmers and markets.”

Phil explains that the first priority of the project was to map the cowpea genome.

“The map helps us locate the genes that play a role in expressing key traits such as drought tolerance, disease resistance or pest resistance,” says Phil. “Once we know where these genes are, we can use molecular marker tools to identify and help select for the traits. This is a lot quicker than growing the plant and observing if the trait is present or not.”

To use an analogy, think of the plant’s genome as a story: its words are the plant’s genes, and a molecular marker works as a text highlighter. Molecular markers are not precise enough to highlight specific words (genes), but they can highlight sentences (genomic regions) that contain these words (genes), making it easier and quicker to identify which plants have them. Traditionally, breeders have needed to grow plants to maturity under appropriately challenging conditions to see which ones are likely to have useful traits, but by using markers to flag valuable genes they are able to largely skip this step, and test large amounts of material to choose the best parents for their crosses, then check which of the progeny have inherited the gene or genes.

Diversity of cowpea seed.

Breeding new varieties faster, using modern techniques

A farmer pleased with her cowpea plants.

The main focus of the cowpea component in TLI was to optimise marker-assisted recurrent selection (MARS) and marker-assisted backcrossing (MABC) breeding techniques for sub-Saharan African environments and relevant traits.

MARS identifies regions of the genome that control important traits. In the case of cowpeas, these include drought tolerance and insect resistance. It uses molecular markers to explore more combinations in the plant populations, thus increasing breeding efficiency.

MABC is the simplest form of marker-assisted breeding, in which the goal is to incorporate a major gene from an agronomically inferior source (the donor parent) into an elite cultivar or breeding line (the recurrent parent). Major genes by themselves have a significant effect; it’s therefore easier to find a major gene associated with a desired trait, than having to find and clone several minor genes. The aim is to produce a line made up almost entirely of the recurrent parent genotype, with only the selected major gene from the donor parent.

Using the genome map and molecular markers, the UCR team identified 30 cowpea lines with drought tolerance and pest resistance from 5,000 varieties in its collection, providing the raw material for marker-assisted breeding. “Once we knew which lines had the drought-tolerance and pest-resistance genes we were looking for, we crossed them with high-yielding lines to develop 20 advanced cowpea lines, which our African partners field tested,” says Phil.

The lines underwent final field tests in 2014, and the best-yielding drought-tolerant lines will be used locally in Burkina Faso, Mozambique and Senegal to develop new higher yielding varieties that will be available to growers by 2016.

“While we are still some time off from releasing these varieties, we already feel we are two or three years ahead of where we would be if we were doing things using only conventional breeding methods,” says Ndiaga.

A parasitic Striga plant, in a cowpea experimental plot.

The genome map and molecular markers have helped cowpea breeders like Ousmane Boukar, cowpea breeder and Kano Station Representative with the International Institute of Tropical Agriculture (IITA), headquartered in Nigeria, to locate the genes in cowpeas that play a role in expressing desirable traits.

Ousmane, who was GCP’s cowpea Product Delivery Coordinator, says, “We have used this technology to develop advanced breeding lines that are producing higher yields in drier conditions and displaying resistance to several pests and diseases like thrips and Striga. We expect these lines to be available to plant breeders by the end of 2015.

“TLI has had a huge impact in Africa in terms of developing capacity to carry out marker-assisted breeding,” he says. “This form of breeding helps us to breed new varieties in three to five years instead of seven to ten years.”

Burkina Faso – evaluating new lines to improve the country’s economy

Cowpea is an important crop for the people of Burkina Faso. Over 10 million farmers produce on average 800,000 tonnes of cowpeas each year, making the country the third largest producer in the world, behind neighbours Nigeria and Niger.

Much of Burkina Faso’s cowpea crop is consumed domestically, but the government sees potential in increasing productivity for export to Côte d’Ivoire and Ghana in the south. This new venture would improve the country’s gross domestic product (GDP), which is the third lowest in the world.

“The government is very interested in our research to improve cowpea yields and secure them against drought and disease,” says Issa Drabo, lead cowpea breeder with the Institut de l’Environnement et de Recherches Agricoles (INERA) in Burkina Faso.

“We’ve been working closely with UCR to evaluate advanced breeding lines that we can use in our own breeding programme. So far we have several promising lines, some of which breeders are using to create varieties for release to farmers – some as early as this year.”

Farmers in Burkina Faso discuss cowpea varieties during participatory varietal selection activities.

Outsourcing the molecular work

Issa says his team has mainly been using conventional breeding techniques and outsourcing the molecular breeding work to the UK and USA. “We send leaf samples to the UK to be genotyped by a private company [LGC Genomics], who then forward the data to UCR, who analyse it and tell us which plants contain the desired genes and would be suitable for crossing.”

The whole process takes four to six weeks, from taking the samples to making a decision on which plants to cross.

“This system works well for countries that don’t have the capacity or know-how to do the molecular work,” says Darshna Vyas, a plant genetics specialist with LGC Genomics. “Genotyping has advanced to a point where even larger labs around the world choose to outsource their genotyping work, as it is cheaper and quicker than if they were to equip their lab and do it themselves. We do hundreds of thousands of genotyping samples a day – day in, day out. It’s our business.”

Darshna says LGC Genomics have also developed plant kits, as a result of working more with GCP partners from developing countries. “We would receive plant tissue that was not properly packaged and had become mouldy on the journey. The plant kits help researchers package their tissue correctly. The genotyping data you get from undamaged tissue compared to damaged tissue is a thousand times better.”

Getting the genotyping expertise on the ground

A trader bagging cowpeas at Bodija market, Ibadan, Nigeria.

To reduce their African partners’ reliance on UCR, researchers from the university, including Phil, have been training young plant breeders and PhD students from collaborating institutes. Independent of the cowpea project, they have also been joining GCP’s Integrated Breeding Platform (IBP) training events in Africa to help breeders understand the new technologies.

“All this capacity building we do really gets at the issue of leaving expertise on the ground when the project ends,” says Phil. “If these breeders don’t have the expertise to use the modern breeding technologies, then we won’t make much progress.”

GCP Capacity Building Theme Leader and TLI Project Manager Ndeye Ndack Diop has been impressed by UCR’s enthusiasm to build capacity in its partner countries. “Capacity building is a core objective for GCP and the TLI project,” says Ndeye Ndack. “While it is built into almost all GCP projects, UCR have gone over and above what was expected of them and contributed towards building capacity not only among its partner institutions, but in many other African national breeding institutes as well.”

Issa Drabo reports that in 2014 two of his young researchers from Burkina Faso completed their training in GCP’s Integrated Breeding Multiyear Course, conducted by UCR and the IBP team.

One of Issa’s researchers at INERA, Jean-Baptiste de la Salle Tignegré, says the course helped him understand more about the background genetics, statistical analysis and data management involved in the process of molecular breeding. “Because of the course, we are now able to analyse the genotype data from LGC,” he says.

Mozambique – insects and drought are the problem

In 2010, the Universidade Eduardo Mondlane (UEM) joined the cowpea component of TLI, three years after the project started. “We were a little late to the party because we were busy setting up Mozambique’s first cowpea breeding programme, which only began in 2008,” recalls Rogerio Chiulele, a lecturer at the university’s Faculty of Agronomy and Forestry Engineering and lead scientist for cowpea research in Mozambique for TLI.

That year (2008), UEM received a GCP Capacity building à la carte grant to establish a cowpea-breeding programme for addressing some of the constraints limiting cowpea production and productivity, particularly drought, pests and diseases.

As in Burkina Faso and Senegal, in Mozambique cowpeas are an important source of food, for both protein and profit, particularly for the poor. Cowpeas rank as the fourth most cultivated crop in Mozambique, accounting for about nine percent of the total cultivated area, or an estimated four million hectares of smallholder farms.

Cowpea plants infested by aphids.

Rogerio says that farmers in his country, just as in other parts of Africa, struggle to reach their full yield potential because of climate, pests and diseases. “Several insect pests – such as aphids, flower thrips, nematodes and pod-sucking pests – can substantially reduce cowpea yield and productivity in Mozambique,” he says.

“Cowpea aphids can cause problems at any time in the growing season, but are most damaging during dry weather when they infest seedlings that are stressed from lack of water. In wetter parts of the country, flower thrips – which feed on floral buds – are the most damaging insect pest.” These insects are also major pests in Burkina Faso and Senegal, along with hairy caterpillar (Amsacta moloneyi), which can completely destroy swaths of cowpea seedlings.

Rogerio says breeding for insect resistance and drought tolerance, using marker-assisted techniques, improves breeders’ chances of increased cowpea productivity. “Productivity is key to increasing rural incomes, and new resources can then be invested in other activities that help boost total family income,” says Rogerio. “These new breeding techniques will help us achieve this quicker.”

Three high-yielding varieties to hit the Mozambique market in 2015

Mature cowpea pods ready for harvesting.

Since 2010, Rogerio’s team have quickly caught up to Burkina Faso and Senegal and plan to release three higher yielding new lines with drought tolerance in 2015. One of these lines, CB46, is based on a local cowpea variety crossed with a UCR-sourced American black-eyed pea variety that displays drought tolerance, which potentially has huge market appeal.

“Local varieties fetch, on average, half a US dollar per kilogram, compared to black-eyed pea varieties, whose price is in the region of four to five US dollars,” says Rogerio. “Obviously this is beneficial to the growers, but the benefits for consumers are just as appealing. The peas are better quality and tastier, and they take half as long to cook compared to local varieties.”

All these extra qualities are important to consider in any breeding programme and are a key objective of the Tropical Legume II (TLII) project (see box above). TLII activities, led by ICRISAT, seek to apply products from TLI to make an impact among farmers.

“TLII focuses on translating research outputs from TLI into tangible products, including new varieties,” says Ousmane Boukar, who works closely with Ndiaga, Issa and Rogerio in TLI and TLII.

Building a community of breeders to sustain success

Cowpea flower with developing pods.

Part of Ousmane’s GCP role as Product Delivery Coordinator for cowpeas was to lead a network of African cowpea and soybean breeders, and he champions the need for breeders to share information and materials as well as collaborating in other ways so as to sustain their breeding programmes post-GCP.

“To sustain integrated breeding practices post-2014, GCP has established Communities of Practice (CoP) that are discipline- and commodity-oriented,” says Ndeye Ndack. “The ultimate goal is to provide a platform for community problem solving, idea generation and information sharing.”

Ousmane says the core of this community was already alive and well before the CoP. “Ndiaga, Issa and I have over 80 years combined experience working on cowpea. We have continually crossed paths and have even been working together on other non-GCP projects over the past seven years.”

One such project the trio worked together on was to release a new drought-tolerant cowpea breeding line, IT97K-499-35, in Nigeria. “The performance of this variety impressed farmers in Mali, who named it jiffigui, which means ‘hope’,” says Ousmane. “We shared these new lines with our partners in Mali and Niger so they could conduct adaptation trials in their own countries.”

For young breeders like Rogerio, the CoP has provided an opportunity to meet and learn from these older partners. “I’ve really enjoyed our annual project meetings and feeling more a part of the world of cowpea breeding, particularly since we in Mozambique are isolated geographically from larger cowpea-producing countries in West Africa.”

For Phil Roberts, instances where more-established researchers mentor younger researchers in different countries give him hope that all the work UCR has done to install new breeding techniques will pay off. “Young researchers represent the future. If they can establish a foothold in breeding programmes in their national programmes, they can make an impact. Beyond having the know-how, it is vital to have the support of the national programme to develop modern breeding effort in cowpea – or any crop.”

Setting up breeders for the next 20 years

Farmer harvesting mature cowpea pods.

In Senegal, Ndiaga is hopeful that the work that the GCP project has accomplished has set up cowpea breeders in his country and others for the next 20 years.

“Both GCP’s and UCR’s commitment to build capacity in developing countries like Senegal cannot be valued less than the new higher yielding, drought-tolerant varieties that we are breeding,” says Ndiaga. “They have provided us with the tools and skills now to continue this research well into the future.

“We are close to releasing several new drought-tolerant and pest- and disease-resistant lines, which is our ultimate goal towards securing Senegal’s food and helping minimise the impact of the hungry period.”

Sweetpotato: lifesaver that gets a genetic lifeline

Africa, Capacity building, Genetics, Genomics, Latin America, Phase I crops, Sweetpotatoes No Responses »

Jun 052015

Farmer Maria Mtele holds recently harvested orange-fleshed sweetpotatoes in a field in Mwasonge, Tanzania.

Sweetpotato has a long history as a lifesaver. The Japanese used it when typhoons demolished their rice fields. It kept millions from starvation in famine-plagued China in the early 1960s and came to the rescue in Uganda in the 1990s, when a virus ravaged the cassava crop.

In sub-Saharan Africa, sweetpotato is proving crucial in the fight against blindness, disease and premature death among children under five. And, as agriculture becomes more market-oriented across the continent, sweetpotato has some significant advantages: it requires fewer inputs and less labour than other crops such as maize, tolerates marginal growing areas and can mature within four months.

On these fertile grounds, researchers across the globe are not underestimating the importance of sweetpotato as a staple crop.

“Yields achieved by resource-poor farmers in sub-Saharan Africa are typically low,” says Roland Schafleitner of the International Potato Center (CIP), based in Peru.

“Improved and well-adapted sweetpotato varieties with increased tolerance to drought, pests and diseases will have a positive impact on food and income security in sub-Saharan Africa and can significantly contribute to increasing productivity,” he says.

Roland was Principal Investigator of two research projects funded by the CGIAR Generation Challenge Programme (GCP), which developed genetic and genomic resources for breeding improved sweetpotato.

At the outset of the work, Roland says: “Breeding efforts were limited by the crop’s genetic complexity and the lack of information available about its genetic resources.

“It was clear that if we could develop genetic tools and make concerted efforts towards understanding the gene pool of sweetpotato, the breeding potential of the crop would improve.”

Farmer Mwanaidi Rhamdani at work in an orange-fleshed sweetpotato field in Mwasonge, Tanzania.

Sub-Saharan Africans getting their vitamin A from sweetpotato

Sweetpotato diversity.

Malnutrition does not always mean a simple lack of calories; research suggests that nutrient shortfalls are an even bigger killer. Vitamin A deficiency is a leading cause of blindness, infectious disease and premature death among children under five and pregnant women in sub-Saharan Africa and Asia.

Sweetpotato comes in a wide range of colours. Varieties with dark orange flesh are naturally very rich in the pigment beta-carotene, which the body converts into vitamin A. However, the sweetpotatoes traditionally grown in Africa are pale-fleshed and low in beta-carotene. African consumers were not used to eating colourful sweetpotato – and these orange-fleshed varieties were in any case not well adapted African growing conditions.

Recent years have therefore seen a collaborative effort by researchers across the world to breed orange-fleshed sweetpotato varieties fortified with high levels of beta-carotene, and even enriched with other nutrients, that have also been crossed with local varieties and so are adapted to local conditions and tastes. A crucial part of these efforts has also been to create public awareness and encourage people to grow, eat and buy these new varieties.

Two cheeky young chappies from Mozambique enjoy the sweet taste of orange-fleshed sweetpotato rich in beta-carotene, or pro-vitamin A.

All of this adds to the growing momentum behind sweetpotato. The growing awareness of sweetpotato’s potential nutritional benefits for the poor and food insecure, as well as its value for subsistence farmers as a reliable crop that withstands drought and requires minimal inputs, mean that it is growing in significance.

Orange-fleshed sweetpotato can be used to make a variety of tasty products from doughnuts to chapati.

More than 95% of the world’s sweetpotato crop is grown in developing countries, where it is the fifth most important staple food crop. It is particularly important in many African countries: Madagascar in Southern Africa; Nigeria in West Africa; and those surrounding the Great Lakes in East and Central Africa – Uganda, Malawi, Angola and Mozambique.

According to 2013 figures from the Food and Agriculture Organization of the United Nations, 3.6 million hectares of sweetpotato were harvested in Africa. While the average global yield of sweetpotato per hectare was 14.8 tonnes, across all East African countries in 2013 it was only half this, at 7.1 tonnes per hectare. In West African nations the average yield was even worse, at 3.7 tonnes per hectare.

Farmers are unable to make the most of their crops because the varieties available to them, including traditional varieties (or landraces) have low resistance to viral diseases and insect pests, and poor tolerance to drought. It is therefore crucial that when developing new varieties breeders are able to efficiently incorporate pest and disease resistance and drought tolerance traits.

New DNA markers identified for sweetpotato disease

The sweetpotato virus disease (SPVD) is the most serious disease affecting sweetpotato in sub-Saharan Africa. It often causes serious yield losses of up to 80–90 percent.

The disease is the result of joint infection by two viruses: the sweetpotato feathery mottle virus and the sweetpotato chlorotic stunt virus. Of the two, the stunt virus is the more problematic.

Wolfgang Grüneberg, also from CIP, says that, in the years 2006–2008, 52 new DNA markers were developed as part of GCP-funded research to improve marker-assisted selection for resistance to the disease.

“The results,” says Wolfgang, Principal Investigator for the research, “looked promising for developing a large number of orange-fleshed sweetpotatoes with resistance to SPVD.”

Immediately following the development of the markers, two varieties of sweetpotato were developed using a cloned gene, Resistan, known to confer resistance to the virus. The first variety was used to improve an SPVD test system so that the disease could be diagnosed earlier if a crop was affected. The second variety underwent field tests in regions in Uganda that were highly affected by the disease.

Sweetpotato vines and roots.

Mobilising the genetic diversity of sweetpotato for breeding

The goals of the GCP-supported work were to develop a diverse genetic resource base for sweetpotato and stimulate the use of new tools in ongoing breeding programmes.

To help transfer this work from high-end laboratories to resource-poor research labs in developing countries, GCP promoted collaboration across institutions and borders. Researchers from Brazil, Mozambique, Uganda and Uruguay worked together on sweetpotato genetic research projects.

As Roland explains, the basic first steps needed to begin to ‘mobilise’ the genetic diversity of sweetpotato were developing a reference set of varieties and improving genomics tools to work with polyploid crops, i.e. those possessing multiple sets of chromosomes, such as sweetpotato.

GCP-supported researchers in Peru and sub-Saharan Africa defined a reference set of 472 varieties of sweetpotato, carefully selected and honed to represent both the diversity of the crop and its most important agronomical and nutritional traits.

“Based on a reference set, genetic markers can be developed that are associated with important characteristics of the crop and can help breeders to select favourable genotypes,” says Roland.

The gene sequences developed during the Programme are now available as a Sweetpotato Gene Index.

“Based on these sequences,” says Roland, “molecular markers have been designed that can help breeders and gene-bank curators to assess the genetic diversity of their accessions and to perform genetic mapping studies.

“Today, techniques that yield a much larger number of markers for genetic studies and selection are accessible for sweetpotato,” he says.

Mwanaidi Rhamdani (left) works with Maria Mtele in an orange-fleshed sweetpotato field in rural Tanzania.

The genetic lifelines reach Africa

Sweetpotato is one of the most important staple crops in Mozambique, ranking in third position after cassava and maize. The areas harvested in Mozambique in 2013 were 1.7 million hectares of maize, 780,000 hectares of cassava and 120,000 hectares of sweetpotato.

A child eats cooked orange-fleshed sweetpotato in Uganda.

GCP funded breeders in Mozambique and Uganda to learn how to identify genetic markers that would prove useful for future sweetpotato breeding.

“Our African partners visited us at CIP and helped us complete the work on identifying markers,” recalls Roland. “This provided the opportunity for direct ‘technology transfer’ to breeders in the target region.”

The collaboration had, for the first time, created a critical amount of genetic and genomics resources for sweetpotato. The resulting Sweetpotato Gene Index and the new markers were published in a peer-reviewed journal, BMC Genomics (2010) 11:604.

The new genetic resources are in use at CIP in Peru and in breeding programmes in Burkina Faso, Mozambique, Uganda, Uruguay and the USA for the assessment of the genetic diversity of germplasm collections.

“The markers have been used for diversity analysis, especially at the CIP gene bank, and also in Africa,” says Roland, who says the markers will help future research.

“Such analysis guides germplasm conservation decisions, and diversity studies are a great tool to develop core collections and composite genotype sets – subsets of the whole collection – which allow for more practical screening for specific traits than large collections.”

Handling big data

Clearing the bottleneck

Providing help where it is needed

Breeding rice and maize more efficiently using IBP

From the GCP nest to world-scale deployment

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Transformation for Chiedozie – and for cassava

Building African capacity

A paradigm shift

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Ghana gains a new centre of excellence

Capacity building à la carte a real ‘life changer’

A ‘kick-start’ for plant science and for people

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Turning point: cassava to help the vulnerable

Challenges and opportunities

A place at the table, and sharing joy

Nurturing women

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Developing and leading Africa’s cassava research

Feeding a giant

Empowering African researchers

Continuing the momentum

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Bridging the gap between the lab and farmers

Things are speeding up in Tanzania

Tanzania’s new zest for advanced plant breeding

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A grounding in the history of Africa’s groundnuts

How Africa lost its groundnut export market

Ancestral genes could hold the key to drought tolerance and disease resistance

Genetics alone will not lift productivity – farmers’ local knowledge is vital

Local knowledge and high-end genetics working together in Tanzania

Similar breeding success in Senegal

It’s all about poverty

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What makes a plant drought tolerant?

Fat beans indicate plants coping with drought stress

Drought is but one plant stressor – diseases and pests wreak havoc too

Ethiopia’s new bean breeders

Kenya chasing higher bean yields

Commercialising beans

Success built on a solid foundation

Developing physical capacity

Delivering the right beans to farmers

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Cowpea production – almost all of it comes from Africa

Mapping the cowpea genome

Breeding new varieties faster, using modern techniques

Burkina Faso – evaluating new lines to improve the country’s economy

Outsourcing the molecular work

Getting the genotyping expertise on the ground

Mozambique – insects and drought are the problem

Three high-yielding varieties to hit the Mozambique market in 2015

Building a community of breeders to sustain success

Setting up breeders for the next 20 years

More links

Sub-Saharan Africans getting their vitamin A from sweetpotato

New DNA markers identified for sweetpotato disease

Mobilising the genetic diversity of sweetpotato for breeding

The genetic lifelines reach Africa

More links