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The Generation Challenge Programme: a tale of partnership

History, Partnerships, Themes No Responses »

Nov 062015

Where to begin a decade-long story like that of the CGIAR Generation Challenge Programme (GCP)? This time-bound programme concluded in 2014 after successfully catalysing the use of advanced plant breeding techniques in the developing world.

Like all good tales, the GCP story had a strong theme: building partnerships in modern crop breeding for food security. It had a strong cast of characters: a palpable community of staff, consultants and partners from all over the world. And it had a formidable structure – two distinct phases split equally over the decade to first discover new plant genetic information and tools, and then to apply what the researchers learnt to breed more tolerant and resilient crops.

In October 2014, at the final General Research Meeting in Thailand, GCP Director Jean-Marcel Ribaut paid tribute to GCP’s cast and crew: “To all the people involved in GCP over the last 12 years, you are the real asset of the Programme,” he told them.

“In essence, our work has been all about partnerships and networking, bringing together players in crop research who may otherwise never have worked together,” says Jean-Marcel. “GCP’s impact is not easy to evaluate but it’s extremely important for effective research into the future. We demonstrated proofs of concept that can be scaled up for powerful results.”

A significant aspect of GCP’s legacy is the abundance of collaborations it forged and fostered between international researchers. A typical GCP project brought together public and private partners from both developing and developed nations and from CGIAR Centres. In all, more than 200 partners collaborated on GCP projects.

Just some of the extended GCP family assembled for the Programme’s final General Research Meeting in 2014.

The idea that the ‘community would pave the way towards success’ was always a key foundation of GCP, according to Dave Hoisington, who was involved with GCP from its conception and was latterly Chair of GCP’s Consortium Committee. “We designed GCP to provide opportunities for researchers to work together,” says Dave. He is a senior research scientist and program director at the University of Georgia, and was formerly Director of Research at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) and Director of the Genetic Resources Program and of the Applied Biotechnology Center at the International Maize and Wheat Improvement Center (CIMMYT).

“GCP was the mechanism that would help us to complete our mission – to tap into the rich genetic diversity of crops and package it so that breeding programme researchers could integrate it into their operations,” says Dave.

A little girl tucks into sorghum porridge in Mali.

The dawn of a new generation

Food security in the developing world continues to be one of the greatest global challenges of our time. One in nine people worldwide – or more than 820 million people – go hungry every day.

Although this figure is currently diminishing, a changing global climate is making food production more challenging for farmers. Farmers need higher yielding crops that can grow with less water, tolerate higher temperatures and poorer soils, and resist pests and diseases.

The turn of the millennium saw rapid technological developments emerging in international molecular plant science. New tools and approaches were developed that enabled plant scientists, particularly in the developing world, to make use of genetic diversity in plants that was previously largely inaccessible to them. These tools had the potential to increase plant breeders’ capacity to rapidly develop crop varieties able to tolerate extreme environments and yield more in farmers’ fields.

Photo: J van de Gevel/Bioversity International

Wheat varieties in a field trial.

Dave was one scientist who early on recognised the significance and potential of this new dawn in plant science. In 2002, while working at CIMMYT, he teamed up with the Center’s then Director General, Masa Iwanaga, and its then Executive Officer for Research, Peter Ninnes – another long-term member of the GCP family who at the other end of the Programme’s lifespan became its Transition Manager. Together with a Task Force of other collaborators from CIMMYT, the International Rice Research Institute (IRRI) and IPGRI (now Bioversity International), they drafted and presented a joint proposal to form a CGIAR Challenge Programme – and so GCP was conceived.

The five CGIAR Challenge Programmes were the early precursors of the current CGIAR Research Programs. They introduced a new model for collaboration among CGIAR Research Centers and with external institutes, particularly national breeding programmes in developing countries.

A programme where the spirit is palpable

Failed harvest: this Ghanaian farmer’s maize ears are undersized and poorly developed due to drought.

From the beginning, GCP had collaboration and capacity building at its heart. As encapsulated in its tagline, “partnerships in modern crop breeding for food security,” GCP’s aim was to bring breeders together and give them the tools to more effectively breed crops for the benefit of the resource-poor farmers and their families, particularly in marginal environments.

GCP’s primary focus on was on drought tolerance and breeding for drought-prone farming systems, since this is the biggest threat to food security worldwide – and droughts are already becoming more frequent and severe with climate change. However, the Programme made major advances in breeding for resilience to other major stresses in a number of different crops, including acid soils and important pests and diseases. It also sought improved yields and nutritional quality.

The model for the Programme was that it would work by contracting partner institutes to conduct research, initially through competitive projects and later through commissioning. These partnerships would ensure that GCP’s overall objectives were met. For Dave, GCP set the groundwork for modern plant breeding.

“GCP demonstrated that you can tap into genetic resources and that they can be valuable and can have significant impacts on breeding programmes,” he says.

“I think GCP started to guide the process. Without GCP, the adoption, testing and use of molecular technologies would probably have been delayed.”

Photo: Meena Kadri/Flickr (Creative Commons)

Harvesting wheat in India.

Masa Iwanaga, who is now President of the Japan International Research Center for Agricultural Sciences (JIRCAS), says that the key to the proposal and ultimate success of GCP was the focus on building connections between partners worldwide. “By providing the opportunity for researchers from developed countries to partner with researchers in developing countries, it helped enhance the capacity of national programmes in developing countries to use advanced technology for crop improvement.”

While not all partnerships were fruitful, Jean-Marcel has observed that those participants who invested in partnerships and built trust, understanding and communication produced some of the most successful results. “We created this amazing chain of people, stretching from the labs to the fields,” said Jean-Marcel, discussing the Programme in a 2012 interview.

“Perhaps the best way I can describe it is as a ‘GCP spirit’ created by the researchers we worked with.

“The Programme’s environment is friendly, open to sharing and is marked by a strong sense of community and belonging. The GCP spirit is visible and palpable: you can recognise people working with us have a spirit that is typical of the Programme.”

Exploring gene banks to uncover genetic wealth

GCP started operations in 2004 and was designed in two five-year phases, 2004–2008 and 2009–2013. 2014 was a transition year for orderly closure.

Phase I focussed on upstream research to generate knowledge and tools for modern plant breeding. It mainly consisted of exploration and discovery projects, funded on a competitive basis, pursuing the most promising molecular research and high-potential partnerships.

“GCP’s first task was to go in and identify the genetic wealth held within the CGIAR gene banks,” says Dave Hoisington.

Gene bank samples give a small snapshot of cowpea diversity.

CGIAR’s gene banks were originally conceived purely for conservation, but breeders increasingly recognised the tremendous value of studying and utilising these collections. Over the years they were able to use gene banks as a valuable source of new breeding material, but were hampered by having to choose seeds almost blindly, with limited knowledge of what useful traits they might contain.

“We realised we could use molecular tools to help scan the genomes and discover genes in crops of interest and related species,” says Dave. “The genes we were most interested in were ones that helped increase yield in harsh environments, particularly under drought.”

By studying the genomes of wild varieties of wheat, for example, researchers found genes that increase wheat’s tolerance of water stress.

Photo: International Potato Center (CIP)

Sweetpotato diversity.

GCP-supported projects analysed naturally occurring genetic diversity to produce cloned genes, informative markers and reference sets for 21 important food crops. ‘Reference sets’, or ‘reference collections’ reduce search time for researchers: they are representative selections of a few hundred plant samples (‘accessions’) that encapsulate each crop’s genetic diversity, narrowed down from the many thousands of gene bank accessions available. The resources developed through GCP have already proved enormously valuable, and will continue to benefit researchers for years to come.

For example, researchers developed 52 new molecular (DNA) markers for sweetpotato to enable marker-assisted selection for resistance to sweet potato virus disease (SPVD). For lentils, a reference set of about 150 accessions was produced, a distillation down to 15 percent of the global collection studied. And for barley, 90 percent of all the different characteristics of barley were captured within 300 representative plant lines.

Harvesting barley in Ethiopia.

The leader of GCP’s barley research, Michael Baum, who directs the Biodiversity and Integrated Gene Management Program at the International Center for Agricultural Research in the Dry Areas (ICARDA), says the reference set is a particular boon for a researcher new to barley.

“By looking at 300 lines, they see the diversity of 3,000 lines without any duplication,” says Michael. “This is much better and quicker for a plant breeder.”

Similarly, the lentil reference set serves as a common resource for ICARDA’s team of lentil breeders, facilitating efficient collaboration, according to Aladdin Hamweih of ICARDA, who was charged with developing the lentil collection for GCP.

“These materials can be accessed to achieve farming goals – to produce tough plants suitable for local environments. In doing this, we give farmers a greater likelihood of success, which ultimately leads to improving food security for the wider population,” Aladdin says.

An important aspect of the efforts within Phase I was GCP’s emphasis on developing genomic resources such as reference sets for historically under-resourced crops that had received relatively little investment in genetic research. These made up most of GCP’s target crops, and included: bananas and plantains; cassava; coconuts; common beans; cowpeas; chickpeas; groundnuts; lentils; finger, foxtail and pearl millets; pigeonpeas; potatoes; sorghum; sweetpotatoes and yams.

Although not all of these historically under-resourced crops continued to receive research funding into Phase II, the outcomes from Phase I provided valuable genetic resources and a solid basis for the ongoing use of modern, molecular-breeding techniques. Indeed, thanks to their GCP boost, some of these previously neglected species have become model crops for genetic and genomic research – even overtaking superstar crops such as wheat, whose highly complex genome hampers scientists’ progress.

Banana harvest for sale in Rwanda.

A need to focus and deliver products

“Phase I provided plenty of opportunity for researchers to tap into genetic diversity,” says Jean-Marcel. “We opened the door for a lot of different topics which helped us to identify projects worth pursuing further, as well as identifying productive partnerships. But at the same time, we were losing focus by spreading ourselves too thinly across so many crops.”

This notion was confirmed by the authors of an external review conducted in 2008, commissioned by CGIAR. This recommended consolidating GCP’s research in order to optimise efficiency and increase outputs during GCP’s second phase, while also enhancing potential for longer term impact.

Transparency and a willingness to respond and adapt were always core GCP values. The Programme embraced external review throughout its lifetime, and was able to make dynamic changes in direction as the best ways to achieve impact emerged. Markus Palenberg, Managing Director of the Institute for Development Strategy in Germany, was a member of the 2008 evaluation panel.

“One major recommendation from the evaluation was to focus on crops and tools which would provide the greatest impact in terms of food security,” recounts Markus, who later joined GCP’s Executive Board. “This resulted in the Programme refocusing its research on only nine core crops.” These were cassava, beans, chickpeas, cowpeas, groundnuts, maize, rice, sorghum and wheat.

Hard work: harvesting groundnut in Malawi.

GCP’s decision-making process on how to focus its Phase II efforts was partly guided by research the Programme had commissioned, documented in its Pathways to impact brief No 1: Where in the world do we start? This took global data on the number of stunted – i.e., severely malnourished – children, as a truer indicator of poverty than a monetary definition, and overlaid it on maps showing where drought was most likely to occur and have a serious impact on crop productivity. This combination of poverty and vulnerable harvests was used to determine the farming systems where GCP might have most impact.

The Programme also attempted to maintain a balance between types of crops, including each of the following categories: cereals (maize, rice, sorghum, wheat), legumes (beans, chickpeas, cowpeas, groundnuts), and roots and tubers (cassava).

The crops were organised into six crop- specific Research Initiatives (RIs) – legumes were consolidated into one – plus a seventh, Comparative Genomics, which focused on exploiting genetic similarities among rice, maize and sorghum to find and deploy sources of tolerance to acid soils.

Child eating rice.

The research under the RIs built on GCP’s achievements in Phase I, moving from exploration to application. The change in focus was underpinned by the planned shift from competitive to commissioned projects, allowing the Programme to continue to support its strongest partnerships and research strands.

“The RIs focused on promoting the use of modern integrated breeding approaches, using both conventional and molecular breeding methods, to improve each crop through a series of specific projects undertaken in more than 30 countries,” says Jean-Marcel. “More importantly, the RIs were focused on creating new genetic material and varieties of plants that would ultimately benefit farmers.”

Such products released on the ground included new varieties of:

cassava resistant to several diseases, tolerant to drought, nutritionally enhanced to provide high levels of vitamin A, and with higher starch content for high-quality cassava flour and starch processing
chickpea tolerant to drought and able to thrive in semi-arid conditions, already providing improved food and income security for smallholder African farmers – yields have doubled in Ethiopia – and set to help them supply growing demand for the legume in India
maize with higher yields, tolerant to high levels of aluminium in acid soils, resistant to disease, adapted to local conditions in Africa – and with improved phosphorus efficiency in the pipeline
rice with tolerance to drought and low levels of phosphorus in acid soils, disease resistance, high grain quality, and tolerance to soil salinity – with improved aluminium tolerance on the way too

Harvesting rice in India.

Over the coming years, many more varieties developed through GCP projects are expected to be available to farmers, as CGIAR Research Centres and national programmes continue their work.

These will include varieties of:

common bean resistant to disease and tolerant to drought and heat, with higher yields in drier conditions – due for release in several African countries from 2015 onwards
cowpea resistant to diseases and insect pests, with higher yields, and able to tolerate worsening drought – set for release in several countries from 2015, to secure and improve harvests in sub-Saharan Africa
groundnut tolerant to drought and resistant to pests, diseases, and the fungi that cause aflatoxin contamination, securing harvests and raising incomes in some of the poorest regions of Africa
maize tolerant to drought and adapted to local conditions and tastes in Asia
sorghum that is even more robust and adapted to increasing drought in the arid areas of sub-Saharan Africa – plus sorghum varieties able to tolerate high aluminium levels in acid soils, set for imminent release
wheat with heat and drought tolerance – as well as improved yield and grain quality – for India and China, the two largest wheat producers in the world

Groundnut harvest, Ghana.

Giving a voice to all the cast and crew

The 2008 external review also recommended slight changes in governance. It suggested GCP receive more guidance from two proposed panels: a Consortium Committee and an independent Executive Board.

Dave Hoisington, who chaired the Committee from 2010, succeeding the inaugural Chair Yves Savidan, explains: “GCP was not a research programme run by a single institute, but a consortium of 18 institutes. By having a committee of the key players in research as well as an independent board comprising people who had no conflict of interest with the Programme, we were able to make sure both the ‘players’ and ‘referees’ were given a voice.”

Jean-Marcel says providing this voice to everyone involved was an important facet of effective management. “Given that GCP was built on its people and partnerships, it was important that we restructured our governance to provide everyone with a representative to voice their thoughts on the Programme. We have always tried to be very transparent.”

The seven-member Executive Board was instated in June 2008 to provide oversight of the scientific strategy of the Programme. Board members had a wide variety of skills and backgrounds, with expertise ranging across molecular biology, development assistance, socioeconomics, academia, finance, governance and change management.

Andrew Bennett, who followed inaugural Chair Calvin Qualset into the role in 2009, has more than 45 years of experience in international development and disaster management and has worked in development programmes in Africa, Asia, Latin America, the Pacific and the Caribbean.

“The Executive Board’s first role was to provide advice and to help the Consortium Committee and management refocus the Programme,” says Andrew.

Rice seed diversity.

‘Advice’ and ‘helping’ are not usually words associated with how a Board works but, like so much of GCP’s ‘family’, this was not a typical board. Because GCP was hosted by CIMMYT, the Board did not have to deal with any policy issues; that was the responsibility of the Consortium Committee. As Andrew explains, “Our role was to advise on and help with decision-making and implementation, which was great as we were able to focus on the Programme’s science and people.”

Andrew has been impressed by what GCP has been able to achieve in its relatively short lifespan in comparison with other research programmes. “I think this programme has demonstrated that a relatively modest amount of money used intelligently can move with the times and help identify areas of potential benefit.”

Developing capacity and leadership in Africa

As GCP’s focus shifted from exploration and discovery to application and impact between Phases I and II, project leadership shifted too. More and more projects were being led by developing-country partners.

Harold Roy-Macauley, GCP Board member and Executive Director of the West and Central African Council for Agricultural Research and Development (WECARD), advised GCP about how to develop capacity, community and leadership among African partners so that products would reach farmers.

“The objective was to make sure that we were influencing development within local research communities,” says Harold. “GCP has played a very important role in creating synergies between the different institutions in Africa. Bringing the right people together, who are working on similar problems, and providing them with the opportunity to lead, has brought about change in the way researchers are doing research.”

In the early years of the Programme, only about 25 percent of the research budget was allocated to research institutes in developing countries; this figure was more than 50 percent in 2012 and 2013.

Jean-Marcel echoes Harold’s comments: “To make a difference in rural development – to truly contribute to improved food security through crop improvement and incomes for poor farmers – we knew that building capacity had to be a cornerstone of our strategy,” he says. Throughout its 10 years, GCP invested 15 percent of its resources in developing capacity.

“Providing this capacity has enabled people, research teams and institutes to grow, thrive and stand on their own, and this is deeply gratifying. It is very rewarding to see people from developing countries growing and becoming leaders,” says Jean-Marcel.

“For me, seeing developing-country partners come to the fore and take the reins of project leadership was one of the major outcomes of the Programme. Providing them with the opportunity, along with the appropriate capacity, allowed them to build their self-confidence. Now, many have become leaders of other transnational projects.”

Emmanuel Okogbenin and Chiedozie Egesi, two plant breeders at Nigeria’s National Root Crops Research Institute (NRCRI), are notable examples. They are leading an innovative new project using marker-assisted breeding techniques they learnt during GCP projects to develop higher-yielding, stress-tolerant cassava varieties. For this project, they are partnering with the Bill & Melinda Gates Foundation, Cornell University in the USA, the International Institute of Tropical Agriculture (IITA) and Uganda’s National Crops Resources Research Institute (NaCRRI).

Chiedozie says this would not have been possible without GCP helping African researchers to build their profiles. “GCP helped us to build an image for ourselves in Nigeria and in Africa,” he says, “and this created a confidence in other global actors, who, on seeing our ability to deliver results, are choosing to invest in us.”

Nigerian cassava farmer.

A ‘sweet and sour’ sunset

Photo: Daryl Marquardt/Flickr (Creative Commons)

Maize at sunset.

Jean-Marcel defined GCP’s final General Research Meeting in Thailand in 2014 as a ‘sweet-and-sour experience’.

Summing up the meeting, Jean-Marcel said, “It was sour in terms of GCP’s sunset, and sweet in terms of seeing you all here, sharing your stories and continuing your conversations with your partners and communities.”

From the outset, GCP was set up as a time-bound programme, which gave partners specific time limits and goals, and the motivation to deliver products. However, much of the research begun during GCP projects will take longer than 10 years to come to full fruition, so it was important for GCP to ensure that the research effort could be sustained and would continue to deliver farmer-focused outcomes.

During the final two years of the Programme, the Executive Board, Consortium Committee and Management Team played a large role in ensuring this sustainability through a thoroughly planned handover.

“We knew we weren’t going to be around forever, so we had a plan from early on to hand over the managerial reins to other institutes, including CGIAR Research Programs,” says Jean-Marcel.

One of the largest challenges was to ensure the continuity and future success of the Integrated Breeding Platform (IBP). IBP is a web-based, one-stop shop for information, tools and related services to support crop breeders in designing and carrying out integrated breeding projects, including both conventional and marker-assisted breeding methods.

While there are already a number of other analytical and data management breeding systems on the market, IBP combines all the tools that a breeder needs to carry out their day-to-day logistics, plan crosses and trials, manage and analyse data, and analyse and refine breeding decisions. IBP is also unique in that it is geared towards supporting breeders in developing countries – although it is already proving valuable to a wide range of breeding teams across the world. The Platform is set up to grow and improve as innovative ideas emerge, as users can develop and share their own tools.

Beyond the communities and relationships fostered by GCP community, Jean-Marcel sees IBP as the most important legacy of the Programme. “I think that the impact of IBP will be huge – so much larger than GCP. It will really have impact on how people do their business, and adopt best practice.”

While the sun is setting on GCP, it is rising for IBP, which is in an exciting phases as it grows and seeks long-term financial stability. The Platform is now independent, with its headquarters hosted at CIMMYT, and has established a number of regional hubs to provide localised support and training around the world, with more to follow.

It is envisaged that IBP will be invaluable to researchers in both developing and developed countries for many years to come, helping them to get farmers the crop varieties they need more efficiently. IBP is also helping to sustain some of the networks that GCP built and nurtured, as it is hosting the crop-specific Communities of Practice established by GCP.

2014 may be the end of GCP’s story but its legacy will live on. It will endure, of course, in the Programme’s scientific achievements – for many crops, genetic research and the effective use of genetic diversity in molecular breeding are just beginning, and GCP has helped to kick-start a long and productive scientific journey – and in the valuable tools brought together in IBP. And most of all, GCP’s character, communities and spirit will live on in all those who formed part of the GCP family.

For Chiedozie Egesi, the partnerships fostered by GCP have changed the way he does research: “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.

Fellow cassava breeder Elizabeth Parkes of Ghana agrees that GCP’s impact will be a lasting one: “All the agricultural research institutes and individual scientists who came into contact with GCP have been fundamentally transformed.”

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.

Ousmane Boukar: committed to cowpeas

Africa, Cowpeas, Legumes, Researchers No Responses »

Oct 082015

Ousmane Boukar

“There is a clear need to develop a range of varieties that meet diverse requirements”

For 30 years, Ousmane Boukar has been working towards a singular goal: to improve and secure cowpea production in sub-Saharan Africa.

“Cowpeas are very important in sub-Saharan Africa,” he says. “They are an important source of protein, and contribute to the livelihood and food security of millions.”

Despite their dietary importance, cowpea yields in Africa are low – on average a mere 10 to 30 percent of their potential. This is primarily because of attacks from insects and diseases, but is often further compounded by chronic drought.

Since 2007, Ousmane has worked for the International Institute of Tropical Agriculture (IITA) as cowpea breeder and Station Representative in Kano, Nigeria. As a breeder, his mission is to improve yields by identifying additional genetic sources of resistance to pests and diseases, tolerance of parasitic weeds, improved drought tolerance and adaptation to low soil fertility.

To accomplish this, he searches for genes associated with these kinds of valuable traits. He then uses this information to develop breeding populations comprising of plant lines with multiple useful traits, and works with farmers to grow these populations to make sure they do grow well in the field before releasing them as new varieties.

“Cowpea breeding is very challenging because of the range of production environments and cropping systems, and the diverse preferences among consumers and producers for grain, leaves, pods and fodder,” Ousmane says. “There is a clear need to develop a range of varieties that meet those diverse requirements, combining high yield potential and resistance to the major production constraints.”

A farmer’s field full of cowpea plants (with maize at the background) in Kano, Nigeria.

Joining an international programme

The same year Ousmane joined IITA, he joined forces in a new collaboration with cowpea breeders and geneticists from Burkina Faso, Mozambique, Senegal and the USA. He was Product Delivery Coordinator for the cowpea component of the Tropical Legumes I project (TLI) – a seven-year project funded by the CGIAR Generation Challenge Programme (GCP) that sought to use marker-assisted breeding techniques to breed high yielding, drought-tolerant and insect- and disease-resistant varieties of four important legumes.

Cowpea plants at podding stage.

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

Key outcomes from the cowpea component of the project were a cowpea genome map and molecular markers that have helped breeders like Ousmane locate the genes in cowpeas that determine and regulate desirable traits. These markers can be used like flags to indicate which potential parent plants have useful genes, and which of the progeny from each cross have inherited them, making breeding more efficient.

“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 such as thrips [insects which feed on cowpeas] and Striga [a parasitic weed]. We expect these lines to be available to plant breeders by the end of 2015.”

Cowpea seed.

Ousmane says the success of the cowpea component of TLI owes much to the pre-existing relationships the partners had before the project. “TLI was an extension of a USAID collaborative project [Bean/Cowpea Collaborative Research Support Program] we had been working on since 2002,” he explains. “I had also crossed paths with breeders in Senegal, Burkina Faso and USA many times when I worked with the Institute of Agricultural Research for Development [IRAD] in Cameroon.”

Striga in a cowpea plot.

Ousmane was with IRAD in his home country of Cameroon from 1990 to 2007. He also worked by correspondence during this time to complete both his Master’s and Doctoral degrees in Plant Breeding and Genomics from the University of Purdue in Indiana, USA. His thesis involved characterising and mapping Striga resistance in cowpeas. Striga is a parasitic weed widespread in West Africa, which can reduce susceptible cultivar yields by up to 100 percent. Resistance within the host plant is the only practical control method (see ‘Cowpea in between’, GCP Partner and Product Highlights 2006, page 23).

A trader sells cowpeas in Moniya market, Ibadan, Nigeria.

Taking the lead in the Community of Practice

In 2011, in addition to his TLI and Product Delivery Coordinator roles, Ousmane became the coordinator of the Cowpea Community of Practice (CoP) – a newly created network founded by GCP to develop capacity in Africa and help GCP researchers share their new expertise in molecular breeding.

“The CoP was designed for cowpea researchers and people interested in cowpeas to ask questions and to share their expertise and knowledge, particularly with people who don’t have the experience, such as graduate students or breeders new to cowpeas,” Ousmane explains. Members are from Burkina Faso, Cameroon, Kenya, Malawi, Mali, Mozambique, Niger, Nigeria, Senegal, Tanzania and USA.

“My role as coordinator is to collect ideas, find funding opportunities, and understand member expertise and resources so I can direct members of the community to the right people.”

Ghanaian farmer Alanig Bawa drying cowpeas.

Ousmane says the position has opened his eyes to all the new research going on in cowpea. The number of new researchers in the field also heartens him. “There are more researchers that are practising molecular breeding than ever before, which is great, because we can enhance their impact and efficiency in cowpea breeding.”

As membership grows, Ousmane is confident that the community and capacity that have developed with help from GCP will remain sustainable after GCP’s close at the end of 2014. “Governments in Nigeria and Burkina Faso understand the importance of cowpeas and are investing in our research. As the set of skills and the number of personnel grow in other sub-Saharan countries, we are confident that cowpea research will expand and produce higher yielding varieties for their farmers.”

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.

Chickpea’s promise: to be win-win for Africa and India

Africa, Asia, Capacity building, Chickpeas, Crop breeding, Genetics, Legumes No Responses »

Jun 012015

Crop science and collaboration help African farmers feed India’s appetite for chickpeas

Indian chickpea farmer with her harvest.

India loves chickpeas. With its largely vegetarian population, it has long been the world’s biggest producer and consumer of the nutritious legume. In recent years, however, India’s appetite for chickpea has outstripped production, and the country is also now the world’s biggest importer. With a ready market and new drought-tolerant varieties of chickpea, millions of smallholder African farmers are ready to make up India’s shortfall, improving livelihoods along the way and ensuring food security for some of the world’s most resource-poor countries.

GCP achieved real impacts in chickpea by catalysing and facilitating the deployment of advanced crop science, particularly molecular breeding, in the development of drought-tolerant varieties for both Africa and Asia. Over the course of its research, it also contributed to major advances in chickpea science and genomic knowledge.

Although India boasts the world’s biggest total chickpea harvest, productivity has been low in recent years with yields of less than one tonne per hectare, largely due to drought in the south of the country where much chickpea is grown. The country is relying increasingly on exports from producers in sub-Saharan Africa to supplement its domestic supply.

Drought has been hindering chickpea yields in Africa too, however, and this is a major concern not only for Africa but also for India. Ethiopia and Kenya are Africa’s largest chickpea producers, and both countries have been producing chickpea for export. However, their productivity has been limited, mainly because of heat stress and moisture loss, as well as by a lack of access to basic infrastructure and resources.

Indeed, drought has been the main constraint to chickpea productivity worldwide, and in countries such as Ethiopia and Kenya this is often made worse by crop disease, poor soil quality and limited farmer resources. While total global production of chickpea is around 8.6 million tonnes per year, drought causes losses of around 3.7 million tonnes worldwide.

A decade ago, chickpea researchers, supported by the CGIAR Generation Challenge Programme (GCP), started to consider the potential for developing new drought-tolerant varieties that could help boost the world’s production.

They posed this question: If struggling African farmers were armed with adequate resources, could they make up India’s shortfall by growing improved chickpea varieties for export? Empowering farmers to stimulate and sustain their own food production, it was proposed, would not only offer food security to millions of farmers, but could ultimately secure future chickpea exports to India.

An Ethiopian farmer harvests her chickpea crop.

In 2007, GCP kicked off a plan for a multiphased, multithemed Tropical Legumes I (TLI) project, which later became part of, and the largest project within, the GCP Legumes Research Initiative (RI; see box below) – the chickpea component of which would involve collaboration between researchers from India, Ethiopia and Kenya. The scope was not only to develop improved, drought-tolerant chickpeas that would thrive in semiarid conditions, but also to ensure that these varieties would be growing in farmers’ fields across Africa and South Asia within a decade.

“We knew our task would not be complete until we had improved varieties in the hands of farmers,” says GCP researcher Paul Kimurto from the Faculty of Agriculture, Egerton University, Kenya.

The success of GCP research in achieving these goals has opened up great opportunities for East African countries such as Ethiopia and Kenya, which are primed and ready to take advantage of a guaranteed chickpea market.

How drought affects chickpea

Chickpea is a pretty tough customer overall, being able to withstand and thrive on the most rugged and dry terrains, surviving with no irrigation – only the moisture left deep in the soil at the end of the rainy season.

Yet the legume does have one chink in its armour: if no rain falls at its critical maturing or ripening stage (otherwise known as the grain-filling period), crop yields will be seriously affected. The size and weight of chickpea legumes is determined by how successful this maturing stage is. Any stress, such as drought or disease, that occurs at this time will reduce the crop’s yield dramatically.

In India, this has been a particular problem for the past 40 years or so, as chickpea cropping areas have shifted from the cooler north to the warmer south.

“In the 1960s and 1970s when the agricultural Green Revolution introduced grain crops to northern India, chickpeas began to be replaced there by wheat or rice, and grown more in the south,” says Pooran Gaur from the International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), headquartered in India. Pooran was an Activity Leader for the first phase of TLI and Product Delivery Coordinator for the chickpea component of the Legumes RI.

This shift meant the crop was no longer being grown in cooler, long-season environments, but in warmer, short-season environments where drought and diseases like Fusarium wilt have inhibited productivity.

“We have lost about four or five million hectares of chickpea growing area in northern India in the decades since that time,” says Pooran. “In the central and southern states, however, chickpea area more than doubled to nearly five million hectares.”

Escaping drought in India

“The solution we came up with was to develop varieties that were not only high yielding, but could also mature earlier and therefore have more chance of escaping terminal drought,” Pooran explains.

“Such varieties could also allow cereal farmers to produce a fast-growing crop in between the harvest and planting of their main higher yielding crops,” he says.

New short-duration varieties are expected to play a key role in expanding chickpea area into new niches where the available crop-growing seasons are shorter.

“In southern India now we are already seeing these varieties growing well, and their yield is very high,” says Pooran. “In fact, productivity has increased in the south by about seven to eight times in the last 10–12 years.”

The southern state of Andhra Pradesh, once considered unfavourable for chickpea cultivation, today has the highest chickpea yields (averaging 1.4 tonnes/hectare) in India, producing almost as much chickpea as Australia, Canada, Mexico and Myanmar combined.

Indian chickpea farmer with her harvest.

Developing new varieties: Tropical Legumes I in action

GCP-supported drought-tolerance breeding activities in chickpea created hugely valuable breeding materials and tools during the Programme’s decade of existence, focussing not only in India but African partner countries of Ethiopia and Kenya too. A key first step in Phase I of TLI was to create and phenotype – i.e. measure and record the observable characteristics of – a chickpea reference set. This provided the raw information on physical traits needed to make connections between phenotype and genotype, and allowed breeders to identify materials likely to contain drought tolerance genes. This enabled the creation in Phase II of breeding populations with superior genotypes, and so the development of new drought-tolerant prebreeding lines to feed into TLII.

A significant number of markers and other genomic resources were identified and made available during this time, including simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs) and Diversity Array Technologies (DArT) arrays. The combination of genetic maps with phenotypic information led to the identification of an important ‘hot spot’ region containing quantitative trait loci (QTLs) for several drought-related traits.

Two of the most important molecular-breeding approaches, marker-assisted backcrossing (MABC) and marker-assisted recurrent selection (MARS), were then employed extensively in the selection of breeding materials and introgression of these drought-tolerance QTLs and other desired traits into elite chickpea varieties.

Developing chickpea pods

Markers – DNA sequences with known locations on a chromosome – are like flags on the genetic code. Using them in molecular breeding involves several steps. Scientists must first discover a large number of markers, of which only a small number are likely to be polymorphic, i.e. to have different variants. These are then mapped and compared with phenotypic information, in the hope that just one or two might be associated with a useful trait. When this is the case, breeders can test large quantities of breeding materials to find out which have genes for, say, drought tolerance without having to grow plants to maturity.

The implementation of techniques such as MABC and MARS has become ever more effective over the course of GCP’s work in chickpea, thanks to the emergence and development of increasingly cost-effective types of markers such as SNPs, which can be discovered and explored in large numbers relatively cheaply. The integration of SNPs into chickpea genetic maps significantly accelerated molecular breeding.

The outcome of all these molecular-breeding efforts has been the development and release of locally adapted, drought-tolerant chickpea varieties in each of the target countries – Ethiopia, Kenya and India – where they are already changing lives with their significantly higher yields. Further varieties are in the pipeline and due for imminent release, and it is anticipated that, with partner organisations adopting the use of molecular markers as a routine part of their breeding programmes, many more will be developed over the coming years.

Molecular breeding in TLI was done in conjunction with target-country partners, with at least one cross carried out in each country. ICRISAT also backed up MABC activities with additional crosses. The elite lines that were developed underwent multilocation phenotyping in the three target countries and the best-adapted, most drought-tolerant lines were promoted in TLII.

The project placed heavy emphasis on capacity building for the target-country partners. Efforts were made, for instance, to help researchers and breeders at Egerton University in Kenya and the Ethiopian Institute of Agricultural Research (EIAR) in Ethiopia to undertake molecular breeding activities. At least one PhD and two Master’s students each from Kenya, Ethiopia and India were supported throughout this capacity-building process.

The magic of genetic diversity

One of the important advances in chickpea science supported by GCP, as part of TLI and its mission to develop drought-tolerant chickpea genotypes, was the development of the first ever chickpea multiparent advanced generation intercross (MAGIC) population.

It was created using eight well-adapted and drought-tolerant desi chickpea cultivars and elite lines from different genetic origins and backgrounds, including material from Ethiopia, Kenya, India and Tanzania. These were drawn from the chickpea reference set that GCP had previously developed and phenotyped, allowing an effective strategic selection of parental lines. The population was created by crossing these over several generations in such a way as to maximise the mix of genes in the offspring and ensure varied combinations.

MAGIC populations like these are a valuable genetic resource that makes trait mapping and gene discovery much easier, helping scientists identify useful genes and create varieties with enhanced genetic diversity. They can also be directly used as source material in breeding programmes; already, phenotyping a subset of the chickpea MAGIC population has led to the identification of valuable chickpea breeding lines that had favourable alleles for drought tolerance.

Through links with future molecular-breeding projects, it is expected that the investment in the development of MAGIC populations will benefit both African and South Asian chickpea production. GCP was also involved in developing MAGIC populations for cowpea, rice and sorghum, which were used to combine elite alleles for both simple traits, such as aluminium tolerance in sorghum and submergence tolerance in rice, and complex traits, such as drought or heat tolerance.

Decoding the chickpea genome

Chickpea seed

In 2013, GCP scientists, working with other research organisations around the world, announced the successful sequencing of the chickpea genome. This major breakthrough is expected to lead to the development of even more superior varieties that will transform chickpea production in semiarid environments.

A collaboration of 20 international research organisations under the banner of the International Chickpea Genome Sequencing Consortium (ICGSC), led by ICRISAT, identified more than 28,000 genes and several million genetic markers. These are expected to illuminate important genetic traits that may enhance new varieties.

“The value of this new resource for chickpea improvement cannot be overstated,” says Doug Cook from the University of California, Davis (UC Davis), United States. “It will provide the basis for a wide range of studies, from accelerated breeding, to identifying the molecular basis of a range of key agronomic traits, to basic studies of chickpea biology.”

Doug was one of three lead authors on the publication of the chickpea genome, along with Rajeev Varshney of ICRISAT, who was Principal Investigator for the chickpea work in GCP’s Legumes RI, and Jun Wang, Director of the Beijing Genomics Institute (BGI) of China.

“Making the chickpea genome available to the global research community is an important milestone in bringing chickpea improvement into the 21st century, to address the nutritional security of the poor – especially the rural poor in South Asia and Africa,” he says.

Increased food security will mean higher incomes and a better standard of living for farmers across sub-Saharan Africa.

For Pooran Gaur, GCP played the role of catalyst in this revolution in genomic resource development. “GCP got things started; it set the foundation. Now we are in a position to do further molecular breeding in chickpea.”

The chickpea genome-sequencing project was partly funded by GCP. Other collaborators included UC Davis and BGI-Shenzhen, with key involvement of national partners in India, Canada, Spain, Australia, Germany and the Czech Republic.

In September 2014, ICRISAT received a grant from the Indian Government for a three-year project to further develop chickpea genomic resources, by utilising the genome-sequence information to improve chickpea.

Indian women roast fresh green chickpeas for an evening snack in Andhra Pradesh, India.

Chickpea success in Africa: new varieties already changing lives

With high-yielding, drought tolerant chickpea varieties emerging from the research efforts in molecular breeding, GCP’s partners also needed to reach out to farmers. Teaching African farmers about the advantages of growing chickpeas, either as a main crop or a rotation crop between cereals, has brought about a great uptake in chickpea production in recent years.

A key focus during the second phase of TLI, and onward into TLII, was on enhancing the knowledge, skills and resources of local breeders who have direct links to farmers, especially in Ethiopia and Kenya, and so also build the capacity of farmers themselves.

“We’ve held open days where farmers can interact with and learn from breeders,” says Asnake Fikre, Crop Research Director for EIAR and former TLI country coordinator of the chickpea work in Ethiopia.

“Farmers are now enrolled in farmer training schools at agricultural training centres, and there are also farmer participatory trials.

“This has given them the opportunity to participate in varietal selection with breeders, share their own knowledge and have their say in which varieties they prefer and know will give better harvest, in the conditions they know best.”

EIAR has also been helping train farmers to improve their farm practices to boost production and to become seed producers of these high-yielding chickpea varieties.

“Our goal was to have varieties that would go to farmers’ fields and make a clearly discernible difference,” says Asnake. “Now we are starting to make that kind of impact in my country.”

In fields across Ethiopia, the introduction of new, drought-tolerant varieties has already brought a dramatic increase in productivity, with yields doubling in recent years. This has transformed Ethiopia’s chickpea from simple subsistence crop to one of great commercial significance.

“Targeted farmers are now planting up to half their land with chickpea,” Asnake says. “This has not only improved the fertility of their soil but has had direct benefits for their income and diets.”

Varieties like the large-seeded and high-valued kabuli have presented new opportunities for farmers to earn extra income through the export industry, and indeed chickpea exports from eastern Africa have substantially increased since 2001.

“The high yields of the drought-tolerant and pest-resistant chickpea, and the market value, meant that I am no longer seen as a poor widow but a successful farmer,” says Ethiopian farmer Temegnush Dabi.

“Ultimately, by making wealth out of chickpea and chickpea technologies in this country, people are starting to change their lives,” says Asnake. “They are educating their children to the university level and constructing better houses, even in towns. This will have a massive impact on the next generation.”

A similar success story is unfolding in Kenya, where GCP efforts during TLI led to the release of six new varieties of chickpea in the five years prior to GCP’s close at the end of 2014; more are expected to be ready within the next three years.

While chickpea is a relatively new crop in Kenya it has been steadily gaining popularity, especially in the drylands, which make up over 80 percent of Kenya’s total land surface and support nearly 10 million Kenyans – about 34 percent of the country’s population.

Drought tolerance experiments in chickpea at Egerton University, Njoro, Kenya.

“It wasn’t until my university went into close collaboration with ICRISAT during TLII and gained more resources and training options – facilitated by GCP – that chickpea research gained leverage in Kenya,” Paul Kimurto explains. “Through GCP and ICRISAT, we had more opportunities to promote the crop in Kenya. It is still on a small scale here, but it is spreading into more and more areas.”

Kenyan farmers are now discovering the benefits of chickpea as a rotational or ‘relay’ crop, he says, due to its ability to enhance soil fertility. In the highlands where fields are normally left dry and nothing is planted from around November to February, chickpea is a very good option to plant instead of letting fields stay fallow until the next season.

“By fixing nitrogen and adding organic matter to the soil, chickpeas can minimise, even eliminate, the need for costly fertilisers,” says Paul. “This is certainly enough incentive for cereal farmers to switch to pulse crops such as chickpea that can be managed without such costs.”

Households in the drylands have often been faced with hunger due to frequent crop failure of main staples, such as maize and beans, on account of climate change, Paul explains. With access to improved varieties, however, farmers can now produce a fast-growing chickpea crop between the harvest and planting of their main cereals. In the drylands they are now growing chickpeas after wheat and maize harvests during the short rains, when the land would otherwise lie fallow.

“Already, improved chickpeas have increased the food security and nutritional status of more than 27,000 households across the Baringo, Koibatek, Kerio Valley and Bomet areas of Kenya,” Paul says.

It is a trend he hopes will continue right across sub-Saharan Africa in the years to come, attracting more and more resource-poor farmers to grow chickpea.

Chickpea’s promise meeting future challenges

Beyond the end of GCP and the funding it provided, chickpea researchers are hopeful they will be able to continue working directly with farmers in the field, to ensure that their interests and needs are being addressed.

“To sustain integrated breeding practices post-2014, GCP has established Communities of Practice (CoPs) that are discipline- and commodity-oriented,” says Ndeye Ndack Diop, GCP’s Capacity Building Leader and TLI Project Manager. “The ultimate goal of the CoPs is to provide a platform for community problem solving, idea generation and information sharing.”

Ndeye Ndack has been impressed with the way the chickpea community has embraced the CoP concept, noting that Pooran has played an important part in this and the TLI projects. “Pooran was able to bring developing-country partners outside of TLI into the CoP and have them work on TLI-related activities. Being part of the community means they have been able to source breeding material and learn from others. In so doing, we are seeing these partners in Kenya and Ethiopia develop their own germplasm.

“Furthermore, much of this new germplasm has been developed by Master’s and PhD students, which is great for the future of these breeding programmes.”

“GCP played a catalytic role in this regard,” explains Rajeev Varshney. “GCP provided a community environment in ways that very few other organisations can, and in ways that made the best use of resources,” he says. “It brought together people from all kinds of scientific disciplines: from genomics, bioinformatics, biology, molecular biology and so on. Such a pooling of complementary expertise and resources made great achievements possible.”

An Ethiopian farmer loads his bounteous chickpea harvest onto his donkey.

For Rajeev, the challenge facing chickpea research beyond GCP’s sunset is whether an adequate framework will be there to continue bringing this kind of community together.

“But that’s what we’re trying to do in the next phase of the Tropical Legumes Project (Tropical Legumes III, or TLIII), which kicks off in 2015,” explains Rajeev, who will be TLIII’s Principal Investigator. TLIII is to be led by ICRISAT.

“We will continue to work with the major partners as we did during GCP, which will involve, first of all, upscaling the activities we are doing now,” he says. “India currently has the capacity, the resources, to do this.”

Rajeev is hopeful that the relatively smaller national partners from Ethiopia and Kenya, and associated partners such as Egerton University, EIAR and maybe others, will have similar opportunities. “We hope they can also start working with their governments, or with agencies like USAID, and be successful at convincing them to fund these projects into the future, as GCP has been doing,” he says.

“The process is like a jigsaw puzzle: we have the borders done, and a good idea of what the picture is and where the rest of the pieces will fit,” he says.

Certainly for Paul Kimurto, the picture is clear for the future of chickpea breeding in Kenya.

“Improvements in chickpea resources cannot end now that new varieties have started entering farmers’ fields,” he says. “We’ve managed to develop a good, solid breeding programme here at Egerton University. The infrastructure is in place, the facilities are here – we are indeed equipped to maintain the life and legacy of GCP well beyond 2015.”

This can only be good news for lovers of the legume in India. With millions of smallholder farmers in Kenya and Ethiopia poised to exploit a ready market for new varieties that will change their families’ lives, chickpea’s potential for ensuring food security across the developing world seems more promising than ever.

Brazilian Corporation of Agricultural Research finds kindred spirit in GCP

Africa, Comparative genomics in cereals, Genomics, Groundnuts, Latin America, Legumes, Maize, Partnerships, Sorghum No Responses »

May 292015

A little over a decade ago, a PhD student in Brazil was poring over sorghum genes, trying to isolate one that helps plants withstand acidic soils.

Sorghum

Scientists at the Brazilian Corporation of Agricultural Research (EMBRAPA) had been researching plants that can grow well in acidic soils since the mid-1970s.

“What we have done within the Generation Challenge Programme,” explains Jurandir Magalhães, now a senior scientist for EMBRAPA, as he reflects back on the past decade, “is speed up maize and sorghum breeding for acidic soil adaptation”.

EMBRAPA partnered with the CGIAR Generation Challenge Programme (GCP) to advance plant genetics so as to breed aluminium-tolerant crops that will improve yields in harsh environments, in turn improving the quality of life for farmers.

Almost 70 percent of Brazil’s arable land is made up of acidic soils. That means the soil has toxic levels of aluminium and low levels of phosphorous – a lethal combination that makes crop production unsustainable. Aluminium toxicity in soil comes close to rivalling drought as a food-security threat in critical tropical food-producing regions. This is because acidic soils reduce root growth and deprive plants of the nutrients and water they need to grow.

Robert Schaffert – EMBRAPA’s longest-serving sorghum breeder – had developed mapping populations for aluminium tolerance in sorghum; these populations were the basis for the work supported by GCP.

During the first four years of the 10-year Programme, Jurandir was able to identify and clone the major aluminium-tolerance gene in sorghum – Alt_SB – using these mapping populations. The cloned gene has since enabled researchers across Africa and Asia to quickly and efficiently breed improved sorghum and maize plants that can withstand acidic soils.

Jurandir, speaking today about the work to advance sorghum genetic resources, says: “Wherever there are acidic soils with aluminium toxicity and low phosphorous availability, our results should be applicable.”

His story with EMBRAPA is one of many where GCP-supported projects have been instrumental in helping global research centres achieve their goals, which ultimately will help farmers worldwide.

Common objectives

Jurandir is now a research scientist in molecular genetics and genomics at the EMBRAPA Maize & Sorghum research centre. He and colleagues at the centre partnered with scientists in Africa, Asia and the US to identify and clone genes in sorghum, maize and rice that confer resistance or tolerance to stresses such as soil acidity, phosphorus efficiency, drought, pests and diseases.

Maize growing in Brazil.

“One important focus of GCP was linking basic research to applied crop breeding,” Jurandir says. “This is also the general orientation of our programme at EMBRAPA. We develop projects and research to produce, adapt and diffuse knowledge and technologies in maize and sorghum production by the efficient and rational use of natural resources.

“GCP provided both financial support and a rich scientific community that were useful to help us attain our common objectives.”

EMBRAPA’s work on cloning the Alt_SB gene would prove to be one of the first steps in GCP’s foundation sorghum and maize projects, both of which sought to provide farmers in the developing world with crops that will not only survive but thrive in the acidic soils where aluminium toxicity reduces crop production.

Leon Kochian of Cornell University in the US was Jurandir’s supervisor at the time when they applied for GCP funding. Leon was a Principal Investigator for various GCP research projects, researching how to improve grain yields of crops grown in acidic soils.

“The breeders are so important,” says Leon about the importance of supporting institutes such as EMBRAPA to advance plant genetics. “Ultimately, they are the cliché of ‘the rubber hits the road’. They’re the ones who translate what we’re trying to figure out into the actual crop improvements. That’s really what it’s all about.”

“That’s why EMBRAPA is a unique institution. Their mission is to get improved seed out, new germplasm out, for the farmers. They have the researchers in sorghum and maize breeding [Robert Schaffert and Sidney Parentoni] and molecular biology [Jurandir Magalhães and Claudia Guimarães].”

Maize farmers in Brazil.

Great minds think alike

Jurandir’s EMBRAPA colleague Claudia Guimarães, a plant molecular geneticist focusing on maize, says GCP promoted ‘products’, which also echoed the mission statement of EMBRAPA’s Maize & Sorghum research centre.

The centre’s mission is to: ‘Generate, adapt and transfer knowledge and technology that allows for the efficient production and use of maize, sorghum, and natural resources as well as promotes competitiveness in the agriculture sector, sustainable development, and the well-being of society.’

GCP, says Claudia, “wanted to extract something else from the science – products – the idea of a real, touchable product. You have to have progress: germplasm, lines, markers; they are quite practical things.

“The major goal of GCP is to deliver products that can improve people’s lives worldwide. So it needs to be readily available and useful for other scientists and for the whole community.”

GCP wanted to ensure that research products could and would be adopted, adapted and applied for the ultimate benefit of resource-poor farmers. The Programme therefore set out to catalyse interactions between the various players who are needed to bridge the gap between strategic research in advanced labs and resource-poor farmers.

GCP and EMBRAPA were both working towards tangible applied outcomes, says Claudia: “GCP was not only giving you money, they are really serious about what are you doing: ‘Did you deliver everything you promised?’”

Claudia delivered. She and her team at EMBRAPA were able to find an important aluminium-tolerance gene in maize similar to the sorghum gene. This outcome provided the basic materials for molecular-breeding programmes focusing on improving maize production and stability on acidic soils in Africa and other developing regions.

Maize trials in the field at EMBRAPA. The maize plants on the left are aluminium-tolerant while those on the right are not.

Multifaceted and tangible results

Through further GCP funding, EMBRAPA researchers Robert Schaffert and Sidney Parentoni were able to work together with two researchers from Kenya, Dickson Ligeyo and Samuel Gudu, to develop a breeding programme to combine the improved Brazilian germplasm with locally adapted Kenyan materials. A new base of improved germplasm was established for Kenyan breeders, which allowed the development of varieties adapted to acidic soils in Kenya.

Sidney, a maize breeder for GCP projects and now the deputy head of research and development for EMBRAPA Maize & Sorghum, says that the benefits of being part of GCP are multifaceted: “It was very important, not only for EMBRAPA as an institute, but also individually for each of the participants that had the opportunity to interact with partners in different parts of the word,” says Sidney.

A Kenyan farmer with her sorghum crop.

“Each of them adds a piece to build the results achieved by GCP, which from my perspective promoted a number of advances in the areas of genetics and breeding.

“Technologies such as root image scanning developed at Cornell [University] were transferred to EMBRAPA and allowed us to do large-scale screening in a number of maize and sorghum genotypes with large impacts in phosphorous-efficiency studies.

“Scientists from Africa were trained in breeding and screening techniques at EMBRAPA, and Brazilian scientists had the opportunity to go to Africa and interact with African researchers to jointly develop strategies for breeding maize and sorghum for low-phosphorous and acidic soils.

“These trainings and exchanges of experiences were very important for the people and for the institutions involved,” says Sidney.

Sustainable partnerships to break ground for groundnut

Groundnut

Soraya Leal-Bertioli is a researcher in the EMBRAPA Genetic Resources & Biotechnology centre. She works on groundnut (also known as peanut), and formed part of the GCP team working on groundnut with tolerance to drought and resistance to diseases and fungal contamination. She concurs that GCP united researchers from all over the globe in a common goal.

“GCP not only identified groups, but it went out, searched for people and invited contributions, offered resources to get them together. GCP brought partnerships to a whole new level,” Soraya says.

“Last time I checked there were 200 partners in 50 countries. No one is able to do that. It required a lot of money, a lot of resources, but the way it was dealt with in GCP was: ‘Let’s reach out for the main players, the ones who have the technology, and also the ones who can use the technology’.

“GCP used the resources for the benefit of the community and brought everybody together.”

Soraya says the traditional way of funding research often had ‘no structure’.

“Sometimes a university or funding body receives a large amount of money and decides to build something, a new institute in the middle of the jungle somewhere, but they don’t have anybody to run it; it is not sustainable.

“What GCP did was help to provide the structure and the agents for the whole system. They helped train the people to run the whole system. This is a very sustainable model, which is very likely to give good results in a much shorter time frame than other programmes.”

Watch Soraya – and other members of the team – discuss the complex personality of groundnut and groundnut research in our video series:

Genetic stocks AND people are products

The products and outcomes of the collaboration with GCP have included both the tangible and the not-so-tangible. Sidney says that a large quantity of Brazilian improved maize and sorghum lines tolerant to acidic soils has been developed over the years at EMBRAPA.

“These materials were shared with partners in Africa, and this was a major contribution to Kenyan farmers, as part of this collaborative work done in the scope of GCP.

“To be part of the programme has been very important for EMBRAPA’s research team. It has given us the opportunity to interact with a diversity of institutes.”

Sidney mentions institutes they gave worked with through GCP, including Cornell University and Texas A&M University in the US, the Japan International Research Center for Agricultural Sciences (JIRCAS), the International Rice Research Institute (IRRI), the International Maize and Wheat Improvement Center (CIMMYT), and various institutes in Africa, such as Moi University, Kenya, and the Kenya Agricultural and Livestock Research Organisation (KALRO).

Sidney concludes: “In this large network of partnerships, EMBRAPA was able to learn and to share information in a highly productive way.

“From my perspective, the involvement with GCP projects allowed me to grow as a researcher and as a person, and also at the same time to share and to acquire new knowledge in a number of areas. I think it was a ‘win-win’ interaction for all the participants.”

Many of the products generated within the scope of GCP, such as markers and germplasm, are already available within EMBRAPA’s breeding programmes. Avenues for further research have been paved based on the GCP achievements, and these new research lines will be continued within new projects.

As Claudia says: “The strong partnerships built along the way with GCP will be maintained by us joining with new research teams from other institutes and countries to work on new projects.”

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