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Nov 062015


 Photo: C Schubert/CCAFSWhere 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.

Photo: GCP

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

Photo: N Palmer/CIAT

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.

Photo: IITA

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.

Photo: N Palmer/CIAT

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.

Photo: Mann/ILRI

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.

Photo: IRRI

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
Photo: CSISA

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
Photo: N Palmer/CIAT

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.

Photo: IRRI

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.”

Photo: IITA

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.”

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Photo: E Hermanowicz/Bioversity International

Cowpea seeds dried in their pods.

Oct 162015
Photo: A Paul-Bossuet/ICRISAT

Pigeonpea farmers in India.

The tagline of the CGIAR Generation Challenge Programme (GCP) is ‘Partnerships in modern crop breeding for food security’. One of GCP’s many rewarding partnerships was with the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT).

The Institute was a source of valuable partnerships with highly regarded agricultural scientists and researchers, as well as of germplasm and genetic resources from its gene bank. With assistance from GCP, these resources have enabled scientists and crop breeders throughout Africa, Asia and Latin America to achieve crop improvements for chickpea, groundnut, pearl millet, pigeonpea and sorghum, all of which are staple crops that millions of people depend upon for survival.

“The philosophy of GCP at the start was to tap into and use the genomic recourses we had in our gene banks to develop ICRISAT’s and our partners’ breeding programmes,” says Pooran Gaur, GCP’s Product Delivery Coordinator for chickpeas, and Principal Scientist for chickpea genetics and breeding at ICRISAT.

ICRISAT’s gene bank is a global repository of crop genetic diversity. It contains 123,023 germplasm accessions – in the form of seed samples – assembled from 144 countries, making it one of the largest gene banks in the world.

The collection serves as insurance against genetic loss and as a source of resistance to diseases and pests, tolerance to climatic and other environmental stresses, and improved quality and yield traits for crop breeding.

Pooran says the ultimate goal of the GCP–ICRISAT partnership was to use the resources in the gene bank to develop drought-tolerant varieties that would thrive in semi-arid conditions and to make these varieties available to farmers’ fields within a decade.

Photo: S Kilungu/CCAFS

Harvesting sorghum in Kenya.

Setting a foundation for higher yielding, drought-tolerant chickpeas

Pooran was involved with GCP from its beginning in 2004 and was instrumental in coordinating chickpea projects.


Chickpea harvest, India.

“GCP got things started; it set a foundation for using genomic resources to breed chickpeas,” says Pooran. During Phase I of GCP (2004–2009), ICRISAT was involved in developing reference sets for chickpeas and developing mapping populations for drought-tolerance traits. It also collaborated with 19 other international research organisations to successfully sequence the chickpea genome in 2013 – a major breakthrough that paved the way for the development of even more superior chickpea varieties to transform production in semi-arid environments.

The International Chickpea Genome Sequencing Consortium, led by ICRISAT and partly funded by GCP, identified more than 28,000 genes and several million genetic markers. Pooran says these are expected to illuminate important genetic traits that may enhance new varieties.

The trait of most interest to many chickpea breeders is drought tolerance. In recent years, droughts in the south of India, the largest producer of chickpeas, have reduced yields to less than one tonne per hectare. Droughts have also diminished chickpea yields in Ethiopia and Kenya, Africa’s largest chickpea producers and exporters to India. While total global production of chickpeas is around 8.6 million tonnes per year, drought causes losses of around 3.7 million tonnes worldwide.


Putting it to the test: Rajeev Varshney (left, see below) and Pooran Gaur (right) inspecting a chickpea field trial.

Pooran says the foundation work supported by GCP was particularly important for identifying drought-tolerance traits. “We had identified plants with early maturing traits. This allowed us to develop chickpea varieties that have more chance of escaping drought when cereal farmers produce a fast-growing crop in between the harvest and planting of their main crops,” he says.

New varieties that grow and develop more quickly are expected to play a key role in expanding the area suitable for chickpeas 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.”

Developing capacity by involving partners in Kenya and Ethiopia

Photo: GCP

Monitoring the water use of chickpea plants in experiments at Egerton University, Njoro, Kenya.

As part of GCP’s Tropical Legumes I project (TLI), incorporated within its Legume Research Initiative (RI), ICRISAT partnered with Egerton University in Kenya and the Ethiopian Institute of Agricultural Research (EIAR) to share breeding skills and resources to produce higher yielding, drought-tolerant chickpea varieties.

“When we first started working on this project in mid-2007, our breeding programme was very weak,” says Paul Kimurto of the Faculty of Agriculture at Egerton University, who was Lead Scientist for chickpea research in the TLI project. “We have since accumulated a lot of germplasm, a chickpea reference set and a mapping population, all of which have greatly boosted our breeding programme.”

Paul says that with this increased capacity, his team in Kenya had released six new varieties of chickpea in the five years prior to GCP’s close at the end of 2014, and were expecting more to be ready within in the next three years.

In fields across Ethiopia, meanwhile, the introduction of new varieties has already brought a dramatic increase in productivity, with yields doubling in recent years, according to Asnake Fikre, Crop Research Directorate Director for EIAR.

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. This has transformed Ethiopia’s chickpeas from simple subsistence crop to one of great commercial significance.

Photo: S Sridharan/ICRISAT

This chickpea seller in Ethiopia says that kabuli varieties are becoming more popular.

Decoding pigeonpea genome

Two years prior to the decoding of the chickpea genome, GCP’s Director Jean-Marcel Ribaut announced that a six-year, GCP-funded collaboration led by ICRISAT had already sequenced almost three-quarters of the pigeonpea genome.

“This will have significant impact on resource-poor communities in the semi-arid regions, because they will have the opportunity to improve their livelihoods and increase food availability,” Jean-Marcel stated in January 2012.

Pigeonpea, the grains of which make a highly nutritious and protein-rich food, is a hardy and drought-tolerant crop. It is grown in the semi-arid tropics and subtropics of Asia, Africa, the Americas and the Caribbean. This crop’s prolific seed production and tolerance to drought help reduce farmers’ vulnerability to potential food shortages during dry periods.

Photo: B Sreeram/ICRISAT

A pigeonpea farmer in his field in India.

The collaborative project brought together 12 participating institutes operating under the umbrella of the International Initiative for Pigeonpea Genomics. The initiative was led by Rajeev K Varshney, GCP’s Genomics Theme Leader and Director of the Center of Excellence in Genomics at ICRISAT. Other participants included BGI in Shenzhen, China; four universities; and five other advanced research entities, both private and public. The Plant Genome Research Program of the National Science Foundation, USA, also funded part of this research.

“We were able to assemble over 70 percent of the genome. This was sufficient to enable us to change breeding approaches for pigeonpea,” says Rajeev. “That is, we can now combine conventional and molecular breeding methods – something we couldn’t do as well before – and access enough genes to create many new pigeonpea varieties that will effectively help improve the food security and livelihoods of resource-poor communities.”

Pigeonpea breeders are now able to use markers for genetic mapping and trait identification, marker-assisted selection, marker-assisted recurrent selection and genomic selection. These techniques, Rajeev says, “considerably cut breeding time by doing away with several cropping cycles. This means new varieties reach dryland areas of Africa and Asia more quickly, thus improving and increasing the sustainability of food production systems in these regions.”

Several genes, unique to pigeonpea, were also identified for drought tolerance by the project. Future research may find ways of transferring these genes to other legumes in the same family – such as soybean, cowpea and common bean – helping these crops also become more drought tolerant. This would be a significant asset in view of the increasingly drier climates in these crops’ production areas.

“We cannot help but agree with William Dar, Director General of ICRISAT, who observed that the ‘mapping of the pigeonpea genome is a breakthrough that could not have come at a better time’,” says Jean-Marcel.


East African farmers inspect pigeonpea at flowering time.

Securing income-generating groundnut crops in Africa

Groundnut, otherwise known as peanut, is one of ICRISAT’s mandate crops. Groundnuts provide a key source of nutrition for Africa’s farming families and have the potential to sustain a strong African export industry in future.

“The groundnut is one of the most important income-generating crops for my country and other countries in East Africa,” says Patrick Okori, who is a groundnut breeder and Principal Scientist with ICRISAT in Malawi and who was 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

It is the same in West Africa, according to groundnut breeder Issa Faye from the Institut Sénégalais de Recherches Agricoles (ISRA), 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 groundnut in West Africa.”

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, including those from ICRISAT, 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.

Photo: S Sridharan/ICRISAT

Drying groundnut harvest, Mozambique.

“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 science

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.

Supporting key crops in West Africa

Photo: N Palmer/CIAT

Harvested pearl millet and sorghum in Ghana.

With a focus on the semi-arid tropics, ICRISAT has been working closely with partners for 30 years to improve rainfed farming systems in West Africa. One sorghum researcher who has been working on the ground with local partners in Mali since 1998 is Eva Weltzien-Rattunde. She is an ICRISAT Principal Scientist in sorghum breeding and genetic resources, based in Mali, and was Principal Investigator for GCP’s Sorghum Research Initiative.

Eva and her team collaborated with local researchers at Mali’s Institut d’Economie Rurale (IER) and France’s Centre de coopération internationale en recherche agronomique pour le développement (CIRAD; Agricultural Research for Development) on a project to test a novel molecular-breeding approach: backcross nested association mapping (BCNAM). Eva says this method has the potential to halve the time it takes to develop local sorghum varieties with improved yield and adaptability to poor soil fertility conditions.

In another project, under GCP’s Comparative Genomics Research Initiative, Eva and her team are using molecular markers developed through the RI to select for aluminium-tolerant and phosphorus-efficient varieties and validating their performance in field trials across 29 environments in three countries in West Africa.

“Low phosphorus availability is a key problem for farmers on the coast of West Africa, and breeding phosphorus-efficient crops to cope with these conditions has been a main objective of ICRISAT in West Africa for some time,” says Eva.

“We’ve had good results in terms of field trials. We have at least 20 lines we are field testing at the moment, which we selected from 1,100 lines that we tested under high and low phosphorous conditions.” Eva says that some of these lines could be released as new varieties as early as 2015.

Ibrahima Sissoko, a data curator working with Eva’s team at ICRISAT in Mali, also adds that the collaborations and involvement with GCP have increased his and other developing country partners’ capacity in data management and statistical analysis, as well as helping to expand their network. “I can get help from other members of my sorghum community,” he says.

In summing up, Eva says: “Overall, we feel the GCP partnerships are enhancing our capacity here in Mali, and that we are closer to delivering more robust sorghum varieties that will help farmers and feed the ever-growing population in West Africa.”

Photo: A Paul-Bossuet/ICRISAT

Enjoying a tasty dish of sorghum.

Tom Hash, millet breeder and Principal Scientist at ICRISAT and GCP Principal Investigator for millet, shares Eva’s sentiments on GCP and the impact it is having in West Africa.

Between 2005 and 2007, GCP invested in genetic research for millet, which is the sixth most important cereal crop globally and a staple food (along with sorghum) in Burkina Faso, Chad, Eritrea, Mali, Niger, northern Nigeria, Senegal and Sudan.

With financial support from GCP, and drawing on lessons learnt from parallel GCP genetic research, including in sorghum and chickpea, ICRISAT was able to mine its considerable pearl millet genetic resources for desirable traits.

Hari D Upadhyaya, Principal Scientist and Head of Genebank at ICRISAT in India, led this task to develop and genotype a ‘composite collection’ of pearl millet. The team created a selection that strategically reduced the 21,594 accessions in the gene bank down to just 1,021. This collection includes lines developed at ICRISAT and material from other sources, with a range of valuable traits including tolerance to drought, heat and soil salinity and resistance to blast, downy mildew, ergot, rust and smut, and even resistance to multiple diseases.

The team then used molecular markers to fingerprint the DNA of plants grown from the collection.

“GCP supported collaboration with CIRAD, and our pearl millet breeding teams learnt how to do marker-based genetic diversity analysis,” says Tom. “This work, combined with the genomic resources work, did make some significant contributions to pearl millet research.”

Over 100 new varieties of pearl millet have recently been developed and released in Africa by the African Centre for Crop Improvement in South Africa, another developing country partner of ICRISAT and GCP. Tom says the initial genetic research was pivotal to this happening.

Photo: N Palmer/CIAT

A Ghanaian farmer examines his pearl millet harvest.

From poverty to prosperity through partnerships

Patrick Okori says that GCP has enabled his organisation to make a much stronger contribution to the quality of science.

“Prior to GCP, ICRISAT was already one of the big investors in legume research, because that was its mandate. The arrival of GCP, however, expanded the number of partners that ICRISAT had, both locally and globally, through the resources, strategic meetings and partnership arrangements that GCP provided as a broad platform for engaging in genomic research and the life sciences.”

This expansion of ICRISAT, facilitated by GCP, also enabled researchers from across the world and in diverse fields to interact in ways they had never had the opportunity to before, says Vincent Vadez.

“GCP has allowed me to make contact with people working on other legumes, for example,” he says. “It has allowed us to test hypotheses in other related crops, and we’ve generated quite a bit of good science from that.”

Pooran Gaur has had a similar experience with his chickpea research at ICRISAT.

“GCP provided the first opportunity for us to work with the bean and cowpea groups, learning from each other. That cross-learning from other crops really helped us. You learn many things working together, and I think we have developed a good relationship, a good community for legumes now.”

This community environment has made the best use of an unusual variety of skills, knowledge and resources, agrees Rajeev Varshney.

“It brought together people from all kinds of scientific disciplines – from genomics, bioinformatics, biology, molecular biology and so on,” he says. “Such a pooling of complementary expertise and resources made great achievements possible.”

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Photo: A Paul-Bossuet/ICRISAT

Man and beast team up to transport chickpeas in Ethiopia.


Sep 242015

Hei Leung has always been passionate about diversity, especially genetic diversity, and that’s one reason why he leapt at the chance to get involved with the CGIAR Generation Challenge Programme (GCP) right from its inception more than a decade ago.

Photo: IRRIBut GCP’s attraction for Hei wasn’t just about genetic diversity; it was also about working with diverse institutes and researchers. At the time, Hei had been working for the International Rice Research Institute (IRRI) for some 10 years, on and off, including a stint at Washington State University in the USA.

“The whole idea of the Challenge Programme was to bring people together from different places instead of an individual CGIAR Centre doing things,” he says.

Hei also saw the likely spin-offs from rice research to other crops such as wheat, maize and sorghum, which are also crucial to food security.

Rice is a ‘model crop’ because of its small genome. This means researchers in major cereals like wheat and maize, which have much bigger genomes but share genes of similar functions, can benefit from our work with rice.”

Photo: Jeffreyw/Flickr (Creative Commons)

From little pizzas great programmes grow!

It all began in 2003, over pizza, in Rome. Hei remembers that his commitment to GCP started when he met with a small group of people including Robert Zeigler, who was to become the first Director of GCP, and who is currently Director General of IRRI.

“Little did we know that pizza was so inspiring,” Hei says, recalling that it was during that meeting that they agreed on the name: the Generation Challenge Programme.

GCP was formally launched in 2004 in Brisbane, Australia, at the 4th International Crop Science Congress.

Making the Programme ‘pro-poor’

Hei was initially involved with GCP as Subprogramme Leader for Comparative Genomics for Gene Discovery between 2004 and 2007, and later as a Principal Investigator for the Rice Research Initiative. Taking on his leadership role, Hei recognised from the start that many crops important to developing communities in Asia and Africa needed to become more drought-tolerant because of the increasing effects of climate change.

“We wanted to have a programme that is what we call ‘pro-poor’,” he says. “The majority of the world’s people depend on crops such as rice, wheat and maize for food.”

“I always feel that if you can solve eastern India’s problems, you can solve most of the problems in the world,” Hei adds. “If you travel in eastern India, you can see climate change happening day in, day out. You don’t have to wait 10 years or 50 years; it’s happening already. They either have too much or too little water. It’s a high-stress environment.”

Photo: N Palmer/CIAT

Women at work threshing rice near Sangrur, Punjab, India.

Rice is the world’s most widely consumed cereal crop, and is particularly important as the staple food of 2.4 billion people in Asia. GCP recognised rice’s importance and invested almost USD 29.5 million in rice research and development.

Furthermore, the genetic breeding lessons learnt from rice can also be applied to other staple crops such as wheat, maize and sorghum.

Other GCP-supported researchers used comparative genetics to determine if the same or similar genes – for example, the phosphorus starvation tolerance (PSTOL1) protein kinase gene found in rice – was also present and operating in the same manner in sorghum and maize.

They found sorghum and maize varieties that contained genes, similar to rice’s PSTOL1, that also conferred tolerance to phosphorus-deficient soils by enhancing the plant’s root system. They were then able to develop molecular markers to help breeders in Brazil and Africa to identify lines with these genes, which can now be used in breeding and developed as varieties for farmers growing crops, particularly in acidic soils.

Seeing the potential for novel researcher interactions

Hei also recognised that crops that received less scientific attention but remained important as regional staple foods, such as bananas and plantains (of the genus Musa), could benefit from comparative genomics research.

“We had a highly motivated group of researchers willing to devote their efforts to Musa,” remembers Hei, who is currently IRRI Program Leader of Genetic Diversity and Gene Discovery.

“GCP’s community could offer a framework for novel interactions among banana-related actors and players working on other crops, such as rice. So, living up to its name as a Challenge Programme, GCP decided to take the gamble on banana genomics and help it fly.”

Photo:  Asian Development Bank

A banana farmer at work in the Philippines.

However, after four years, Hei found it difficult to maintain his GCP leadership role as well as keep on top of his IRRI work: “They said I was 50 percent with IRRI and 50 percent with GCP, but it is never like that in reality. I was always doing two jobs, or at least one-and-a-half jobs, and I didn’t think I was doing a good enough job for either. I thought it was time for other people to come into GCP.”

While Hei stepped down from a leadership role, he remained active working on GCP projects throughout the life of the Programme.

Hei says that during the last five years of GCP, a lot of technology to characterise genetic diversity evolved “to bring high-quality science to accelerate our mission to help the poor areas of Asia and Africa.”

Streamlining GCP reporting: from three reports a year down to just one One of the things that initially bothered Hei during his GCP time was the reporting requirements: “I remember we used to ask people to submit a mid-year report, end-of-year report and an update. “So I stuck my neck out during the last couple of years, and I said: ‘Guys, stop it. Don’t ask for these reports. They become mechanical. People just fill in the blanks. Ask for just one report before or after our annual meeting: just one report that people are excited to write about. And that was adopted.”

A MAGIC affair

The development of MAGIC (multi-parent advanced generation intercross) populations is the project that Hei gets most excited about. From these populations, created by crossing different combinations of multiple parents, plant lines can be selected that have useful characteristics such as drought tolerance, salinity tolerance and the ability to produce better quality grain.

“Now many crop breeders are calling for MAGIC populations,” says Hei. “I feel proud that at GCP we decided to support this concept and activity. This is one of GCP’s most important legacies and it’s one of my most favourite things.”

Photo: IRRI

Hei Leung looking relaxed in the lab at IRRI.

Honoured as a Fellow of the American Phytopathological Society (APS), Hei is recognised “for his leadership in the international community toward building and distributing rice genetic and genomic resources and creating capacity in plant pathology in the developing countries of Asia.”

Hei’s GCP leadership and research have clearly provided him with an important platform for taking on leadership and champion roles linking many individuals and organisations across Asia and Africa. His ASP profile concludes: “His promotion of collaborative research and his leadership in such programmes in the developing world have contributed to the building of a dynamic research community that promotes both basic knowledge and food security for Asia and the world.”

Making a difference to food security and farmer’s lives in developing countries is what GCP is all about. Such differences have been made possible through collaborative links that connect a diversity of organisations and people with the latest research in genetic diversity and breeding techniques.

Photo: IRRI

A farmer transplants rice in the Philippines.

It’s amore!

hei quoteHei recalls his personal and professional journey with GCP with much affection: “I think that it has been a wonderful scientific journey in terms of knowing the science and opening up my mind to being more receptive to alternative ways of doing things.

“There have been so many friends I have met through networking with GCP. Sometimes you go through bumpy roads, but anything you do will have bumpy times. And it’s very unusual to have a programme so illuminating. We honoured our commitment to finish in 10 years. It is a programme that had a fresh start and a clean ending.

“Most importantly, GCP has enabled plant breeders to embrace cutting-edge science through partnerships that focused on improving crop yields in areas previously deemed unproductive,” he says. “GCP is unique, one-of-a-kind, and I love it!”

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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.

Photo: Bill & Melinda Gates Foundation

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.

Groundnut facts and figures •	About one-third of groundnuts produced globally are eaten and two-thirds are crushed for oil  •	The residue from oil processing is used as an animal feed and fertiliser •	Oils and solvents derived from groundnuts are used in medicines, textiles, cosmetics, nitro-glycerine, plastics, dyes, paints, varnishes, lubricating oils, leather dressings, furniture polish, insecticides and soap •	Groundnut shells are used to make plastic, wallboard, abrasives, fuel, cellulose and glue; they can also be converted to biodiesel

“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.”

Photo: Joseph Hill/Flickr (Creative Commons)

Harvested groundnuts in Senegal.

How Africa lost its groundnut export market

Photo: V Vadez

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.”

Photo: S Sridharan/ICRISAT

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.

Photo: IITA

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.

Photo: N Palmer/CIAT

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.”

The Tropical Legumes I project (TLI) was initiated by GCP in 2007 and subsequently incorporated into the Programme’s Legumes Research Initiative (RI). The goal of the RI was to improve the productivity of four legumes – beans, chickpeas, cowpeas and groundnuts – that are important in food security and poverty reduction in developing countries, by providing solutions to overcome drought, poor soils, pests and diseases. TLI was led by GCP and focussed on Africa. Work on groundnut within TLI was coordinated by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). The partners in the four target countries were Malawi’s Chitedze Research Station, Senegal’s Institut Sénégalais de Recherches Agricoles (ISRA), and Tanzania’sAgricultural Research Institute (ARI). Other partners were France’s Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), the Brazilian Corporation of Agricultural Research (EMBRAPA) and Universidade de Brasil in Brazil, and University of Georgia in the USA. Tropical Legumes II (TLII) was a sister project to TLI, led by ICRISAT on behalf of the International Institute of Tropical Agriculture (IITA) and International Center for Tropical Agriculture (CIAT). It focussed on large-scale breeding, seed multiplication and distribution primarily in sub-Saharan Africa and South Asia, thus applying the ‘upstream’ research results from TLI and translating them into breeding materials for the ultimate benefit of resource-poor farmers. Many partners in TLI also worked on projects in TLII.

Photo: A Diama/ ICRISAT

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.

Photo: C Schubert/CCAFS

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.

Photo: C Schubert/CCAFS

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

Photo: C Schubert/CCAFS

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.

Photo: S Sridharan/ICRISAT

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.”

Photo: S Sridharan/ICRISAT

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.

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Photo: S Sridharan/ICRISAT

Oswin Madzonga, Scientific Officer at ICRISAT-Lilongwe, visits on-farm trials near Chitala Research Station in Salima, Malawi, where promising disesase-resistant varieties are being tested real life conditions.

Jun 122015
Photo: IITA

Growing cowpea pods.

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

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

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

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

Photo: IITA

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

Cowpea production – almost all of it comes from Africa

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

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

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

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

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

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

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

Photo: IITA

Farmers in Northern Nigeria transport their cowpea harvest.

Mapping the cowpea genome

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

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

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

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

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

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

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

Photo: IITA

Diversity of cowpea seed.

Breeding new varieties faster, using modern techniques


A farmer pleased with her cowpea plants.

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

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

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

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

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

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

Photo: IITA

A parasitic Striga plant, in a cowpea experimental plot.

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

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

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

The Tropical Legumes I project (TLI) was initiated by GCP in 2007 and subsequently incorporated into the Programme’s Legumes Research Initiative (RI). The goal of the RI was to improve the productivity of four legumes – beans, chickpeas, cowpeas and groundnuts – that are important in food security and poverty reduction in developing countries, by providing solutions to overcome drought, poor soils, pests and diseases. TLI was led by GCP and focussed on Africa. Work on cowpea within TLI was coordinated by the University of California, Riverside in the USA. Target-country partners were Institut de l’Environnement et de Recherches Agricoles (INERA) in Burkina Faso, Universidade Eduardo Mondlane in Mozambique and Institut Sénégalais de Recherches Agricoles (ISRA; Senegalese Agricultural Research Institute) in Senegal. Other partners were the International Institute of Tropical Agriculture (IITA) and USA’s Feed the Future Innovation Labs for Collaborative Research on Grain Legumes and for Climate-Resilient Cowpea. Tropical Legumes II (TLII) was a sister project to TLI, led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) on behalf of IITA and the International Centre for Tropical Agriculture (CIAT). It focussed on large-scale breeding, seed multiplication and distribution primarily in sub-Saharan Africa and South Asia, thus applying the ‘upstream’ research results from TLI and translating them into breeding materials for the ultimate benefit of resource-poor farmers. Many partners in TLI also worked on projects in TLII.

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

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

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

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

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

Photo: IITA

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

Outsourcing the molecular work

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

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

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

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

Getting the genotyping expertise on the ground

Photo: IITA

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

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

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

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

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

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

Mozambique – insects and drought are the problem

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

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

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

Photo: IITA

Cowpea plants infested by aphids.

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

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

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

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

Photo: IITA

Mature cowpea pods ready for harvesting.

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

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

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

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

Building a community of breeders to sustain success

Photo: C Peacock/IITA

Cowpea flower with developing pods.

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

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

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

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

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

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

Setting up breeders for the next 20 years

Photo: IITA

Farmer harvesting mature cowpea pods.

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

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

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

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Mar 172015


Photo: IRRI

Harvesting rice by hand in The Philippines.

Rice plays a key role in global food security, particularly in Asia, where 90 percent of the world’s rice is grown and eaten. By 2050, Asia’s population is estimated to grow by one billion to 5.2 billion people, who will continue to depend on rice as their major staple food.

But with rising demand for rice has also come increasing salinity, droughts and other stresses, along with decreasing areas of land available for farming the crop.

And that’s why the CGIAR Generation Challenge Programme (GCP) placed a major focus on rice throughout its 10 years of existence.

Key ingredient in the rice research fest was GCP’s relationship with the International Rice Research Institute (IRRI), headquartered in The Philippines. GCP supported IRRI in its endeavours to use the latest molecular plant-breeding techniques, along with traditional plant-breeding tools, to develop rice crops better able to cope with various stresses and still be productive.

“These ‘super’ crops will revolutionise rice farming,” says IRRI Director General Robert Zeigler, who was also the first Director of GCP.

For more on GCP’s rice research see our Sunset Story ‘The power of rice unlocked’.

Rice that can survive increasingly salty water

Climate change is one of the major threats facing rice production. As sea levels rise, salt water enters further up rivers with the high tides and affects rice production areas.

Each year in Bangladesh, during the boro rice season from November to May, salinity is so high that a white film of salt covers the country’s coastal paddy fields. For Bangladeshi farmers, this white colour is a warning sign that their land is ‘sick’. Around the world, Bangladesh, India, Myanmar and parts of Africa are most affected by increasing salinity.

Right from the beginning of GCP, salinity was a problem firmly on the rice research agenda.

Photos: IRRI

Highly saline soils in India (left), and a close-up showing a surface crust of salt on afflicted soil (right).

Leading this research was IRRI plant physiologist Abdelbagi Ismail, who dreamed of the ‘super’ rice crop that could “tolerate salinity, drought and submergence”.

Abdelbagi has managed and overseen most of the progress made during the discovery of a major genetic region, or quantitative trait locus (QTL), associated with salinity tolerance and named Saltol.

Photo: IRRI

Abdelbagi Ismail examines rice plants in the field in Bangladesh.

Its insertion into well-known rice varieties used by farmers in Bangladesh, Indonesia and The Philippines is part of the revolution taking place in rice research.

Abdelbagi says Saltol was mapped and markers were developed for its use in breeding more salt-tolerant rice varieties. Its salt-tolerance code is now being transferred into several varieties evaluated with IRRI partners in South and Southeast Asia.

“These projects also provided opportunities for both degree training and non-degree training to several of our partners in the countries involved,” he adds.

“Partnerships are crucial for us to build the capacity of the researchers in these countries and to ensure our outputs and outcomes reach the farmers that need them.

“All our partners benefitted from salt-tolerant varieties developed conventionally through this project, and they also provided pipelines for uptake and dissemination by farmers.”

Having developed new lines following the discovery of the Saltol QTL, Abdelbagi’s GCP-supported team trained plant breeders in country programmes to successfully breed for salt tolerance and other stresses.

In this way, Abdelbagi says, they are improving the capacity of researchers in developing countries to take up new breeding techniques, such as the use of molecular markers. “This can reduce the time it takes to breed new varieties, from six to ten years at the moment, down to two or three years,” he says.

This means that benefits to smallholder rice farmers struggling with salinity will happen sooner rather than later. And Abdelbagi credits GCP’s partnership approach, working directly with the countries in need, for the success so far.

“The salt-tolerant varieties are now being widely distributed,” he says. “Some of these varieties have doubled farmers’ productivity in affected areas.

“The work developed technologies of value to our needy farmers.

“We do believe this is the start of a second Green Revolution, especially for those who farm in less favourable areas and that missed this opportunity during the first Green Revolution.”

Partnership approach key to new rice gene for uptake of phosphorus

More than 60 percent of rainfed lowland rice is produced on poor and problem soils, including those that are naturally low in phosphorus. This is an essential for nutrient growing crops, but providing phosphorus through fertilisers is costly and unfeasible for many smallholder rice growers.

Photo: IRRI

IRRI’s Sheryl Catausan prepares the roots of a rice plant for scanning as part of the work of the PSTOL1, phosphorus uptake research team at IRRI.

This problem was the focus of GCP’s rice phosphorus-uptake project led by IRRI molecular biologist Sigrid Heuer.

The project was enormously successful, with its discovery of the PSTOL1 (‘phosphorus starvation tolerance 1’) gene within the Pup1 locus, which was published in the prestigious journal Nature.

“We wanted it in Nature for a couple of reasons,” she says. “To raise awareness about phosphorus deficiency and phosphorus being a limited resource, especially in poorer countries; and to draw attention to how we do molecular breeding these days, which is a speedier, easier and more cost-effective approach to developing crops that have the potential to alleviate such problems.”

Following the PSTOL1 discovery, researchers are now working with developing-country researchers and extension agencies to help them understand how to breed local varieties of rice that can be grown in phosphorus-deficient soils. They are also collaborating with other crop breeders looking to breed similar maize, sorghum and wheat varieties.

Tobias Kretzschmar, a molecular biologist with IRRI, says that GCP’s partnership approach was the key to the project having an impact on the rice farmers who needed it most.

“For me, the collaborations that were forged through these inter-institutional projects made the difference,” he says.

Sigrid agrees: “GCP was always there supporting us and giving us confidence, even when we were not sure.”

Solving the insoluble: a gene for drought tolerance

Rice is a crop that not only needs water, but loves water. So developing a drought-tolerant rice variety is a quest to find a seemingly impossible gene.

However, GCP-supported researchers did just that: they solved the insoluble.

“They were very successful in terms of getting drought tolerance,” says Hei Leung of IRRI, who was GCP Subprogramme Leader for the Comparative Genomics Research Initiative between 2004 and 2007, and also a Principal Investigator for the Rice Research Initiative. “They’re now getting a 1.5 tonne rice yield advantage under water stress. I mean, that’s unheard of! This is a crop that needs water.

“This is one of GCP’s big success stories; that you can actually get drought tolerance is a seemingly impossible task for a water-loving rice plant.”

As Subprogramme Leader, Hei played a critical role in the creation, management, delivery and communication of a wide portfolio of research projects. He credits the nature of how GCP was set up for accelerating the breeding programme for drought-tolerant rice.

“The advantage of GCP is that it is run by a small group of people who can make fast decisions,” he says. “This means they can respond to the needs of researchers: ‘Okay, we are going to invest on that. We’re going to have a meeting on this’.

“The real advantage of GCP is its agility. Usually with other organisations you have new ideas and then have to slave away for a year to get the funding to implement them. But GCP was quick.”

Photo: C Quintana/IRRI

Hei Leung (right) explains rice screening processes to a visiting scholar at IRRI.

IRRI and GCP deliver genetic resources to those who need them most

Tobias says one of the main objectives of GCP and IRRI is to make genetic stocks available to breeders, particularly in developing countries.

“Without that, IRRI would fail in its central mission to reduce hunger and poverty,” he says. “In order to achieve this mission, tight collaboration with our agricultural and extension partners in other countries is the key.”

What is a genetic stock? “A genetic stock is a line that has been created by modern breeders and researchers, using conventional technologies, specifically to address some specified scientific purpose, typically for gene discovery,” explains Ruaraidh Sackville Hamilton, an evolutionary biologist and head of the International Rice Genebank maintained by IRRI in The Philippines. This definition includes the notion of perpetuation (a ‘line’), which is central to genetic stocks: either the materials are genetically stabilised through sexual reproduction, or they can be distributed through vegetative propagation.

In fact, this idea of protecting the future through genetic material was influential in the choice of GCP as a CGIAR Challenge Program name. Hei, who was involved from the start with GCP, talks about the meeting in a Rome pizzeria where participants came up with the name: “When we talk about ‘generation’, we are really talking about the work we do with genetic diversity; it is about the future generation,” he says.

Part of that future generation is about sharing genetic resources or stocks, but first the genetic diversity of such stocks needs to be characterised. Hei remembers that one of the first GCP projects in 2004 brought together researchers in various countries to characterise the genetic diversity of various crops, including rice.

“But everyone was using different genotyping platforms and markers, and the technology back then was not what we have now,” he recalls.

“So we spent a lot of resources getting poor quality data. In a sense, it was a failure. On the other hand, it was also a success because we alerted people to the importance of characterising diversity in every single crop. The whole concept of getting all the national partners doing genetic resource characterisation is a good one.

“We have evolved the technology together over the last 10 years of GCP. Now the country partners feel enabled. They are not scared of the technology.”

Abdelbagi agrees that characterising genetic diversity is essential, and adds that making such genetic stocks readily available to breeders is also vital.

“This has not been an issue before,” he explains. “With the new regulations of germplasm control and intellectual property issues, it became extremely difficult to exchange germplasm with some countries. One important lesson we learnt was to engage in direct discussion with our partners in efforts to influence their policies and guidelines to allow essential exchange of genetic stocks and breeding material, at least at the regional level.”

Abdelbagi adds that another big challenge has been to provide country partners with materials and DNA markers for marker-assisted selection programmes and to make sure these were properly used in breeding programmes.

“We solved this by hosting a workshop at IRRI and with continued visits with GCP collaborators,” he says.

Photo: IRRI

Rice terraces in Ifugao Province in The Philippines.

‘Super’ crops: something ‘magic’ happens

Hei says that the GCP project he’s most passionate about, and one that leaves a lasting legacy, is the development of multiparent advanced generation intercross (MAGIC) populations, which will potentially yield lines that are tolerant to environmental stresses, grow well in poor soils and produce better quality grain.

“MAGIC populations will leave behind a very good resource towards improving different crop species,” says Hei. “I’m sure that they will expand on their own.”

Making MAGIC MAGIC – multiparent advanced generation intercross – allows crop breeders to identify the genes controlling quantitative traits, such as salinity tolerance, by crossing different combinations of multiple parents. The results of these crosses are plants whose genome is a mosaic of their multiple parents. MAGIC has multiple advantages compared with existing approaches, as it permits a more precise identification of genes that are responsible for particular rice traits. Even genes with minor effects can be pinpointed. Standard crosses (between two parents) show a poor correlation between the diversity found in the DNA (genetic diversity) and the diversity of the observable characteristics displayed by the plant (phenotypic diversity) when it grows as part of a crop. Because the MAGIC populations are created from multiple parents rather than by simply crossing two lines, making them more genetically diverse, and are the product of numerous generations of intercrossing the original founders or parent plants, creating greater opportunities for recombination and so ‘milling’ the genetic contributions from the different lines ever finer, scientists are able to more accurately identify the genes underlying important traits.  There are three main advantages of the MAGIC approach compared to existing approaches: 1. It enables scientists to more precisely identify the specific regions of the genome controlling key traits. 2. MAGIC populations incorporate a large proportion of the genetic diversity within elite rice varieties from around the world. 3. MAGIC enables the discovery of the best combinations of genes for important traits.

GCP funded the development of four kinds of rice populations, including indica MAGIC, which is the most advanced of the MAGIC populations developed so far. These populations contain multiple desirable traits, including: blast and bacterial blight-resistance, salinity and submergence tolerance and grain quality.

New generation of researchers working on a new rice revolution

Photo: IRRI

Rice farmer in her field in Rwanda.

Robert Zeigler’s dream of a new rice Green Revolution with ‘super crops’ is coming true, thanks in part to GCP’s focus on combining cutting-edge molecular plant-breeding techniques with conventional plant breeding.

“With all this going for us, the second Green Revolution means we can meet the great challenges ahead with unprecedented efforts that will result in unparalleled impacts,” he says. “This will range from mining the rice genomes for needed traits to developing climate change-ready rice.”

IRRI researchers like Abdelbagi agree that new plant-breeding techniques, such as those fostered by GCP, are making ‘super’ crops more likely: “I’m committed to understand how plants can be manipulated to adapt to, and better tolerate, extreme environmental stresses, which seems more feasible today than it has ever been before.

“GCP-supported work has provided mechanisms for developing varieties with multiple stress tolerances, besides the improvements in yield and quality.”

And for Hei, GCP’s 10-year legacy is not just about the technology but also about the people.

“Over ten years you have three generations of PhD students,” he says. “Many people became a ‘new generation’ scientist through this programme. Many people have benefitted. GCP is one of a kind. I’m just in love with it.”

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Mar 102015


Niaba Témé

Niaba Témé

“I can’t talk enough about the positive stories from the Generation Challenge Programme [GCP]. It initiated something new. I cannot measure its benefits for my country, for myself and for the sorghum-breeding and -producer communities. Right now, GCP has reached its sunset; but for me it is a sunrise, because what we have been left with is so very important.”

Growing up in a farming community in Mali, on the southern edge of the Sahara Desert, plant breeder Niaba Témé knows the ups and downs of farming in the harsh, volatile semiarid regions of Africa.

“I used to love harvesting the millet and helping my mother with her groundnut crops,” he remembers fondly. “We grew other dryland crops too, like sorghum, cowpeas, Bambara nuts, sesame and dah.”

Niaba’s village of Yendouma-Sogol is one of many villages balanced along the edge of the Bandiagara escarpment – 150 kilometres of sandstone cliffs soaring hundreds of metres above the sandy plains below. The region is considered one of the most challenging places in the world to be a farmer. The climate is harsh, with the average daily temperature on the dry, sun-scorched plains rarely falling below 30°C and often exceeding 40°C during the hottest months of the year. With no major water source available for drinking, cropping and livestock husbandry, the threat of drought is ever-present here, as it is across much of Africa’s semiarid landscape.

While much of Mali’s irrigated agriculture relies on water from the River Niger, villages like Niaba’s depend entirely on the 500 or so millimetres of rainfall they receive during the July–August wet season. In the years that the rains didn’t come, Niaba’s family were unable to harvest anything at all. The repeated failure of his parents’ crops – coupled with a natural interest in science – inspired Niaba to embark on a career where he could help farming families like his own defend themselves against the risks of drought and extreme temperatures.

Photo: F Fiondella/CCAFS

Farmland in Diouna, Mali. Farmers here must contend with the Sahel’s dry, sandy soil and whatever limited rainfall the clouds bring to grow sorghum, millet, maize, and other crops.

Niaba’s journey

Niaba’s first big step along the research road was when he enrolled to study agronomy at Mali’s Institut Polytechnique Rural de Formation et de Recherche Appliquée in Eastern Bamako. Within two years he was offered a scholarship to study plant breeding at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in Hyderabad, India. He then worked at the Cinzana Research Station in Mali.

Niaba later spent 11 years in the USA completing a bachelor’s degree, master’s degree and finally PhD in agronomy at Texas Tech University before returning home to Mali in 2007, where he was soon recruited by Mali’s Institut d’Économie Rurale (IER) to take charge of their new biotechnology lab at the Centre Régional de Recherche Agronomique.

His journey with the Generation Challenge Programme began in 2010 when IER received GCP funding to carry out sorghum research in Africa as part of GCP’s Sorghum Research Initiative (RI) launched that same year. The project was a collaboration with ICRISAT and France’s Centre de coopération internationale en recherche agronomique pour le développement (Agropolis–CIRAD; Agricultural Research for Development). With an initial focus on Mali, the project’s results would expand to encompass five other countries in the Sudano-Sahelian region: Burkina Faso, Ethiopia, Kenya, Niger and Sudan.

Sorghum the survivor gets even tougher


Hand milling of sorghum grains – an arduous task, mostly carried out by poor women in the drylands of Africa.

Drought-hardy crops such as sorghum are ideal for Mali’s conditions, where more water-intensive crops such as maize simply cannot survive. Millions of poor rural people across Africa depend on sorghum in their day-to-day lives: it is eaten in many forms, used to make alcoholic beverages and as animal fodder, and is converted into biofuel for cooking.

But even sorghum has its limits. While the demand for it has doubled in West Africa in the last 20 years, productivity has generally remained low, with an average yield of only one tonne per hectare for traditional varieties in Mali. This is mostly due to post-flowering drought, poor soils and farming conditions, and limited access to quality, high-yielding seed. As rainfall patterns become increasingly erratic and variable across the world, scientists warn of the need to improve sorghum’s broad adaptability to drought, to ensure future food security in Africa.

The GCP Sorghum RI, with Niaba’s help, aimed to support the development of new breeds of sorghum that could survive better on less water in drought-stricken parts of Africa. It sought to improve sorghum yield and quality for African farmers and, in turn, improve the livelihoods and food security of communities across sub-Saharan Africa.

In 2012, Niaba found himself travelling once again, this time to Australia with IER colleague Sidi B Coulibaly. They spent three weeks working alongside, and training with, Andrew Borrell and his sorghum research team at the Queensland Government Department of Agriculture, Fisheries and Forestry’s (DAFF) Hermitage Research Facility in Warwick.

“We have been collaborating with researchers at DAFF and The University of Queensland since 2009, to introduce what is called the ‘stay-green’ drought-resistant gene into our local sorghum varieties,” says Niaba.

Photo provided by A Borrell

Left to right: Niaba Témé with David Jordan (Australia), Sidi B Coulibaly (Mali) and Andrew Borrell (Australia), visiting an experiment at Hermitage Research Facility in Queensland, Australia.

Niaba’s no longer green when it comes to using stay-green

Stay-green is a drought adaptation trait that allows sorghum plants to stay alive and maintain green leaves for longer during post-flowering drought. This means the plants can keep growing and produce more grain in drier conditions. It has contributed significantly to an increase in sorghum yields, using less water, in north-eastern Australia and southern USA for the last two decades.

GCP’s stay-green project aimed to evaluate the potential for introducing stay-green into Mali’s local sorghum varieties, enriching Malian pre-breeding material for the trait, and training African sorghum researchers, such as Niaba, in the methods of improving yields and drought resistance in sorghum breeding lines from both Australia and Mali.

Photo provided by E Weltzein-Rattunde

A sorghum farmer in Mali.

“In Australia we learnt about association mapping, population genetics and diversity, molecular breeding, crop modelling using climate forecasts, and sorghum physiology,” says Niaba.

Learning to use molecular markers was particularly exciting, he says, “because molecular markers make it easier to see if the plant being bred has the gene related to drought tolerance, without having to go through the lengthy process of growing the plant to maturity and risk missing the trait through visual inspection.”

Niaba says the molecular training he received in Australia complemented previous training he had received through a collaborative GCP-funded project with Agropolis–CIRAD and Syngenta Foundation for Sustainable Agriculture, in which he learnt to use molecular markers to identify and monitor key regions of sorghum’s genome in consecutive breeding generations through a process called marker-assisted recurrent selection (MARS).

A large part of GCP’s focus is building such capacity among developing country partners to carry out crop research and breeding independently in the future, so they can continue developing new varieties with drought adaptation relevant to their own environmental conditions.

“Our time in Australia was an intense but rewarding experience, more so for the fact that between the efforts of Australia and Mali, we have now developed new drought-tolerant crops which will enhance food security for my country,” says Niaba. “Similarly with the help of Agropolis–CIRAD and Syngenta, we are using molecular markers to improve breeding efficiency of sorghum varieties more adapted to the variable environment of Mali.”

Photo provided by A Borrell

Niaba (foreground) examining a sorghum panicle at trials in Mali in 2009.

Sorghum sunrise in Mali

On the back of the MARS project, Niaba successfully obtained GCP funding in 2010 to carry out similar research with Agropolis–CIRAD and collaborators in Africa at ICRISAT.

“In that project, we were trying to enhance sorghum grain yield and quality for the Sudano-Sahelian zone of West Africa using the backcross nested association mapping (BCNAM) approach,” explains Niaba. “This involved using an elite recurrent parent that is already adapted to local drought conditions. The benefit of this approach is that it can lead to detecting elite varieties much faster.”

The approach has the potential to halve the time it takes to develop local sorghum varieties with improved yield and adaptability to drought. The project developed 100 lines for 50 populations from backcrosses carried out with 30 recurrent parents. The lines are now being validated in Mali.

Photo: P St-Jacques/DFATD-MAECD

Agronomists inspect a field of sorghum in Mali.

Niaba says such successful collaborations and capacity development opportunities have been made possible only through GCP support.

“We had some contacts before, but we didn’t have the funds or skills to really get into a collaboration. Now we’re motivated and are making connections with other people so we can continue working with the material we have developed.

“GCP’s time may be ending, but it very much represents a new day – a sunrise for the work we are doing with sorghum here in Mali.”

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Photo: N Palmer/CIAT

Sorghum for sale.

Mar 062015


Photo: IITA

A woman holds yam tubers in her hands in a market in West Africa.

Yam production in West Africa is plagued by unsustainable and suboptimal practices. Most farmers continue to grow local varieties that produce poor yields – and also lack aesthetic qualities that appeal to consumers, such as smooth skin and elegant tuber shape.

For a better future and a sustainable food supply, farmers need access to improved yam varieties that can tolerate changes in the climate and environment, as well as resist pests and diseases. Adopting new practices will also help farmers to increase their yields.

Yams play a key role in the food security, income generation and sociocultural life of at least 60 million people in Africa, where more than 95 percent of the world’s yam supply is produced. Worldwide, the tuber vegetable is grown and consumed across the tropics and subtropics of Asia, the Caribbean, the Pacific, and West and Central Africa. Such is the reliance on yams in parts of Africa that communities hold annual festivals to revere and celebrate the crop. The Igbo people in Nigeria hold a ‘new yam harvest’ festival every year at the end of the rainy season in August or September, when the yams are ready for harvest. People in both Nigeria and Ghana hold the ‘new yam eating’ festival, also known as the ‘hoot at hunger’ festival, which symbolises the end of a harvest and the beginning of the next cropping cycle.

Despite the importance of yams in West Africa, breeding efforts for improved varieties have been limited for a number of reasons. One is that local yam cultivars have different names in different communities, making germplasm management and research difficult. Another obstacle is the constraints on yam growth – the plants have a long growth cycle and are highly susceptible to pests and diseases, poor soil, weeds and drought.

Photo: J Haskins/Global Crop Diversity Trust

Dancers celebrate at a new yam festival in Nigeria.

Unique collaborations get yam research rolling

Photo: J Haskins/Global Crop Diversity Trust

A farmer in his yam field in Nigeria.

In 2004, the CGIAR Generation Challenge Programme (GCP) recognised the need to provide resource-poor farmers in West Africa with yam varieties that combine high yields with drought tolerance, pest and disease resistance, and good tuber quality. The Programme was created to advance plant genetics for 21 crops, with a view to improving the resources and capabilities of local breeders in developing countries. Yams were one of the crops that received funding for the first half of the 10-year Programme.

Robert Asiedu, Principal Investigator for GCP’s project assessing the genetic diversity of yams in West Africa, says the Programme improved yam breeding through its unique collaborations.

“The work was brief but the partnership arrangement was useful,” says Robert, who is Director of Research for Development at the International Institute of Tropical Agriculture (IITA), based in Nigeria.

Photo: IITA

A Nigerian farmer displays her healthy yam tubers.

His GCP-funded team included researchers from Centre de coopération internationale en recherche agronomique pour le développement (Agropolis–CIRAD; Agricultural Research for Development) in France, the International Potato Center (CIP) headquartered in Peru, the International Centre for Tropical Agriculture (CIAT) based in Colombia, the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) headquartered in India, Chile’s Instituto de Investigaciones Agropecuarias (INIA; Agricultural Research Institute), and the United States Department of Agriculture, plus experts in genome profiling and genetic analysis from Diversity Arrays Technology (DArT) in Australia. DArT provided high-throughput genotyping services that helped to profile yam’s genome.

Andrzej Kilian, DArT’s founder and director, says: “My company had a range of interactions with GCP, and I hope we had some positive impact on the outcomes.”

The researchers used molecular breeding tools – simple sequence repeat markers, or SSRs – to assess the genetic diversity of more than 500 yam accessions from Benin, DR Congo, Côte d’Ivoire, Equatorial Guinea, Gabon, Ghana, Nigeria, Sierra Leone and Togo. The assessment was a huge step forward in expanding the scientific knowledge of yam genetics, and ultimately in identifying suitable material for use in breeding programmes.

Photo: J Haskins/Global Crop Diversity Trust

Walking in yam fields.

IITA research scientist Maria Kolesnikova-Allen, also funded by GCP, says the yam work had two main objectives.

Photo: IITA

Yam vines twist up bamboo staking in a yam field.

“The primary focus of the first projects on yams involving molecular markers was to assess genetic diversity among yams originating from different West African countries and to find relationships between species. This information is important for future breeding and conservation efforts,” she says.

“Also, we were interested in confirming the use of molecular markers for analysis of yams and their potential use in breeding programmes.

“By confirming their usefulness in yam studies, we have offered a robust tool set for further studies on this crop.”

Photo: IITA

A trader displays clean and dried yam tubers at Bodija market, Ibadan, Nigeria.

As a result of the research, she says, “more knowledge and understanding has been achieved in terms of the genetic structure of yam populations in West and Central Africa, providing breeders with important knowledge for accessions selection to be included in breeding programmes.”

The genetic information that has been generated for yams will directly benefit countries in West Africa, according to Maria, “especially with IITA being positioned in the middle of the region and providing expert advice and dissemination of this information to local breeders and farmers.”

As part of her GCP-supported work, Maria supervised West African PhD students Jude Obidiegwu from Nigeria and Emmanuel Otoo from Ghana. Jude, a researcher at the National Root Crops Research Institute (NRCRI) in Nigeria, was responsible for GCP’s work on the genetic diversity of yams. His PhD assessed the genetic diversity of the West African yam collection.

African researchers carry GCP torch forward for yams

Jude is an example of how GCP focussed on fostering a base of experts on the ground in the countries where yams play an important role in people’s lives.

He was a participant in GCP’s Plant Genetic Diversity and Molecular Marker Assisted Breeding workshop held in Pretoria in June 2005. There he learned genomic DNA extraction methods, genetic and quantitative trait locus (QTL) mapping, development of core collections, and scientific proposal writing.

Photo: IITA

Woman counting money from the sales of yams at a yam market in Accra, Ghana.

“Our students at PhD level from Nigeria and Ghana were the main drivers of the projects at laboratory and field experiments level,” says Maria.

“Being involved in the projects allowed them to gain international exposure in their respective research fields and later advance their scientific career, becoming fully fledged yam scientists in their own right.

“If there be any hope of applying advanced genetics and genomics tools to the improvement of yam, it is researchers like Jude who will be the foot soldiers of that work in Africa.”

Photo: J Haskins/Global Crop Diversity Trust

A drummer adds his music to a new yam festival in Nigeria.

Maria feels there are strong foundations for further development of yam’s genetic resources after GCP’s sunset at the end of 2014.

“I would like to hope the future is bright,” she says. “As programmes for reducing hunger and poverty are multiplying and gaining momentum worldwide, I am sure the research on staple crops will be given much-needed financial support.

“I strongly believe in a partnership approach,” she maintains, drawing an analogy between GCP’s focus on crop genetics and the Human Genome Project that involved more than 300 partners collaborating between 1990 and 2003 to identify, map and sequence the human genome.

Robert agrees, forecasting that: “New projects will raise the capacity for yam breeding in West Africa by developing high-yielding and robust varieties of yams preferred by farmers and suited to market demands.”

Photo: IITA

A woman offers yam flour (known as elubo isu) for sale in Bodija market, Ibadan, Nigeria.

Mar 042015


Photo: IRRI

A woman harvests rice in Ifugao, The Philippines.

Plant geneticist Sigrid Heuer remembers very clearly entering the transgenic greenhouse in Manila to see her postdoctoral student holding up a rice plant with ‘monster’ roots.

“They were enormous,” she recalls. “This is when I knew we had the right gene. It confirmed years of work. That was our eureka moment.

So massive was the effect of that gene that I knew we had the right one.”

This genetic discovery – described in more detail a little later – is one of the shining lights of the 10-year-long CGIAR Generation Challenge Programme (GCP) established in 2004.

GCP-supported researchers aimed high: they wanted to contribute to food security in the developing world by using the latest advances in crop science and plant breeding.

And with the lives of half of the world’s population directly reliant on their own agriculture, there is a lot at stake. Land degradation, salinity, pollution and excessive fertiliser use are just some of the challenges.

Rice is one of the most critical crops worldwide

Amelia Henry, drought physiology group leader at the International Rice Research Institute (IRRI), explains why rice was such a critical crop for GCP research. She says rice is grown in a diverse set of environmental settings, often characterised by severe flooding, poor soils and disease.

Photo: A Barclay/IRRI

Cycling through rice fields in Odisha, India.

In Asia, 40 percent of rice is produced in rainfed systems with little or no water control or protection from floods and droughts – meaning rice plants are usually faced with too much or too little water, and rarely get just enough. In addition, 60 percent (29 million hectares) of the rainfed lowland rice is produced on poor and problem soils, including those that are naturally low in phosphorus.

Phosphorus deficiency and aluminium toxicity are two of the most widespread environmental causes of poor crop productivity in acidic soils, where high acid levels upset the balance of available nutrients. And drought makes these problems even worse.

Phosphorus is essential for growing crops. Its commercial use in fertilisers is due to the need to replace the phosphorus that plants have extracted from the soil as they grow. Soils lacking phosphorus are an especially big problem in Africa, and the continent is a major user of phosphate fertilisers. However, inappropriate use of fertilisers can, ironically, acidify soil further, since excess nitrogen fertiliser decreases soil pH.

Meanwhile, high levels of aluminium in soil cause damage to roots and impair crop growth, reducing their uptake both of nutrients like phosphorus and of water – making plants more vulnerable to drought. Aluminium toxicity is a major limitation on crop production for more than 30 percent of farmland in Southeast Asia and South America and approximately 20 percent in East Asia, sub-Saharan Africa and North America.

Rice is a staple for nearly half of the world’s seven billion people, and global consumption is rising. More than 90 percent of all the rice produced is consumed in Asia, where it is a staple for 2.4 billion people – a majority of the population. Outside Asia, rice consumption continues to rise steadily, with the fastest growth in sub-Saharan Africa, where people are eating 50 percent more rice than they were two decades ago. More than 90 percent of the world’s rice is produced by farmers in six countries: China, India, Indonesia, Bangladesh, Vietnam and Japan. China and India account for nearly half of that, with an output of more than 700 million tonnes.

The challenge today is to tap into the genetic codes of key crops such as rice and wheat to feed a growing global population. Science plays a crucial role in identifying genes for traits that help plants tolerate more difficult environmental conditions, and producing crop varieties that contain these genes.

Plant biologists are already developing new rice lines that produce higher yields in the face of reduced water, increasingly scant fertiliser as costs rise, and unproductive soils. However, ‘super’ crops are needed that can combine these qualities and withstand climate changes such as increasing temperatures and reduced rainfall in a century when the world’s population is estimated to reach nearly 10 billion people by 2050.

Bringing the best scientific minds to improve rice varieties

Ambitious in concept, the GCP research focussed on bringing together experts to work on these critical problems of rice production for some of the world’s poorest farmers.

The programme was rolled out in two phases that sought to explore the genetic diversity of key crops and use the most important genes for valuable traits, such as Sigrid’s discovery made in a rice variety that is tolerant of phosphorus-poor soils. Each phase involved dedicated teams in partner countries.

GCP: a two-act tale Phase I (2004–08) involved ‘discovery’ projects for 21 crops: beans, cassava, chickpeas, cowpeas, groundnuts, maize, rice, sorghum, wheat, bananas (and plantains), barley, coconuts, finger millet, foxtail millet, lentils, pearl millet, pigeonpeas, potatoes, soya beans, sweetpotatoes and yams. Phase II (2009–14) focussed on nine of these 21: beans, cassava, chickpeas, cowpeas, groundnuts, maize, rice, sorghum and wheat.

GCP Principal Investigator Hei Leung, from IRRI, says GCP is unique, one of kind: “I love it.” He says GCP has enabled rice researchers and breeders to embrace cutting-edge science through partnerships focussed on improving crop yields in areas previously deemed unproductive.

Hei says GCP wanted to target research during its second phase on those crops that most poor people depend upon. “We wanted to have a programme that is what we call ‘pro-poor’, meaning the majority of the world’s people depends on those crops,” he says.

Rice is the ‘chosen one’ of GCP’s cereal crop research and development, with the biggest slice of GCP’s research activities dedicated to this, the most widely consumed staple food.

It is crucial to increase rice supplies by applying research and development such as that carried out by GCP researchers over the past 10 years, Hei says.

For more on the relationship between GCP and IRRI – and an extra sprinkling of salt on your rice (fields) – see our Sunset Story ‘Rice research reaps a rich harvest of products, people and partners’.

Relying on rice’s small genome in the hunt for drought-tolerance genes

Researchers had been trying to map the genomes of key cereal crops for over two decades. Rice’s genome was mapped in 2004, just as GCP started.

Rice has a relatively small genome, one-sixth the size of the maize genome and 40 times smaller than the wheat genome. This makes it a useful ‘model’ crop for researchers to compare with other crops.

“People like to compare with rice because wheat and maize have very big genomes, and they don’t have the resources,” explains Hei.

After the rice genome had been sequenced, the next step was to focus down to a more detailed level: the individual genes that give rice plants traits such as drought tolerance. Identifying useful genes, and markers that act as genetic ‘tags’ to point them out, gives scientists an efficient way to choose which plants to use in breeding.

One of GCP’s Principal Investigators for rice was Marie-Noëlle Ndjiondjop, a senior molecular scientist with the Africa Rice Center.

“Rice is becoming a very important crop in Africa,” she says. “Production has been reduced by a lot of constraints, and drought is one of the most important constraints that we face in Africa.”

Meet Marie-Noëlle below (or on YouTube), in our series of Q&A videos on rice research in Africa.


Marie-Noëlle’s team recognised that drought tolerance was likely to be a complex trait in rice, involving many genes, due to the mix of physiological, genetic and environmental components that affect how well a plant can tolerate drought conditions. To help discover the rice varieties likely to have improved drought tolerance, Marie-Noëlle’s team used an innovative approach known as bi-parental marker-assisted recurrent selection (MARS).

“With such a complex trait, you really need to have all the tools and infrastructure necessary; through GCP we were able to buy the necessary equipment and put in the infrastructure needed to find and test the drought trait in rice lines.

“By using the MARS approach we identified the genetic regions associated with drought and are moving towards developing new rice lines that the African breeder and farmer will be using in the next decade to grow crops that are better able to withstand drought conditions.”

Likewise, Amelia Henry’s IRRI team also developed drought-tolerant lines, particularly for drought-prone areas of South Asia. She says many of the promising deep-rooted or generally drought-tolerant varieties identified in the early decades after IRRI’s foundation in 1960 are still used today as ‘drought donors’.

“Since the strength of our project was the compilation of results from many different sites, this work couldn’t have been done without the GCP partners,” she says. “They taught me a lot about how rice grows in different countries and what problems rice farmers face.”

Hei agrees that GCP partnerships have been crucial, including in the successful breeding of rice with drought tolerance: “They’re getting a 1.5-tonne rice yield advantage under water stress. I mean, that’s unheard of! This is a crop that needs water.”

Photo: IRRI

A rice farmer in Rwanda.

But the researchers could not rest with just one of rice’s problems solved.

Hei says GCP’s initial focus on drought was a good one but then, “I remember saying, ‘We cannot just go for drought. Rice, like all crops, needs packages of traits’.”

He knows that drought is just one problem facing rice farmers, noting “this broadened our research portfolio to include seeking to breed rice varieties with traits of tolerance to aluminium toxicity, salt and poor soils.”

The scope widens: phosphorus-hungry rice and a huge success

Sigrid Heuer was in The Philippines working for IRRI when she became involved in the ground-breaking phosphorus-uptake project for rice.

She took over the project being headed by Matthias Wissuwa. Much earlier, Matthias had noted that Kasalath – a traditional northern Indian rice variety that grew successfully in low-phosphorus soil – must contain advantageous genes. His postdoctoral supervisor, Noriharu Ae, thought that longer roots were likely to be the secret to some rice varieties being able to tolerate phosphorus-deficient soils.

Matthias, now a senior scientist in the Crop, Livestock and Environment Division at the Japan International Research Center for Agricultural Sciences (JIRCAS), says that for a long time he was not sure if it was just long roots: “It was a real chicken-and-egg scenario – does strong phosphorus uptake spur root growth, or is it the other way around?”

Photo: IRRI

Screening for phosphorus-efficient rice, able to make the best of low levels of available phosphorus, on an IRRI experimental plot in The Philippines. Some types of rice have visibly done much better than others.

Sigrid Heuer used her background in molecular breeding to take up the challenge with GCP to find the genes responsible for the Kasalath variety’s long roots.

“I spent years looking for the gene,” Sigrid says. “It was like trying to find a needle in a haystack; the genomic region where the gene is located is very complex.

“We had little biogenomics support at the time and I had three jobs and two kids; I was spending all my nights trying to find this gene.”

Photo: IRRI

Sigrid Heuer in the field at IRRI.

But one day, Sigrid’s postdoctoral student Rico Gamuyao excitedly called her downstairs to the transgenic greenhouses. “Rico had used transgenic plants to see whether this gene had any effect. He was digging out plants from experimental pods.”

Sigrid says that moment in the Manila labs was the turning point for the project’s researchers.

Matthias’ team had previously identified a genomic region, or locus, named Pup1 (‘phosphorus uptake 1’) that was linked to phosphorus uptake in lines of traditional rice growing in poor soils. However, its functional mechanism remained elusive until the breakthrough GCP-funded project sequenced the locus, showing the presence of a Pup1-specific protein kinase gene, which was named PSTOL1 (‘phosphorus starvation tolerance 1’). The discovery was reported in the prestigious scientific journal Nature on 23 August 2012 and picked up by media around the world.

The gene instructs the plant to grow larger and longer roots, increasing its surface area – which Sigrid compares to having a bigger sponge to absorb more water and nutrients in the soil.

“Plants growing longer roots have more uptake of phosphorus – and PSTOL1 is responsible for this.

“GCP was always there, supporting us and giving us confidence, even when we weren’t sure we were going to succeed,” she recalls. “They really wanted us to succeed, so, financially and from a motivational point of view, this gave us more enthusiasm.”

She adds, jokingly, “With so many people having expectations about the project, it was better not to disappoint.”

For some insight straight from the source, listen to Matthias in our podcosts below. In these two bitesized chunks of wisdom he discusses the importance of phosphorus deficiency and of incorporating PSTOL1 into national breeding programmes; his work in Africa and the possibility of uncovering an African ‘Pup2; what the PSTOL1 discovery has meant for him; and the essential contribution of international partnerships and GCP’s support.

Photo: IRRI

Members of the IRRI PSTOL1, phosphorus uptake research team chat in the field in 2012. From left to right they are are: Sigrid Heuer, Cheryl Dalid, Rico Gamuyao, Matthias Wissuwa and Joong Hyoun Chin.

Phosphorus-uptake gene not all it seemed – an imposter?

But PSTOL1 was definitely not what it seemed. “It was identified under phosphorus-deficient conditions and the original screen was set up for that,” says Sigrid.

Researchers eventually discovered that Pup1 and the PSTOL1 gene within it were not really all about phosphorus at all: “It turns out it is actually a root-growth gene, which just happens to enhance uptake of phosphorus and other nutrients such as nitrogen and potassium.

“The result is big root growth and maintenance of that growth under stress. If you have improved root growth, there is more access to soil resources, as a plant can explore more soil area with more root fingers.”

Her team showed that overexpression of PSTOL1 gene significantly improves grain yield in varieties growing in phosphorus-deficient soil – by up to 60 percent compared to rice varieties that did not have the gene.

In field tests in Indonesia and The Philippines, rice with the PSTOL1 gene produced about 20 percent more grain than rice without the gene. This is important in countries where rice is grown in poor soils.

Photo: T Saputro/CIFOR

A farmer harvests rice in South Sulawesi, Indonesia.

Sigrid, now based in Adelaide at the Australian Centre for Plant Functional Genomics, says the introduction of the new gene into locally adapted rice varieties in different locations across Asia and Africa is expected to boost productivity under low-phosphorus conditions.

“The ultimate measure for these kinds of projects is whether a gene works in different environments. I think we have a lot of evidence that says it does,” she says.

The discovery of PSTOL1 promises to improve the food security of rice farmers on phosphorus-deficient land though assisting them to grow more rice and earn more.

Titbits of further research successes: aluminium tolerance and MAGIC genes

Drought, low-phosphorus soils, aluminium toxicity, diseases, acid soils, climate change… the list seems never-ending for challenges to growing rice. Apart from the successes with drought and phosphorus that GCP scientists achieved, there was to be much more in the works from other GCP researchers.

During GCP Phase I, a team led by Leon Kochian of Cornell University, USA, with colleagues at the Brazilian Corporation of Agricultural Research (EMBRAPA), JIRCAS and Moi University, Kenya, successfully identified and cloned a major sorghum aluminium-tolerance gene.

In Phase II, they worked towards breeding aluminium-tolerant sorghum lines for sub-Saharan Africa, as well as applying what they learnt to discover similar genes in rice and maize.

Hei Leung says GCP leaves a lasting legacy in the development of multiparent advanced generation intercross (MAGIC) populations. These help breeders to identify valuable genes, and from among the populations they can also select lines to use in breeding that have favourable traits, such as being tolerant to environmental stresses, having an ability to grow well in poor soils or being able to produce better quality grain.

“MAGIC populations will leave behind a very good resource towards improving different crop species,” says Hei. “I’m sure that they will expand on their own.”

GCP funded the development of four different MAGIC populations for rice, including both indica and japonica types. And the idea of developing MAGIC populations has spread to other crops, including chickpeas, cowpeas and sorghum.

For more on MAGIC see our Sunset Story ‘Rice research reaps a rich harvest of products, people and partners’.

Photo: IRRI

A farmer harvests rice in Nepal.

Meeting the challenges and delivering outcomes to farmers

But with success come the frustrations of getting there, according to Nourollah Ahmadi, GCP Product Delivery Coordinator for rice across Africa. “This is because things are not always going as well as you want.”

Nourollah, from Centre de coopération internationale en recherche agronomique pour le développement (Agropolis–CIRAD; Agricultural Research for Development), says sometimes he felt overwhelmed coordinating GCP’s rice projects because “the challenges were perhaps too big.”

Project Delivery Coordinators monitor projects first-hand, conducting on-site visits, advising project leaders and partners and helping them implement delivery plans.

“One of the problems was the overall level of basic education of people who were involved in the project,” Nourollah says.

Photo: L Hartless/ACDI VOCA/USAID

Rice cultivation in Mali is on the rise.

His work with GCP has opened up new prospects for some of the poorest farmers in the world: “For five years, I have been coordinating one of the rice initiatives implemented by the Africa Rice Center and involving three African countries.” These are Burkina Faso, Mali and Nigeria.

He says GCP has brought much-needed expertise and technical skills to countries which can now use genetic insights to produce improved crops tolerant of drought conditions and poor soils and resistant to diseases. Using new molecular-breeding techniques has provided a more effective way to move forward, still firmly focussed on helping the world’s poorest farmers achieve food security.

“We don’t change direction, we change tools – sometimes you have a bicycle, sometimes you have a car,” Nourollah says.

Hei agrees there have been challenges: “It’s been a bumpy road to get to this point. But the whole concept of getting all the national partners doing genetic resource characterisation is a very good one.

Right now they are enabled; they are not scared about the technology. They can apply it.”

Sigrid says applied research is judged on two scales: “One is the publications and science you’re doing. The other is whether the work has any impact in the field, whether it works in the field. Bringing these two together is sometimes a challenge.”

GCP has managed to meet both challenges. New crop varieties have been released to farmers, and more than 450 scientifically reviewed papers have been published since 2004.

Building on the rice success story and leaving a lasting legacy

The work that GCP-supported researchers have done for rice is also being used in other crops. For example, researchers used comparative genomics to determine if genes the same as or similar to those found in rice are present and operating in the same manner in sorghum and maize.

The GCP team found sorghum and maize varieties that contained genes, similar to rice’s PSTOL1, that also confer tolerance of phosphorus-deficient soil with an enhanced root system. They were then able to develop markers to help breeders in Brazil and Africa identify phosphorus-efficient lines.

Making the most of comparative genomics Over the last 20 years, genetic researchers all over the world have been mapping the genomes of various crops. A genome is the total of all genes that make up the genetic code of an individual. Genome maps are now being used by geneticists and plant breeders to identify similarities and differences between the genes of different crop species. This process is termed comparative genomics and was an important tool for GCP during its second phase (2008–2014).

The knowledge that GCP-supported rice researchers have generated is shared through communities of practice, through websites, publications, research meetings and the Integrated Breeding Platform.

As Amelia Henry notes, GCP’s achievements will be defined by “the spirit of dedication to openness with research data, results and germplasm and giving credit and support to partners in developing countries.” The work in rice in many ways exemplifies GCP’s collaborative approach, commitment to capacity building and deeply held belief that together we can go so much further in helping farmers.

Unlocking genetic diversity in crops for the resource-poor was at the heart of GCP’s mission, which in 2003 promised ‘a new, unique public platform for accessing and developing new genetic resources using new molecular technologies and traditional means’.

Certainly for poor rice farmers in Asia and Africa, the work that GCP has supported in applying the latest molecular-breeding techniques will lead to rice varieties that will help them produce better crops on poor soils in a changing climate.

Photo: A Erlangga/CIFOR

Rice farmers in Indonesia.

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