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The Generation Challenge Programme: a tale of partnership

History, Partnerships, Themes No Responses »

Nov 062015

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

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

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

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

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

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

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

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

A little girl tucks into sorghum porridge in Mali.

The dawn of a new generation

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

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

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

Photo: J van de Gevel/Bioversity International

Wheat varieties in a field trial.

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

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

A programme where the spirit is palpable

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

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

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

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

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

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

Photo: Meena Kadri/Flickr (Creative Commons)

Harvesting wheat in India.

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

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

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

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

Exploring gene banks to uncover genetic wealth

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

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

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

Gene bank samples give a small snapshot of cowpea diversity.

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

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

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

Photo: International Potato Center (CIP)

Sweetpotato diversity.

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

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

Harvesting barley in Ethiopia.

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

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

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

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

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

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

Banana harvest for sale in Rwanda.

A need to focus and deliver products

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

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

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

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

Hard work: harvesting groundnut in Malawi.

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

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

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

Child eating rice.

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

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

Such products released on the ground included new varieties of:

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

Harvesting rice in India.

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

These will include varieties of:

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

Groundnut harvest, Ghana.

Giving a voice to all the cast and crew

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

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

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

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

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

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

Rice seed diversity.

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

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

Developing capacity and leadership in Africa

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

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

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

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

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

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

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

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

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

Nigerian cassava farmer.

A ‘sweet and sour’ sunset

Photo: Daryl Marquardt/Flickr (Creative Commons)

Maize at sunset.

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

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

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

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

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

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

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

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

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

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

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

For Chiedozie Egesi, the partnerships fostered by GCP have changed the way he does research: “We now have a network of cassava breeders that you can count on and relate with in different countries. This has really widened our horizons.

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

Markers for favourable genes boost crop yields, economies and spirits

Africa, Asia, Beans, Cassava, Chickpeas, Comparative genomics in cereals, Crop breeding, Genetic resources, Genomics, Maize, Rice, Sorghum, Themes, Wheat No Responses »

Oct 272015

GCP sowed the seeds of a genetic resources revolution.

“In the last 10 years we have had a revolution in terms of developing the genetic resources of crops.”

So says Pooran Gaur, Principal Scientist for chickpea genetics and breeding at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), and Product Delivery Coordinator for chickpeas for the CGIAR Generation Challenge Programme (GCP).

He attributes this revolution in large part to GCP, saying it “played the role of catalyst. It got things started. It set the foundation. Now we are in a position to do further molecular breeding in chickpeas.”

Led by Pooran, researchers from India, Ethiopia and Kenya worked together not only to develop improved, drought-tolerant chickpeas that would thrive in semiarid conditions, but also to ensure these varieties would be growing in farmers’ fields across Africa within a decade.

The 10-year Generation Challenge Programme, with the goal of improving food security in developing countries, aimed to leave plant genetic assets as an important part of its legacy.

Diagnostic, or informative, molecular markers – which act like ‘tags’ for beneficial genes scientists are looking for – are an increasingly important genetic tool for breeders in developing resilient, improved varieties, and have been a key aspect of GCP’s research.

Chickpeas, ready to harvest.

What is a diagnostic molecular marker?

Developments in plant genetics over the past 10–15 years have provided breeders with powerful tools to detect beneficial traits of plants much more quickly than ever before.

Scientists can identify individual genes and explore which ones are responsible for, or contribute to, valuable characteristics such as tolerance to drought or poor soils, or resistance to pests or diseases.

Once a favourable gene for a target agronomic trait is discovered and located in the plant’s genome, the next step is to find a molecular marker that will effectively tag it. A molecular marker is simply a variation in the plant’s DNA sequence that can be detected by scientists using any of a range of methods. When one of these genetic variants is found close on the genome to a gene of interest (or even within the gene itself), it can be used to indicate the gene’s presence.

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

Once a marker is found to be associated with a gene, or multiple genes, and determined to be significant to a target trait, it is designated an informative marker, diagnostic marker or predictive marker. Some simple traits such as flower colour are controlled by one gene, but more complex traits such as drought tolerance are controlled by multiple genes. Diagnostic markers enable plant breeders to practise molecular breeding.

Breeders use markers to predict plant traits

Hard work: a Ugandan bean farmer’s jembe, or hoe.

In the process known as marker-assisted selection, plant breeders use diagnostic molecular markers early in the breeding process to determine whether plants they are developing will have the desired qualities. By testing only a small amount of seed or seedling tissue, breeders are able to choose the best parent plants for crossing, and easily see which of the progeny have inherited useful genes. This considerably shortens the time it takes to develop new crop varieties.

“We use diagnostic markers to check for favourable genes in plants under selection. If the genes are present, we grow the seed or plant and observe how the genes are expressed as plant characteristics in the field [phenotyping]; if the genes are not present, we throw the seed or plant away,” explains Steve Beebe, a leading bean breeder with the International Center for Tropical Agriculture (CIAT) and GCP’s Product Delivery Coordinator for beans.

“This saves us resources and time, as instead of a growing few thousand plants to maturity, most of which would not possess the gene, by using markers to make our selection we need to grow and phenotype only a few hundred plants which we know have the desired genes.”

GCP supported 25 projects to discover and develop markers for genes that control traits that enable key crops, including bean and chickpea, to tolerate drought and poor soils and resist pests and diseases.

Genomic resources, including genetic maps and genotyping datasets, were developed during GCP’s first phase (2004–2008) and were then used in molecular-breeding projects during the second five years of the Programme (2009–2014).

“GCP’s philosophy was that we have, in breeding programmes, genomic resources that can be utilised. Now we are well placed, and we should be able to continue even after GCP with our molecular-breeding programme,” says Pooran.

A small selection of the rice diversity in the International Rice Research Institute gene bank – raw material for the creation of genomic resources.

Markers developed for drought tolerance

Cracked earth.

With climate change making droughts more frequent and severe, breeding for drought tolerance was a key priority for GCP from its inception.

Different plants may use similar strategies to tolerate drought, for example, having longer roots or reducing water loss from leaves. But drought tolerance is a complex trait to breed, as in each crop a large number of genes are involved.

Wheat, for example, has many traits – each controlled by different genes – that allow the crop to tolerate extreme temperature and/or lack of moisture. Identifying drought tolerance in wheat is therefore a search for many genes. In the particular case of wheat, this search is compounded by its genetic make-up, which is one of the most complex in the plant kingdom.

The difficulty of identifying genes that play a significant role in drought tolerance makes it all the more impressive when researchers successfully collaborate to overcome these challenges. GCP-supported scientists were able to develop and use diagnostic markers in chickpea, rice, sorghum and wheat to breed for drought tolerance. The first new drought-tolerant varieties bred using marker-assisted selection have already been released to farmers in Africa and Asia and are making significant contributions to food and income security.

Tanzanian sorghum farmer.

Markers developed for pests and diseases

A bumper harvest of cassava roots at the International Institute of Tropical Agriculture (IITA) in Nigeria.

Cassava mosaic disease (CMD) is the biggest threat to cassava production in Africa – where more cassava is grown and eaten than any other crop. A principal source of CMD resistance is CMD2, a dominant gene that confers high levels of resistance.

Nigerian GCP-supported researchers worked on identifying and validating diagnostic markers that are associated with CMD2. These markers are being used in marker-assisted selection work to transfer CMD resistance to locally-adapted, farmer-preferred varieties.

In the common bean, GCP-supported researchers identified genes for resistance to pests such as bean stem maggot in Ethiopia, as well as diseases such as the common mosaic necrosis potyvirus and common bacterial blight, which reduce bean quality and yields and in some cases means total crop losses.

Markers developed for acidic and saline soils

Sifting rice in Nepal.

Aluminium toxicity and phosphorus deficiency, caused by imbalanced nutrient availability in acid soils, are major factors in inhibiting crop productivity throughout the world. Aluminium toxicity also exacerbates the effects of drought by inhibiting root growth.

Diagnostic markers for genes that confer tolerance to high levels of aluminium and improve phosphorus uptake were identified in sorghum, maize and rice. The markers linked to these two sets of similar major genes have been used efficiently in breeding programmes in Africa and Asia.

Salt stress is also a major constraint across many rice-producing areas, partly because modern rice varieties are highly sensitive to salinity. Farmers in salt-affected areas have therefore continued growing their traditional crop varieties, which are more resilient but give low yields with poor grain quality. To address this issue, GCP supported work to develop and use markers to develop popular Bangladeshi varieties with higher tolerance to salt. GCP also funded several PhD students working in this area, one of whom was Armin Bhuiya.

Markers mean information, which means power

Diagnostic molecular markers are, in their most essential form, data. That means they are easily stored and maintained as data in publicly accessible databases and publications. Breeders can now access the molecular markers developed for various crops through the Integrated Breeding Platform – a web-based one-stop shop for integrated breeding information (including genetic resources), tools and support, which was established by GCP and is now continuing independently following GCP’s close – in order to design and carry out breeding projects.

“We could not have done that much in developing genomic resources without GCP support,” says Pooran. “Now the breeding products are coming; the markers are strengthening our work; and you will see in the next five to six years more products coming from molecular breeding.

“For me, GCP has improved the efficiency of the breeding programme – that is the biggest advantage.”

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

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

Oct 092015

Elizabeth Parkes

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

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

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

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

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

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

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

Turning point: cassava to help the vulnerable

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

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

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

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

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

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

Healthy cassava plants.

Challenges and opportunities

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

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

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

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

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

A place at the table, and sharing joy

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

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

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

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

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

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

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

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

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

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

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

Nurturing women

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

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

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

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

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

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

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

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

Sorghum sunrise: collaborating across continents to lift West African yields

Africa, Crop breeding, Sorghum No Responses »

Sep 282015

Sorghum is already a drought-hardy crop, and is a critical food source across Africa’s harsh, semi-arid regions where water-intensive crops simply cannot survive. Now, as rainfall patterns become increasingly erratic and variable worldwide, scientists warn of the need to improve sorghum’s broad adaptability to drought.

Crop researchers across the world are now on the verge of doing just that. Through support from the CGIAR Generation Challenge Programme (GCP), advanced breeding methods are enhancing the capacity of African sorghum breeders to deliver more robust varieties that will help struggling farmers and feed millions of poor people across sub-Saharan Africa.

A farmer in her sorghum field in Tanzania.

Sorghum at home in Africa

From Sudanese savannah to the Sahara’s desert fringes, sorghum thrives in a diverse range of environments. First domesticated in East Africa some 6000 years ago, it is well adapted to hot, dry climates and low soil fertility, although still depends on receiving some rainfall to grow and is very sensitive to flooding.

In developed countries such as Australia, sorghum is grown almost exclusively to make feed for cattle, pigs and poultry, but in many African countries millions of poor rural people directly depend on the crop in their day-to-day lives.

A Malian woman and her child eating sorghum.

In countries like Mali sorghum is an important staple crop. It is eaten in many forms such as couscous or tô (a kind of thick porridge), it is used for making local beer, and its straw is a vital source of feed for livestock.

While the demand for, and total production of, sorghum has doubled in West Africa in the last 20 years, yields have generally remained low due to a number of causes, from drought and problematic soils, to pests and diseases.

“In Mali, for instance, the average grain yield for traditional varieties of sorghum has been less than one tonne per hectare,” says Eva Weltzein-Rattunde, Principal Scientist for Mali’s sorghum breeding programme at the International Crops Research Institute for the Semi-Arid-Tropics (ICRISAT).

In a continued quest to integrate ways to increase productivity, GCP launched its Sorghum Research Initiative (RI) in 2010. This aimed to investigate and apply the approaches by which genetics and molecular breeding could be used to improve sorghum yields through better adaptability, particularly in the drylands of West Africa where cropping areas are large and rainfall is becoming increasingly rare.

Kick starting the work was a GCP-funded collaboration between project Principal Investigator Niaba Témé, plant breeder at Mali’s Institut d’économie rurale (IER) and the RI’s Product Delivery Coordinator Jean-François Rami of the Centre de coopération internationale en recherche agronomique pour le développement (CIRAD; Agricultural Research for Development), France, with additional support from the Syngenta Foundation for Sustainable Agriculture in Switzerland.

The collaboration aimed to develop ways to improve sorghum’s productivity and adaptation in the Sudano-Sahelian zone, starting with Mali in West Africa, and expanding later across the continent to encompass Burkina Faso, Ethiopia, Kenya, Niger and Sudan.

A farmer harvest sorghum in Sudan.

Sorghum gains from molecular research

Since 2008, with the help of CIRAD and Syngenta, Niaba and his team at IER have been learning how to use molecular markers to develop improved sorghum germplasm through identifying parental lines that are more tolerant and better adapted to the arid and volatile environments of Mali.

The two breeding methods used in the collaboration are known as marker-assisted recurrent selection (MARS) and backcross nested association mapping (BCNAM).

MARS

“MARS identifies regions of the genome that control important traits,” explains Jean-François. “It uses molecular markers to explore more combinations in the plant populations, and thus increases breeding efficiency.”

Syngenta, he explains, became involved through its long experience in implementing MARS in maize.

“Syngenta advised the team on how to conduct MARS and ways we could avoid critical pitfalls,” he says. “They gave us access to using the software they have developed for the analysis of data, and this enabled us to start the programme immediately.”

With the help of the IER team, two bi-parental populations from elite local varieties were developed, targeting two different environments found in sorghum cropping areas in Mali. “We were then able to use molecular markers through MARS to identify and monitor key regions of the genome in consecutive breeding generations,” says Jean-François.

“When we have identified the genome regions on which to focus, we cross the progenies and monitor the resulting new progenies,” he says. “The improved varieties subsequently go to plant breeders in Mali’s national research program, which will later release varieties to farmers.”

Jean-François is pleased with the success of the MARS project so far. “The development of MARS addressed a large range of breeding targets for sorghum in Mali, including adaptation to the environment and grain productivity, as well as grain quality, plant morphology and response to diseases,” he says. “It proved to be efficient in elucidating the complex relationships between the large number of traits that the breeder has to deal with, and translating this into target genetic ideotypes that can be constructed using molecular markers.”

Jean-François says several MARS breeding lines have already shown superior and stable performance in farm testing as compared to current elite lines, and these will be available to breeders in Mali in 2015 to develop new varieties.

Eva Weltzein-Rattunde examines sorghum plants with farmers in Mali.

BCNAM

Like MARS, the BCNAM approach shows promise for being able to quickly gain improvements in sorghum yield and adaptability to drought, explains Niaba, who is Principal Investigator of the BCNAM project. BCNAM may be particularly effective, he says, in developing varieties that have the grain quality preferences of Malian farmers, as well as the drought tolerance that has until now been unavailable.

“BCNAM involves using an elite recurrent parent that is already adapted to local drought conditions, then crossing it with several different specific or donor parents to build up larger breeding populations,” he explains. “The benefit of this approach is it can lead to detecting elite varieties much faster.”

Eva and her team at ICRISAT have also been collaborating with researchers at IER and CIRAD on the BCNAM project. The approach, she says, has the potential to halve the time it takes to develop local sorghum varieties with improved yield and adaptability to poor soil fertility conditions.

“We don’t have these types of molecular-breeding resources available in Mali, so it’s really exciting to be a part of this project,” she says. “Overall, we feel the experience is enhancing our capacity here, and that we are closer to delivering more robust sorghum varieties which will help farmers and feed the ever-growing population in West Africa.”

Indeed, during field testing in Mali, BCNAM lines derived from the elite parent variety Grinkan have produced more than twice the yields of Grinkan itself. As they are rolled out in the form of new varieties, the team anticipates that they will have a huge positive impact on farmers’ livelihoods.

Malian sorghum farmers.

Mali and Queensland – similar problem, different soil

In Mali and the wider Sahel region within West Africa, cropping conditions are ideal for sorghum. The climate is harsh, with daily temperatures on the dry, sun-scorched lower plains rarely falling below 30°C. With no major river system, the threat of drought is ever-present, and communities are entirely dependent on the 500 millimetres of rain that falls during the July and August wet season.

“All the planting and harvesting is done during the rainy season,” says Niaba. “We have lakes that are fed by the rain, but when these lakes start to dry up farmers rely mostly on the moisture remaining in the soil.”

Over 17 thousand kilometres to the east of Mali, in north-eastern Australia’s dryland cropping region, situated mainly in the state of Queensland, sorghum is the main summer crop, and is considered a good rotational crop as it performs well under heat and moisture stress. The environment here is similar to Mali’s, with extreme drought a big problem.

Average yields for sorghum in Queensland are double those in Mali—around two tonnes per hectare—yet growers still consider them low, directly limited by the crop’s predominantly water-stressed production environment in Australia.

One of the differentiating factors is soil. “Queensland has a much deeper and more fertile soil compared to Mali, where the soil is shallow, with no mulch or organic matter,” says Niaba. “Also, there is no management at the farm level in Mali, so when rain comes, if the soil cannot take it, we lose it.”

Photo: Bart Sedgwick/Flickr (Creative Commons)

Sorghum in Queensland, Australia.

Making sorghum stay green, longer

Another key reason for the difference in yields between Queensland and Mali is that growers in Queensland are sowing a sorghum variety of with a genetic trait that makes it more tolerant to drought.

This trait is called ‘stay-green’, and over the last two decades it has proven valuable in increasing sorghum yields, using less water, in north-eastern Australia and the southern United States.

Stay-green allows sorghum plants to stay alive and maintain green leaves for longer during post-flowering drought—that is, drought that occurs after the plant has flowered. This means the plants can keep growing and produce more grain in drier conditions.

“We’ve found that stay-green can improve yields by up to 30 percent in drought conditions with very little downside during a good year,” says Andrew Borrell from the Queensland Alliance for Agriculture and Food Innovation (QAAFI) at the University of Queensland (UQ) in Australia.

“Plant breeders have known about stay-green for some 30 years,” he says. “They’d walk their fields and see that the leaves of certain plants would remain green while others didn’t. They knew it was correlated with high yield under drought conditions, but didn’t know why.”

Stay-green’s potential in Mali

With their almost 20 years working on understanding how stay-green works, Andrew and his colleagues at UQ were invited by GCP in 2012 to take part in the IER/CIRAD collaborative project, to evaluate the potential for introducing stay-green into Mali’s local sorghum varieties and enriching Malian pre-breeding material for the trait.

A pivotal stage in this new alliance was a 12-month visit to Australia by Niaba and his IER colleague Sidi Coulibaly, to work with Andrew and his team to understand how stay-green drought resistance works in tall Malian sorghum varieties.

“African sorghum is very tall and sensitive to variation in day length,” explains Andrew. “We have been looking to investigate if the stay-green mechanism operates in tall African sorghums (around four metres tall) in the same way that it does in short Australian sorghum (one metre tall).”

Having just completed a series of experiments at the end of 2014, the UQ team consider their data as preliminary at this stage. “But it looks like we can get a correlation between stay-green and the size and yield of these Malian lines,” says Andrew. “We think it’s got great potential.”

Sorhum growing in Mozambique.

Sharing knowledge as well as germplasm

Eva Weltzein-Rattunde has played more of an on-the-ground capacity development role in Mali since accepting her position at ICRISAT in 1998. She says “the key challenges have been improving the infrastructure of the national research facilities [in Mali] to do the research as well as increasing the technical training for local agronomists and researchers.”

A Malian farmer harvests Sorghum.

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

A key objective of the IER team’s Australian visit was to receive training in the methods for improving yields and drought resistance in sorghum breeding lines from both Australia and Mali.

“We learnt about association mapping, population genetics and diversity, molecular breeding, crop modelling using climate forecasts, and sorghum physiology, plus a lot more,” says Niaba. This training complemented previous training Niaba and IER researchers had from CIRAD and ICRISAT through the MARS and BCNAM projects.

“We [CIRAD] have a long collaboration in sorghum research in Mali and training young scientists has always been part of our mission,” says Jean-François. “We’ve hosted several IER students here in France and we are always interacting with our colleagues in Mali either over the phone or travelling to Mali to give technical workshops in molecular breeding.”

Photo: Rita Willaert/Flickr (Creative Commons)

Harvested sorghum in Sudan.

Working together to implement MARS in the sorghum breeding program in Mali represented many operational challenges, Jean-François explains. “The approach requires a very tight integration of different and complementary skills, including a strong conventional breeding capacity, accurate breeders’ knowledge, efficient genotyping technologies, and skills for efficient genetic analyses,” he says.

Because of this requirement, he adds, there are very few reported experiences of the successful implementation of MARS. It is also the reason why these kinds of projects would normally not be undertaken in a developing country like Mali, but for the support of GCP and the dedicated mentorship of Jean-François.

“GCP provided the perfect environment to develop the MARS approach,” says Jean-François. “It brought together people with complementary skills, developed the Integrated Breeding Platform (IPB), and provided tools and services to support the programme.”

In addition to developing capacity, Jean-François says one of the great successes of both the MARS and the BCNAM projects was how they brought together Mali’s sorghum research groups working at IER and ICRISAT in a common effort to develop new genetic resources for sorghum breeding.

“This work has strengthened the IER and ICRISAT partnerships around a common resource. The large multiparent populations that have been developed are analysed collectively to decipher the genetic control of important traits for sorghum breeding in Mali,” says Jean-François. “This community development is another major achievement of the Sorghum Research Initiative.” The major challenge, he adds, will be whether this community can be kept together beyond GCP.

Considering the numerous ‘non-GCP’ activities that have already been initiated in Africa as a result of the partnerships forged through GCP research, Jean-François sees a clear indication that these connections will endure well beyond GCP’s time frame.

GCP’s sunset is Mali’s sunrise

Sorghum at sunset in Mozambique.

Among the new activities Jean-François lists are both regional and national projects aimed at building on what has already been achieved through GCP and linking national partners together. These include the West African Agricultural Productivity Program (WAAPP), the West Africa Platform being launched by CIRAD as a continuation of the MARS innovation, and another MARS project in Senegal and Niger through the Feed the Future Innovation Lab for Collaborative Research on Sorghum and Millet at Kansas State University.

“These are all activities which will help maintain the networks we’ve built,” Jean-François says. “I think it is very important that these networks of people with common objectives stick together.”

For Niaba, GCP provided the initial boost needed for these networks to emerge and thrive. “We had some contacts before, but we didn’t have the funds to really get into a collaboration. This has been made possible by GCP. Now we’re motivated and are making connections with other people on how we can continue working with the material we have developed.”

“I can’t talk enough of the positive stories from GCP,” he adds. “GCP initiated something, and the benefits for me and my country I cannot measure. Right now, GCP has reached its sunset; but for me it is a sunrise, because what we have been left with is so important.”

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

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

Jun 122015

Growing cowpea pods.

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

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

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

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

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

Cowpea production – almost all of it comes from Africa

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

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

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

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

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

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

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

Farmers in Northern Nigeria transport their cowpea harvest.

Mapping the cowpea genome

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

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

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

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

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

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

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

Diversity of cowpea seed.

Breeding new varieties faster, using modern techniques

A farmer pleased with her cowpea plants.

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

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

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

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

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

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

A parasitic Striga plant, in a cowpea experimental plot.

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

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

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

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

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

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

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

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

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

Outsourcing the molecular work

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

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

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

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

Getting the genotyping expertise on the ground

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

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

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

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

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

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

Mozambique – insects and drought are the problem

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

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

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

Cowpea plants infested by aphids.

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

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

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

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

Mature cowpea pods ready for harvesting.

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

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

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

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

Building a community of breeders to sustain success

Cowpea flower with developing pods.

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

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

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

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

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

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

Setting up breeders for the next 20 years

Farmer harvesting mature cowpea pods.

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

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

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

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

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

Jun 012015

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

Indian chickpea farmer with her harvest.

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

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

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

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

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

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

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

An Ethiopian farmer harvests her chickpea crop.

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

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

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

How drought affects chickpea

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

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

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

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

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

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

Escaping drought in India

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

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

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

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

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

Indian chickpea farmer with her harvest.

Developing new varieties: Tropical Legumes I in action

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

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

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

Developing chickpea pods

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

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

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

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

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

The magic of genetic diversity

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

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

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

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

Decoding the chickpea genome

Chickpea seed

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

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

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

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

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

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

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

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

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

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

Chickpea success in Africa: new varieties already changing lives

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Chickpea’s promise meeting future challenges

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Brazilian Corporation of Agricultural Research finds kindred spirit in GCP

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

May 292015

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

Sorghum

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

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

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

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

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

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

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

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

Common objectives

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

Maize growing in Brazil.

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

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

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

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

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

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

Maize farmers in Brazil.

Great minds think alike

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

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

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

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

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

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

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

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

Multifaceted and tangible results

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

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

A Kenyan farmer with her sorghum crop.

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

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

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

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

Sustainable partnerships to break ground for groundnut

Groundnut

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

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

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

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

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

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

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

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

Genetic stocks AND people are products

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

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

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

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

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

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

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

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

GCP Sunset Blog

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