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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.”

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

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

Oct 192015

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

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

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

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

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

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

Breeders access IBP’s services through its Web Portal.

Handling big data

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

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

An abundant harvest of nutrient-enriched cassava in Nigeria.

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

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

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

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

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

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

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

Clearing the bottleneck

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

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

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

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

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

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

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

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

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

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

Freshly threshed rice in India.

Providing help where it is needed

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

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

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

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

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

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

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

IBP Regional Hubs worldwide.

Breeding rice and maize more efficiently using IBP

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

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

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

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

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

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

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

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

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

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

From the GCP nest to world-scale deployment

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

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

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

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

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

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

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

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

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

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

Genetic stocks: the secret to more productive and efficient crops

Crop breeding, Genetic resources, Genetics, Themes No Responses »

Oct 192015

Precious sorghum seed diversity.

Humans are a protective species. We like to hoard away our precious items in vaults and safes made of concrete and steel, safe from thieves and catastrophes.

One not-so-obvious precious item, which many people take for granted, is seed. Without seeds, farmers would not be able to grow the grains, legumes, vegetables and fruits we eat.

For centuries, farmers have harvested seeds to store and protect for planting the following year. Most of the time, farmers will only keep seeds harvested from plants that have excelled in their environment – that have produced high yields or have favourable qualities such as larger or tastier grain. This simple iterative process of selecting primarily for high yields means that many crops today are closely related genetically, which can make them more vulnerable to evolving diseases and pests.

Without diversity, a severe epidemic can completely wipe out a farmer’s crop — and even a whole region’s crop. One of the best-known historical examples of just such a disastrous crop failure is the Irish Potato Famine of the 19^th century, when potato blight disease caused extensive death, human suffering and social upheaval. A number of crops around the world are in similar danger today, including wheat, threatened by the Ug99 strain of stem rust disease, to which almost all the world’s wheat is susceptible, and cassava, menaced by African cassava mosaic virus (ACMV).

The solution – genetic diversity

Plant breeders are looking at ways to increase diversity among cultivated crops, mitigating the risks of pests and diseases and introducing genes that help plants thrive in their local environments. To do this they are looking for useful traits in traditional cultivars, related species and wild ancestors. Such traits may include tolerance to drought, heat, and poor soils as well as insect and disease resistance. Breeders cross these donor parents with high-yielding elite breeding lines. The resulting new varieties have all the preferred traits of their parents and none of the deficiencies.

The genetic diversity of crops and their wild relatives is held by gene banks. There are thousands of gene banks worldwide, which collect and store seeds from hundreds of thousands of varieties. Breeders and researchers submit seed and tissue of wild and cultivated varieties as well as of lines of new varieties they are trying to breed.

Staff hard at work in the medium-term storage room of the International Rice Genebank at IRRI.

“For years, gene banks were primarily repositories, but with genetics evolving, and its subsequent application in plant breeding growing over the past 10 years, breeders and geneticists are now mining gene banks for wild and exotic species that might have favourable genes for desired traits,” explains Ruaraidh Sackville Hamilton, evolutionary biologist and head of the International Rice Genebank maintained by the International Rice Research Institute (IRRI) at its headquarters in The Philippines.

Sifting through all these gene-bank collections for plants with desired traits is challenging for breeders, even for traits that are easy to select for through visual screening. For example, Ruaraidh says the rice collection held at the International Rice Genebank contains more than 117,000 different types of rice, or accessions.

In recognition of this challenge, the initial rationale of the CGIAR Generation Challenge Programme’s (GCP) genetic stocks activity was to make the diversity in gene banks more easily accessible and practical for the study – and application – of genetic diversity.

Taking stock of genetic stocks

The first step towards making diversity accessible to breeders was to develop reference sets, representing as much genetic diversity as possible within a small proportion of gene bank accessions, selected through pedigree and molecular marker information.

“Reference sets reduce the number of choices that breeders have to search through, from thousands down to a few hundred,” says Jean Christophe Glaszmann, a plant geneticist at France’s Centre de coopération internationale en recherche agronomique pour le développement (CIRAD; Agricultural Research for Development), who held a managing role at GCP between 2004 and 2010, overseeing much of the reference-set work as GCP’s Subprogramme Leader on Genetic Diversity during GCP’s Phase I.

“A reference set represents the whole diversity found in the collections. Breeders can then use this sample to make crosses with their preferred varieties to try and integrate specific genes from the reference-set lines into those varieties.”

During the first phase of GCP (2004–2008), the Programme focused on identifying and characterising reference sets, each of roughly 300 lines, for banana, barley, cassava, chickpea, coconut, common bean, cowpea, faba bean, finger millet, foxtail millet, groundnut, lentil, maize, pearl millet, pigeonpea, potato, rice, sorghum, sweetpotato, wheat and yam. For most crops phenotyping data – information about physical plant traits – were also being made available for the reference sets, helping researchers to select material of interest for breeding.

A trainee at the International Maize and Wheat Improvement Center (CIMMYT) shows off diverse wheat ears, a small sample of the thousands of different lines found in the centre’s gene bank.

A further aspect of the work was the development of data-kits, which included molecular markers used to genotype and verify the sets. These kits allow plant scientists to assess and compare the diversity of their own collections with that of the reference sets, thus facilitating the introduction of new diversity in their prebreeding programmes.

Jean Christophe says the reference sets and data-kits were pivotal to the success of GCP’s molecular-breeding projects as they allowed researchers in different institutes to simultaneously work on the same genetic materials. “The sets served as consistent reference material that everybody collaborating on the project could analyse,” he explains. “Some of these collaborations involved hundreds of researchers, particularly those projects seeking to map genomes and identify genes.”

During the second phase of GCP (2009–2014), the reference sets for GCP’s Phase II target crops (cassava, chickpea, common bean, cowpea, groundnut, maize, rice, sorghum and wheat) were thoroughly phenotyped under different environments, including biotic and abiotic stresses. Jean Christophe says this work helped to identify new alleles (alternative forms of a gene or genetic locus) associated with desired traits that could be used for breeding purposes. Reference sets have been used successfully to identify and use new plant material in breeding programmes to improve various traits, particularly disease resistance and even more complex traits such as drought tolerance in cassava, chickpea, cowpea, maize, sorghum and wheat.

Broadening groundnut’s genetic base to prevent disease

A farmer in Senegal shows off her groundnut crop, almost ripe for harvest.

Another objective of GCP’s genetic stocks activity was to create new diversity within domesticated cultivated crops that have narrow genetic diversity, such as groundnut.

“The groundnuts we grow today are not too dissimilar to the ones that were first created naturally five to six thousand years ago,” says David Bertioli, a plant geneticist at the University of Brasília, Brazil. “This means that they are genetically very similar and have a narrow genetic base – the narrowest of any cultivated crop.”

This genetic similarity means that all cultivated groundnuts are very susceptible to diseases, particularly leaf spot, requiring expensive agrochemicals, especially fungicides. Without agrochemicals, which smallholder farmers in Africa and Asia often cannot afford, yields can be very low.

David says groundnut breeders always recognised the need to increase diversity, but because cultivated groundnuts have had a narrow base for so long, they became radically different from their wild relatives, making it very difficult to successfully cross wild species with cultivated species.

New genetic diversity is created through recombination, that is, through crossing contrasting varieties to create novel lines. Researchers can study these recombinants to identify genes associated with desired traits or use them in further crosses to develop new varieties.

“One of our first jobs was to make wild-species recombinants to trace out the relatedness of the wild-species genomes,” says David. “Once we could see the relatedness, we could see which wild species we could cross with cultivated lines. We had to do a lot of these crosses, but we eventually started to broaden the genetic diversity of the cultivated lines.”

David says this painstaking work, carried out under GCP, also formed the platform for sequencing the groundnut genome for the first time.

“That gave us an even greater understanding of the genetic structure, which is laying the groundwork for new varieties with traits such as added disease resistance and drought tolerance,” says David.

An additional key outcome of the groundnut aspect of the Legumes Research Initiative was developing ‘wild × domesticated’ synthetic lines, which are being crossed with domesticated groundnut varieties in Malawi, Niger, Senegal and Tanzania to introduce higher drought tolerance.

Like many areas of Africa struck by climate change, this village in Tanzania is suffering the effects of drought, with temperature increases and increasingly unpredictable rainfall.

Genetic gain by exploiting genetic stocks

The genetic stocks activity has generated a large and diverse array of resources across GCP’s target crops, not just for groundnut.

Recombinant inbred lines (RILs) incorporating specific traits of interest – particularly drought tolerance – have been developed for cowpea, maize, rice, sorghum and wheat. RILs are stabilised genetic stocks, created over several years by crossing two inbred lines followed by repeated generations of sibling mating to produce inbred lines that are genetically identical. These can then be used to discover and verify the role of particular genes and groups of genes associated with desired traits.

Near-isogenic lines (NILs) are RILs that possess identical genetic codes, except for differences at a few specific genetic loci. This enables researchers to evaluate particular genes and groups of genes that they may want to incorporate into breeding lines, particularly genes that have come from plants that otherwise do not perform well agronomically, such as wild relatives or older varieties. Sorghum NILs incorporating the Alt_SB locus for aluminium tolerance are being tested in Burkina Faso, Mali and Niger on problematic acid soils.

Multiparent advanced generation intercross (MAGIC) populations are a form of recombinants developed from crossing several parental lines from different genetic origins and, in some cases, exotic backgrounds to maximise the mix of genes from the parental lines in the offspring. MAGIC populations have been developed for chickpea, cowpea, rice and sorghum, and are being developed for common bean. Selected parental lines have been used to combine elite alleles for simple traits such as aluminium tolerance in sorghum and submergence tolerance in rice, as well as for complex traits such as drought or heat tolerance.

The further evaluation and use of the genetic stocks stemming from GCP-supported projects, as well as the generation of new genetic stocks, will continue beyond GCP through CGIAR’s Research Programs as well as through those institutes and national breeding programmes associated with GCP. There will be a continuing and evolving need to identify new genes associated with desired traits to improve cultivated germplasm.

Transplanting rice plants in Myanmar.

Sustaining genetic stocks into the future

Sustainability of genetic stocks has always been an issue, as stocks are generally not managed in a centralised way but are left under the direct responsibility of the scientists who developed them. These resources have therefore usually been handled in a highly ad hoc manner.

Because of high staff turnover in CGIAR Centers and breeding programmes in developing countries, and also because their management is neither centralised nor coordinated, these resources are also often lost as staff move from one organisation to another.

Although different genetic resources require different management protocols and storage timelines, the idea that gene bank curators take on the management of genetic stocks was proposed several years ago. For Centers such as IRRI, this is already a reality – for at least some of the genetic resources developed.

However, with the growing popularity of tapping into the rich diversity in gene banks that GCP’s genetic stocks activity has helped drive, gene bank supervisors such as Ruaraidh Sackville Hamilton are concerned about how genetic stocks will be sustained.

“The more popular molecular breeding and genetic stock become, the more funds we need to help us curate and disseminate them,” says Ruaraidh. He proposes to recover costs for managing genetic resources through a chargeback system on a two-tier scale, with non-profit organisations receiving stock at lower costs than commercial organisations. “Such a system would be sustainable and reduce the burden on gene bank institutes,” he says.

Still, the costs are of concern to institutes, particularly CGIAR Centers, which maintain most of the world’s plant crop gene banks.

CGIAR, a global partnership that unites 15 research Centres, including IRRI, is engaged in research for a food-secure future. CGIAR also created GCP. “CGIAR’s main priority is to conserve genetic resources for all humankind,” says Dave Hoisington, Senior Research Scientist and Program Director at the University of Georgia in the US. He 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) (both CGIAR Centers) and Chair of the GCP Consortium Committee.

“In both of the CGIAR Centers I worked in,” says Dave, “we always maintained the position that if the Center were to shut down, the last thing we’d do would be to turn out the lights of the gene bank. Even when we had funding cuts, we would never cut the budget for the gene bank.”

At work in the maize active collection in the gene bank at CIMMYT, which keeps maize and wheat diversity in trust for the world.

New programme to fund crop diversity

To alleviate some of the funding burden on CGIAR Centers and free up more money to use in research and development, CGIAR created a new CGIAR Research Program for Managing and Sustaining Crop Collections. The comprehensive five-year programme is managed by the Crop Trust (formerly Global Crop Diversity Trust).

“The Trust is a financial mechanism to raise an endowment, to ensure the conservation and availability of crop diversity,” says Charlotte Lusty, Genebank Programmes Coordinator at the Global Crop Diversity Trust. “The new programme is an extension of the Trust’s work. We aim to raise a USD 500 million endowment by 2016. The interest from this will be divided between the CGIAR Centers to cover all their long-term conservation operations.”

The new programme is also reviewing how gene banks within CGIAR are being managed, with a view to developing a quality management system, which it hopes will make gene banks run more efficiently. Charlotte says it is also encouraging stronger gene banks, such as IRRI and CIMMYT, to lend their expertise and experience to smaller gene banks so they can meet and build on their management quality.

Dave Hoisington believes that the new programme will provide CGIAR’s gene banks with greater capacity and make them even more attractive for researchers wanting to make use of their rich diversity.

A wide diversity of rice seed from the collection of the International Rice Genebank at IRRI.

Looking forward 30 years

Tapping into new diversity was really at the heart of GCP, and was a major, if not the primary, rationale for its establishment. Over its 10-year lifespan, has invested almost USD 28 million, or 18 percent of its budget, in developing genetic stocks, both reference sets and recombinants, for over 20 different crops.

Although these products don’t directly benefit farmers, they do indirectly help by significantly increasing breeding efficiency.

“All this research is fairly new and I am amazed, as a geneticist and plant breeder, by how far we’ve come since GCP started in 2004,” says David Bertioli.

“What we’ve been able to do in groundnut – that is, broaden the genetic base – hasn’t occurred naturally or through conventional breeding for thousands of years. And we’ve been able to do it in less than ten years.”

David recognises that the true value of the research will only be realised when new disease-resistant varieties are available for farmers to grow, which may be in five to seven years. “Only then will we be able to look back and consider the worth of all the hard work and cooperation that went into developing these precious varieties.”

GCP’s genetic stock activities have generated a large and diverse array of resources. These resources lay the foundation for further genetic stock development and will aid in researchers’ quests to tap into genetic diversity well into the future.

Chiedozie Egesi: cassava champion for poor African farmers

Africa, Capacity building, Cassava, Researchers No Responses »

Oct 182015

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

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

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

Peeling cassava roots.

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

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

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

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

Transformation for Chiedozie – and for cassava

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

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

Nigerian women at work processing cassava.

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

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

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

Cassava leaves.

Building African capacity

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

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

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

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

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

A paradigm shift

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

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

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

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

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

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

ICRISAT researchers agree, partnerships can alleviate poverty

Africa, Asia, Chickpeas, Crop breeding, Genetics, Groundnuts, Partnerships, Pearl millet, Phase I crops, Pigeonpeas, Sorghum No Responses »

Oct 162015

Pigeonpea farmers in India.

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

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

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

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

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

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

Harvesting sorghum in Kenya.

Setting a foundation for higher yielding, drought-tolerant chickpeas

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

Chickpea harvest, India.

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

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

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

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

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

New varieties that grow and develop more quickly are expected to play a key role in expanding the area suitable for chickpeas into new niches where the available crop-growing seasons are shorter.

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

Developing capacity by involving partners in Kenya and Ethiopia

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

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

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

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

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

Varieties like the large-seeded and high-valued kabuli have presented new opportunities for farmers to earn extra income through the export industry, and indeed chickpea exports from eastern Africa have substantially increased since 2001. This has transformed Ethiopia’s chickpeas from simple subsistence crop to one of great commercial significance.

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

Decoding pigeonpea genome

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

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

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

A pigeonpea farmer in his field in India.

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

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

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

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

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

East African farmers inspect pigeonpea at flowering time.

Securing income-generating groundnut crops in Africa

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

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

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

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

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

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

Drying groundnut harvest, Mozambique.

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

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

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

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

Supporting key crops in West Africa

Harvested pearl millet and sorghum in Ghana.

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

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

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

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

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

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

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

Enjoying a tasty dish of sorghum.

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

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

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

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

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

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

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

A Ghanaian farmer examines his pearl millet harvest.

From poverty to prosperity through partnerships

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

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

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

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

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

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

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

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

Ghana’s plant researchers blossom in their own fields

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

Oct 132015

The vibrant colours of a cassava leaf.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Cassava chips on sale in a Ghanaian market.

Ghana gains a new centre of excellence

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

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

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

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

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

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

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

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

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

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

Capacity building à la carte a real ‘life changer’

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

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

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

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

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

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

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

A Ghanaian farmer holds a just-harvested maize ear.

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

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

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

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

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

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

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

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

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

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

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

Scientists paint a rainbow over maize research

Africa, Asia, Comparative genomics in cereals, Crop breeding, Genomics, Latin America, Maize No Responses »

Oct 122015

Photo: One Acre Fund/Flickr (Creative Commons)

A Kenyan farmer harvesting her maize.

“The map of Kenya’s maize-growing regions mirrors the map of the nation’s acid soils.”

So says Dickson Ligeyo, senior research officer at the Kenya Agricultural and Livestock Research Organisation (KALRO; formerly the Kenya Agricultural Research Institute, or KARI), who believes this paints a sombre picture for his country’s maize farmers.

Maize is a staple crop for Kenyans, with 90 percent of the population depending on it for food. However, acid soils cause yield losses of 17–50 percent across the nation.

Soil acidity is a major environmental and economic concern in many more countries around the world. The availability of nutrients in soil is affected by pH, so acid conditions make it harder for plants to get a balanced diet. High acidity causes two major problems: perilously low levels of phosphorus and toxically high levels of aluminium. Aluminium toxicity affects 38 percent of farmland in Southeast Asia, 31 percent in Latin America and 20 percent in East Asia, sub-Saharan Africa and North America.

Aluminium toxicity in soil comes close to rivalling drought as a food-security threat in critical tropical food-producing regions. By damaging roots, acid soils deprive plants of the nutrients and water they need to grow – a particularly bitter effect when water is scarce.

Maize, meanwhile, is one of the most economically important food crops worldwide. It is grown in virtually every country in the world, and it is a staple food for more than 1.2 billion people in developing countries across sub-Saharan Africa and Latin America. In many cultures it is consumed primarily as porridge: polenta in Italy; angu in Brazil; and isitshwala, nshima, pap, posho,sadza or ugali in Africa.

Photo: Allison Mickel/Flickr (Creative Commons)

Ugali, a stiff maize porridge that is a staple dish across East Africa, being prepared in Tanzania.

Maize is also a staple food for animals reared for meat, eggs and dairy products. Around 60 percent of global maize production is used for animal feed.

The world demand for maize is increasing at the same time as global populations burgeon and climate changes. Therefore, improving the ability of maize to withstand acid soils and produce higher yields with less reliable rainfall is paramount. This is why the CGIAR Generation Challenge Programme (GCP) invested almost USD 12.5 million into maize research between 2004 and 2014.

GCP’s goal was to facilitate the use of genetic diversity and advanced plant science to improve food security in developing countries through the breeding of ‘super’ crops – including maize – able to tolerate drought and poor soils and resist diseases.

Researchers take on the double whammy of acid soils and drought

Part of successfully breeding higher-yielding drought-tolerant maize varieties involves improving plant genetics for acid soils. In these soils, aluminium toxicity inhibits root growth, reducing the amount of water and nutrients that the plant can absorb and compounding the effects of drought.

Improving plant root development for aluminium tolerance and phosphorous efficiency can therefore have the positive side effect of higher plant yield when water is limited.

A farmer in Tanzania shows the effects of drought on her maize crop. The maize ears are undersized with few grains.

Although plant breeders have exploited the considerable variation in aluminium tolerance between different maize varieties for many years, aluminium toxicity has been a significant but poorly understood component of plant genetics. It is a particularly complex trait in maize that involves multiple genes and physiological mechanisms.

The solution is to take stock of what maize germplasm is available worldwide, characterise it, clone the sought-after genes and implement new breeding methods to increase diversity and genetic stocks.

Scientists join hands to unravel maize complexity

Scientists from the International Maize and Wheat Improvement Center (CIMMYT) and the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) got their heads together between 2005 and 2008 to itemise what maize stocks were available.

Marilyn Warburton, then a molecular geneticist at CIMMYT, led this GCP-funded project. Her goal was to discover how all the genetic diversity in maize gene-bank collections around the globe might be used for practical plant improvement. She first gathered samples from gene banks all over the world, including those of CIMMYT and the International Institute of Tropical Agriculture (IITA). Scientists from developing country research centres in China, India, Indonesia, Kenya, Nigeria, Thailand and Vietnam also contributed by supplying DNA from their local varieties.

Maize diversity.

Researchers then used molecular markers and a bulk fingerprinting method – which Marilyn was instrumental in developing – for three purposes: to characterise the structure of maize populations, to better understand how maize migrated across the world, and to complete the global picture of maize biodiversity. Scientists were also using markers to search for new genes associated with desirable traits.

Allen Oppong, a maize pathologist and breeder from Ghana’s Crops Research Institute (CRI), of the Council for Scientific and Industrial Research, was supported by GCP from 2007 to 2010 to characterise Ghana’s maize germplasm. Trained in using the fingerprinting technique, Allen was able to identify distinctly different maize germplasm in the north of Ghana (with its dry savanna landscape) and in the south (with its high rainfall). He also identified mixed germplasm, which he says demonstrates that plant germplasm often finds its way to places where it is not suitable for optimal yield and productivity. Maize yields across the country are low.

Stocktaking a world’s worth of maize for GCP was a challenge, but not the only one, according to Marilyn. “In the first year it was hard to see how all the different partners would work together. Data analysis and storage was the hardest; everyone seemed to have their own idea about how the data could be stored, accessed and analysed best.

“The science was also evolving, even as we were working, so you could choose one way to sequence or genotype your data, and before you were even done with the project, a better way would be available,” she recalls.

Maize ears drying in Ghana.

Comparing genes: sorghum gene paves way for maize aluminium tolerance

In parallel to Marilyn’s work, scientists at the Brazilian Corporation of Agricultural Research (EMBRAPA) had already been advancing research on plant genetics for acid soils and the effects of aluminium toxicity on sorghum – spurred on by the fact that almost 70 percent of Brazil’s arable land is made up of acid soils.

What was of particular interest to GCP in 2004 was that the Brazilians, together with researchers at Cornell University in the USA, had recently mapped and identified the major sorghum aluminium tolerance locus Alt_SB, and were working on isolating the major gene within it with a view to cloning it. Major genes were known to control aluminium tolerance in sorghum, wheat and barley and produce good yields in soils that had high levels of aluminium. The gene had also been found in rape and rye.

GCP embraced the opportunity to fund more of this work with a view to speeding up the development of maize – as well as sorghum and rice – germplasm that can withstand the double whammy of acid soils and drought.

Maize trials in the field at EMBRAPA. The maize plants on the left are aluminium-tolerant and so able to withstand acid soils, while those on the right are not.

Leon Kochian, Director of the Robert W Holley Center for Agriculture and Health, United States Department of Agriculture – Agricultural Research Service and Professor at Cornell University, was a Principal Investigator for various GCP research projects investigating how to improve grain yields of crops grown in acid soils. “GCP was interested in our work because we were working with such critical crops,” he says.

“The idea was to use discoveries made in the first half of the GCP’s 10-year programme – use comparative genomics to look into genes of rice and maize to see if we can see relations in those genes – and once you’ve cloned a gene, it is easier to find a gene that can work for other crops.”

The intensity of GCP-supported maize research shifted up a gear in 2007, after the team led by Jurandir Magalhães, research scientist in molecular genetics and genomics of maize and sorghum at EMBRAPA, used positional cloning to identify the major sorghum aluminium tolerance gene SbMATE responsible for the Alt_SB aluminium tolerance locus. The team comprised researchers from EMBRAPA, Cornell, the Japan International Research Center for Agricultural Sciences (JIRCAS) and Moi University in Kenya.

By combing the maize genome searching for a similar gene to sorghum’s SbMATE, Jurandir’s EMBRAPA colleague Claudia Guimarães and a team of GCP-supported scientists discovered the maize aluminium tolerance gene ZmMATE1. High expression of this gene, first observed in maize lines with three copies of ZmMATE1, has been shown to increase aluminium tolerance. ZmMATE1 improves grain yields in acid soil by up to one tonne per hectare when introgressed in an aluminium-sensitive line.

Photos: 1 – V Alves ; 2 – F Mendes; both edited by C Guimarães

The genetic region, or locus, containing the ZmMATE1 aluminium tolerance gene is known as qALT6. Photo 1 shows a rhyzobox containing two layers of soil: a corrected top-soil and lower soils with 15 percent aluminium saturation. On the right, near-isogenic lines (NILs) introgressed with qALT6 show deeper roots and longer secondary roots in the acidic lower soil, whereas on the left the maize line without qALT6, L53, shows roots mainly confined to the corrected top soil. Photo 2 shows maize ears from lines without qALT6 (above) and with qALT6 (below); the lines with qALT6 maintain their size and quality even under high aluminium levels of 40 percent aluminium saturation.

The outcomes of these GCP-supported research projects provided the basic materials, such as molecular markers and donor sources of the positive alleles, for molecular-breeding programmes focusing on improving maize production and stability on acid soils in Latin America, Africa and other developing regions.

Kenya deploys powerful maize genes

One of those researchers crucial to achieving impact in GCP’s work in maize was Samuel (Sam) Gudu of Moi University, Kenya. From 2010 he was the Principal Investigator for GCP’s project on using marker-assisted backcrossing (MABC) to improve aluminium tolerance and phosphorous efficiency in maize in Kenya. This project combined molecular and conventional breeding approaches to speed up the development of maize varieties adapted to the acid soils of Africa, and was closely connected to the other GCP comparative genomics projects in maize and sorghum.

MABC is a type of marker-assisted selection (see box), which Sam’s team – including Dickson Ligeyo of KALRO – used to combine new molecular materials developed through GCP with Kenyan varieties. They have thus been able to significantly advance the breeding of maize varieties suitable for soils in Kenya and other African countries.

Maize and Comparative Genomics were two of seven Research Initiatives (RIs) where GCP concentrated on advancing researchers’ and breeders’ skills and resources in developing countries. Through this work, scientists have been able to characterise maize germplasm using improved trait observation and characterisation methods (phenotyping), implement molecular-breeding programmes, enhance strategic data management and build local human and infrastructure capacity.

The ultimate goal of the international research collaboration on comparative genomics in maize was to improve maize yields grown on acidic soils under drought conditions in Kenya and other African countries, as well as in Latin America. Seven institutes partnered up to for the comparative genomics research: Moi University, KALRO, EMBRAPA, Cornell University, the United States Department of Agriculture (USDA), JIRCAS and the International Rice Research Institute (IRRI).

“Before funding by GCP, we were mainly working on maize to develop breeding products resistant to disease and with increased yield,” says Sam. “At that time we had not known that soil acidity was a major problem in the parts of Kenya where we grow maize and sorghum. GCP knew that soil acidity could limit yields, so in the work with GCP we managed to characterise most of our acid soils. We now know that it was one of the major problems for limiting the yield of maize and sorghum.

“The relationship to EMBRAPA and Cornell University is one of the most important links we have. We developed material much faster through our collaboration with our colleagues in the advanced labs. I can see that post-GCP we will still want to communicate and interact with our colleagues in Brazil and the USA to enable us to continue to identify molecular materials that we discover,” he says. Sam and other maize researchers across Kenya, including Dickson, have since developed inbred, hybrid and synthetic varieties with improved aluminium tolerance for acid soils, which are now available for African farmers.

A Kenyan maize farmer.

“We crossed them [the new genes identified to have aluminium tolerance] with our local material to produce the materials we required for our conditions,” says Sam.

“The potential for aluminium-tolerant and phosphorous-efficient material across Africa is great. I know that in Ethiopia, aluminium toxicity from acid soil is a problem. It is also a major problem in Tanzania. It is a major problem in South Africa and a major problem in Kenya. So our breeding work, which is starting now to produce genetic materials that can be used directly, or could be developed even further in these other countries, is laying the foundation for maize improvement in acid soils.”

Sam is very proud of the work: “Several times I have felt accomplishment, because we identified material for Kenya for the first time. No one else was working on phosphorous efficiency or aluminium tolerance, and we have come up with materials that have been tested and have become varieties. It made me feel that we’re contributing to food security in Kenya.”

Maize grain for sale.

Maize for meat: GCP’s advances in maize genetics help feed Asia’s new appetites

Reaping from the substantial advances in maize genetics and breeding, researchers in Asia were also able to enhance Asian maize genetic resources.

A pig roots among maize ears on a small farm in Nepal.

Bindiganavile Vivek, a senior maize breeder for CIMMYT based in India, has been working with GCP since 2008 on improving drought tolerance in maize, especially for Asia, for two reasons: unrelenting droughts and a staggering growth the importance of maize as a feedstock. This work was funded by GCP as part of its Maize Research Initiative.

“People’s diets across Asia changed after government policies changed in the 1990s. We had a more free market economy, and along with that came more money that people could spend. That prompted a shift towards a non vegetarian diet,” Vivek recounts.

“Maize, being the number one feed crop of the world, started to come into demand. From the year 2000 up to now, the growing area of maize across Asia has been increasing by about two percent every year. That’s a phenomenal increase. It’s been replacing other crops – sorghum and rice. There’s more and more demand.

“Seventy percent of the maize that is produced in Asia is used as feed. And 70 percent of that feed is poultry feed.”

In Vietnam, for example, the government is actively promoting the expansion of maize acreage, again displacing rice. Other Asian nations involved in the push for maize include China, Indonesia and The Philippines.

A farmer in Indonesia transports his maize harvest by motorcycle.

The problem with this growth is that 80 percent of the 19 million hectares of maize in South and Southeast Asia relies on rain as its only source of water, so is prone to drought: “Wherever you are, you cannot escape drought,” says Vivek. And resource-poor farmers have limited access to improved maize products or hybrids appropriate for their situation.

Vivek’s research for GCP focused on the development – using marker-assisted breeding methods, specifically marker-assisted recurrent selection (MARS) – of new drought-tolerant maize adapted to many countries in Asia. His goal was to transfer the highest expression of drought tolerance in maize into elite well-adapted Asian lines targeted at drought-prone or water-constrained environments.

Asia’s existing maize varieties had no history of breeding for drought tolerance, only for disease resistance. To make a plant drought tolerant, many genes have to be incorporated into a new variety. So Vivek asked: “How do you address the increasing demand for maize that meets the drought-tolerance issue?”

The recent work on advancing maize genetics for acid soils in the African and Brazilian GCP projects meant it was a golden opportunity for Vivek to reap some of the new genetic resources.

“This was a good opportunity to use African germplasm, bring it into India and cross it to some Asia-adapted material,” he says.

Stored maize ears hanging in long bunches outside a house in China.

A key issue Vivek faced, however, was that most African maize varieties are white, and most Asian maize varieties are yellow. “You cannot directly deploy what you breed in Africa into Asia,” Vivek says. “Plus, there’s so much difference in the environments [between Africa and Asia] and maize is very responsive to its environment.”

The advances in marker-assisted breeding since the inception of GCP contributed significantly towards the success of Vivek’s team.

“In collaboration with GCP, IITA, Cornell University and Monsanto, CIMMYT has initiated the largest public sector MARS breeding approach in the world,” says Vivek.

The outcome is good: “We now have some early-generation, yellow, drought-tolerant inbred germplasm and lines suitable for Asia.

“GCP gave us a good start. We now need to expand and build on this,” says Vivek.

GCP’s supported work laid the foundation for other CIMMYT projects, such as the Affordable, Accessible, Asian Drought-Tolerant Maize project funded by the Syngenta Foundation for Sustainable Agriculture. This project is developing yet more germplasm with drought tolerance.

A better picture: GCP brightens maize research

Dickson Ligeyo’s worries of a stormy future for Kenya’s maize production have lifted over the 10 years of GCP. At the end of 2014, Kenya had two new varieties that were in the final stage of testing in the national performance trials before being released to farmers.

“There is a brighter picture for Kenya’s maize production since we have acquired acid-tolerant germplasm from Brazil, which we are using in our breeding programmes,” Dickson says.

In West Africa, researchers are also revelling in the opportunity they have been given to help enhance local yields in the face of a changing climate. “My institute benefited from GCP not only in terms of human resource development, but also in provision of some basic equipment for field phenotyping and some laboratory equipment,” says Allen Oppong in Ghana.

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

The main challenge now for breeders, according to Allen, is getting the new varieties out to farmers: “Most people don’t like change. The new varieties are higher yielding, disease resistant, nutritious – all good qualities. But the challenge is demonstrating to farmers that these materials are better than what they have.”

This Kenyan farmer is very happy with his healthy maize crop, grown using an improved variety during a period of drought.

Certainly GCP has strengthened the capacity of researchers across Africa, Asia and Latin America, training researchers in maize breeding, data management, statistics, trial evaluations and phenotyping. The training has been geared so that scientists in developed countries can use genetic diversity and advanced plant science to improve crops for greater food security in the developing world.

Elliot Tembo, a maize breeder with the private sector in sub-Saharan Africa says: “As a breeder and a student, I have been exposed to new breeding tools through GCP. Before my involvement, I was literally blind in the use of molecular tools. Now, I am no longer relying only on pedigree data – which is not always reliable – to classify germplasm.”

Allen agrees: “GCP has had tremendous impact on my life as a researcher. The capacity-building programme supported my training in marker-assisted selection training at CIMMYT in Mexico. This training exposed me to modern techniques in plant breeding and genomics. Similarly, it built my confidence and work efficiency.”

There is no doubt that GCP research has brightened the picture for maize research and development where it is most needed: with researchers in developing countries where poor farmers and communities rely on maize as their staple food and main crop.

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

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

Oct 092015

Elizabeth Parkes

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

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

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

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

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

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

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

Turning point: cassava to help the vulnerable

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

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

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

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

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

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

Healthy cassava plants.

Challenges and opportunities

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

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

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

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

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

A place at the table, and sharing joy

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

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

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

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

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

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

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

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

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

Nurturing women

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

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

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

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

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

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

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

Ousmane Boukar: committed to cowpeas

Africa, Cowpeas, Legumes, Researchers No Responses »

Oct 082015

Ousmane Boukar

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

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

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

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

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

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

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

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

Joining an international programme

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

Cowpea plants at podding stage.

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

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

“We have used this technology to develop advanced breeding lines that are producing higher yields in drier conditions and displaying resistance to several pests and diseases such as thrips [insects which feed on cowpeas] and Striga [a parasitic weed]. We expect these lines to be available to plant breeders by the end of 2015.”

Cowpea seed.

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

Striga in a cowpea plot.

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

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

Taking the lead in the Community of Practice

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

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

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

Ghanaian farmer Alanig Bawa drying cowpeas.

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

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

The dawn of a new generation

A programme where the spirit is palpable

Exploring gene banks to uncover genetic wealth

A need to focus and deliver products

Giving a voice to all the cast and crew

Developing capacity and leadership in Africa

A ‘sweet and sour’ sunset

More links

What is a diagnostic molecular marker?

Breeders use markers to predict plant traits

Markers developed for drought tolerance

Markers developed for pests and diseases

Markers developed for acidic and saline soils

Markers mean information, which means power

More links

Handling big data

Clearing the bottleneck

Providing help where it is needed

Breeding rice and maize more efficiently using IBP

From the GCP nest to world-scale deployment

More links

The solution – genetic diversity

Taking stock of genetic stocks

Broadening groundnut’s genetic base to prevent disease

Genetic gain by exploiting genetic stocks

Sustaining genetic stocks into the future

New programme to fund crop diversity

Looking forward 30 years

More links

Transformation for Chiedozie – and for cassava

Building African capacity

A paradigm shift

More links

Setting a foundation for higher yielding, drought-tolerant chickpeas

Developing capacity by involving partners in Kenya and Ethiopia

Decoding pigeonpea genome

Securing income-generating groundnut crops in Africa

Supporting key crops in West Africa

From poverty to prosperity through partnerships

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Ghana gains a new centre of excellence

Capacity building à la carte a real ‘life changer’

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

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Researchers take on the double whammy of acid soils and drought

Scientists join hands to unravel maize complexity

Comparing genes: sorghum gene paves way for maize aluminium tolerance

Kenya deploys powerful maize genes

Maize for meat: GCP’s advances in maize genetics help feed Asia’s new appetites

A better picture: GCP brightens maize research

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Turning point: cassava to help the vulnerable

Challenges and opportunities

A place at the table, and sharing joy

Nurturing women

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Joining an international programme

Taking the lead in the Community of Practice

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