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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.”

Cloned genes an asset in push for food security in developing countries

Africa, Asia, Comparative genomics in cereals, Genetic resources, Genetics, Latin America, Maize, Rice, Sorghum, Themes No Responses »

Oct 262015

Photo: HK Tang/Flickr (Creative Commons)

An Indian patchwork of rice and maize fields.

“Once you’ve cloned a major gene in one crop, it is possible to find a counterpart gene that has the same function in another crop, and this is easier than finding useful genes from scratch” explains Leon Kochian, Professor in Plant Biology and Crop and Soil Sciences at Cornell University, USA, and Director of the Robert W Holley Center for Agriculture and Health, United States Department of Agriculture – Agricultural Research Service.

Leon was the Product Delivery Coordinator for the Comparative Genomics Research Initiative of the CGIAR Generation Challenge Programme (GCP). The Programme set out in 2004 to advance plant genetics in a bid to provide sustainable food-security solutions.

Between 2004 and 2014, GCP invested in projects to clone two genes and deploy them in elite local varieties. The first gene, SbMATE, encodes aluminium tolerance traits in sorghum; the work was a collaborative effort led by the Brazilian Corporation of Agricultural Research (EMBRAPA) and Cornell University, and gave rise to locally-adapted sorghum varieties released in South America and Africa. The second gene, PSTOL1, produces traits that improve phosphorus uptake in rice. This research was a collaboration between the Japan International Research Center for Agricultural Sciences (JIRCAS) and the International Rice Research Institute (IRRI). PSTOL1 has now been extensively deployed in Asian rice varieties.

Aluminium toxicity and low phosphorus levels in acid soils are major factors that hinder cereal productivity worldwide, particularly in sub-Saharan Africa, South America and Southeast Asia. Globally, acid soils are outranked only by drought when it comes to stresses that threaten food security.

Tolerance to high levels of aluminium and low phosphorus is conferred by major genes, which lend themselves to cloning. Major genes are genes that by themselves have a significant and evident effect in producing a particular trait; it’s therefore easier to find and deploy a major gene associated with a desired trait than having to find and clone several minor genes.

Harvesting sorghum in Kenya.

Cloning major genes instrumental in hunt for resilient varieties

Locating a single gene within a plant’s DNA is like looking for a needle in a haystack. Instead of searching for a gene at random, geneticists need a plan for finding it.

The first step is to conduct prolonged phenotyping – that is, measuring and recording of plants’ observable characteristics in the field. By coupling and comparing this knowledge with genetic sequencing data, scientists can identify and locate quantitative trait loci (QTLs) – discrete genetic regions that contain genes associated with a desired trait, in this instance tolerance to aluminium or improved phosphorus uptake. They then dissect the QTL to single out the gene responsible for the desired trait. In the case of sorghum, researchers had identified the aluminium tolerance locus Alt_SB, and were looking for the gene responsible.

Once the gene has been identified, the next step is to clone it – that is, make copies of the stretch of DNA that makes up the gene. Geneticists need millions of copies of the same gene for their research: to gain information about the nucleotide sequence of the gene, create molecular markers to help identify the presence of the gene in plants and help compare versions of the gene from different species, and understand the mechanisms it controls and ways it interacts with other genes.

Drying the sorghum harvest in India.

Sorghum was one of the simpler crops to work with, according to Claudia Guimarães.

“Sorghum has a smaller genome… with clear observable traits, which are often controlled by one major gene,” she says.

The first breakthrough was the identification and cloning of SbMATE, the aluminium tolerance gene in sorghum behind the Alt_SB locus. The next was finding a diagnostic marker for the gene so that it could be used in breeding.

Marking genes to quickly scan plants for desired traits

Harvesting rice in The Philippines.

Once a desired gene is identified, a specific molecular marker must be found for it. This is a variation in the plant’s DNA, associated with a gene of interest, that scientists can use to flag up the gene’s presence. We can compare this process to using a text highlighter in a book, where the words represent the genes making up a genome. Each marker is like a coloured highlighter, marking sentences (genomic regions) containing particular keywords (genes) and making them easier to find.

In molecular breeding, scientists can use markers to quickly scan hundreds or thousands of DNA samples of breeding materials for a gene, or genes, that they want to incorporate into new plant varieties. This enables them to select parents for crosses more efficiently, and easily see which of the next generation have inherited the gene. This marker-assisted breeding method can save significant time and money in getting new varieties out into farmers’ fields.

Leon, who was also the Principal Investigator for various GCP-funded research projects, says that the cloning of SbMATE helped advance sorghum as a model for the further exploration of aluminium tolerance and the discovery of new molecular solutions for improving crop yields.

“This research also has environmental implications for badly needed increases in food production on marginal soils in developing countries,” says Leon. “For example, if we can increase food production on existing lands, it could limit agriculture’s encroachment into other areas.”

Rice field trials in Tanzania.

Aluminium toxicity is the result of aluminum becoming more available to plants when the soil pH is lower, and affects 38 percent of farmland in Southeast Asia, 31 percent in South America and 20 percent in East Asia, sub-Saharan Africa and North America. Meanwhile phosphorus, the second most important inorganic plant nutrient after nitrogen, becomes less available to plants in acid soils because it binds with aluminium and iron oxides. Almost half of the ricelands across the globe are currently phosphorus deficient. The research therefore has the potential for significant impact across the world.

The GCP-funded scientists used markers to search rice and maize for genes equivalent to sorghum’s SbMATE. In maize they successfully identified a similar gene, ZmMATE1, which is now being validated in Brazil, Kenya and Mali. In rice the search continues, but will become easier now that markers for ZmMATE1 have been developed.

Similarly, having validated, cloned and developed markers for PSTOL1 gene in rice, researchers at IRRI and JIRCAS then worked with researchers at EMBRAPA and Cornell University to use PSTOL1 markers to search for comparable genes in sorghum and maize. In both crops, genes similar to PSTOL1 have been identified and shown to improve grain yields under low-phosphorus soil conditions, albeit through different mechanisms.

The GCP-funded discoveries are already being used in marker-assisted selection in national breeding programmes in Brazil, Kenya, Niger, Indonesia, Japan, The Philippines and USA in sorghum, maize and rice. They have led to the release of new, aluminium-tolerant sorghum varieties in Brazil, with more currently being developed, along with phosphorus-efficient rice varieties.

Showing off freshly harvested sorghum in Kenya.

Cloning a worthwhile investment

Gene cloning was a relatively small cost in GCP’s research budget – about five percent (approximately USD 7 million) of a total research budget of USD 150 million spread over 10 years.

The gene-cloning component nonetheless yielded important genes for aluminium tolerance and phosphorus-uptake efficiency, within and across genomes. The molecular markers that have been developed are helping plant breeders across the world produce improved crop varieties.

Jean-Marcel Ribaut, Director of GCP, concludes: “The new markers developed for major genes in rice, sorghum and maize will have a significant impact on plant-breeding efficiency in developing countries.

“Breeders will be able to identify aluminium-tolerance and phosphorus-efficiency traits quicker, which, in time, will enable them to develop new varieties that will survive and thrive in the acid soils that make up more than half of the world’s arable soils.”

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.

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