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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.”

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.

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.”

Cassava: ‘there is life’ for African farmers

Africa, Cassava, Crop breeding No Responses »

Oct 052015

Cassava brings life to African people

Beyond the glittering coastline of what was once known as the Gold Coast, Ghana’s shrublands and rich forested hills are split by forking rivers that reach inland through the country’s lush tropics, into drier western Africa. In the past 40 years, seven major droughts have battered the people of Africa – with the most significant and devastating occurring in the Sahel region and the Horn of Africa in the early 1970s and 1980s.

Photo: Y Wachira/Bioversity International

This little girl in Kenya already seems to know that cassava roots are precious.

But despite the massive social disruption and human suffering that these droughts cause, life goes on. In south-eastern Ghana and in Togo, the three-million-plus people who speak the Ewe language have a word for this. It is agbeli: ‘There is life’. It is no coincidence that this word is also their name for a tropical and subtropical crop that survives through the worst times to feed Africa’s families: cassava.

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, and it is grown by nearly every farming family in sub-Saharan Africa, supplying about a third of the region’s daily energy intake. In the centuries since Portuguese traders introduced this Amazonian plant to Africa, cassava has flourished, yielding up to 40 tonnes per hectare.

Hear more on just why cassava is so important to food security from Emmanuel Okogbenin, of Nigeria’s National Root Crops Research Institute, in the video below (or watch on Youtube):

African countries produced nearly 140 million tonnes of cassava in 2012 – but most of the production is subsistence farming by small-scale farmers. Even the undisputed global cassava giant, Nigeria, currently produces only just enough to feed its population – and although the country is increasingly moving towards production of cassava for export as an industrial raw material, the poorest farmers often do not produce enough to sell, or have access to these markets.

Because cassava does so well on poor soils, on marginal land and with little rainfall, it can outlast its more sophisticated crop competitors: wheat, rice and maize. In fact, under harsh conditions such as drought, the amount of energy a given area of cassava plants can produce in the form of starchy carbohydrates outstrips all other crops. Chiedozie Egesi, a plant breeder and geneticist at Nigeria’s National Root Crops Research Institute (NRCRI), describes cassava as “the crop you can bet on when every other thing is failing”.

Despite cassava’s superhero cape, however, there’s no denying that its production is not at its highest when faced with diseases, pests, low-nutrient soils and drought. How plants deal with problems like low nutrients or dry conditions is called ‘stress tolerance’ by scientists. Improving this tolerance – plus resistance to diseases and pests – is the long-term goal for staple crops around the world so that they have higher yields in the face of capricious weather and evolving threats.

In the 1980s, catastrophe struck cassava production in East and Central Africa. A serious outbreak of cassava mosaic disease (CMD) – which first slowly shrivels and yellows cassava leaves, then its roots – lasted for almost 15 years and nearly halved cassava yields in that time. Food shortages led to localised famines in 1993 and 1997.

Other diseases affecting cassava include cassava brown streak disease (CBSD), cassava bacterial blight, cassava anthracnose disease and root rot. CBSD is impossible to detect above ground. Its damage is revealed only after harvest, when it can be seen that the creeping brown lesions have spoilt the white flesh of the tubers, rendering them inedible. Many cassava diseases are transmitted through infected cuttings, affecting the next generation in the next season. Pests that also prey on cassava include the cassava green mite and the variegated grasshopper.

Between the effects of drought, diseases, pests and low soil nutrients, cassava yields vary widely – losses can total between 50 and 100 percent in the worst times.

Symptoms of cassava mosaic disease (CMD) and cassava brown streak disease (CBSD), both of which can cripple cassava yields.

GCP takes the first steps to kick start cassava research

The next step forward for cassava appeared to be research towards breeding stronger and more resilient cassava varieties. However, cassava research had long been neglected – scientists say it’s a tricky crop that has garnered far less policy, scientific and monetary interest than the comparatively glamorous crops of maize, rice and wheat.

Watch as Emmanuel tells us more about the complexities and challenges of cassava breeding in the video below (or on YouTube):

Cassava is a plant which ‘drags its feet’: creating new plants has to be done from cuttings, which are costly to cut and handle and don’t store well; the plant takes up to two years to grow to maturity; and it is onerous to harvest. Elizabeth Parkes, of Ghana’s Crops Research Institute (CRI) (currently on secondment at the International Institute of Tropical Agriculture, IITA), says the long wait can be difficult.

This is where the work of scientists funded by the CGIAR Generation Challenge Programme (GCP) came in. Plant breeder and molecular geneticist Emmanuel Okogbenin of NRCRI led the cassava research push launched in 2010. He explains that before GCP, “most national programmes didn’t really have established crop breeding programmes, and didn’t have the manpower” to do the scale of research GCP supported.

Usually, researchers looking to breed crops that are more resistant to drought, diseases and pests would use conventional breeding methods that could take considerable time to deliver any results, especially given cassava’s slow path to maturity. Researchers would be trying to select disease- and pest-resistant plants by looking at how they’re growing in the field, without any way to see the different genetic strengths each plant has.

An IITA researcher exams cassava roots in the field.

This is where new ‘molecular breeding’ tools are particularly useful, given that – genetically – cassava presents more of a challenge to breeders than its cereal counterparts. Like many other vegetatively propagated crops, cassava is highly heterozygous, meaning that the counterpart genes on paired chromosomes tend to be different versions, or alleles, rather than the same. This makes it difficult to identify good parent plants for breeding and, after these are crossed, to accurately select progeny with desired traits. Useful – or detrimental – genes can be present in a cassava plant’s genetic code but not reflected in the plant itself, making breeding more unpredictable – and adding extra obstacles to the hunt for the exact genes that code for better varieties of cassava.

Although late to the world of molecular breeding, cassava had not missed its chance. Guided by GCP’s ambitious remit to increase food security through modern crop breeding, GCP-supported scientists have applied and developed molecular breeding methods that shorten the breeding process by identifying which plants have good genes, even before starting on that long cassava growth cycle. Increasing the capacity of local plant breeders to apply these methods has great potential for delivering better varieties to farmers much faster than has traditionally been the case.

Charting cassava’s genetic material was the first step in the researchers’ molecular quest. Part of the challenge for African and South American researchers was to create a genetic map of the cassava genome. Emmanuel describes the strong foundation that these early researchers built for those coming after: “It was significant when the first draft of the cassava genome sequence was released. It enabled rapid progress in cassava research activities and outcomes, both for GCP and cassava researchers worldwide.”

Cassava on sale in Kampala, Uganda.

Once cassava’s genome had been mapped, the pace picked up. In just one year, GCP-supported scientists phenotyped and genotyped more than 1000 genetically different cassava plants – that is, measured and collected a large amount of information about both their physical and their genetic traits – searching for ‘superstar’ plants with resistance to more than one crop threat. During this process, scientists compare plant’s physical characteristics with their genetic makeup, looking for correlations that reveal regions of the DNA that seem to contain genes that confer traits they are looking for, such as resistance to a particular disease. Within these, scientists then identify sequences of DNA, or ‘molecular markers’, associated with these valuable genes or genetic regions.

Plant breeders can use this knowledge to apply an approach known as marker-assisted selection, choosing their breeding crosses based directly on which plants contain useful genes, using markers like tags. This makes producing better plant varieties dramatically faster and more efficient. “It narrowed the search at an early stage,” explains Emmanuel, “so we could select only material that displayed markers for the genetic traits we’re looking for. There is no longer any need to ship in tonnes of plant material to Africa.”

Like breadcrumbs leading to a clue, breeders use markers to lead to identifying actual genes (rather than just a site on the genome) that give certain plants desirable characteristics. However, this is a particularly difficult process in cassava. Genes are often obscured, partly due to cassava’s highly heterozygous nature. In trials in Africa, where CMD is widespread, resistant types were hard to spot when challenged with the disease, and reliably resistant parents were hard to pin down.

This meant that two decades of screening cassava varieties from South America – where CMD does not yet exist yet – had identified no CMD-resistance genes. But screening of cassava from Nigeria eventually yielded markers for a CMD-resistance gene – a great success for the international collaborative team led by Martin Fregene, who was based in Colombia at the International Center for Tropical Agriculture (CIAT).

This finding was a win for African plant breeders, as it meant they could use molecular breeding to combine the genes producing high-quality and high-yielding cassava from South America with the CMD-resistance gene found in cassava growing in Nigeria.

Chiedozie Egesi, who led the work on biotic trait markers, explains the importance of combining varieties from South America with varieties from Africa: “Because cassava is not native to Africa, those varieties are not as genetically diverse, so we needed to bring genetic diversity from the centre of origin: South America. Coupling resistance genes from African varieties with genes for very high yields from South America was critical.”

Cassava research leaps forward with new varieties to benefit farmers

GCP’s first investment phase into cassava research stimulated a sturdy injection of people, passion, knowledge and funds into the second phase of research. From the genome maps created during the first phase, some of the world’s best geneticists would now apply genomic tools and molecular breeding approaches to increase and accelerate the genetic gains during breeding, combining farmers’ favourite characteristics with strong resistances and tolerances to abiotic and biotic constraints.

In the sprawling, tropical city of Accra on Ghana’s coast, the second phase of the research was officially launched at the end of the wet season in mid-2010. NRCRI’s Emmanuel Okogbenin coordinated product delivery from the projects, but the roles of Principal Investigator for the different projects were shared between another four individuals.

These were breeder and geneticist Chiedozie Egesi (NRCRI, Nigeria), molecular geneticist Morag Ferguson (IITA), genomic scientist Pablo Rabinowicz (University of Maryland, USA) and physiologist and geneticist Alfredo Alves (Brazilian Corporation of Agricultural Research, EMBRAPA). The team shared the vision of enabling farmers to increase cassava production for cash, well beyond subsistence levels.

Garri, or gari, a kind of granular cassava flour used to prepare a range of foods.

If the Accra launch set the stage for the next five years of cassava collaboration, a breakthrough in Nigeria at the end of 2010 set the pace, with the release of Africa’s first cassava variety developed using molecular-breeding techniques. “It was both disease-resistant and highly nutritious – a world-first,” recalls Emmanuel proudly.

Known as UMUCASS33 (or CR41-10), it took its high yield and nutritional value from its South American background, and incorporated Nigerian resistance to devastating CMD attacks thanks to marker-assisted selection. It was also resistant to several other pests and diseases. UMUCASS33 was swiftly followed by a stream of similar disease-busting varieties, released and supplied to farmers.

Never before had cassava research been granted such a boost of recognition, scientific might and organisational will. And never before had there been so much farmer consultation or so many on-farm trials.

“Cassava was an orphan crop and with the help of GCP it is becoming more prominent,” says Chiedozie. “GCP highlighted and enhanced cassava’s role as a major and reliable staple that is important to millions of poor Africans.”

Another important challenge for scientists was to develop a higher-yielding cassava for water-limited environments. The aim was to keep mapping genes for resistance to other diseases and pests and then combine them with favourable genetics that increase yield in drought conditions – no easy feat. Drought’s wicked effect on cassava is to limit the bulk of the tuber, or sometimes to stop the tuber forming altogether. Emmanuel led the work on marker-assisted recurrent selection for drought.

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):

Many traits and many varieties

As closely as the cassava teams in Africa were working together, Chiedozie recalls that each country’s environment demanded different cassava characteristics: “We had to select for what worked best in each country, then continue with the research from there. What works fine for East Africa may not be so successful in Nigeria or Ghana”. A core reference set representing most of the diversity of cassava in Africa was improved with the addition of over 564 varieties. Improving the reference set, says project leader Morag Ferguson, “enables the capture of many diverse features of cassava” within a relatively small collection, providing a pathway for more efficient trait and gene discovery.

While mapping of cassava’s genetic makeup carried on, with a focus on drought tolerance, researchers continued to develop a suite of new varieties. They mapped out further genes that provided CMD resistance. In Tanzania, four new varieties were released that combined resistance to both CMD and CBSD – two for the coastal belt and two for the semi-arid areas of central Tanzania. These new varieties had the potential to double the yield of existing commercial varieties. In Ghana too, disease-resistant varieties were being developed.

Built-in disease resistance can make a huge difference to the health of cassava crops. This photo shows a cassava variety resistant to African cassava mosaic virus (ACMV), which causes cassava mosaic disease (CMD), growing on the left, alongside a susceptible variety on the right.

Meanwhile in Nigeria, another variety was released in 2012 with very high starch content – an essential factor in good cassava. This is a critical element to breeding any crop, explains Chiedozie: “A variety may be scientifically perfect, based on a researcher’s perspective, but farmers will not grow it if it fails the test in terms of taste, texture, colour or starchiness.”

Geoffrey Mkamilo, cassava research leader at Tanzania’s Agricultural Research Institute, Naliendele, says that farmer awareness and adoption go hand in hand. Once they had the awareness, he says, “the farmers were knocking on our doors for improved varieties. They and NGOs were knocking and calling.”

After groundwork in Ghana and Nigeria to find potential sources of resistance, cassava varieties that are resistant to bacterial blight and green mites were also developed in Tanzania and then tested. By the time GCP closed in December 2014, these varieties were on their way to commercial breeders for farmers to take up.

Scientists seeking to resolve the bigger challenge of drought resistance have achieved significant answers as well. Researchers have been able to map genetic regions that largely account for how well the crops deal with drought.

Hunt for ‘super powered’ cassava

The hunt was on for drought-tolerance genes in African cassava plants. The end goal was to find as many different drought-related genes as possible, then to put them all together with the applicable disease and pest resistance genes, to make a ‘super powered’ set of cassava lines. Molecular breeders call this process ‘pyramiding’, and in Ghana, Elizabeth Parkes led these projects.

With the help of Cornell University scientists, the researchers compared plants according to their starch content, how they endured a dry season, how they used sunlight and how they dealt with pests and diseases.

Fourteen gene regions or quantitative trait loci (QTLs) were identified for 10 favourable traits from the genetic material in Ghana, while nine were found for the plants in Nigeria – with two shared between the plants from both Ghana and Nigeria. After that success, the identified genes were used in breeding programmes to develop a new generation of cassava with improved productivity.

Pyramiding is important in effective disease resistance; Chiedozie explains in the video below (or on YouTube):

New cassava varieties rich in pro-vitamin A have a telltale golden hue.

The research has also delivered results in terms of Vitamin A levels in cassava. In 2011, the NRCRI team, together with 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. Since then, the team has aimed to increase this figure to 50 percent. In 2014, they released three more pro-vitamin A varieties with even higher concentrations of beta-carotene.

A field worker at IITA proudly displays a high-yielding, pro-vitamin A-rich cassava variety (right), compared with a traditional variety (left).

The new varieties developed with GCP support are worth their weight in gold, says Chiedozie: “Through these varieties, people’s livelihoods can be improved. 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.”

Turning from Nigeria to Tanzania, Geoffrey has some remarkable numbers. He says that the national average cassava yield is 10.5 tonnes per hectare. He adds that a new cassava variety, PWANI, developed with GCP support and released in 2012, has the potential to increase yields to 51 tonnes per hectare. And they don’t stop there: the Tanzanian researchers want to produce three million cuttings and directly reach over 2,000 farmers with these new varieties, then scale up further.

A farmer tends her cassava field in northern Tanzania.

Cassava grows up: looking ahead to supporting African families

Emmanuel reflects on how the first release of a new disease-resistant high-yielding cassava variety took fundamental science towards tangible realities for the world’s farmers: “It was a great example of a practical application of marker technology for selecting important new traits, and it bodes well for the future as markers get fully integrated into cassava breeding.”

Emmanuel further believes that GCP’s Cassava Research Initiative has given research communities “a framework for international support from other investors to do research and development in modern breeding using genomic resources.” Evaluations have demonstrated that molecular-assisted breeding can slash between three and five years from the timeline of developing better crops.

Women tend to bear most of the burden of cassava cultivation and preparation. Here a Congolese woman pounds cassava leaves – eaten in many regions in addition to cassava roots – prior to cooking a meal for her family.

But, like cassava’s long growth cycle underground, Emmanuel knows there is still a long road to maturity for cassava as a crop for Africa and in research. “Breeding is just playing with genetics, but when you’re done with that, there is still a lot to do in economics and agronomics,” he says. Revolutionising cassava is about releasing improved varieties carefully buttressed by financial incentives and marketing opportunities.

Rural women in particular stand to benefit from improved varieties – they carry most of the responsibility for producing, processing and marketing cassava. So far, Elizabeth explains: “Most women reported an increase in their household income as a result of the improved cassava, but that is still dependent on extra time spent on cassava-related tasks” – a burden which she aims to diminish.

Elizabeth emphasises that future improvement research has to take a bottom-up approach, first talking to female farmers to ensure that improved crops retain characteristics they already value in addition to the new traits. “Rural families are held together by women, so if you are able to change their lot, you can make a real mark,” she says. Morag echoes this hope: “We are just starting to implement this now in Uganda; it’s a more farmer-centric approach to breeding”. The cassava teams emphasise the importance of supporting women in science too; the Tanzanians teams are aiming for a target of 40 percent women in their training courses.

Meet Elizabeth in the podcast below (or on PodOmatic), and be inspired by her passion when it comed to women in agriculture and in science:

This direct impact goes much further than individuals, says Chiedozie. “GCP’s daring has enabled many national programmes to be self-empowered, where new avenues are unfolding for enhanced collaboration at the local, national and regional level. We’re seeing a paradigm shift.” And Chiedozie’s objectives reach in a circle back to his compatriots: “Through GCP, I’ve been able to achieve my aims of using the tools of science and technology to make the lives of poor Africans better by providing them with improved crops.”

GCP has been crucial for developing the capacity of countries to keep doing this level of research, says Chiedozie: “The developing-country programmes were never taken seriously,” he says. “But when the GCP opportunity to change this came up we seized it, and now the developing-country programmes have the boldness, capacity and visibility to do this for themselves.”

Emmanuel says his proudest moment was when GCP was looking for Africans to take up leadership roles. “They felt we could change things around and set a precedent to bring people back to the continent,” he says. “They appreciated our values and the need to install African leaders on the ground in Africa rather than in Europe, Asia or the Americas.”

“If you want to work for the people, you have to walk with the people – that’s an African concept. Then when you work with the people, you really understand what they want. When you speak, they know they can trust you.” GCP trusted and trod where others had not before, Chiedozie says.

Elizabeth agrees: “In the past, the assumption was always that ‘Africa can’t do this.’ Now, people see that when given a chance to get around circumstances – as GCP has done for us through the provision of resources, motivation, encouragement and training – Africa can achieve so much!”

Barley: the ‘last crop grown before the desert’

Africa, Asia, Barley, Genetics, Genomics, Phase I crops No Responses »

Jun 162015

Ripening barley.

Barley is thought to have been one of the first crops ever cultivated by humankind. This is largely because it is a tough plant able to withstand dry and salty conditions. Its fortitude is especially important for the small land-holders living on the fringes of deserts in West Asia and North Africa, where it is “the last crop grown before the desert,” says Dr Michael Baum, who led barley research for the CGIAR Generation Challenge Programme (GCP).

Michael, who is Director of the Biodiversity and Integrated Gene Management Programme at the International Center for Agricultural Research in the Dry Areas (ICARDA), says one of the GCP’s first tasks was to find where the useful genes were in wild barley.

“Looking at wild barley is especially important for low-input agriculture, such as is found in developing countries,” he says. “Wild barley grows in, and is very adapted to, the harsh conditions at the edge of the deserts in the Fertile Crescent of West Asia: Iraq, Syria, Jordan and Turkey.”

In some regions, wild barley produces an even higher yield of grain when there is a drought. And this was the kind of useful trait that GCP researchers were looking for in their work on barley during the first phase of GCP, when the internationally funded Programme set out to enhance genetic stocks and plant-breeding skills that will help developing nations cope with increasingly extreme drought conditions.

Barley a ‘chosen one’ for research

Photo: Peter Haden/Flickr (Creative Commons)

Preparing barley in Ethiopia.

During its first five years, GCP chose barley as one of its focus crops as advances had already been made in understanding its genetic makeup and in using new molecular plant-breeding technologies to find and incorporate useful genes into barley varieties.

“At the same time, we needed to find the genes or characteristics we did not want in cultivated barley so we could avoid these traits,” says Michael. “This includes the way wild barley disperses its seed when its brittle spikes shatter. Domesticated barley has non-shattering spikes, making it much easier to harvest.”

Resource-poor farmers mostly grow barley in poor environments, where yields of key crops are chronically low, and crop failures are common. Resilient, high-yielding varieties could make a big difference to livelihoods.

Farmers in Central and West Asia and North Africa (CWANA) plant more than five million hectares of barley each year, where it is largely used as feed for the sheep and goats that are the main source of meat, milk and milk products for rural populations. In these environments, barley grain is harvested only two to three times over a five-year period. In years when it is too dry, sheep are sent into the barley field to graze on the straw.

Barley-based livestock system on marginal drylands in Morocco.

Finding the clues to help breeders select barley’s best DNA

Photo: Dave Shea/Flickr (Creative Commons)

Malted barley.

The quest for better barley varieties – those that yield more, have more protein, can resist pests and diseases and can tolerate drought – means understanding what genes for what characteristics are available to plant breeders.

With 2,692 different barley accessions (or genetically different types of barley) in the ICARDA collection, from 84 different countries, this is no mean feat. GCP-supported researchers selected seed from 1,000 of the most promising accessions and planted single plants, whose seed was then ‘fingerprinted’, or genotyped, according to its DNA composition.

“From this, we selected 300 different barley lines that represented 90 percent of all the different characteristics of barley,” says Michael.

“This [reference set] is really good for someone new to barley. By looking at 300 lines they are seeing the diversity of almost 3,000 lines without any duplication,” he says. “This is much better and quicker for a plant breeder.”

The reference set of 300 barley lines is now available to plant breeders through the ICARDA gene bank.

Barley growing on experimental fields in Morocco.

Checking out the effects of the environment on gene expression

Harvesting barley in Nepal.

It’s not enough to discover what genes are present in different varieties of barley. It’s also important to understand how these genes express themselves in terms of barley’s yield, quality (especially protein content) and adaptation to stresses such as drought when grown in different environments.

To make this happen, GCP improved collaboration across research centres. This increased the probability of relatively quick advances in identifying new traits and opportunities to improve barley varieties for the poorer farmers of CWANA.

GCP funded a collaborative project between ICARDA and researchers in Australia (the University of Adelaide and the Australian Centre for Plant Functional Genomics), Italy (l’Università degli Studi di Udine) and Syria (Tishreen University) to apply a new method, analysing allele-specific expression (ASE), to understand how genes express themselves in barley, using experimental hybrid plants (cultivated plants crossed with wild barley plants). Over three years, the collaboration tested 30 genes and 10 gene-cross combinations and found that there were changes in genetic expression when plants were grown in drought conditions.

“This is a project we could not have done without the partners in the GCP collaboration,” says Michael. “We gained important insights into how genes are regulated and how gene expression changes under different environmental conditions, such as drought, or during growth stages, such as early plant development or grain filling. We published our results in a high-impact journal [The Plant Journal (2009) 59(1):14–26], which was a great outcome for a project with such a limited timespan.”

This project was designed not so much for the practical plant breeder, but for those using molecular-breeding technologies where it is important to understand that there is a change in the expression of genes over the lifetime of a plant. “This affects the selection of genes for breeding programmes,” says Michael.

Preparing barley in Ethiopia.

Making the most of wild barley

Photo: Rahel Jaskow/Flickr (Creative Commons)

Wild barley in flower.

Once some of the fundamental research into barley’s building blocks had been done, GCP revisited the potential of wild barley, with the aim to identify specific DNA that increased or decreased drought tolerance.

“Whenever you can’t find the characteristics you are looking for in a cultivated crop, you go back to look again at the wild varieties,” says Michael.

Once again, a collaborative effort – this time between ICARDA, the Scottish Crop Research Institute (since renamed to the James Hutton Institute), the University of California, Riverside, the University of Oregon and Chile’s Instituto de Investigaciones Agropecuarias (INIA; Agricultural Research Institute) – was the key to success.

Joanne Russell from the James Hutton Institute says success came when “we combined the power of genomics with a unique population of 140 barley lines to identify segments of the donor genome that confer drought tolerance”.

The barley lines were composed of an advanced elite genetic background combined with introduced segments of DNA from wild barley that came from the Fertile Crescent.

“We were successful in identifying parts of the DNA from hybrid plants that confer a significant increase in yield under drought,” says Joanne.

Leader of this GCP project from the James Hutton Institute, Professor Robbie Waugh, adds that GCP provided a unique opportunity for their laboratory to interact with international colleagues on a project focussed on improving the plight of some of the world’s poorest subsistence farmers.

“The genetic technologies we had developed prior to the GCP project starting were, at the time, state of the art – even in the more developed world,” says Robbie. “Our ability to then apply these technologies to wild barley genetic material from ICARDA and to varieties derived from wild × cultivated crosses allowed us to learn a lot about patterns of genetic and phenotypic variation in the wider barley gene pool.

“Indeed, we are still working on one of the genetic populations of barley that we studied in the GCP program, now using sophisticated phenotyping tools and approaches to explore how genes in defined segments of the wild barley genome help provide yield stability under drought conditions through architectural variation in the root system.”

Photo: Richard Weil/Flickr (Creative Commons)

Women harvesting barley in India.

GCP builds genetic resources through ongoing collaboration

Photo: Diana Prichard/ONE.org/Flickr (Creative Commons)

Barley in rural Ethiopia.

For Michael, one of the most important outcomes of the GCP work was the ability to meet and work with researchers from other centres across the world.

“Before GCP, I had only visited two other CGIAR centres,” he says. “GCP was the first attempt to develop a programme across the CGIAR centres and to work on a specific topic, which was genetic resources. I would give GCP high marks for stimulating this cross-centre cooperation, particularly through their annual GCP meeting.”

And when the decision came to end barley research after the first phase of GCP, Michael found that he missed the GCP meetings: “I would have found it useful if I could have continued to attend the annual meetings,” he says. “These were much more important to me than getting the project funding out of GCP.”

Despite this and despite dealing with the challenge that some countries, such as China, were unable to provide the barley germplasm (samples of materials) that they initially promised, Michael has continued his relationships with some of the people he first met through GCP. “I’m still collaborating with China through a continuous bilateral effort on barley. Ten years later, the collaborations are still ongoing. Often when a project finishes, the collaboration finishes, but we are still continuing our collaboration on barley.”

Most importantly, Michael believes the GCP-supported and -funded collaborations brought a new approach to providing plant genetic resources to breeders. “The reference sets we assembled for barley and other crops provided a new way to look at large germplasm collections,” he says.

“This was one aim of GCP: about how to have a more rational look at germplasm collections. Now plant breeders don’t have to ask for five to ten thousand accessions of a crop, and then spend several years on evaluation.

“Now they have a higher chance of finding the genetic characteristics they want more quickly from the much smaller reference collection.”

And although the reference-set approach has been further refined since GCP’s first phase of research concluded, Michael believes it builds on what GCP started through its collaborative teams, with barley being just one example.

“GCP helped make it all happen,” he says.

For research and breeding products, see the GCP Product Catalogue and search for barley.

Photo: Oleksii Leonov/Flickr (Creative Commons)

Field of barley.

Sweetpotato: lifesaver that gets a genetic lifeline

Africa, Capacity building, Genetics, Genomics, Latin America, Phase I crops, Sweetpotatoes No Responses »

Jun 052015

Farmer Maria Mtele holds recently harvested orange-fleshed sweetpotatoes in a field in Mwasonge, Tanzania.

Sweetpotato has a long history as a lifesaver. The Japanese used it when typhoons demolished their rice fields. It kept millions from starvation in famine-plagued China in the early 1960s and came to the rescue in Uganda in the 1990s, when a virus ravaged the cassava crop.

In sub-Saharan Africa, sweetpotato is proving crucial in the fight against blindness, disease and premature death among children under five. And, as agriculture becomes more market-oriented across the continent, sweetpotato has some significant advantages: it requires fewer inputs and less labour than other crops such as maize, tolerates marginal growing areas and can mature within four months.

On these fertile grounds, researchers across the globe are not underestimating the importance of sweetpotato as a staple crop.

“Yields achieved by resource-poor farmers in sub-Saharan Africa are typically low,” says Roland Schafleitner of the International Potato Center (CIP), based in Peru.

“Improved and well-adapted sweetpotato varieties with increased tolerance to drought, pests and diseases will have a positive impact on food and income security in sub-Saharan Africa and can significantly contribute to increasing productivity,” he says.

Roland was Principal Investigator of two research projects funded by the CGIAR Generation Challenge Programme (GCP), which developed genetic and genomic resources for breeding improved sweetpotato.

At the outset of the work, Roland says: “Breeding efforts were limited by the crop’s genetic complexity and the lack of information available about its genetic resources.

“It was clear that if we could develop genetic tools and make concerted efforts towards understanding the gene pool of sweetpotato, the breeding potential of the crop would improve.”

Farmer Mwanaidi Rhamdani at work in an orange-fleshed sweetpotato field in Mwasonge, Tanzania.

Sub-Saharan Africans getting their vitamin A from sweetpotato

Sweetpotato diversity.

Malnutrition does not always mean a simple lack of calories; research suggests that nutrient shortfalls are an even bigger killer. Vitamin A deficiency is a leading cause of blindness, infectious disease and premature death among children under five and pregnant women in sub-Saharan Africa and Asia.

Sweetpotato comes in a wide range of colours. Varieties with dark orange flesh are naturally very rich in the pigment beta-carotene, which the body converts into vitamin A. However, the sweetpotatoes traditionally grown in Africa are pale-fleshed and low in beta-carotene. African consumers were not used to eating colourful sweetpotato – and these orange-fleshed varieties were in any case not well adapted African growing conditions.

Recent years have therefore seen a collaborative effort by researchers across the world to breed orange-fleshed sweetpotato varieties fortified with high levels of beta-carotene, and even enriched with other nutrients, that have also been crossed with local varieties and so are adapted to local conditions and tastes. A crucial part of these efforts has also been to create public awareness and encourage people to grow, eat and buy these new varieties.

Two cheeky young chappies from Mozambique enjoy the sweet taste of orange-fleshed sweetpotato rich in beta-carotene, or pro-vitamin A.

All of this adds to the growing momentum behind sweetpotato. The growing awareness of sweetpotato’s potential nutritional benefits for the poor and food insecure, as well as its value for subsistence farmers as a reliable crop that withstands drought and requires minimal inputs, mean that it is growing in significance.

Orange-fleshed sweetpotato can be used to make a variety of tasty products from doughnuts to chapati.

More than 95% of the world’s sweetpotato crop is grown in developing countries, where it is the fifth most important staple food crop. It is particularly important in many African countries: Madagascar in Southern Africa; Nigeria in West Africa; and those surrounding the Great Lakes in East and Central Africa – Uganda, Malawi, Angola and Mozambique.

According to 2013 figures from the Food and Agriculture Organization of the United Nations, 3.6 million hectares of sweetpotato were harvested in Africa. While the average global yield of sweetpotato per hectare was 14.8 tonnes, across all East African countries in 2013 it was only half this, at 7.1 tonnes per hectare. In West African nations the average yield was even worse, at 3.7 tonnes per hectare.

Farmers are unable to make the most of their crops because the varieties available to them, including traditional varieties (or landraces) have low resistance to viral diseases and insect pests, and poor tolerance to drought. It is therefore crucial that when developing new varieties breeders are able to efficiently incorporate pest and disease resistance and drought tolerance traits.

New DNA markers identified for sweetpotato disease

The sweetpotato virus disease (SPVD) is the most serious disease affecting sweetpotato in sub-Saharan Africa. It often causes serious yield losses of up to 80–90 percent.

The disease is the result of joint infection by two viruses: the sweetpotato feathery mottle virus and the sweetpotato chlorotic stunt virus. Of the two, the stunt virus is the more problematic.

Wolfgang Grüneberg, also from CIP, says that, in the years 2006–2008, 52 new DNA markers were developed as part of GCP-funded research to improve marker-assisted selection for resistance to the disease.

“The results,” says Wolfgang, Principal Investigator for the research, “looked promising for developing a large number of orange-fleshed sweetpotatoes with resistance to SPVD.”

Immediately following the development of the markers, two varieties of sweetpotato were developed using a cloned gene, Resistan, known to confer resistance to the virus. The first variety was used to improve an SPVD test system so that the disease could be diagnosed earlier if a crop was affected. The second variety underwent field tests in regions in Uganda that were highly affected by the disease.

Sweetpotato vines and roots.

Mobilising the genetic diversity of sweetpotato for breeding

The goals of the GCP-supported work were to develop a diverse genetic resource base for sweetpotato and stimulate the use of new tools in ongoing breeding programmes.

To help transfer this work from high-end laboratories to resource-poor research labs in developing countries, GCP promoted collaboration across institutions and borders. Researchers from Brazil, Mozambique, Uganda and Uruguay worked together on sweetpotato genetic research projects.

As Roland explains, the basic first steps needed to begin to ‘mobilise’ the genetic diversity of sweetpotato were developing a reference set of varieties and improving genomics tools to work with polyploid crops, i.e. those possessing multiple sets of chromosomes, such as sweetpotato.

GCP-supported researchers in Peru and sub-Saharan Africa defined a reference set of 472 varieties of sweetpotato, carefully selected and honed to represent both the diversity of the crop and its most important agronomical and nutritional traits.

“Based on a reference set, genetic markers can be developed that are associated with important characteristics of the crop and can help breeders to select favourable genotypes,” says Roland.

The gene sequences developed during the Programme are now available as a Sweetpotato Gene Index.

“Based on these sequences,” says Roland, “molecular markers have been designed that can help breeders and gene-bank curators to assess the genetic diversity of their accessions and to perform genetic mapping studies.

“Today, techniques that yield a much larger number of markers for genetic studies and selection are accessible for sweetpotato,” he says.

Mwanaidi Rhamdani (left) works with Maria Mtele in an orange-fleshed sweetpotato field in rural Tanzania.

The genetic lifelines reach Africa

Sweetpotato is one of the most important staple crops in Mozambique, ranking in third position after cassava and maize. The areas harvested in Mozambique in 2013 were 1.7 million hectares of maize, 780,000 hectares of cassava and 120,000 hectares of sweetpotato.

A child eats cooked orange-fleshed sweetpotato in Uganda.

GCP funded breeders in Mozambique and Uganda to learn how to identify genetic markers that would prove useful for future sweetpotato breeding.

“Our African partners visited us at CIP and helped us complete the work on identifying markers,” recalls Roland. “This provided the opportunity for direct ‘technology transfer’ to breeders in the target region.”

The collaboration had, for the first time, created a critical amount of genetic and genomics resources for sweetpotato. The resulting Sweetpotato Gene Index and the new markers were published in a peer-reviewed journal, BMC Genomics (2010) 11:604.

The new genetic resources are in use at CIP in Peru and in breeding programmes in Burkina Faso, Mozambique, Uganda, Uruguay and the USA for the assessment of the genetic diversity of germplasm collections.

“The markers have been used for diversity analysis, especially at the CIP gene bank, and also in Africa,” says Roland, who says the markers will help future research.

“Such analysis guides germplasm conservation decisions, and diversity studies are a great tool to develop core collections and composite genotype sets – subsets of the whole collection – which allow for more practical screening for specific traits than large collections.”

Collective ‘intelligence’ cracks banana’s genetic code, clearing way for breeders

Africa, Asia, Bananas, Genetics, Genomics, Latin America, Phase I crops No Responses »

Jun 022015

A farmer transports bananas to market by bicycle in Uganda.

At whatever time of the day or night you are reading this, somewhere in the world there are sure to be farmers trekking many kilometres to take their bananas to local markets. These small-scale farmers produce almost 90 percent of the world’s bananas, and make up a significant portion of the 400 million people around the globe’s tropical girdle – Africa, Asia and Latin America – who rely on bananas for food and a source of income.

Bananas are often called the world’s most popular fruit, and global production in 2012 was almost 140 million tonnes. India is the largest producer, while South and Central American farmers supply the most to international supermarket shelves, exporting 80 percent of their bananas.

The importance of the banana as a food crop in tropical areas cannot be underestimated. More than a simple snack, plantain-type bananas in particular are a key component in savoury dishes. In Central and East African countries – like Cameroon, Gabon, Rwanda and Uganda – one person will eat an average of between 100 kg and 250 kg of banana each year. That equates to somewhere between 800 and 2000 average-sized bananas. In those four countries, bananas account for up to a quarter of people’s daily calorie intake.

Photo: A Vezina/Bioversity International

A stallholder offers bananas for sale at a fruit market in Nairobi, Kenya.

Banana’s asexuality inhibits its resilience

Bananas growing in Rwanda.

Banana propagates though asexual reproduction. This means that all the bananas of each variety are genetically identical, or nearly so, and therefore susceptible to the same diseases. Indeed, the world has already lost almost its entire banana crop once: before the 1950s, the Gros Michel cultivar dominated banana exports, but it was gradually wiped out in most regions by Panama disease, caused by the fungus Fusarium oxysporum. Furthermore, with reproduction being asexual, it is difficult to develop new, resistant varieties through conventional breeding.

At the turn of the twenty-first century, pests and diseases were once again becoming a real threat to global banana production. Little genetic research had been done on the fruit, and only a small portion of its genes had been used in breeding new varieties in its 7,000-year history as a cultivated crop.

“Several research groups had developed genetic markers for bananas [‘flags’ on the genome that can be linked to physical traits], but there was no coordination and only sketchy germplasm studies,” recalls Jean Christophe Glaszmann from CIRAD (Centre de coopération internationale en recherche agronomique pour le développement; Agricultural Research for Development) in France.

A plantain farmer walks through a plantation in Quindió, Colombia.

“It was not a priority,” says Jean Christophe, who was Subprogramme Leader for Genetic Diversity for the CGIAR Generation Challenge Programme (GCP), an international initiative established in 2004 to encourage the use of genetic diversity and advanced plant science to improve crops.

But between 2004 and 2012, under GCP, a wealth of research work was undertaken that culminated in the complete genetic sequencing of banana. It was a long process, says Jean Christophe, but the GCP-funded work on banana made a significant contribution to important results.

The extensive data on the genetics of banana are now available to scientists worldwide, who can use it to delve deeper into banana’s genes to breed varieties that can sustain the poorer populations in developing countries.

Once finally sequenced, the banana genome was published in one of the most prestigious scientific journals, Nature, in July 2012: “The reference Musa [banana and plantains] genome sequence represents a major advance in the quest to unravel the complex genetics of this vital crop, whose breeding is particularly challenging. Having access to the entire Musa gene repertoire is a key to identifying genes responsible for important agronomic characters, such as fruit quality and pest resistance.”

Passionate people pooled for the work

A banana seller in Hanoi, Vietnam.

Plans to sequence the banana genome started taking shape in 2001 at Bioversity International (a CGIAR centre), where a group of scientists formed the Global Musa Genomics Consortium. At that time, the only plant whose genome had been sequenced was Arabidopsis thaliana (a small flowering plant related to cabbage and mustard, used as a model organism in plant science), with rice close behind.

CGIAR established GCP in 2004 “to tap into the rich genetic diversity of crops via a global network of partnerships and breeding programmes,” according to Hei Leung, who was instrumental to GCP’s foundation and a Subprogramme Leader for Comparative Genomics. (During its first phase GCP was organised by Subprogramme; these were later replaced by Research Themes and Research Initiatives.)

Hei acknowledges that banana was ‘somewhat on the fringe’ of GCP’s main focus on improving drought tolerance in crops. However, he says, it was still relevant for GCP to support the emergence of improved genetics for banana.

“The work we did in genetic diversity is about future generations. We wanted a programme that is pro-poor, meaning that the majority of the people in the world are depending on [the crop].

A typical banana and plantain market at Ikire in Osun State, Nigeria.

“Drought tolerance is a good candidate because drought affects a lot of poor areas, but you really cannot just take one trait as pro-poor. We had a highly motivated group of researchers willing to devote their efforts to Musa,” says Hei.

“Nicolas Roux at Bioversity International was a passionate advocate for the partnership,” notes Hei. “The GCP community offered a framework for novel interactions among banana-related actors and players working on other crops, such as rice.”

Nicolas concurs on the potential for a little banana research to have great value: “Even though banana is among the most important basic food crops for 400 million people, and 100 million tonnes are grown annually on over 10 million hectares in 120 countries, it’s still under-researched and underfunded.”

The resultant research team was led by Japan’s National Institute of Agrobiological Sciences, which had vast experience in rice genome sequencing.

“So, living up to its name as a Challenge Programme, GCP decided to take the gamble on banana genomics and help it fly,” says Hei.

To advance genetics, you first need the intelligence

Banana bunches on an experimental plot at IITA.

Three global research agencies were charged with working together to develop a reference set for banana: Bioversity International, CIRAD, and the International Institute of Tropical Agriculture (IITA).

Creating a reference set – a careful, tactical selection representing the genetic diversity of a crop – is an invaluable first step in enabling scientists to work together to develop more ‘intelligent’ genetic data.

“Initially, we put together a community of institutions that have collections [of banana germplasm],” explains Jean Christophe. “And then we put together these initial materials that we sample in order to develop representative subsamples – this is called a ‘composite’ set because it comes from different institutions.

“Then we genotype this composite collection, and the genotyping allows us to understand how all this [genetic material] is structured. Based on how it is structured, we can re sample a smaller representation – this is what becomes a reference set.”

So, in the case of crops with an extensive genetic resource base, such as rice, there may be more than 100,000 different plant samples, or accessions, that are reduced to a few thousand. For banana, which has a smaller genetic resource base, a few hundred thousand accessions can be reduced to a few dozen.

“A couple of hundred accessions or fewer become manageable for plant breeders or crop specialists. And we want this to serve as a reference, shared among people, so that everybody works on the same reference material,” says Jean Christophe.

“If you work on the same reference material, you can compile information that is more intelligent – you can have the crop specialist who says ‘this is resistant; this is tolerant; this is susceptible’, and you can also have the biochemist, you can have the physiologist; in the end, you can compile the information.”

“We analysed about 500 accessions and narrowed it down to 50,” says Jean Christophe. This reference collection is currently stored at the University of Leuven in Belgium.

The refined data collected on the banana reference set enabled the researchers to unravel the origin and genealogy of the most important dessert banana: the Cavendish, the cultivar subgroup that dominates banana exports worldwide. Thanks to the early GCP work, they were able to show that Cavendish bananas evolved from three markedly different subspecies.

65-year-old Cambodian farmer, Khout Sorn, stands in front of his banana trees in Aphiwat Village, Tipo commune, Cambodia.

Malaysian wild subspecies fully sequenced

During these preliminary years of GCP-supported research on banana, the Programme funded several other smaller projects to consolidate genomic resources available for banana. Scientists developed libraries of artificial chromosomes that can be used in sequencing the DNA of banana, as well as genetic maps, which according to Jean Christophe are essential for improving the quality of the sequence.

These projects contributed to the full genome sequencing of a wild banana from Malaysia’s Pahang province in 2008. The ‘Pahang’ subspecies is one of the Cavendish variety’s three ancestors, and has also been shown to have had a role in the origin of many other banana cultivars, including those that are most important for food and economic security.

“GCP did not fund the sequence [of the Pahang banana], but it funded several things that made it possible to undertake full-scale sequencing,” Jean Christophe says. “It supported the development of particular resources and tools, and this made it possible for researchers to start the full-length sequencing.”

A farmer at work on a banana plantation, Mindanao, the Philippines.

Breeders now need to set to work

The more that is known about the genes responsible for disease resistance and other desirable traits in banana, the more researchers will be able to help farmers in developing countries to improve their yields.

“The road remains long, but now we have a good understanding of genetic diversity,” says Jean Christophe. “We have done a range of studies aimed at unravelling the genes that could control sterility in the species.

“This is undoubtedly an inspiring challenge towards unlocking the genetic diversity in this crop.

“If we have more money in the future, we are going to sequence others of the subspecies so that we can have the full coverage of the current Cavendish genome. But that was a good start,” says Jean Christophe.

“What we have to do now is to create the right populations [of banana] in the field so that we can separate out the characteristics we want to breed for.”

The new intelligence on banana genetics has given breeders the material they need that will ultimately help 400 million people in the tropics sustain food supplies and livelihoods.

Giants make giant strides in quest for drought-tolerant wheat

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

Mar 262015

Wheat growing in China.

For as long as peoples and countries have traded wheat, drought has continually played a part in dictating its availability and price. Developed countries have become more able to accommodate the bad years by using intensive agricultural practices to grow and store more wheat during more favourable years. However, farmers, traders and consumers are still at the mercy of drought when it comes to wheat availability and prices.

A recent example where drought in just one country inflated the world’s wheat prices was in the People’s Republic of China during 2010–11.

For almost six months, eight provinces in the north of China received little to no rain. Known as the breadbasket of China, these eight provinces grow more than 80 percent of the country’s total wheat and collectively produce more wheat than anywhere else in the world.

It was the worst drought to hit the provinces in 60 years.

With over 1.3 billion mouths to feed, China’s demand for wheat is high and ever increasing. When this demand was coupled with the reduced wheat yield caused by the severe 2010–11 drought, wheat prices around the world rose. While this price rise was beneficial for wheat growers in other countries, it made wheat unaffordable for many consumers and traders in developing nations.

Although this was a one-in-60-year event, previous droughts had already made locals question the sustainability of wheat production in this naturally dry region of China, where water consumption has increased in the past 50 years due to intensive agriculture, industry and a growing and increasingly urbanised population.

Wheat growers and breeders know they need to find wheat varieties and apply practices that will help them adapt to and tolerate drier conditions and still produce sustainable yields.

Luckily, they have help from a community of breeders around the world.

An Uyghur baker displays his bread in Kashi, Xinjiang, China.

Sharing knowledge to improve breeding efficiency and sustainability

In March 2009, 70 international plant breeding leaders and experts from the public and private sector converged in Montpellier, France, as part of a CGIAR Generation Challenge Programme (GCP) initiative to draw up roadmaps to improve plant-breeding efficiency in developing countries.

Richard Trethowan, professor in plant breeding at the University of Sydney, Australia, remembers the meeting distinctly. “We all got together and thought how we could use what we had learnt during the first phase of GCP [2004–2009] – all the genetics and molecular-breeding work – to deliver new varieties of crops, particularly in countries where it will have the greatest impact.”

The resulting roadmap for wheat became the GCP Wheat Research Initiative (RI), with Richard as Product Delivery Coordinator. It had two very clear destinations in mind: China and India.

Richard explains why China and India were targeted – as the world’s two wheat-production giants – in the video below.

Wheat Research Initiative developed capacity and infrastructure in China and India The Wheat RI aimed to integrate genetic diversity for water-use efficiency and heat tolerance into Chinese and Indian breeding programmes. Some aspects of the RI sprang from work led by Francis Ogbonnaya of the International Center for Agricultural Research in the Dry Areas (ICARDA) and by Peter Langridge of the Australian Centre for Plant Functional Genomics (ACPFG). Jean-Marcel Ribaut, GCP Director, says of the work: “The GCP’s RI approach was not about large impacts in the short term. Rather, what GCP demonstrated was definitive proof-of-concept of the power of molecular breeding to increase crop productivity, thereby improving food security. Other agencies are now able to upscale and outscale the proven concept at the national, or even at the regional level.”

Like China, India is an extremely water-stressed country, with the water table in many places falling at an alarming rate. In North Gujarat alone, an established wheat district in western India, the water table is reported to be dropping by as much as six metres per year.

Delivering wheat varieties that have improved water-use efficiency and higher tolerance to drought will have the greatest impact in these countries, given they are the two largest producers of wheat worldwide.

“Even though the Initiative is set to conclude in 2015, the outcomes have already been absolutely phenomenal for such a short time-bound project, given that wheat is such a complex plant to work with,” exclaims Richard. “While we are still a few years away from releasing new drought-tolerant varieties, we have been able to develop systems and build capacity to reduce the time it takes to develop and release these varieties.”

Tapping into genetic diversity to enhance wheat’s drought and heat tolerance

Spikes of emmer wheat.

One project that impressed Richard was that led by Satish Misra, GCP Principal Investigator and senior wheat breeder at Agharkar Research Institute, Pune, India.

In a collaboration with the University of Sydney, Australia, and the International Maize and Wheat Improvement Center (CIMMYT), the project identified novel genes associated with drought- and heat-tolerance traits in ancestral wheat lines (of emmer wheat).

Emmer wheat is a minor crop grown mainly in marginal lands, where farmers can produce a small harvest but nowhere near the yield of more elite cultivated lines. Satish explains that emmer wheat lines are very useful for breeders because they have a larger diversity of novel genes than more popular wheat types, such as durum or bread wheat.

Durum wheat spike.

“Durum lines are more commonly used by breeders because of their high yield and hard grain, which is used to make bread wheat and pasta,” Satish says. “However, because of their popularity and continual use in breeding, durum wheat lines have become less and less diverse with years of cultivation.”

The first task was to identify emmer lines that might have genes for drought and heat tolerance. Satish says that CIMMYT played an important part in this process. “They gave us access to their gene bank, which contains almost 2,000 emmer lines. More importantly, they helped us develop a reference set that encapsulated all the diversity found in the emmer lines they had.”

A reference set reduces the number of choices that breeders have to search through, from thousands down to a few hundred – in this case, 300 emmer lines.

“CIMMYT also developed 30 synthetic emmer wheat lines by crossing wild emmer wheat species with domesticated wheat species,” says Satish. “The synthetic lines contain the novel drought- and heat-tolerance genes.”

Satish and Richard’s teams crossed these synthetic lines with durum wheat lines and identified 41 resulting lines with high levels of stress tolerance. These are undergoing further evaluation in India and Australia.

“What Satish has been able to do in five years is amazing and is currently having a big impact in wheat breeding in India and Australia,” says Richard. “We’ve had local breeding companies here in Australia come to us requesting the lines we developed. The same is happening in India, too.”

Reaping existing skills

A baker butters naan bread in Hyderabad, India.

For Richard, the preliminary success of the Wheat RI is due, at least in part, to the speed with which national breeding programmes in both China and India are learning and incorporating new molecular-breeding techniques.

“This was another reason why we chose to focus on China and India: they had the infrastructure and human capacity to start doing this almost immediately,” says Richard. “In other countries where GCP is investing, more time is going into teaching breeders the basics of molecular breeding and genetics. In China and India, they already have that basic understanding and are able to quickly incorporate it into their current programmes.”

This does not mean, however, that the work is not focused on building capacity, given that molecular breeding is still a relatively new concept for many breeders around the world.

Ruilian Jing says the China project is continually working to educate and train wheat breeders in molecular-breeding techniques.

“When we started the project, we found that most institutions that focus on wheat breeding in China had the equipment to do marker-assisted breeding but were unsure how to use it,” says Ruilian, professor in plant breeding at the Chinese Academy of Agricultural Sciences (CAAS) and Principal Investigator for the Wheat RI’s drought-tolerant wheat project in China.

Much of Ruilian’s work in China has been in educating these breeders so they can start achieving outcomes.

Younger researchers taking a lead

Ruilian explains that those leading the charge to become educated in molecular-breeding techniques are young researchers, including seven PhD students and one Master’s student supported by the project in China.

One such researcher who is enthusiastically applying these new approaches is Yonggui Xiao, a molecular plant breeder at the Institute of Crop Science, CAAS.

“Working as part of this GCP project gave me my first opportunity to practice using molecular-breeding techniques to improve the quality and yield of wheat under drought conditions,” says Yonggui.

“We have so far successfully used several molecular markers to produce an advanced variety, with higher yield and preferred qualities [taste, grain colour] under water stress, and this will be released to farmers [in 2015].”

Women of the Nakhi people harvest wheat in Songzanlinsi, Yunnan, China.

Yonggui is now expanding the application of the technology to develop varieties with resistance to powdery mildew, a fungal disease that can reduce wheat yields and quality during non-drought years. “Overall, we have been impressed by how these new techniques complement our conventional breeding techniques to improve selection efficiency, in turn reducing the time and costs of producing advanced varieties,” says Yonggui.

Success stories like these make Ruilian’s job easier as she tries to encourage more and more plant breeders to experiment with these new breeding techniques.

At the same time, she is impressed by this new generation of molecular wheat breeders who will ensure that these techniques benefit wheat research in many years to come: “This form of capacity, the human capacity, which we are building, is what will leave the largest legacy in China and help this technology spread from generation to generation and crop to crop.”

Overcoming complex traits, genes and wary breeders

Wheat farmer in India.

Across the Himalayas, Ruilian’s Indian counterpart, Vinod Prabhu, is just as pleased with the progress and results his team are producing.

“Over the last five years, we have discovered several water-use efficiency traits and their related genes, bred new lines to incorporate the genes and traits and run national trials, all of which would be unheard of using only conventional breeding practices,” says Vinod, Head of the Genetics Division at the Indian Agricultural Research Institute in New Delhi and the Principal Investigator for the Wheat RI’s drought-tolerant wheat project in India.

By the end of the projects in November 2015, partners in China and India will deliver 15–20 new wheat lines with drought and heat tolerance, adapted to each country’s conditions. An additional target for both China and India is to produce four wheat varieties with improved water-use efficiency and higher heat tolerance. These varieties will have the potential to cover about 24 million hectares and minimise yield loss from heat or drought, or both, by up to 20–50 percent.

Vinod confides that all these outcomes are far more than what he initially expected they would achieve: “When we started, we had a lot of reservations about the complexity of breeding for drought tolerance in wheat as well as the acceptance and uptake of these new breeding techniques by conventional breeders.”

Vinod’s primary role has been to coordinate the Indian centres working on the project (see box at end). But he has also been working to convince Indian plant breeders that these unconventional, new breeding techniques will improve their efficiency and aid in their quest to breed for heat- and drought-tolerant wheat varieties.

“Many world-leading wheat breeders were wary at first, but they have definitely started to see the merit in using the technology to enhance their conventional methods as we edge closer towards releasing new varieties in such a short time,” says Vinod.

Wheat seed ready for planting in Punjab, India.

Incorporating conventional methods

An aspect of the Wheat RI that Ruilian and Vinod have been continually promoting is the importance of conventional breeding methods. “These new molecular-breeding techniques are only a small part of the whole breeding process,” says Ruilian. “Yes, they provide a big impact, but in the grand scheme of things they need to be viewed as one tool in a breeder’s tool box.”

For more information on conventional versus molecular breeding, or marker-assisted breeding, see our quick guide here on the Sunset Blog.

Phenotyping: How to manage a subjective process

One of the most important processes of the Wheat RI, and plant breeding in general, is phenotyping: measuring and recording observable characteristics of the plant such as drought tolerance or susceptibility to pests and diseases. Breeders phenotype the plants they have developed to see which ones have the traits they are interested in and also – for molecular breeding to be possible – to establish links between specific genes and specific traits.

Unfortunately, phenotyping has caused a bit of trouble for both Chinese and Indian partners. The challenge stems from the fact that one person’s observations about a plant’s phenotype or characteristics may not be the same as another person’s.

“This is always a challenge for any collaborative plant-breeding project,” says Vinod. “Unless all trials are inspected by one person, there will always be a risk of inconsistent observations.

Scientists from South Asia learn phenotyping on a training course at CIMMYT.

To help overcome this inconsistency, one of the first activities of the Wheat RI was to develop phenotyping protocols that allowed researchers in different research institutes and countries to collect comparable data. GCP enlisted Matthew Reynolds, a wheat physiologist at CIMMYT, to help with this.

“Each breeder has their own ways to do things, so it’s important to develop standardised protocols, particularly for a transnational project like this,” explains Matthew. “We developed a few standardised phenotyping manuals and travelled to China to give some intensive hands-on training.”

This problem is not unique to China and India. Another GCP wheat project is providing promising results to help overcome the risk of inconsistency and increase the efficiency and accuracy of phenotyping. Led by Fernanda Dreccer, based at Australia’s Commonwealth Scientific and Industrial Research Organisation (CSIRO), in collaboration with the International Center for Agricultural Research in the Dry Areas (ICARDA), the project is developing a reliable phenotyping approach to detect drought-adaptive traits in wheat crops using cheap and simple tools.

“For example, using just a camera you can analyse crop cover, which is an important trait for shading the crop and/or trapping heat,” says Fernanda. “The idea was to test different non-invasive, low-cost tools and compare them to find something that would provide accurate and useful data related to identifying drought-tolerance traits.”

Another important aspect of phenotyping that Fernanda’s project is helping with is constant and consistent analysis of a crop’s surroundings. “It’s just as important to measure the environment of the crop as it is [to measure] the crop itself to make a correlation between an environmental impact and a plant’s reaction,” says Fernanda.

Since the static nature of single observations can give a misleading or incomplete picture, Fernanda’s team is integrating live crop, weather and soil data through mobile sensors in the field with the aim of producing constant phenotypic information. “This will provide new insights into the interaction between the genotype and the environment. This in turn will help to accelerate the detection of wheat genotypes better suited to cope with drought.”

A young farmer in her wheat field in India.

Managing the tsunami of phenotyping data

Although a plant breeder’s work should be simplified and made more efficient by combining molecular-breeding technologies with advanced phenotyping techniques and protocols, the reality is not necessarily so easy.

There are many steps to the plant-breeding puzzle, all of which produce data. The more advanced the techniques and – in the case of wheat – the more complex the plant’s genome, the more pieces of data breeders need to sift through to find solutions.

Before the Wheat RI started, Richard saw that this impending tsunami of data was going to be a problem in both China and India: “Both countries had the skills to carry out these advanced techniques, but they didn’t have in place a strong culture of data management.”

This problem is by no means unique to China and India, Richard says: “Most of the time, plant breeders keep a log of all their data in a book or Excel sheet. However, these data often get lost once a project is completed.”

GCP recognised this problem before the RIs began and has, since 2009, been developing the Breeding Management System (BMS) – a suite of interconnected software designed to manage the mass of data – as part of its Integrated Breeding Platform (IBP).

“The BMS is the first tool that can help breeders record and collate their data in a coordinated way,” says Richard. “This is vital in a project like this, which has several institutes across three countries working towards a similar product.”

Vinod agrees with Richard, adding that the BMS was relatively easy for his Indian partners to learn and use: “The BMS is great as we have no way of losing data.”

Rolling out the BMS in China, though, has been more difficult due to the language barrier. Ruilian explains: “We are now working towards translating the IBP, but it will be an ongoing challenge as the platform continually changes and is updated.”

Ruilian is optimistic that a translated BMS will become a viable tool for Chinese breeders in the future. “The more that we collaborate with other countries, the more a tool like this becomes important to have.”

Watch Richard on adoption of IBP tools in the video below.

Friendly competition helping inspire India’s wheat breeders

Vinod credits two things for the successful development of new wheat varieties and integration of new breeding techniques and data-management systems: a clear, logical plan and friendly competition between China and India to breed the first new drought-tolerant varieties.

“The initial plan, which Richard helped develop in Montpellier, was logical and well thought out. Although we initially thought it was overambitious in its objectives, we have been able to meet them so far, which is a great credit to the team and their enthusiasm to try these new technologies and see for themselves the benefits first hand.

“What has also helped is our competitive spirit, as we would like to achieve the objectives before the Chinese breeders do. Our breeders are always asking me for updates on how China is progressing!” Vinod adds, with a chuckle.

Ruilian agrees with Vinod’s assessment, adding: “The project would not have been as successful if it was solely national. It needed the international collaboration and friendly competition to help build confidence and drive.”

For Richard this international collaboration, between two very different and proud cultures, allowed the project to broaden its scope and troubleshoot quicker than usual.

“They [the Chinese and Indian researchers] think about problems in different ways. When you get a group of people in a room from different backgrounds, you can come up with great integrated plans, things you would never have come up with within just a national team,” says Richard.

Watch Richard on the beauty of diversity in research partnerships in the video below.

Securing wheat production into the future

With the project concluding in 2015, both the Chinese and Indian researchers are working towards completing national trials and releasing their new, advanced drought-tolerant varieties to farmers and other breeders. However, for Richard, the impact of the Wheat RI may not be fully recognised for 10–20 years.

“The initial new varieties that both China and India develop will help farmers in the short term. However, as both countries become more advanced in using the technology, future varieties are sure to be more and more robust. What’s more, these techniques and tools are sure to filter through to other national wheat-breeding programmes, as well as to other crops.”

In the case of wheat, new drought-tolerant varieties will help secure both China’s and India’s wheat industries, helping to stabilise wheat yields, and consequently prices, the world over. These new varieties may not be the silver bullet for eliminating the risks of drought, but they will go a long way to mitigating its impact.

Donkeys bring home the wheat harvest in Qinghai, China.

A little research goes a long way for lentils

Africa, Asia, Genetics, Integrated Breeding Platform, Legumes, Lentils, Phase I crops No Responses »

Jan 302015

“Little had been done to advance the genetic diversity of lentils.” This was the picture back in 2005, recalls Aladdin Hamwieh, a scientist at the International Center for Agricultural Research in the Dry Areas (ICARDA) based in Lebanon.

“Lentil has a narrow genetic base, meaning not too many varieties are used in production,” he explains.

A small sample of the lentil diversity available in the ICARDA gene bank.

It was on this premise that Aladdin joined a three-year global effort to capture and understand the genetic diversity of the world’s lentil varieties – a protein-rich crop that plays an integral part in the lives of many people in Central and West Asia and North Africa (CWANA), South Asia and North America.

He was funded by the CGIAR Generation Challenge Programme (GCP) to develop a refined set of genetic reference materials for lentils so that plant breeders across the globe could access the best gene pool available to be able to improve food security in developing countries.

“Essentially, the genetic make-up of lentil was repeatedly filtered until 15 percent of ICARDA’s gene bank was collected,” says Aladdin.

ICARDA has the largest collection of lentil genes in the world. Some work had been done on improving the genetics of lentils to withstand harsh, dry conditions. But it was not enough to prepare for the challenge the world is now facing – feeding almost 10 billion people by 2050 and climate conditions that mean longer dry periods and more erratic rainfall.

The reference set captures the existing genetic diversity of lentils and makes it easier for scientists to search for genes that can help overcome the challenges to lentil production. It consists of about 150 accessions, or 15 per cent of the global collection studied (see box).

Creating the reference set immediately helped researchers to understand more about lentils. “The major outcome was that different gene pools were identified where accessions from Europe and America were clearly separated from Asia and Africa,” Aladdin says. “Accessions from India, Afghanistan and Pakistan were also separated from accessions from the Middle East and North Africa.”

A common resource for lentil breeders

International cooperation and knowledge sharing are hallmarks of GCP, with one of the Programme’s key goals being to facilitate collaboration between scientists from across the globe in breeding new varieties of crops that can not only tolerate drought, but also resist diseases and tolerate poor soils. Ashutosh Sarker, a former lentil breeder and currently Coordinator and Food Legume Breeder for ICARDA’s South Asia and China Regional Program, says production challenges for lentils vary from country to country. While demand is rising globally, he says, some developing countries are having trouble meeting their own need for this staple food.

A woman farmer with lentils in Bihar, India.

This was where the GCP work came in; its purpose, according to Aladdin, was to “develop a diverse reference set that is small and easy to handle. This way, it can be sent around the world for scientists to simultaneously screen for desirable or undesirable traits. This has important implications for developing countries.”

The reference collection serves as a common resource for all lentil breeders interested in the same crop.

“These materials can be accessed to achieve farming goals – to produce tough plants suitable for local environments. In doing this, farmers have a greater likelihood of success, which ultimately improves the wider population’s food security.”

When Aladdin’s team studied the reference collection, they were able to identify favourable genes.

“This enables us to look at the genes of plants and highlight those traits that best suit certain environments,” he says, “and then breed plants to be better adapted.”

Diversity is key to searching for valuable breeding traits

Shiv Kumar Agrawal, who joined ICARDA in 2009, uses the reference set developed for GCP to identify and create markers for drought-tolerant and early-maturing traits for key lentil-producing countries, including Bangladesh, Ethiopia and India.

“Developing more markers will help mitigate lentil’s barriers to production,” says Shiv, pointing to climate change and rising temperatures in production zones as adversely affecting lentil yields.

Markers are like genetic ‘tags’ that indicate which plants or seeds have particular genes, so markers related to relevant genes – for traits such as heat tolerance, for example – can help breeders choose which plant materials to use when developing a new variety.

“Breeding for this should be a priority,” he continues. “Developing heat-tolerant lentil plants would help to expand the area of legume cultivation, stabilise yield in areas prone to heat stress and mitigate impacts of global climate change in the future.”

This is the same for other traits, he says, which would improve food security in developing countries: “Developing extra-early breeds of lentils has great scope in diversifying cropping methods and gives more flexibility for farmers.”

Photo: T Wolday/Bioversity International

Farmers in Ethiopia winnow orange lentils.

Karthika Rajendran, a postdoctoral student working with Shiv at ICARDA, uses both conventional and molecular-breeding approaches to develop heat-tolerant lentil cultivars that mature early. The products of GCP, she says, are “helpful to identify the source of genetic diversity and molecular markers for the traits identified under each research targets.”

Like Shiv, Karthika stresses the value of heat-tolerant varieties for heat-stressed areas and in reducing the impacts of climate change, and adds that improving other traits alongside also has significant impacts: “The development of machine-harvestable lentils reduces the production cost, increases the farm profit, reduces the drudgery of women and improves the nutritional and food security of smallholder farmers in developing countries.”

Farmer Minto with lentils in his field in Bangladesh.

While achieving such lentil varieties may be some way down the track, Shiv and Karthika offer a small glimpse of what the future holds and the promise of making even more from GCP’s genetic reference set than what has been achieved so far.

Preserving genetic resources

Aladdin Hamwieh is also looking to the future: “We don’t know what tomorrow brings, so people need to understand the value of such genetic reference material.”

He reflects on the reality of how civil unrest in developing countries often means local agriculture is disrupted and crops destroyed, which can mean the loss of traditional varieties.

“We could lose interesting genes from these,” says Aladdin. “We must therefore maintain and protect the ICARDA database, because it stores important information that the next generation won’t be able to study in nature.”

Aladdin is adamant that this is important not only for developing countries but for the whole world. “We can’t make genes in future so this one we cannot lose,” he stresses.

A ‘backup’ duplicate copy of ICARDA’s lentil collection is stored in the Arctic Circle at the Svalbard Global Seed Vault.

Groundwork on lentils ‘gave orientation to future breeding efforts’

Although GCP’s genetic research work on lentils came to an end in 2007, scientists all over the world can still access the materials – and are reaping other benefits from GCP’s work too. For example, ICARDA is using GCP’s Integrated Breeding Platform (IBP) – particularly the Breeding Management System (BMS) – for its lentil-breeding programme.

Reflecting GCP’s collaborative spirit, Shiv explains that his team have not only successfully integrated use of BMS within their own programme, but have also included it in regular training programmes for developing country partners.

Karthika says, “We use the BMS to store historical data of crossing blocks and germplasm collections and to create fieldbooks, field maps and labels of yield trials. We use the crossing manager to build up the list of the crossing blocks, and the breeding manager to maintain the pedigree of the breeding programme.”

She explains that within the BMS, “the breeding view demonstrated a great potential to analyse the phenotypic and genotypic data for single and multienvironmental conditions,” and notes that “the Molecular Breeding Design Tool would be useful in the process of marker-assisted selection.”

ICARDA plans to implement the BMS to develop fieldbooks for Lentil International Elite Nurseries, using the IBFieldbook tool, and to distribute the books to developing country partners for data collection.

“Once the database is centralised, it will facilitate rapid access to breeding material and easy sharing of knowledge and technology to the developing country partners,” says Karthika.

Such ongoing advances in breeding technologies since the outset of GCP mean the refining process can continue.

“We should not stop,” says Aladdin, encouraging other lentil breeders and researchers to continue their work.

A female farmer in India helps to harvest lentils by sifting them after fellow workers have beaten the stalks to remove the seeds from their pods.

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

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

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

More links

Cassava brings life to African people

GCP takes the first steps to kick start cassava research

Cassava research leaps forward with new varieties to benefit farmers

Many traits and many varieties

Hunt for ‘super powered’ cassava

Cassava grows up: looking ahead to supporting African families

More links

Barley a ‘chosen one’ for research

Finding the clues to help breeders select barley’s best DNA

Checking out the effects of the environment on gene expression

Making the most of wild barley

GCP builds genetic resources through ongoing collaboration

Sub-Saharan Africans getting their vitamin A from sweetpotato

New DNA markers identified for sweetpotato disease

Mobilising the genetic diversity of sweetpotato for breeding

The genetic lifelines reach Africa

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Banana’s asexuality inhibits its resilience

Passionate people pooled for the work

To advance genetics, you first need the intelligence

Malaysian wild subspecies fully sequenced

Breeders now need to set to work

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Sharing knowledge to improve breeding efficiency and sustainability

Tapping into genetic diversity to enhance wheat’s drought and heat tolerance

Reaping existing skills

Younger researchers taking a lead

Overcoming complex traits, genes and wary breeders

Incorporating conventional methods

Phenotyping: How to manage a subjective process

Managing the tsunami of phenotyping data

Friendly competition helping inspire India’s wheat breeders

Securing wheat production into the future

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A common resource for lentil breeders

Diversity is key to searching for valuable breeding traits

Preserving genetic resources

Groundwork on lentils ‘gave orientation to future breeding efforts’