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Nov 062015
 

 

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

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

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

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

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

Photo: GCP

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

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

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

Photo: ICRISAT

A little girl tucks into sorghum porridge in Mali.

The dawn of a new generation

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

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

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

Photo: J van de Gevel/Bioversity International

Wheat varieties in a field trial.

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

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

A programme where the spirit is palpable

Photo: N Palmer/CIAT

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

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

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

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

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

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

Photo: Meena Kadri/Flickr (Creative Commons)

Harvesting wheat in India.

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

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

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

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

Exploring gene banks to uncover genetic wealth

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

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

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

Photo: IITA

Gene bank samples give a small snapshot of cowpea diversity.

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

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

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

Photo: International Potato Center (CIP)

Sweetpotato diversity.

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

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

Photo: ICARDA

Harvesting barley in Ethiopia.

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

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

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

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

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

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

Photo: N Palmer/CIAT

Banana harvest for sale in Rwanda.

A need to focus and deliver products

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

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

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

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

Photo: Mann/ILRI

Hard work: harvesting groundnut in Malawi.

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

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

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

Photo: IRRI

Child eating rice.

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

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

Such products released on the ground included new varieties of:

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

Harvesting rice in India.

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

These will include varieties of:

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

Groundnut harvest, Ghana.

Giving a voice to all the cast and crew

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

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

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

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

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

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

Photo: IRRI

Rice seed diversity.

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

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

Developing capacity and leadership in Africa

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

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

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

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

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

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

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

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

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

Photo: IITA

Nigerian cassava farmer.

A ‘sweet and sour’ sunset

Photo: Daryl Marquardt/Flickr (Creative Commons)

Maize at sunset.

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

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

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

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

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

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

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

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

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

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

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

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

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

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Photo: E Hermanowicz/Bioversity International

Cowpea seeds dried in their pods.

Oct 192015
 

 

Photo: ICRISAT

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 19th 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.

Photo: IRRI

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.

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

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.

Photo: P Kosina/CIMMYT

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

Photo: V Meadu/CCAFS

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.

Photo: C Schubert/CCAFS

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 AltSB 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.

Photo: K Zaw/Bioversity International

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.”

Photo: X Fonseca/CIMMYT

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.

Photo: IRRI

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

Looking forward 30 years

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

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

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

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

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

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

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Oct 162015
 
Photo: A Paul-Bossuet/ICRISAT

Pigeonpea farmers in India.

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

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

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

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

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

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

Photo: S Kilungu/CCAFS

Harvesting sorghum in Kenya.

Setting a foundation for higher yielding, drought-tolerant chickpeas

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

Photo: ICRISAT

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.

Photo: ICRISAT

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

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

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

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

Developing capacity by involving partners in Kenya and Ethiopia

Photo: GCP

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

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

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

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

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

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

Photo: S Sridharan/ICRISAT

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

Decoding pigeonpea genome

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

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

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

Photo: B Sreeram/ICRISAT

A pigeonpea farmer in his field in India.

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

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

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

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

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

Photo: ICRISAT

East African farmers inspect pigeonpea at flowering time.

Securing income-generating groundnut crops in Africa

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

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

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

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

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

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

Photo: S Sridharan/ICRISAT

Drying groundnut harvest, Mozambique.

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

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

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

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

Supporting key crops in West Africa

Photo: N Palmer/CIAT

Harvested pearl millet and sorghum in Ghana.

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

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

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

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

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

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

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

Photo: A Paul-Bossuet/ICRISAT

Enjoying a tasty dish of sorghum.

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

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

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

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

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

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

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

Photo: N Palmer/CIAT

A Ghanaian farmer examines his pearl millet harvest.

From poverty to prosperity through partnerships

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

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

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

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

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

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

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

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

More links

Photo: A Paul-Bossuet/ICRISAT

Man and beast team up to transport chickpeas in Ethiopia.

 

Oct 122015
 

 

Photo: One Acre Fund/Flickr (Creative Commons)

A Kenyan farmer harvesting her maize.

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

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

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

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

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

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

Photo: Allison Mickel/Flickr (Creative Commons)

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

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

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

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

 By weight, more maize is produced each year than any other grain: global production is more than 850 million tonnes. Maize production is increasing at twice the annual rate of rice and three times that of wheat. In 2020, demand for maize in developing countries alone is expected to exceed 500 million tonnes and will surpass the demand for both rice and wheat.  This projected rapid increase in demand is mainly because maize is the grain of choice to feed animals being reared for meet – but it is placing strain on the supply of maize for poor human consumers. Demand for maize as feed for poultry and pigs is growing, particularly in East and Southeast Asia, as an ever-increasing number of people in Asia consume meat. In some areas of Asia, maize is already displacing sorghum and rice. Acreage allocated to maize production in South and Southeast Asia has been expanding by 2.2 percent annually since 2001. In its processed form, maize is also used for biofuel (ethanol), and the starch and sugars from maize end up in beer, ice cream, syrup, shoe polish, glue, fireworks, ink, batteries, mustard, cosmetics, aspirin and paint.

Researchers take on the double whammy of acid soils and drought

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

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

Photo: A Wangalachi/CIMMYT

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

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

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

Scientists join hands to unravel maize complexity

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

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

Photo: X Fonseca/CIMMYT

Maize diversity.

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

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

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

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

Photo: N Palmer/CIAT

Maize ears drying in Ghana.

Comparing genes: sorghum gene paves way for maize aluminium tolerance

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

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

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

Photo: L Kochian

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

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

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

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

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

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

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

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

Kenya deploys powerful maize genes

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

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

Marker-assisted selection helps breeders like Sam Gudu more quickly develop plants that have desirable genes. When two plants are sexually crossed, both positive and negative traits are inherited. The ongoing process of selecting plants with more desirable traits and crossing them with other plants to transfer and combine such traits takes many years using conventional breeding techniques, as each generation of plants must be grown to maturity and phenotyped – that is, the observable characteristics of the plants must be measured to determine which plants might contain genes for valuable traits.   By using molecular markers that are known to be linked to useful genes such as ZmMATE1, breeders can easily test plant materials to see whether or not these genes are present. This helps them to select the best parent plants to use in their crosses, and accurately identify which of the progeny have inherited the gene or genes in question without having to grow them all to maturity. Marker-assisted selection therefore reduces the number of years it takes to breed plant varieties with desired traits.

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

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

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

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

Photo: N Palmer/CIAT

A Kenyan maize farmer.

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

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

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

Photo: N Palmer/CIAT

Maize grain for sale.

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

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

Photo: D Mowbray/CIMMYT

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

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

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

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

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

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

Photo: A Erlangga/CIFOR

A farmer in Indonesia transports his maize harvest by motorcycle.

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

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

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

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

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

Photo: E Phipps/CIMMYT

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

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

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

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

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

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

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

A better picture: GCP brightens maize research

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

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

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

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

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

Photo: CIMMYT

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

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

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

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

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

More links

Photo: N Palmer/CIAT

A farmer displays maize harvested on his farm in Laos.

Jun 162015
 
Ripening barley.

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.

Signs of barley being domesticated and grown for human use in the Fertile Crescent date back to more than 8,000 BCE. It was a staple cereal of ancient Egypt, where it was used to make bread and beer.  The Fertile Crescent is a crescent-shaped region containing comparatively moist and fertile land within otherwise arid and semiarid West Asia and the Nile Valley and Nile Delta of Northeast Africa. The modern-day countries with significant territory within the Crescent are Cyprus, Egypt, Iraq, Israel, Jordan, Kuwait, Lebanon and Syria; it also includes the southeastern fringe of Turkey and the western fringes of Iran.  Today barley is an important crop for many of these countries, and while production in many other parts of the world is declining it is increasing in this region. Worldwide, barley is grown in more than 100 countries, yielding more than 120 million tonnes a year for food, livestock feed and beer production. This makes it the world’s fourth most important cereal crop, after maize, rice and wheat.

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 grain is used as animal feed, malt and human food. Barley straw is used as animal feed, for animal bedding and for roofing huts. In many developing countries, livestock graze on the stubble after barley is harvested. Barley is also used for green grazing or is cut before maturity and either directly fed to animals or used for silage. In the highlands of Tibet, Nepal, Ethiopia, Eritrea, in the Andean countries and in North Africa, barley is also an important food source.

Barley-based livestock system on marginal drylands in Morocco.

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.

Morocco researchers use GCP barley reference set to improve food security In Morocco, barley is the second most important cereal after wheat. Farmers produce about 1.3 million tonnes a year from a cultivated area of almost 1.9 million hectares. In this North African country, barley is used as food as well as for animal feed. It plays an important role in food security, as the per capita barley consumption is the highest in the world. However, production is constrained by diseases, pests, and stresses such as drought, and climate change has further aggravated the problem. Morocco imports cereals to meet its domestic demand.  Moroccan varieties of barley have a narrow genetic base, making it difficult to breed better varieties. In this context, the GCP barley reference set was introduced to Morocco from ICARDA and used in the breeding programme. “This has helped my country to develop new varieties,” says Fouad Abbad Andaloussi, Head of the Plant Protection Department at L'Institut National De La Recherche Agronomique (INRA; National Institute for Agricultural Research). “GCP has also greatly enhanced my personal scientific contacts and helped me to explore new developments in plant genetics and biotechnology.”

Photo: ICARDA

Barley growing on experimental fields in Morocco.

Checking out the effects of the environment on gene expression

Photo: World Bank Photo Collection

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.

Barley: Food of gladiators Barley contains about 75 percent carbohydrate, 9 percent protein and 2 percent fat. Barley grain is rich in zinc (up to 50 ppm), iron (up to 60 ppm) and soluble fibres and has a higher content of Vitamins A and E than other major cereals. Barley has been documented as a high-energy food since the Roman times, when the gladiators were called ‘hordearii’, meaning barley men or barley eaters, because they were fed a barley diet before going to an arena to fight. Some varieties of barley are also remarkably high in protein. For example, some Ethiopian varieties have up to 18 percent protein.

Photo: Peter Haden/Flickr (Creative Commons)

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.

Jun 052015
 
Photo: Bill & Melinda Gates Foundation

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.”

Photo: Bill & Melinda Gates Foundation

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

Sub-Saharan Africans getting their vitamin A from sweetpotato

Photo: CIP

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.

Photo: HarvestPlus

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.

Photo: HarvestPlus

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.

Sweetpotato, in spite of its name, is only distantly related to the potato. Unlike the potato – which is a tuber, or thickened stem – the sweetpotato is a root. Sweetpotato is not related to the yam either, despite the physical similarity between the two. Sweetpotato can grow at altitudes ranging from sea level to 2,500 metres. It requires fewer inputs and less labour than other crops such as maize, and, in contrast to the potato, it can tolerate heat.

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.

Photo: HarvestPlus

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.

Photo: Bill & Melinda Gates Foundation

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.

Photo: CIP

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.”

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Photo: P Casier/CGIAR

Kenyan farmer Emily Marigu with her sweetpotatoes.

Mar 262015
 

 

Photo: R Cheung/Flickr

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.

Photo: E Zotov/Flickr

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

Photo: Rasbak/Wikimedia Commons

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.

Photo: X Fonseca/CIMMYT

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  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.”

Reaping existing skills

Photo: R Pamnani/Flickr

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].”

Photo: R Saltori/Flickr

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

Photo: CCAFS

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.

Photo: N Palmer/CIAT

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.”

Conventional vs marker-assisted breeding To conventionally breed a new wheat variety, two wheat plants are sexually crossed. The aim is to combine the favourable traits from both parent plants and exclude their unwanted traits in a new and better plant variety. This is achieved by selecting the best plants from among the progeny over several generations. Marker-assisted breeding allows breeders to be much more efficient and targeted in their activities. It still requires breeders to sexually cross plants, but they can use genetic information to tell them which plants have particular genes for useful traits, which helps them to choose which parent plants to cross, and then to confirm which of the progeny have inherited the desired gene without necessarily growing and phenotyping all of them under conditions that would express that trait.

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.

Photo: CIMMYT

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.”

Photo: R Martin/CIMMYT

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.

Photo: Rosino/Flickr

Donkeys bring home the wheat harvest in Qinghai, China.

The GCP Wheat Research Initiative involved 10 institutes from China, India and Australia: China – Chinese Academy of Agricultural Sciences (Institute of Crop Science; National Key Facility for Crop Gene Resources and Genetic Improvement) Hebei Academy of Agricultural Sciences Shanxi Academy of Agricultural Sciences  Xinjiang Academy of Agricultural Sciences India – Indian Agricultural Research Institute Punjab Agricultural University Agharkar Research Institute  National Research Centre on Plant Biotechnology Jawaharlal Nehru Krishi Vishwa Vidyalaya Australia – Plant Breeding Institute, University of Sydney The Wheat RI built on several previous GCP projects conducted by the International Maize and Wheat Improvement Center (CIMMYT) and International Center for Agricultural Research in the Dry Areas (ICARDA).

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Mar 192015
 
Photo: N Palmer/CIAT

A farmer harvests her pearl millet crop in Ghana’s Upper West Region.

Pearl millet is the only cereal crop that can be grown in some of the hottest and driest regions of Asia and Africa. It is a staple provider of food, nutrition and income for millions of resource-poor people living on these harsh agricultural lands.

Even though pearl millet is well adapted to growing in areas characterised by drought, poor soil fertility and high temperatures, “there are limited genetic tools available for this orphan crop,” reported researcher Tom Hash at the International Crop Science Congress 10 years ago.

“The people who relied on this crop in such extreme environments had not benefitted from the ‘biotechnology revolution’, or even the ‘green revolution’ that dramatically increased food grain production on irrigated lands over a generation ago,” adds Tom, now Principal Scientist (Millet Breeding) in the Dryland Cereals Research Program of the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). This lack of research dividends was despite the fact that pearl millet is the sixth most important cereal crop globally.

It was at this time – in 2005 – that the CGIAR Generation Challenge Programme (GCP) stepped up to invest in more genetic research for pearl millet (along with finger and foxtail millet).

Photo: S Mann/ILRI

Newly harvested pearl millet heads in Niger.

The use of genetic technologies to improve pearl millet had already made some advances through work carried out in the United Kingdom. The GCP initiative was established to improve food security in developing countries by expanding such available genetic work to create crops bred to tolerate drought, disease and poor soils.

With financial support from GCP, and with the benefit of lessons learnt from parallel GCP genetic research, ICRISAT scientists were able to develop more advanced tools for breeding pearl millet.

Pearl millet is used for food for humans and animals and is an essential component of dryland crop-livestock production systems like those of the Sahel region of Africa. It is a main staple (along with sorghum) in Burkina Faso, Chad, Eritrea, Mali, Niger, northern Nigeria, Senegal and Sudan. It has the highest protein content of any cereal, up to 22 percent, and a protein digestibility of about 95 percent, which makes it a far better source of protein than other crops such as sorghum and maize. Pearl millet grain is also a crucial source of iron and zinc. Pearl millet is the most widely grown millet (a general term for grain harvested from small-seeded grasses), and accounts for approximately 50 percent of the total world millet production. It has been grown in Africa and South Asia, particularly in India, since prehistoric times and was first domesticated in West Africa. It is the millet of choice in hot, dry regions of Asia, Africa and the Americas because it is well adapted to growing in areas characterised by drought, poor soil fertility and high temperatures; it even performs well in soils with high salinity or low levels of phosphorous. In short, thanks to its tolerance to harsh environments, it can be grown in areas where other cereals such as maize or wheat do not survive or do not yield well.

Protein in pearl millet ‘critical’ for nutrition

Photo: P Casier/ICRISAT HOPE

A farmer harvests millet in Mali.

Mark Laing, Director of the African Centre for Crop Improvement (ACCI) at the University of KwaZulu-Natal in South Africa, says the GCP-supported work on pearl millet will have long-term impacts.

He says it is the high protein content of pearl millet that makes it such a crucial crop for developing countries – in Africa, this is the reason people use pearl millet for weaning babies.

“It was interesting to us that African people have used pearl millet as a weaning food for millennia. The reason why was not clear to us until we assessed the protein content,” says Mark. “Its seed has 13–22 percent protein, remarkable for a cereal crop, whereas maize has only eight percent protein, and sorghum has only two percent digestible protein.”

Photo: S Kilungu/CCAFS

Pearl millet growing in Kenya.

Tom Hash agrees, adding: “More importantly, pearl millet grain has much higher levels of the critically important mineral micronutrients iron and zinc, which are important for neurological and immune system development.

“These mineral micronutrients, although not present in a highly available form, can improve blood iron levels when used in traditional pearl millet-based foods. Pearl millet grain, when fed to poultry, can provide a potentially important source of omega-3 fatty acids, which are also essential for normal neurological development.”

Pearl millet endowed with genetic potential

Photo: AS Rao/ICRISAT

A farmer with his pearl millet harvest in India.

In a treasure-trove of plant genetic resources, thousands of samples, or accessions, of pearl millet and its wild relatives are kept at ICRISAT’s gene banks in India and Niger.

For pearl millet alone, in 2004 ICRISAT had 21,594 types of germplasm in its vaults at its headquarters in India. This represents a huge reservoir of genetic diversity that can be mined for data and for genetic traits that can be used to improve pearl millet and other crops.

Between 2005 and 2007, with support from GCP, scientists from ICRISAT set to work to do just that, mining these resources for qualities based on observed traits, geographical origin and taxonomy.

Hari D Upadhyaya, Principal Scientist and Director of Genebank at ICRISAT, led the task of developing and genotyping a ‘composite collection’ of pearl millet. To do this, the team created a selection that reduced 21,594 accessions down to 1,021. This collection includes lines that are tolerant to drought, heat and soil salinity; others resistant to blast, downy mildew, ergot, rust and smut; and accessions resistant to multiple diseases.

Photo: C Bonham/Bioversity International

A traditional pearl millet variety growing in India.

The collection also includes types of pearl millet with high seed iron and zinc content (from traditional farmer varieties, or landraces, from Benin, Burkina Faso, Ghana and Togo), high seed protein content, high stalk sugar content, and other known elite breeding varieties.

The final collection comprised 710 landraces, 251 advanced breeding lines, and 60 accessions from seven wild species.

The GCP-supported scientists then used molecular markers to fingerprint the DNA of plants grown from the collection. Molecular markers are known variations in the sequence of the genetic code, found in different versions within a species, which act as flags in the genome sequence. Some individual markers may be associated with particular useful genes, but markers are useful even without known associations, as the different flags can be compared between samples. In the pearl millet research, scientists searched for similarities and differences among these DNA markers to assess how closely or distantly related the 1,021 accessions were to each other.

This was not only a big step forward for the body of scientific knowledge on pearl millet, but also for the knowledge and skills of the scientists involved. “The GCP work did make some significant contributions to pearl millet research,” says Tom, “mainly by helping a critical mass of scientists working on pearl millet to learn how to appropriately use the genetic tools that have been developed in better-studied fungi, plants and animals (including people).”

GCP extends know-how to Africa

Photos: N Palmer/CIAT

Comparisons of good and bad pearl millet yields in Ghana’s Upper West Region, which has suffered failed rains and rising temperatures.

The semiarid areas of northern and eastern Uganda are home to a rich history and culture, but they are difficult environments for successful food production and security.

In this region, pearl millet is grown for both commercial and local consumption. Its yields, although below the global average, are reasonable given that it is grown on poor sandy soils where other crops fail. Yet despite being a survivor in these harsh drylands, pearl millet can still be affected by severe drought and disease.

GCP helped kick-start work to tackle these problems. With financial support from GCP, and through ACCI, Geofrey Lubade, a scientist from Uganda, was able to study and explore breeding pearl millet that would be suitable for northern Uganda and have higher yields, drought tolerance and rust resistance.

Geofrey now plans to develop the best of his pearl millet lines for registration and release in Uganda, which he expects will go a long way in helping the resource-poor.

But Geofrey’s success is just one example of the benefits from GCP-support. Thanks to GCP, Mark Laing says that his students at ACCI have learnt invaluable skills that save significant time and money in the plant-breeding process.

“Many of our students, with GCP support, have been involved in diversity studies to select for desirable traits,” says Mark – and these students are now working on releasing new crop varieties.

He says that African scientists directly benefitted from the GCP grants for training in biotechnology and genetic studies.

Their work, along with that of a number of other scientists, will have a huge impact on plant breeding in developing countries – long term.

Photo: N Palmer/CIAT

A farmer inspects his millet crop in northwest Ghana.

As Mark explains, once breeders have built up a head of steam there is no stopping them. “Plant breeders take time to start releasing varieties, but once they get started, then they can keep generating new varieties every year for many years,” he says. “And a good variety can have a very long life, even more than 50 years.

“We have already had a significant impact on plant breeding in some African countries,” says Mark. But perhaps more importantly, he says, the work has changed the status of plant breeding and pearl millets as a subject: “It used to be disregarded, but now it is taken seriously as a way to have an impact on agriculture.”

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

Mar 062015
 

 

Photo: IITA

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

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

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

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

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

Photo: J Haskins/Global Crop Diversity Trust

Dancers celebrate at a new yam festival in Nigeria.

Unique collaborations get yam research rolling

Photo: J Haskins/Global Crop Diversity Trust

A farmer in his yam field in Nigeria.

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

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

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

Photo: IITA

A Nigerian farmer displays her healthy yam tubers.

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

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

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

Photo: J Haskins/Global Crop Diversity Trust

Walking in yam fields.

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

Photo: IITA

Yam vines twist up bamboo staking in a yam field.

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

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

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

Photo: IITA

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

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

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

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

African researchers carry GCP torch forward for yams

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

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

Photo: IITA

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

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

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

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

Photo: J Haskins/Global Crop Diversity Trust

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

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

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

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

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

Photo: IITA

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

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.

Photo: ICARDA

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.

ICARDA has a global mandate for research on lentil improvement. As such, ICARDA houses the world’s collection of lentils, held in trust as a global public good. It includes 8,789 different types of seed of cultivated lentils from 70 countries, 1,146 breeding lines and 574 new seed samples from 4 wild lentil species representing 23 countries. From this, a collection of 1,000 plants was identified for use as GCP reference materials, consisting of traditional farmer varieties, wild relatives and elite varieties and cultivars. Individual plants of each were planted in 2005 so that seed could be collected at the end of the growing season.

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.

Photo: P Casier/CGIAR

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.”

Lentils – with a protein content ranging from 22 to 35 percent – are an important source of dietary protein in both human and animal diets, second only to soya beans as a source of usable protein. Lentils are currently grown on 3.8 million hectares worldwide, with a total annual production of over 3.5 million tonnes. The major producers of lentils are countries the South Asia and CWANA regions, and Canada, Australia and the USA. Productivity is low in developing countries, largely because the crop is grown on marginal lands in semiarid environments, without irrigation, weeding or pest control.

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.”

Photo: E Huttner/ACIAR

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.

Photo: Bill & Melinda Gates Foundation

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.