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

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

Jun 012015

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

Indian chickpea farmer with her harvest.

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

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

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

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

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

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

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

An Ethiopian farmer harvests her chickpea crop.

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

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

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

How drought affects chickpea

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

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

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

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

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

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

Escaping drought in India

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

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

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

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

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

Indian chickpea farmer with her harvest.

Developing new varieties: Tropical Legumes I in action

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

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

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

Developing chickpea pods

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

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

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

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

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

The magic of genetic diversity

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

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

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

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

Decoding the chickpea genome

Chickpea seed

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

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

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

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

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

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

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

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

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

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

Chickpea success in Africa: new varieties already changing lives

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Chickpea’s promise meeting future challenges

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Brazilian Corporation of Agricultural Research finds kindred spirit in GCP

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

May 292015

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

Sorghum

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

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

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

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

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

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

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

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

Common objectives

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

Maize growing in Brazil.

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

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

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

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

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

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

Maize farmers in Brazil.

Great minds think alike

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

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

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

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

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

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

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

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

Multifaceted and tangible results

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

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

A Kenyan farmer with her sorghum crop.

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

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

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

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

Sustainable partnerships to break ground for groundnut

Groundnut

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

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

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

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

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

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

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

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

Genetic stocks AND people are products

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

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

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

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

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

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

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

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

Giants make giant strides in quest for drought-tolerant wheat

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

Mar 262015

Wheat growing in China.

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

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

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

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

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

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

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

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

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

Sharing knowledge to improve breeding efficiency and sustainability

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

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

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

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

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

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

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

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

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

Spikes of emmer wheat.

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

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

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

Durum wheat spike.

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

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

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

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

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

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

Reaping existing skills

A baker butters naan bread in Hyderabad, India.

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

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

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

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

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

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

Younger researchers taking a lead

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

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

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

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

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

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

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

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

Overcoming complex traits, genes and wary breeders

Wheat farmer in India.

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

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

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

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

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

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

Wheat seed ready for planting in Punjab, India.

Incorporating conventional methods

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

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

Phenotyping: How to manage a subjective process

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

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

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

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

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

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

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

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

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

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

A young farmer in her wheat field in India.

Managing the tsunami of phenotyping data

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

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

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

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

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

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

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

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

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

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

Friendly competition helping inspire India’s wheat breeders

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

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

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

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

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

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

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

Securing wheat production into the future

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

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

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

Donkeys bring home the wheat harvest in Qinghai, China.

Protein-rich pearl millet, pearl of the harsh lands

Africa, Asia, Capacity building, Genetics, Pearl millet, Phase I crops No Responses »

Mar 192015

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).

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.

Protein in pearl millet ‘critical’ for nutrition

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.”

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

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

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.

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.

Rice research reaps a rich harvest of products, people and partners

Asia, Comparative genomics in cereals, Crop breeding, Genetics, Partnerships, Rice No Responses »

Mar 172015

Harvesting rice by hand in The Philippines.

Rice plays a key role in global food security, particularly in Asia, where 90 percent of the world’s rice is grown and eaten. By 2050, Asia’s population is estimated to grow by one billion to 5.2 billion people, who will continue to depend on rice as their major staple food.

But with rising demand for rice has also come increasing salinity, droughts and other stresses, along with decreasing areas of land available for farming the crop.

And that’s why the CGIAR Generation Challenge Programme (GCP) placed a major focus on rice throughout its 10 years of existence.

Key ingredient in the rice research fest was GCP’s relationship with the International Rice Research Institute (IRRI), headquartered in The Philippines. GCP supported IRRI in its endeavours to use the latest molecular plant-breeding techniques, along with traditional plant-breeding tools, to develop rice crops better able to cope with various stresses and still be productive.

“These ‘super’ crops will revolutionise rice farming,” says IRRI Director General Robert Zeigler, who was also the first Director of GCP.

For more on GCP’s rice research see our Sunset Story ‘The power of rice unlocked’.

Rice that can survive increasingly salty water

Climate change is one of the major threats facing rice production. As sea levels rise, salt water enters further up rivers with the high tides and affects rice production areas.

Each year in Bangladesh, during the boro rice season from November to May, salinity is so high that a white film of salt covers the country’s coastal paddy fields. For Bangladeshi farmers, this white colour is a warning sign that their land is ‘sick’. Around the world, Bangladesh, India, Myanmar and parts of Africa are most affected by increasing salinity.

Right from the beginning of GCP, salinity was a problem firmly on the rice research agenda.

Highly saline soils in India (left), and a close-up showing a surface crust of salt on afflicted soil (right).

Leading this research was IRRI plant physiologist Abdelbagi Ismail, who dreamed of the ‘super’ rice crop that could “tolerate salinity, drought and submergence”.

Abdelbagi has managed and overseen most of the progress made during the discovery of a major genetic region, or quantitative trait locus (QTL), associated with salinity tolerance and named Saltol.

Abdelbagi Ismail examines rice plants in the field in Bangladesh.

Its insertion into well-known rice varieties used by farmers in Bangladesh, Indonesia and The Philippines is part of the revolution taking place in rice research.

Abdelbagi says Saltol was mapped and markers were developed for its use in breeding more salt-tolerant rice varieties. Its salt-tolerance code is now being transferred into several varieties evaluated with IRRI partners in South and Southeast Asia.

“These projects also provided opportunities for both degree training and non-degree training to several of our partners in the countries involved,” he adds.

“Partnerships are crucial for us to build the capacity of the researchers in these countries and to ensure our outputs and outcomes reach the farmers that need them.

“All our partners benefitted from salt-tolerant varieties developed conventionally through this project, and they also provided pipelines for uptake and dissemination by farmers.”

Having developed new lines following the discovery of the Saltol QTL, Abdelbagi’s GCP-supported team trained plant breeders in country programmes to successfully breed for salt tolerance and other stresses.

In this way, Abdelbagi says, they are improving the capacity of researchers in developing countries to take up new breeding techniques, such as the use of molecular markers. “This can reduce the time it takes to breed new varieties, from six to ten years at the moment, down to two or three years,” he says.

This means that benefits to smallholder rice farmers struggling with salinity will happen sooner rather than later. And Abdelbagi credits GCP’s partnership approach, working directly with the countries in need, for the success so far.

“The salt-tolerant varieties are now being widely distributed,” he says. “Some of these varieties have doubled farmers’ productivity in affected areas.

“The work developed technologies of value to our needy farmers.

“We do believe this is the start of a second Green Revolution, especially for those who farm in less favourable areas and that missed this opportunity during the first Green Revolution.”

Partnership approach key to new rice gene for uptake of phosphorus

More than 60 percent of rainfed lowland rice is produced on poor and problem soils, including those that are naturally low in phosphorus. This is an essential for nutrient growing crops, but providing phosphorus through fertilisers is costly and unfeasible for many smallholder rice growers.

IRRI’s Sheryl Catausan prepares the roots of a rice plant for scanning as part of the work of the PSTOL1, phosphorus uptake research team at IRRI.

This problem was the focus of GCP’s rice phosphorus-uptake project led by IRRI molecular biologist Sigrid Heuer.

The project was enormously successful, with its discovery of the PSTOL1 (‘phosphorus starvation tolerance 1’) gene within the Pup1 locus, which was published in the prestigious journal Nature.

“We wanted it in Nature for a couple of reasons,” she says. “To raise awareness about phosphorus deficiency and phosphorus being a limited resource, especially in poorer countries; and to draw attention to how we do molecular breeding these days, which is a speedier, easier and more cost-effective approach to developing crops that have the potential to alleviate such problems.”

Following the PSTOL1 discovery, researchers are now working with developing-country researchers and extension agencies to help them understand how to breed local varieties of rice that can be grown in phosphorus-deficient soils. They are also collaborating with other crop breeders looking to breed similar maize, sorghum and wheat varieties.

Tobias Kretzschmar, a molecular biologist with IRRI, says that GCP’s partnership approach was the key to the project having an impact on the rice farmers who needed it most.

“For me, the collaborations that were forged through these inter-institutional projects made the difference,” he says.

Sigrid agrees: “GCP was always there supporting us and giving us confidence, even when we were not sure.”

Solving the insoluble: a gene for drought tolerance

Rice is a crop that not only needs water, but loves water. So developing a drought-tolerant rice variety is a quest to find a seemingly impossible gene.

However, GCP-supported researchers did just that: they solved the insoluble.

“They were very successful in terms of getting drought tolerance,” says Hei Leung of IRRI, who was GCP Subprogramme Leader for the Comparative Genomics Research Initiative between 2004 and 2007, and also a Principal Investigator for the Rice Research Initiative. “They’re now getting a 1.5 tonne rice yield advantage under water stress. I mean, that’s unheard of! This is a crop that needs water.

“This is one of GCP’s big success stories; that you can actually get drought tolerance is a seemingly impossible task for a water-loving rice plant.”

As Subprogramme Leader, Hei played a critical role in the creation, management, delivery and communication of a wide portfolio of research projects. He credits the nature of how GCP was set up for accelerating the breeding programme for drought-tolerant rice.

“The advantage of GCP is that it is run by a small group of people who can make fast decisions,” he says. “This means they can respond to the needs of researchers: ‘Okay, we are going to invest on that. We’re going to have a meeting on this’.

“The real advantage of GCP is its agility. Usually with other organisations you have new ideas and then have to slave away for a year to get the funding to implement them. But GCP was quick.”

Hei Leung (right) explains rice screening processes to a visiting scholar at IRRI.

IRRI and GCP deliver genetic resources to those who need them most

Tobias says one of the main objectives of GCP and IRRI is to make genetic stocks available to breeders, particularly in developing countries.

“Without that, IRRI would fail in its central mission to reduce hunger and poverty,” he says. “In order to achieve this mission, tight collaboration with our agricultural and extension partners in other countries is the key.”

In fact, this idea of protecting the future through genetic material was influential in the choice of GCP as a CGIAR Challenge Program name. Hei, who was involved from the start with GCP, talks about the meeting in a Rome pizzeria where participants came up with the name: “When we talk about ‘generation’, we are really talking about the work we do with genetic diversity; it is about the future generation,” he says.

Part of that future generation is about sharing genetic resources or stocks, but first the genetic diversity of such stocks needs to be characterised. Hei remembers that one of the first GCP projects in 2004 brought together researchers in various countries to characterise the genetic diversity of various crops, including rice.

“But everyone was using different genotyping platforms and markers, and the technology back then was not what we have now,” he recalls.

“So we spent a lot of resources getting poor quality data. In a sense, it was a failure. On the other hand, it was also a success because we alerted people to the importance of characterising diversity in every single crop. The whole concept of getting all the national partners doing genetic resource characterisation is a good one.

“We have evolved the technology together over the last 10 years of GCP. Now the country partners feel enabled. They are not scared of the technology.”

Abdelbagi agrees that characterising genetic diversity is essential, and adds that making such genetic stocks readily available to breeders is also vital.

“This has not been an issue before,” he explains. “With the new regulations of germplasm control and intellectual property issues, it became extremely difficult to exchange germplasm with some countries. One important lesson we learnt was to engage in direct discussion with our partners in efforts to influence their policies and guidelines to allow essential exchange of genetic stocks and breeding material, at least at the regional level.”

Abdelbagi adds that another big challenge has been to provide country partners with materials and DNA markers for marker-assisted selection programmes and to make sure these were properly used in breeding programmes.

“We solved this by hosting a workshop at IRRI and with continued visits with GCP collaborators,” he says.

Rice terraces in Ifugao Province in The Philippines.

‘Super’ crops: something ‘magic’ happens

Hei says that the GCP project he’s most passionate about, and one that leaves a lasting legacy, is the development of multiparent advanced generation intercross (MAGIC) populations, which will potentially yield lines that are tolerant to environmental stresses, grow well in poor soils and produce better quality grain.

“MAGIC populations will leave behind a very good resource towards improving different crop species,” says Hei. “I’m sure that they will expand on their own.”

GCP funded the development of four kinds of rice populations, including indica MAGIC, which is the most advanced of the MAGIC populations developed so far. These populations contain multiple desirable traits, including: blast and bacterial blight-resistance, salinity and submergence tolerance and grain quality.

New generation of researchers working on a new rice revolution

Rice farmer in her field in Rwanda.

Robert Zeigler’s dream of a new rice Green Revolution with ‘super crops’ is coming true, thanks in part to GCP’s focus on combining cutting-edge molecular plant-breeding techniques with conventional plant breeding.

“With all this going for us, the second Green Revolution means we can meet the great challenges ahead with unprecedented efforts that will result in unparalleled impacts,” he says. “This will range from mining the rice genomes for needed traits to developing climate change-ready rice.”

IRRI researchers like Abdelbagi agree that new plant-breeding techniques, such as those fostered by GCP, are making ‘super’ crops more likely: “I’m committed to understand how plants can be manipulated to adapt to, and better tolerate, extreme environmental stresses, which seems more feasible today than it has ever been before.

“GCP-supported work has provided mechanisms for developing varieties with multiple stress tolerances, besides the improvements in yield and quality.”

And for Hei, GCP’s 10-year legacy is not just about the technology but also about the people.

“Over ten years you have three generations of PhD students,” he says. “Many people became a ‘new generation’ scientist through this programme. Many people have benefitted. GCP is one of a kind. I’m just in love with it.”

West Africa gets its own ‘fully fledged’ yam scientists

Africa, Capacity building, Genetics, Phase I crops, Yams No Responses »

Mar 062015

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.

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

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.

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.

Walking in yam fields.

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

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.”

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.

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.”

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.”

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

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