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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.”

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Photo: A Paul-Bossuet/ICRISAT

Man and beast team up to transport chickpeas in Ethiopia.

 

Sep 282015
 

 

Photo: Agência BrasíliaSorghum is already a drought-hardy crop, and is a critical food source across Africa’s harsh, semi-arid regions where water-intensive crops simply cannot survive. Now, as rainfall patterns become increasingly erratic and variable worldwide, scientists warn of the need to improve sorghum’s broad adaptability to drought.

Crop researchers across the world are now on the verge of doing just that. Through support from the CGIAR Generation Challenge Programme (GCP), advanced breeding methods are enhancing the capacity of African sorghum breeders to deliver more robust varieties that will help struggling farmers and feed millions of poor people across sub-Saharan Africa.

Photo: ICRISAT

A farmer in her sorghum field in Tanzania.

Sorghum at home in Africa

From Sudanese savannah to the Sahara’s desert fringes, sorghum thrives in a diverse range of environments. First domesticated in East Africa some 6000 years ago, it is well adapted to hot, dry climates and low soil fertility, although still depends on receiving some rainfall to grow and is very sensitive to flooding.

In developed countries such as Australia, sorghum is grown almost exclusively to make feed for cattle, pigs and poultry, but in many African countries millions of poor rural people directly depend on the crop in their day-to-day lives.

Photo: ICRISAT

A Malian woman and her child eating sorghum.

In countries like Mali sorghum is an important staple crop. It is eaten in many forms such as couscous or (a kind of thick porridge), it is used for making local beer, and its straw is a vital source of feed for livestock.

While the demand for, and total production of, sorghum has doubled in West Africa in the last 20 years, yields have generally remained low due to a number of causes, from drought and problematic soils, to pests and diseases.

“In Mali, for instance, the average grain yield for traditional varieties of sorghum has been less than one tonne per hectare,” says Eva Weltzein-Rattunde, Principal Scientist for Mali’s sorghum breeding programme at the International Crops Research Institute for the Semi-Arid-Tropics (ICRISAT).

In a continued quest to integrate ways to increase productivity, GCP launched its Sorghum Research Initiative (RI) in 2010. This aimed to investigate and apply the approaches by which genetics and molecular breeding could be used to improve sorghum yields through better adaptability, particularly in the drylands of West Africa where cropping areas are large and rainfall is becoming increasingly rare.

Kick starting the work was a GCP-funded collaboration between project Principal Investigator Niaba Témé, plant breeder at Mali’s Institut d’économie rurale (IER) and the RI’s Product Delivery Coordinator Jean-François Rami of the Centre de coopération internationale en recherche agronomique pour le développement (CIRAD; Agricultural Research for Development), France, with additional support from the Syngenta Foundation for Sustainable Agriculture in Switzerland.

The collaboration aimed to develop ways to improve sorghum’s productivity and adaptation in the Sudano-Sahelian zone, starting with Mali in West Africa, and expanding later across the continent to encompass Burkina Faso, Ethiopia, Kenya, Niger and Sudan.

Photo: F Noy/UN Photo

A farmer harvest sorghum in Sudan.

Sorghum gains from molecular research

Since 2008, with the help of CIRAD and Syngenta, Niaba and his team at IER have been learning how to use molecular markers to develop improved sorghum germplasm through identifying parental lines that are more tolerant and better adapted to the arid and volatile environments of Mali.

The two breeding methods used in the collaboration are known as marker-assisted recurrent selection (MARS) and backcross nested association mapping (BCNAM).

MARS

Photo: N Palmer/CIAT“MARS identifies regions of the genome that control important traits,” explains Jean-François. “It uses molecular markers to explore more combinations in the plant populations, and thus increases breeding efficiency.”

Syngenta, he explains, became involved through its long experience in implementing MARS in maize.

“Syngenta advised the team on how to conduct MARS and ways we could avoid critical pitfalls,” he says. “They gave us access to using the software they have developed for the analysis of data, and this enabled us to start the programme immediately.”

With the help of the IER team, two bi-parental populations from elite local varieties were developed, targeting two different environments found in sorghum cropping areas in Mali. “We were then able to use molecular markers through MARS to identify and monitor key regions of the genome in consecutive breeding generations,” says Jean-François.

“When we have identified the genome regions on which to focus, we cross the progenies and monitor the resulting new progenies,” he says. “The improved varieties subsequently go to plant breeders in Mali’s national research program, which will later release varieties to farmers.”

Jean-François is pleased with the success of the MARS project so far. “The development of MARS addressed a large range of breeding targets for sorghum in Mali, including adaptation to the environment and grain productivity, as well as grain quality, plant morphology and response to diseases,” he says. “It proved to be efficient in elucidating the complex relationships between the large number of traits that the breeder has to deal with, and translating this into target genetic ideotypes that can be constructed using molecular markers.”

Jean-François says several MARS breeding lines have already shown superior and stable performance in farm testing as compared to current elite lines, and these will be available to breeders in Mali in 2015 to develop new varieties.

Photo: ICRISAT

Eva Weltzein-Rattunde examines sorghum plants with farmers in Mali.

BCNAM

Like MARS, the BCNAM approach shows promise for being able to quickly gain improvements in sorghum yield and adaptability to drought, explains Niaba, who is Principal Investigator of the BCNAM project. BCNAM may be particularly effective, he says, in developing varieties that have the grain quality preferences of Malian farmers, as well as the drought tolerance that has until now been unavailable.

“BCNAM involves using an elite recurrent parent that is already adapted to local drought conditions, then crossing it with several different specific or donor parents to build up larger breeding populations,” he explains. “The benefit of this approach is it can lead to detecting elite varieties much faster.”

Eva and her team at ICRISAT have also been collaborating with researchers at IER and CIRAD on the BCNAM project. The approach, she says, has the potential to halve the time it takes to develop local sorghum varieties with improved yield and adaptability to poor soil fertility conditions.

“We don’t have these types of molecular-breeding resources available in Mali, so it’s really exciting to be a part of this project,” she says. “Overall, we feel the experience is enhancing our capacity here, and that we are closer to delivering more robust sorghum varieties which will help farmers and feed the ever-growing population in West Africa.”

Indeed, during field testing in Mali, BCNAM lines derived from the elite parent variety Grinkan have produced more than twice the yields of Grinkan itself. As they are rolled out in the form of new varieties, the team anticipates that they will have a huge positive impact on farmers’ livelihoods.

Photo: E Weltzein-Rattunde/ICRISAT

Malian sorghum farmers.

Mali and Queensland similar problem, different soil

In Mali and the wider Sahel region within West Africa, cropping conditions are ideal for sorghum. The climate is harsh, with daily temperatures on the dry, sun-scorched lower plains rarely falling below 30°C. With no major river system, the threat of drought is ever-present, and communities are entirely dependent on the 500 millimetres of rain that falls during the July and August wet season.

“All the planting and harvesting is done during the rainy season,” says Niaba. “We have lakes that are fed by the rain, but when these lakes start to dry up farmers rely mostly on the moisture remaining in the soil.”

Over 17 thousand kilometres to the east of Mali, in north-eastern Australia’s dryland cropping region, situated mainly in the state of Queensland, sorghum is the main summer crop, and is considered a good rotational crop as it performs well under heat and moisture stress. The environment here is similar to Mali’s, with extreme drought a big problem.

Average yields for sorghum in Queensland are double those in Mali—around two tonnes per hectare—yet growers still consider them low, directly limited by the crop’s predominantly water-stressed production environment in Australia.

One of the differentiating factors is soil. “Queensland has a much deeper and more fertile soil compared to Mali, where the soil is shallow, with no mulch or organic matter,” says Niaba. “Also, there is no management at the farm level in Mali, so when rain comes, if the soil cannot take it, we lose it.”

Photo: Bart Sedgwick/Flickr (Creative Commons)

Sorghum in Queensland, Australia.

Making sorghum stay green, longer

Another key reason for the difference in yields between Queensland and Mali is that growers in Queensland are sowing a sorghum variety of with a genetic trait that makes it more tolerant to drought.

This trait is called ‘stay-green’, and over the last two decades it has proven valuable in increasing sorghum yields, using less water, in north-eastern Australia and the southern United States.

Stay-green allows sorghum plants to stay alive and maintain green leaves for longer during post-flowering drought—that is, drought that occurs after the plant has flowered. This means the plants can keep growing and produce more grain in drier conditions.

“We’ve found that stay-green can improve yields by up to 30 percent in drought conditions with very little downside during a good year,” says Andrew Borrell from the Queensland Alliance for Agriculture and Food Innovation (QAAFI) at the University of Queensland (UQ) in Australia.

“Plant breeders have known about stay-green for some 30 years,” he says. “They’d walk their fields and see that the leaves of certain plants would remain green while others didn’t. They knew it was correlated with high yield under drought conditions, but didn’t know why.”

Stay-green’s potential in Mali

With their almost 20 years working on understanding how stay-green works, Andrew and his colleagues at UQ were invited by GCP in 2012 to take part in the IER/CIRAD collaborative project, to evaluate the potential for introducing stay-green into Mali’s local sorghum varieties and enriching Malian pre-breeding material for the trait.

A pivotal stage in this new alliance was a 12-month visit to Australia by Niaba and his IER colleague Sidi Coulibaly, to work with Andrew and his team to understand how stay-green drought resistance works in tall Malian sorghum varieties.

“African sorghum is very tall and sensitive to variation in day length,” explains Andrew. “We have been looking to investigate if the stay-green mechanism operates in tall African sorghums (around four metres tall) in the same way that it does in short Australian sorghum (one metre tall).”

Having just completed a series of experiments at the end of 2014, the UQ team consider their data as preliminary at this stage. “But it looks like we can get a correlation between stay-green and the size and yield of these Malian lines,” says Andrew. “We think it’s got great potential.”

Photo: S Sridharan/ICRISAT

Sorhum growing in Mozambique.

Sharing knowledge as well as germplasm

Eva Weltzein-Rattunde has played more of an on-the-ground capacity development role in Mali since accepting her position at ICRISAT in 1998. She says “the key challenges have been improving the infrastructure of the national research facilities [in Mali] to do the research as well as increasing the technical training for local agronomists and researchers.”

Photo: ICRISAT

A Malian farmer harvests Sorghum.

A large part of GCP’s focus is building just such capacity among developing country partners to carry out crop research and breeding independently in future, so they can continue developing new varieties with drought adaptation relevant to their own environmental conditions.

A key objective of the IER team’s Australian visit was to receive training in the methods for improving yields and drought resistance in sorghum breeding lines from both Australia and Mali.

“We learnt about association mapping, population genetics and diversity, molecular breeding, crop modelling using climate forecasts, and sorghum physiology, plus a lot more,” says Niaba. This training complemented previous training Niaba and IER researchers had from CIRAD and ICRISAT through the MARS and BCNAM projects.

“We [CIRAD] have a long collaboration in sorghum research in Mali and training young scientists has always been part of our mission,” says Jean-François. “We’ve hosted several IER students here in France and we are always interacting with our colleagues in Mali either over the phone or travelling to Mali to give technical workshops in molecular breeding.”

Photo: Rita Willaert/Flickr (Creative Commons)

Harvested sorghum in Sudan.

Working together to implement MARS in the sorghum breeding program in Mali represented many operational challenges, Jean-François explains. “The approach requires a very tight integration of different and complementary skills, including a strong conventional breeding capacity, accurate breeders’ knowledge, efficient genotyping technologies, and skills for efficient genetic analyses,” he says.

Because of this requirement, he adds, there are very few reported experiences of the successful implementation of MARS.  It is also the reason why these kinds of projects would normally not be undertaken in a developing country like Mali, but for the support of GCP and the dedicated mentorship of Jean-François.

sorghum quote 2“GCP provided the perfect environment to develop the MARS approach,” says Jean-François. “It brought together people with complementary skills, developed the Integrated Breeding Platform (IPB), and provided tools and services to support the programme.”

In addition to developing capacity, Jean-François says one of the great successes of both the MARS and the BCNAM projects was how they brought together Mali’s sorghum research groups working at IER and ICRISAT in a common effort to develop new genetic resources for sorghum breeding.

“This work has strengthened the IER and ICRISAT partnerships around a common resource. The large multiparent populations that have been developed are analysed collectively to decipher the genetic control of important traits for sorghum breeding in Mali,” says Jean-François. “This community development is another major achievement of the Sorghum Research Initiative.” The major challenge, he adds, will be whether this community can be kept together beyond GCP.

Considering the numerous ‘non-GCP’ activities that have already been initiated in Africa as a result of the partnerships forged through GCP research, Jean-François sees a clear indication that these connections will endure well beyond GCP’s time frame.

GCP’s sunset is Mali’s sunrise

Photo: S Sridharan/ICRISAT

Sorghum at sunset in Mozambique.

Among the new activities Jean-François lists are both regional and national projects aimed at building on what has already been achieved through GCP and linking national partners together. These include the West African Agricultural Productivity Program (WAAPP), the West Africa Platform being launched by CIRAD as a continuation of the MARS innovation, and another MARS project in Senegal and Niger through the Feed the Future Innovation Lab for Collaborative Research on Sorghum and Millet at Kansas State University.

“These are all activities which will help maintain the networks we’ve built,” Jean-François says. “I think it is very important that these networks of people with common objectives stick together.”

sorghum quoteFor Niaba, GCP provided the initial boost needed for these networks to emerge and thrive. “We had some contacts before, but we didn’t have the funds to really get into a collaboration. This has been made possible by GCP. Now we’re motivated and are making connections with other people on how we can continue working with the material we have developed.”

“I can’t talk enough of the positive stories from GCP,” he adds. “GCP initiated something, and the benefits for me and my country I cannot measure. Right now, GCP has reached its sunset; but for me it is a sunrise, because what we have been left with is so important.”

More links

Photo: ICRISAT

A sorghum farmer in her field in Tanzania.

Jun 122015
 
Photo: IITA

Growing cowpea pods.

Each year, millions of people in Senegal go hungry for several months, many surviving on no more than one meal a day. Locals call this time soudure – the hungry period. It typically lasts from June through to September, when previous winter and spring cereal supplies are exhausted and people wait anxiously for a bountiful autumn cereal harvest.

During this period, a bowl of fresh green cowpea pods once a day is the best that many people can hope for. Cowpeas are the first summer crop to mature, with some varieties ready to harvest in as little as 60 days.

While cowpeas provide valued food security in Africa, yields remain low. In Senegal, average cowpea yields are 450 kilograms per hectare, a mere 10–30 percent of their potential. This poor productivity is primarily because of losses due to insects and diseases, but is sometimes further compounded by chronic drought.

In 2007, the CGIAR Generation Challenge Programme (GCP) brought together a team of plant breeders and geneticists from Burkina Faso, Mozambique, Nigeria, Senegal and the USA to collaborate on cowpea. Their goal was to breed varieties that would be higher yielding, drought tolerant and resistant to pests and diseases, and so help secure and improve local cowpea production in sub-Saharan African countries.

Photo: IITA

A trader selling cowpea at Bodija market, Ibadan, Nigeria.

Cowpea production – almost all of it comes from Africa

A type of legume originating in West Africa, cowpeas are also known as niébé in francophone Africa and as black-eyed peas in the USA.  They are well adapted to drier, warmer regions and grow well in poor soils. In Africa, they are mostly grown in the hot, drought-prone savannas and very arid sub-Saharan regions, often together with pearl millet and sorghum.

Nutritionally, cowpeas are a major source of dietary protein in many developing countries. Young leaves, unripe pods and peas are used as vegetables, and the mature grain is processed for various snacks and main meal dishes. As a cash crop, both for grain and animal fodder, cowpea is highly valued in sub-Saharan Africa.

Worldwide, an estimated 14.5 million hectares of land is planted with cowpea each year. Global production of dried cowpeas in 2010 was 5.5 million tonnes, 94 percent of which was grown in Africa.

“In Senegal, cowpeas cover more than 200,000 hectares,” says Ndiaga Cissé, cowpea breeder at L’institut sénégalais de recherches agricoles (ISRA; Senegalese Agricultural Research Institute). “This makes it the second most grown legume in Senegal, after groundnuts.”

In 2011, Senegal experienced its third drought within a decade. Low and erratic rainfall led to poor harvests in 2011 and 2012: yields of cereal crops (wheat, barley and maize) fell by 36 percent compared to 2010. Consequently, the hungry period in 2012 started three months earlier than usual, making gap-fillers like cowpea even more important. In fact, cereal production in sub-Saharan African countries has not seen substantial growth over the last two decades – total area, yield and production grew by only 4.3 percent, 1.5 percent and 5.8 percent, respectively.

Climate change is expected to further compound this situation across sub-Saharan Africa. Droughts are forecast to occur more frequently, weakening plants and making them more vulnerable to pests and diseases.

“Improved varieties of cowpeas are urgently needed to narrow the gap between actual and potential yields,” says Ndiaga. “They will not only provide security to farmers in the face of climate change, but will also help with food security and overall livelihoods.”

Photo: IITA

Farmers in Northern Nigeria transport their cowpea harvest.

Mapping the cowpea genome

For over 30 years, Phil Roberts, a professor in the Department of Nematology at the University of California, Riverside (UCR), has been breeding new varieties of cowpea. “UCR has a long history of research in cowpea breeding that goes back to the mid-seventies,” explains Phil. “One of the reasons we were commissioned by GCP in 2007 was to use our experience, particularly in using molecular breeding, to help African cowpea-breeding programmes produce higher yielding cowpeas.”

For seven years, Phil and his team at UCR coordinated the cowpea component of the Tropical Legumes I (TLI) project led by GCP (see box below).  The objective of this work was to advance cowpea breeding by applying modern, molecular breeding techniques, tools and knowledge to develop lines and varieties with drought tolerance and resistance to pests and diseases in the sub-Saharan African countries Burkina Faso, Mozambique, Nigeria and Senegal.

The molecular breeding technology that UCR uses for cowpeas is based on finding genes that help cowpea plants tolerate insects and diseases, identifying markers that can indicate the presence of known genes, and using these to incorporate valuable genes into higher yielding varieties.

“Using molecular breeding techniques is a lot easier and quicker, and certainly less hit-or-miss, than conventional breeding techniques,” says Phil. “We can shorten the time needed to breed better adapted cowpea varieties preferred by farmers and markets.”

Phil explains that the first priority of the project was to map the cowpea genome.

“The map helps us locate the genes that play a role in expressing key traits such as drought tolerance, disease resistance or pest resistance,” says Phil. “Once we know where these genes are, we can use molecular marker tools to identify and help select for the traits. This is a lot quicker than growing the plant and observing if the trait is present or not.”

To use an analogy, think of the plant’s genome as a story: its words are the plant’s genes, and a molecular marker works as a text highlighter. Molecular markers are not precise enough to highlight specific words (genes), but they can highlight sentences (genomic regions) that contain these words (genes), making it easier and quicker to identify which plants have them. Traditionally, breeders have needed to grow plants to maturity under appropriately challenging conditions to see which ones are likely to have useful traits, but by using markers to flag valuable genes they are able to largely skip this step, and test large amounts of material to choose the best parents for their crosses, then check which of the progeny have inherited the gene or genes.

Photo: IITA

Diversity of cowpea seed.

Breeding new varieties faster, using modern techniques

Photo: ICRISAT

A farmer pleased with her cowpea plants.

The main focus of the cowpea component in TLI was to optimise marker-assisted recurrent selection (MARS) and marker-assisted backcrossing (MABC) breeding techniques for sub-Saharan African environments and relevant traits.

MARS identifies regions of the genome that control important traits. In the case of cowpeas, these include drought tolerance and insect resistance. It uses molecular markers to explore more combinations in the plant populations, thus increasing breeding efficiency.

MABC is the simplest form of marker-assisted breeding, in which the goal is to incorporate a major gene from an agronomically inferior source (the donor parent) into an elite cultivar or breeding line (the recurrent parent). Major genes by themselves have a significant effect; it’s therefore easier to find a major gene associated with a desired trait, than having to find and clone several minor genes. The aim is to produce a line made up almost entirely of the recurrent parent genotype, with only the selected major gene from the donor parent.

Using the genome map and molecular markers, the UCR team identified 30 cowpea lines with drought tolerance and pest resistance from 5,000 varieties in its collection, providing the raw material for marker-assisted breeding. “Once we knew which lines had the drought-tolerance and pest-resistance genes we were looking for, we crossed them with high-yielding lines to develop 20 advanced cowpea lines, which our African partners field tested,” says Phil.

The lines underwent final field tests in 2014, and the best-yielding drought-tolerant lines will be used locally in Burkina Faso, Mozambique and Senegal to develop new higher yielding varieties that will be available to growers by 2016.

“While we are still some time off from releasing these varieties, we already feel we are two or three years ahead of where we would be if we were doing things using only conventional breeding methods,” says Ndiaga.

Photo: IITA

A parasitic Striga plant, in a cowpea experimental plot.

The genome map and molecular markers have helped cowpea breeders like Ousmane Boukar, cowpea breeder and Kano Station Representative with the International Institute of Tropical Agriculture (IITA), headquartered in Nigeria, to locate the genes in cowpeas that play a role in expressing desirable traits.

Ousmane, who was GCP’s cowpea Product Delivery Coordinator, says, “We have used this technology to develop advanced breeding lines that are producing higher yields in drier conditions and displaying resistance to several pests and diseases like thrips and Striga. We expect these lines to be available to plant breeders by the end of 2015.

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

The Tropical Legumes I project (TLI) was initiated by GCP in 2007 and subsequently incorporated into the Programme’s Legumes Research Initiative (RI). The goal of the RI was to improve the productivity of four legumes – beans, chickpeas, cowpeas and groundnuts – that are important in food security and poverty reduction in developing countries, by providing solutions to overcome drought, poor soils, pests and diseases. TLI was led by GCP and focussed on Africa. Work on cowpea within TLI was coordinated by the University of California, Riverside in the USA. Target-country partners were Institut de l’Environnement et de Recherches Agricoles (INERA) in Burkina Faso, Universidade Eduardo Mondlane in Mozambique and Institut Sénégalais de Recherches Agricoles (ISRA; Senegalese Agricultural Research Institute) in Senegal. Other partners were the International Institute of Tropical Agriculture (IITA) and USA’s Feed the Future Innovation Labs for Collaborative Research on Grain Legumes and for Climate-Resilient Cowpea. Tropical Legumes II (TLII) was a sister project to TLI, led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) on behalf of IITA and the International Centre for Tropical Agriculture (CIAT). It focussed on large-scale breeding, seed multiplication and distribution primarily in sub-Saharan Africa and South Asia, thus applying the ‘upstream’ research results from TLI and translating them into breeding materials for the ultimate benefit of resource-poor farmers. Many partners in TLI also worked on projects in TLII.

Burkina Faso – evaluating new lines to improve the country’s economy

Cowpea is an important crop for the people of Burkina Faso. Over 10 million farmers produce on average 800,000 tonnes of cowpeas each year, making the country the third largest producer in the world, behind neighbours Nigeria and Niger.

Much of Burkina Faso’s cowpea crop is consumed domestically, but the government sees potential in increasing productivity for export to Côte d’Ivoire and Ghana in the south. This new venture would improve the country’s gross domestic product (GDP), which is the third lowest in the world.

“The government is very interested in our research to improve cowpea yields and secure them against drought and disease,” says Issa Drabo, lead cowpea breeder with the Institut de l’Environnement et de Recherches Agricoles (INERA) in Burkina Faso.

“We’ve been working closely with UCR to evaluate advanced breeding lines that we can use in our own breeding programme. So far we have several promising lines, some of which breeders are using to create varieties for release to farmers – some as early as this year.”

Photo: IITA

Farmers in Burkina Faso discuss cowpea varieties during participatory varietal selection activities.

Outsourcing the molecular work

Issa says his team has mainly been using conventional breeding techniques and outsourcing the molecular breeding work to the UK and USA. “We send leaf samples to the UK to be genotyped by a private company [LGC Genomics], who then forward the data to UCR, who analyse it and tell us which plants contain the desired genes and would be suitable for crossing.”

The whole process takes four to six weeks, from taking the samples to making a decision on which plants to cross.

“This system works well for countries that don’t have the capacity or know-how to do the molecular work,” says Darshna Vyas, a plant genetics specialist with LGC Genomics. “Genotyping has advanced to a point where even larger labs around the world choose to outsource their genotyping work, as it is cheaper and quicker than if they were to equip their lab and do it themselves. We do hundreds of thousands of genotyping samples a day – day in, day out. It’s our business.”

Darshna says LGC Genomics have also developed plant kits, as a result of working more with GCP partners from developing countries. “We would receive plant tissue that was not properly packaged and had become mouldy on the journey. The plant kits help researchers package their tissue correctly. The genotyping data you get from undamaged tissue compared to damaged tissue is a thousand times better.”

Getting the genotyping expertise on the ground

Photo: IITA

A trader bagging cowpeas at Bodija market, Ibadan, Nigeria.

To reduce their African partners’ reliance on UCR, researchers from the university, including Phil, have been training young plant breeders and PhD students from collaborating institutes. Independent of the cowpea project, they have also been joining GCP’s Integrated Breeding Platform (IBP) training events in Africa to help breeders understand the new technologies.

“All this capacity building we do really gets at the issue of leaving expertise on the ground when the project ends,” says Phil. “If these breeders don’t have the expertise to use the modern breeding technologies, then we won’t make much progress.”

GCP Capacity Building Theme Leader and TLI Project Manager Ndeye Ndack Diop has been impressed by UCR’s enthusiasm to build capacity in its partner countries. “Capacity building is a core objective for GCP and the TLI project,” says Ndeye Ndack. “While it is built into almost all GCP projects, UCR have gone over and above what was expected of them and contributed towards building capacity not only among its partner institutions, but in many other African national breeding institutes as well.”

Issa Drabo reports that in 2014 two of his young researchers from Burkina Faso completed their training in GCP’s Integrated Breeding Multiyear Course, conducted by UCR and the IBP team.

One of Issa’s researchers at INERA, Jean-Baptiste de la Salle Tignegré, says the course helped him understand more about the background genetics, statistical analysis and data management involved in the process of molecular breeding. “Because of the course, we are now able to analyse the genotype data from LGC,” he says.

Mozambique – insects and drought are the problem

In 2010, the Universidade Eduardo Mondlane (UEM) joined the cowpea component of TLI, three years after the project started. “We were a little late to the party because we were busy setting up Mozambique’s first cowpea breeding programme, which only began in 2008,” recalls Rogerio Chiulele, a lecturer at the university’s Faculty of Agronomy and Forestry Engineering and lead scientist for cowpea research in Mozambique for TLI.

That year (2008), UEM received a GCP Capacity building à la carte grant to establish a cowpea-breeding programme for addressing some of the constraints limiting cowpea production and productivity, particularly drought, pests and diseases.

As in Burkina Faso and Senegal, in Mozambique cowpeas are an important source of food, for both protein and profit, particularly for the poor. Cowpeas rank as the fourth most cultivated crop in Mozambique, accounting for about nine percent of the total cultivated area, or an estimated four million hectares of smallholder farms.

Photo: IITA

Cowpea plants infested by aphids.

Rogerio says that farmers in his country, just as in other parts of Africa, struggle to reach their full yield potential because of climate, pests and diseases. “Several insect pests – such as aphids, flower thrips, nematodes and pod-sucking pests – can substantially reduce cowpea yield and productivity in Mozambique,” he says.

“Cowpea aphids can cause problems at any time in the growing season, but are most damaging during dry weather when they infest seedlings that are stressed from lack of water. In wetter parts of the country, flower thrips – which feed on floral buds – are the most damaging insect pest.” These insects are also major pests in Burkina Faso and Senegal, along with hairy caterpillar (Amsacta moloneyi), which can completely destroy swaths of cowpea seedlings.

Rogerio says breeding for insect resistance and drought tolerance, using marker-assisted techniques, improves breeders’ chances of increased cowpea productivity. “Productivity is key to increasing rural incomes, and new resources can then be invested in other activities that help boost total family income,” says Rogerio. “These new breeding techniques will help us achieve this quicker.”

Three high-yielding varieties to hit the Mozambique market in 2015

Photo: IITA

Mature cowpea pods ready for harvesting.

Since 2010, Rogerio’s team have quickly caught up to Burkina Faso and Senegal and plan to release three higher yielding new lines with drought tolerance in 2015. One of these lines, CB46, is based on a local cowpea variety crossed with a UCR-sourced American black-eyed pea variety that displays drought tolerance, which potentially has huge market appeal.

“Local varieties fetch, on average, half a US dollar per kilogram, compared to black-eyed pea varieties, whose price is in the region of four to five US dollars,” says Rogerio. “Obviously this is beneficial to the growers, but the benefits for consumers are just as appealing. The peas are better quality and tastier, and they take half as long to cook compared to local varieties.”

All these extra qualities are important to consider in any breeding programme and are a key objective of the Tropical Legume II (TLII) project (see box above). TLII activities, led by ICRISAT, seek to apply products from TLI to make an impact among farmers.

“TLII focuses on translating research outputs from TLI into tangible products, including new varieties,” says Ousmane Boukar, who works closely with Ndiaga, Issa and Rogerio in TLI and TLII.

Building a community of breeders to sustain success

Photo: C Peacock/IITA

Cowpea flower with developing pods.

Part of Ousmane’s GCP role as Product Delivery Coordinator for cowpeas was to lead a network of African cowpea and soybean breeders, and he champions the need for breeders to share information and materials as well as collaborating in other ways so as to sustain their breeding programmes post-GCP.

“To sustain integrated breeding practices post-2014, GCP has established Communities of Practice (CoP) that are discipline- and commodity-oriented,” says Ndeye Ndack. “The ultimate goal is to provide a platform for community problem solving, idea generation and information sharing.”

Ousmane says the core of this community was already alive and well before the CoP. “Ndiaga, Issa and I have over 80 years combined experience working on cowpea. We have continually crossed paths and have even been working together on other non-GCP projects over the past seven years.”

One such project the trio worked together on was to release a new drought-tolerant cowpea breeding line, IT97K-499-35, in Nigeria. “The performance of this variety impressed farmers in Mali, who named it jiffigui, which means ‘hope’,” says Ousmane. “We shared these new lines with our partners in Mali and Niger so they could conduct adaptation trials in their own countries.”

For young breeders like Rogerio, the CoP has provided an opportunity to meet and learn from these older partners. “I’ve really enjoyed our annual project meetings and feeling more a part of the world of cowpea breeding, particularly since we in Mozambique are isolated geographically from larger cowpea-producing countries in West Africa.”

For Phil Roberts, instances where more-established researchers mentor younger researchers in different countries give him hope that all the work UCR has done to install new breeding techniques will pay off. “Young researchers represent the future. If they can establish a foothold in breeding programmes in their national programmes, they can make an impact. Beyond having the know-how, it is vital to have the support of the national programme to develop modern breeding effort in cowpea – or any crop.”

Setting up breeders for the next 20 years

Photo: IITA

Farmer harvesting mature cowpea pods.

In Senegal, Ndiaga is hopeful that the work that the GCP project has accomplished has set up cowpea breeders in his country and others for the next 20 years.

“Both GCP’s and UCR’s commitment to build capacity in developing countries like Senegal cannot be valued less than the new higher yielding, drought-tolerant varieties that we are breeding,” says Ndiaga. “They have provided us with the tools and skills now to continue this research well into the future.

“We are close to releasing several new drought-tolerant and pest- and disease-resistant lines, which is our ultimate goal towards securing Senegal’s food and helping minimise the impact of the hungry period.”

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

Photo: ICRISAT

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.

Photo: S Sridharan/ ICRISAT

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.

The Tropical Legumes I project (TLI) was initiated by GCP in 2007 and subsequently incorporated into the Programme’s Legumes Research Initiative (RI). The goal of the RI was to improve the productivity of four legumes – beans, chickpeas, cowpeas and groundnuts – that are important in food security and poverty reduction in developing countries, by providing solutions to overcome drought, poor soils, pests and diseases. TLI was led by GCP and focussed on Africa. Work on chickpea within TLI was coordinated by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). Target-country partners were the Ethiopian Institute of Agricultural Research (EIAR), Egerton University in Kenya and the Indian Institute of Pulses Research. The National Center for Genome Resources in the USA was also a partner. Tropical Legumes II (TLII) was a sister project to TLI, led by ICRISAT on behalf of the International Institute of Tropical Agriculture (IITA) and the International Center for Tropical Agriculture (CIAT). It focussed on large-scale breeding, seed multiplication and distribution primarily in sub-Saharan Africa and South Asia, thus applying the ‘upstream’ research results from TLI and filtering them downstream into breeding materials for the ultimate benefit of resource-poor farmers. Many partners in TLI also worked on projects in TLII.

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.

Photo: ICRISAT

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.

Photo: L Vidyasagar/ ICRISAT

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

Photo: ICRISAT

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.

 Photo: L Vidyasagar/ICRISAT

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.

Photo: A Paul-Bossuet/ICRISAT

“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.

Photo: GCP

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.”

Photo: A Paul-Bossuet/ ICRISAT

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.

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Mar 102015
 

 

Niaba Témé

Niaba Témé

“I can’t talk enough about the positive stories from the Generation Challenge Programme [GCP]. It initiated something new. I cannot measure its benefits for my country, for myself and for the sorghum-breeding and -producer communities. Right now, GCP has reached its sunset; but for me it is a sunrise, because what we have been left with is so very important.”

Growing up in a farming community in Mali, on the southern edge of the Sahara Desert, plant breeder Niaba Témé knows the ups and downs of farming in the harsh, volatile semiarid regions of Africa.

“I used to love harvesting the millet and helping my mother with her groundnut crops,” he remembers fondly. “We grew other dryland crops too, like sorghum, cowpeas, Bambara nuts, sesame and dah.”

Niaba’s village of Yendouma-Sogol is one of many villages balanced along the edge of the Bandiagara escarpment – 150 kilometres of sandstone cliffs soaring hundreds of metres above the sandy plains below. The region is considered one of the most challenging places in the world to be a farmer. The climate is harsh, with the average daily temperature on the dry, sun-scorched plains rarely falling below 30°C and often exceeding 40°C during the hottest months of the year. With no major water source available for drinking, cropping and livestock husbandry, the threat of drought is ever-present here, as it is across much of Africa’s semiarid landscape.

While much of Mali’s irrigated agriculture relies on water from the River Niger, villages like Niaba’s depend entirely on the 500 or so millimetres of rainfall they receive during the July–August wet season. In the years that the rains didn’t come, Niaba’s family were unable to harvest anything at all. The repeated failure of his parents’ crops – coupled with a natural interest in science – inspired Niaba to embark on a career where he could help farming families like his own defend themselves against the risks of drought and extreme temperatures.

Photo: F Fiondella/CCAFS

Farmland in Diouna, Mali. Farmers here must contend with the Sahel’s dry, sandy soil and whatever limited rainfall the clouds bring to grow sorghum, millet, maize, and other crops.

Niaba’s journey

Niaba’s first big step along the research road was when he enrolled to study agronomy at Mali’s Institut Polytechnique Rural de Formation et de Recherche Appliquée in Eastern Bamako. Within two years he was offered a scholarship to study plant breeding at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in Hyderabad, India. He then worked at the Cinzana Research Station in Mali.

Niaba later spent 11 years in the USA completing a bachelor’s degree, master’s degree and finally PhD in agronomy at Texas Tech University before returning home to Mali in 2007, where he was soon recruited by Mali’s Institut d’Économie Rurale (IER) to take charge of their new biotechnology lab at the Centre Régional de Recherche Agronomique.

His journey with the Generation Challenge Programme began in 2010 when IER received GCP funding to carry out sorghum research in Africa as part of GCP’s Sorghum Research Initiative (RI) launched that same year. The project was a collaboration with ICRISAT and France’s Centre de coopération internationale en recherche agronomique pour le développement (Agropolis–CIRAD; Agricultural Research for Development). With an initial focus on Mali, the project’s results would expand to encompass five other countries in the Sudano-Sahelian region: Burkina Faso, Ethiopia, Kenya, Niger and Sudan.

Sorghum the survivor gets even tougher

Photo: ICRISAT

Hand milling of sorghum grains – an arduous task, mostly carried out by poor women in the drylands of Africa.

Drought-hardy crops such as sorghum are ideal for Mali’s conditions, where more water-intensive crops such as maize simply cannot survive. Millions of poor rural people across Africa depend on sorghum in their day-to-day lives: it is eaten in many forms, used to make alcoholic beverages and as animal fodder, and is converted into biofuel for cooking.

But even sorghum has its limits. While the demand for it has doubled in West Africa in the last 20 years, productivity has generally remained low, with an average yield of only one tonne per hectare for traditional varieties in Mali. This is mostly due to post-flowering drought, poor soils and farming conditions, and limited access to quality, high-yielding seed. As rainfall patterns become increasingly erratic and variable across the world, scientists warn of the need to improve sorghum’s broad adaptability to drought, to ensure future food security in Africa.

The GCP Sorghum RI, with Niaba’s help, aimed to support the development of new breeds of sorghum that could survive better on less water in drought-stricken parts of Africa. It sought to improve sorghum yield and quality for African farmers and, in turn, improve the livelihoods and food security of communities across sub-Saharan Africa.

In 2012, Niaba found himself travelling once again, this time to Australia with IER colleague Sidi B Coulibaly. They spent three weeks working alongside, and training with, Andrew Borrell and his sorghum research team at the Queensland Government Department of Agriculture, Fisheries and Forestry’s (DAFF) Hermitage Research Facility in Warwick.

“We have been collaborating with researchers at DAFF and The University of Queensland since 2009, to introduce what is called the ‘stay-green’ drought-resistant gene into our local sorghum varieties,” says Niaba.

Photo provided by A Borrell

Left to right: Niaba Témé with David Jordan (Australia), Sidi B Coulibaly (Mali) and Andrew Borrell (Australia), visiting an experiment at Hermitage Research Facility in Queensland, Australia.

Niaba’s no longer green when it comes to using stay-green

Stay-green is a drought adaptation trait that allows sorghum plants to stay alive and maintain green leaves for longer during post-flowering drought. This means the plants can keep growing and produce more grain in drier conditions. It has contributed significantly to an increase in sorghum yields, using less water, in north-eastern Australia and southern USA for the last two decades.

GCP’s stay-green project aimed to evaluate the potential for introducing stay-green into Mali’s local sorghum varieties, enriching Malian pre-breeding material for the trait, and training African sorghum researchers, such as Niaba, in the methods of improving yields and drought resistance in sorghum breeding lines from both Australia and Mali.

Photo provided by E Weltzein-Rattunde

A sorghum farmer in Mali.

“In Australia we learnt about association mapping, population genetics and diversity, molecular breeding, crop modelling using climate forecasts, and sorghum physiology,” says Niaba.

Learning to use molecular markers was particularly exciting, he says, “because molecular markers make it easier to see if the plant being bred has the gene related to drought tolerance, without having to go through the lengthy process of growing the plant to maturity and risk missing the trait through visual inspection.”

Niaba says the molecular training he received in Australia complemented previous training he had received through a collaborative GCP-funded project with Agropolis–CIRAD and Syngenta Foundation for Sustainable Agriculture, in which he learnt to use molecular markers to identify and monitor key regions of sorghum’s genome in consecutive breeding generations through a process called marker-assisted recurrent selection (MARS).

A large part of GCP’s focus is building such capacity among developing country partners to carry out crop research and breeding independently in the future, so they can continue developing new varieties with drought adaptation relevant to their own environmental conditions.

“Our time in Australia was an intense but rewarding experience, more so for the fact that between the efforts of Australia and Mali, we have now developed new drought-tolerant crops which will enhance food security for my country,” says Niaba. “Similarly with the help of Agropolis–CIRAD and Syngenta, we are using molecular markers to improve breeding efficiency of sorghum varieties more adapted to the variable environment of Mali.”

Photo provided by A Borrell

Niaba (foreground) examining a sorghum panicle at trials in Mali in 2009.

Sorghum sunrise in Mali

On the back of the MARS project, Niaba successfully obtained GCP funding in 2010 to carry out similar research with Agropolis–CIRAD and collaborators in Africa at ICRISAT.

“In that project, we were trying to enhance sorghum grain yield and quality for the Sudano-Sahelian zone of West Africa using the backcross nested association mapping (BCNAM) approach,” explains Niaba. “This involved using an elite recurrent parent that is already adapted to local drought conditions. The benefit of this approach is that it can lead to detecting elite varieties much faster.”

The approach has the potential to halve the time it takes to develop local sorghum varieties with improved yield and adaptability to drought. The project developed 100 lines for 50 populations from backcrosses carried out with 30 recurrent parents. The lines are now being validated in Mali.

Photo: P St-Jacques/DFATD-MAECD

Agronomists inspect a field of sorghum in Mali.

Niaba says such successful collaborations and capacity development opportunities have been made possible only through GCP support.

“We had some contacts before, but we didn’t have the funds or skills to really get into a collaboration. Now we’re motivated and are making connections with other people so we can continue working with the material we have developed.

“GCP’s time may be ending, but it very much represents a new day – a sunrise for the work we are doing with sorghum here in Mali.”

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Photo: N Palmer/CIAT

Sorghum for sale.

Mar 042015
 

 

Photo: IRRI

A woman harvests rice in Ifugao, The Philippines.

Plant geneticist Sigrid Heuer remembers very clearly entering the transgenic greenhouse in Manila to see her postdoctoral student holding up a rice plant with ‘monster’ roots.

“They were enormous,” she recalls. “This is when I knew we had the right gene. It confirmed years of work. That was our eureka moment.

So massive was the effect of that gene that I knew we had the right one.”

This genetic discovery – described in more detail a little later – is one of the shining lights of the 10-year-long CGIAR Generation Challenge Programme (GCP) established in 2004.

GCP-supported researchers aimed high: they wanted to contribute to food security in the developing world by using the latest advances in crop science and plant breeding.

And with the lives of half of the world’s population directly reliant on their own agriculture, there is a lot at stake. Land degradation, salinity, pollution and excessive fertiliser use are just some of the challenges.

Rice is one of the most critical crops worldwide

Amelia Henry, drought physiology group leader at the International Rice Research Institute (IRRI), explains why rice was such a critical crop for GCP research. She says rice is grown in a diverse set of environmental settings, often characterised by severe flooding, poor soils and disease.

Photo: A Barclay/IRRI

Cycling through rice fields in Odisha, India.

In Asia, 40 percent of rice is produced in rainfed systems with little or no water control or protection from floods and droughts – meaning rice plants are usually faced with too much or too little water, and rarely get just enough. In addition, 60 percent (29 million hectares) of the rainfed lowland rice is produced on poor and problem soils, including those that are naturally low in phosphorus.

Phosphorus deficiency and aluminium toxicity are two of the most widespread environmental causes of poor crop productivity in acidic soils, where high acid levels upset the balance of available nutrients. And drought makes these problems even worse.

Phosphorus is essential for growing crops. Its commercial use in fertilisers is due to the need to replace the phosphorus that plants have extracted from the soil as they grow. Soils lacking phosphorus are an especially big problem in Africa, and the continent is a major user of phosphate fertilisers. However, inappropriate use of fertilisers can, ironically, acidify soil further, since excess nitrogen fertiliser decreases soil pH.

Meanwhile, high levels of aluminium in soil cause damage to roots and impair crop growth, reducing their uptake both of nutrients like phosphorus and of water – making plants more vulnerable to drought. Aluminium toxicity is a major limitation on crop production for more than 30 percent of farmland in Southeast Asia and South America and approximately 20 percent in East Asia, sub-Saharan Africa and North America.

Rice is a staple for nearly half of the world’s seven billion people, and global consumption is rising. More than 90 percent of all the rice produced is consumed in Asia, where it is a staple for 2.4 billion people – a majority of the population. Outside Asia, rice consumption continues to rise steadily, with the fastest growth in sub-Saharan Africa, where people are eating 50 percent more rice than they were two decades ago. More than 90 percent of the world’s rice is produced by farmers in six countries: China, India, Indonesia, Bangladesh, Vietnam and Japan. China and India account for nearly half of that, with an output of more than 700 million tonnes.

The challenge today is to tap into the genetic codes of key crops such as rice and wheat to feed a growing global population. Science plays a crucial role in identifying genes for traits that help plants tolerate more difficult environmental conditions, and producing crop varieties that contain these genes.

Plant biologists are already developing new rice lines that produce higher yields in the face of reduced water, increasingly scant fertiliser as costs rise, and unproductive soils. However, ‘super’ crops are needed that can combine these qualities and withstand climate changes such as increasing temperatures and reduced rainfall in a century when the world’s population is estimated to reach nearly 10 billion people by 2050.

Bringing the best scientific minds to improve rice varieties

Ambitious in concept, the GCP research focussed on bringing together experts to work on these critical problems of rice production for some of the world’s poorest farmers.

The programme was rolled out in two phases that sought to explore the genetic diversity of key crops and use the most important genes for valuable traits, such as Sigrid’s discovery made in a rice variety that is tolerant of phosphorus-poor soils. Each phase involved dedicated teams in partner countries.

GCP: a two-act tale Phase I (2004–08) involved ‘discovery’ projects for 21 crops: beans, cassava, chickpeas, cowpeas, groundnuts, maize, rice, sorghum, wheat, bananas (and plantains), barley, coconuts, finger millet, foxtail millet, lentils, pearl millet, pigeonpeas, potatoes, soya beans, sweetpotatoes and yams. Phase II (2009–14) focussed on nine of these 21: beans, cassava, chickpeas, cowpeas, groundnuts, maize, rice, sorghum and wheat.

GCP Principal Investigator Hei Leung, from IRRI, says GCP is unique, one of kind: “I love it.” He says GCP has enabled rice researchers and breeders to embrace cutting-edge science through partnerships focussed on improving crop yields in areas previously deemed unproductive.

Hei says GCP wanted to target research during its second phase on those crops that most poor people depend upon. “We wanted to have a programme that is what we call ‘pro-poor’, meaning the majority of the world’s people depends on those crops,” he says.

Rice is the ‘chosen one’ of GCP’s cereal crop research and development, with the biggest slice of GCP’s research activities dedicated to this, the most widely consumed staple food.

It is crucial to increase rice supplies by applying research and development such as that carried out by GCP researchers over the past 10 years, Hei says.

For more on the relationship between GCP and IRRI – and an extra sprinkling of salt on your rice (fields) – see our Sunset Story ‘Rice research reaps a rich harvest of products, people and partners’.

Relying on rice’s small genome in the hunt for drought-tolerance genes

Researchers had been trying to map the genomes of key cereal crops for over two decades. Rice’s genome was mapped in 2004, just as GCP started.

Rice has a relatively small genome, one-sixth the size of the maize genome and 40 times smaller than the wheat genome. This makes it a useful ‘model’ crop for researchers to compare with other crops.

“People like to compare with rice because wheat and maize have very big genomes, and they don’t have the resources,” explains Hei.

After the rice genome had been sequenced, the next step was to focus down to a more detailed level: the individual genes that give rice plants traits such as drought tolerance. Identifying useful genes, and markers that act as genetic ‘tags’ to point them out, gives scientists an efficient way to choose which plants to use in breeding.

One of GCP’s Principal Investigators for rice was Marie-Noëlle Ndjiondjop, a senior molecular scientist with the Africa Rice Center.

“Rice is becoming a very important crop in Africa,” she says. “Production has been reduced by a lot of constraints, and drought is one of the most important constraints that we face in Africa.”

Meet Marie-Noëlle below (or on YouTube), in our series of Q&A videos on rice research in Africa.

 

Marie-Noëlle’s team recognised that drought tolerance was likely to be a complex trait in rice, involving many genes, due to the mix of physiological, genetic and environmental components that affect how well a plant can tolerate drought conditions. To help discover the rice varieties likely to have improved drought tolerance, Marie-Noëlle’s team used an innovative approach known as bi-parental marker-assisted recurrent selection (MARS).

“With such a complex trait, you really need to have all the tools and infrastructure necessary; through GCP we were able to buy the necessary equipment and put in the infrastructure needed to find and test the drought trait in rice lines.

“By using the MARS approach we identified the genetic regions associated with drought and are moving towards developing new rice lines that the African breeder and farmer will be using in the next decade to grow crops that are better able to withstand drought conditions.”

Likewise, Amelia Henry’s IRRI team also developed drought-tolerant lines, particularly for drought-prone areas of South Asia. She says many of the promising deep-rooted or generally drought-tolerant varieties identified in the early decades after IRRI’s foundation in 1960 are still used today as ‘drought donors’.

“Since the strength of our project was the compilation of results from many different sites, this work couldn’t have been done without the GCP partners,” she says. “They taught me a lot about how rice grows in different countries and what problems rice farmers face.”

Hei agrees that GCP partnerships have been crucial, including in the successful breeding of rice with drought tolerance: “They’re getting a 1.5-tonne rice yield advantage under water stress. I mean, that’s unheard of! This is a crop that needs water.”

Photo: IRRI

A rice farmer in Rwanda.

But the researchers could not rest with just one of rice’s problems solved.

Hei says GCP’s initial focus on drought was a good one but then, “I remember saying, ‘We cannot just go for drought. Rice, like all crops, needs packages of traits’.”

He knows that drought is just one problem facing rice farmers, noting “this broadened our research portfolio to include seeking to breed rice varieties with traits of tolerance to aluminium toxicity, salt and poor soils.”

The scope widens: phosphorus-hungry rice and a huge success

Sigrid Heuer was in The Philippines working for IRRI when she became involved in the ground-breaking phosphorus-uptake project for rice.

She took over the project being headed by Matthias Wissuwa. Much earlier, Matthias had noted that Kasalath – a traditional northern Indian rice variety that grew successfully in low-phosphorus soil – must contain advantageous genes. His postdoctoral supervisor, Noriharu Ae, thought that longer roots were likely to be the secret to some rice varieties being able to tolerate phosphorus-deficient soils.

Matthias, now a senior scientist in the Crop, Livestock and Environment Division at the Japan International Research Center for Agricultural Sciences (JIRCAS), says that for a long time he was not sure if it was just long roots: “It was a real chicken-and-egg scenario – does strong phosphorus uptake spur root growth, or is it the other way around?”

Photo: IRRI

Screening for phosphorus-efficient rice, able to make the best of low levels of available phosphorus, on an IRRI experimental plot in The Philippines. Some types of rice have visibly done much better than others.

Sigrid Heuer used her background in molecular breeding to take up the challenge with GCP to find the genes responsible for the Kasalath variety’s long roots.

“I spent years looking for the gene,” Sigrid says. “It was like trying to find a needle in a haystack; the genomic region where the gene is located is very complex.

“We had little biogenomics support at the time and I had three jobs and two kids; I was spending all my nights trying to find this gene.”

Photo: IRRI

Sigrid Heuer in the field at IRRI.

But one day, Sigrid’s postdoctoral student Rico Gamuyao excitedly called her downstairs to the transgenic greenhouses. “Rico had used transgenic plants to see whether this gene had any effect. He was digging out plants from experimental pods.”

Sigrid says that moment in the Manila labs was the turning point for the project’s researchers.

Matthias’ team had previously identified a genomic region, or locus, named Pup1 (‘phosphorus uptake 1’) that was linked to phosphorus uptake in lines of traditional rice growing in poor soils. However, its functional mechanism remained elusive until the breakthrough GCP-funded project sequenced the locus, showing the presence of a Pup1-specific protein kinase gene, which was named PSTOL1 (‘phosphorus starvation tolerance 1’). The discovery was reported in the prestigious scientific journal Nature on 23 August 2012 and picked up by media around the world.

The gene instructs the plant to grow larger and longer roots, increasing its surface area – which Sigrid compares to having a bigger sponge to absorb more water and nutrients in the soil.

“Plants growing longer roots have more uptake of phosphorus – and PSTOL1 is responsible for this.

“GCP was always there, supporting us and giving us confidence, even when we weren’t sure we were going to succeed,” she recalls. “They really wanted us to succeed, so, financially and from a motivational point of view, this gave us more enthusiasm.”

She adds, jokingly, “With so many people having expectations about the project, it was better not to disappoint.”

For some insight straight from the source, listen to Matthias in our podcosts below. In these two bitesized chunks of wisdom he discusses the importance of phosphorus deficiency and of incorporating PSTOL1 into national breeding programmes; his work in Africa and the possibility of uncovering an African ‘Pup2; what the PSTOL1 discovery has meant for him; and the essential contribution of international partnerships and GCP’s support.


Photo: IRRI

Members of the IRRI PSTOL1, phosphorus uptake research team chat in the field in 2012. From left to right they are are: Sigrid Heuer, Cheryl Dalid, Rico Gamuyao, Matthias Wissuwa and Joong Hyoun Chin.

Phosphorus-uptake gene not all it seemed – an imposter?

But PSTOL1 was definitely not what it seemed. “It was identified under phosphorus-deficient conditions and the original screen was set up for that,” says Sigrid.

Researchers eventually discovered that Pup1 and the PSTOL1 gene within it were not really all about phosphorus at all: “It turns out it is actually a root-growth gene, which just happens to enhance uptake of phosphorus and other nutrients such as nitrogen and potassium.

“The result is big root growth and maintenance of that growth under stress. If you have improved root growth, there is more access to soil resources, as a plant can explore more soil area with more root fingers.”

Her team showed that overexpression of PSTOL1 gene significantly improves grain yield in varieties growing in phosphorus-deficient soil – by up to 60 percent compared to rice varieties that did not have the gene.

In field tests in Indonesia and The Philippines, rice with the PSTOL1 gene produced about 20 percent more grain than rice without the gene. This is important in countries where rice is grown in poor soils.

Photo: T Saputro/CIFOR

A farmer harvests rice in South Sulawesi, Indonesia.

Sigrid, now based in Adelaide at the Australian Centre for Plant Functional Genomics, says the introduction of the new gene into locally adapted rice varieties in different locations across Asia and Africa is expected to boost productivity under low-phosphorus conditions.

“The ultimate measure for these kinds of projects is whether a gene works in different environments. I think we have a lot of evidence that says it does,” she says.

The discovery of PSTOL1 promises to improve the food security of rice farmers on phosphorus-deficient land though assisting them to grow more rice and earn more.

Titbits of further research successes: aluminium tolerance and MAGIC genes

Drought, low-phosphorus soils, aluminium toxicity, diseases, acid soils, climate change… the list seems never-ending for challenges to growing rice. Apart from the successes with drought and phosphorus that GCP scientists achieved, there was to be much more in the works from other GCP researchers.

During GCP Phase I, a team led by Leon Kochian of Cornell University, USA, with colleagues at the Brazilian Corporation of Agricultural Research (EMBRAPA), JIRCAS and Moi University, Kenya, successfully identified and cloned a major sorghum aluminium-tolerance gene.

In Phase II, they worked towards breeding aluminium-tolerant sorghum lines for sub-Saharan Africa, as well as applying what they learnt to discover similar genes in rice and maize.

Hei Leung says GCP leaves a lasting legacy in the development of multiparent advanced generation intercross (MAGIC) populations. These help breeders to identify valuable genes, and from among the populations they can also select lines to use in breeding that have favourable traits, such as being tolerant to environmental stresses, having an ability to grow well in poor soils or being able to 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 different MAGIC populations for rice, including both indica and japonica types. And the idea of developing MAGIC populations has spread to other crops, including chickpeas, cowpeas and sorghum.

For more on MAGIC see our Sunset Story ‘Rice research reaps a rich harvest of products, people and partners’.

Photo: IRRI

A farmer harvests rice in Nepal.

Meeting the challenges and delivering outcomes to farmers

But with success come the frustrations of getting there, according to Nourollah Ahmadi, GCP Product Delivery Coordinator for rice across Africa. “This is because things are not always going as well as you want.”

Nourollah, from Centre de coopération internationale en recherche agronomique pour le développement (Agropolis–CIRAD; Agricultural Research for Development), says sometimes he felt overwhelmed coordinating GCP’s rice projects because “the challenges were perhaps too big.”

Project Delivery Coordinators monitor projects first-hand, conducting on-site visits, advising project leaders and partners and helping them implement delivery plans.

“One of the problems was the overall level of basic education of people who were involved in the project,” Nourollah says.

Photo: L Hartless/ACDI VOCA/USAID

Rice cultivation in Mali is on the rise.

His work with GCP has opened up new prospects for some of the poorest farmers in the world: “For five years, I have been coordinating one of the rice initiatives implemented by the Africa Rice Center and involving three African countries.” These are Burkina Faso, Mali and Nigeria.

He says GCP has brought much-needed expertise and technical skills to countries which can now use genetic insights to produce improved crops tolerant of drought conditions and poor soils and resistant to diseases. Using new molecular-breeding techniques has provided a more effective way to move forward, still firmly focussed on helping the world’s poorest farmers achieve food security.

“We don’t change direction, we change tools – sometimes you have a bicycle, sometimes you have a car,” Nourollah says.

Hei agrees there have been challenges: “It’s been a bumpy road to get to this point. But the whole concept of getting all the national partners doing genetic resource characterisation is a very good one.

Right now they are enabled; they are not scared about the technology. They can apply it.”

Sigrid says applied research is judged on two scales: “One is the publications and science you’re doing. The other is whether the work has any impact in the field, whether it works in the field. Bringing these two together is sometimes a challenge.”

GCP has managed to meet both challenges. New crop varieties have been released to farmers, and more than 450 scientifically reviewed papers have been published since 2004.

Building on the rice success story and leaving a lasting legacy

The work that GCP-supported researchers have done for rice is also being used in other crops. For example, researchers used comparative genomics to determine if genes the same as or similar to those found in rice are present and operating in the same manner in sorghum and maize.

The GCP team found sorghum and maize varieties that contained genes, similar to rice’s PSTOL1, that also confer tolerance of phosphorus-deficient soil with an enhanced root system. They were then able to develop markers to help breeders in Brazil and Africa identify phosphorus-efficient lines.

Making the most of comparative genomics Over the last 20 years, genetic researchers all over the world have been mapping the genomes of various crops. A genome is the total of all genes that make up the genetic code of an individual. Genome maps are now being used by geneticists and plant breeders to identify similarities and differences between the genes of different crop species. This process is termed comparative genomics and was an important tool for GCP during its second phase (2008–2014).

The knowledge that GCP-supported rice researchers have generated is shared through communities of practice, through websites, publications, research meetings and the Integrated Breeding Platform.

As Amelia Henry notes, GCP’s achievements will be defined by “the spirit of dedication to openness with research data, results and germplasm and giving credit and support to partners in developing countries.” The work in rice in many ways exemplifies GCP’s collaborative approach, commitment to capacity building and deeply held belief that together we can go so much further in helping farmers.

Unlocking genetic diversity in crops for the resource-poor was at the heart of GCP’s mission, which in 2003 promised ‘a new, unique public platform for accessing and developing new genetic resources using new molecular technologies and traditional means’.

Certainly for poor rice farmers in Asia and Africa, the work that GCP has supported in applying the latest molecular-breeding techniques will lead to rice varieties that will help them produce better crops on poor soils in a changing climate.

Photo: A Erlangga/CIFOR

Rice farmers in Indonesia.

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