Generation Challenge Programme
GCP website
Integrated Breeding
IBP website
GCP Blog
GCP blog
  Connect with us GCP on Facebook GCP on Twitter GCP on LinkedIn Subscribe to GCP Newsletter Subscribe to GCP RSS feeds
Oct 272015
 

 

Photo: N Palmer/CIAT

GCP sowed the seeds of a genetic resources revolution.

“In the last 10 years we have had a revolution in terms of developing the genetic resources of crops.”

So says Pooran Gaur, Principal Scientist for chickpea genetics and breeding at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), and Product Delivery Coordinator for chickpeas for the CGIAR Generation Challenge Programme (GCP).

He attributes this revolution in large part to GCP, saying it “played the role of catalyst. It got things started. It set the foundation. Now we are in a position to do further molecular breeding in chickpeas.”

Led by Pooran, researchers from India, Ethiopia and Kenya worked together not only to develop improved, drought-tolerant chickpeas that would thrive in semiarid conditions, but also to ensure these varieties would be growing in farmers’ fields across Africa within a decade.

The 10-year Generation Challenge Programme, with the goal of improving food security in developing countries, aimed to leave plant genetic assets as an important part of its legacy.

Diagnostic, or informative, molecular markers – which act like ‘tags’ for beneficial genes scientists are looking for – are an increasingly important genetic tool for breeders in developing resilient, improved varieties, and have been a key aspect of GCP’s research.

Photo: ICARDA

Chickpeas, ready to harvest.

What is a diagnostic molecular marker?

Developments in plant genetics over the past 10–15 years have provided breeders with powerful tools to detect beneficial traits of plants much more quickly than ever before.

Scientists can identify individual genes and explore which ones are responsible for, or contribute to, valuable characteristics such as tolerance to drought or poor soils, or resistance to pests or diseases.

Once a favourable gene for a target agronomic trait is discovered and located in the plant’s genome, the next step is to find a molecular marker that will effectively tag it. A molecular marker is simply a variation in the plant’s DNA sequence that can be detected by scientists using any of a range of methods. When one of these genetic variants is found close on the genome to a gene of interest (or even within the gene itself), it can be used to indicate the gene’s presence.

To use an analogy, think of a story as the plant’s genome: its words are the plant’s genes, and a molecular marker works like a text highlighter. Molecular markers are not precise enough to highlight specific words (genes), but they can highlight sentences (genomic regions) that contain these words, making it easier and quicker to identify whether or not they are present.

Once a marker is found to be associated with a gene, or multiple genes, and determined to be significant to a target trait, it is designated an informative marker, diagnostic marker or predictive marker. Some simple traits such as flower colour are controlled by one gene, but more complex traits such as drought tolerance are controlled by multiple genes. Diagnostic markers enable plant breeders to practise molecular breeding.

Breeders use markers to predict plant traits

Photo: N Palmer/CIAT

Hard work: a Ugandan bean farmer’s jembe, or hoe.

In the process known as marker-assisted selection, plant breeders use diagnostic molecular markers early in the breeding process to determine whether plants they are developing will have the desired qualities. By testing only a small amount of seed or seedling tissue, breeders are able to choose the best parent plants for crossing, and easily see which of the progeny have inherited useful genes. This considerably shortens the time it takes to develop new crop varieties.

“We use diagnostic markers to check for favourable genes in plants under selection. If the genes are present, we grow the seed or plant and observe how the genes are expressed as plant characteristics in the field [phenotyping]; if the genes are not present, we throw the seed or plant away,” explains Steve Beebe, a leading bean breeder with the International Center for Tropical Agriculture (CIAT) and GCP’s Product Delivery Coordinator for beans.

“This saves us resources and time, as instead of a growing few thousand plants to maturity, most of which would not possess the gene, by using markers to make our selection we need to grow and phenotype only a few hundred plants which we know have the desired genes.”

GCP supported 25 projects to discover and develop markers for genes that control traits that enable key crops, including bean and chickpea, to tolerate drought and poor soils and resist pests and diseases.

Genomic resources, including genetic maps and genotyping datasets, were developed during GCP’s first phase (2004–2008) and were then used in molecular-breeding projects during the second five years of the Programme (2009–2014).

“GCP’s philosophy was that we have, in breeding programmes, genomic resources that can be utilised. Now we are well placed, and we should be able to continue even after GCP with our molecular-breeding programme,” says Pooran.

Photo: IRRI

A small selection of the rice diversity in the International Rice Research Institute gene bank – raw material for the creation of genomic resources.

Markers developed for drought tolerance

Photo: N Palmer/CIAT

Cracked earth.

With climate change making droughts more frequent and severe, breeding for drought tolerance was a key priority for GCP from its inception.

Different plants may use similar strategies to tolerate drought, for example, having longer roots or reducing water loss from leaves. But drought tolerance is a complex trait to breed, as in each crop a large number of genes are involved.

Wheat, for example, has many traits – each controlled by different genes – that allow the crop to tolerate extreme temperature and/or lack of moisture. Identifying drought tolerance in wheat is therefore a search for many genes. In the particular case of wheat, this search is compounded by its genetic make-up, which is one of the most complex in the plant kingdom.

The difficulty of identifying genes that play a significant role in drought tolerance makes it all the more impressive when researchers successfully collaborate to overcome these challenges. GCP-supported scientists were able to develop and use diagnostic markers in chickpea, rice, sorghum and wheat to breed for drought tolerance. The first new drought-tolerant varieties bred using marker-assisted selection have already been released to farmers in Africa and Asia and are making significant contributions to food and income security.

Photo: ICRISAT

Tanzanian sorghum farmer.

Markers developed for pests and diseases

Photo: IITA

A bumper harvest of cassava roots at the International Institute of Tropical Agriculture (IITA) in Nigeria.

Cassava mosaic disease (CMD) is the biggest threat to cassava production in Africa – where more cassava is grown and eaten than any other crop. A principal source of CMD resistance is CMD2, a dominant gene that confers high levels of resistance.

Nigerian GCP-supported researchers worked on identifying and validating diagnostic markers that are associated with CMD2. These markers are being used in marker-assisted selection work to transfer CMD resistance to locally-adapted, farmer-preferred varieties.

In the common bean, GCP-supported researchers identified genes for resistance to pests such as bean stem maggot in Ethiopia, as well as diseases such as the common mosaic necrosis potyvirus and common bacterial blight, which reduce bean quality and yields and in some cases means total crop losses.

Markers developed for acidic and saline soils

Photo: N Palmer/CIAT

Sifting rice in Nepal.

Aluminium toxicity and phosphorus deficiency, caused by imbalanced nutrient availability in acid soils, are major factors in inhibiting crop productivity throughout the world. Aluminium toxicity also exacerbates the effects of drought by inhibiting root growth.

Diagnostic markers for genes that confer tolerance to high levels of aluminium and improve phosphorus uptake were identified in sorghum, maize and rice. The markers linked to these two sets of similar major genes have been used efficiently in breeding programmes in Africa and Asia.

Salt stress is also a major constraint across many rice-producing areas, partly because modern rice varieties are highly sensitive to salinity. Farmers in salt-affected areas have therefore continued growing their traditional crop varieties, which are more resilient but give low yields with poor grain quality. To address this issue, GCP supported work to develop and use markers to develop popular Bangladeshi varieties with higher tolerance to salt. GCP also funded several PhD students working in this area, one of whom was Armin Bhuiya.

Markers mean information, which means power

Diagnostic molecular markers are, in their most essential form, data. That means they are easily stored and maintained as data in publicly accessible databases and publications. Breeders can now access the molecular markers developed for various crops through the Integrated Breeding Platform – a web-based one-stop shop for integrated breeding information (including genetic resources), tools and support, which was established by GCP and is now continuing independently following GCP’s close – in order to design and carry out breeding projects.

“We could not have done that much in developing genomic resources without GCP support,” says Pooran. “Now the breeding products are coming; the markers are strengthening our work; and you will see in the next five to six years more products coming from molecular breeding.

“For me, GCP has improved the efficiency of the breeding programme – that is the biggest advantage.”

More links

Photo: N Palmer/CIAT

Beans on sale in Uganda.

Oct 162015
 
Photo: A Paul-Bossuet/ICRISAT

Pigeonpea farmers in India.

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

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

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

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

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

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

Photo: S Kilungu/CCAFS

Harvesting sorghum in Kenya.

Setting a foundation for higher yielding, drought-tolerant chickpeas

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

Photo: ICRISAT

Chickpea harvest, India.

“GCP got things started; it set a foundation for using genomic resources to breed chickpeas,” says Pooran. During Phase I of GCP (2004–2009), ICRISAT was involved in developing reference sets for chickpeas and developing mapping populations for drought-tolerance traits. It also collaborated with 19 other international research organisations to successfully sequence the chickpea genome in 2013 – a major breakthrough that paved the way for the development of even more superior chickpea varieties to transform production in semi-arid environments.

The International Chickpea Genome Sequencing Consortium, led by ICRISAT and partly funded by GCP, identified more than 28,000 genes and several million genetic markers. Pooran says these are expected to illuminate important genetic traits that may enhance new varieties.

The trait of most interest to many chickpea breeders is drought tolerance. In recent years, droughts in the south of India, the largest producer of chickpeas, have reduced yields to less than one tonne per hectare. Droughts have also diminished chickpea yields in Ethiopia and Kenya, Africa’s largest chickpea producers and exporters to India. While total global production of chickpeas is around 8.6 million tonnes per year, drought causes losses of around 3.7 million tonnes worldwide.

Photo: ICRISAT

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

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

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

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

Developing capacity by involving partners in Kenya and Ethiopia

Photo: GCP

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

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

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

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

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

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

Photo: S Sridharan/ICRISAT

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

Decoding pigeonpea genome

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

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

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

Photo: B Sreeram/ICRISAT

A pigeonpea farmer in his field in India.

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

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

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

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

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

Photo: ICRISAT

East African farmers inspect pigeonpea at flowering time.

Securing income-generating groundnut crops in Africa

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

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

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

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

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

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

Photo: S Sridharan/ICRISAT

Drying groundnut harvest, Mozambique.

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

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

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

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

Supporting key crops in West Africa

Photo: N Palmer/CIAT

Harvested pearl millet and sorghum in Ghana.

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

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

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

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

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

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

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

Photo: A Paul-Bossuet/ICRISAT

Enjoying a tasty dish of sorghum.

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

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

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

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

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

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

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

Photo: N Palmer/CIAT

A Ghanaian farmer examines his pearl millet harvest.

From poverty to prosperity through partnerships

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

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

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

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

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

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

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

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

More links

Photo: A Paul-Bossuet/ICRISAT

Man and beast team up to transport chickpeas in Ethiopia.

 

Oct 122015
 

 

Photo: One Acre Fund/Flickr (Creative Commons)

A Kenyan farmer harvesting her maize.

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

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

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

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

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

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

Photo: Allison Mickel/Flickr (Creative Commons)

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

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

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

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

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

Researchers take on the double whammy of acid soils and drought

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

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

Photo: A Wangalachi/CIMMYT

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

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

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

Scientists join hands to unravel maize complexity

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

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

Photo: X Fonseca/CIMMYT

Maize diversity.

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

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

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

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

Photo: N Palmer/CIAT

Maize ears drying in Ghana.

Comparing genes: sorghum gene paves way for maize aluminium tolerance

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

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

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

Photo: L Kochian

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

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

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

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

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

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

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

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

Kenya deploys powerful maize genes

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

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

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

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

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

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

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

Photo: N Palmer/CIAT

A Kenyan maize farmer.

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

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

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

Photo: N Palmer/CIAT

Maize grain for sale.

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

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

Photo: D Mowbray/CIMMYT

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

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

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

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

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

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

Photo: A Erlangga/CIFOR

A farmer in Indonesia transports his maize harvest by motorcycle.

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

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

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

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

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

Photo: E Phipps/CIMMYT

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

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

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

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

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

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

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

A better picture: GCP brightens maize research

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

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

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

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

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

Photo: CIMMYT

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

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

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

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

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

More links

Photo: N Palmer/CIAT

A farmer displays maize harvested on his farm in Laos.

Sep 242015
 

Hei Leung has always been passionate about diversity, especially genetic diversity, and that’s one reason why he leapt at the chance to get involved with the CGIAR Generation Challenge Programme (GCP) right from its inception more than a decade ago.

Photo: IRRIBut GCP’s attraction for Hei wasn’t just about genetic diversity; it was also about working with diverse institutes and researchers. At the time, Hei had been working for the International Rice Research Institute (IRRI) for some 10 years, on and off, including a stint at Washington State University in the USA.

“The whole idea of the Challenge Programme was to bring people together from different places instead of an individual CGIAR Centre doing things,” he says.

Hei also saw the likely spin-offs from rice research to other crops such as wheat, maize and sorghum, which are also crucial to food security.

Rice is a ‘model crop’ because of its small genome. This means researchers in major cereals like wheat and maize, which have much bigger genomes but share genes of similar functions, can benefit from our work with rice.”

Photo: Jeffreyw/Flickr (Creative Commons)

From little pizzas great programmes grow!

It all began in 2003, over pizza, in Rome. Hei remembers that his commitment to GCP started when he met with a small group of people including Robert Zeigler, who was to become the first Director of GCP, and who is currently Director General of IRRI.

“Little did we know that pizza was so inspiring,” Hei says, recalling that it was during that meeting that they agreed on the name: the Generation Challenge Programme.

GCP was formally launched in 2004 in Brisbane, Australia, at the 4th International Crop Science Congress.

Making the Programme ‘pro-poor’

Hei was initially involved with GCP as Subprogramme Leader for Comparative Genomics for Gene Discovery between 2004 and 2007, and later as a Principal Investigator for the Rice Research Initiative. Taking on his leadership role, Hei recognised from the start that many crops important to developing communities in Asia and Africa needed to become more drought-tolerant because of the increasing effects of climate change.

“We wanted to have a programme that is what we call ‘pro-poor’,” he says. “The majority of the world’s people depend on crops such as rice, wheat and maize for food.”

“I always feel that if you can solve eastern India’s problems, you can solve most of the problems in the world,” Hei adds. “If you travel in eastern India, you can see climate change happening day in, day out. You don’t have to wait 10 years or 50 years; it’s happening already. They either have too much or too little water. It’s a high-stress environment.”

Photo: N Palmer/CIAT


Women at work threshing rice near Sangrur, Punjab, India.

Rice is the world’s most widely consumed cereal crop, and is particularly important as the staple food of 2.4 billion people in Asia. GCP recognised rice’s importance and invested almost USD 29.5 million in rice research and development.

Furthermore, the genetic breeding lessons learnt from rice can also be applied to other staple crops such as wheat, maize and sorghum.

Other GCP-supported researchers used comparative genetics to determine if the same or similar genes – for example, the phosphorus starvation tolerance (PSTOL1) protein kinase gene found in rice – was also present and operating in the same manner in sorghum and maize.

They found sorghum and maize varieties that contained genes, similar to rice’s PSTOL1, that also conferred tolerance to phosphorus-deficient soils by enhancing the plant’s root system. They were then able to develop molecular markers to help breeders in Brazil and Africa to identify lines with these genes, which can now be used in breeding and developed as varieties for farmers growing crops, particularly in acidic soils.

Seeing the potential for novel researcher interactions

Hei also recognised that crops that received less scientific attention but remained important as regional staple foods, such as bananas and plantains (of the genus Musa), could benefit from comparative genomics research.

“We had a highly motivated group of researchers willing to devote their efforts to Musa,” remembers Hei, who is currently IRRI Program Leader of Genetic Diversity and Gene Discovery.

“GCP’s community could offer a framework for novel interactions among banana-related actors and players working on other crops, such as rice. So, living up to its name as a Challenge Programme, GCP decided to take the gamble on banana genomics and help it fly.”

Photo:  Asian Development Bank

A banana farmer at work in the Philippines.

However, after four years, Hei found it difficult to maintain his GCP leadership role as well as keep on top of his IRRI work: “They said I was 50 percent with IRRI and 50 percent with GCP, but it is never like that in reality. I was always doing two jobs, or at least one-and-a-half jobs, and I didn’t think I was doing a good enough job for either. I thought it was time for other people to come into GCP.”

While Hei stepped down from a leadership role, he remained active working on GCP projects throughout the life of the Programme.

Hei says that during the last five years of GCP, a lot of technology to characterise genetic diversity evolved “to bring high-quality science to accelerate our mission to help the poor areas of Asia and Africa.”

Streamlining GCP reporting: from three reports a year down to just one One of the things that initially bothered Hei during his GCP time was the reporting requirements: “I remember we used to ask people to submit a mid-year report, end-of-year report and an update. “So I stuck my neck out during the last couple of years, and I said: ‘Guys, stop it. Don’t ask for these reports. They become mechanical. People just fill in the blanks. Ask for just one report before or after our annual meeting: just one report that people are excited to write about. And that was adopted.”

A MAGIC affair

The development of MAGIC (multi-parent advanced generation intercross) populations is the project that Hei gets most excited about. From these populations, created by crossing different combinations of multiple parents, plant lines can be selected that have useful characteristics such as drought tolerance, salinity tolerance and the ability to produce better quality grain.

“Now many crop breeders are calling for MAGIC populations,” says Hei. “I feel proud that at GCP we decided to support this concept and activity. This is one of GCP’s most important legacies and it’s one of my most favourite things.”

Photo: IRRI

Hei Leung looking relaxed in the lab at IRRI.

Honoured as a Fellow of the American Phytopathological Society (APS), Hei is recognised “for his leadership in the international community toward building and distributing rice genetic and genomic resources and creating capacity in plant pathology in the developing countries of Asia.”

Hei’s GCP leadership and research have clearly provided him with an important platform for taking on leadership and champion roles linking many individuals and organisations across Asia and Africa. His ASP profile concludes: “His promotion of collaborative research and his leadership in such programmes in the developing world have contributed to the building of a dynamic research community that promotes both basic knowledge and food security for Asia and the world.”

Making a difference to food security and farmer’s lives in developing countries is what GCP is all about. Such differences have been made possible through collaborative links that connect a diversity of organisations and people with the latest research in genetic diversity and breeding techniques.

Photo: IRRI

A farmer transplants rice in the Philippines.

It’s amore!

hei quoteHei recalls his personal and professional journey with GCP with much affection: “I think that it has been a wonderful scientific journey in terms of knowing the science and opening up my mind to being more receptive to alternative ways of doing things.

“There have been so many friends I have met through networking with GCP. Sometimes you go through bumpy roads, but anything you do will have bumpy times. And it’s very unusual to have a programme so illuminating. We honoured our commitment to finish in 10 years. It is a programme that had a fresh start and a clean ending.

“Most importantly, GCP has enabled plant breeders to embrace cutting-edge science through partnerships that focused on improving crop yields in areas previously deemed unproductive,” he says. “GCP is unique, one-of-a-kind, and I love it!”

More links

Jun 012015
 

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.

More links

Mar 262015
 

 

Photo: R Cheung/Flickr

Wheat growing in China.

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

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

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

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

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

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

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

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

Photo: E Zotov/Flickr

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

Sharing knowledge to improve breeding efficiency and sustainability

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

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

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

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


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

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

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

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

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

Photo: Rasbak/Wikimedia Commons

Spikes of emmer wheat.

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

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

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

Photo: X Fonseca/CIMMYT

Durum wheat spike.

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

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

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

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

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

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

Reaping existing skills  For Richard, the preliminary success of the Wheat RI is due, at least in part, to the speed with which national breeding programmes in both China and India are learning and incorporating new molecular-breeding techniques. “This was another reason why we chose to focus on China and India: they had the infrastructure and human capacity to start doing this almost immediately,” says Richard. “In other countries where GCP is investing, more time is going into teaching breeders the basics of molecular breeding and genetics. In China and India, they already have that basic understanding and are able to quickly incorporate it into their current programmes.”

Reaping existing skills

Photo: R Pamnani/Flickr

A baker butters naan bread in Hyderabad, India.

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

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

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

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

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

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

Younger researchers taking a lead

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

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

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

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

Photo: R Saltori/Flickr

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

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

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

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

Overcoming complex traits, genes and wary breeders

Photo: CCAFS

Wheat farmer in India.

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

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

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

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

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

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

Photo: N Palmer/CIAT

Wheat seed ready for planting in Punjab, India.

Incorporating conventional methods

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

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

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

Phenotyping: How to manage a subjective process

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

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

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

Photo: CIMMYT

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

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

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

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

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

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

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

Photo: R Martin/CIMMYT

A young farmer in her wheat field in India.

Managing the tsunami of phenotyping data

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

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

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

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

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

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

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

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

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

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

Friendly competition helping inspire India’s wheat breeders

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

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

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

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

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

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

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

Securing wheat production into the future

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

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

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

Photo: Rosino/Flickr

Donkeys bring home the wheat harvest in Qinghai, China.

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

More links

Mar 192015
 
Photo: N Palmer/CIAT

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

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

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

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

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

Photo: S Mann/ILRI

Newly harvested pearl millet heads in Niger.

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

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

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

Protein in pearl millet ‘critical’ for nutrition

Photo: P Casier/ICRISAT HOPE

A farmer harvests millet in Mali.

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

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

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

Photo: S Kilungu/CCAFS

Pearl millet growing in Kenya.

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

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

Pearl millet endowed with genetic potential

Photo: AS Rao/ICRISAT

A farmer with his pearl millet harvest in India.

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

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

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

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

Photo: C Bonham/Bioversity International

A traditional pearl millet variety growing in India.

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

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

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

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

GCP extends know-how to Africa

Photos: N Palmer/CIAT

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

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

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

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

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

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

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

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

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

Photo: N Palmer/CIAT

A farmer inspects his millet crop in northwest Ghana.

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

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

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

Mar 172015
 

 

Photo: IRRI

Harvesting rice by hand in The Philippines.

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

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

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

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

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

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

Rice that can survive increasingly salty water

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

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

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

Photos: IRRI

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

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

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

Photo: IRRI

Abdelbagi Ismail examines rice plants in the field in Bangladesh.

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

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

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

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

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

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

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

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

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

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

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

Partnership approach key to new rice gene for uptake of phosphorus

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

Photo: IRRI

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

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

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

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

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

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

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

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

Solving the insoluble: a gene for drought tolerance

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

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

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

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

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

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

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

Photo: C Quintana/IRRI

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Photo: IRRI

Rice terraces in Ifugao Province in The Philippines.

‘Super’ crops: something ‘magic’ happens

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

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

Making MAGIC MAGIC – multiparent advanced generation intercross – allows crop breeders to identify the genes controlling quantitative traits, such as salinity tolerance, by crossing different combinations of multiple parents. The results of these crosses are plants whose genome is a mosaic of their multiple parents. MAGIC has multiple advantages compared with existing approaches, as it permits a more precise identification of genes that are responsible for particular rice traits. Even genes with minor effects can be pinpointed. Standard crosses (between two parents) show a poor correlation between the diversity found in the DNA (genetic diversity) and the diversity of the observable characteristics displayed by the plant (phenotypic diversity) when it grows as part of a crop. Because the MAGIC populations are created from multiple parents rather than by simply crossing two lines, making them more genetically diverse, and are the product of numerous generations of intercrossing the original founders or parent plants, creating greater opportunities for recombination and so ‘milling’ the genetic contributions from the different lines ever finer, scientists are able to more accurately identify the genes underlying important traits.  There are three main advantages of the MAGIC approach compared to existing approaches: 1. It enables scientists to more precisely identify the specific regions of the genome controlling key traits. 2. MAGIC populations incorporate a large proportion of the genetic diversity within elite rice varieties from around the world. 3. MAGIC enables the discovery of the best combinations of genes for important traits.

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

New generation of researchers working on a new rice revolution

Photo: IRRI

Rice farmer in her field in Rwanda.

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

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

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

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

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

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

More links

Jan 302015
 

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

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

Photo: ICARDA

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

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

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

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

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

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

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

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

A common resource for lentil breeders

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

Photo: P Casier/CGIAR

A woman farmer with lentils in Bihar, India.

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

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

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

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

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

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

Diversity is key to searching for valuable breeding traits

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

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

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

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

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

Photo: T Wolday/Bioversity International

Farmers in Ethiopia winnow orange lentils.

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

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

Photo: E Huttner/ACIAR

Farmer Minto with lentils in his field in Bangladesh.

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

Preserving genetic resources

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

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

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

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

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

Groundwork on lentils ‘gave orientation to future breeding efforts’

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

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

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

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

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

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

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

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

Photo: Bill & Melinda Gates Foundation

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