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Jun 012015

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


Indian chickpea farmer with her harvest.

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

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

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

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

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

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

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

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.


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


Chickpea seed

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

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

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

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

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

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

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

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

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

 Photo: L Vidyasagar/ICRISAT

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

Chickpea success in Africa: new varieties already changing lives

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

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

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

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

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

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

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

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

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

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

Photo: A Paul-Bossuet/ICRISAT

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

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

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

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

Photo: GCP

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

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

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

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

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

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

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

Chickpea’s promise meeting future challenges

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

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

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

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

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

Photo: A Paul-Bossuet/ ICRISAT

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

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

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

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

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

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

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

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

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

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Mar 042015


Photo: IRRI

A woman harvests rice in Ifugao, The Philippines.

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

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

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

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

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

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

Rice is one of the most critical crops worldwide

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

Photo: A Barclay/IRRI

Cycling through rice fields in Odisha, India.

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

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

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

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

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

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

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

Bringing the best scientific minds to improve rice varieties

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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

Photo: IRRI

A rice farmer in Rwanda.

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

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

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

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

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

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

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

Photo: IRRI

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

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

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

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

Photo: IRRI

Sigrid Heuer in the field at IRRI.

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

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

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

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

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

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

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

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

Photo: IRRI

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

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

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

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

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

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

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

Photo: T Saputro/CIFOR

A farmer harvests rice in South Sulawesi, Indonesia.

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

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

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

Titbits of further research successes: aluminium tolerance and MAGIC genes

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

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

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

Hei Leung says GCP leaves a lasting legacy in the development of multiparent advanced generation intercross (MAGIC) populations. These help breeders to identify valuable genes, and from among the populations they can also select lines to use in breeding that have favourable traits, such as being tolerant to environmental stresses, having an ability to grow well in poor soils or being able to produce better quality grain.

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

GCP funded the development of four different MAGIC populations for rice, including both indica and japonica types. And the idea of developing MAGIC populations has spread to other crops, including chickpeas, cowpeas and sorghum.

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

Photo: IRRI

A farmer harvests rice in Nepal.

Meeting the challenges and delivering outcomes to farmers

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

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

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

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

Photo: L Hartless/ACDI VOCA/USAID

Rice cultivation in Mali is on the rise.

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

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

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

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

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

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

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

Building on the rice success story and leaving a lasting legacy

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

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

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

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

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

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

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

Photo: A Erlangga/CIFOR

Rice farmers in Indonesia.

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Feb 242015
Photo provided by S Gudu

Sam Gudu

Kenyan crop scientist Samuel (Sam) Gudu loves nothing more than getting his hands dirty out on the land.

Photo: J Agalo

Seeing the true impact of research and doing what he likes to do best: Sam in a maize field in Kenya.

“Although these days I spend most of my time inside doing administrative work, I go out to the field at least once a month, as this is the only way I can truly see how our research is helping to make the lives of Kenyan farmers a lot more profitable and sustainable,” he says.

A love for the land began in Sam’s childhood on the banks of Lake Victoria in western Kenya, where he learnt the value of “hard and honest” work and a sense of responsibility for the welfare of his community.

“Growing up in a small fishing village, I was always helping my parents to fish and garden, or my grandparents to muster cattle. I remember spending long hours before and after school either on the lake or in the field helping to catch, harvest and produce enough food to eat and support our family,” he says.

It was in his high school classroom some 40 years ago that Sam’s outdoor enthusiasm grew into a keen thirst for knowledge of the world. “I became very interested in biology, as I wanted to know how nature worked,” he says. “I was particularly captivated by the study of genetics, as it focussed on what controlled life.” Today, a quick glance through Sam’s CV leaves no doubt as to his dedication since his youth to advancing plant genetics and biotechnology. His passion was firmly grounded at the University of Nairobi, where he completed his undergraduate degree and Master of Science in Agriculture, focussing on genetics and plant breeding.  Realising the potential of biotechnology to combat the agricultural, health and environmental challenges facing developing countries like his own, Sam then secured a scholarship to undertake a PhD in plant genetics and biotechnology at the University of Guelph, Canada, between 1988 and 1993. Returning to Kenya in 1993, Sam took a teaching position in the Department of Botany at Moi University in Eldoret, in western Kenya, and was eventually promoted to Professor there in 2003 and later Deputy Vice Chancellor (Planning and Development). He is now also Principal of Rongo University College (a constituent college of Moi University).

Sam and GCP embrace biotechnology and emerging scientists

Sam’s relationship with the CGIAR Generation Challenge Programme (GCP) began in 2009 via a series of collaborative projects to advance maize and sorghum genetics for acid soils. Along with some of his students at Moi University, he worked primarily with researchers at the Brazilian Corporation of Agricultural Research (EMBRAPA), Cornell University in the USA and Niger’s Institut National de la Recherche Agronomique du Niger.

Photo: C Schubert/CCAFS

A farmer in her maize field in Kenya.

To take the example of maize, the challenge they face is that small-scale farms across Kenya yield less than one tonne per hectare, and this figure is declining. This compares with a possible yield of five to eight tonnes under controlled research conditions. Constraints to maize production in Kenya are threefold: soil acidity and poor fertility, pests and diseases, and frequent droughts.

Through GCP, Sam was also able to work with senior researchers at the International Rice Research Institute in The Philippines, the International Crops Research Institute for the Semi-Arid Tropics in India and the Japan International Research Center for Agricultural Sciences.

“Collaborating with these advanced colleagues in their advanced labs has enabled us to develop [breeding] materials much faster,” says Sam, talking about the virtues of improved breeding efficiency in delivering new and improved crop varieties more quickly and ultimately benefitting farmers sooner. “I can see that post-GCP we will still want to communicate and interact with these colleagues to enable us to continue to identify molecular materials that we discover.”

Photo: J Agalo

Sam (left) addressing a mixed group of farmers and researchers at Sega, Western Kenya, in June 2009.

Both EMBRAPA and Cornell University hosted several of Sam’s PhD students as part of GCP-supported research. “These students are now returning to Kenya with a far greater understanding of molecular breeding, which they are then sharing with us to advance our national breeding programme,” says Sam.

In parallel to his own career progression, Sam has been a strong proponent for promoting the next generation of Kenyan scientists. He has recruited many talented graduates in plant genetics, plant breeding, molecular and cell biology and biotechnology. He has also been instrumental in sourcing advanced laboratory equipment for research labs in Kenya that enable practical teaching and research in molecular biology.

“The Kenyan Government recently increased its funding for science and research,” explains Sam. “GCP has also made considerable investment into field research infrastructure. This support has not only helped us compete in the world of research but has also helped raise the profile of science as a career in this country.”

Photo: AgCommons

Sam Gudu (right) consults with Onkware Augustino (left) and Hannibal Muhtar (centre, who was contracted to work with GCP partners in planning and implementing infrastructure improvement) at the Sega phenotyping site in Western Kenya in February 2010. Field infrastructure improvements to the site were funded by GCP and implemented by its Integrated Breeding Platform, and included drip irrigation, fencing and a weather station.

The importance of supporting emerging scientists in Africa cannot be overstated, explains Sam. In fact, he considers the greatest achievements of his own career to be those that have benefitted his students, as well as Kenyan farmers.

“I wouldn’t be where I am now were it not for all the assistance I received from my teachers, lecturers and supervisors,” he says. “So I’ve always tried my best to give the same assistance to my students. It’s been hard work but very rewarding, especially when you see them graduate to become peers and colleagues.

“Having funding to support PhD students and provide them with the resources they need to complete their research is very fulfilling, and GCP has provided the funds for a number of my students. This support will go a long way to enhance the long-term success of our goal: to provide Kenyan farmers with cereal varieties that will improve their yields and make their livelihoods more secure and sustainable.”

Photo: J Agalo

Sam (second from right), with some of his young charges: Thomas Matonyei (far left), Edward Saina (second from left) and Evans Ouma (far right).

Sam and GCP exchange strengths

Sam’s work on improving maize and sorghum tolerance to acid soils, supported by GCP, is already having a positive impact. In sorghum, his team have developed five lines highly adapted to acid soils, which are currently undergoing registration for release as new varieties by the Kenyan national variety release authority. In maize, they have developed eight aluminium-tolerant lines and seven phosphorus-efficient lines.

Sam’s team share their results and materials with their partners across countries and continents. He says these lines will provide sorghum and maize breeders working in other African countries that have acid soils – including Ethiopia, Kenya, Niger, South Africa and Tanzania – with new breeding germplasm, which they can use to breed higher yielding maize and sorghum varieties for their countries’ farmers.

Photo: S Kilungu/CCAFS

A Kenyan farmer examines a sorghum variety in the field.

“Knowing which genes are responsible for aluminium tolerance and phosphorus efficiency has allowed us to more precisely select for this in our breeding programmes, reducing the time it takes to breed varieties with improved yields in acid soils without the use of costly inputs such as lime or fertiliser,” Sam explains.

“This means being able to select for, and breed, new maize varieties faster – varieties that are suitable not only for Kenyan soils, but also for other African countries.

“No one else has worked on this before in Kenya. It makes me feel that we’re truly contributing to food security for Kenyan people.”

While Sam has attracted externally funded competitive research projects throughout his career, it was the international collaborative nature of GCP that gave Sam something a little more personal: “I have improved how to communicate, how to develop relationships, how to maintain friendships. I think I have developed much more with GCP because I had many people to communicate with and I had the opportunity to visit other labs.

“GCP has not only developed my professional career but has also allowed me to interact with labs – and people – that I would probably not have interacted with.”

Photo: N Palmer/CIAT

A Kenyan maize farmer shows off her healthy crop.

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Dec 052014

It’s a cruel feature of some of the most populous areas of the world, particularly in the tropics and subtropics: acid soils. They cover a third of the world’s total land area – including significant swathes of Africa, Asia and Latin America – and 60 percent of land we could use for growing food. Today around 30 percent of all arable land reaches levels of acidity that are toxic to crops.

Soil acidity occurs naturally in higher rainfall areas and varies according to the landscape and soil. But we also make the problem worse through intensive agricultural practices. The main cause of soil acidification is the overuse of nitrogen fertilisers, which farmers apply to crops to increase production. Ironically, the inefficient use of nitrogen fertiliser can instead make matters worse by decreasing the soil pH.

60 percent of the world’s potential crop-growing land is highly acidic. Map courtesy of Leon Kochian.

60 percent of the world’s potential crop-growing land is highly acidic. Map courtesy of Leon Kochian.

Acidity prevents crops from accessing the right balance of nutrients in the soil, limiting farmers’ yields. Its negative effect on world yield is second only to drought and is particularly hard felt by subsistent and smallholder farmers who cannot afford to correct soil pH using calcium-rich lime. As a result, these farmers are forced to grow less profitable, acid-tolerant crops like millet, or suffer huge yield losses when growing more popular cereal crops like wheat, rice or maize.

“In Kenya, acidic soils cover almost 90 percent of the maize-growing areas and can reduce yields by almost 60 percent,” says Samuel Gudu, Professor and Deputy Vice-Chancellor (Planning & Development) at Moi University in Kenya. “Farmers know that the soil affects their yields, but they still grow maize because it is so popular.”

As is true in many other sub-Saharan countries, maize is a staple of the Kenyan diet: the average Kenyan consumes 98 kilograms of it each year. But maize prices in Kenya are among the highest in Africa, which directly affects the poorest quarter of the population, who spend 28 percent of their income on the crop.

“Yield losses play a big part in this economic imbalance and are why we need affordable agronomic options to help our farmers improve yields,” says Samuel, who was a Principal Investigator of a GCP comparative genomics project which sought to provide some of these options.

A Kenyan farmer prepares her maize plot for planting. Acid soils cover almost 90 percent of Kenya’s maize-growing area, and can more than halve yields.

A Kenyan farmer prepares her maize plot for planting. Acid soils cover almost 90 percent of Kenya’s maize-growing area, and can more than halve yields.

Aluminium toxicity and phosphorus deficiency: Public enemies number one and two in the fight against acidic soils

Between 2004 and 2014, crop researchers and plant breeders across five continents collaborated on several GCP projects to develop local varieties of maize, rice and sorghum that can withstand phosphorus deficiency and aluminium toxicity – two of the most widespread constraints leading to poor crop productivity in acidic soils.

Aluminium toxicity is the primary limitation on crop production for more than 30 percent of farmland in Southeast Asia and Latin America and approximately 20 percent in East Asia, sub-Saharan Africa and North America. Aluminium becomes more soluble in acid souls, creating a toxic glut of aluminium ions that damage roots and impair their growth and function. This results in reduced nutrient and water uptake, which in turn depresses yield.

Phosphorus deficiency is the next biggest soil deficiency after nitrogen to limit plant production. In acid soils, phosphorus is stuck (fixed) in forms that plants cannot take up. All plants need phosphorus to survive and thrive; it is a key element in plant metabolism, root growth, maturity and yield. Plants deficient in phosphorus are often stunted.

In a double whammy, the damage that aluminium toxicity causes to roots means that plants cannot efficiently access native soil phosphorus or even added phosphorus fertiliser – and adding phosphorus is an option that is rapidly becoming less viable.

“The world is running out of phosphorus as quickly as it is running out of oil,” says Leon Kochian, a Professor in the Departments of Plant Biology and Crop and Soil Science at Cornell University in the USA. “This is making its application a more expensive and less sustainable option for all farmers wanting to improve yields on acidic soils.” Indeed, the price of rock phosphate has more than doubled since 2007.

For 30 years, Leon has combined lecturing and supervising duties at Cornell University and the United States Department of Agriculture with his scientific quest to understand the genetic and physiological mechanisms that allow some cereals to tolerate acidic soils while others wither. And for the last 10 years, he has played an important leading role in GCP’s effort to develop new, higher yielding varieties of maize, rice and sorghum that tolerate acidic soils.

GCP builds on past crop breeding successes

The rationale behind GCP’s efforts stems from two independent and concurrent projects, which had been flourishing on different sides of the Pacific well before GCP was created.

One of those projects was co-led by Leon at Cornell University in collaboration with a previous PhD student of his, Jurandir Magalhães, at the Brazilian Corporation of Agricultural Research (EMBRAPA) Maize & Sorghum research centre.

Working on the understanding that the cells in grasses like barley and wheat use ‘membrane transporters’ to insulate themselves against excessive subsoil aluminium, Leon and Jurandir searched for a similar transporter in the cells of sorghum varieties that were known to tolerate aluminium.

“In wheat, when aluminium levels are high, these membrane transporters prompt organic acid release from the tip of the root,” explains Jurandir. “The organic acid binds with the aluminium ion, preventing it from entering the root.” Jurandir’s team found that in certain sorghum varieties, the gene SbMATE encodes a specialised organic acid transport protein, which stimulates the release of citric acid. They cloned the gene and found it was very active in aluminium-tolerant sorghum varieties. They also discovered that the activity of SbMATE increases the longer the plant is exposed to high levels of aluminium.

The rice variety on the left (IR-74) has the the gene locus Pup1, conferring phosphorus-efficient longer roots, while the rice on the right does not.

The rice variety on the left (IR-74) has the the gene locus Pup1, conferring phosphorus-efficient longer roots, while that on the right does not.

The other project, co-led by Matthias Wissuwa at Japan International Research Centre for Agricultural Sciences (JIRCAS) and Sigrid Heur at the International Rice Research Institute (IRRI) in The Philippines, was looking for genes that could improve rice yields in phosphorus-deficient soils. They had already identified a gene locus (a section of the genome containing a collection of genes) that produced a protein which allowed rice varieties with to grow successfully in low-phosphorous conditions. The locus was termed ‘phosphorus uptake 1’ or Pup1 for short. With GCP support, the team were able to make the breakthrough of discovering the protein kinase gene responsible, PSTOL1 (‘phosphorus starvation tolerance 1’), and understanding its mechanism.

“In phosphorus-poor soils, this protein instructs the plant to grow larger, longer roots, which are able to forage through more soil to absorb and store more nutrients,” explains Sigrid, a plant geneticist at IRRI and a GCP Principal Investigator. “By having a larger root surface area, plants can explore a greater area in the soil and find more phosphorus than usual. It’s like having a larger sponge to absorb more water.”

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

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

Leon clarifies that both projects were fairly advanced before they became part of the GCP fold. “Our team had already identified the gene SbMATE and were in the process of cloning it for breeding purposes. The IRRI and JIRCAS team had also identified Pup1 and were in the process of identifying and cloning the gene.”

The purpose of cloning these genes was to create molecular markers to help breeders identify whether the genes were present in the varieties they were working with. As an analogy, think of ‘reading’ a plant’s genome as you would read a story: the story’s words are the plant’s genes, and a molecular marker works as a text highlighter. Different markers can highlight or tag different keywords in the story. Tagging the location of beneficial genes in the DNA of plant genomes allows scientists to see which of the plants or seeds they are interested in – perhaps only a few out of hundreds or thousands – contain these genes. This forms the basis of marker-assisted breeding, which can help plant breeders halve the time it takes them to breed new high-yielding varieties for acidic soil conditions.

Leon says that GCP provided both projects with the opportunity to validate their discoveries and to use what they had found to develop new aluminium-tolerant sorghum varieties and phosphorus-efficient rice varieties for farmers. But it’s what happened next that made this GCP initiative unique.

Finding the best genes within the crop family

Sorghum, rice, maize and wheat are all part of the Poaceae (true grasses) family, evolving from a common grass ancestor 65 million years ago. Over this time, they have become very different from each other. However, at the genetic level they still have a lot in common.

Over the last 20 years, genetic researchers all over the world have been mapping these cereals’ genomes. These maps are now being used by geneticists and plant breeders to identify similarities and differences between the genes of different cereal species. This process is termed ‘comparative genomics’ and was a fundamental research theme for GCP during its second phase (2008–2014).

“The objective during GCP Phase I (2004-2007) was to study the genomes of important crops and identify genes conferring resistance or tolerance to various stresses, such as drought,” says Rajeev Varshney, Director of the Center of Excellence in Genomics at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). “This research was long and intensive, but it set a firm foundation for the work in GCP’s second phase, which sought to use what we have learnt in the laboratory and apply it to breed better varieties of crops.”

Rajeev oversaw GCP’s comparative genomics research projects on aluminium tolerance and phosphorus deficiency in sorghum, maize and rice, as part of his GCP role as Leader of the Comparative and Applied Genomics Research Theme.

“The idea behind the sorghum, maize and rice initiative was to use the discoveries we had independently made in sorghum and rice to see if we could find the same genes in the other crop,” explains Rajeev. “In other words, we wanted to see if we could find PSTOL1 in sorghum and SbMATE in rice.”

Working together through a number of comparative genomics projects, the researchers were highly successful in reaching this goal, discovering valuable sister genes and beginning to introduce them into new improved crop varieties for farmers.

Extending research in sorghum and rice to maize

Researchers at Cornell and EMBRAPA had already been using similar comparative techniques to look for SbMATE in maize because of its close familial connection to sorghum. This research was overseen by Leon and another EMBRAPA researcher, Claudia Guimarães.

“We used the knowledge that Jurandir and Leon’s SbMATE project produced to prove that we had a major aluminium-tolerance gene,” reflects Claudia.

The SbMATE gene in sorghum explains about 80 percent of its aluminium tolerance, but Claudia says that in maize it explains only about 20 per cent, making it harder for researchers to find without a little help knowing what to look for. “So we had to dig a little deeper for other similar genes that confer aluminium tolerance, and we found ZmMATE.”

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

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

ZmMATE1 has a similar genetic sequence to SbMATE and encodes a similar protein membrane transporter that releases citric acid from the roots. Just as in sorghum, citric acid binds to aluminium in the soil, making it difficult for it to enter plant roots. The team have also discovered related gene ZmMATE2, which also encodes a transporter protein, but appears to confer aluminium tolerance via a different mechanism, as yet unclear.

Claudia has developed a number of molecular markers for ZmMATE, which have been successfully used by breeders at EMBRAPA as well as by African partners in Niger and Kenya, such as Samuel Gudu, to identify maize breeding lines that have the gene.

“We used aluminium-tolerant maize varieties sourced locally and from Brazil to develop a range of potential new varieties,” says Samuel. “The goal is to develop varieties that are suited to our environment and not too dissimilar to varieties that Kenyan farmers like to grow, except they have a higher tolerance to aluminium toxicity.”

Left to right (foreground): Leon Kochian, Jurandir Magalhães and Samuel Gudu examine crosses between Kenyan and Brazilian maize, at the Kenya Agricultural Research Institute (KARI), Kitale, in May 2010.

Left to right (foreground): Leon Kochian, Jurandir Magalhães and Samuel Gudu examine crosses between Kenyan and Brazilian maize, at the Kenya Agricultural Research Institute (KARI), Kitale, in May 2010.

Involving farmers in the crop breeding process is an important part of such programs being successful, explains Samuel. “They help us identify maize varieties that they have observed have higher tolerance to acidic soils. We also try to incorporate other features that they want, such as disease resistance and higher yield. By incorporating their feedback into the breeding process they are more likely to grow any new varieties, as they have played a part in their development.”

Samuel says they have developed some local aluminium-tolerant varieties, which rank among the best for aluminium tolerance. Interestingly, these varieties seem to have a different aluminium-tolerance mechanism to the Brazilian varieties.

“From the work Samuel has done, we’ve possibly identified a novel source of aluminium tolerance in Kenyan maize varieties,” says Claudia. “We are now working together with Leon to identify the genes that are conferring this tolerance so we can develop markers to help Kenyan maize breeders also identify these varieties more efficiently.”

To help in the process, Samuel and his team are developing single-cross hybrids with a combination of both the novel Kenyan sources of aluminium tolerance and ZmMATE from Brazil, which will be even more tolerant to acidic soils.

Breeding for multiple stresses is a step-by-step process

Suradiyo, a farmer from Bojong Village near Yogyakarta, Indonesia, harvests rice.

Suradiyo, a farmer from Bojong Village near Yogyakarta, Indonesia, harvests rice.

In Asia, about 60 percent of rainfed rice is grown on soils that are affected by multiple stresses. These typically include phosphorus deficiency as well as aluminium toxicity, salinity and drought.

These stresses are particularly hard felt in Indonesia, which is the world’s third-largest rice producer. Joko Prasetiyono is a molecular rice breeder at the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD). His team have been collaborating with IRRI and JIRCAS for many years and contributed to validating the effect of Pup1 by embedding it into three popular local rice varieties – Dodokan, Situ Bagendit and Batur – which were then able to tolerate phosphorus-deficient conditions.

“The aim [with GCP research] was to breed varieties identical to those that farmers already know and trust, except that they have PSTOL1 and an improved ability to take up soil phosphorus,” says Joko.

Joko says that these varieties – which will be available in one to two years – will yield as well as, if not better than, traditional varieties, and will need 30–50 percent less fertiliser.

But the work is only partly finished for Joko and his Asian partners. They are now building on previous work done at Cornell and EMBRAPA to include the SbMATE gene in their varieties. “Higher yields will only be possible if the plant can also tolerate excess aluminium, which severely inhibits root growth and thereby water and nutrient uptake,” explains Joko. “We are also looking at incorporating salt-tolerance and drought-tolerance genes. It’s a step-by-step process where we hope to build tolerance to the multiple stresses that afflict most rice-growing areas throughout Asia and the world.”

Introducing PSTOL1 into maize and sorghum

At EMBRAPA, Claudia is also interested in building up tolerance to multiple stresses and was involved in the project to look for genes similar to PSTOL1 in maize. “As soon as IRRI and JIRCAS had cloned the gene and created markers, we started using the markers to search for the gene in maize, as Jurandir did in sorghum,” she says.

Women farmers in India bring home their sorghum harvest.

Women farmers in India bring home their sorghum harvest.

Finding genes that confer phosphorus-efficiency traits in maize and sorghum has been a more challenging project, according to Leon. “From the rice work, we knew a big part of phosphorus efficiency was to do with root architecture – you want to have shallow horizontal roots instead of roots that grow down, which is often the case in maize and sorghum,” he explains. “This is because there is less accessible phosphorus further down the soil profile.”

Observing root architecture is difficult in ordinary soil, so the team had to develop new ways to visualise the plants’ roots. They grew plants in a transparent nutrient gel, which they then photographed to create three-dimensional images of the root structure.

The team found sorghum and maize varieties that contained genes similar to PSTOL1 in rice, but which also have longer root systems that radiated outwards rather than downwards in gels with higher concentration of aluminium. “These observations helped validate multiple PSTOL1 regions in sorghum and maize, which we’ve been able to develop markers for to help breeders identify these traits more easily,” says Leon.

These markers have successfully been used by sorghum breeders in Brazil and Africa to identify phosphorus-efficient varieties. Maize breeders in both Brazil and Africa are expected to use similar markers to validate their varieties in 2015.

New sorghum varieties prove their worth in the field

Eva Weltzien is one Africa-based sorghum breeder who has benefited from these PSTOL1 and SbMATE markers. Based in Mali at ICRISAT, Eva and her team have been using the markers 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.

She says the markers have helped evolve the way they do their breeding. “Using molecular markers, we are able to identify whether the lines we are breeding have genes that confer the traits that we want,” explains Eva. “It has really revolutionised our breeding program and helped it make great progress in the past three to four years.”

In Mali, sorghum is an important staple crop. It is used to make (a thick porridge), couscous, and local beers. Part of its popularity is its adaptability to various climates – in Mali it is grown in very dry environments as well as in forest/rainforest zones. However, it is widely affected by acidic soils.

Sorghum farmers at work in the field in Mali.

Sorghum farmers at work in the field in Mali.

“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 next year.

“Overall, we feel the GCP partnership with EMBRAPA and Cornell is 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.”

Leon notes that the work by Eva in Mali and by other African partners in Niger and Kenya is imperative for the research. “Just because plants have these genes, doesn’t mean they will all display aluminium tolerance or phosphorus efficiency. You still need to test and observe for these traits in the field and determine what other factors might affect plants grown in acidic soils.”

One surprising observation that has Leon intrigued is a local sorghum variety with a phosphorus-efficiency gene that is close to where the SbMATE gene resides in the sorghum genome. “This suggests that SbMATE, which aids with aluminium tolerance, may also improve phosphorus efficiency. This means we could use SbMATE markers to look for both phosphorus efficiency and aluminium tolerance,” he says. Leon and Jurandir will continue to validate this result post-GCP.

Working together to improve food security worldwide

GCP’s comparative genomics projects have laid a significant foundation for further research into and breeding for tolerance to multiple plant stresses.

A Kenyan farmer in her maize field.

A Kenyan farmer in her maize field.

“We’re in a golden age of biology where we are learning more and more about the complexities and commonalities of plants, which is allowing us to manipulate them ever so slightly to help them tolerate multiple environmental stresses,” says Leon. “As a geneticist, I am extremely proud to be part of this, particularly seeing the potential impact that the basic research we do in the laboratory can have on crop improvement and the lives of people in poorer countries.”

Although not all projects produced new and improved varieties ready for release, they are well and truly in the pipeline. Each partner institute is committed to work together and source new funding to continue on their quest to produce further products.

“GCP has really installed in us a spirit to see this work through and expand on it,” says Leon. “I mean, we are now working with other countries and institutes to share what we have learnt with them and help them make the discoveries that we have. It’s a credit to GCP for bringing us all together; that was a key to the success of the project. Each partner has brought their expertise to the table – genomics, molecular biology, plant breeding – and it has been great to see the impact filter into Africa and Asia.”

In Kenya, Samuel agrees with Leon’s assessment. “GCP gave us an opportunity to build our expertise and start interacting with the rest of the world,” he says. “But more importantly, it means that we’re contributing to food security in Kenya, and that makes us really proud.”

Although the sun is setting on GCP, work on comparative genomics projects is still in progress, with all parties still working towards delivering important new acid-beating varieties to farmers.

A boy rides his bicycle next to a rice field in the Philippines. With acid soils affecting half the world’s current arable land, acid-beating crop varieties will help farmers feed their families – and the world – into the future.

A boy rides his bicycle next to a rice field in the Philippines. With acid soils affecting half the world’s current arable land, acid-beating crop varieties will help farmers feed their families – and the world – into the future.

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