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Oct 262015


Photo: HK Tang/Flickr (Creative Commons)

An Indian patchwork of rice and maize fields.

“Once you’ve cloned a major gene in one crop, it is possible to find a counterpart gene that has the same function in another crop, and this is easier than finding useful genes from scratch” explains Leon Kochian, Professor in Plant Biology and Crop and Soil Sciences at Cornell University, USA, and Director of the Robert W Holley Center for Agriculture and Health, United States Department of Agriculture – Agricultural Research Service.

Leon was the Product Delivery Coordinator for the Comparative Genomics Research Initiative of the CGIAR Generation Challenge Programme (GCP). The Programme set out in 2004 to advance plant genetics in a bid to provide sustainable food-security solutions.

Between 2004 and 2014, GCP invested in projects to clone two genes and deploy them in elite local varieties. The first gene, SbMATE, encodes aluminium tolerance traits in sorghum; the work was a collaborative effort led by the Brazilian Corporation of Agricultural Research (EMBRAPA) and Cornell University, and gave rise to locally-adapted sorghum varieties released in South America and Africa. The second gene, PSTOL1, produces traits that improve phosphorus uptake in rice. This research was a collaboration between the Japan International Research Center for Agricultural Sciences (JIRCAS) and the International Rice Research Institute (IRRI). PSTOL1 has now been extensively deployed in Asian rice varieties.

Aluminium toxicity and low phosphorus levels in acid soils are major factors that hinder cereal productivity worldwide, particularly in sub-Saharan Africa, South America and Southeast Asia. Globally, acid soils are outranked only by drought when it comes to stresses that threaten food security.

Tolerance to high levels of aluminium and low phosphorus is conferred by major genes, which lend themselves to cloning. Major genes are genes that by themselves have a significant and evident effect in producing a particular trait; it’s therefore easier to find and deploy a major gene associated with a desired trait than having to find and clone several minor genes.

Photo: S Kilungu/CCAFS

Harvesting sorghum in Kenya.

Cloning major genes instrumental in hunt for resilient varieties

Locating a single gene within a plant’s DNA is like looking for a needle in a haystack. Instead of searching for a gene at random, geneticists need a plan for finding it.

The first step is to conduct prolonged phenotyping – that is, measuring and recording of plants’ observable characteristics in the field. By coupling and comparing this knowledge with genetic sequencing data, scientists can identify and locate quantitative trait loci (QTLs) – discrete genetic regions that contain genes associated with a desired trait, in this instance tolerance to aluminium or improved phosphorus uptake. They then dissect the QTL to single out the gene responsible for the desired trait. In the case of sorghum, researchers had identified the aluminium tolerance locus AltSB, and were looking for the gene responsible.

Once the gene has been identified, the next step is to clone it – that is, make copies of the stretch of DNA that makes up the gene. Geneticists need millions of copies of the same gene for their research: to gain information about the nucleotide sequence of the gene, create molecular markers to help identify the presence of the gene in plants and help compare versions of the gene from different species, and understand the mechanisms it controls and ways it interacts with other genes.


Drying the sorghum harvest in India.

Sorghum was one of the simpler crops to work with, according to Claudia Guimarães.

“Sorghum has a smaller genome… with clear observable traits, which are often controlled by one major gene,” she says.

The first breakthrough was the identification and cloning of SbMATE, the aluminium tolerance gene in sorghum behind the AltSB locus. The next was finding a diagnostic marker for the gene so that it could be used in breeding.

Marking genes to quickly scan plants for desired traits

Photo: IRRI

Harvesting rice in The Philippines.

Once a desired gene is identified, a specific molecular marker must be found for it. This is a variation in the plant’s DNA, associated with a gene of interest, that scientists can use to flag up the gene’s presence. We can compare this process to using a text highlighter in a book, where the words represent the genes making up a genome. Each marker is like a coloured highlighter, marking sentences (genomic regions) containing particular keywords (genes) and making them easier to find.

In molecular breeding, scientists can use markers to quickly scan hundreds or thousands of DNA samples of breeding materials for a gene, or genes, that they want to incorporate into new plant varieties. This enables them to select parents for crosses more efficiently, and easily see which of the next generation have inherited the gene. This marker-assisted breeding method can save significant time and money in getting new varieties out into farmers’ fields.

Leon, who was also the Principal Investigator for various GCP-funded research projects, says that the cloning of SbMATE helped advance sorghum as a model for the further exploration of aluminium tolerance and the discovery of new molecular solutions for improving crop yields.

“This research also has environmental implications for badly needed increases in food production on marginal soils in developing countries,” says Leon. “For example, if we can increase food production on existing lands, it could limit agriculture’s encroachment into other areas.”

Photo: IRRI

Rice field trials in Tanzania.

Aluminium toxicity is the result of aluminum becoming more available to plants when the soil pH is lower, and affects 38 percent of farmland in Southeast Asia, 31 percent in South America and 20 percent in East Asia, sub-Saharan Africa and North America. Meanwhile phosphorus, the second most important inorganic plant nutrient after nitrogen, becomes less available to plants in acid soils because it binds with aluminium and iron oxides. Almost half of the ricelands across the globe are currently phosphorus deficient. The research therefore has the potential for significant impact across the world.

The GCP-funded scientists used markers to search rice and maize for genes equivalent to sorghum’s SbMATE. In maize they successfully identified a similar gene, ZmMATE1, which is now being validated in Brazil, Kenya and Mali. In rice the search continues, but will become easier now that markers for ZmMATE1 have been developed.

Similarly, having validated, cloned and developed markers for PSTOL1 gene in rice, researchers at IRRI and JIRCAS then worked with researchers at EMBRAPA and Cornell University to use PSTOL1 markers to search for comparable genes in sorghum and maize. In both crops, genes similar to PSTOL1 have been identified and shown to improve grain yields under low-phosphorus soil conditions, albeit through different mechanisms.

The GCP-funded discoveries are already being used in marker-assisted selection in national breeding programmes in Brazil, Kenya, Niger, Indonesia, Japan, The Philippines and USA in sorghum, maize and rice. They have led to the release of new, aluminium-tolerant sorghum varieties in Brazil, with more currently being developed, along with phosphorus-efficient rice varieties.

Photo: S Kilungu/CCAFS

Showing off freshly harvested sorghum in Kenya.

Cloning a worthwhile investment

Gene cloning was a relatively small cost in GCP’s research budget – about five percent (approximately USD 7 million) of a total research budget of USD 150 million spread over 10 years.

The gene-cloning component nonetheless yielded important genes for aluminium tolerance and phosphorus-uptake efficiency, within and across genomes. The molecular markers that have been developed are helping plant breeders across the world produce improved crop varieties.

Jean-Marcel Ribaut, Director of GCP, concludes: “The new markers developed for major genes in rice, sorghum and maize will have a significant impact on plant-breeding efficiency in developing countries.

“Breeders will be able to identify aluminium-tolerance and phosphorus-efficiency traits quicker, which, in time, will enable them to develop new varieties that will survive and thrive in the acid soils that make up more than half of the world’s arable soils.”

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Photo: CSISA

A rice farmer in Bihar, India.

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.”


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.

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Photo: N Palmer/CIAT

A farmer displays maize harvested on his farm in Laos.

Oct 072015

Young Nigerian scientists often leave Africa and look for jobs with international research agencies overseas. But with the CGIAR Generation Challenge Programme (GCP)-funded Cassava Research Initiative (RI), two young nationals have been leading the international collaboration and injecting confidence into Africa’s research capacity.

Leadership is a quality admired and consistently sought after, particularly when overcoming a challenge. Some leaders direct from afar; others rise through the ranks and work with their peers on the ground – winning respect from the people they lead as they get their hands dirty.

Photo: G Norton

Dream team: Emmanuel Okogbenin (left) and Chiedozie Egesi (right), both of Nigeria’s National Root Crops Research Institute.

“If you want to work for the people, you have to walk with the people – that’s an African concept,” says Emmanuel Okogbenin, a plant breeder and geneticist at Nigeria’s National Root Crops Research Institute (NRCRI). “Then when you work with the people, you really understand what they want. When you speak, they know they can trust you.”

This powerful sentiment is one reason why GCP sought the collaboration of NRCRI in overcoming the challenge of sustaining Africa’s, and indeed the world’s, cassava production.

Having started as a small farm in 1923, NRCRI has taken giant strides to become one of Nigeria’s best research institutes, contributing immensely to the country’s economic development and making it the leading producer of cassava in the world. NRCRI Executive Director Julius Chukwuma Okonkwo says, “This would not have been attainable if not for the trust and support that GCP had in us when they made two of our young cassava researchers the leaders of an international collaboration.”

The two researchers to whom Julius refers are Emmanuel and his colleague Chiedozie Egesi, also a plant breeder and geneticist at NRCRI. Their combined 36 years’ of cassava research experience is matched by their passion to get the best out of Nigeria’s main staple crop.

And they are happy to get some dirt under their fingernails. “It’s just as important to work with the farmers in the field and understand what they want, as it is to do the research in the lab,” says Emmanuel. “At the end of the day we need to please the farmers, as they are the ones who will be using the new varieties that we are developing to sustain their livelihoods.”

Photo: IITA

Nigerian farmers display their cassava harvest.

Developing and leading Africa’s cassava research

Between 2010 and 2014, both Emmanuel and Chiedozie led three different projects within GCP’s Cassava RI, working with other colleagues in national breeding programmes in Ghana, Tanzania and Uganda, as well as the International Institute of Tropical Agriculture (IITA), the International Center for Tropical Agriculture (CIAT), the Brazilian Corporation of Agricultural Research (EMBRAPA) and Cornell University in the USA. The aim of the initiative was to use molecular-breeding techniques to accelerate the development of high-starch cassava varieties with resistance to diseases and tolerance to drought – and so ensure both food supplies and income for farmers.

Meet Chiedozie and Emmanuel in the video playlist below, learn more about cassava in Africa, and hear all about their research (or watch on Youtube):

Emmanuel explains that before GCP, “most African national programmes didn’t really have established crop-breeding programmes, and didn’t have the resources” to do the scale of research GCP assisted with. Nor did they have the capacity to use molecular-breeding techniques, which can potentially halve the time it takes to develop new varieties.

With help from GCP and CIAT, NRCRI was able to equip a new molecular-breeding laboratory, and staff were trained to incorporate molecular-breeding techniques into their breeding programme. “GCP was there not only to provide technology, but also to guide us in how to operate that technology,” explains Chiedozie.

Julius points out that both Chiedozie and Emmanuel were also influential in disseminating this knowledge and, in turn, building and sustaining NRCRI’s human capacity. “They both mentored many young scientists who have chosen a career in cassava and molecular breeding because of this.”

Photo: IITA

Transporting a bountiful cassava harvest from farm to market in Nigeria.

With training and infrastructure in place, NRCRI led an international collaboration that in 2010 released Africa’s first cassava variety developed using molecular-breeding techniques. Known as UMUCASS33 (or CR 41-10), it was resistant to cassava mosaic disease (CMD) – a devastating plant disease that can wipe out farmers’ entire cassava crops – and also highly nutritious. This was swiftly followed by a second similar variety, CR 36-5, and supplied to farmers.

Between this landmark release and GCP’s close in 2014, the cassava team had already released nearly 20 higher yielding, more nutritious varieties resistant to diseases and pests, and had begun working on developing drought-tolerant varieties.

These new and improved varieties – all generated as a direct or indirect result of his engagement in GCP projects – are, Chiedozie says, worth their weight in gold: “Through these materials, people’s livelihoods can be improved. The food people grow should be nutritious, resistant and high-yielding enough to allow them to sell some of it and make money for other things in life, such as building a house, getting a motorbike or sending their kids to school.” This social aspect is particularly pertinent in Nigeria, where these cassava varieties will have the greatest impact.

Five years, 20 new varieties for African farmers Between 2010 and 2014, NRCRI and its collaborators developed and released multiple new cassava varieties with a combination of traits. This work has continued after the closure of GCP, with more releases in the pipeline. Disease and pest resistance During 2010-2014 the team released several varieties of cassava resistant to cassava mosaic disease (CMD) for different environments in Nigeria, Ghana, Uganda and Tanzania as well as several varieties resistant to cassava brown streak disease (CBSD) – a similarly devastating disease originating in Tanzania but quickly spreading into Uganda and further west. They have also developed new varieties with combined resistance to CMD and CBSD. These have the potential to double the yield of existing commercial varieties. The team has also worked with Tanzanian breeders to develop cassava varieties that are resistant to bacterial blight and green mites. These new Tanzanian varieties are on their way to commercial breeders and will be available to farmers by 2015–16. High starch content In 2012 the team released a variety with very high starch content – an essential element of good cassava.  Improved nutrition In 2011, the NRCRI team, together with IITA and HarvestPlus (another CGIAR Challenge Programme focussed on the nutritional enrichment of crops), released three cassava varieties rich in pro-vitamin A, which hold the potential to provide children under five and women of reproductive age with up to 25 percent of their daily vitamin A requirement. Since then, the team has aimed to increase this figure to 50 percent. In 2014, they released three more pro-vitamin A varieties with higher concentrations of beta-carotene.

Feeding a giant

Photo: IITA

Nigerian farmer with his bountiful cassava harvest.

Nigeria is often referred to as the ‘Giant of Africa’. It is the most populous African country, with over 174 million inhabitants. The population’s main staple food is cassava, making Nigeria the world’s largest producer and consumer of the crop. At the same time, the country imports almost USD 4 billion of wheat every year – a figure that is expected to quadruple by 2030 if wheat consumption continues to grow at the same rate it is today.

The government is wary of this ‘overreliance’ on imported grain and is working towards making the country less reliant on wheat by imposing a wheat tariff. It also hopes to boost cassava production and commercialisation by promoting 20 percent substitution of cassava flour for wheat in breadmaking.

“The government feels that to quickly change the fortunes of farmers, cassava is the way to go,” explains Emmanuel, who liaises with the Nigerian Government to promote to farmers the benefit of cassava varieties with high starch concentrations. It is the flour from these varieties that is being used to partially replace wheat flour to make bread. GCP support has been crucial here too, in providing vital scientific information to the government. Emmanuel explains: “The tariff from wheat is expected to be ploughed back to support agricultural development – especially in the cassava sector – as the government seeks to increase cassava production to support flour mills.”

Cassava offers a huge opportunity to transform the agricultural economy, stimulate rural development and further improve Nigeria’s gross domestic product. In 2014, Nigeria’s economy surpassed that of South Africa’s to become the largest on the continent. By 2050, Nigeria is expected to rise further and become one of the world’s top 20 economies.

Unfortunately, however, like many growing economies worldwide, Nigeria is still working to address severe inequality, including in the distribution of wealth and in feeding the country’s expanding population.

Photo: IITA

A woman with her children at work in a cassava processing centre in Nigeria.

It’s a problem Chiedozie understands well: “Nigeria is an oil-producing country, but you still see grinding poverty in some cases,” he says. “Coming from a small town in the southeast of the country, I grew up in an environment where you see people who are struggling, weak from disease, poor, and with no opportunities to send their children to school,” he reveals. The poverty challenge, he explains, hits smallholder farmers particularly hard: “Urban development caught up with them in the end: some of them don’t even have access to the land that they inherited, so they’re forced to farm along the street.”

For Chiedozie, the seemingly bleak picture only served to ignite a fierce determination and motivation to act: “Despite the social injustice around me, I always thought there was opportunity to improve people’s lives.” And thus galvanised by the plight of Nigerian farmers, Chiedozie promptly shelved his plans for a career in medical surgery and pursued biological sciences and a PhD in crop genetics, a course he interspersed with training stints in the USA at Cornell University and the University of Washington, before returning to his homeland to accept a job as head of the cassava breeding team, and – following a promotion in 2010 – to become Assistant Director of the Biotechnology Department at NRCRI.

Empowering African researchers

Photo: IITA

Carrying cassava at a processing centre in Nigeria.

Emmanuel, who followed a similar educational route to Chiedozie, says both he and his colleague are exceptions to the norm in Africa, where African researchers tend to look for opportunities at international or private institutes rather than in national breeding programmes.

“It is difficult being a researcher in Africa,” says Emmanuel. “We don’t get paid as much as breeders in more developed countries, and funding is very hard to obtain.”

Emmanuel says his proudest moment was when GCP was looking for Africans to take up leadership roles. “They felt we could change things around and set a precedent to bring people back to the continent,” he says. “They appreciated our values and the need to install African leaders on the ground in Africa rather than in Europe, Asia or the Americas.”

Jean-Marcel Ribaut, GCP’s Director, says that seeking this local leadership was a novel approach for a transnational programme like GCP at the time, and proved to be an imperative feature for all GCP Research Initiatives. “The reasoning behind the approach is two-fold: Firstly, it’s important that our national partners share in feeling ownership of the projects and outcomes; secondly, they are gaining experience in the role so they can continue to do so after the close of the Programme in 2014,” he says. “We feel that most of our leading institutes, NRCRI included, are in a better position now than when they joined the project, and that this, along with their experience, has already gained them more exposure and funding opportunities.”

This is indeed true of the NRCRI cassava team, which is engaging with the Bill & Melinda Gates Foundation, Cornell University, IITA and Uganda’s National Crop Resources Research Institute in an initiative that Chiedozie promises will be at the front of cutting-edge technology. “We are still working out specifics, but it will see us continuing to use marker-assisted breeding techniques to develop higher yielding, stress-tolerant cassava varieties.”

Chiedozie adds this would not have been possible without GCP, which helped them to develop their capacity in Nigeria and in Africa, and this has “created a confidence in other global actors, who, on seeing our ability to deliver results, are choosing to invest in us.”

Photo: IITA

Before GCP came along, cassava was something of an orphan crop in agricultural research. Among the challenges to efficient breeding of cassava are that it is slow to grow and is propagated, not by seed, but using cut sections of stem like those shown. But with investment and capacity building from GCP, particularly in molecular breeding tools, African cassava scientists have gained a new confidence and prestige.

Continuing the momentum

One organisation that has been impressed by the work done at NRCRI is the CGIAR Research Program on Roots, Tubers and Bananas (RTB). RTB Director Graham Thiele has been following the work done at NRCRI since 2010 with great interest. “We have been really impressed to see a national programme like NRCRI playing a leading role in these successful GCP projects, and grow as a result of this,” he says.

One area of research that has particularly impressed Graham is Chiedozie and Emmanuel’s pre-emptive breeding for cassava brown streak disease (CBSD) resistance. “CBSD isn’t currently an issue in Nigeria but it has the potential to wipe out all crops, as it has in Uganda and Tanzania, if it continues to spread west from these countries,” he explains.

“What Chiedozie and Emmanuel are doing is using molecular markers, developed in collaboration with IITA, to search for genes in their varieties that confer resistance to brown streak virus. They can then use these when breeding for CBSD resistance without exposing cassava to the virus. It’s very exciting and forward thinking, as normally people breed for resistance only when the disasters happen.”

As GCP approached its sunset in December 2014, Chiedozie and Emmanuel were reaching out to RTB to seek funding to continue this and other projects they are currently working on. “They’ve already created some great varieties but have plenty more in the pipeline, so we want to help them finish this work and, most importantly, keep the momentum going,” says Graham.

Chiedozie looks forward to the next steps with optimism, confirming that the new collaboration will continue in the quest to “give African farmers varieties of cassava that they will love to grow.”

More links

Photo: IITA

Healthy improved cassava varieties growing in the field.


Oct 052015

Cassava brings life to African people

Photo: N Palmer/CIATBeyond the glittering coastline of what was once known as the Gold Coast, Ghana’s shrublands and rich forested hills are split by forking rivers that reach inland through the country’s lush tropics, into drier western Africa. In the past 40 years, seven major droughts have battered the people of Africa – with the most significant and devastating occurring in the Sahel region and the Horn of Africa in the early 1970s and 1980s.

Photo: Y Wachira/Bioversity International

This little girl in Kenya already seems to know that cassava roots are precious.

But despite the massive social disruption and human suffering that these droughts cause, life goes on. In south-eastern Ghana and in Togo, the three-million-plus people who speak the Ewe language have a word for this. It is agbeli: ‘There is life’. It is no coincidence that this word is also their name for a tropical and subtropical crop that survives through the worst times to feed Africa’s families: cassava.

Cassava is a lifeline for African people, and is a particularly important staple food for poorer farmers. More cassava is produced in Africa than any other crop, and it is grown by nearly every farming family in sub-Saharan Africa, supplying about a third of the region’s daily energy intake. In the centuries since Portuguese traders introduced this Amazonian plant to Africa, cassava has flourished, yielding up to 40 tonnes per hectare.

Hear more on just why cassava is so important to food security from Emmanuel Okogbenin, of Nigeria’s National Root Crops Research Institute, in the video below (or watch on Youtube):


African countries produced nearly 140 million tonnes of cassava in 2012 – but most of the production is subsistence farming by small-scale farmers. Even the undisputed global cassava giant, Nigeria, currently produces only just enough to feed its population – and although the country is increasingly moving towards production of cassava for export as an industrial raw material, the poorest farmers often do not produce enough to sell, or have access to these markets.

Because cassava does so well on poor soils, on marginal land and with little rainfall, it can outlast its more sophisticated crop competitors: wheat, rice and maize. In fact, under harsh conditions such as drought, the amount of energy a given area of cassava plants can produce in the form of starchy carbohydrates outstrips all other crops. Chiedozie Egesi, a plant breeder and geneticist at Nigeria’s National Root Crops Research Institute (NRCRI), describes cassava as “the crop you can bet on when every other thing is failing”.

Benefits of cassava to African farmers and families Most cassava grown is consumed as food – for instance, as starchy, fine powder called tapioca or the fermented, flaky garri. The tubers can also be eaten boiled or fried in chunks, and are used in many other local dishes.  If cassava is grown in favourable conditions, its firm, white flesh can be rich in calcium and vitamin C and contain other vitamins such as B1, B2 and niacin. Some improved varieties are fortified with increased vitamin A levels, giving them a golden hue.   As well as being eaten directly, cassava can also be processed into ingredients for animal feed, alcohol production, confectionery, sweeteners, glues, plywood, textiles, paper and drugs.  Cassava tubers are easy to save for a rainy day – unlike other crops, they can be left in the ground for up to two years, so harvesting can be delayed until extra food is needed, or to await more optimal processing or marketing conditions.

Despite cassava’s superhero cape, however, there’s no denying that its production is not at its highest when faced with diseases, pests, low-nutrient soils and drought. How plants deal with problems like low nutrients or dry conditions is called ‘stress tolerance’ by scientists. Improving this tolerance – plus resistance to diseases and pests – is the long-term goal for staple crops around the world so that they have higher yields in the face of capricious weather and evolving threats.

In the 1980s, catastrophe struck cassava production in East and Central Africa. A serious outbreak of cassava mosaic disease (CMD) – which first slowly shrivels and yellows cassava leaves, then its roots – lasted for almost 15 years and nearly halved cassava yields in that time. Food shortages led to localised famines in 1993 and 1997.

Other diseases affecting cassava include cassava brown streak disease (CBSD), cassava bacterial blight, cassava anthracnose disease and root rot. CBSD is impossible to detect above ground. Its damage is revealed only after harvest, when it can be seen that the creeping brown lesions have spoilt the white flesh of the tubers, rendering them inedible. Many cassava diseases are transmitted through infected cuttings, affecting the next generation in the next season. Pests that also prey on cassava include the cassava green mite and the variegated grasshopper.

Between the effects of drought, diseases, pests and low soil nutrients, cassava yields vary widely – losses can total between 50 and 100 percent in the worst times.

Photo: IITA

Symptoms of cassava mosaic disease (CMD) and cassava brown streak disease (CBSD), both of which can cripple cassava yields.

GCP takes the first steps to kick start cassava research

The next step forward for cassava appeared to be research towards breeding stronger and more resilient cassava varieties. However, cassava research had long been neglected – scientists say it’s a tricky crop that has garnered far less policy, scientific and monetary interest than the comparatively glamorous crops of maize, rice and wheat.

Watch as Emmanuel tells us more about the complexities and challenges of cassava breeding in the video below (or on YouTube):


Cassava is a plant which ‘drags its feet’: creating new plants has to be done from cuttings, which are costly to cut and handle and don’t store well; the plant takes up to two years to grow to maturity; and it is onerous to harvest. Elizabeth Parkes, of Ghana’s Crops Research Institute (CRI) (currently on secondment at the International Institute of Tropical Agriculture, IITA), says the long wait can be difficult.

This is where the work of scientists funded by the CGIAR Generation Challenge Programme (GCP) came in. Plant breeder and molecular geneticist Emmanuel Okogbenin of NRCRI led the cassava research push launched in 2010. He explains that before GCP, “most national programmes didn’t really have established crop breeding programmes, and didn’t have the manpower” to do the scale of research GCP supported.

Usually, researchers looking to breed crops that are more resistant to drought, diseases and pests would use conventional breeding methods that could take considerable time to deliver any results, especially given cassava’s slow path to maturity. Researchers would be trying to select disease- and pest-resistant plants by looking at how they’re growing in the field, without any way to see the different genetic strengths each plant has.

Photo: M Mitchell/IFPRI

An IITA researcher exams cassava roots in the field.

This is where new ‘molecular breeding’ tools are particularly useful, given that – genetically – cassava presents more of a challenge to breeders than its cereal counterparts. Like many other vegetatively propagated crops, cassava is highly heterozygous, meaning that the counterpart genes on paired chromosomes tend to be different versions, or alleles, rather than the same. This makes it difficult to identify good parent plants for breeding and, after these are crossed, to accurately select progeny with desired traits. Useful – or detrimental – genes can be present in a cassava plant’s genetic code but not reflected in the plant itself, making breeding more unpredictable – and adding extra obstacles to the hunt for the exact genes that code for better varieties of cassava.

Although late to the world of molecular breeding, cassava had not missed its chance. Guided by GCP’s ambitious remit to increase food security through modern crop breeding, GCP-supported scientists have applied and developed molecular breeding methods that shorten the breeding process by identifying which plants have good genes, even before starting on that long cassava growth cycle. Increasing the capacity of local plant breeders to apply these methods has great potential for delivering better varieties to farmers much faster than has traditionally been the case.

Charting cassava’s genetic material was the first step in the researchers’ molecular quest. Part of the challenge for African and South American researchers was to create a genetic map of the cassava genome. Emmanuel describes the strong foundation that these early researchers built for those coming after: “It was significant when the first draft of the cassava genome sequence was released. It enabled rapid progress in cassava research activities and outcomes, both for GCP and cassava researchers worldwide.”

Photo: N Palmer/CIAT

Cassava on sale in Kampala, Uganda.

Once cassava’s genome had been mapped, the pace picked up. In just one year, GCP-supported scientists phenotyped and genotyped more than 1000 genetically different cassava plants – that is, measured and collected a large amount of information about both their physical and their genetic traits – searching for ‘superstar’ plants with resistance to more than one crop threat. During this process, scientists compare plant’s physical characteristics with their genetic makeup, looking for correlations that reveal regions of the DNA that seem to contain genes that confer traits they are looking for, such as resistance to a particular disease. Within these, scientists then identify sequences of DNA, or ‘molecular markers’, associated with these valuable genes or genetic regions.

Plant breeders can use this knowledge to apply an approach known as marker-assisted selection, choosing their breeding crosses based directly on which plants contain useful genes, using markers like tags. This makes producing better plant varieties dramatically faster and more efficient. “It narrowed the search at an early stage,” explains Emmanuel, “so we could select only material that displayed markers for the genetic traits we’re looking for. There is no longer any need to ship in tonnes of plant material to Africa.”

Like breadcrumbs leading to a clue, breeders use markers to lead to identifying actual genes (rather than just a site on the genome) that give certain plants desirable characteristics. However, this is a particularly difficult process in cassava. Genes are often obscured, partly due to cassava’s highly heterozygous nature. In trials in Africa, where CMD is widespread, resistant types were hard to spot when challenged with the disease, and reliably resistant parents were hard to pin down.

This meant that two decades of screening cassava varieties from South America – where CMD does not yet exist yet – had identified no CMD-resistance genes. But screening of cassava from Nigeria eventually yielded markers for a CMD-resistance gene – a great success for the international collaborative team led by Martin Fregene, who was based in Colombia at the International Center for Tropical Agriculture (CIAT).

This finding was a win for African plant breeders, as it meant they could use molecular breeding to combine the genes producing high-quality and high-yielding cassava from South America with the CMD-resistance gene found in cassava growing in Nigeria.

Chiedozie Egesi, who led the work on biotic trait markers, explains the importance of combining varieties from South America with varieties from Africa: “Because cassava is not native to Africa, those varieties are not as genetically diverse, so we needed to bring genetic diversity from the centre of origin: South America. Coupling resistance genes from African varieties with genes for very high yields from South America was critical.”

Cassava research leaps forward with new varieties to benefit farmers

GCP’s first investment phase into cassava research stimulated a sturdy injection of people, passion, knowledge and funds into the second phase of research. From the genome maps created during the first phase, some of the world’s best geneticists would now apply genomic tools and molecular breeding approaches to increase and accelerate the genetic gains during breeding, combining farmers’ favourite characteristics with strong resistances and tolerances to abiotic and biotic constraints.

In the sprawling, tropical city of Accra on Ghana’s coast, the second phase of the research was officially launched at the end of the wet season in mid-2010. NRCRI’s Emmanuel Okogbenin coordinated product delivery from the projects, but the roles of Principal Investigator for the different projects were shared between another four individuals.

These were breeder and geneticist Chiedozie Egesi (NRCRI, Nigeria), molecular geneticist Morag Ferguson (IITA), genomic scientist Pablo Rabinowicz (University of Maryland, USA) and physiologist and geneticist Alfredo Alves (Brazilian Corporation of Agricultural Research, EMBRAPA). The team shared the vision of enabling farmers to increase cassava production for cash, well beyond subsistence levels.

Photo: A Hoel/World Bank

Garri, or gari, a kind of granular cassava flour used to prepare a range of foods.

If the Accra launch set the stage for the next five years of cassava collaboration, a breakthrough in Nigeria at the end of 2010 set the pace, with the release of Africa’s first cassava variety developed using molecular-breeding techniques. “It was both disease-resistant and highly nutritious – a world-first,” recalls Emmanuel proudly.

Known as UMUCASS33 (or CR41-10), it took its high yield and nutritional value from its South American background, and incorporated Nigerian resistance to devastating CMD attacks thanks to marker-assisted selection. It was also resistant to several other pests and diseases. UMUCASS33 was swiftly followed by a stream of similar disease-busting varieties, released and supplied to farmers.

Never before had cassava research been granted such a boost of recognition, scientific might and organisational will. And never before had there been so much farmer consultation or so many on-farm trials.

“Cassava was an orphan crop and with the help of GCP it is becoming more prominent,” says Chiedozie. “GCP highlighted and enhanced cassava’s role as a major and reliable staple that is important to millions of poor Africans.”

Another important challenge for scientists was to develop a higher-yielding cassava for water-limited environments. The aim was to keep mapping genes for resistance to other diseases and pests and then combine them with favourable genetics that increase yield in drought conditions – no easy feat. Drought’s wicked effect on cassava is to limit the bulk of the tuber, or sometimes to stop the tuber forming altogether. Emmanuel led the work on marker-assisted recurrent selection for drought.

Hear from Chiedozie on the beneficial outcomes of GCP – in terms not only of variety releases but also of attracting further projects, prestige, and enthusiastic young breeders – in the video below (or on YouTube):

Many traits and many varieties

As closely as the cassava teams in Africa were working together, Chiedozie recalls that each country’s environment demanded different cassava characteristics: “We had to select for what worked best in each country, then continue with the research from there. What works fine for East Africa may not be so successful in Nigeria or Ghana”. A core reference set representing most of the diversity of cassava in Africa was improved with the addition of over 564 varieties. Improving the reference set, says project leader Morag Ferguson, “enables the capture of many diverse features of cassava” within a relatively small collection, providing a pathway for more efficient trait and gene discovery.

While mapping of cassava’s genetic makeup carried on, with a focus on drought tolerance, researchers continued to develop a suite of new varieties. They mapped out further genes that provided CMD resistance. In Tanzania, four new varieties were released that combined resistance to both CMD and CBSD – two for the coastal belt and two for the semi-arid areas of central Tanzania. These new varieties had the potential to double the yield of existing commercial varieties. In Ghana too, disease-resistant varieties were being developed.

Photo: IITA

Built-in disease resistance can make a huge difference to the health of cassava crops. This photo shows a cassava variety resistant to African cassava mosaic virus (ACMV), which causes cassava mosaic disease (CMD), growing on the left, alongside a susceptible variety on the right.

Meanwhile in Nigeria, another variety was released in 2012 with very high starch content – an essential factor in good cassava. This is a critical element to breeding any crop, explains Chiedozie: “A variety may be scientifically perfect, based on a researcher’s perspective, but farmers will not grow it if it fails the test in terms of taste, texture, colour or starchiness.”

Geoffrey Mkamilo, cassava research leader at Tanzania’s Agricultural Research Institute, Naliendele, says that farmer awareness and adoption go hand in hand. Once they had the awareness, he says, “the farmers were knocking on our doors for improved varieties. They and NGOs were knocking and calling.”

After groundwork in Ghana and Nigeria to find potential sources of resistance, cassava varieties that are resistant to bacterial blight and green mites were also developed in Tanzania and then tested. By the time GCP closed in December 2014, these varieties were on their way to commercial breeders for farmers to take up.

Scientists seeking to resolve the bigger challenge of drought resistance have achieved significant answers as well. Researchers have been able to map genetic regions that largely account for how well the crops deal with drought.

Developing new varieties takes people, and time The numbers of new cassava varieties so far released through GCP-supported research do not tell the full story.   They certainly do not illustrate the patience and skill required from many different people to get to that end-stage of having a new cassava variety. In the first step, after the plants that seem to have resistance to CMD are identified, those plants are cloned and grown.   The DNA of these plantlets is then exposed to markers specific to valuable resistance genes, or regions of the genome known as quantitative trait loci (QTLs), in order to confirm the presence of the gene or QTL in question. Confirmed plants can be used as parents in breeding crosses after growing out and flowering – although sometimes plants don’t flower, another hurdle for the cassava breeder.  This parental selection using genetic information is a powerful way to make cassava breeding more efficient. Breeders also use markers to identify which of the progeny from each cross have inherited the genes they are interested in. Over several generations of crosses, scientists can combine genes and QTLs for useful traits from different plant lines, to eventually develop a new variety for cultivation.  In cassava, this complex process can take seven years – although it takes even longer using only conventional breeding techniques. While fruition is slow, the research aided by GCP has sown the seeds for many more new varieties and bumper harvests for farmers into the future.

Hunt for ‘super powered’ cassava

The hunt was on for drought-tolerance genes in African cassava plants. The end goal was to find as many different drought-related genes as possible, then to put them all together with the applicable disease and pest resistance genes, to make a ‘super powered’ set of cassava lines. Molecular breeders call this process ‘pyramiding’, and in Ghana, Elizabeth Parkes led these projects.

With the help of Cornell University scientists, the researchers compared plants according to their starch content, how they endured a dry season, how they used sunlight and how they dealt with pests and diseases.

Fourteen gene regions or quantitative trait loci (QTLs) were identified for 10 favourable traits from the genetic material in Ghana, while nine were found for the plants in Nigeria – with two shared between the plants from both Ghana and Nigeria. After that success, the identified genes were used in breeding programmes to develop a new generation of cassava with improved productivity.

Pyramiding is important in effective disease resistance; Chiedozie explains in the video below (or on YouTube):

Photo: HarvestPlus

New cassava varieties rich in pro-vitamin A have a telltale golden hue.

The research has also delivered results in terms of Vitamin A levels in cassava. In 2011, the NRCRI team, together with IITA and HarvestPlus (another CGIAR Challenge Programme focussed on the nutritional enrichment of crops), released three cassava varieties rich in pro-vitamin A, which hold the potential to provide children under five and women of reproductive age with up to 25 percent of their daily vitamin A requirement. Since then, the team has aimed to increase this figure to 50 percent. In 2014, they released three more pro-vitamin A varieties with even higher concentrations of beta-carotene.

Photo: IITA

A field worker at IITA proudly displays a high-yielding, pro-vitamin A-rich cassava variety (right), compared with a traditional variety (left).

The new varieties developed with GCP support are worth their weight in gold, says Chiedozie: “Through these varieties, people’s livelihoods can be improved. The food people grow should be nutritious, resistant and high-yielding enough to allow them to sell some of it and make money for other things in life, such as building a house, getting a motorbike or sending their kids to school.”

Turning from Nigeria to Tanzania, Geoffrey has some remarkable numbers. He says that the national average cassava yield is 10.5 tonnes per hectare. He adds that a new cassava variety, PWANI, developed with GCP support and released in 2012, has the potential to increase yields to 51 tonnes per hectare. And they don’t stop there: the Tanzanian researchers want to produce three million cuttings and directly reach over 2,000 farmers with these new varieties, then scale up further.

Photo: N Palmer/CIAT

A farmer tends her cassava field in northern Tanzania.

Cassava grows up: looking ahead to supporting African families

Emmanuel reflects on how the first release of a new disease-resistant high-yielding cassava variety took fundamental science towards tangible realities for the world’s farmers: “It was a great example of a practical application of marker technology for selecting important new traits, and it bodes well for the future as markers get fully integrated into cassava breeding.”

Emmanuel further believes that GCP’s Cassava Research Initiative has given research communities “a framework for international support from other investors to do research and development in modern breeding using genomic resources.” Evaluations have demonstrated that molecular-assisted breeding can slash between three and five years from the timeline of developing better crops.

Photo: M Perret/UN Photo

Women tend to bear most of the burden of cassava cultivation and preparation. Here a Congolese woman pounds cassava leaves – eaten in many regions in addition to cassava roots – prior to cooking a meal for her family.

But, like cassava’s long growth cycle underground, Emmanuel knows there is still a long road to maturity for cassava as a crop for Africa and in research. “Breeding is just playing with genetics, but when you’re done with that, there is still a lot to do in economics and agronomics,” he says. Revolutionising cassava is about releasing improved varieties carefully buttressed by financial incentives and marketing opportunities.

Rural women in particular stand to benefit from improved varieties – they carry most of the responsibility for producing, processing and marketing cassava. So far, Elizabeth explains: “Most women reported an increase in their household income as a result of the improved cassava, but that is still dependent on extra time spent on cassava-related tasks” – a burden which she aims to diminish.

Elizabeth emphasises that future improvement research has to take a bottom-up approach, first talking to female farmers to ensure that improved crops retain characteristics they already value in addition to the new traits. “Rural families are held together by women, so if you are able to change their lot, you can make a real mark,” she says. Morag echoes this hope: “We are just starting to implement this now in Uganda; it’s a more farmer-centric approach to breeding”. The cassava teams emphasise the importance of supporting women in science too; the Tanzanians teams are aiming for a target of 40 percent women in their training courses.

Meet Elizabeth in the podcast below (or on PodOmatic), and be inspired by her passion when it comed to women in agriculture and in science:


This direct impact goes much further than individuals, says Chiedozie. “GCP’s daring has enabled many national programmes to be self-empowered, where new avenues are unfolding for enhanced collaboration at the local, national and regional level. We’re seeing a paradigm shift.” And Chiedozie’s objectives reach in a circle back to his compatriots: “Through GCP, I’ve been able to achieve my aims of using the tools of science and technology to make the lives of poor Africans better by providing them with improved crops.”

GCP has been crucial for developing the capacity of countries to keep doing this level of research, says Chiedozie: “The developing-country programmes were never taken seriously,” he says. “But when the GCP opportunity to change this came up we seized it, and now the developing-country programmes have the boldness, capacity and visibility to do this for themselves.”

Emmanuel says his proudest moment was when GCP was looking for Africans to take up leadership roles. “They felt we could change things around and set a precedent to bring people back to the continent,” he says. “They appreciated our values and the need to install African leaders on the ground in Africa rather than in Europe, Asia or the Americas.”

“If you want to work for the people, you have to walk with the people – that’s an African concept. Then when you work with the people, you really understand what they want. When you speak, they know they can trust you.” GCP trusted and trod where others had not before, Chiedozie says.

Elizabeth agrees: “In the past, the assumption was always that ‘Africa can’t do this.’ Now, people see that when given a chance to get around circumstances – as GCP has done for us through the provision of resources, motivation, encouragement and training – Africa can achieve so much!”

More links

Photo: A Hoel/World Bank

Walking into the future: farmer Felicienne Soton in her cassava field in Benin.

May 292015

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

Photo: B Nichols/USDA


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

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

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

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

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

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

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

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

Common objectives

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

Photo: R Silva/EMBRAPA

Maize growing in Brazil.

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

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

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

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

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

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

Photo: CIFOR

Maize farmers in Brazil.

Great minds think alike

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

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

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

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

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

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

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

Photo: L Kochian

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

Multifaceted and tangible results

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

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

Photo: Bioversity International

A Kenyan farmer with her sorghum crop.

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

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

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

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

Sustainable partnerships to break ground for groundnut

Photo: N Palmer/CIAT


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

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

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

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

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

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

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

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

Genetic stocks AND people are products

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

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

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

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

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

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

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

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

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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.

More links

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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