He attributes this revolution in large part to GCP, saying it “played the role of catalyst. It got things started. It set the foundation. Now we are in a position to do further molecular breeding in chickpeas.”
Led by Pooran, researchers from India, Ethiopia and Kenya worked together not only to develop improved, drought-tolerant chickpeas that would thrive in semiarid conditions, but also to ensure these varieties would be growing in farmers’ fields across Africa within a decade.
The 10-year Generation Challenge Programme, with the goal of improving food security in developing countries, aimed to leave plant genetic assets as an important part of its legacy.
Diagnostic, or informative, molecular markers – which act like ‘tags’ for beneficial genes scientists are looking for – are an increasingly important genetic tool for breeders in developing resilient, improved varieties, and have been a key aspect of GCP’s research.
Chickpeas, ready to harvest.
What is a diagnostic molecular marker?
Developments in plant genetics over the past 10–15 years have provided breeders with powerful tools to detect beneficial traits of plants much more quickly than ever before.
Scientists can identify individual genes and explore which ones are responsible for, or contribute to, valuable characteristics such as tolerance to drought or poor soils, or resistance to pests or diseases.
Once a favourable gene for a target agronomic trait is discovered and located in the plant’s genome, the next step is to find a molecular marker that will effectively tag it. A molecular marker is simply a variation in the plant’s DNA sequence that can be detected by scientists using any of a range of methods. When one of these genetic variants is found close on the genome to a gene of interest (or even within the gene itself), it can be used to indicate the gene’s presence.
To use an analogy, think of a story as the plant’s genome: its words are the plant’s genes, and a molecular marker works like a text highlighter. Molecular markers are not precise enough to highlight specific words (genes), but they can highlight sentences (genomic regions) that contain these words, making it easier and quicker to identify whether or not they are present.
Once a marker is found to be associated with a gene, or multiple genes, and determined to be significant to a target trait, it is designated an informative marker, diagnostic marker or predictive marker. Some simple traits such as flower colour are controlled by one gene, but more complex traits such as drought tolerance are controlled by multiple genes. Diagnostic markers enable plant breeders to practise molecular breeding.
Breeders use markers to predict plant traits
Hard work: a Ugandan bean farmer’s jembe, or hoe.
In the process known as marker-assisted selection, plant breeders use diagnostic molecular markers early in the breeding process to determine whether plants they are developing will have the desired qualities. By testing only a small amount of seed or seedling tissue, breeders are able to choose the best parent plants for crossing, and easily see which of the progeny have inherited useful genes. This considerably shortens the time it takes to develop new crop varieties.
“We use diagnostic markers to check for favourable genes in plants under selection. If the genes are present, we grow the seed or plant and observe how the genes are expressed as plant characteristics in the field [phenotyping]; if the genes are not present, we throw the seed or plant away,” explains Steve Beebe, a leading bean breeder with the International Center for Tropical Agriculture (CIAT) and GCP’s Product Delivery Coordinator for beans.
“This saves us resources and time, as instead of a growing few thousand plants to maturity, most of which would not possess the gene, by using markers to make our selection we need to grow and phenotype only a few hundred plants which we know have the desired genes.”
GCP supported 25 projects to discover and develop markers for genes that control traits that enable key crops, including bean and chickpea, to tolerate drought and poor soils and resist pests and diseases.
Genomic resources, including genetic maps and genotyping datasets, were developed during GCP’s first phase (2004–2008) and were then used in molecular-breeding projects during the second five years of the Programme (2009–2014).
“GCP’s philosophy was that we have, in breeding programmes, genomic resources that can be utilised. Now we are well placed, and we should be able to continue even after GCP with our molecular-breeding programme,” says Pooran.
A small selection of the rice diversity in the International Rice Research Institute gene bank – raw material for the creation of genomic resources.
Markers developed for drought tolerance
Cracked earth.
With climate change making droughts more frequent and severe, breeding for drought tolerance was a key priority for GCP from its inception.
Different plants may use similar strategies to tolerate drought, for example, having longer roots or reducing water loss from leaves. But drought tolerance is a complex trait to breed, as in each crop a large number of genes are involved.
Wheat, for example, has many traits – each controlled by different genes – that allow the crop to tolerate extreme temperature and/or lack of moisture. Identifying drought tolerance in wheat is therefore a search for many genes. In the particular case of wheat, this search is compounded by its genetic make-up, which is one of the most complex in the plant kingdom.
The difficulty of identifying genes that play a significant role in drought tolerance makes it all the more impressive when researchers successfully collaborate to overcome these challenges. GCP-supported scientists were able to develop and use diagnostic markers in chickpea, rice, sorghum and wheat to breed for drought tolerance. The first new drought-tolerant varieties bred using marker-assisted selection have already been released to farmers in Africa and Asia and are making significant contributions to food and income security.
Tanzanian sorghum farmer.
Markers developed for pests and diseases
A bumper harvest of cassava roots at the International Institute of Tropical Agriculture (IITA) in Nigeria.
Cassava mosaic disease (CMD) is the biggest threat to cassava production in Africa – where more cassava is grown and eaten than any other crop. A principal source of CMD resistance is CMD2, a dominant gene that confers high levels of resistance.
Nigerian GCP-supported researchers worked on identifying and validating diagnostic markers that are associated with CMD2. These markers are being used in marker-assisted selection work to transfer CMD resistance to locally-adapted, farmer-preferred varieties.
In the common bean, GCP-supported researchers identified genes for resistance to pests such as bean stem maggot in Ethiopia, as well as diseases such as the common mosaic necrosis potyvirus and common bacterial blight, which reduce bean quality and yields and in some cases means total crop losses.
Markers developed for acidic and saline soils
Sifting rice in Nepal.
Aluminium toxicity and phosphorus deficiency, caused by imbalanced nutrient availability in acid soils, are major factors in inhibiting crop productivity throughout the world. Aluminium toxicity also exacerbates the effects of drought by inhibiting root growth.
Diagnostic markers for genes that confer tolerance to high levels of aluminium and improve phosphorus uptake were identified in sorghum, maize and rice. The markers linked to these two sets of similar major genes have been used efficiently in breeding programmes in Africa and Asia.
Salt stress is also a major constraint across many rice-producing areas, partly because modern rice varieties are highly sensitive to salinity. Farmers in salt-affected areas have therefore continued growing their traditional crop varieties, which are more resilient but give low yields with poor grain quality. To address this issue, GCP supported work to develop and use markers to develop popular Bangladeshi varieties with higher tolerance to salt. GCP also funded several PhD students working in this area, one of whom was Armin Bhuiya.
Markers mean information, which means power
Diagnostic molecular markers are, in their most essential form, data. That means they are easily stored and maintained as data in publicly accessible databases and publications. Breeders can now access the molecular markers developed for various crops through the Integrated Breeding Platform – a web-based one-stop shop for integrated breeding information (including genetic resources), tools and support, which was established by GCP and is now continuing independently following GCP’s close – in order to design and carry out breeding projects.
“We could not have done that much in developing genomic resources without GCP support,” says Pooran. “Now the breeding products are coming; the markers are strengthening our work; and you will see in the next five to six years more products coming from molecular breeding.
“For me, GCP has improved the efficiency of the breeding programme – that is the biggest advantage.”
“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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.”
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.
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.
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.
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.
Beyond 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.
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”.
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.
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.
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.”
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.
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.
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.
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):
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.
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.
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.
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
Profiles here on the Sunset Blog: Elizabeth’s story | Chiedozie’s story
And an extra Sunset helping of cassava in the stories of our partnerships: ARI, Tanzania | CRI, Ghana | NRCRI, Nigeria
Sorghum is already a drought-hardy crop, and is a critical food source across Africa’s harsh, semi-arid regions where water-intensive crops simply cannot survive. Now, as rainfall patterns become increasingly erratic and variable worldwide, scientists warn of the need to improve sorghum’s broad adaptability to drought.
Crop researchers across the world are now on the verge of doing just that. Through support from the CGIAR Generation Challenge Programme (GCP), advanced breeding methods are enhancing the capacity of African sorghum breeders to deliver more robust varieties that will help struggling farmers and feed millions of poor people across sub-Saharan Africa.
A farmer in her sorghum field in Tanzania.
Sorghum at home in Africa
From Sudanese savannah to the Sahara’s desert fringes, sorghum thrives in a diverse range of environments. First domesticated in East Africa some 6000 years ago, it is well adapted to hot, dry climates and low soil fertility, although still depends on receiving some rainfall to grow and is very sensitive to flooding.
In developed countries such as Australia, sorghum is grown almost exclusively to make feed for cattle, pigs and poultry, but in many African countries millions of poor rural people directly depend on the crop in their day-to-day lives.
A Malian woman and her child eating sorghum.
In countries like Mali sorghum is an important staple crop. It is eaten in many forms such as couscous or tô (a kind of thick porridge), it is used for making local beer, and its straw is a vital source of feed for livestock.
While the demand for, and total production of, sorghum has doubled in West Africa in the last 20 years, yields have generally remained low due to a number of causes, from drought and problematic soils, to pests and diseases.
“In Mali, for instance, the average grain yield for traditional varieties of sorghum has been less than one tonne per hectare,” says Eva Weltzein-Rattunde, Principal Scientist for Mali’s sorghum breeding programme at the International Crops Research Institute for the Semi-Arid-Tropics (ICRISAT).
In a continued quest to integrate ways to increase productivity, GCP launched its Sorghum Research Initiative (RI) in 2010. This aimed to investigate and apply the approaches by which genetics and molecular breeding could be used to improve sorghum yields through better adaptability, particularly in the drylands of West Africa where cropping areas are large and rainfall is becoming increasingly rare.
Since 2008, with the help of CIRAD and Syngenta, Niaba and his team at IER have been learning how to use molecular markers to develop improved sorghum germplasm through identifying parental lines that are more tolerant and better adapted to the arid and volatile environments of Mali.
The two breeding methods used in the collaboration are known as marker-assisted recurrent selection (MARS) and backcross nested association mapping (BCNAM).
MARS
“MARS identifies regions of the genome that control important traits,” explains Jean-François. “It uses molecular markers to explore more combinations in the plant populations, and thus increases breeding efficiency.”
Syngenta, he explains, became involved through its long experience in implementing MARS in maize.
“Syngenta advised the team on how to conduct MARS and ways we could avoid critical pitfalls,” he says. “They gave us access to using the software they have developed for the analysis of data, and this enabled us to start the programme immediately.”
With the help of the IER team, two bi-parental populations from elite local varieties were developed, targeting two different environments found in sorghum cropping areas in Mali. “We were then able to use molecular markers through MARS to identify and monitor key regions of the genome in consecutive breeding generations,” says Jean-François.
“When we have identified the genome regions on which to focus, we cross the progenies and monitor the resulting new progenies,” he says. “The improved varieties subsequently go to plant breeders in Mali’s national research program, which will later release varieties to farmers.”
Jean-François is pleased with the success of the MARS project so far. “The development of MARS addressed a large range of breeding targets for sorghum in Mali, including adaptation to the environment and grain productivity, as well as grain quality, plant morphology and response to diseases,” he says. “It proved to be efficient in elucidating the complex relationships between the large number of traits that the breeder has to deal with, and translating this into target genetic ideotypes that can be constructed using molecular markers.”
Jean-François says several MARS breeding lines have already shown superior and stable performance in farm testing as compared to current elite lines, and these will be available to breeders in Mali in 2015 to develop new varieties.
Eva Weltzein-Rattunde examines sorghum plants with farmers in Mali.
BCNAM
Like MARS, the BCNAM approach shows promise for being able to quickly gain improvements in sorghum yield and adaptability to drought, explains Niaba, who is Principal Investigator of the BCNAM project. BCNAM may be particularly effective, he says, in developing varieties that have the grain quality preferences of Malian farmers, as well as the drought tolerance that has until now been unavailable.
“BCNAM involves using an elite recurrent parent that is already adapted to local drought conditions, then crossing it with several different specific or donor parents to build up larger breeding populations,” he explains. “The benefit of this approach is it can lead to detecting elite varieties much faster.”
Eva and her team at ICRISAT have also been collaborating with researchers at IER and CIRAD on the BCNAM project. The approach, she says, has the potential to halve the time it takes to develop local sorghum varieties with improved yield and adaptability to poor soil fertility conditions.
“We don’t have these types of molecular-breeding resources available in Mali, so it’s really exciting to be a part of this project,” she says. “Overall, we feel the experience is enhancing our capacity here, and that we are closer to delivering more robust sorghum varieties which will help farmers and feed the ever-growing population in West Africa.”
Indeed, during field testing in Mali, BCNAM lines derived from the elite parent variety Grinkan have produced more than twice the yields of Grinkan itself. As they are rolled out in the form of new varieties, the team anticipates that they will have a huge positive impact on farmers’ livelihoods.
Malian sorghum farmers.
Mali and Queensland – similar problem, different soil
In Mali and the wider Sahel region within West Africa, cropping conditions are ideal for sorghum. The climate is harsh, with daily temperatures on the dry, sun-scorched lower plains rarely falling below 30°C. With no major river system, the threat of drought is ever-present, and communities are entirely dependent on the 500 millimetres of rain that falls during the July and August wet season.
“All the planting and harvesting is done during the rainy season,” says Niaba. “We have lakes that are fed by the rain, but when these lakes start to dry up farmers rely mostly on the moisture remaining in the soil.”
Over 17 thousand kilometres to the east of Mali, in north-eastern Australia’s dryland cropping region, situated mainly in the state of Queensland, sorghum is the main summer crop, and is considered a good rotational crop as it performs well under heat and moisture stress. The environment here is similar to Mali’s, with extreme drought a big problem.
Average yields for sorghum in Queensland are double those in Mali—around two tonnes per hectare—yet growers still consider them low, directly limited by the crop’s predominantly water-stressed production environment in Australia.
One of the differentiating factors is soil. “Queensland has a much deeper and more fertile soil compared to Mali, where the soil is shallow, with no mulch or organic matter,” says Niaba. “Also, there is no management at the farm level in Mali, so when rain comes, if the soil cannot take it, we lose it.”
Sorghum in Queensland, Australia.
Making sorghum stay green, longer
Another key reason for the difference in yields between Queensland and Mali is that growers in Queensland are sowing a sorghum variety of with a genetic trait that makes it more tolerant to drought.
This trait is called ‘stay-green’, and over the last two decades it has proven valuable in increasing sorghum yields, using less water, in north-eastern Australia and the southern United States.
Stay-green allows sorghum plants to stay alive and maintain green leaves for longer during post-flowering drought—that is, drought that occurs after the plant has flowered. This means the plants can keep growing and produce more grain in drier conditions.
“Plant breeders have known about stay-green for some 30 years,” he says. “They’d walk their fields and see that the leaves of certain plants would remain green while others didn’t. They knew it was correlated with high yield under drought conditions, but didn’t know why.”
Stay-green’s potential in Mali
With their almost 20 years working on understanding how stay-green works, Andrew and his colleagues at UQ were invited by GCP in 2012 to take part in the IER/CIRAD collaborative project, to evaluate the potential for introducing stay-green into Mali’s local sorghum varieties and enriching Malian pre-breeding material for the trait.
A pivotal stage in this new alliance was a 12-month visit to Australia by Niaba and his IER colleague Sidi Coulibaly, to work with Andrew and his team to understand how stay-green drought resistance works in tall Malian sorghum varieties.
“African sorghum is very tall and sensitive to variation in day length,” explains Andrew. “We have been looking to investigate if the stay-green mechanism operates in tall African sorghums (around four metres tall) in the same way that it does in short Australian sorghum (one metre tall).”
Having just completed a series of experiments at the end of 2014, the UQ team consider their data as preliminary at this stage. “But it looks like we can get a correlation between stay-green and the size and yield of these Malian lines,” says Andrew. “We think it’s got great potential.”
A large part of GCP’s focus is building just such capacity among developing country partners to carry out crop research and breeding independently in future, so they can continue developing new varieties with drought adaptation relevant to their own environmental conditions.
A key objective of the IER team’s Australian visit was to receive training in the methods for improving yields and drought resistance in sorghum breeding lines from both Australia and Mali.
“We learnt about association mapping, population genetics and diversity, molecular breeding, crop modelling using climate forecasts, and sorghum physiology, plus a lot more,” says Niaba. This training complemented previous training Niaba and IER researchers had from CIRAD and ICRISAT through the MARS and BCNAM projects.
“We [CIRAD] have a long collaboration in sorghum research in Mali and training young scientists has always been part of our mission,” says Jean-François. “We’ve hosted several IER students here in France and we are always interacting with our colleagues in Mali either over the phone or travelling to Mali to give technical workshops in molecular breeding.”
Harvested sorghum in Sudan.
Working together to implement MARS in the sorghum breeding program in Mali represented many operational challenges, Jean-François explains. “The approach requires a very tight integration of different and complementary skills, including a strong conventional breeding capacity, accurate breeders’ knowledge, efficient genotyping technologies, and skills for efficient genetic analyses,” he says.
Because of this requirement, he adds, there are very few reported experiences of the successful implementation of MARS. It is also the reason why these kinds of projects would normally not be undertaken in a developing country like Mali, but for the support of GCP and the dedicated mentorship of Jean-François.
“GCP provided the perfect environment to develop the MARS approach,” says Jean-François. “It brought together people with complementary skills, developed the Integrated Breeding Platform (IPB), and provided tools and services to support the programme.”
In addition to developing capacity, Jean-François says one of the great successes of both the MARS and the BCNAM projects was how they brought together Mali’s sorghum research groups working at IER and ICRISAT in a common effort to develop new genetic resources for sorghum breeding.
“This work has strengthened the IER and ICRISAT partnerships around a common resource. The large multiparent populations that have been developed are analysed collectively to decipher the genetic control of important traits for sorghum breeding in Mali,” says Jean-François. “This community development is another major achievement of the Sorghum Research Initiative.” The major challenge, he adds, will be whether this community can be kept together beyond GCP.
Considering the numerous ‘non-GCP’ activities that have already been initiated in Africa as a result of the partnerships forged through GCP research, Jean-François sees a clear indication that these connections will endure well beyond GCP’s time frame.
GCP’s sunset is Mali’s sunrise
Sorghum at sunset in Mozambique.
Among the new activities Jean-François lists are both regional and national projects aimed at building on what has already been achieved through GCP and linking national partners together. These include the West African Agricultural Productivity Program (WAAPP), the West Africa Platform being launched by CIRAD as a continuation of the MARS innovation, and another MARS project in Senegal and Niger through the Feed the Future Innovation Lab for Collaborative Research on Sorghum and Millet at Kansas State University.
“These are all activities which will help maintain the networks we’ve built,” Jean-François says. “I think it is very important that these networks of people with common objectives stick together.”
For Niaba, GCP provided the initial boost needed for these networks to emerge and thrive. “We had some contacts before, but we didn’t have the funds to really get into a collaboration. This has been made possible by GCP. Now we’re motivated and are making connections with other people on how we can continue working with the material we have developed.”
“I can’t talk enough of the positive stories from GCP,” he adds. “GCP initiated something, and the benefits for me and my country I cannot measure. Right now, GCP has reached its sunset; but for me it is a sunrise, because what we have been left with is so important.”
Across Africa, governments and scientists alike are heralding groundnuts’ potential to lead resource-poor farmers out of poverty.
Around 5,000 years ago in the north of Argentina, two species of wild groundnuts got together to produce a natural hybrid. The result of this pairing is the groundnut grown today across the globe, particularly in Africa and Asia. Now, scientists are discovering the treasures hidden in the genes of these ancient ancestors.
Nearly half of the world’s groundnut growing area lies within the African continent, yet Africa’s production of the legume has, until recently, accounted for only 25 percent of global yield. Drought, pests, diseases and contamination are all culprits in reducing yields and quality. But through the CGIAR Generation Challenge Programme (GCP), scientists have been developing improved varieties using genes from the plant’s ancient ancestors. These new varieties are destined to make great strides towards alleviating poverty in some of the world’s most resource-poor countries.
A Ugandan farmer at work weeding her groundnut field.
A grounding in the history of Africa’s groundnuts
From simple bar snack in the west to staple food in developing countries, groundnuts – also commonly known as peanuts – have a place in the lives of many peoples across the world. First domesticated in the lush valleys of Paraguay, groundnuts have been successfully bred and cultivated for millennia. Today they form a billion-dollar industry in China, India and the USA, while also sustaining the livelihoods of millions of farming families across Africa and Asia.
“The groundnut is one of the most important income-generating crops for my country and other countries in East Africa,” says Malawian groundnut breeder Patrick Okori, Principal Scientist at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), who was also GCP’s Product Delivery Coordinator for groundnuts.
“It’s like a small bank for many smallholder farmers, one that can be easily converted into cash, fetching the highest prices,” he says.
The situation is similar in West Africa, according to groundnut breeder Issa Faye from the Institut Sénégalais de Recherches Agricoles (ISRA; Senegalese Agricultural Research Institute), who has been involved in GCP since 2008. “It’s very important for Senegal,” he says. “It’s the most important cash crop here – a big source of revenue for farmers around the country. Senegal is one of the largest exporters of peanut in West Africa.”
Groundnuts have good potential for sustaining a strong African export industry in future, while providing a great source of nutrition for Africa’s regional farming families.
“We believe that by using what we have learnt through GCP, we will be able to boost the production and exportation of groundnuts from Senegal to European countries, and even to Asian countries,” says Issa. “So it’s very, very important for us.”
Harvested groundnuts in Senegal.
How Africa lost its groundnut export market
Groundnuts in distress under drought conditions.
In Africa, groundnuts have mostly been grown by impoverished smallholder farmers, in infertile soils and dryland areas where rainfall is both low and erratic. Drought and disease cause about USD 500 million worth of losses to groundnut production in Africa every year.
“Because groundnut is self-pollinating, most of the time poor farmers can recycle the seed and keep growing it over and over,” Patrick says. “But for such a crop you need to refresh the seed frequently, and after a certain period you should cull it. So the absence of, or limited access to, improved seed for farmers is one of the big challenges we have. Because of this, productivity is generally less than 50 percent of what would be expected.”
Rosette virus damage to groundnut above and below ground.
Diseases such as the devastating groundnut rosette virus – which is only found in Africa and has been known to completely wipe out crops in some areas – as well as pests and preharvest seed contamination have all limited crop yields and quality and have subsequently shut out Africa’s groundnuts from export markets.
The biggest blow for Africa came in the 1980s from a carcinogenic fungal toxin known as aflatoxin, explains Patrick.
Aflatoxin-contaminated groundnut kernels from Mozambique.
Aflatoxin is produced by mould species of the genus Aspergillus, which can naturally occur in the soil in which groundnuts are grown. When the fungus infects the legume it produces a toxin which, if consumed in high enough quantities, can be fatal or cause cancer. Groundnut crops the world over are menaced by aflatoxin, but Africa lost its export market because of high contamination levels.
“That’s why a substantial focus of the GCP research programme has been to develop varieties of groundnuts with resistance to the fungus,” says Patrick.
After a decade of GCP support, a suite of new groundnut varieties representing a broad diversity of characteristics is expected to be rolled out in the next two or three years. This suite will provide a solid genetic base of resistance from which today’s best commercial varieties can be improved, so the levels of aflatoxin contamination in the field can ultimately be reduced.
Ancestral genes could hold the key to drought tolerance and disease resistance
In April 2014, the genomes of the groundnut’s two wild ancestral parents were successfully sequenced by the International Peanut Genome Initiative – a multinational group of crop geneticists, who had been working in collaboration for several years.
The sequencing work has given breeders access to 96 percent of all groundnut genes and provided the molecular map needed to breed drought-tolerant and disease-resistant higher-yielding varieties, faster.
“The wild relatives of a number of crops contain genetic stocks that hold the most promise to overcome drought and disease,” says Vincent Vadez, ICRISAT Principal Scientist and groundnut research leader for GCP’s Legumes Research Initiative. And for groundnut, these stocks have already had a major impact in generating the genetic tools that are key to making more rapid and efficient progress in crop breeding.
“Genetically, the groundnut has always been a really tough nut to crack,” says GCP collaborator David Bertioli, from the University of Brasilia in Brazil. “It has a complex genetic structure, narrow genetic diversity and a reputation for being slow and difficult to breed. Until its genome was sequenced, the groundnut was bred relatively blindly compared to other crops, so it has remained among the less studied crops,” he says.
With the successful genome sequencing, however, researchers can now understand groundnut breeding in ways they could only dream of before.
Groundnut cracked.
“Working with a wild species allows you to bring in new versions of genes that are valuable for the crop, like disease resistance, and also other unexpected things, like improved yield under drought,” David says. “Even things like seed size can be altered this way, which you don’t really expect.”
The sequencing of the groundnut genome was funded by The Peanut Foundation, Mars Inc. and three Chinese academies (the Chinese Academy of Agricultural Sciences, the Henan Academy of Agricultural Sciences, and the Shandong Academy of Agricultural Sciences), but David credits GCP work for paving the way. “GCP research built up the populations and genetic maps that laid the groundwork for the material that then went on to be sequenced.”
Chair of GCP’s Consortium Committee, David Hoisington – formerly ICRISAT’s Director of Research and now Senior Research Scientist and Program Director at the University of Georgia – says the sequencing could be a huge step forward for boosting agriculture in developing countries.
“Researchers and plant breeders now have much better tools available to breed more productive and more resilient groundnut varieties, with improved yields and better nutrition,” he says.
These resilient varieties should be available to farmers across Africa within a few years.
Genetics alone will not lift productivity – farmers’ local knowledge is vital
Improvements in the yield, quality and share of the global market of groundnuts produced by developing countries are already being seen as a result of GCP support, says Vincent Vadez. “But for this trend to continue, the crop’s ability to tolerate drought and resist diseases must be improved without increasing the use of costly chemicals that most resource-poor farmers simply cannot afford,” he says.
While genetic improvements are fundamental to developing the disease resistance and drought tolerance so desperately needed by African farmers, there are other important factors that can influence the overall outcome of a breeding programme, he explains. Understanding the plant itself, the soil and the climate of a region are all vital in creating the kinds of varieties farmers need and can grow in their fields.
Kenyan groundnut farmer Patrick Odima with some of his crop.
“I have grown increasingly convinced that overlooking these aspects in our genetic improvements would be to our peril,” Vincent warns. “There are big gains to be made from looking at very simple sorts of agronomic management changes, like sowing density – the number of seeds you plant per square metre. Groundnuts are often cultivated at seeding rates that are unlikely to achieve the best possible yields, especially when they’re grown in infertile soils.”
For Omari Mponda, now Director of Tanzania’s Agricultural Research Institute at Naliendele (ARI–Naliendele), previously Zonal Research Coordinator and plant breeder, and country groundnut research leader for GCP’s Tropical Legumes I project (TLI; see box below), combining good genetics with sound agronomic management is a matter of success or failure for any crop-breeding programme, especially in poverty-stricken countries.
“Molecular markers by themselves will not address the productivity on the ground,” he says, agreeing with Vincent. “A new variety of groundnut may have very good resistance, but its pods may be too hard, making shelling very difficult. This does not help the poor people, because they can’t open the shells with their bare hands.”
And helping the poor of Africa is the real issue, Omari says. “We must remind ourselves of that.”
This means listening to the farmers: “It means finding out what they think and experience, and using that local knowledge. Only then should the genetics come in. We need to focus on the connections between local knowledge and scientific knowledge. This is vital.”
Participants at a farmer field day in Mali interact with ICRISAT staff and examine different groundnut varieties and books on aflatoxin control and management options.
Local knowledge and high-end genetics working together in Tanzania
Like Malawi, Tanzania has also experienced the full spectrum of constraints to groundnut production – from drought, aflatoxin contamination, poor soil and limited access to new seed, to a lack of government extension officers visiting farmers to ensure they have the knowledge and skills needed to improve their farming practices and productivity.
Although more than one million hectares of Tanzania is groundnut cropping land, the resources supplied by the government have until now been minimal, says Omari, compared to those received for traditional cash crops such as cashews and coffee.
A farmer and her children near Dodoma, Tanzania, an area where climate change is causing increasing heat and drought. Groundnut is an important crop for local famers, forming the basis of their livelihood together with maize and livestock.
“But the groundnut is now viewed differently by the government in my country as a result of GCP’s catalytic efforts,” Omari says. “More resources are being put into groundnut research.”
In the realm of infrastructure, for instance, the use of GCP funds to build a new irrigation system at Naliendele has since prompted Tanzania’s government to invest further in irrigation for breeder seed production.
“They saw it was impossible for us to irrigate our crops with only one borehole, for instance, so they injected new funds into our irrigation system. We now have two boreholes and a whole new system, which has helped expand the seed production flow. Without GCP, this probably wouldn’t have happened.”
Irrigation, for Omari, ultimately means being able to get varieties to the farmers much faster: “maybe three times as fast,” he says. “This means we’ll be able to speed up the multiplication of seeds – in the past we were relying on rainfed seed, which took longer to bulk and get to farmers.”
With such practical outcomes from GCP’s research and funding efforts and the new genetic resources becoming available, breeders like Omari see a bright future for groundnut research in Tanzania.
Groundnut farmer near Dodoma, Tanzania.
The gains being made at Naliendele are not only sustainable, Omari explains, but have given the researchers independence and autonomy. “Before we were only learning – now we have become experts in what we do.”
Prior to GCP, Omari and his colleagues were used to conventional breeding and lacked access to cutting-edge science.
“We used to depend on germplasm supplied to us by ICRISAT, but now we see the value in learning to use molecular markers in groundnut breeding to grow our own crosses, and we are rapidly advancing to a functional breeding programme in Tanzania.”
Omari says he and his team now look forward to the next phase of their research, when they expect to make impact by practically applying their knowledge to groundnut production in Tanzania.
Similar breeding success in Senegal
Harvesting groundnuts in Senegal.
Issa Faye became involved in GCP in 2008 when the programme partly funded his PhD in fresh seed dormancy in groundnuts. “I was an example of a young scientist who was trained and helped by GCP in groundnut research,” he says.
“I remember when I was just starting my thesis, my supervisor would say, ‘You are very lucky because you will not be limited to using conventional breeding. You are starting at a time when GCP funding is allowing us to use marker-assisted selection [MAS] in our breeding programme’.”
The importance of MAS in groundnut breeding, Issa says, cannot be overstated.
“It is very difficult to distinguish varieties of cultivated groundnut because most of them are morphologically very similar. But if you use molecular markers you can easily distinguish them and know the diversity of the matter you are using, which makes your programme more efficient. It makes it easier to develop varieties, compared to the conventional breeding programme we were using before we started working with GCP.”
By using markers that are known to be linked to useful genes for traits such as drought tolerance, disease resistance, or resistance to aflatoxin-producing fungi, breeders can test plant materials to see whether or not they 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, saving time and money.
These women in Salima District, Malawi, boil groundnuts at home and carry their tubs to the Siyasiya roadside market.
Senegal, like other developing countries, does not have enough of its own resources for funding research activities, explains Issa. “We can say we are quite lucky here because we have a well-developed and well-equipped lab, which is a good platform for doing molecular MAS. But we need to keep improving it if we want to be on the top. We need more human resources and more equipment for boosting all the breeding programmes in Senegal and across other regions of West Africa.”
Recently, Issa says, the Senegalese government has demonstrated awareness of the importance of supporting these activities. “We think that we will be receiving more funds from the government because they have seen that it’s a kind of investment. If you want to develop agriculture, you need to support research. Funding from the government will be more important in the coming years,” he says.
“Now that we have resources developed through GCP, we hope that some drought-tolerant varieties will come and will be very useful for farmers in Senegal and even for other countries in West Africa that are facing drought.”
It’s all about poverty
“The achievements of GCP in groundnut research are just the beginning,” says Vincent. The legacy of the new breeding material GCP has provided, he says, is that it is destined to form the basis of new and ongoing research programmes, putting research well ahead of where it would otherwise have been.
“There wasn’t time within the scope of GCP to develop finished varieties because that takes such a long time, but these products will come,” he says.
For Vincent, diverse partnerships facilitated by GCP have been essential for this to happen. “The groundnut work led by ICRISAT and collaborators in the target countries – Malawi, Senegal, and Tanzania – has been continuously moving forward.”
Groundnut harvesting at Chitedze Agriculture Research Station, Malawi.
Issa agrees: “It was fantastic to be involved in this programme. We know each other now and this will ease our collaborations. We hope to keep working with all the community, and that will obviously have a positive impact on our work.”
For Omari, a lack of such community and collaboration can only mean failure when it comes to addressing poverty.
“If we all worked in isolation, a lot of money would be spent developing new varieties but nothing would change on the ground,” he says. “Our work in Tanzania is all about the problem of poverty, and as scientists we want to make sure the new varieties are highly productive for the farmers around our area. This means we need to work closely with members of the agricultural industry, as a team.”
Omari says he and his colleagues see themselves as facilitators between the farmers of Tanzania and the ‘upstream end’ of science represented by ICRISAT and GCP. “We are responsible for bringing these two ends together and making the collaboration work,” he says.
Only from there can we come up with improved technologies that will really succeed at helping to reduce poverty in Africa.”
As climate change threatens to aggravate poverty more and more in the future, the highly nutritious, drought-tolerant groundnut may well be essential to sustain a rapidly expanding global population.
By developing new, robust varieties with improved adaptation to drought, GCP researchers are well on the way to increasing the productivity and profitability of the groundnut in some of the poorest regions of Africa, shifting the identity of the humble nut to potential crop champion for future generations.
Oswin Madzonga, Scientific Officer at ICRISAT-Lilongwe, visits on-farm trials near Chitala Research Station in Salima, Malawi, where promising disesase-resistant varieties are being tested real life conditions.
“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”.
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.
“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].”
Maize farmers in Brazil.
Great minds think alike
Jurandir’s EMBRAPA colleague Claudia Guimarães, a plant molecular geneticist focusing on maize, says GCP promoted ‘products’, which also echoed the mission statement of EMBRAPA’s Maize & Sorghum research centre.
The centre’s mission is to: ‘Generate, adapt and transfer knowledge and technology that allows for the efficient production and use of maize, sorghum, and natural resources as well as promotes competitiveness in the agriculture sector, sustainable development, and the well-being of society.’
GCP, says Claudia, “wanted to extract something else from the science – products – the idea of a real, touchable product. You have to have progress: germplasm, lines, markers; they are quite practical things.
“The major goal of GCP is to deliver products that can improve people’s lives worldwide. So it needs to be readily available and useful for other scientists and for the whole community.”
GCP wanted to ensure that research products could and would be adopted, adapted and applied for the ultimate benefit of resource-poor farmers. The Programme therefore set out to catalyse interactions between the various players who are needed to bridge the gap between strategic research in advanced labs and resource-poor farmers.
GCP and EMBRAPA were both working towards tangible applied outcomes, says Claudia: “GCP was not only giving you money, they are really serious about what are you doing: ‘Did you deliver everything you promised?’”
Claudia delivered. She and her team at EMBRAPA were able to find an important aluminium-tolerance gene in maize similar to the sorghum gene. This outcome provided the basic materials for molecular-breeding programmes focusing on improving maize production and stability on acidic soils in Africa and other developing regions.
Maize trials in the field at EMBRAPA. The maize plants on the left are aluminium-tolerant while those on the right are not.
Multifaceted and tangible results
Through further GCP funding, EMBRAPA researchers Robert Schaffert and Sidney Parentoni were able to work together with two researchers from Kenya, Dickson Ligeyo and Samuel Gudu, to develop a breeding programme to combine the improved Brazilian germplasm with locally adapted Kenyan materials. A new base of improved germplasm was established for Kenyan breeders, which allowed the development of varieties adapted to acidic soils in Kenya.
Sidney, a maize breeder for GCP projects and now the deputy head of research and development for EMBRAPA Maize & Sorghum, says that the benefits of being part of GCP are multifaceted: “It was very important, not only for EMBRAPA as an institute, but also individually for each of the participants that had the opportunity to interact with partners in different parts of the word,” says Sidney.
A Kenyan farmer with her sorghum crop.
“Each of them adds a piece to build the results achieved by GCP, which from my perspective promoted a number of advances in the areas of genetics and breeding.
“Technologies such as root image scanning developed at Cornell [University] were transferred to EMBRAPA and allowed us to do large-scale screening in a number of maize and sorghum genotypes with large impacts in phosphorous-efficiency studies.
“Scientists from Africa were trained in breeding and screening techniques at EMBRAPA, and Brazilian scientists had the opportunity to go to Africa and interact with African researchers to jointly develop strategies for breeding maize and sorghum for low-phosphorous and acidic soils.
“These trainings and exchanges of experiences were very important for the people and for the institutions involved,” says Sidney.
Sustainable partnerships to break ground for groundnut
Groundnut
Soraya Leal-Bertioli is a researcher in the EMBRAPA Genetic Resources & Biotechnology centre. She works on groundnut (also known as peanut), and formed part of the GCP team working on groundnut with tolerance to drought and resistance to diseases and fungal contamination. She concurs that GCP united researchers from all over the globe in a common goal.
“GCP not only identified groups, but it went out, searched for people and invited contributions, offered resources to get them together. GCP brought partnerships to a whole new level,” Soraya says.
“Last time I checked there were 200 partners in 50 countries. No one is able to do that. It required a lot of money, a lot of resources, but the way it was dealt with in GCP was: ‘Let’s reach out for the main players, the ones who have the technology, and also the ones who can use the technology’.
“GCP used the resources for the benefit of the community and brought everybody together.”
Soraya says the traditional way of funding research often had ‘no structure’.
“Sometimes a university or funding body receives a large amount of money and decides to build something, a new institute in the middle of the jungle somewhere, but they don’t have anybody to run it; it is not sustainable.
“What GCP did was help to provide the structure and the agents for the whole system. They helped train the people to run the whole system. This is a very sustainable model, which is very likely to give good results in a much shorter time frame than other programmes.”
Watch Soraya – and other members of the team – discuss the complex personality of groundnut and groundnut research in our video series:
Genetic stocks AND people are products
The products and outcomes of the collaboration with GCP have included both the tangible and the not-so-tangible. Sidney says that a large quantity of Brazilian improved maize and sorghum lines tolerant to acidic soils has been developed over the years at EMBRAPA.
“These materials were shared with partners in Africa, and this was a major contribution to Kenyan farmers, as part of this collaborative work done in the scope of GCP.
“To be part of the programme has been very important for EMBRAPA’s research team. It has given us the opportunity to interact with a diversity of institutes.”
Sidney 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.”
A farmer harvests her pearl millet crop in Ghana’s Upper West Region.
Pearl millet is the only cereal crop that can be grown in some of the hottest and driest regions of Asia and Africa. It is a staple provider of food, nutrition and income for millions of resource-poor people living on these harsh agricultural lands.
Even though pearl millet is well adapted to growing in areas characterised by drought, poor soil fertility and high temperatures, “there are limited genetic tools available for this orphan crop,” reported researcher Tom Hash at the International Crop Science Congress 10 years ago.
“The people who relied on this crop in such extreme environments had not benefitted from the ‘biotechnology revolution’, or even the ‘green revolution’ that dramatically increased food grain production on irrigated lands over a generation ago,” adds Tom, now Principal Scientist (Millet Breeding) in the Dryland Cereals Research Program of the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). This lack of research dividends was despite the fact that pearl millet is the sixth most important cereal crop globally.
It was at this time – in 2005 – that the CGIAR Generation Challenge Programme (GCP) stepped up to invest in more genetic research for pearl millet (along with finger and foxtail millet).
Newly harvested pearl millet heads in Niger.
The use of genetic technologies to improve pearl millet had already made some advances through work carried out in the United Kingdom. The GCP initiative was established to improve food security in developing countries by expanding such available genetic work to create crops bred to tolerate drought, disease and poor soils.
With financial support from GCP, and with the benefit of lessons learnt from parallel GCP genetic research, ICRISAT scientists were able to develop more advanced tools for breeding pearl millet.
He says it is the high protein content of pearl millet that makes it such a crucial crop for developing countries – in Africa, this is the reason people use pearl millet for weaning babies.
“It was interesting to us that African people have used pearl millet as a weaning food for millennia. The reason why was not clear to us until we assessed the protein content,” says Mark. “Its seed has 13–22 percent protein, remarkable for a cereal crop, whereas maize has only eight percent protein, and sorghum has only two percent digestible protein.”
Pearl millet growing in Kenya.
Tom Hash agrees, adding: “More importantly, pearl millet grain has much higher levels of the critically important mineral micronutrients iron and zinc, which are important for neurological and immune system development.
“These mineral micronutrients, although not present in a highly available form, can improve blood iron levels when used in traditional pearl millet-based foods. Pearl millet grain, when fed to poultry, can provide a potentially important source of omega-3 fatty acids, which are also essential for normal neurological development.”
Pearl millet endowed with genetic potential
A farmer with his pearl millet harvest in India.
In a treasure-trove of plant genetic resources, thousands of samples, or accessions, of pearl millet and its wild relatives are kept at ICRISAT’s gene banks in India and Niger.
For pearl millet alone, in 2004 ICRISAT had 21,594 types of germplasm in its vaults at its headquarters in India. This represents a huge reservoir of genetic diversity that can be mined for data and for genetic traits that can be used to improve pearl millet and other crops.
Between 2005 and 2007, with support from GCP, scientists from ICRISAT set to work to do just that, mining these resources for qualities based on observed traits, geographical origin and taxonomy.
Hari D Upadhyaya, Principal Scientist and Director of Genebank at ICRISAT, led the task of developing and genotyping a ‘composite collection’ of pearl millet. To do this, the team created a selection that reduced 21,594 accessions down to 1,021. This collection includes lines that are tolerant to drought, heat and soil salinity; others resistant to blast, downy mildew, ergot, rust and smut; and accessions resistant to multiple diseases.
A traditional pearl millet variety growing in India.
The collection also includes types of pearl millet with high seed iron and zinc content (from traditional farmer varieties, or landraces, from Benin, Burkina Faso, Ghana and Togo), high seed protein content, high stalk sugar content, and other known elite breeding varieties.
The final collection comprised 710 landraces, 251 advanced breeding lines, and 60 accessions from seven wild species.
The GCP-supported scientists then used molecular markers to fingerprint the DNA of plants grown from the collection. Molecular markers are known variations in the sequence of the genetic code, found in different versions within a species, which act as flags in the genome sequence. Some individual markers may be associated with particular useful genes, but markers are useful even without known associations, as the different flags can be compared between samples. In the pearl millet research, scientists searched for similarities and differences among these DNA markers to assess how closely or distantly related the 1,021 accessions were to each other.
This was not only a big step forward for the body of scientific knowledge on pearl millet, but also for the knowledge and skills of the scientists involved. “The GCP work did make some significant contributions to pearl millet research,” says Tom, “mainly by helping a critical mass of scientists working on pearl millet to learn how to appropriately use the genetic tools that have been developed in better-studied fungi, plants and animals (including people).”
GCP extends know-how to Africa
Comparisons of good and bad pearl millet yields in Ghana’s Upper West Region, which has suffered failed rains and rising temperatures.
The semiarid areas of northern and eastern Uganda are home to a rich history and culture, but they are difficult environments for successful food production and security.
In this region, pearl millet is grown for both commercial and local consumption. Its yields, although below the global average, are reasonable given that it is grown on poor sandy soils where other crops fail. Yet despite being a survivor in these harsh drylands, pearl millet can still be affected by severe drought and disease.
GCP helped kick-start work to tackle these problems. With financial support from GCP, and through ACCI, Geofrey Lubade, a scientist from Uganda, was able to study and explore breeding pearl millet that would be suitable for northern Uganda and have higher yields, drought tolerance and rust resistance.
Geofrey now plans to develop the best of his pearl millet lines for registration and release in Uganda, which he expects will go a long way in helping the resource-poor.
But Geofrey’s success is just one example of the benefits from GCP-support. Thanks to GCP, Mark Laing says that his students at ACCI have learnt invaluable skills that save significant time and money in the plant-breeding process.
“Many of our students, with GCP support, have been involved in diversity studies to select for desirable traits,” says Mark – and these students are now working on releasing new crop varieties.
He says that African scientists directly benefitted from the GCP grants for training in biotechnology and genetic studies.
Their work, along with that of a number of other scientists, will have a huge impact on plant breeding in developing countries – long term.
A farmer inspects his millet crop in northwest Ghana.
As Mark explains, once breeders have built up a head of steam there is no stopping them. “Plant breeders take time to start releasing varieties, but once they get started, then they can keep generating new varieties every year for many years,” he says. “And a good variety can have a very long life, even more than 50 years.
“We have already had a significant impact on plant breeding in some African countries,” says Mark. But perhaps more importantly, he says, the work has changed the status of plant breeding and pearl millets as a subject: “It used to be disregarded, but now it is taken seriously as a way to have an impact on agriculture.”
For research and breeding products, see the GCP Product Catalogue and search for pearl millet.
Rice plays a key role in global food security, particularly in Asia, where 90 percent of the world’s rice is grown and eaten. By 2050, Asia’s population is estimated to grow by one billion to 5.2 billion people, who will continue to depend on rice as their major staple food.
But with rising demand for rice has also come increasing salinity, droughts and other stresses, along with decreasing areas of land available for farming the crop.
Key ingredient in the rice research fest was GCP’s relationship with the International Rice Research Institute (IRRI), headquartered in The Philippines. GCP supported IRRI in its endeavours to use the latest molecular plant-breeding techniques, along with traditional plant-breeding tools, to develop rice crops better able to cope with various stresses and still be productive.
“These ‘super’ crops will revolutionise rice farming,” says IRRI Director General Robert Zeigler, who was also the first Director of GCP.
Climate change is one of the major threats facing rice production. As sea levels rise, salt water enters further up rivers with the high tides and affects rice production areas.
Each year in Bangladesh, during the boro rice season from November to May, salinity is so high that a white film of salt covers the country’s coastal paddy fields. For Bangladeshi farmers, this white colour is a warning sign that their land is ‘sick’. Around the world, Bangladesh, India, Myanmar and parts of Africa are most affected by increasing salinity.
Right from the beginning of GCP, salinity was a problem firmly on the rice research agenda.
Highly saline soils in India (left), and a close-up showing a surface crust of salt on afflicted soil (right).
Leading this research was IRRI plant physiologist Abdelbagi Ismail, who dreamed of the ‘super’ rice crop that could “tolerate salinity, drought and submergence”.
Abdelbagi has managed and overseen most of the progress made during the discovery of a major genetic region, or quantitative trait locus (QTL), associated with salinity tolerance and named Saltol.
Abdelbagi Ismail examines rice plants in the field in Bangladesh.
Its insertion into well-known rice varieties used by farmers in Bangladesh, Indonesia and The Philippines is part of the revolution taking place in rice research.
Abdelbagi says Saltol was mapped and markers were developed for its use in breeding more salt-tolerant rice varieties. Its salt-tolerance code is now being transferred into several varieties evaluated with IRRI partners in South and Southeast Asia.
“These projects also provided opportunities for both degree training and non-degree training to several of our partners in the countries involved,” he adds.
“Partnerships are crucial for us to build the capacity of the researchers in these countries and to ensure our outputs and outcomes reach the farmers that need them.
“All our partners benefitted from salt-tolerant varieties developed conventionally through this project, and they also provided pipelines for uptake and dissemination by farmers.”
Having developed new lines following the discovery of the Saltol QTL, Abdelbagi’s GCP-supported team trained plant breeders in country programmes to successfully breed for salt tolerance and other stresses.
In this way, Abdelbagi says, they are improving the capacity of researchers in developing countries to take up new breeding techniques, such as the use of molecular markers. “This can reduce the time it takes to breed new varieties, from six to ten years at the moment, down to two or three years,” he says.
This means that benefits to smallholder rice farmers struggling with salinity will happen sooner rather than later. And Abdelbagi credits GCP’s partnership approach, working directly with the countries in need, for the success so far.
“The salt-tolerant varieties are now being widely distributed,” he says. “Some of these varieties have doubled farmers’ productivity in affected areas.
“The work developed technologies of value to our needy farmers.
“We do believe this is the start of a second Green Revolution, especially for those who farm in less favourable areas and that missed this opportunity during the first Green Revolution.”
Partnership approach key to new rice gene for uptake of phosphorus
More than 60 percent of rainfed lowland rice is produced on poor and problem soils, including those that are naturally low in phosphorus. This is an essential for nutrient growing crops, but providing phosphorus through fertilisers is costly and unfeasible for many smallholder rice growers.
IRRI’s Sheryl Catausan prepares the roots of a rice plant for scanning as part of the work of the PSTOL1, phosphorus uptake research team at IRRI.
This problem was the focus of GCP’s rice phosphorus-uptake project led by IRRI molecular biologist Sigrid Heuer.
The project was enormously successful, with its discovery of the PSTOL1 (‘phosphorus starvation tolerance 1’) gene within the Pup1 locus, which was published in the prestigious journal Nature.
“We wanted it in Nature for a couple of reasons,” she says. “To raise awareness about phosphorus deficiency and phosphorus being a limited resource, especially in poorer countries; and to draw attention to how we do molecular breeding these days, which is a speedier, easier and more cost-effective approach to developing crops that have the potential to alleviate such problems.”
Following the PSTOL1 discovery, researchers are now working with developing-country researchers and extension agencies to help them understand how to breed local varieties of rice that can be grown in phosphorus-deficient soils. They are also collaborating with other crop breeders looking to breed similar maize, sorghum and wheat varieties.
Tobias Kretzschmar, a molecular biologist with IRRI, says that GCP’s partnership approach was the key to the project having an impact on the rice farmers who needed it most.
“For me, the collaborations that were forged through these inter-institutional projects made the difference,” he says.
Sigrid agrees: “GCP was always there supporting us and giving us confidence, even when we were not sure.”
Solving the insoluble: a gene for drought tolerance
Rice is a crop that not only needs water, but loves water. So developing a drought-tolerant rice variety is a quest to find a seemingly impossible gene.
However, GCP-supported researchers did just that: they solved the insoluble.
“They were very successful in terms of getting drought tolerance,” says Hei Leung of IRRI, who was GCP Subprogramme Leader for the Comparative Genomics Research Initiative between 2004 and 2007, and also a Principal Investigator for the Rice Research Initiative. “They’re now getting a 1.5 tonne rice yield advantage under water stress. I mean, that’s unheard of! This is a crop that needs water.
“This is one of GCP’s big success stories; that you can actually get drought tolerance is a seemingly impossible task for a water-loving rice plant.”
As Subprogramme Leader, Hei played a critical role in the creation, management, delivery and communication of a wide portfolio of research projects. He credits the nature of how GCP was set up for accelerating the breeding programme for drought-tolerant rice.
“The advantage of GCP is that it is run by a small group of people who can make fast decisions,” he says. “This means they can respond to the needs of researchers: ‘Okay, we are going to invest on that. We’re going to have a meeting on this’.
“The real advantage of GCP is its agility. Usually with other organisations you have new ideas and then have to slave away for a year to get the funding to implement them. But GCP was quick.”
Hei Leung (right) explains rice screening processes to a visiting scholar at IRRI.
IRRI and GCP deliver genetic resources to those who need them most
Tobias says one of the main objectives of GCP and IRRI is to make genetic stocks available to breeders, particularly in developing countries.
“Without that, IRRI would fail in its central mission to reduce hunger and poverty,” he says. “In order to achieve this mission, tight collaboration with our agricultural and extension partners in other countries is the key.”
In fact, this idea of protecting the future through genetic material was influential in the choice of GCP as a CGIAR Challenge Program name. Hei, who was involved from the start with GCP, talks about the meeting in a Rome pizzeria where participants came up with the name: “When we talk about ‘generation’, we are really talking about the work we do with genetic diversity; it is about the future generation,” he says.
Part of that future generation is about sharing genetic resources or stocks, but first the genetic diversity of such stocks needs to be characterised. Hei remembers that one of the first GCP projects in 2004 brought together researchers in various countries to characterise the genetic diversity of various crops, including rice.
“But everyone was using different genotyping platforms and markers, and the technology back then was not what we have now,” he recalls.
“So we spent a lot of resources getting poor quality data. In a sense, it was a failure. On the other hand, it was also a success because we alerted people to the importance of characterising diversity in every single crop. The whole concept of getting all the national partners doing genetic resource characterisation is a good one.
“We have evolved the technology together over the last 10 years of GCP. Now the country partners feel enabled. They are not scared of the technology.”
Abdelbagi agrees that characterising genetic diversity is essential, and adds that making such genetic stocks readily available to breeders is also vital.
“This has not been an issue before,” he explains. “With the new regulations of germplasm control and intellectual property issues, it became extremely difficult to exchange germplasm with some countries. One important lesson we learnt was to engage in direct discussion with our partners in efforts to influence their policies and guidelines to allow essential exchange of genetic stocks and breeding material, at least at the regional level.”
Abdelbagi adds that another big challenge has been to provide country partners with materials and DNA markers for marker-assisted selection programmes and to make sure these were properly used in breeding programmes.
“We solved this by hosting a workshop at IRRI and with continued visits with GCP collaborators,” he says.
Rice terraces in Ifugao Province in The Philippines.
‘Super’ crops: something ‘magic’ happens
Hei says that the GCP project he’s most passionate about, and one that leaves a lasting legacy, is the development of multiparent advanced generation intercross (MAGIC) populations, which will potentially yield lines that are tolerant to environmental stresses, grow well in poor soils and produce better quality grain.
“MAGIC populations will leave behind a very good resource towards improving different crop species,” says Hei. “I’m sure that they will expand on their own.”
GCP funded the development of four kinds of rice populations, including indica MAGIC, which is the most advanced of the MAGIC populations developed so far. These populations contain multiple desirable traits, including: blast and bacterial blight-resistance, salinity and submergence tolerance and grain quality.
New generation of researchers working on a new rice revolution
Rice farmer in her field in Rwanda.
Robert Zeigler’s dream of a new rice Green Revolution with ‘super crops’ is coming true, thanks in part to GCP’s focus on combining cutting-edge molecular plant-breeding techniques with conventional plant breeding.
“With all this going for us, the second Green Revolution means we can meet the great challenges ahead with unprecedented efforts that will result in unparalleled impacts,” he says. “This will range from mining the rice genomes for needed traits to developing climate change-ready rice.”
IRRI researchers like Abdelbagi agree that new plant-breeding techniques, such as those fostered by GCP, are making ‘super’ crops more likely: “I’m committed to understand how plants can be manipulated to adapt to, and better tolerate, extreme environmental stresses, which seems more feasible today than it has ever been before.
“GCP-supported work has provided mechanisms for developing varieties with multiple stress tolerances, besides the improvements in yield and quality.”
And for Hei, GCP’s 10-year legacy is not just about the technology but also about the people.
“Over ten years you have three generations of PhD students,” he says. “Many people became a ‘new generation’ scientist through this programme. Many people have benefitted. GCP is one of a kind. I’m just in love with it.”
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.
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.
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 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.
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.”
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?”
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.”
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.
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.
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.
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.
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.”
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.
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.
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.
And get an extra Sunset helping of rice in our tale of GCP’s relationship with IRRI, with more on MAGIC populations and breeding for salinity tolerance
Kenyan crop scientist Samuel (Sam) Gudu loves nothing more than getting his hands dirty out on the land.
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.
Sam and GCP embrace biotechnology and emerging scientists
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.
“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.”
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.”
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.”
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.
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.”
