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.
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.
Barley is thought to have been one of the first crops ever cultivated by humankind. This is largely because it is a tough plant able to withstand dry and salty conditions. Its fortitude is especially important for the small land-holders living on the fringes of deserts in West Asia and North Africa, where it is “the last crop grown before the desert,” says Dr Michael Baum, who led barley research for the CGIAR Generation Challenge Programme (GCP).
“Looking at wild barley is especially important for low-input agriculture, such as is found in developing countries,” he says. “Wild barley grows in, and is very adapted to, the harsh conditions at the edge of the deserts in the Fertile Crescent of West Asia: Iraq, Syria, Jordan and Turkey.”
In some regions, wild barley produces an even higher yield of grain when there is a drought. And this was the kind of useful trait that GCP researchers were looking for in their work on barley during the first phase of GCP, when the internationally funded Programme set out to enhance genetic stocks and plant-breeding skills that will help developing nations cope with increasingly extreme drought conditions.
Barley a ‘chosen one’ for research
Preparing barley in Ethiopia.
During its first five years, GCP chose barley as one of its focus crops as advances had already been made in understanding its genetic makeup and in using new molecular plant-breeding technologies to find and incorporate useful genes into barley varieties.
“At the same time, we needed to find the genes or characteristics we did not want in cultivated barley so we could avoid these traits,” says Michael. “This includes the way wild barley disperses its seed when its brittle spikes shatter. Domesticated barley has non-shattering spikes, making it much easier to harvest.”
Resource-poor farmers mostly grow barley in poor environments, where yields of key crops are chronically low, and crop failures are common. Resilient, high-yielding varieties could make a big difference to livelihoods.
Farmers in Central and West Asia and North Africa (CWANA) plant more than five million hectares of barley each year, where it is largely used as feed for the sheep and goats that are the main source of meat, milk and milk products for rural populations. In these environments, barley grain is harvested only two to three times over a five-year period. In years when it is too dry, sheep are sent into the barley field to graze on the straw.
Barley-based livestock system on marginal drylands in Morocco.
Finding the clues to help breeders select barley’s best DNA
Malted barley.
The quest for better barley varieties – those that yield more, have more protein, can resist pests and diseases and can tolerate drought – means understanding what genes for what characteristics are available to plant breeders.
With 2,692 different barley accessions (or genetically different types of barley) in the ICARDA collection, from 84 different countries, this is no mean feat. GCP-supported researchers selected seed from 1,000 of the most promising accessions and planted single plants, whose seed was then ‘fingerprinted’, or genotyped, according to its DNA composition.
“From this, we selected 300 different barley lines that represented 90 percent of all the different characteristics of barley,” says Michael.
“This [reference set] is really good for someone new to barley. By looking at 300 lines they are seeing the diversity of almost 3,000 lines without any duplication,” he says. “This is much better and quicker for a plant breeder.”
The reference set of 300 barley lines is now available to plant breeders through the ICARDA gene bank.
Barley growing on experimental fields in Morocco.
Checking out the effects of the environment on gene expression
Harvesting barley in Nepal.
It’s not enough to discover what genes are present in different varieties of barley. It’s also important to understand how these genes express themselves in terms of barley’s yield, quality (especially protein content) and adaptation to stresses such as drought when grown in different environments.
To make this happen, GCP improved collaboration across research centres. This increased the probability of relatively quick advances in identifying new traits and opportunities to improve barley varieties for the poorer farmers of CWANA.
GCP funded a collaborative project between ICARDA and researchers in Australia (the University of Adelaide and the Australian Centre for Plant Functional Genomics), Italy (l’Università degli Studi di Udine) and Syria (Tishreen University) to apply a new method, analysing allele-specific expression (ASE), to understand how genes express themselves in barley, using experimental hybrid plants (cultivated plants crossed with wild barley plants). Over three years, the collaboration tested 30 genes and 10 gene-cross combinations and found that there were changes in genetic expression when plants were grown in drought conditions.
“This is a project we could not have done without the partners in the GCP collaboration,” says Michael. “We gained important insights into how genes are regulated and how gene expression changes under different environmental conditions, such as drought, or during growth stages, such as early plant development or grain filling. We published our results in a high-impact journal [The Plant Journal (2009) 59(1):14–26], which was a great outcome for a project with such a limited timespan.”
This project was designed not so much for the practical plant breeder, but for those using molecular-breeding technologies where it is important to understand that there is a change in the expression of genes over the lifetime of a plant. “This affects the selection of genes for breeding programmes,” says Michael.
Preparing barley in Ethiopia.
Making the most of wild barley
Wild barley in flower.
Once some of the fundamental research into barley’s building blocks had been done, GCP revisited the potential of wild barley, with the aim to identify specific DNA that increased or decreased drought tolerance.
“Whenever you can’t find the characteristics you are looking for in a cultivated crop, you go back to look again at the wild varieties,” says Michael.
Joanne Russell from the James Hutton Institute says success came when “we combined the power of genomics with a unique population of 140 barley lines to identify segments of the donor genome that confer drought tolerance”.
The barley lines were composed of an advanced elite genetic background combined with introduced segments of DNA from wild barley that came from the Fertile Crescent.
“We were successful in identifying parts of the DNA from hybrid plants that confer a significant increase in yield under drought,” says Joanne.
Leader of this GCP project from the James Hutton Institute, Professor Robbie Waugh, adds that GCP provided a unique opportunity for their laboratory to interact with international colleagues on a project focussed on improving the plight of some of the world’s poorest subsistence farmers.
“The genetic technologies we had developed prior to the GCP project starting were, at the time, state of the art – even in the more developed world,” says Robbie. “Our ability to then apply these technologies to wild barley genetic material from ICARDA and to varieties derived from wild × cultivated crosses allowed us to learn a lot about patterns of genetic and phenotypic variation in the wider barley gene pool.
“Indeed, we are still working on one of the genetic populations of barley that we studied in the GCP program, now using sophisticated phenotyping tools and approaches to explore how genes in defined segments of the wild barley genome help provide yield stability under drought conditions through architectural variation in the root system.”
Women harvesting barley in India.
GCP builds genetic resources through ongoing collaboration
Barley in rural Ethiopia.
For Michael, one of the most important outcomes of the GCP work was the ability to meet and work with researchers from other centres across the world.
“Before GCP, I had only visited two other CGIAR centres,” he says. “GCP was the first attempt to develop a programme across the CGIAR centres and to work on a specific topic, which was genetic resources. I would give GCP high marks for stimulating this cross-centre cooperation, particularly through their annual GCP meeting.”
And when the decision came to end barley research after the first phase of GCP, Michael found that he missed the GCP meetings: “I would have found it useful if I could have continued to attend the annual meetings,” he says. “These were much more important to me than getting the project funding out of GCP.”
Despite this and despite dealing with the challenge that some countries, such as China, were unable to provide the barley germplasm (samples of materials) that they initially promised, Michael has continued his relationships with some of the people he first met through GCP. “I’m still collaborating with China through a continuous bilateral effort on barley. Ten years later, the collaborations are still ongoing. Often when a project finishes, the collaboration finishes, but we are still continuing our collaboration on barley.”
Most importantly, Michael believes the GCP-supported and -funded collaborations brought a new approach to providing plant genetic resources to breeders. “The reference sets we assembled for barley and other crops provided a new way to look at large germplasm collections,” he says.
“This was one aim of GCP: about how to have a more rational look at germplasm collections. Now plant breeders don’t have to ask for five to ten thousand accessions of a crop, and then spend several years on evaluation.
“Now they have a higher chance of finding the genetic characteristics they want more quickly from the much smaller reference collection.”
And although the reference-set approach has been further refined since GCP’s first phase of research concluded, Michael believes it builds on what GCP started through its collaborative teams, with barley being just one example.
“GCP helped make it all happen,” he says.
For research and breeding products, see the GCP Product Catalogue and search for barley.
Each year, millions of people in Senegal go hungry for several months, many surviving on no more than one meal a day. Locals call this time soudure – the hungry period. It typically lasts from June through to September, when previous winter and spring cereal supplies are exhausted and people wait anxiously for a bountiful autumn cereal harvest.
During this period, a bowl of fresh green cowpea pods once a day is the best that many people can hope for. Cowpeas are the first summer crop to mature, with some varieties ready to harvest in as little as 60 days.
While cowpeas provide valued food security in Africa, yields remain low. In Senegal, average cowpea yields are 450 kilograms per hectare, a mere 10–30 percent of their potential. This poor productivity is primarily because of losses due to insects and diseases, but is sometimes further compounded by chronic drought.
In 2007, the CGIAR Generation Challenge Programme (GCP) brought together a team of plant breeders and geneticists from Burkina Faso, Mozambique, Nigeria, Senegal and the USA to collaborate on cowpea. Their goal was to breed varieties that would be higher yielding, drought tolerant and resistant to pests and diseases, and so help secure and improve local cowpea production in sub-Saharan African countries.
A trader selling cowpea at Bodija market, Ibadan, Nigeria.
Cowpea production – almost all of it comes from Africa
A type of legume originating in West Africa, cowpeas are also known as niébé in francophone Africa and as black-eyed peas in the USA. They are well adapted to drier, warmer regions and grow well in poor soils. In Africa, they are mostly grown in the hot, drought-prone savannas and very arid sub-Saharan regions, often together with pearl millet and sorghum.
Nutritionally, cowpeas are a major source of dietary protein in many developing countries. Young leaves, unripe pods and peas are used as vegetables, and the mature grain is processed for various snacks and main meal dishes. As a cash crop, both for grain and animal fodder, cowpea is highly valued in sub-Saharan Africa.
Worldwide, an estimated 14.5 million hectares of land is planted with cowpea each year. Global production of dried cowpeas in 2010 was 5.5 million tonnes, 94 percent of which was grown in Africa.
In 2011, Senegal experienced its third drought within a decade. Low and erratic rainfall led to poor harvests in 2011 and 2012: yields of cereal crops (wheat, barley and maize) fell by 36 percent compared to 2010. Consequently, the hungry period in 2012 started three months earlier than usual, making gap-fillers like cowpea even more important. In fact, cereal production in sub-Saharan African countries has not seen substantial growth over the last two decades – total area, yield and production grew by only 4.3 percent, 1.5 percent and 5.8 percent, respectively.
Climate change is expected to further compound this situation across sub-Saharan Africa. Droughts are forecast to occur more frequently, weakening plants and making them more vulnerable to pests and diseases.
“Improved varieties of cowpeas are urgently needed to narrow the gap between actual and potential yields,” says Ndiaga. “They will not only provide security to farmers in the face of climate change, but will also help with food security and overall livelihoods.”
Farmers in Northern Nigeria transport their cowpea harvest.
Mapping the cowpea genome
For over 30 years, Phil Roberts, a professor in the Department of Nematology at the University of California, Riverside (UCR), has been breeding new varieties of cowpea. “UCR has a long history of research in cowpea breeding that goes back to the mid-seventies,” explains Phil. “One of the reasons we were commissioned by GCP in 2007 was to use our experience, particularly in using molecular breeding, to help African cowpea-breeding programmes produce higher yielding cowpeas.”
For seven years, Phil and his team at UCR coordinated the cowpea component of the Tropical Legumes I (TLI) project led by GCP (see box below). The objective of this work was to advance cowpea breeding by applying modern, molecular breeding techniques, tools and knowledge to develop lines and varieties with drought tolerance and resistance to pests and diseases in the sub-Saharan African countries Burkina Faso, Mozambique, Nigeria and Senegal.
The molecular breeding technology that UCR uses for cowpeas is based on finding genes that help cowpea plants tolerate insects and diseases, identifying markers that can indicate the presence of known genes, and using these to incorporate valuable genes into higher yielding varieties.
“Using molecular breeding techniques is a lot easier and quicker, and certainly less hit-or-miss, than conventional breeding techniques,” says Phil. “We can shorten the time needed to breed better adapted cowpea varieties preferred by farmers and markets.”
Phil explains that the first priority of the project was to map the cowpea genome.
“The map helps us locate the genes that play a role in expressing key traits such as drought tolerance, disease resistance or pest resistance,” says Phil. “Once we know where these genes are, we can use molecular marker tools to identify and help select for the traits. This is a lot quicker than growing the plant and observing if the trait is present or not.”
To use an analogy, think of the plant’s genome as a story: its words are the plant’s genes, and a molecular marker works as a text highlighter. Molecular markers are not precise enough to highlight specific words (genes), but they can highlight sentences (genomic regions) that contain these words (genes), making it easier and quicker to identify which plants have them. Traditionally, breeders have needed to grow plants to maturity under appropriately challenging conditions to see which ones are likely to have useful traits, but by using markers to flag valuable genes they are able to largely skip this step, and test large amounts of material to choose the best parents for their crosses, then check which of the progeny have inherited the gene or genes.
Diversity of cowpea seed.
Breeding new varieties faster, using modern techniques
A farmer pleased with her cowpea plants.
The main focus of the cowpea component in TLI was to optimise marker-assisted recurrent selection (MARS) and marker-assisted backcrossing (MABC) breeding techniques for sub-Saharan African environments and relevant traits.
MARS identifies regions of the genome that control important traits. In the case of cowpeas, these include drought tolerance and insect resistance. It uses molecular markers to explore more combinations in the plant populations, thus increasing breeding efficiency.
MABC is the simplest form of marker-assisted breeding, in which the goal is to incorporate a major gene from an agronomically inferior source (the donor parent) into an elite cultivar or breeding line (the recurrent parent). Major genes by themselves have a significant effect; it’s therefore easier to find a major gene associated with a desired trait, than having to find and clone several minor genes. The aim is to produce a line made up almost entirely of the recurrent parent genotype, with only the selected major gene from the donor parent.
Using the genome map and molecular markers, the UCR team identified 30 cowpea lines with drought tolerance and pest resistance from 5,000 varieties in its collection, providing the raw material for marker-assisted breeding. “Once we knew which lines had the drought-tolerance and pest-resistance genes we were looking for, we crossed them with high-yielding lines to develop 20 advanced cowpea lines, which our African partners field tested,” says Phil.
The lines underwent final field tests in 2014, and the best-yielding drought-tolerant lines will be used locally in Burkina Faso, Mozambique and Senegal to develop new higher yielding varieties that will be available to growers by 2016.
“While we are still some time off from releasing these varieties, we already feel we are two or three years ahead of where we would be if we were doing things using only conventional breeding methods,” says Ndiaga.
A parasitic Striga plant, in a cowpea experimental plot.
The genome map and molecular markers have helped cowpea breeders like Ousmane Boukar, cowpea breeder and Kano Station Representative with the International Institute of Tropical Agriculture (IITA), headquartered in Nigeria, to locate the genes in cowpeas that play a role in expressing desirable traits.
Ousmane, who was GCP’s cowpea Product Delivery Coordinator, says, “We have used this technology to develop advanced breeding lines that are producing higher yields in drier conditions and displaying resistance to several pests and diseases like thrips and Striga. We expect these lines to be available to plant breeders by the end of 2015.
“TLI has had a huge impact in Africa in terms of developing capacity to carry out marker-assisted breeding,” he says. “This form of breeding helps us to breed new varieties in three to five years instead of seven to ten years.”
Burkina Faso – evaluating new lines to improve the country’s economy
Cowpea is an important crop for the people of Burkina Faso. Over 10 million farmers produce on average 800,000 tonnes of cowpeas each year, making the country the third largest producer in the world, behind neighbours Nigeria and Niger.
Much of Burkina Faso’s cowpea crop is consumed domestically, but the government sees potential in increasing productivity for export to Côte d’Ivoire and Ghana in the south. This new venture would improve the country’s gross domestic product (GDP), which is the third lowest in the world.
“We’ve been working closely with UCR to evaluate advanced breeding lines that we can use in our own breeding programme. So far we have several promising lines, some of which breeders are using to create varieties for release to farmers – some as early as this year.”
Farmers in Burkina Faso discuss cowpea varieties during participatory varietal selection activities.
Outsourcing the molecular work
Issa says his team has mainly been using conventional breeding techniques and outsourcing the molecular breeding work to the UK and USA. “We send leaf samples to the UK to be genotyped by a private company [LGC Genomics], who then forward the data to UCR, who analyse it and tell us which plants contain the desired genes and would be suitable for crossing.”
The whole process takes four to six weeks, from taking the samples to making a decision on which plants to cross.
“This system works well for countries that don’t have the capacity or know-how to do the molecular work,” says Darshna Vyas, a plant genetics specialist with LGC Genomics. “Genotyping has advanced to a point where even larger labs around the world choose to outsource their genotyping work, as it is cheaper and quicker than if they were to equip their lab and do it themselves. We do hundreds of thousands of genotyping samples a day – day in, day out. It’s our business.”
Darshna says LGC Genomics have also developed plant kits, as a result of working more with GCP partners from developing countries. “We would receive plant tissue that was not properly packaged and had become mouldy on the journey. The plant kits help researchers package their tissue correctly. The genotyping data you get from undamaged tissue compared to damaged tissue is a thousand times better.”
Getting the genotyping expertise on the ground
A trader bagging cowpeas at Bodija market, Ibadan, Nigeria.
To reduce their African partners’ reliance on UCR, researchers from the university, including Phil, have been training young plant breeders and PhD students from collaborating institutes. Independent of the cowpea project, they have also been joining GCP’s Integrated Breeding Platform (IBP) training events in Africa to help breeders understand the new technologies.
“All this capacity building we do really gets at the issue of leaving expertise on the ground when the project ends,” says Phil. “If these breeders don’t have the expertise to use the modern breeding technologies, then we won’t make much progress.”
GCP Capacity Building Theme Leader and TLI Project Manager Ndeye Ndack Diop has been impressed by UCR’s enthusiasm to build capacity in its partner countries. “Capacity building is a core objective for GCP and the TLI project,” says Ndeye Ndack. “While it is built into almost all GCP projects, UCR have gone over and above what was expected of them and contributed towards building capacity not only among its partner institutions, but in many other African national breeding institutes as well.”
Issa Drabo reports that in 2014 two of his young researchers from Burkina Faso completed their training in GCP’s Integrated Breeding Multiyear Course, conducted by UCR and the IBP team.
One of Issa’s researchers at INERA, Jean-Baptiste de la Salle Tignegré, says the course helped him understand more about the background genetics, statistical analysis and data management involved in the process of molecular breeding. “Because of the course, we are now able to analyse the genotype data from LGC,” he says.
Mozambique – insects and drought are the problem
In 2010, the Universidade Eduardo Mondlane (UEM) joined the cowpea component of TLI, three years after the project started. “We were a little late to the party because we were busy setting up Mozambique’s first cowpea breeding programme, which only began in 2008,” recalls Rogerio Chiulele, a lecturer at the university’s Faculty of Agronomy and Forestry Engineering and lead scientist for cowpea research in Mozambique for TLI.
That year (2008), UEM received a GCP Capacity building à la carte grant to establish a cowpea-breeding programme for addressing some of the constraints limiting cowpea production and productivity, particularly drought, pests and diseases.
As in Burkina Faso and Senegal, in Mozambique cowpeas are an important source of food, for both protein and profit, particularly for the poor. Cowpeas rank as the fourth most cultivated crop in Mozambique, accounting for about nine percent of the total cultivated area, or an estimated four million hectares of smallholder farms.
Cowpea plants infested by aphids.
Rogerio says that farmers in his country, just as in other parts of Africa, struggle to reach their full yield potential because of climate, pests and diseases. “Several insect pests – such as aphids, flower thrips, nematodes and pod-sucking pests – can substantially reduce cowpea yield and productivity in Mozambique,” he says.
“Cowpea aphids can cause problems at any time in the growing season, but are most damaging during dry weather when they infest seedlings that are stressed from lack of water. In wetter parts of the country, flower thrips – which feed on floral buds – are the most damaging insect pest.” These insects are also major pests in Burkina Faso and Senegal, along with hairy caterpillar (Amsacta moloneyi), which can completely destroy swaths of cowpea seedlings.
Rogerio says breeding for insect resistance and drought tolerance, using marker-assisted techniques, improves breeders’ chances of increased cowpea productivity. “Productivity is key to increasing rural incomes, and new resources can then be invested in other activities that help boost total family income,” says Rogerio. “These new breeding techniques will help us achieve this quicker.”
Three high-yielding varieties to hit the Mozambique market in 2015
Mature cowpea pods ready for harvesting.
Since 2010, Rogerio’s team have quickly caught up to Burkina Faso and Senegal and plan to release three higher yielding new lines with drought tolerance in 2015. One of these lines, CB46, is based on a local cowpea variety crossed with a UCR-sourced American black-eyed pea variety that displays drought tolerance, which potentially has huge market appeal.
“Local varieties fetch, on average, half a US dollar per kilogram, compared to black-eyed pea varieties, whose price is in the region of four to five US dollars,” says Rogerio. “Obviously this is beneficial to the growers, but the benefits for consumers are just as appealing. The peas are better quality and tastier, and they take half as long to cook compared to local varieties.”
All these extra qualities are important to consider in any breeding programme and are a key objective of the Tropical Legume II (TLII) project (see box above). TLII activities, led by ICRISAT, seek to apply products from TLI to make an impact among farmers.
“TLII focuses on translating research outputs from TLI into tangible products, including new varieties,” says Ousmane Boukar, who works closely with Ndiaga, Issa and Rogerio in TLI and TLII.
Building a community of breeders to sustain success
Cowpea flower with developing pods.
Part of Ousmane’s GCP role as Product Delivery Coordinator for cowpeas was to lead a network of African cowpea and soybean breeders, and he champions the need for breeders to share information and materials as well as collaborating in other ways so as to sustain their breeding programmes post-GCP.
“To sustain integrated breeding practices post-2014, GCP has established Communities of Practice (CoP) that are discipline- and commodity-oriented,” says Ndeye Ndack. “The ultimate goal is to provide a platform for community problem solving, idea generation and information sharing.”
Ousmane says the core of this community was already alive and well before the CoP. “Ndiaga, Issa and I have over 80 years combined experience working on cowpea. We have continually crossed paths and have even been working together on other non-GCP projects over the past seven years.”
One such project the trio worked together on was to release a new drought-tolerant cowpea breeding line, IT97K-499-35, in Nigeria. “The performance of this variety impressed farmers in Mali, who named it jiffigui, which means ‘hope’,” says Ousmane. “We shared these new lines with our partners in Mali and Niger so they could conduct adaptation trials in their own countries.”
For young breeders like Rogerio, the CoP has provided an opportunity to meet and learn from these older partners. “I’ve really enjoyed our annual project meetings and feeling more a part of the world of cowpea breeding, particularly since we in Mozambique are isolated geographically from larger cowpea-producing countries in West Africa.”
For Phil Roberts, instances where more-established researchers mentor younger researchers in different countries give him hope that all the work UCR has done to install new breeding techniques will pay off. “Young researchers represent the future. If they can establish a foothold in breeding programmes in their national programmes, they can make an impact. Beyond having the know-how, it is vital to have the support of the national programme to develop modern breeding effort in cowpea – or any crop.”
Setting up breeders for the next 20 years
Farmer harvesting mature cowpea pods.
In Senegal, Ndiaga is hopeful that the work that the GCP project has accomplished has set up cowpea breeders in his country and others for the next 20 years.
“Both GCP’s and UCR’s commitment to build capacity in developing countries like Senegal cannot be valued less than the new higher yielding, drought-tolerant varieties that we are breeding,” says Ndiaga. “They have provided us with the tools and skills now to continue this research well into the future.
“We are close to releasing several new drought-tolerant and pest- and disease-resistant lines, which is our ultimate goal towards securing Senegal’s food and helping minimise the impact of the hungry period.”
Farmer Maria Mtele holds recently harvested orange-fleshed sweetpotatoes in a field in Mwasonge, Tanzania.
Sweetpotato has a long history as a lifesaver. The Japanese used it when typhoons demolished their rice fields. It kept millions from starvation in famine-plagued China in the early 1960s and came to the rescue in Uganda in the 1990s, when a virus ravaged the cassava crop.
In sub-Saharan Africa, sweetpotato is proving crucial in the fight against blindness, disease and premature death among children under five. And, as agriculture becomes more market-oriented across the continent, sweetpotato has some significant advantages: it requires fewer inputs and less labour than other crops such as maize, tolerates marginal growing areas and can mature within four months.
On these fertile grounds, researchers across the globe are not underestimating the importance of sweetpotato as a staple crop.
“Yields achieved by resource-poor farmers in sub-Saharan Africa are typically low,” says Roland Schafleitner of the International Potato Center (CIP), based in Peru.
“Improved and well-adapted sweetpotato varieties with increased tolerance to drought, pests and diseases will have a positive impact on food and income security in sub-Saharan Africa and can significantly contribute to increasing productivity,” he says.
Roland was Principal Investigator of two research projects funded by the CGIAR Generation Challenge Programme (GCP), which developed genetic and genomic resources for breeding improved sweetpotato.
At the outset of the work, Roland says: “Breeding efforts were limited by the crop’s genetic complexity and the lack of information available about its genetic resources.
“It was clear that if we could develop genetic tools and make concerted efforts towards understanding the gene pool of sweetpotato, the breeding potential of the crop would improve.”
Farmer Mwanaidi Rhamdani at work in an orange-fleshed sweetpotato field in Mwasonge, Tanzania.
Sub-Saharan Africans getting their vitamin A from sweetpotato
Sweetpotato diversity.
Malnutrition does not always mean a simple lack of calories; research suggests that nutrient shortfalls are an even bigger killer. Vitamin A deficiency is a leading cause of blindness, infectious disease and premature death among children under five and pregnant women in sub-Saharan Africa and Asia.
Sweetpotato comes in a wide range of colours. Varieties with dark orange flesh are naturally very rich in the pigment beta-carotene, which the body converts into vitamin A. However, the sweetpotatoes traditionally grown in Africa are pale-fleshed and low in beta-carotene. African consumers were not used to eating colourful sweetpotato – and these orange-fleshed varieties were in any case not well adapted African growing conditions.
Recent years have therefore seen a collaborative effort by researchers across the world to breed orange-fleshed sweetpotato varieties fortified with high levels of beta-carotene, and even enriched with other nutrients, that have also been crossed with local varieties and so are adapted to local conditions and tastes. A crucial part of these efforts has also been to create public awareness and encourage people to grow, eat and buy these new varieties.
Two cheeky young chappies from Mozambique enjoy the sweet taste of orange-fleshed sweetpotato rich in beta-carotene, or pro-vitamin A.
All of this adds to the growing momentum behind sweetpotato. The growing awareness of sweetpotato’s potential nutritional benefits for the poor and food insecure, as well as its value for subsistence farmers as a reliable crop that withstands drought and requires minimal inputs, mean that it is growing in significance.
Orange-fleshed sweetpotato can be used to make a variety of tasty products from doughnuts to chapati.
More than 95% of the world’s sweetpotato crop is grown in developing countries, where it is the fifth most important staple food crop. It is particularly important in many African countries: Madagascar in Southern Africa; Nigeria in West Africa; and those surrounding the Great Lakes in East and Central Africa – Uganda, Malawi, Angola and Mozambique.
According to 2013 figures from the Food and Agriculture Organization of the United Nations, 3.6 million hectares of sweetpotato were harvested in Africa. While the average global yield of sweetpotato per hectare was 14.8 tonnes, across all East African countries in 2013 it was only half this, at 7.1 tonnes per hectare. In West African nations the average yield was even worse, at 3.7 tonnes per hectare.
Farmers are unable to make the most of their crops because the varieties available to them, including traditional varieties (or landraces) have low resistance to viral diseases and insect pests, and poor tolerance to drought. It is therefore crucial that when developing new varieties breeders are able to efficiently incorporate pest and disease resistance and drought tolerance traits.
New DNA markers identified for sweetpotato disease
The sweetpotato virus disease (SPVD) is the most serious disease affecting sweetpotato in sub-Saharan Africa. It often causes serious yield losses of up to 80–90 percent.
The disease is the result of joint infection by two viruses: the sweetpotato feathery mottle virus and the sweetpotato chlorotic stunt virus. Of the two, the stunt virus is the more problematic.
Wolfgang Grüneberg, also from CIP, says that, in the years 2006–2008, 52 new DNA markers were developed as part of GCP-funded research to improve marker-assisted selection for resistance to the disease.
“The results,” says Wolfgang, Principal Investigator for the research, “looked promising for developing a large number of orange-fleshed sweetpotatoes with resistance to SPVD.”
Immediately following the development of the markers, two varieties of sweetpotato were developed using a cloned gene, Resistan, known to confer resistance to the virus. The first variety was used to improve an SPVD test system so that the disease could be diagnosed earlier if a crop was affected. The second variety underwent field tests in regions in Uganda that were highly affected by the disease.
Sweetpotato vines and roots.
Mobilising the genetic diversity of sweetpotato for breeding
The goals of the GCP-supported work were to develop a diverse genetic resource base for sweetpotato and stimulate the use of new tools in ongoing breeding programmes.
To help transfer this work from high-end laboratories to resource-poor research labs in developing countries, GCP promoted collaboration across institutions and borders. Researchers from Brazil, Mozambique, Uganda and Uruguay worked together on sweetpotato genetic research projects.
As Roland explains, the basic first steps needed to begin to ‘mobilise’ the genetic diversity of sweetpotato were developing a reference set of varieties and improving genomics tools to work with polyploid crops, i.e. those possessing multiple sets of chromosomes, such as sweetpotato.
GCP-supported researchers in Peru and sub-Saharan Africa defined a reference set of 472 varieties of sweetpotato, carefully selected and honed to represent both the diversity of the crop and its most important agronomical and nutritional traits.
“Based on a reference set, genetic markers can be developed that are associated with important characteristics of the crop and can help breeders to select favourable genotypes,” says Roland.
The gene sequences developed during the Programme are now available as a Sweetpotato Gene Index.
“Based on these sequences,” says Roland, “molecular markers have been designed that can help breeders and gene-bank curators to assess the genetic diversity of their accessions and to perform genetic mapping studies.
“Today, techniques that yield a much larger number of markers for genetic studies and selection are accessible for sweetpotato,” he says.
Mwanaidi Rhamdani (left) works with Maria Mtele in an orange-fleshed sweetpotato field in rural Tanzania.
The genetic lifelines reach Africa
Sweetpotato is one of the most important staple crops in Mozambique, ranking in third position after cassava and maize. The areas harvested in Mozambique in 2013 were 1.7 million hectares of maize, 780,000 hectares of cassava and 120,000 hectares of sweetpotato.
A child eats cooked orange-fleshed sweetpotato in Uganda.
GCP funded breeders in Mozambique and Uganda to learn how to identify genetic markers that would prove useful for future sweetpotato breeding.
“Our African partners visited us at CIP and helped us complete the work on identifying markers,” recalls Roland. “This provided the opportunity for direct ‘technology transfer’ to breeders in the target region.”
The collaboration had, for the first time, created a critical amount of genetic and genomics resources for sweetpotato. The resulting Sweetpotato Gene Index and the new markers were published in a peer-reviewed journal, BMC Genomics (2010) 11:604.
The new genetic resources are in use at CIP in Peru and in breeding programmes in Burkina Faso, Mozambique, Uganda, Uruguay and the USA for the assessment of the genetic diversity of germplasm collections.
“The markers have been used for diversity analysis, especially at the CIP gene bank, and also in Africa,” says Roland, who says the markers will help future research.
“Such analysis guides germplasm conservation decisions, and diversity studies are a great tool to develop core collections and composite genotype sets – subsets of the whole collection – which allow for more practical screening for specific traits than large collections.”
A farmer transports bananas to market by bicycle in Uganda.
At whatever time of the day or night you are reading this, somewhere in the world there are sure to be farmers trekking many kilometres to take their bananas to local markets. These small-scale farmers produce almost 90 percent of the world’s bananas, and make up a significant portion of the 400 million people around the globe’s tropical girdle – Africa, Asia and Latin America – who rely on bananas for food and a source of income.
Bananas are often called the world’s most popular fruit, and global production in 2012 was almost 140 million tonnes. India is the largest producer, while South and Central American farmers supply the most to international supermarket shelves, exporting 80 percent of their bananas.
The importance of the banana as a food crop in tropical areas cannot be underestimated. More than a simple snack, plantain-type bananas in particular are a key component in savoury dishes. In Central and East African countries – like Cameroon, Gabon, Rwanda and Uganda – one person will eat an average of between 100 kg and 250 kg of banana each year. That equates to somewhere between 800 and 2000 average-sized bananas. In those four countries, bananas account for up to a quarter of people’s daily calorie intake.
A stallholder offers bananas for sale at a fruit market in Nairobi, Kenya.
Banana’s asexuality inhibits its resilience
Bananas growing in Rwanda.
Banana propagates though asexual reproduction. This means that all the bananas of each variety are genetically identical, or nearly so, and therefore susceptible to the same diseases. Indeed, the world has already lost almost its entire banana crop once: before the 1950s, the Gros Michel cultivar dominated banana exports, but it was gradually wiped out in most regions by Panama disease, caused by the fungus Fusarium oxysporum. Furthermore, with reproduction being asexual, it is difficult to develop new, resistant varieties through conventional breeding.
At the turn of the twenty-first century, pests and diseases were once again becoming a real threat to global banana production. Little genetic research had been done on the fruit, and only a small portion of its genes had been used in breeding new varieties in its 7,000-year history as a cultivated crop.
“Several research groups had developed genetic markers for bananas [‘flags’ on the genome that can be linked to physical traits], but there was no coordination and only sketchy germplasm studies,” recalls Jean Christophe Glaszmann from CIRAD (Centre de coopération internationale en recherche agronomique pour le développement; Agricultural Research for Development) in France.
A plantain farmer walks through a plantation in Quindió, Colombia.
“It was not a priority,” says Jean Christophe, who was Subprogramme Leader for Genetic Diversity for the CGIAR Generation Challenge Programme (GCP), an international initiative established in 2004 to encourage the use of genetic diversity and advanced plant science to improve crops.
But between 2004 and 2012, under GCP, a wealth of research work was undertaken that culminated in the complete genetic sequencing of banana. It was a long process, says Jean Christophe, but the GCP-funded work on banana made a significant contribution to important results.
The extensive data on the genetics of banana are now available to scientists worldwide, who can use it to delve deeper into banana’s genes to breed varieties that can sustain the poorer populations in developing countries.
Once finally sequenced, the banana genome was published in one of the most prestigious scientific journals, Nature, in July 2012: “The reference Musa [banana and plantains] genome sequence represents a major advance in the quest to unravel the complex genetics of this vital crop, whose breeding is particularly challenging. Having access to the entire Musa gene repertoire is a key to identifying genes responsible for important agronomic characters, such as fruit quality and pest resistance.”
Passionate people pooled for the work
A banana seller in Hanoi, Vietnam.
Plans to sequence the banana genome started taking shape in 2001 at Bioversity International (a CGIAR centre), where a group of scientists formed the Global Musa Genomics Consortium. At that time, the only plant whose genome had been sequenced was Arabidopsis thaliana (a small flowering plant related to cabbage and mustard, used as a model organism in plant science), with rice close behind.
CGIAR established GCP in 2004 “to tap into the rich genetic diversity of crops via a global network of partnerships and breeding programmes,” according to Hei Leung, who was instrumental to GCP’s foundation and a Subprogramme Leader for Comparative Genomics. (During its first phase GCP was organised by Subprogramme; these were later replaced by Research Themes and Research Initiatives.)
Hei acknowledges that banana was ‘somewhat on the fringe’ of GCP’s main focus on improving drought tolerance in crops. However, he says, it was still relevant for GCP to support the emergence of improved genetics for banana.
“The work we did in genetic diversity is about future generations. We wanted a programme that is pro-poor, meaning that the majority of the people in the world are depending on [the crop].
A typical banana and plantain market at Ikire in Osun State, Nigeria.
“Drought tolerance is a good candidate because drought affects a lot of poor areas, but you really cannot just take one trait as pro-poor. We had a highly motivated group of researchers willing to devote their efforts to Musa,” says Hei.
“Nicolas Roux at Bioversity International was a passionate advocate for the partnership,” notes Hei. “The GCP community offered a framework for novel interactions among banana-related actors and players working on other crops, such as rice.”
Nicolas concurs on the potential for a little banana research to have great value: “Even though banana is among the most important basic food crops for 400 million people, and 100 million tonnes are grown annually on over 10 million hectares in 120 countries, it’s still under-researched and underfunded.”
Creating a reference set – a careful, tactical selection representing the genetic diversity of a crop – is an invaluable first step in enabling scientists to work together to develop more ‘intelligent’ genetic data.
“Initially, we put together a community of institutions that have collections [of banana germplasm],” explains Jean Christophe. “And then we put together these initial materials that we sample in order to develop representative subsamples – this is called a ‘composite’ set because it comes from different institutions.
“Then we genotype this composite collection, and the genotyping allows us to understand how all this [genetic material] is structured. Based on how it is structured, we can re sample a smaller representation – this is what becomes a reference set.”
So, in the case of crops with an extensive genetic resource base, such as rice, there may be more than 100,000 different plant samples, or accessions, that are reduced to a few thousand. For banana, which has a smaller genetic resource base, a few hundred thousand accessions can be reduced to a few dozen.
“A couple of hundred accessions or fewer become manageable for plant breeders or crop specialists. And we want this to serve as a reference, shared among people, so that everybody works on the same reference material,” says Jean Christophe.
“If you work on the same reference material, you can compile information that is more intelligent – you can have the crop specialist who says ‘this is resistant; this is tolerant; this is susceptible’, and you can also have the biochemist, you can have the physiologist; in the end, you can compile the information.”
“We analysed about 500 accessions and narrowed it down to 50,” says Jean Christophe. This reference collection is currently stored at the University of Leuven in Belgium.
The refined data collected on the banana reference set enabled the researchers to unravel the origin and genealogy of the most important dessert banana: the Cavendish, the cultivar subgroup that dominates banana exports worldwide. Thanks to the early GCP work, they were able to show that Cavendish bananas evolved from three markedly different subspecies.
65-year-old Cambodian farmer, Khout Sorn, stands in front of his banana trees in Aphiwat Village, Tipo commune, Cambodia.
Malaysian wild subspecies fully sequenced
During these preliminary years of GCP-supported research on banana, the Programme funded several other smaller projects to consolidate genomic resources available for banana. Scientists developed libraries of artificial chromosomes that can be used in sequencing the DNA of banana, as well as genetic maps, which according to Jean Christophe are essential for improving the quality of the sequence.
These projects contributed to the full genome sequencing of a wild banana from Malaysia’s Pahang province in 2008. The ‘Pahang’ subspecies is one of the Cavendish variety’s three ancestors, and has also been shown to have had a role in the origin of many other banana cultivars, including those that are most important for food and economic security.
“GCP did not fund the sequence [of the Pahang banana], but it funded several things that made it possible to undertake full-scale sequencing,” Jean Christophe says. “It supported the development of particular resources and tools, and this made it possible for researchers to start the full-length sequencing.”
A farmer at work on a banana plantation, Mindanao, the Philippines.
Breeders now need to set to work
The more that is known about the genes responsible for disease resistance and other desirable traits in banana, the more researchers will be able to help farmers in developing countries to improve their yields.
“The road remains long, but now we have a good understanding of genetic diversity,” says Jean Christophe. “We have done a range of studies aimed at unravelling the genes that could control sterility in the species.
“This is undoubtedly an inspiring challenge towards unlocking the genetic diversity in this crop.
“If we have more money in the future, we are going to sequence others of the subspecies so that we can have the full coverage of the current Cavendish genome. But that was a good start,” says Jean Christophe.
“What we have to do now is to create the right populations [of banana] in the field so that we can separate out the characteristics we want to breed for.”
The new intelligence on banana genetics has given breeders the material they need that will ultimately help 400 million people in the tropics sustain food supplies and livelihoods.
“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 woman holds yam tubers in her hands in a market in West Africa.
Yam production in West Africa is plagued by unsustainable and suboptimal practices. Most farmers continue to grow local varieties that produce poor yields – and also lack aesthetic qualities that appeal to consumers, such as smooth skin and elegant tuber shape.
For a better future and a sustainable food supply, farmers need access to improved yam varieties that can tolerate changes in the climate and environment, as well as resist pests and diseases. Adopting new practices will also help farmers to increase their yields.
Despite the importance of yams in West Africa, breeding efforts for improved varieties have been limited for a number of reasons. One is that local yam cultivars have different names in different communities, making germplasm management and research difficult. Another obstacle is the constraints on yam growth – the plants have a long growth cycle and are highly susceptible to pests and diseases, poor soil, weeds and drought.
Dancers celebrate at a new yam festival in Nigeria.
Unique collaborations get yam research rolling
A farmer in his yam field in Nigeria.
In 2004, the CGIAR Generation Challenge Programme (GCP) recognised the need to provide resource-poor farmers in West Africa with yam varieties that combine high yields with drought tolerance, pest and disease resistance, and good tuber quality. The Programme was created to advance plant genetics for 21 crops, with a view to improving the resources and capabilities of local breeders in developing countries. Yams were one of the crops that received funding for the first half of the 10-year Programme.
Robert Asiedu, Principal Investigator for GCP’s project assessing the genetic diversity of yams in West Africa, says the Programme improved yam breeding through its unique collaborations.
Andrzej Kilian, DArT’s founder and director, says: “My company had a range of interactions with GCP, and I hope we had some positive impact on the outcomes.”
The researchers used molecular breeding tools – simple sequence repeat markers, or SSRs – to assess the genetic diversity of more than 500 yam accessions from Benin, DR Congo, Côte d’Ivoire, Equatorial Guinea, Gabon, Ghana, Nigeria, Sierra Leone and Togo. The assessment was a huge step forward in expanding the scientific knowledge of yam genetics, and ultimately in identifying suitable material for use in breeding programmes.
Walking in yam fields.
IITA research scientist Maria Kolesnikova-Allen, also funded by GCP, says the yam work had two main objectives.
Yam vines twist up bamboo staking in a yam field.
“The primary focus of the first projects on yams involving molecular markers was to assess genetic diversity among yams originating from different West African countries and to find relationships between species. This information is important for future breeding and conservation efforts,” she says.
“Also, we were interested in confirming the use of molecular markers for analysis of yams and their potential use in breeding programmes.
“By confirming their usefulness in yam studies, we have offered a robust tool set for further studies on this crop.”
A trader displays clean and dried yam tubers at Bodija market, Ibadan, Nigeria.
As a result of the research, she says, “more knowledge and understanding has been achieved in terms of the genetic structure of yam populations in West and Central Africa, providing breeders with important knowledge for accessions selection to be included in breeding programmes.”
The genetic information that has been generated for yams will directly benefit countries in West Africa, according to Maria, “especially with IITA being positioned in the middle of the region and providing expert advice and dissemination of this information to local breeders and farmers.”
As part of her GCP-supported work, Maria supervised West African PhD students Jude Obidiegwu from Nigeria and Emmanuel Otoo from Ghana. Jude, a researcher at the National Root Crops Research Institute (NRCRI) in Nigeria, was responsible for GCP’s work on the genetic diversity of yams. His PhD assessed the genetic diversity of the West African yam collection.
African researchers carry GCP torch forward for yams
Jude is an example of how GCP focussed on fostering a base of experts on the ground in the countries where yams play an important role in people’s lives.
Woman counting money from the sales of yams at a yam market in Accra, Ghana.
“Our students at PhD level from Nigeria and Ghana were the main drivers of the projects at laboratory and field experiments level,” says Maria.
“Being involved in the projects allowed them to gain international exposure in their respective research fields and later advance their scientific career, becoming fully fledged yam scientists in their own right.
“If there be any hope of applying advanced genetics and genomics tools to the improvement of yam, it is researchers like Jude who will be the foot soldiers of that work in Africa.”
A drummer adds his music to a new yam festival in Nigeria.
Maria feels there are strong foundations for further development of yam’s genetic resources after GCP’s sunset at the end of 2014.
“I would like to hope the future is bright,” she says. “As programmes for reducing hunger and poverty are multiplying and gaining momentum worldwide, I am sure the research on staple crops will be given much-needed financial support.
“I strongly believe in a partnership approach,” she maintains, drawing an analogy between GCP’s focus on crop genetics and the Human Genome Project that involved more than 300 partners collaborating between 1990 and 2003 to identify, map and sequence the human genome.
Robert agrees, forecasting that: “New projects will raise the capacity for yam breeding in West Africa by developing high-yielding and robust varieties of yams preferred by farmers and suited to market demands.”
A woman offers yam flour (known as elubo isu) for sale in Bodija market, Ibadan, Nigeria.
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
