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Groundnut boom may help crack poverty in Africa

Africa, Capacity building, Crop breeding, Genetics, Genomics, Groundnuts, Legumes No Responses »

Jun 222015

Photo: Joseph Hill/Flickr (Creative Commons)

Groundnut plants growing in Senegal.

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.

Photo: Y Wachira/Bioversity International

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.

Superior bean pods boost yields in face of drought

Africa, Beans, Capacity building, Crop breeding, Legumes No Responses »

Jun 192015

Bean Market in Kampala, Uganda.

Common beans are the world’s most important food legume, particularly for subsistence and smallholder farmers in East and Southern Africa. They are a crucial source of protein, are easy to grow, are very adaptable to different cropping systems, and mature quickly.

To some, beans are ‘a near-perfect food’ because of their high protein and fibre content plus their complex carbohydrates and other nutrients. One cup of beans provides at least half the recommended daily allowance of folate, or folic acid – a B vitamin that is especially important for pregnant women to prevent birth defects. One cup also supplies 25–30 percent of the daily requirement of iron, 25 percent of that of magnesium and copper, and 15 percent of the potassium and zinc requirement.

Unfortunately, yields in Africa are well below their potential – between 20 and 30 percent below. The main culprit is drought, which affects 70 percent of Africa’s major bean-producing regions. Drought is especially severe in the mid-altitudes of Ethiopia, Kenya, Malawi and Zimbabwe, as well as across Southern Africa.

“For the past seven or eight years, rains have been very unreliable in central and northern Malawi,” says Virginia Chisale, a bean breeder with Malawi’s Department of Agricultural Research and Technical Services.

“In the past, rains used to be very reliable and people were able to know the right time to plant to meet the rains in critical conditions,” she says. “Now these primary agriculture regions are either not receiving rain for long periods of time, or rains are not falling at the right time.”

Virginia recounts that during the 2011/12 cropping season there were no rains soon after planting, when it is important that beans receive moisture. Such instances can cut bean yields by half.

Steve Beebe in the field.

“Drought is a recurrent problem of rainfed agriculture throughout the world,” says Steve Beebe, a leading bean breeder with the International Center for Tropical Agriculture (CIAT). “Since over 80 percent of the world’s cultivated lands are rainfed, drought stress has major implications for global economy and trade.”

Steve was the Product Delivery Coordinator for the beans component of the Legumes Research Initiative (RI), part of Phase II of the CGIAR Generation Challenge Programme (GCP). The RI incorporated several projects, the biggest of which was Tropical Legumes I (TLI) (see box). The main objective of the work on beans within TLI was to identify and develop drought-tolerant varieties using marker-assisted breeding techniques. The resulting new varieties were then evaluated for their performance in Ethiopia, Kenya, Malawi and Zimbabwe.

“It’s vital that we develop high-yielding drought-tolerant varieties so as to help farmers, particularly in developing countries, adapt to drought and produce sustained yields for their families and local economies,” says Steve.

For an overview of the work on beans from the perspectives of four different partners, watch our video below, “The ABCs of bean breeding”.

What makes a plant drought tolerant?

The question of what makes a plant drought tolerant is one that breeders have debated for centuries. No single plant characteristic or trait can be fully responsible for protecting the plant from the stress of intense heat and reduced access to water.

“It’s a difficult question to answer for any plant, including beans,” says Steve. “Once you do isolate a trait genetically, it can often be difficult to identify this trait in a plant in the field, for example, identifying the architecture and length of a plant’s roots.”

Phenotyping is an important process in conventional plant breeding. It involves identifying and measuring the presence of physical traits such as seed colour, pod size, stem thickness or root length. Gathering data about a range of such characteristics across a number of different plant lines helps breeders decide which plants to use as parents in crosses and which of the progeny have inherited useful traits.

Root length has long been thought of as a drought-tolerance trait: the longer the root, the more chance it has of tapping into moisture stored deeper in the soil profile.

Given, however, that it is difficult to inspect root length in the field, researchers at CIAT have been exploring other more accessible drought-tolerance traits they can more easily identify and measure. One of these is measuring the weight of the plants’ seeds.

Comparison between varieties in trials of drought tolerant beans at CIAT’s headquarters in Colombia.

Fat beans indicate plants coping with drought stress

“We measure seed weight because we are discovering that under drought stress, drought-tolerant bean varieties will divert sugars from their leaves, stems and pods to their seed,” says Steve. “We call this trait ‘pod filling’, and for us it is the most important drought-tolerance trait to be found over the last several years.”

Finding bean plants with larger, heavier seeds when growing under drought conditions indicates that the plants are coping well, and means farmers’ yields are maintained.

As part of GCP’s Legumes RI, African partners like Virginia have been measuring the seed weight of several advanced breeding lines, which can be used as parents to develop new varieties. These breeding lines have been bred by CIAT and demonstrate this pod-filling process and consequent tolerance of drought.

Although this measurement is relatively cheap and easy for breeders all over the world to do, Steve and his team are interested in finding an even more efficient way to spot plants that maintain full pods under drought.

“We are trying to understand which genes control this trait so we can use molecular-assisted breeding techniques to determine when the trait is present,” says Steve. Having identified several regions of genes related to pod filling, he and his team have developed molecular markers to help breeders identify which plants have these desired genes. “The use of molecular markers in selection significantly reduces the time and cost of the breeding process, making it more efficient. This means that we get improved varieties out to farmers more quickly.”

Bean farmer in Rwanda.

Molecular markers (also known as DNA markers) are used by researchers as ‘flags’ to identify particular genes within a plant’s genome (DNA) that control desired traits, such as drought tolerance. These markers are themselves fragments of DNA that highlight particular genes or regions of genes by binding near them.

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 (genes), making it easier and quicker to identify whether or not they are present.

Beans from Rwanda.

Plant breeders can use molecular markers from early on in the breeding process to choose parents for their crosses and determine whether progeny they have produced have the desired trait, based on testing only a small amount of seed or seedling tissue.

“If the genes are present, we grow the progeny and conduct the appropriate phenotyping; if not, we throw the progeny away,” explains Steve. “This saves us resources and time because we need to grow and phenotype only the few hundred progeny which we know have the desired genes, instead of a few thousand progeny, most of which would not possess the gene.”

GCP has supported this foundation work, building on the extensive bean research already done by CIAT dating back to the 1970s, to develop molecular markers not only for drought-tolerance traits such as pod filling, but also for traits associated with resistance to important insect and disease menaces.

“Under drought conditions, plants become more susceptible to pests and diseases, so it was important that we also try to identify and include resistance traits in the drought-tolerant progeny,” says Steve.

Drought is but one plant stressor – diseases and pests wreak havoc too

Common bacterial blight on bean.

The bean diseases that farmers in Ethiopia, Kenya, Malawi and Zimbabwe continually confront are angular leaf spot, bean common mosaic virus, common bacterial blight and rust. Key insect pests are bean stem maggot and aphids.

“We’ve had reports of bean stem maggot and bean common mosaic virus wiping out a whole field of beans,” says Virginia. “Although angular leaf spot and common bacterial blight are not as damaging, they can still reduce yields by over 50 percent.”

Virginia says this is devastating for farmers in Malawi, many of whom only have enough land and money to grow beans to feed their families and sell what little excess there is at market to purchase other necessities.

“This is why we are excited by the prospect of developing not just drought-tolerant varieties, but drought-tolerant varieties with disease and pest resistance as well,” says Virginia.

Virginia’s team in Malawi – along with other breeders in Ethiopia, Kenya and Zimbabwe – are currently using over 200 Mesoamerican and Andean bean breeding lines supplied by CIAT to help breed for drought tolerance and disease and pest resistance. Although many do not yet have the capacity to do molecular breeding in their countries, thanks to advances in plant science it is becoming more feasible and cheaper to outsource molecular breeding stages of the process (see box above).

“With help from GCP and CIAT, we have successfully crossed a line from CIAT with some local varieties to produce plants that are high yielding and resistant to most common bean diseases,” Virginia says.

Malawian farmer Jinny Lemson grows beans to feed her livestock.

Ethiopia’s new bean breeders

Young women sorting beans after a harvest in Ethiopia.

One man who has been helping build this new breeding capacity is Bodo Raatz, a molecular geneticist who joined CIAT and GCP’s Legumes RI in late 2011.

“We’ve [CIAT] hosted several African PhD students here in Colombia and have conducted several workshops in Colombia and Africa too,” says Bodo.

“At the workshops we teach local breeders and technicians how to use genetic tools and markers for advanced breeding methods, phenotyping and data management. The more people there are who can do this work, the quicker new varieties will filter through to farmers.”

Bodo says he has found delivering the training both personally and professionally rewarding, especially “seeing the participants understand the concepts and start using the tools and techniques to develop new lines [of bean varieties] and contribute to the project.”

One national breeder whom Bodo has seen advance from the training is Daniel Ambachew, then a bean breeder at the Southern Agricultural Research Institute (SARI) in Ethiopia.

Daniel started as a GCP-funded Master’s student enrolled at Haramaya University, Ethiopia, evaluating bean varieties with both tolerance to drought and resistance to bean stem maggot. He eventually became the Ethiopian project leader for beans within GCP’s Legumes RI.

“Daniel is currently one of only a handful of bean breeders in Ethiopia who are using molecular-assisted breeding techniques to breed new varieties,” says Bodo. “It’s quite an achievement, especially now that he has taken on the lead role in Ethiopia.”

Buying and selling at a bean market in Kampala, Uganda.

For Daniel, learning about and using the new molecular-breeding techniques has been an exciting new challenge. “The most interesting part of the technology is that it helps us understand what is going on in the plant at a molecular level and lets us know if the crosses we are making are successful and the genes we want are present,” says Daniel. “All this helps improve our efficiency and speeds up the time it takes us to breed and release new varieties for farmers.”

By the end of 2014, Daniel and his team had finished the third year of trials and had several drought-tolerant lines ready for national trials in 2015 and eventual release in 2016.

Between 2012 and 2014, Daniel, and two other breeders from SARI, attended GCP’s three-year Integrated Breeding Multiyear Course, learning how to design molecular-assisted breeding trials; collect, analyse and interpret genotypic and phenotypic data from the trials; and manage data using the GCP’s Integrated Breeding Platform (IBP), particularly its Breeding Management System (BMS).

“The IBP is a really fantastic tool,” says Daniel. “During the course we learnt about the importance of recording clear and consistent phenotypic data, and the IBP helps us to do this as well as store it in a database. It makes it easier to refer to and learn from the past. I’m now trying to pass on the knowledge I’ve learnt as well as create and implement a data-management policy for all plant breeders and technicians in our institute.”

Bodo agrees with Daniel about the importance of IBP and believes it will be a true legacy of GCP beyond the Programme’s end in 2014. “The Platform has been designed to be the main data-management platform for plant breeders. It allows breeders to talk the same language and will reduce the need for learning new systems.”

Daniel says the challenge for his institute now is to build further capacity among staff – and to retain it. “At the moment we only have two bean breeders,” says Daniel. “It’s hard to retain research staff in Ethiopia as salaries are very low, so people move on to new, higher paying positions when they get the chance. It’s not unique to Ethiopia, but true of all Africa.”

Bean trials at KALRO in Kenya.

Kenya chasing higher bean yields

Across the border, Kenya has also been facing staffing issues.

“We are behind Ethiopia, Malawi and Zimbabwe in terms of our capacity and our trials,” says David Karanja, a bean breeder and project leader at the Kenya Agricultural and Livestock Research Organisation (KALRO, formerly the Kenya Agricultural Research Institute, or KARI). “At the start of the project, we didn’t have a breeder to lead the project for almost two years. However, we are now rapidly catching up with the others.”

And it’s a good thing too, as the country is in need of higher yielding beans to accommodate its population’s insatiable appetite for the crop. Out of the four target African countries, Kenya is the largest bean producer and consumer. As such, the country relies on beans imports from Ethiopia, Malawi, Tanzania and Uganda.

“A lot of families eat beans every day,” says David. “On average, the population eats 14–16 kilograms per person each year, but in western Kenya the average is over 60 kilograms.”

Githeri, a Kenyan staple food made with maize and beans.

Kenyans consume an average total of 400,000 tonnes of beans each year, consistently more than the country produces. Projected trends in population growth indicate that this demand for beans will continue to increase by three to four percent annually.

Even though the area planted to beans has been increasing, David says farmers and breeders need to work together to improve productivity, which is well below where it should be. “The national average yield is 100 kilograms per hectare, which can range from 50 kilograms up to 700 kilograms, depending on whether we experience a drought, or a pest or disease epidemic,” explains David. “The minimum target we should be aiming for is 1,200 kilograms per hectare.”

Such a figure may seem impossible, but David believes that new breeding techniques and the varieties KALRO are producing with the help of CIAT are providing hope that farmers can reach these lofty goals.

“We have several bean lines that are showing good potential to produce higher yields under drought conditions and also have resistance to diseases like rust and mosaic virus,” says David. “They are currently under national trials, and we are confident these will be released to farmers in 2015.”

Varieties fare differently in KALRO bean trials in Kenya.

Commercialising beans

Maturing bean pods.

“Many subsistence farmers have limited access to good quality bean seeds; they lack knowledge of good crop, pest and disease management; and they have poor post-harvest storage facilities,” says Godwill Makunde, who was previously a breeder at Zimbabwe’s Crop Breeding Institute (CBI) and leader of GCP’s Legumes RI bean project in Zimbabwe.

TLI’s sister project, Tropical Legumes II (TLII, see box above), led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), provided the route by which the upstream work of TLI would have impact in helping these farmers, seeking to deliver the new varieties developed under TLI into their hands. As part of TLII, Godwill, his successor Bruce Mutari, and other African partners worked on developing sustainable seed systems.

“Because beans are self-pollinating, which means each crop is capable of producing seed exactly as it was sown, farmers tend to propagate seed on farm,” says Godwill. “While this can be cost effective, it can reduce farmers’ access to higher yielding, tolerant lines, like the ones we are currently producing.”

In none of the partner countries of TLI and TLII are there formal systems for producing and disseminating bean seeds. Godwill and other partners are working with seed companies on developing a sustainable model where both farmers and seed companies can benefit.

Success built on a solid foundation

Field workers tend beans in Rwanda.

A key to the success of the beans component of GCP’s Legumes RI, according to Ndeye Ndack Diop, GCP’s Capacity Building Theme Leader and TLI Project Manager, has been partners’ existing relationships with each other.

“Many of the partners are part of a very strong network of bean breeders: the Bean Coordinated Agricultural Project [BeanCAP],” explains Ndeye Ndack, adding that the TLI and BeanCAP networks benefited each other.

BeanCAP released more than 1,500 molecular markers to TLI researchers, which have helped broaden the genetic tools available to developing-country bean breeders.

TLI was also able to leverage and advance previous BeanCAP work and networks. For example, it was through this collaboration that GCP was introduced to LGC Genomics, a company it then worked with on many other crop projects.

To sustain integrated breeding practices beyond the Programme’s close in 2014, GCP established Communities of Practice (CoPs) that are discipline- and commodity-oriented.

“GCP’s CoP for beans has also helped to broaden both the TLI and BeanCAP networks too,” says Ndeye Ndack. “The ultimate goal of the CoPs is to provide a platform for community problem solving, idea generation and information sharing.”

Developing physical capacity

Besides developing human capacity, GCP has also invested in developing infrastructure in Ethiopia, Kenya and Zimbabwe.

SARI now has an irrigation system to enable them to conduct drought trials year round. “We have 12.5 hectares of irrigation now, which we use to increase our efficiency and secure our research,” says Daniel. “We can also increase seed with this irrigation during the off-season and develop early generation seeds for seed producers.”

In Zimbabwe, CBI received specialised equipment that enables them to extract DNA and send it for genotyping in the UK.

Both SARI and CBI also received automatic weather stations from GCP for high-precision climatic data capture, with automated data loading and sharing with other partners in the network.

Delivering the right beans to farmers

Back in Malawi, Virginia says another important facet of the TLII project is that researchers understand what qualities farmers want in their beans. “It’s no use developing higher yielding beans if the farmer doesn’t like the colour, or they don’t taste nice,” she says. “For example, consumers in central Malawi prefer khaki or ‘sugar beans’, which are tan with brown, black or red speckles. While those in southern Malawi tend to prefer red beans. Farmers know this and will grow beans that they know consumers will want.”

Diversity at bean market in Masaka, Uganda.

Breeders in all four countries have been conducting workshops and small trials with farmers to find out this information. In Kenya, David finds farmer participation a great way to promote the work they are doing and show the impact the new drought-tolerant and disease-resistant lines can have.

“Farmers are excited and want to grow these varieties immediately when they see for themselves the difference in yield these new varieties can produce compared to their regular varieties,” says David. “They understand the pressure on them to produce more yields and are grateful that these varieties are becoming more readily available as well as tailored to their needs.”

For Steve, such anecdotes provide him and his collaborators with incentives to continue their quest to discover more molecular markers associated with drought tolerance, post-GCP.

“It’s a testament to everyone involved that we have been able to develop these advanced lines with pod-filling traits using molecular techniques, and make them available to farmers in six years instead of ten,” says Steve.

Cowpea research helps secure food supply during the ‘hungry months’ in Africa

Africa, Capacity building, Cowpeas, Crop breeding, Genetics, Genomics, Legumes No Responses »

Jun 122015

Growing cowpea pods.

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 Senegal, cowpeas cover more than 200,000 hectares,” says Ndiaga Cissé, cowpea breeder at L’institut sénégalais de recherches agricoles (ISRA; Senegalese Agricultural Research Institute). “This makes it the second most grown legume in Senegal, after groundnuts.”

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.

“The government is very interested in our research to improve cowpea yields and secure them against drought and disease,” says Issa Drabo, lead cowpea breeder with the Institut de l’Environnement et de Recherches Agricoles (INERA) in Burkina Faso.

“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.”

Sweetpotato: lifesaver that gets a genetic lifeline

Africa, Capacity building, Genetics, Genomics, Latin America, Phase I crops, Sweetpotatoes No Responses »

Jun 052015

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.”

Collective ‘intelligence’ cracks banana’s genetic code, clearing way for breeders

Africa, Asia, Bananas, Genetics, Genomics, Latin America, Phase I crops No Responses »

Jun 022015

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.

Photo: A Vezina/Bioversity International

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.”

The resultant research team was led by Japan’s National Institute of Agrobiological Sciences, which had vast experience in rice genome sequencing.

“So, living up to its name as a Challenge Programme, GCP decided to take the gamble on banana genomics and help it fly,” says Hei.

To advance genetics, you first need the intelligence

Banana bunches on an experimental plot at IITA.

Three global research agencies were charged with working together to develop a reference set for banana: Bioversity International, CIRAD, and the International Institute of Tropical Agriculture (IITA).

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.

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