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Poverty eradication through crop breeding for abundant harvests

Crop breeding, Drought, GCP, Poverty eradication No Responses »

Oct 152014

In recognition of the International Day for the Eradication of Poverty, October 17th, we are reflecting on what poverty means, how crop breeding helps eradicate poverty and transform lives, and how we have tried to maximise and measure those impacts.

In the early days of GCP, we were largely on uncharted seas and needed to chart a course to where our efforts would have the greatest impact, a process documented in our Pathways to impact brief No 1: Where in the world do we start? Instead of using a monetary definition of poverty, since this varies so widely between places and contexts, we took a different approach. As an indicator of true poverty, we used data on the number of stunted – ie, severely malnourished – children, overlaying this on maps showing where drought was most likely to occur. Our thinking was clear and simple: poverty + drought = where GCP needed to be.

Whatever else you may think they may lack, these children in Sibi village, Burkina Faso, definitely have verve, and look full of the energy they need to play!

A boy plays with an improvised hoop in Lukolela, Democratic Republic of Congo.

Drought routinely reduces harvests, and can be catastrophic. For example, nearly half (40 percent) of Africa’s maize-lands face occasional drought, reducing yields by between 10 and 25 percent, while a quarter suffers frequent drought, with overall losses of up to half the harvest – and total losses for some individual farmers. With climate change making droughts ever more common, drought was a natural priority for GCP from its inception.

Drought-tolerant crops are therefore the most important focus for the breeders of the GCP family, though not an exclusive one. Other key traits our breeders consider include resistance to pests and diseases and nutritional fortification, depending on the crop and location – and of course all varieties should yield well in good years too. Resilient improved varieties are particularly important for the poorest farmers, as they do not usually have access to measures such as irrigation or pesticides to combat environmental menaces. Typically, the poorest farmers also live in the most drought-prone drylands. Helping poor farmers to reap consistently abundant nutritious harvests means more food for their families and often a surplus to sell –reducing child malnourishment, and poverty in general.

A little girl eats fresh roti at home in the district of Dinajpur, Bangladesh.

A girl eats rice with her family in the Philippines.

Together we stand

The theme of the International Day for the Eradication of Poverty 2014 is Leave no one behind: think, decide and act together against extreme poverty, and it is one that echoes beautifully with the ethos of GCP. Collaboration and partnership have always been hallmarks of our approach, particularly in terms of empowering researchers in developing countries to implement – and lead – cutting-edge science. You can find a wealth of posts on our blog about our partnerships and the ‘GCP spirit’.

Collaboration is particularly important in crop breeding because one crop is often faced by all kinds of threats at once – a selection from the world’s least tasty smorgasbord of drought, heat, waterlogging pests, diseases, soil infertility, and much more. It is likely to be of no use breeding a super-crop that goes untouched by disease if it turns up its toes after a few dry days, or if no one likes the taste. That means researchers with different areas of expertise need to work together – and with farmers and extensionists too. Read the case for collective action in our Pathways to impact brief No 2: A call for collective action in agricultural research.

Girls help in the fields in Luang Prabang, Laos.

Eyes dancing with past, present or future mischief, two cheeky young chappies from Mozambique enjoy the sweet taste of orange sweet potato enriched with pro-vitamin A.

Impact by the numbers

GCP believes that using marker-assisted breeding (a range of efficient crop-breeding approaches that use genetic information to work out which plants have useful traits) to create improved varieties faster and more effectively is worth its extra cost, and has a real impact on farmers’ incomes. This cannot be taken for granted however, so get an introduction to the numerical approach in our Pathways to impact brief No 3: Molecular and conventional breeding through an economic lens. Our study found that women in Nigeria reported increased household incomes from growing improved cassava varieties, but also more time spent on cassava-related tasks – emphasising the need for researchers to be aware of the characteristics farmers – in this case predominantly women – value.

Hard at work, a boy helps to peel a mountain of cassava in Nigeria.

As we mark this year’s International Day for the Eradication of Poverty, we at GCP are proud to be contributing to the eradication of poverty by creating partnerships, expertise, and ultimately crop varieties that promise abundant harvests for the world’s poorest farmers and their families – helping their children grow up big, strong and free from poverty.

At play: children of the Sao Felix community in the Brazilian Amazon.

Enjoy the game, but keep off the plants! Boys play football next to maize fields in Khulungira, central Malawi.

Tribute to cassava: Princess, pauper, mother, orphan, queen

Africa, Cassava, Latin America No Responses »

Oct 142014

Things fall apart… and come together

By Eloise Phipps

Cassava – the tough, gutsy daughter of a poignant confluence of cultures, and the benevolent mother of millions when times get tough – is bursting onto the science scene after years of neglect. For October 15th, the International Day of Rural Women, we crown her the Queen of Crops. Read on to see why …

His mother and sisters worked hard enough, but they grew women’s crops, like coco-yams, beans and cassava. Yam, the king of crops, was a man’s crop.”

So wrote Chinua Achebe in his great novel, Things Fall Apart, set among the Igbo people in southeast Nigeria. His words are a reminder that men’s and women’s experiences, needs, activities and ambitions in the agricultural sphere can often be different – and that women’s contributions are all too often undervalued.

Cassava feeds more than half a billion people in the in the developing world. After rice and maize, it is the third-largest source of carbohydrates for people in the tropics, where it is grown across Africa, Asia and Latin America. Yet tough, unassuming cassava is a bit of an underdog – just like the women who grow it. We are celebrating the International Day of Rural Women by taking a special look at cassava, what it means for women, and the extraordinary things that can happen when Things Come Together!

A bright spot in a sea of green: a farmer in her field of cassava, in the village of Tiniu, near Mwanza, northern Tanzania.

It thrives on poor soils where other plants struggle, and it survives droughts that leave other crops biting the dust. For many rural mothers, cassava is the crop that keeps their families alive…”

“We must sing for you, great cassava…”

Hefty chunks of cassava – full of energy and nutrients – on sale in Kampala, Uganda.

Cassava’s story is one that is inextricably linked to centuries of pain and struggle. It was introduced to Africa in the 16^th century by Portuguese traders who brought it from Brazil – and took Africans back to Brazil as slaves.

Yam, native to Africa, was firmly established as the staple food of the Igbo people. Dominating their farming activities, it thus dominated the very routine of existence. So, control of yam affirmed men’s position at the top of the pinnacle. When cassava arrived, no one thought very much of it. For the Portuguese, it was a cheap source of carbohydrates. For the Igbo, it was a decidedly inferior crop to the long-beloved and much-revered yam.

Since the men were generally not much interested, Igbo women gradually adopted cassava as ‘their’ crop, a process that has been reinforced over the centuries. For example, Nigerian troop conscription during the First World War and the subsequent influenza pandemic caused a serious shortage of labour, particularly manpower. Women needed to grow more food, and cassava – more flexible and less labour-intensive than yam – was the natural choice, being also free from the cultural constraints that made yam the exclusive domain of men.

While no one would call cassava glamorous, plenty of women over the years have turned out to be quite happy that such a valuable crop ended up in their sphere of influence. While cassava is not often much of a cash crop in Africa, it is tough, resilient, and very useful for survival in difficult times. It thrives on poor soils where other plants struggle, and it survives droughts that leave other crops biting the dust. For many rural mothers, cassava is the crop that keeps their families alive.

The hard-working hands of Angelique Ipanga, a teacher and farmer, as she tends her cassava crop in Lukolela, Democratic Republic of Congo.

What better words to sing cassava’s praises than those of Flora Nwapa, Nigeria’s first female novelist, in her Cassava Song? In ancient Igbo tradition, women sing their work, singing it into being and into completion, and her poem is a tribute to those work-songs.

And here, we have another Nigerian to join the chorus of praise – watch Emmanuel Okogbenin, molecular plant breeder, on the importance of cassava:

While our spotlight on Nigeria thus far has been purely coincidental, let’s also not forget that Nigeria is the global cassava giant, being far and away the world’s biggest producer and consumer of cassava. But do buckle up and let’s cross the great ocean, to another part of the planet, for an equally captivating cassava story…

… legend has it that the first cassava was birthed by a human woman…”

Crossing continents: A virgin-born, Amazonian Snow White planted in the earth

Of course, cassava is not exclusively a female province – it is grown by both women and men farmers around the world. But can you blame us for imparting it with a special feminine mystique, when legend has it that the first cassava was birthed by a human woman caught at the confluence of two cultures?

Many centuries before the Europeans arrived, cassava – often known in the New World as manioc – sustained peoples and cultures throughout the tropical lowlands of the Americas. The Tupí people of Brazil tell how, many years ago, the daughter of a chief became pregnant. Although she said that she had not been with a man, her father did not believe her, and threatened to kill her if she did not tell him the name of the child’s father. When he slept, however, he dreamt of a white-skinned warrior who told him that his daughter was telling the truth, and that one day, she would bear a great gift for all his tribe.

The chief’s daughter gave birth to a little girl, Maní, whose skin was as white as the moon and eyes were as dark as the night. She grew into a happy and beautiful baby, but died suddenly after her first birthday. Her mother watered the grave every day, as was the custom, and one day, a strange plant grew there that no one had ever seen before. Later, the earth cracked open, and the Tupí people saw a fruit that was as white as the dead child. They drew it from the ground, peeled and cooked it, and to their surprise found that it was delicious, and even renewed their strength. They called it mandioca or manioca, meaning ‘House of Maní’.

It is a haunting tale, rich with echoes of the cultural upheavals that followed the coming of the Europeans, ancient fears of female impurity, and the realities of infant mortality. But it leaves one thing in no doubt: poor little Maní’s legacy was a precious treasure, not just for the Tupí but for the world.

Under the hot sun, the work goes on: a farmer tends her cassava crop in Colombia’s southwestern Cauca department.

Proud in pink and polka dots: a farmer shows off a healthy cassava leaf in a plantation in Kampong Cham, Cambodia.

A busy Bea grows her way to cassava glory – with a little help from her friends

Female farmer reloaded: Being a rural woman farmer does not mean you have to have dirt under your fingernails all the time. Here’s Bea looking as elegant and regal as any queen.

Ghanaian cassava researcher Elizabeth Parkes is no puny pushover, but even so she met her match in gutsy and determined farmer Bea. Elizabeth laughs as she remembers how the story began: “She hadn’t planted cassava before in her life, but she wanted to go into cassava production. She came to me – she pestered me actually! I was tired of it, because she didn’t know anything and it was a time when I was finishing my PhD, and I thought no, this lady cannot take this precious time from me.”

When most people think of a farmer, they probably think of a man in a straw hat. But in defiance of this stereotype, women make up 43 percent of the agricultural labour force in developing countries, rising to at least 50 percent in sub-Saharan Africa and Eastern Asia. These millions of rural women have incredibly diverse lives, but a few things stay surprisingly constant. Female farmers tend to produce less than their male counterparts – not because they are worse at farming, but because they have less access to all kinds of resources and opportunities. These include anything from land itself to improved seed and new technologies, and from education and information to financial credit.

If this gap could be completely sealed, women could increase their harvests by 20 to 30 percent, translating to millions fewer hungry and malnourished people worldwide. Fortunately, with the right kind of support, female farmers can – and do – transform their lives in remarkable ways. Bea’s story came to just such a happy ending: with guidance from Elizabeth, her cassava-growing skills took off like a rocket, and she became so successful that she was recognised as the best farmer in her community. “These are things that make me glad… that at least I have impacted somebody who hadn’t planted cassava before, and it’s amazing,” says Elizabeth. “There are people out there who need us, and when we give them our best, they will give the world their best as well.”

Listen to Elizabeth in the podcast below, and you are bound to pick up her infectious enthusiasm!

When scientists like these come together, with a dash of the right support, marvellous things happen… cassava has been given a voice.”

Things Come Together

Elizabeth Parkes is a woman from Ghana, and Chiedozie Egesi is a man from Nigeria, himself of the Igbo people and a yam breeder in a past life. However, the two have a lot in common. They are dynamic African scientists with a passion for social justice, and for helping the poorest and most disadvantaged rural people through their work on cassava. When scientists like these come together, with a dash of the right support, marvellous things happen.

Read Elizabeth’s story here and more from her here, and catch up with Chiedozie here and here.

Cassava has traditionally been a forgotten ‘orphan’ in crop science research. Humble and unfashionable, it also has some special challenges for breeders, like its long growth cycle and complicated genetics, while its tough and uncomplaining nature meant that many people thought of it as an “anywhere, anyhow” crop – a very misleading myth, if ever there was one (with thanks to myth-buster Joseph Adjebeng, for that memorable cassava quote). Although the idea grew from a kernel of truth, cassava, like any other crop, needs a little love, and yields less when plagued by problems such as diseases or degraded and infertile soils. But, like Harry Potter, in recent years this orphan has come out from the cupboard under the stairs, and the magic has begun.

Wreathed in sunlight and smiles, a cassava farmer inspects her crop in Kratie, Cambodia.

Cassava’s no waif – luckily, as its tuberous roots are packed with staple carbohydrates. Here Ghanaian researcher, Elizabeth Parkes, shows off some huge and healthy cassava. These days Elizabeth is a pro when it comes to things crop-related, but it was not always so. “I remember we used to uproot volunteer cocoyam from a serious, busy lady farmer’s farm and we put it in our garden expecting to have a fast-growing plant overnight,” she admits. “The crops died and the busy woman farmer had to come and warn us never to step in her farm again. That was the first hard lesson learnt.” Elizabeth remains ready to learn, with a healthy respect for the knowledge and skills of the farmers she works with, an attitude she learned early on when she visited cocoa farms near her home town. “I loved the way farmers called colleagues by making unique sounds,” she says. “There are many paths to the farm but everyone knew the many routes to our many farms. This still amazes me.”

The plus side of cassava being neglected for so long is that it only needed a relatively small initial investment in local capacity-building and applying modern breeding methods to make a big impact, and set the ball rolling for serious cassava research. “GCP helped us to build an image for ourselves in Nigeria and in Africa, and this created a confidence in other global actors, who, on seeing our ability to deliver results, are choosing to invest in us,” explains Chiedozie.

His team have released new cassava varieties that are resistant to diseases and rich in pro-vitamin A, providing the vitamin A that is particularly important for small children and childbearing women. He believes that these have the potential to transform the lives of the people – mainly rural women – who grow them. “The food people grow should be nutritious, resistant and high-yielding enough to allow them sell some of it and make money for other things in life, such as building a house, getting a motorbike, or sending their kids to school,” he says.

Elizabeth agrees that a new, “blessed and privileged era” has begun for cassava. “Thanks to funders such as GCP, who recognised that we couldn’t afford to turn a blind eye to the plight of this struggling crop, cassava has been given a voice.”

It seems that things have come together for cassava at last, and for Elizabeth, the personal rewards of being able to make real impacts are great. “I see African communities where poverty and hunger are seemingly huge problems with no way out; I’m fortunate to be working on a crop whereby, if I put in enough effort, I can bring some solutions.”

After all, it seems that being a ‘woman’s crop’ might not be a put-down, but something to celebrate. Cassava has come a long way, from a pale princess lying under the earth, to a steadfast mother keeping the family going in the toughest of times, to a confident and majestic queen with a glorious reign ahead of her.

And so, for October 15th, in honour of the International Day of Rural Women, we crown her the Queen of Crops. Long live Queen Cassava!

Colourful streamers for the coronation? No, they’re cassava noodles being made in Kampong Cham, Cambodia.

A regal African beauty tends her gorgeous cassava plants.

Earth to MARS! On the way to breeding drought-resistant maize for Asia

Asia, Crop breeding, Maize 2 Responses »

Sep 012014

Scouring the planet for breeding solutions

Bindiganavile Vivek

Bindiganavile Vivek (pictured) is a maize breeder working at the International Maize and Wheat Improvement Center (CIMMYT), based in Hyderabad, India. For the past five years, Vivek and his team have been developing drought-tolerant germplasm for Asia using relatively new molecular-breeding approaches – marker-assisted recurrent selection (MARS), applied in a genomewide selection (GWS) mode. Their work in the Asian Maize Drought-Tolerance (AMDROUT) project is implemented through GCP’s Maize Research Initiative, with Vivek as the AMDROUT Principal Investigator.

Driven by consumer demand for drought-tolerant maize varieties in Asia, the AMDROUT research team has focussed on finding suitable drought-tolerant donors from Africa and Mexico. Most of these donors are white-seeded, yet in Asia, market and consumer preferences predominantly favour yellow-seeded maize. Moreover, maize varieties are very site-specific and this poses yet another challenge. Clearly, breeding is needed for any new target environments, all the while also with an eye on pronounced market and consumer preferences.

(1) Amazing maize and its maze of colour. Maize comes in many colours, hues and shapes. (2) Steeped in saffron: from this marvellous maize mix and mosaic, the Asian market favours yellow maize.

(1) Amazing maize and its maze of colour. Maize comes in many colours and hues. (2) Steeped in saffron: from this marvellous maize mix and mosaic, the flavour in Asia favours yellow maize.

Stalked by drought, tough to catch, but still the next big thing

Around 80 per cent of the 19 million hectares of maize in South and Southeast Asia is grown under rainfed conditions, and is therefore susceptible to drought, when rains fail. Tackling drought can therefore provide excellent returns to rainfed maize research and development investments. As we shall see later, Vivek and his team have already made significant progress in developing drought-tolerant maize.

The stark reality of drought is illustrated in this warning sign on a desiccated drought-scorched landscape, showing the severity of drought in Asia

But they are after a tough target: drought tolerance is dodgy since it is a highly polygenic trait, making it difficult for plant scientists to pinpoint genes for the trait (see this video with an example from rice in Africa). In other words, to make a plant drought-tolerant, many genes have to be incorporated into a new variety. As one would expect, the degree of difficulty is directly proportional to the number of genes involved. In the private-sector seed industry, MARS (PDF) has been successfully used in achieving rapid progress towards high grain yield under optimal growth conditions. Therefore, a similar approach could be used to speed up the process of introducing drought tolerance into Asian crops – the reason why the technique is now being used by this project.

More than India: the AMDROUT project also comprises research teams in China, Indonesia, Thailand, The Philippines and Vietnam. In this photo taken during the December 2010 annual project meeting in Penang, Malaysia, the AMDROUT team assessed the progress made by each country team, and team members were trained in data management and drought phenotyping. They also realised that there was a need for more training in genomic selection, and did something about it, as we shall see in the next photo. Pictured here, left to right: Luo Liming, Tan jing Li, Villamor Ladia, V Vengadessan, Muhammad Adnan, Le Quy Kha, Pichet Grudloyma, Vivek, IS Singh, Dan Jeffers (back), Eureka Ocampo (front), Amara Traisiri and Van Vuong.

The rise of maize: clear chicken-and-egg sequence…

Vivek says that the area used for growing maize in India has expanded rapidly in recent years. In some areas, maize is in fact displacing sorghum and rice. And the maize juggernaut rolls beyond India to South and Southeast Asia. In Vietnam, for example, the government is actively promoting the expansion of maize acreage, again displacing rice. Other countries involved in the push for maize include China, Indonesia and The Philippines.

So what’s driving this shift in cropping to modern drought-tolerant maize? The curious answer to this question lies in food-chain dynamics. According to Vivek, the dramatic increase in demand for meat – particularly poultry – is the driver, with 70 percent of maize produced going to animal feed, and 70 percent of that going into the poultry sector alone.

GCP gave us a good start… the AMDROUT project laid the foundation for other CIMMYT projects”

Show and tell: posting and sharing dividends

As GCP approaches its sunset in December 2014, Vivek reports that all the AMDROUT milestones have been achieved. Good progress has been made in developing early-generation yellow drought-tolerant inbred lines. The use of MARS by the team – something of a first in the public sector – has proved to be useful. In addition, regional scientists have benefitted from broad training from experts on breeding trial evaluation and genomic selection (photo-story on continuous capacity-building). “GCP gave us a good start. We now need to expand and build on this,” says Vivek.

AMDROUT calls in on Cambridge for capacity building. AMDROUT country partners were at Cambridge University, UK, in March 2013, for training in quantitative genetics, genomic selection and association mapping. This was a second training session for the team, the first having been September 2012 in India.
Pictured here, left to right – front row: Sri Sunarti, Neni Iriany, Hongmei Chen;
middle row: Ian Mackay (Cambridge), Muhammad Azrai, Le Quy Kha, Artemio Salazar;
back row: Roy Efendy, Alison Bentley (who helped organise, run and teach on the course, alongside Ian) and Suriphat Thaitad.AMDROUT country partners are from China’s Yunnan Academy of Agricultural Sciences (YAAS); the Indonesian Cereals Research Institute (ICERI); the Institute of Plant Breeding at the Unversity of Philppines at Los Baños (UPLB); Thailand’s Nakhon Sawan Field Crops Research Center (NSFCRC); Vietnam’s National Maize Research Institute (NMRI); and private-sector seed companies in India, such as Krishidhan Seeds.Curious on who proposed to whom for this AMDROUT–Cambridge get-together? We have the answer: a Cambridge callout announced the training, and AMDROUT answered by calling in, since course topics were directly relevant to AMDROUT’s research approach.

According to Vivek, the AMDROUT project laid the foundation for other CIMMYT projects such as the Affordable, Accessible, Asian (AAA) Drought-Tolerant Maize (popularly known as the ‘Triple-A project’) funded by the Syngenta Foundation for Sustainable Agriculture. This Triple-A project is building on the success of AMDROUT, developing yet more germplasm for drought tolerance, and going further down the road to develop hybrids.

Outputs from the AMDROUT project will be further refined, tested and deployed through other projects”

Increasing connections, and further into the future

Partly through GCP’s Integrated Breeding Platform (IBP), another area of success has been in informatics. Several systems such as the Integrated Breeding FieldBook, the database Maize Finder and the International Maize Information System (IMIS) now complement each other, and allow for an integrated data system.

There is now also an International Maize Consortium for Asia (IMIC–Asia), coordinated by CIMMYT, comprising a group of 30 commercial companies (ranging from small to large; local to transnational). Through this consortium, CIMMYT is developing maize hybrids for specific environmental conditions, including drought. IMIC–Asia will channel and deploy the germplasms produced by AMDROUT and other projects, with a view to assuring impact in farmers’ fields.

Overall, Vivek’s experience with GCP has been very positive, with the funding allowing him to focus on the agreed milestones, but with adaptations along the way when need arose: Vivek says that GCP was open and flexible regarding necessary mid-course corrections that the team needed to make in their research.

But what next with GCP coming to a close? Outputs from the AMDROUT project will be further refined, tested and deployed through other projects such as Triple A, thus assuring product sustainability and delivery after GCP winds up.

Links

The AMDROUT project | Photos on AMDROUT’s continuous capacity building | Capacity building at GCP
More on the AMDROUT project – Project Updates – 2014 p 25; 2013 p 22 | Project Briefs 2013 p 13 | 2012 Annual Report
3.5 MIN VIDEO – why drought is such a complex customer: a perspective from rice research in Africa. Drought has to do with genetics, physiology and environment, and the interactions between these three elements.
Maize – Research Initiative | InfoCentre | Slides | Blogposts
Marker-assisted recurrent selection (MARS) demystified and explained (PDF)
Vivek’s slides below

GRM 2013: Asian Maize Drought Tolerance (AMDROUT) Project — BS Vivek from CGIAR Generation Challenge Programme

As our Maize Research Initiative does not have a Product Delivery Coordinator, Vivek graciously stepped in to coordinate the maize research group at our General Research Meeting in 2013, for which we thank him yet again. Below are slides summing up the products from this research, and the status of the projects then.

GRM 2013: Maize product catalogue and project status — Projects ongoing, completed, and to be continued post-2014 — BS Vivek from CGIAR Generation Challenge Programme

GRM 2011: Asian Maize Drought Tolerance (AMDROUT) Project from CGIAR Generation Challenge Programme

Eva’s endeavours: a professional path in plant science inspired by Norman Borlaug

Africa, Comparative genomics in cereals, Crop breeding, Researchers, Sorghum, Women in science No Responses »

Aug 292014

“…I wanted to contribute in a similar way” – Eva Weltzien

Eva Weltzien

Learning about the work of Nobel laureate, Norman Borlaug, in high school inspired Eva Weltzien to become a plant breeder so she too could contribute to improving the living conditions in the developing world. Today, Eva is a Principal Scientist in sorghum breeding and genetic resources at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in Mali.

“Not only did Norman Borlaug revolutionise agriculture by breeding high-yielding wheat varieties, he then selflessly distributed these to the countries in the world that most needed them, saving hundreds of millions from starvation,” Eva recollects passionately, as she speaks about her scientific hero. “I remember being inspired when he won his Nobel Prize in 1970, mainly for the fact that agricultural research was actually being seen as contributing to world peace,” says Eva. “I knew then that I wanted to contribute in a similar way.”

I…wanted to take a break from… theory and instead gain an appreciation for plant breeding by working in the field”

The path to plant breeding, and pearls along the way
Eva was raised in her native Germany, as well as in Beirut, Lebanon, where she spent six years when her parents were stationed at the local university there. She credits her parents; both plant pathologists, for instilling in her a scientific mind-set from a tender age.

“They taught me to think outside the box and apply my knowledge and understanding to how I made sense of the world,” Eva recalls. “Being plant pathologists, they also encouraged me to observe the environment carefully and treat the earth with respect.”

Upon graduating from high school, Eva deferred going to university and instead worked as a seed technician for a private company in Germany. “I just wanted to take a break from studying theory and instead gain an appreciation for plant breeding by working in the field,” says Eva.

After one year with the company, Eva was ready to start university. During the decade that followed, she completed a Diploma in Agricultural Biology (University of Hohenheim, 1981) and a PhD in Agriculture (Munich University, 1986).

A year after completing her PhD, Eva accepted a postdoc position at Iowa State University, USA, where she met her future husband Fred Rattunde. After a few years, both Eva and Fred moved to India to work with ICRISAT. “I’ve been working for ICRISAT for almost 27 years now,” says Eva. “When I first started, I was working in pearl millet breeding.”

The key challenges have been improving the infrastructure of the national research facilities… as well as increasing the technical training for local researchers…this has slowly improved, particularly in the last four years with the funding and help through the GCP Sorghum Research Initiative.…we can see our work making an impact on people’s lives…”

Off to Africa, and bearing fruit
In 1998, ICRISAT offered Eva and Fred positions in Mali where they would take responsibility for the Institute’s sorghum-breeding programme in West Africa.

Evaluating Eva: In Dioila district, Mali, evaluating the panicles of a new sorghum line after harvest.

“It was a great challenge that we both wanted to explore,” says Eva. “The key challenges have been improving the infrastructure of the national research facilities to do the research as well as increasing the technical training for local agronomists and researchers. Over the past 15 years, this has slowly improved, particularly in the last four years, with the funding and facilitation through the GCP Sorghum Research Initiative. Now we can see our work making an impact on people’s lives in West Africa.” (see GCP’s work on infrastructure improvement)

…we are closer to delivering more robust sorghum varieties which will help farmers and feed the ever-growing population in West Africa.”

Improving drought tolerance in sorghum for Africa
The second phase of GCP’s Sorghum Research Initiative focuses on Mali, where sorghum-growing areas are large, and distributed over a wide range of rainfall regimes.

Eva and her team are currently collaborating with local researchers at L’Institut d’économie rurale (IER), Mali and France’s Centre de coopération internationale en recherche agronomique pour le développement (CIRAD) on a project to test a novel molecular-breeding approach – backcross nested association mapping (BCNAM). Eva says the approach has the potential to halve the time it takes to develop local sorghum varieties with improved yield and adaptability to poor soil fertility conditions.

“We don’t have these type of molecular-breeding resources available in Mali, so it’s really exciting to be a part of this project.” Still, Eva and her colleagues continue to press forwards in this new frontier in plant science, making good advances in another parallel but closely related project that Eva leads in the GCP Comparative Genomics Research Initiative.

Eva continues, “We’ve had good results in terms of field trials, despite the political situation. Overall, we feel the experience is enhancing our capacity here in Mali, and that we are closer to delivering more robust sorghum varieties which will help farmers and feed the ever-growing population in West Africa.”

Slides (with more links after the slides)

GRM2013: Establishing a molecular breeding program based on the aluminum tolerance gene AltSB and the P efficiency QTL Pup-1, for increasing sorghum production in Sub-Saharan Africa — F Rattunde from CGIAR Generation Challenge Programme

GRM 2013: Enhancing sorghum grain yield and quality for the Sudano-Sahelian zone of West Africa using the Backcross Nested Association Mapping (BCNAM) approach — N Teme from CGIAR Generation Challenge Programme

Links

The project Eva leads
BLOGPOST: Comparative genomics in cereals (maize, rice and sorghum)
Research Initiatives – Sorghum | Comparative genomics in cereals
Sorghum research products
More on Eva’s work in sorghum with other GCP colleagues

Lively Leon: a never-grow-old researcher, and his biological rebirths

Comparative genomics in cereals, Genomics, Maize, Researchers, Sorghum No Responses »

Aug 272014

Leon Kochian

“By being involved with GCP, I’ve had more opportunities to travel to the developing world and witness the problems that local farmers in these countries are facing, as well as to meet with the local researchers who are trying to overcome these problems. It has made me appreciate that these researchers also need the capacity to sustainably deal with agricultural problems once the project money starts to dry up.” – Leon Kochian (pictured), Professor, Cornell University, USA; and Director of Robert W Holley Center for Agriculture and Health, United States Department of Agriculture – Agricultural Research Service. Also Product Delivery Leader for GCP’s Comparative Genomics Research Initiative.

Bright and early beginnings in biology
For as long as Leon Kochian can remember, he’d always wanted to be a biologist.

“I remember my second-grade teacher reading a story to us about the white cliffs of Dover and thinking to myself ‘They’re white because they’re covered in the prehistoric remains of dead protozoan’,”’ says Leon with a chuckle. “Yes, I was a weird kid and that sort of stuff [biology] has always interested me.”

Having completed a Bachelor’s Degree in Botany at the University of California, Berkeley, and a PhD in Plant Physiology at the University of California, Davis (both in USA), Leon joined the United States Department of Agriculture based at Cornell University.

For 30 years, he has combined lecturing and supervising duties at Cornell, with his quest to understand the genetic and physiological mechanisms that allow some cereals to tolerate acidic soils.

The GCP model has always attracted me, particularly its focus on making an impact on farmers’ lives… I had already been a successful researcher having published more than 250 papers, but I felt little of that had made any real impact on the world.”

Identifying genes and breeding tolerant crops for African farmers
Leon and Cornell University have been involved with GCP since the Programme’s inception in 2004, playing a lead role in GCP’s Comparative Genomics Research Initiative, of which Leon is the Product Delivery Coordinator. Cornell University is a member of the GCP Consortium, with Leon as Cornell’s representative in the GCP Consortium Committee.

“The GCP model has always attracted me, particularly its focus on making an impact on farmers’ lives,” says Leon, who has been a Principal Investigator for several Comparative Genomics Research Initiative projects. “I had already been a successful researcher having published more than 250 papers, but I felt little of that had made any real impact on the world.”

During the first phase of the project, Leon led a team comprising of researchers from Cornell, EMBRAPA in Brazil and Moi University in Kenya.

In the foreground, left to right, Leon, Jura and Sam in a maize field in Kenya.

Leon (left) with project colleagues, Jurandir Magalhães (EMBRAPA) and Sam Gudu (Moi University) in a maize field in Kenya in May 2010.

“We had been working for many years with both EMBRAPA and Moi University to identify the genes associated with aluminium tolerance in sorghum and maize and saw the potential to apply our research and expand it to explore other cereals such as rice and wheat,” explains Leon.

During GCP Phase I (2004–2008), the team successfully identified and cloned the major sorghum aluminium tolerance gene (Alt_SB). In Phase II (2009–2014), they are working towards breeding aluminium-tolerant sorghum lines for sub-Saharan Africa as well as applying what they have learnt to discover similar genes in rice and maize.

“Aluminium toxicity is a problem all over the world, but more so in Africa, as most farmers don’t have the money to manage it,” says Leon “These new aluminium-tolerant crops will improve African farmers’ yields, and, in turn, improve their quality of life.”

It’s like match.com for collaborative research and will hopefully foster greater collaboration between the two continents.”

Insights, connections and matchmaking
According to Leon, the funding from GCP has been very beneficial in making significant research progress on the projects he’s been involved with so far, and he is also quick to note the unexpected and very welcome non-monetary benefits from being involved with GCP.

Working with GCP, Leon has designed and run workshops to train African scientists on molecular breeding techniques and hosted several postgraduate researchers at Cornell. He is now working with GCP collaborators to develop a database that will help African scientists find potential collaborators in USA and the rest of the Americas. “It’s like match.com for collaborative research and will hopefully foster greater collaboration between the two continents,” says Leon.

Research is such a fun and social experience! … I still love getting into the lab and discovering new things. I’ve also learnt to enjoy being the old guy in the lab!”

Growing greyer, growing wiser
Leon says his passion for biology and research is steadfast and has not waned through the years. Although he doesn’t get to do much of the hands-on work these days, it still remains the most enjoyable part of his job. “Research is such a fun and social experience! I still love getting into the lab and discovering new things. I’ve also learnt to enjoy being the old guy in the lab! Just watching and helping young researchers grow and develop their skills is really rewarding. Each of the 13 PhD students I’ve supervised is like one of my kids and I still keep in touch with all of them, as I do with my own PhD supervisor, 30 years on!”

Having recently celebrated his 60th birthday, Leon has no plans on slowing down anytime soon. “I’m currently Director of the Robert W Holley Center for Agriculture and Health, lecturing undergraduate and postgraduate students, supervising two PhD students and sitting on several boards, all the while trying to find time to write papers and do some research. It’s hard work but I enjoy it.”

The three faces of Leon: (1) in the lab in Cornell; (2) in the field, courtesy of USDA–ARS; and, (3) delivering opening remarks as Director of the Robert W Holley Center.

Leon tries to impart this philosophy to his students, believing scientists need to enjoy what they are doing, work hard at it, be flexible and creative, and, most importantly, not have ‘fear of failure’. “I don’t care how smart you are. If you’re not willing to work really hard and learn to improve yourself, then you’re not going to succeed.”

With regard to his GCP projects soon coming to a close when GCP sunsets in December 2014, Leon hopes he and team will succeed in meeting all their goals, but even if they don’t, he’s sure they’ll continue the research and try to discover more about aluminium tolerance. More power to them!

Leon’s slides, with links to more supplementary material after the slides

GRM 2013: Cloning, characterization and validation of PUP1/P efficiency in maize — L Kochian from CGIAR Generation Challenge Programme

GRM 2013: Cloning, characterization and validation of AltSB/Al tolerance in rice — L Kochian from CGIAR Generation Challenge Programme

GRM 2013: Status of maize projects in the Comparative Genomics Research Initiative: Products and the future — L Kochian from CGIAR Generation Challenge Programme

Links

BLOGPOST: More on Leon’s work with GCP project colleagues
Leon’s Product Delivery Coordinator profile
The comparative genomics in cereals projects Leon leads – maize | maize and sorghum |rice
Comparative Genomics – Research Initiative | InfoCentre | research products
AUDIO CLIP: To retrace some of the work Leon and team have covered, listen to this 2007 clip (courtesy of WSKG, The DNA files, Aluminium-tolerant sorghum)
FUNTIME! For any of Leon’s younger students and colleagues who think he’s the old guy in the lab, the little boy in Leon is never too far. Hunt for our lively Leon in this high-res group photo, and see what he gets up to when he’s being cheeky around his ‘elders and betters’! Go! (hint: left hand)

Super Sam: Kenya’s nurturing geneticist, and the fruits of his labour

Africa, Capacity building, Comparative genomics in cereals, Crop breeding, Genetics, Genomics, Maize, Researchers 3 Responses »

Aug 152014

Samuel Gudu

“Having funding to support PhD students and provide them with the resources they need to complete their research is very fulfilling and will go a long way to enhance the long-term success of our goal: to provide Kenyan farmers with cereal varieties that will improve their yields and make their livelihood more secure and sustainable.” – Samuel Gudu, Professor and Deputy Vice-Chancellor (Planning & Development) at Moi University, and now Principal, Rongo University College: a Constituent College of Moi University, Kenya.

Growing up, and getting dirty
Learner, teacher and leader. Sam Gudu has been all these, but this doesn’t mean he doesn’t like to get his hands dirty.

Growing up in a small fishing village on the banks of Lake Victoria, in Western Kenya, Sam was always helping his parents to fish and garden, or his grandparents to muster cattle.

“I remember spending long hours before and after school either on the lake or in the field helping to catch, harvest and produce enough food to eat and support our family,” reminisces Sam.

He attributes this “hard and honest” work to why he still enjoys being in the field.

“Even though I now spend most of my days doing administration work, I’m always trying to get out into the field to get my hands dirty and see how our research is helping to make the lives of Kenyan farmers a lot more profitable and sustainable,” he says.

Doing what he likes to do best: Sam in a maize field in Kenya.

I was… captivated by the study of genetics as it focused on what controlled life.”

Taking control: bonded to genetics, at home and away
Sam says his love for the land transferred to an interest and then passion in the classroom during high school. “I became very interested in Biology as I wanted to know how nature worked,” says Sam. “I was particularly captivated by the study of genetics as it focused on what controlled life.”

This interest grew during his undergraduate years at the University of Nairobi where he completed a Bachelor of Science in Agriculture and a Master’s of Science in Agriculture, focusing on genetics and plant breeding.

“I fondly remember a lecturer during my master’s degree studies who would continually give us challenges to test in the field and in the lab. If you had a viable idea he supported you to design an experiment to test your theory. I like to use the same method in teaching my students. I discuss quite a lot with my students and I encourage them to disagree if they use scientific process.”

Driven by an ever-growing passion and enthusiasm, Sam secured a scholarship to travel to Canada to undertake a PhD in Plant Genetics and Biotechnology at the University of Guelph.

[There has been an] influx of young Kenyans who are choosing degrees in science. The Kenyan Government has recently increased its funding for science and research…”

Nurturing the next breed of geneticists
After graduating from Guelph in 1993, Sam returned to Kenya to lecture at Moi University where he initiated and helped expand teaching and research in the disciplines of Genetic Engineering, Biotechnology and Molecular Biology.

In the past two decades, he has recruited young talented graduates in genetics and helped acquire advanced laboratory equipment that has enabled practical teaching and research in molecular biology.

“I wouldn’t be where I am now were it not for all the assistance I received from my teachers, lecturers and supervisors; notably my PhD supervisor – Prof Ken Kasha of the University of Guelph. So I’ve always tried my best to give the same assistance to my students. It’s been hard work but very rewarding, especially when you see your students graduate to become peers and colleagues.” (Meet some of Sam’s students)

Sam (2nd right), with some of his young charges: Thomas Matonyei (far left), Edward Saina (2nd left) and Evans Ouma (far right).

Sam is particularly buoyed by the influx of young Kenyans who are choosing degrees in science.

“The Kenyan Government has recently increased its funding for science and research to two percent of GDP,” explains Sam. “This has not only helped us compete in the world of research but has helped raise the profile of science as a career.”

Knowing which genes are responsible for aluminium tolerance will allow us to more precisely select for aluminium tolerance in our breeding programmes, reducing the time it takes for us to breed varieties that will have improved yields in acidic soils without the use of costly inputs such as lime or fertiliser.” (See the work that Sam does in this area with other partners outside Kenya)

So far we have produced 10 inbred lines that are outstanding for phosphorus efficiency, and two that were outstanding for aluminium toxicity. We are now testing unique verities developed for acid soils of Kenya.”

Slashing costs, increasing yields and resilience: genes to the rescue
Currently, Sam and his team of young researchers at Moi University are working with several other research facilities around the world (Brazilian Agricultural Research Corporation, EMBRAPA; Cornell University, USA; the International Rice Research Institute (IRRI); Japan’s International Research Center for Agricultural Sciences, JIRCAS; and the Kenya Agricultural Research Institute, KARI–Kitale) to develop high-yielding maize varieties adapted to acid soils in East Africa, using molecular and conventional breeding approaches.

Can you spot Sam? It’s a dual life. Here, he sheds his field clothes in this 2011 suit-and-tie moment with Moi University and other colleagues involved in the projects he leads. Left to right: P Kisinyo, J Agalo, V Mugalavai, B Were, D Ligeyo, S Gudu, R Okalebo and A Onkware.

Acid soils cover almost 13 per cent of arable land in Kenya, and most of the maize-growing areas in Kenya. In most of these areas, maize yields are reduced by almost 60 per cent. Aluminium toxicity is partly responsible for the low and declining yields.

“We found that most local maize varieties and landraces grown in acid soils are sensitive to aluminium toxicity. The aluminium reduces root growth and as such the plant cannot efficiently tap into native soil phosphorus, or even added phosphorus fertiliser. However, there are some varieties of maize that are suited to the conditions even if you don’t use lime to improve the soil’s pH. So far we have produced 10 inbred lines that are outstanding for phosphorus efficiency, and two that were outstanding for aluminium toxicity. We are now testing unique varieties developed for acid soils of Kenya.”

Sam (left) a group of farmers and alking to farmers and researchers at Sega, Western Kenya, in June 2009

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

In a related project, Sam is working with the same partners to understand the molecular and genetic basis for aluminium tolerance.

“Knowing which genes are responsible for aluminium tolerance will allow us to more precisely select for aluminium tolerance in our breeding programmes, reducing the time it takes for us to breed varieties that will have improved yields in acidic soils without the use of costly inputs such as lime or fertiliser.”

… my greatest achievements thus far have been those which have benefited farmers and my students.”

Summing up success
For Sam, the greatest two successes in his career have not been personal.

“If I’m honest, I have to say my greatest achievements thus far have been those which have benefited farmers and my students. Having funding to support PhD students and provide them with the resources they need to complete their research is very fulfilling and will go a long way to enhance the long-term success of our goal: to provide Kenyan farmers with cereal varieties that will improve their yields and make their livelihoods more secure and sustainable.”

With a dozen aluminium-tolerant and phosphorus-efficient breeding lines under their belt already, and two lines submitted for National Variety Trials (a pre-requisite step to registration and release to farmers), Sam and his team seem well on their way towards their goal, and we wish them well in their quest and labour.

Links:

PHOTOS:
- Meet some of Sam’s current crop of students
- Infrastructure improvement
The project Sam leads
BLOG: Sam’s work with other partners
Comparative Genomics (cereals) Research Initiative | InfoCentre
Media coverage: Sorghum and food security in Kenya
InfoCentres – Maize| Sorghum

GRM 2013: Marker-assisted breeding for improving phosphorus-use efficiency and tolerance to aluminum toxicity in maize — S Gudu from CGIAR Generation Challenge Programme

Science enlists nature and collaboration to ‘neutralise’ acidic soils

Africa, Asia, Comparative genomics in cereals, Genomics, Latin America, Maize, Rice, Sorghum No Responses »

Jul 232014

DNA spiral

Crop researchers including plant breeders across five continents are collaborating on several GCP projects to develop local varieties of sorghum, maize and rice, which can withstand phosphorus deficiency and aluminium toxicity – two of the most widespread constraints leading to poor crop productivity in acidic soils. These soils account for nearly half the world’s arable soils, with the problem particularly pronounced in the tropics, where few smallholder farmers can afford the costly farm inputs to mitigate the problems. Fortunately, science has a solution, working with nature and the plants’ own defences, and capitalising on cereal ‘family history’ from 65 million years ago. Read on in this riveting story related by scientists, that will carry you from USA to Africa and Asia with a critical stopover in Brazil and back again, so ….

… welcome to Brazil, where there is more going than the 2014 football World Cup! Turning from sports to matters cerebral and science, drive six hours northwest from Rio de Janeiro and you’ll arrive in Sete Lagoas, nerve centre of the EMBRAPA Maize and Sorghum Research Centre. EMBRAPA stands for Empresa Brasileira de Pesquisa Agropecuária ‒ in English, the Brazilian Agricultural Research Corporation.

Jurandir Magalhães

Jurandir Magalhães (pictured), or Jura as he prefers to be called, is a cereal molecular geneticist and principal scientist who’s been at EMBRAPA since 2002.

“EMBRAPA develops 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,” Jura explains.

Such business is also GCP’s bread and butter. So when in 2004, Jura and his former PhD supervisor at Cornell University, Leon Kochian, submitted their first GCP project proposal to clone a major aluminium tolerance gene in sorghum they had been searching for, GCP approved the proposal.

“We were already in the process of cloning the Alt_SB gene,” remembers Jura, “So when this opportunity came along from GCP, we thought it would provide us with the appropriate conditions to carry this out and complete the work.”

Cloning the Alt_SB gene would prove to be one of the first steps in GCP’s foundation sorghum and maize projects, both of which seek to provide farmers in the developing world with crops that will not only survive but thrive in the acidic soils that make up more than half of the world’s arable soils (see map below).

More than half of world’s potentially arable soils are highly acidic.

… identifying the Alt_SB gene was a significant achievement which brought the project closer to their final objective, which is to breed aluminium-tolerant crops that will improve yields in harsh environments, in turn improving the quality of life for farmers.”

A star is born: identifying and cloning Alt_SBFor 30 years, Leon Kochian (pictured below) has combined lecturing and supervising duties at Cornell University and the United States Department of Agriculture, with his quest to understand the genetic and physiological mechanisms behind the ability of some cereals to withstand acidic soils. Leon is also the Product Delivery Coordinator for GCP’s Comparative Genomics Research Initiative.

Leon Kochian

Aluminium toxicity is associated with acidic soils and is the primary limitation on crop production for more than 30 percent of farmland in Southeast Asia and Latin America, and approximately 20 percent in East Asia, sub-Saharan Africa and North America. Aluminium ions damage roots and impair their growth and function. This results in reduced nutrient and water uptake, which in turn depresses yield.

“These effects can be limited by applying lime to increase the soil’s pH. However, this isn’t a viable option for farmers in developing countries,” says Leon, who was the Principal Investigator for the premier Alt_SB project and is currently involved in several off-shoot projects.

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

“In wheat, when aluminium levels are high, these membrane transporters prompt organic acid release from the tip of the root,” explains Leon. “The organic acid binds with the aluminium ion, preventing it from entering the root. We found that in certain sorghum varieties, Alt_SB is the gene that encodes a specialised organic acid transport protein – SbMATE* – which mediates the release of citric acid. From cloning the gene, we found it is highly expressed in aluminium-tolerant sorghum varieties. We also found that the expression increases the longer the plant is exposed to high levels of aluminium.”

[*Editor’s note: different from the gene with the same name, hence not in italics]

Leon says identifying the Alt_SB gene and then cloning it was a significant achievement and it brought the project closer to their final objective, which he says is “to breed aluminium-tolerant crops that will improve yields in harsh environments, in turn improving the quality of life for farmers.”

This research was long and intensive, but it set a firm foundation for the work in GCP Phase II, which seeks to use what we have learnt in the laboratory and apply it to breed crops that are tolerant to biotic or abiotic stress such as aluminium toxicity and phosphorus deficiency.”

Comparative genomics: finding similar genes in different crops
Wheat, maize, sorghum and rice are all part of the Poaceae (grasses) family, evolving from a common grass ancestor 65 million years ago. Over this time they have become very different from each other. However, at a genetic level they still have a lot in common.

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

Rajeev Varshney

“The objective during GCP Phase I was to study the genomes of important crops and identify genes conferring resistance or tolerance to biotic or abiotic stresses,” says Rajeev Varshney (pictured), Director, Center of Excellence in Genomics and Principal Scientist in applied genomics at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). “This research was long and intensive, but it set a firm foundation for the work in GCP Phase II, which seeks to use what we have learnt in the laboratory and apply it to breed crops that are tolerant to biotic or abiotic stress such as aluminium toxicity and phosphorus deficiency.”

Until August 2013, Rajeev had oversight on GCP’s comparative genomics research projects on aluminium tolerance and phosphorus deficiency is sorghum, maize and rice, as part of his GCP role as Leader of the Comparative and Applied Genomics Theme.

“Phosphorus deficiency and aluminium toxicity are soil problems that typically coincide in acidic soils,” says Rajeev. “They are two of the most critical constraints responsible for low crop productivity on acid soils worldwide. These projects are combining the aluminium tolerance work done by EMBRAPA and Cornell University with the phosphorus efficiency work done by IRRI [International Rice Research Institute] and JIRCAS [Japan International Research Centre for Agricultural Sciences] to first identify and validate similar aluminium-tolerance and phosphorus-efficient genes in sorghum, maize and rice, and then, secondly, breed crops with these combined improvements.”

These collaborations are really exciting! They make it possible to answer questions that we could not answer ourselves, or that we would have overlooked, were it not for the partnerships.”

When Alt_SB met Pup1…
Having spent more than a decade identifying and cloning Alt_SB, Jura and Leon have recently turned their attention to identifying and cloning the genes responsible for phosphorus efficiency in sorghum. Luckily, they weren’t starting from scratch this time, as another GCP project on the other side of the world was well on the way to identifying a phosphorus-efficiency gene in rice.

Led by Matthias Wissuwa at JIRCAS and Sigrid Heuer at IRRI, the Asian base GCP project had identified a gene locus, which encoded a particular protein kinase that allowed varieties with this gene to grow successfully in low-phosphorous conditions. They termed the region of the rice genome where this gene resides as ‘phosphorus uptake 1’ or Pup1 as it is commonly referred to in short.

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

Read more about the mechanics of Pup-1 and the evolution of the project.

Jura and Leon are working on the same theory as IRRI and JIRCAS, that larger and longer roots enhance phosphorus efficiency. They are identifying sorghum with these traits, using comparative genomics to identify a locus similar to Pup1 in these low-phosphorus-tolerant varieties, and then verify whether the genes at this locus are responsible for the trait.

“So far, the results are promising and we have evidence that Pup1 homologues may underlie a major QTL for phosphorous uptake in sorghum,” says Jura who is leading the project to identify and validate Pup1 and other phosphorus-efficiency QTLs in sorghum. QTL stands for ‘quantitative trait locus’ which refers to stretches of DNA containing ‒ or linked to ‒ the genes responsible for a quantitative trait “What we have to do now is to see if this carries over in the field, leading to enhanced phosphorus uptake and grain yield in low-phosphorus soils,” he adds.

Jura and Leon are also returning the favour to IRRI and JIRCAS and are collaborating with both institutes to identify and clone in rice similar genes to the Alt_SB gene in sorghum.

“These collaborations are really exciting! They make it possible to answer questions that we could not answer ourselves, or that we would have overlooked, were it not for the partnerships,” says Sigrid.

To make a difference in rural development, to truly contribute to improved food security through crop improvement and incomes for poor farmers, we knew that capacity development had to be a continuing cornerstone in our strategy.”

Building capacity in Africa
In GCP Phase II which is more application oriented, projects must have objectives that deliver products and build capacity in developing-world breeding programmes.

Jean-Marcel Ribaut

“The thought behind the latter requirement is that GCP is not going to be around after 2014 so we need to facilitate these country breeding programmes to take ownership of the science and products so they can continue it locally,” says Jean-Marcel Ribaut, GCP Director (pictured). “To make a difference in rural development, to truly contribute to improved food security through crop improvement and incomes for poor farmers, we knew that capacity development had to be a continuing cornerstone in our strategy.”

Back to Brazil: Jura says this requirement is not uncommon for EMBRAPA projects as the Brazilian government seeks to become a world leader in science and agriculture. “Before GCP started, we had been working with African partners for five to six years through the McKnight Project. It was great when GCP came along as we were able to continue these collaborations.”

Samuel Gudu

One collaboration Jura was most pleased to continue was with his colleague and friend, Sam Gudu (pictured), from Moi University, Kenya. Sam has been collaborating with Jura and Leon on several GCP projects and is the only African Principal Investigator in the Comparative Genomics Research Initiative.

“Our relationship with EMBRAPA and Cornell University has been very fruitful,” says Sam. “We wouldn’t have been able to do as much as we have done without these collaborations or without our other international collaborators at IRRI, JIRCAS, ICRISAT or Niger’s National Institute of Agricultural Research [INRAN].”

Sam is currently working on several projects with these partners looking at validating the genes underlying major aluminium-tolerance and phosphorus-efficiency traits in local sorghum and maize varieties in Kenya, as well as establishing a molecular breeding programme.

“The molecular-marker work has been very interesting. We have selected the best phosphorus-efficient lines from Brazil and Kenya, and have crossed them with local varieties to produce several really good hybrids which we are currently field-testing in Kenya,” explains Sam. “Learning and using these new breeding techniques will enable us to select for and breed new varieties faster.”

Sam is also grateful to both EMBRAPA and Cornell University for hosting several PhD students as part of the project. “This has been a significant outcome as these PhD students are returning to Kenya with a far greater understanding of molecular breeding which they are sharing with us to advance our national breeding programme.”

We’ve used the knowledge that Jura’s and Leon’s Alt_SBprojects have produced to discover and validate similar genes in maize…We identified Kenyan lines carrying the superior allele of ZmMATE …This work will also improve our understanding of what other mechanisms may be working in the Brazilian lines too.”

‘Everyone’ benefits! Applying the Alt_SB gene to maize
Claudia Guimarães (pictured) is a maize geneticist at EMBRAPA. But unlike Jura, her interest lies in maize.

Claudia Guimarães

Working on the same comparative genomics principle used to identify Pup1 in sorghum, Claudia has been leading a GCP project replicating the sorghum aluminium tolerance work in maize.

“We’ve used the knowledge that Jura’s and Leon’s Alt_SBprojects have produced to discover and validate similar genes in maize,” explains Claudia. “From our mapping work we identified ZmMATE as the gene underlying a major aluminium tolerance QTL in maize. It has a similar sequence as the gene found in sorghum and it encodes a similar protein membrane transporter that is responsible for citrate extradition.”

A maize field at EMBRAPA. Maize on the left is aluminum-tolerant while the maize on the right is not.

A maize field at EMBRAPA. Maize on the left is aluminium-tolerant while the maize on the right is not.

Using molecular markers, Claudia and her team of researchers from EMBRAPA, Cornell University and Moi University have developed near-isogenic lines from Brazilian and Kenyan maize varieties that show aluminium tolerance, with ZmMATE present. From preliminary field tests, the Brazilian lines have had improved yields in acidic soils.

“We identified a few Kenyan lines carrying the superior allele of ZmMATE that can be used as donors to develop maize varieties with improved aluminium tolerance,” says Claudia. “This work will also improve our understanding of what other mechanisms may be working in the Brazilian lines too.”

What has pleased Jura and other Principal Investigators the most is the leadership that African partners have taken in GCP projects.

Cherry on the cereal cake
With GCP coming to an end in December 2014, Jura is hopeful that his and other offshoot projects dealing with aluminium tolerance and phosphorus efficiency will deliver on what they set out to do.

“For me, the cherry on the cake for the aluminium-tolerance projects would be if we show that Alt_SB improves tolerance in acidic soils in Africa. If everything goes well, I think this will be possible as we have already developed molecular markers for Alt_SB.”

What has pleased Jura and other Principal Investigators the most is the leadership that African partners have taken in GCP projects.

“This has been a credit to them and all those involved to help build their capacity and encourage them to take the lead. I feel this will help sustain the projects into the future and one day help these developing countries produce varieties of sorghum and maize for their farmers that are able to yield just as well in acidic soils as they do in non-acidic soils.”

In the foreground, left to right, Leon, Jura and Sam in a maize field at the Kenya Agricultural Research Institute (KARI), Kitale, in May 2010. They are examining crosses between Kenyan and Brazilian maize germplasm.

Links

Comparative Genomics Research Initiative on cereals
Comparative and Applied Genomics Theme
Comparative Genomics InfoCentre: for genomic resources, slides, news articles, press releases, videos, podcasts, blogposts, community of researchers, crop databases, and more
Researcher profiles – Claudia Guimarães | Sam Gudu |Leon Kochian | Niaba Témé | Jurandir Magalhães
Selected slides below:

GRM 2013: Cloning, characterization and validation of AltSB/Al tolerance in rice — L Kochian from CGIAR Generation Challenge Programme

GRM 2013: Cloning, characterization and validation of PUP1/P efficiency in maize — L Kochian from CGIAR Generation Challenge Programme

The curious case of cassava’s quirks, narrated in Nigeria

Africa, Cassava 4 Responses »

Jun 242014

Triumphs and tragedies, pitfalls and potential of the ‘camel crop’

We travel through space and time, with a pair of researchers who have a pronounced passion for a plant brought to Africa by seafaring Portuguese traders in the 16^th century. Fastforwarding to today, half a millennium later, the plant is widespread and deep inland, and is the staple food for Africa’s most populous nation – Nigeria.

Meet cassava, the survivor. After rice and maize, cassava is the third-largest source of carbohydrate in the tropics. Surviving, nay thriving, in poor soils and shaking off the vagaries of weather – including an exceptionally high threshold for drought – little wonder that cassava, the ‘camel’ of crops is naturally the main staple in Nigeria. And with that, it has propelled Nigeria to the very top of the cassava totem pole as the world’s leading cassava producer, and consumer: most Nigerians eat cassava in one form or another practically every day.

Great, huh? But there’s also a darker side to cassava, as we will soon find out from our two cassava experts. For starters, the undisputed global cassava giant, Nigeria, produces just enough to feed herself. Even if there were a surplus for the external demand, farming families, which make up 70 percent of the Nigerian population, have limited access to these lucrative external markets. Secondly, cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) are deadly in Africa. Plus, cassava is a late bloomer (up to two years growth cycle, typically one year), so breeding and testing improved varieties takes time. Finally, cassava is most definitely not à la mode at all in modern crop breeding: the crop is an unfashionably late entrant into the world of molecular breeding, owing to its complex genetics which denied cassava the molecular tools that open the door to this glamour world of ‘crop supermodels’.

Emmanuel Okogbenin (left) and Chiedozie Egesi (right) in a cassava field.

But all is not doom and gloom, which inexorably dissolve in the face of dogged determination. All the above notwithstanding, cassava’s green revolution seems to be decidedly on the way in Nigeria, ably led by born-and-bred sons of the soil: Chiedozie Egesi and Emmanuel Okogbenin (pictured right) are plant breeders and geneticists at the National Root Crops Research Institute (NRCRI). With 36 years’ collective cassava research experience between them, the two men are passionate about getting the best out of Nigeria’s main staple crop, and getting their hands into the sod while about it: “I’m a plant breeder,” says Chiedozie, with pride. “I don’t just work in a laboratory. I am also in the field to experience the realities.”

Hitting two birds with one stone…two stones are even better!
As Principal Investigators (PIs) leading three different projects in the GCP-funded Cassava Research Initiative, Chiedozie and Emmanuel, together with other colleagues from across Africa, form a formidable team. They also share a vision to enable farmers increase cassava production for cash, beyond subsistence. This means ensuring farmers have new varieties of cassava that guarantee high starch-rich yields in the face of evolving diseases and capricious weather.

Chiedozie is one of cassava’s biggest fans. His affection for, and connection to, cassava is almost personal and definitely paternal. He is determined to deploy the best plant-breeding techniques to not only enhance cassava’s commercial value, but to also protect the crop against future disease outbreaks, including ‘defensive‘ breading. But more on that later…

Emmanuel is equally committed to the cassava cause. As part of his brief, Emmanuel liaises with the Nigerian government, to develop for – and promote to – farmers high-starch cassava varieties. This ensures a carefully crafted multi-pronged strategy to revolutionise cassava: NRCRI develops and releases improved varieties, buttressed by financial incentives and marketing opportunities that encourage farmers to grow and sell more cassava, which spurs production, thereby simultaneously boosting food security while also improving livelihoods.

Standing tall. Disease resistance and high starch and yield aside, farmers also prefer an upright architecture, which not only significantly increases the number of plants per unit, but also favours intercropping, a perennial favourite for cassava farmers.

Cross-continental crosses and cousins, magic for making time, and clocking a first for cassava

No one has been able to manufacture time yet, so how can breeders get around cassava’s notoriously long breeding cycle? MAS (marker-assisted selection) is crop breeding’s magic key for making time. And just as humans can benefit from healthy donor organ replacement, so too does cassava, with cross-continental cousins donating genes to rescue the cousin in need. Latin American cassava is nutrient-rich, while African cassava is hardier, being more resilient to pests, disease and harsh environments.

Thanks to marker-assisted breeding, CMD resistance from African cassava can now be rapidly ‘injected’ much faster into Latin American cassava for release in Africa. Consequently, in just a three-year span (2010–2012), Chiedozie, Emmanuel, Martin Fregene of the Donald Danforth Plant Science Center (USA) and the NRCRI team, released two new cassava varieties from Latin American genetic backgrounds (CR41-10 and CR36-5). These varieties, developed with GCP funding, are the first molecular-bred cassava ever to be released, meaning they are a momentous milestone in cassava’s belated but steady march towards its own green revolution.

Marker-assisted selection is much cheaper, and more focused.”

On the cusp of a collaborative cassava revolution: on your marks…
With GCP funding, Chiedozie and Emmanuel have been able to use the latest molecular-breeding techniques to speed up CMD resistance. Using marker-assisted selection (MAS) which is much more efficient, the scientists identified plants combining CMD resistance with desirable genetic traits.

“MAS for CMD resistance from Latin American germplasm is much cheaper, and more focused,” explains Emmanuel. “There is no longer any need to ship in tonnes of plant material to Africa. We can narrow down our search at an early stage by selecting only material that displays markers for the genetic traits we’re looking for.” Using markers, combining traits (known as ‘gene pyramiding’) for CMD resistance is faster and more efficient, as it is difficult to distinguish phenotypes with multiple resistance in the field by just observing with the naked eye. This is what makes marker-assisted breeding so effective and desirable in Africa.

GCP’s mode of doing business coupled with its community spirit has spurred the NRCRI scientists to cast their eyes further out to the wider horizon beyond their own borders.

By collaborating with research centres in other parts of the world, Emmanuel and Chiedozie have made remarkable strides in cassava breeding. According to Emmanuel, “GCP helped us make links with advanced laboratories and service providers like LGC Genomics. The outsourcing of genotyping activities for molecular breeding initiatives is very significant, as it enables us to carry out analyses not otherwise possible.”

We can’t afford to sit idle until it comes – we need to be armed and on the ready.”

‘Defensive’ breeding: partnerships to pre-empt catastrophe and combat disease
Closer home in Africa, as PI of the corollary African breeders community of practice (CoP) project, Emmanuel co-organises regular workshops with plant breeders from a dozen other countries (Côte d’Ivoire, DR Congo, Ethiopia, Ghana, Kenya, Liberia, Malawi, Mozambique, Sierra Leone, Tanzania, Uganda and South Sudan). These events are an opportunity to share knowledge on molecular breeding and compare notes.

Of the diseases that afflict cassava, CBSD is the most devastating. Mercifully, in Nigeria, the disease is non-existent, but Chiedozie is emphatic that this is by no means cause for complacency. “If CBSD gets to Nigeria, it would be a monumental catastrophe!” he cautions. “We can’t afford to sit idle until it comes – we need to be armed and on the ready.”

Putting words to action, though this work on CBSD resistance is still in its early stages, more than 1,000 cassava genotypes (different genetic combinations) have already have been screened in the course of just one year. Chiedozie hopes that the team will be able to identify key genetic markers, and validate these in field trials in Tanzania, where CBSD is widespread. This East African stopover, Chiedozie emphasises, is a crucial checkpoint in the West African process. So the cassava CoP not only provides moral but also material support.

And Africa is not the limit. GCP-funded work on CMD resistance is more advanced than the CBSD work, though the real breakthrough in CMD only happened recently, on the international arena within which the African breeders now operate. According to Chiedozie, two entire decades of screening cassava genotypes from Latin America yielded no resistance to CMD. The reason for this is that although it is widespread in Africa, CMD is non-existent in Latin America.

Through international collaborative efforts, cassava scientists, led by Martin Fregene (now based in USA), screened plants from Nigeria and discovered markers for the CMD2 gene, indicating resistance to CMD. Once they had found these markers, the scientists were off and away! By taking the best of the Latin American material and crossing it with Nigerian genotypes that have CMD resistance, promising lines were developed from which the Nigerian team produced two new varieties. These varieties, CR41-10 and CR36-5, have already been released to farmers, and that is not all. More varieties bred using these two as parents are in the pipeline.

“GCP funding has given us the opportunity to show that a national organisation can do the job and deliver.”

Delivery attracts
The success of the CGP-funded cassava research in Nigeria lies in its in-country leadership. Chiedozie, Emmanuel and Martin are native Nigerian scientists and as such are – in many ways – best placed to drive a research collaboration to benefit the country’s farmers and boost food security. “GCP funding has given us the opportunity to show that a national organisation can do the job and deliver,” says Chiedozie.

This proven expertise has helped NRCRI forge other partnerships and attract more financial support, for example from the Bill & Melinda Gates Foundation for a project on genomic selection. GCP support has also bolstered communications with the Nigerian government, which has launched financial instruments, such as a wheat tariff,* to boost cassava production and use.

[Editors note: * wheat tariff: The Nigerian government is trying to reduce wheat import bills and also boost cassava commercialisation by promoting 20 percent wheat substitution in bread-making. Tariffs are being imposed on wheat to dissuade heavy imports and encourage utilisation of high-quality cassava flour for bread.]

“The government feels that to quickly change the fortunes of farmers, cassava is the way to go,” explains Emmanuel. He clarifies, “The tariff from wheat is expected to be ploughed back to support agricultural development – especially the cassava sector – as the government seeks to increase cassava production to support flour mills. Cassava offers a huge opportunity to transform the agricultural economy and stimulate rural development, including rapid creation of employment for youth.”

The Nigerian government is right in step aiding cassava’s march towards the crop’s own green revolution, as is evident in the the Minister of Agriculture’s tweet earlier this year, and in his video interview below. See also related media story, ‘Long wait for cassava bread’.

Clearly, the ‘camel’ crop – once considered an ‘orphan’ in research – has travelled as far in science as in geography, and it is a precious asset to deploy for food production in a climate-change-prone world. As Emmanuel observes, cassava’s future can only be brighter!

Slides by Chiedozie and Emmanuel

GRM 2013: Improving and deploying markers for biotic stresses in cassava — C Egesi from CGIAR Generation Challenge Programme

GRM 2013: Implementing MARS Project for drought tolerance and the Cassava Breeding Community of Practice: Accomplishments in the GCP and the Years Ahead — E Okogbenin from CGIAR Generation Challenge Programme

More links

Chiedozie’s profile
Cassava – Research | Community of practice | InfoCentre | Podcasts | Videos | Data management | Blogposts |Slides
Integrated Breeding Platform (IBP)

‘Milking’ cowpeas in Mozambique for protein and profit… plus a pox upon pests!

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

May 302014

Rogério Chiulele

Today, we travel the Milky Way on a voyage to Mozambique. Our man along the Milky Way is Rogério Marcos Chiulele (pictured), a lecturer at Mozambique’s Universidade Eduardo Mondlane’s Crop Science Department. He is also the lead scientist for cowpea research in Mozambique for the Tropical Legumes I (TLI) project. This gives Rogério a crucial tri-focal down-to-earth and away-from-the-clouds perspective on cowpea pedagogy, research and development. It is through this pragmatic triple-lens prism that Rogerio speaks to us today, once he’s captained us safely back from the stars to Planet Earth, Southeast Africa. After the protein and profit, next stop for him and team is ridding cowpeas of pod-sucking pests, among other things slated for the future. But back from the future to the present and its rooted realities…Problems, yes, but also lots of good scores, plus a deft sleight of hand that are bound to have you starry-eyed, we bet.

…cowpeas rank fourth as the most cultivated crop…”

Q: Tell us about Mozambique and cowpeas: are they important?

The devastating effects of nematodes on cowpea roots.

In Mozambique, cowpeas are an important source of food, for both protein and profit, particularly for the resource-poor households that benefit from cowpea income and nutrition. In terms of cultivation, cowpeas rank fourth as the most cultivated crop after maize, cassava and groundnuts, accounting for about 9 percent of the total cultivated area, and estimated at nearly four million hectares of smallholder farms. The crop is produced for grain and leaves, mostly for household consumption but it is becoming increasingly important as a supplement for household income.

But while its potential for food, protein and income is recognised, the realisation of such potential is still limited by drought due to irregular and insufficient rain; affliction by pests such as aphids, flower thrips and nematodes; diseases such as cowpea aphid mosaic virus and cowpea golden mosaic virus; and cultivation of low-yielding and non-improved varieties.

…we backcross to varieties with traits that farmers prefer…”

Q: And on cowpea research and breeding?
Since 2008, Universidade Eduardo Mondlane [UEM] established a cowpea-breeding programme for addressing some of the limiting constraints affecting cowpea production and productivity. This has been possible through collaboration with different funding institutions such as the Generation Challenge Programme.

2008: Screening of the 300 genotypes.

That same year [2008], a UEM research team that I coordinate qualified for a GCP capacity-building à la carte grant. In this project, we screened 300 Mozambican cowpea lines for drought tolerance. From these, we identified 84 genotypes that were either high-yielding or drought-tolerant. We further evaluated the 84 genotypes for another three seasons in two locations. From the 84, we identified six genotypes that not only had the two sought-after traits, but were also adapted to different environments.

In 2010, the UEM team joined the TLI project. For the six pre-identified genotypes, the UEM breeding programme is using marker-assisted recurrent selection [MARS] and marker-assisted backcrossing [MABC], combining drought tolerance and resistance to major biotic stresses occurring in Mozambique. In MABC, we are conducting a backcross to varieties with traits that farmers prefer, which includes aspects such as large seeds, early maturity and high leaf production.

…we conducted a farmers’ participatory varietal selection to glean farmers’ perceptions and preferences on cowpea varieties and traits…”

Q: What is the main focus in your work, and how and when do farmers come in?
The breeding work conducted by UEM is targeting all Mozambican agroecologies, but with particular focus on southern Mozambique which is drought-prone. In addition to drought, the area is plagued by many pests such as aphids, flower thrips, nematodes and pod-sucking pests. So, in addition to drought tolerance, we are conducting screening and selection for resistance to aphids, flower thrips and nematodes. In the near future, we will start screening for resistance to pod-sucking pests.

2009: field screening of the 84 genotypes in diff locations.

2009: Rogério during field screening of the 84 genotypes in different locations.

In 2009, we conducted a farmers’ participatory varietal selection to glean farmers’ perceptions and preferences on cowpea varieties and traits. From the study, six of the lines passed participatory variety selection with farmers, as they were large-seeded with good leaf production which provides additional food.

we hope to release three varieties in 2015…Our involvement with GCP has not only increased our exposure, but also brought along tangible benefits… I firmly believe black-eyed peas can really make a difference.”

Q: To what would you attribute the successes your team is scoring, and what are your goals for the future, besides screening for pod-sucking pests?
The success of the work that the Eduardo Mondlane team is doing is partly due to the collaboration and partnership with USA’s University of California, Riverside [UCR]. UCR sent us 60 lines from the GCP cowpea reference set* [Editorial note: see explanation at the bottom], which we evaluated for drought tolerance for four seasons in two locations – one with average rainfall and the other drought-prone. As these lines were already drought-tolerant, we tested them for adaptation to the local environment, and for high yield. From the set, we hope to release three varieties in 2015. In addition, for evaluating the different varieties, we also crossed the local varieties with black-eyed peas, which have a huge market appeal: local varieties fetch roughly half a US dollar per kilo, compared to black-eyed peas whose price is in the region of four to five US dollars.

2013: multilocation trials.

Our involvement with GCP has not only increased our exposure, but also brought along tangible benefits. For example, previously, nothing was being done on drought tolerance for cowpeas. But now we receive and exchange material, for example, the black-eyed peas from UCR that we received through GCP, which are set to boost production and markets, thereby improving lives and livelihoods. Amongst the varieties we are proposing to release is one black-eye type. I firmly believe black-eyed peas can really make a difference.

In addition, besides funding a PhD for one of our researchers, Arsenio Ndeve, who is currently at UCR, the Generation Challenge Programme, contributed to improvement on storage and irrigation facilities. We purchased five deep freezers for seed storage and one irrigation pump. Presently, we have adequate storage facilities and we conduct trials even during the off-season, thanks to the irrigation pump provided by GCP.

****

And on that upbeat note even as the challenge ahead is immense, today’s chat with Rogério ends here. To both pod-sucking pests and all manner of plagues on cowpeas, beware, as thy days are numbered: it would seem that Rogério and team firmly say: “A pox on both your houses!”

*A ‘reference set’ is a sub-sample of existing germplasm collections that facilitates and enables access to existing crop diversity for desired traits, such as drought tolerance or resistance to disease or pests

Links

REPORT on Rogério’s groundbreaking cowpea research capacity-building project on pp 130–132 in this PDF. Excerpt: “This project was the first of this nature in the country.”
BLOGPOST: Cowpeas – uncowed and unbowed: believing that what could be can be, in breeding
BLOGPOST: Profile on Jeff Ehlers, previously TLI cowpea research leader, he talks of his past but also his TLI work in this post
Cowpea research | research products | blogposts
Legumes Research initiative | InfoCentre | blogposts
Capacity building

A grounding in the reality of groundnut research in Africa, and why blood is thicker than water

Africa, Genetics, Genomics, Groundnuts, Legumes 2 Responses »

Mar 312014

Vincent Vadez

Today, we travel to yet another sun-kissed spot, leaving California behind but keeping it legumes. We land in Africa for some ground truths on groundnuts with Vincent Vadez (pictured), groundnut research leader for the Tropical Legumes I (TLI) Project. Vincent fills us in on facts and figures on groundnuts and Africa – a tale of ups and downs, triumphs and trials, but also of ‘family’ alliances not feuds, and of problems, yes, but also their present or potential solutions. On to the story then! Read on to find out why groundnuts are…

….A very mixed bag in Africa
Groundnuts (Arachis hypogaea L), also called peanuts, are a significant subsistence and food crop in sub-Saharan Africa. There, groundnuts are grown in practically every country, with the continent accounting for roughly a quarter of the world’s production. Despite this rosy African statistic, problems abound: for example, nearly half (40 percent) of the of the world’s total acreage for groundnuts is in Africa, which dramatically dims the 25 percent global production quota.

In Africa, groundnuts are typically cultivated in moderate rainfall areas across the continent, usually by women. (See editorial note* at the end of the story)

Clearly then, Africa’s yields are low, borne out by telling statistics which show African production at 950 kilos per hectare, in acute contrast to 1.8 tonnes per hectare in Asia.

…every year, yields worth about USD 500 million are lost”

What ails Africa’s production?
The main constraints hampering higher yields and quality in Africa are intermittent drought due to erratic rainfall, as well as terminal drought during maturation. And that is not all, because foliar (leaf) diseases such as the late leaf spot (LLS) or groundnut rosette are also taking their toll. Economically speaking, every year, yields worth about USD 500 million are lost to drought, diseases and pests. Plus, the seeding rates for predominantly bushy groundnut types are low, and therefore insufficient to achieve optimal ground cover. Thus, genetic limitations meet and mingle with major agronomic shortcomings in the cultivation of groundnuts, making it…

…. A tough nut to crack
Groundnuts are mostly cultivated by impoverished farmers living in the semi-arid tropics where rainfall is both low and erratic.

. Tough it may be for crop scientists, but clearly not too tough for these two youngsters shelling groundnuts at Mhperembe Market, Malawi.

“To help double the productivity of this crop over the next 10 years, we need to improve groundnuts’ ability to resist drought and diseases without farmers needing to purchase costly agricultural inputs,” says Vincent.

But the crop’s genetic structure is complex, plus, for resistance to these stresses, its genetic diversity is narrow. “Groundnuts are therefore difficult and slow to breed using conventional methods,” says Vincent. And yet, as we shall see later, groundnuts are distinctly disadvantaged when it comes to molecular breeding. But first, the good news!

…wild relatives have genes for resisting the stresses… molecular markers can play a critical role”

Why blood is thicker than water, and family black sheep are valued
Kith and kin are key in groundnut science. Vincent points out that groundnuts have several wild relatives that carry the necessary genes for resisting the stresses – especially leaf diseases – to which the crop is susceptible. These genes can be transferred from the wild cousins to the cultivated crop by blending conventional and molecular breeding techniques. But that is easier said than done, because cultivated groundnuts can’t cross naturally with their wild relatives owing to chromosomic differences.

Groundnut flower

“In modern breeding, molecular markers can play a critical role,” says Vincent. “Using markers, one can know the locations of genes of interest from an agronomic perspective, and we can then transfer these genes from the wild relatives into the groundnut varieties preferred by farmers and their markets.”

[The] ‘variegated’ partnership has been essential for unlocking wild groundnut diversity…”

Partnerships in and out of Africa, core capacities
“Partners are key to this work,” says Vincent. The groundnut work is led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), with collaborators in the target countries, which are Malawi (Chitedze Agricultural Research Centre), Senegal (Institut sénégalais de recherches agricoles ‒ ISRA) and Tanzania (Agricultural Research Institute, Naliendele), Moving forward together, continuous capacity building for partners in Africa is part and parcel of the project. To this end, there have been several training workshops in core areas such as molecular breeding and phenotyping, farmer field days in the context of participatory varietal selection, as well as longer-term training on more complex topics such as drought, in addition to equipping the partners with the critical infrastructure needed for effective phenotyping.

Freshly dug-up groundnuts.

Further afield out of Africa, Vincent’s team also collaborates with the Brazilian Agricultural Research Corporation (EMBRAPA), France’s Centre de coopération internationale en recherche agronomique pour le développement ‒ CIRAD, and USA’s University of Georgia.

This ‘variegated’ partnership has been essential for unlocking the wild groundnut diversity when about 12 years ago the EMBRAPA team successfully generated a number of ‘synthetic’ groundnuts from their wild relatives. Unlike the wild groundnuts, these synthetic groundnuts can be crossed to the cultivated type, bringing with them treasure troves of beneficial genes pertaining to the wild that would be otherwise unreachable for the cultivated varieties. Taking this one step further, the CIRAD‒ISRA team, in a close North‒South partnership, has used one of the synthetics from the Brazilian programme to generate new genetic diversity in the groundnut cultivar Fleur11. They are using additional synthetics from ICRISAT to further enlarge this genetic diversity in cultivated groundnuts.

These techniques and tools provide signposts on the genome of varieties for characteristics of importance”

A world first for an ‘orphan’, goals achieved, and what next
Among other goals, the team notably achieved a world first: “To produce the first SSR-based genetic linkage map for cultivated groundnuts!” declares Vincent. SSR stands for simple sequence repeat. The map was published in 2009, followed later on by a groundnut consensus map in 2012.

Youngster bearing fresh groundnuts along River Gambia in Senegal.

But what do these maps and their publication mean for groundnut production? Vincent explains: “These techniques and tools provide signposts on the genome of varieties for characteristics of importance ‒ for instance, resistance to a disease ‒ and these are used in combination to speed up the development of groundnut varieties that are more resistant to the stresses found in the harsh environments where most of the tropical world’s poor farmers live. Accelerating development means quicker delivery to farmers who are at high risk of going hungry. TLI Phase I produced synthetic groundnuts with new genes for disease resistance.”

In Phase II of the TLI Project which terminates in mid-2014, the team has continued to identify new genetic and genomic resources, for instance new sources of drought resistance from the germplasm and which are currently being used in the development of new breeding stocks. What is significant about this is that groundnuts ‒ like most other members of the legume family ‒ do not have much in the way of genomic and molecular-genetic resources, and are in fact consequently referred to in some circles as ‘orphans’ of the genome revolution. The focus has also been on resistance to rust, early and late leaf spot, and rosette – all economically critical diseases – by tapping the resilience of GBPD4, a cultivar resistant to rust and leaf spot, and introducing its dual resistance to fortify the most popular varieties against these diseases. The team also hopes to scale up these promising examples.

We believe this team is firmly on the way to fulfilling their two-fold project objectives which were: (1) to develop genomic resources and produce the first molecular-breeding products of the crop by injecting disease resistance (from TLI Phase I work) into farmer- and market-preferred varieties; and, (2) to lay the foundation for future marker-assisted recurrent selection (MARS) breeding by tapping on newly identified sources of drought tolerance.

the genetic stocks that hold the most promise to overcome leaf disease are found in the wild relatives… A thorough reflection is needed to combine good genetics with sound agronomic management”

The future
But the team is not resting on their laurels, as the work will not stop with the fulfillment of project objectives. In many ways, their achievements are in fact just the beginning. The new breeding stocks developed during TLI Phase II need to be evaluated further for their drought tolerance and disease resistance prior to their deployment in breeding programmes, and this activity ‒ among others ‒ is included for the next phase of the work in the proposed Tropical Legumes III project. In particular, the genetic stocks that hold the most promise to overcome leaf disease are found in the wild relatives. Thus, the existing materials need to be fully exploited and more need to be produced to cover the full breadth of potential stresses. Vincent adds “Of course an increasing part of the efforts will be about assuring quality evaluation data, meaning we must continue to significantly enhance the capacity ‒ both human and physical ‒ of our partners in target countries. Last but not least, the good wheat and rice cultivars that directly arose from the green revolution would have been nothing without nitrogen fertiliser and irrigation.” Vincent adds that the same applies to groundnuts: they are cultivated in infertile soil, at seeding rates that are unlikely to optimise productivity.

Groundnut drawing

For this reason, and others explained above, “A thorough reflection is needed to combine good genetics with sound agronomic management,” Vincent concludes, stressing the importance of what he terms as ‘looking beyond the fence’. Vincent’s parting shot, as our conversation draws to close: “In fact, I have grown increasingly convinced over the past year that we probably overlook those agronomic aspects in our genetic improvements at our peril, and we clearly need a re-think of how to better combine genetic improvement with the most suitable and farmer-acceptable agronomic management of the crop.”

Much food for thought there! And probably the beginnings of an animated conversation to which a groundnut crop model, on which Vincent and team are currently working, could soon yield some interesting answers on the most suitable genetic-by-management packages, and therefore guide the most adequate targets for crop improvement.

Links

Photo-story on Flickr
Groundnut research in Africa
Groundnut research Videos | Slides | in Tanzania
Legumes Research Initiative | InfoCentre
Journal articles: advances in groundnut genomics (2012) | Orphan legume crops enter the genomics era! (2009)
Ever wondered why the name groundnuts? Wonder no more, with this answer from the underground

*Editorial note: Erratum – Photo changed on April 8 2014, as the previous one depicted chickpeas, not groundnuts. We apologise to our readers for the error.

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