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James, the agile juggler on the maize research-to-development continuum

 Africa, Capacity building, Crop breeding, Maize, Researchers  1 Response »
Jan 122015
 
James profile

James Gethi and one of the crops closest to his heart – maize. He also has a soft spot for hardy crop varieties that survive harsh and unforgiving drylands, such as Machakos, Kenya, where this June 2011 photo of him with drought-tolerant KARI maize was taken.

As we tell our closing stories on our Sunset Blog, in parallel, we’re also catching up on the backlog of stories still in our store from the time GCP was a going concern. Our next stop is Kenya, and the narrative below is from 2012, but don’t go away as it is an evergreen – a tale that can be told at any time, as it remains fresh as ever. At that time, and for the duration of the partnership with GCP, the Food Crops Research Institute of the Kenya Agricultural and Livestock Research Organisation (KALRO) was then known as the Kenya Agricultural Research Institute (KARI), and we shall therefore stay with this previous name in the story. KARI was also the the name of the Kenyan institute at the time when James Gethi (pictured) left for a sabbatical at the International Maize and Wheat Improvement Center (CIMMYT by its Spanish acronym). On to the story then, and please remember we’re travelling back in time to the year 2012. 

“I got into science by chance, for the fun of it,” muses James, maize breeder and former GCP scientist “With agricultural school promising a flight to overfly the country’s agricultural areas– this was an interesting prospect for a village guy. ‘This could be fun’, I thought!”

And it turned out to be a chance well worth taking.  His first step was getting the requisite education. And so he armed himself with a BSc in Agriculture from the University of Nairobi, Kenya, topped with a Master’s and PhD in Plant Breeding from the University of Alberta (Canada) and Cornell University (USA), respectively. Beyond academics, in the course of his crop science career, James has developed 13 crop varieties, that included maize and cassava, published papers in numerous peer-reviewed papers (including the 2003 prize for Best paper in the field of crop science in the prestigious Crop Science journal. And in leadership, James headed the national maize research programme in his native Kenya. These are just a few of the achievements James has garnered in the course of his career, traversing  and transcending not only the geographical frontiers initially in his sights, but also scientific ones, reaching professional heights that perhaps his younger self might never have dreamt possible.

As a Research Officer at KARI, a typical day sees James juggling his time between hands-on research (developing maize varieties resistant to drought, field and storage pests) and project administration, coordinating public–private partnerships and the maize research programme at both institutional and country level. What motivates the man shouldering much of the responsibility for the buoyancy of his nation’s staple crop? James explains, “Making a difference by providing solutions to farmers. That’s my passion and that’s what makes me get up in the morning and go to work. It’s hugely satisfying!”

Without GCP, I would not be where I am today as a scientist… [it] gave me a chance to work with the best of the best worldwide… You develop bonds and understanding that last well beyond the life of the projects.”

Rapid transitions: trainee to trainer to leader
It was this passion and unequivocal dedication to his vocation – not to mention a healthy dollop of talent – that GCP was quick to recognise back in 2004, when James first climbed aboard the GCP ship. Like a duck to water, he proceeded to engage in all manner of GCP projects and related activities, steadily climbing the ranks from project collaborator to co-Principal Investigator and, finally, Principal Investigator in his own right, leading a maize drought phenotyping project. Along the way, he also secured GCP Capacity building à la carte and Genotyping Support Service grants to further the maize research he and his team were conducting.

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FLASHBACK: At a GCP drought phenotyping course in mid-2006 at Montpellier, France. (1) James (left) pays keen attention during one of the practical sessions. (2) In the spirit of “All work and no play, etc”, taking a break from the course to take in some of the sights with colleagues. Clearly, James, “the guy from the village” is anything but a dull boy! Next to James, second left, is BM Prasanna, currently leader of CIMMYT’s maize programme.

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From trainee to trainer and knowledge-sharer: James (behind the camera) training KARI staff on drought phenotyping in June 2009 at Machakos, in Kenya’s drylands.

The GCP experience, James reveals, has been immensely rewarding: “Without GCP, I would not be where I am today as a scientist,” he asserts. And on the opportunity to work with a capable crew beyond national borders, as opposed to operating as a solo traveller, he says: “GCP gave me a chance to work with the best of the best worldwide, and has opened up new opportunities and avenues for collaboration between developing-country researchers and advanced research institutes, creating and cementing links that were not so concrete before. This has shown that we don’t have to compete with one another; we can work together as partners to derive mutual benefits, finding solutions to problems much faster than we would have done working alone and apart from each other.”

The links James has in mind are not only tangible but also sustainable: “You develop bonds and understanding that last well beyond the life of the projects,” James enthuses, citing additional professional engagements (the African Centre for Crop Improvement in KwaZulu-Natal, South Africa, and the West Africa Centre for Crop Improvement, have both welcomed James and his team into their fold), as well as firm friendships with former GCP project colleagues as two key take-home benefits of his interaction with the Programme. These new personal and professional circles have fostered a happy home for dynamic debates on the latest news and views from the crop-science world, and the resultant healthy cross-fertilisation of ideas, James affirms.

Reflecting on what he describes as a ‘mentor’ role of GCP, and on the vital importance of capacity building in general, he continues: “By enhancing the ability of a scientist to collect germplasm, or to analyse that germplasm, or by providing training and tips on how to write a winning project proposal to get that far in the first place, you’re empowering scientists to make decisions on their own – decisions which make a difference in the lives of farmers. This is tremendous empowerment.”

Another potent tool, says James, is the software made available to him through GCP’s Integrated Breeding Platform (IBP), which is a handy resource package to dip into for – among other things – analysing data and selecting the right varieties at the right time. The next step for IBP, he feels, should be scaling up and aiming for outreach to the wider scientific community, forecasting that such a step could bring nothing but success: “The impacts could be enormous!” he projects, with a palpable and infectious enthusiasm.

People… don’t eat publications, they eat food… I’m not belittling knowledge, but we can do both”

Fast but not loose on the R&D continuum: double agent about?
For James, outreach and impacts are not limited to science alone. In parallel with his activities in upstream genetic science, James’ efforts are equally devoted to the needs of his other client base-–the development community and farmers. For this group, James’ focus is on putting tangible products on the table that will translate into higher crop yields and incomes for farmers. Yet whilst products from any highly complex scientific research project worth its salt are typically late bloomers, often years in the making on a slow burner as demanded by the classic linear R&D view that research must always precede development, adaptation and final adoption, James has been quick to recognise that actors in the world of development and the vulnerable communities they serve do not necessarily have this luxury of time.

August 2008: a huge handful, and more where that came from in Kwale, Kenya. This farmer's healthy harvest came from KARI hybrids.

August 2008: a huge handful, and more where that came from in Kwale, Kenya. This farmer’s healthy harvest came from KARI hybrids.

His solution for this challenge? “Sitting where I sit, I realised from very early on that if I followed the traditional linear scientific approach, my development clients would not take it kindly if I still had no products for them within the three-year lifespan of the project. The challenge then was to deliver results for farmers without compromising or jeopardising their integrity or the science behind the product,” he recalls. In the project he refers to – a GCP-funded project to combat drought and disease in maize and rice – James applied a novel double-pronged approach to get around this seeming conundrum of the need for sound science on the one hand, and the need for rapid results for development on the other hand. Essentially, he simultaneously walked on both tracks of the research–development continuum.

The project – led by Rebecca Nelson of Cornell University and with collaborators including James’ team at KARI (leading the maize component), the International Rice Research Institute (IRRI), researchers in Asia, as well as other universities in USA – initially set out with the long-term goal of dissecting quantitative trait loci (QTLs) for rice and maize with a view to combating drought and disease in these crops. Once QTLs were dissected and gene crosses done, James and his team went about backcrossing these new lines to local parental lines, generating useful products in the short term. The results, particularly given the limited resources and time invested, have been impressive, with seven hybrid varieties developed for drylands and coastal regions having been released in Kenya by 2009, and commercialised from 2010.

James and his colleagues have applied the same innovative approach to other GCP projects, grappling to get a good grasp of the genetic basis of drought tolerance, whilst also generating intermediate products for practical use by farmers along the way. James believes this dual approach paves the way for a win-win situation: “People on the ground don’t eat publications, they eat food,” he says. “As we speak now, there are people out there who don’t know where their next meal will come from. I’m not belittling knowledge, but we can do both – boiled maize on the cob and publications on the boil. But let’s not stop at crop science  and knowledge dissemination – let’s move it to the next level, which means products,” he challenges, adding: “With GCP support, we were able do this, and reach our intended beneficiaries.”

It is perhaps this kind of vision and inherent instinct to play the long game that has taken James this far professionally, and that will no doubt also serve him well in the future.

As our conversation comes to a close, we ask James for a few pearls of wisdom for other young budding crop researchers eager to carve out an equally successful career path for themselves, James offers “Form positive links and collaborations with colleagues and peers. Never give up; never let challenges discourage you. Look for organisations where you can explore the limits of your imagination. Stay focused and aim high, and you’ll reach your goal.”

Upon completion of his ongoing sabbatical at CIMMYT in Zimbabwe, where he is currently working on seed systems, James plans to return to KARI, armed with fresh knowledge and ready to seize – with both hands – any promising collaborative opportunities that may come his way .

Certainly, prospects look plentiful for this ‘village lad’ in full flight, and who doesn’t look set to land any time soon!

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In full flight – Montpellier, Brazil, Benoni, Bangkok, Bamako, Hyderabad… our boy voyaged from the village to Brazil and back, and far beyond that. Sporting the t-shirt from GCP’s Annual Research Meeting in Brazil in 2006, which James attended, he also attended the same meeting the following year, in Benoni, South Africa, in 2007, when this photo was taken. James is a regular at these meetings which are the pinnacle on  GCP’s calendar (http://bit.ly/I9VfP4). But he always sings for his supper and is practically part of the ‘kitchen crew’, but just as comfortable in high company. For example, he was one of the keynote speakers at the 2011 General Research Meeting (see below).

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Jura’s ‘jurassic’ journeys of discovery to and from sorghum’s ‘seven seas sede’

 Africa, Asia, Comparative genomics in cereals, Genetics, Genomics, Latin America, Researchers, Sorghum  No Responses »
Jan 082015
 

Welcome to Brazil! Journey by road six hours northwest from Rio de Janeiro and you’ll arrive to Sete Lagoas,  a city whose name means ‘Seven Lagoons’ in Portuguese. Although cloistered in farmlands, the city is largely a commercial centre, but also the seat of Embrapa Milho e Sorgo, the nerve centre of EMBRAPA’s maize and sorghum research, and so could pass for the ‘sede’ (Portuguese for headquarters) of the these two cereals. EMBRAPA is the Portuguese acronym for Empresa Brasileira de Pesquisa Agropecuária; the Brazilian Agricultural Research Corporation. EMBRAPA is a GCP Consortium member, and contributed to the proposal that founded GCP.

Photo provided by J MagalhãesJurandir Magalhães (pictured), or Jura, as he likes to be referred to in informal settings such as our story today, is a cereal molecular geneticist who has been working at the Embrapa Milho e Sorgo centre since 2002. “The centre 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 qualities are exactly what appeal to GCP, which has supported Jura as a Principal Investigator since 2004. Beyond science and on to governance and advisory issues, Jura is also EMBRAPA’s representative on the GCP Consortium Committee.

Home and away, on a journey of discovery in sorghum
Hailing from Belo Horizonte, Minas Gerais State, where he was born, Jura attended the Federal University of Viçosa in his home state. Upon completing his Master’s degree at the university in 1995, he proceeded to USA’s Cornell University in 1998 for his PhD, under the watchful eye of Leon Kochian, another GCP Principal Investigator.

Sorghum rainbow_A Borrell

No, it’s not photo-shopped. This Australian sorghum-and-double-rainbows shot is from Supa Snappa, Andy Borrell, also a GCP sorghum Principal Investigator. See http://bit.ly/1tBAOMW

At Cornell, Jura worked with Leon on identifying the genes associated with aluminium tolerance in sorghum. “At the time, genes associated with aluminium tolerance were known for cereals in the Triticeae family (wheat, barley and rye). But the same genes were not found in the Poaceae family (sorghum, rice and maize). This suggested that there were different aluminium-tolerance genes at play, so it was a really pioneering project.” Continuing with the Cornell team after his PhD, Jura worked with Leon to  map the location of a major aluminium-tolerance genetic ‘hotspot’ in sorghum, which the project team contracted to  AltSB  for short (aluminium-tolerance gene or locus in Sorghum bicolor). The mapping also marked the next chapter  of what was to be a long-term professional relationship for the pair.

Brazil beckons, joining GCP, leadership and enduring partnerships
But in between, Brazil broke in and beckoned her native son home. And so it was that in 2002, Jura packed his bags and accepted a position with EMBRAPA’s maize and sorghum research centre. And despite the geographical distance, it wasn’t long before he and Leon teamed up again. “When I left Cornell, Leon and I had finished mapping AltSB and we were keen to clone it so we could then develop aluminium-tolerant sorghum varieties more efficiently,” says Jura.

Two years after his return to Brazil,  Leon and Jura – in 2004 – submitted a joint proposal for a competitive grant for their first GCP project on aluminium tolerance in cereals, premised on AltSB. This project contributed to GCP’s foundation work on sorghum in this and other projects, the common goal being a bid to provide farmers in the developing world with sorghum crops that would be able to tolerate harsh soils. But the project contributed much more with a deep taproot in pre-history, as that which we today call ‘sorghum’, ‘maize’ and ‘rice’ were once one millions of ‘Jurassic’ years ago. More on that interesting side-story.

And since this first project, EMBRAPA and Cornell University have collaborated with several other research institutes around the world, particularly in Africa.

Left to right (foreground): Leon Kochian, Jurandir Magalhães (both EMBRAPA) and Sam Gudu (Moi University) examine crosses between Kenyan and Brazilian maize, at the Kenya Agricultural Research Institute (KARI), Kitale, in May 2010.

Left to right (foreground): Leon, Jura and Sam Gudu (Moi University) examine crosses between Kenyan and Brazilian maize, at the Kenya Agricultural Research Institute (KARI), Kitale, in May 2010.

Jura leads several EMBRAPA and GCP collaborative projects across three continents (Africa, Asia and the Americas). The partnerships forged by and through these projects go well beyond project life and frame, and will therefore continue after GCP’s sunset. Jura is both team leader and team player. And a couple of GCP projects in which Jura is part of the project team will run on in 2015 (see page 10), after GCP’s closure in December 2014.

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Peasant lad to leading professor: Paul and his passion for pods

 Africa, Chickpeas, Crop breeding, Legumes, Researchers  No Responses »
Jan 072015
 

Beyond chickpeas to embrace beans, chickpeas, groundnuts and pigeonpeas

Paul_w2As a scientist who comes from the dessicated drylands of the unforgiving Kerio Valley, where severe drought can mean loss of life through loss of food and animals, what comes first is food security… I could start to give something back to the community… It’s been a dream finally coming true.” – Paul Kimurto, Senior Lecturer and Professor in Crop Physiology and Breeding, Egerton University, Kenya

As a son of peasant farmers growing up in a humble home in the Rift Valley of Kenya, agriculture was, for Paul Kimurto (pictured above), not merely a vocation but a way of life: “Coming from a pastoral community, I used to take care of the cattle and other animals for my father. In my community livestock is key, as is farming of food crops such as maize, beans and finger millet.”

Covering some six kilometres each day by foot to bolster this invaluable home education with rural school, an affiliation and ever-blossoming passion for agriculture soon led him to Kenya’s Egerton University.

There, Paul excelled throughout his undergraduate course in Agricultural Sciences, and was thus hand-picked by his professors to proceed to a Master’s degree in Crop Sciences at the self-same university, before going on to obtain a German Academic Exchange Service (DAAD) scholarship to undertake a ‘sandwich’ PhD in Plant Physiology and Crop Breeding at Egerton University and the Leibniz Institute for AgriculturalEngineering (ATB) in Berlin, Germany.

… what comes first is food security… offering alternative drought-tolerant crops… is a dream finally coming true!…  GCP turned out to be one of the best and biggest relationships and collaborations we’ve had.”

Local action, global interaction
With his freshly minted PhD, Paul returned to Egerton’s faculty staff and steadily climbed the ranks to his current position as Professor and Senior Lecturer in Crop Physiology and Breeding at Egerton’s Crop Sciences Department. Yet for Paul, motivating this professional ascent throughout has been one fundamental factor:  “As a scientist who comes from a dryland area of Kerio valley, where severe drought can mean loss of food and animals, what comes first is food security,” Paul explains. “Throughout the course of my time at Egerton, as I began to understand how to develop and evaluate core crop varieties, I could start to give something back to the community, by offering alternative drought-tolerant crops like chickpeas, pigeonpeas, groundnuts and finger millet that provide farmers and their families with food security. It’s been a dream finally coming true.”

And thus one of academia’s true young-guns was forged: with an insatiable thirst for moving his discipline forward by seeking out innovative solutions to real problems on the ground, Paul focused on casting his net wide and enhancing manpower through effective collaborations, having already established fruitful working relationships with the International Maize and Wheat Improvement Center (CIMMYT), the (then) Kenya Agricultural Research Institute (KARI) and the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in earlier collaborative projects on dryland crops in Kenya. It was this strategy that paved the way towards teaming up with GCP, when, in 2008, Paul and his team were commissioned to lead the chickpea work in Kenya for the GCP Tropical Legumes I project (TLI), with local efforts being supported by colleagues at ICRISAT, and friends down the road at KARI undertaking the bean work of the project. Climbing aboard the GCP ship, Paul reveals, was a move worth making: “Our initial engagement with GCP started out as a small idea, but in fact, GCP turned out to be one of the best and biggest relationships and collaborations we’ve had.”

…GCP is people-oriented, and people-driven” 

Power to the people!
The success behind this happy marriage, Paul believes, is really quite simple: “The big difference with GCP is that it is people-oriented, and people-driven,” Paul observes, continuing: “GCP is building individuals: people with ideas become equipped to develop professionally.” Paul elaborates further: “I wasn’t very good at molecular breeding before, but now, my colleagues and I have been trained in molecular tools, genotyping, data management, and in the application of molecular tools in the improvement of chickpeas through GCP’s Integrated Breeding Multiyear Course. This has opened up opportunities for our local chickpea research community and beyond, which, without GCP’s support, would not have been possible for us as a developing-country institution.”

Inspecting maturity, Koibatek FTC, Bomet_R Mulwa_Sep'12_w

Inspecting pod maturity with farmers at Koibatek Farmers Training Centre in Eldama Ravine Division, Baringo County, Kenya, in September 2012. Paul is on the extreme right.

Passionate about his teaching and research work, it’s a journey of discovery Paul is excited to have shares with others: “My co-workers and PhD students have all benefitted. Technicians have been trained abroad. All my colleagues have a story to tell,” he says. And whilst these stories may range from examples of access to training, infrastructure or genomic resources, the common thread throughout is one of self-empowerment and the new-found ability to move forward as a team: “Thanks to our involvement with the GCP’s Genotyping Support Service, we now know how to send plant DNA to the some of the world’s best labs and to analyse the results, as well as to plan for the costs. With training in how to prepare the fields, and infrastructure such as irrigation systems and resources such as tablets, which help us to take data in the field more precisely, we are now generating accurate research results leading to high-quality data.”

The links we’ve established have been tremendous, and we think many of them should be long-lasting too: even without GCP“

Teamwork, international connections and science with a strong sense of mission
Teaming up with other like-minded colleagues from crème de la crème institutions worldwide has also been vital, he explains: “The links we’ve established have been tremendous, and we think many of them should be long-lasting too: even without GCP, we should be able to sustain collaboration with KBioscience [now LGC Genomics] or ICRISAT for example, for genotyping or analysing our data.” He holds similar views towards GCP’s Integrated Breeding Platform (IBP): “IBP is one of the ideas which we think, even after GCP’s exit in December 2014, will continue to support our breeding programmes. My colleagues and I consult IBP regularly for a range of aspects, from markers to protocols to germplasm and the helpdesk, as well as for contacts and content available via the IBP Communities of Practice.” Paul’s colleagues are Richard Mulwa, Alice Kosgei, Serah Songok, Moses Oyier, Paul Korir, Bernard Towett, Nancy Njogu and Lilian Samoei. Paul continues: “We’ve also been encouraging our regional partners to register on IBP – I believe colleagues across Eastern and Central Africa could benefit from this one-stop shop.”

Yet whilst talking animatedly about the greater sophistication and accuracy in his work granted as a result of new infrastructure and the wealth of molecular tools and techniques now available to him and his team, at no point do Paul’s attentions stray from the all-important bigger picture of food security and sustainable livelihoods for his local community: “When we started in 2008, chickpeas were known as a minor crop, with little economic value, and in the unfavoured cluster termed ‘orphan crops’ in research. Since intensifying our work on the crop through TLI, we have gradually seen chickpeas become, thanks to their relative resilience against drought, an important rotational crop after maize and wheat during the short rains in dry highlands of Rift valley and also in the harsh environments of the Kerio Valley and swathes of Eastern Kenya.”

This GCP-funded weather station is at Koibatek Farmers Training Centre, Longisa Division, Bomet County.

This GCP-funded weather station is at Koibatek Farmers Training Centre.

Having such a back-up in place can prove a vital lifeline to farmers, Paul explains, particularly during moments of crisis, citing the 2011–2012 outbreak of the maize lethal necrosis (MLN) disease which wiped out all the maize throughout Kenya’s  Bomet County, where Paul, Richard, Bernard and their team had been working on the chickpea reference set. Those farmers who had planted chickpeas – Paul recalls Toroto and Absalom as two such fortunate souls – were food-secure. Moreover, GCP support for infrastructure such as a weather station have helped farmers in Koibatek County to predict weather patterns and anticipate rainfall, whilst an irrigation system in the area is being used by the Kenyan Ministry of Agriculture to develop improved seed varieties and pasture for farmers.

The science behind the scenes and the resultant products are of course not to be underestimated: in collaboration with ICRISAT, Paul and his team released four drought-resistant chickpea varieties in Kenya in 2012, with the self-same collaboration leading to the integration of at least four varieties of the crop using marker-assisted backcrossing, one of which is in the final stages and soon to be released for field testing. With GCP having contributed to the recent sequencing of the chickpea genome, Paul and his colleagues are now looking to up their game by possibly moving into work on biotic stresses in the crop such as diseases, an ambitious step which Paul feels confident can be realised through effective collaboration, with potential contenders for the mission including ICRISAT (for molecular markers), Ethiopia and Spain (for germplasm) and researchers at the International Center for Agricultural Research in the Dry Areas (ICARDA) for germplasm. Paul first established contact with all of these partners during GCP meetings.

By coming together, pooling skills from biotechnology, agronomy, breeding, statistics and other disciplines, we are stronger as a unit and better equipped to offer solutions to African agriculture and to the current challenges we face.”

Links that flower, a roving eye, and the heat is on!
In the meantime, the fruits of other links established since joining the GCP family are already starting to blossom. For example, TLI products such as certified seeds of chickpea varieties being released in Kenya – and in particular the yet-to-be-released marker-assisted breeding chickpea lines which are currently under evaluation – caught the eye of George Birigwa, Senior Programme Officer at the Program for Africa’s Seed Systems (PASS) initiative of the Alliance for a Green Revolution in Africa (AGRA), which is now supporting the work being undertaken by Paul and his team through the Egerton Seed Unit and Variety Development Centre (of which Paul is currently Director) at the Agro-Based Science Park.

Yet whilst Paul’s love affair with chickpeas has evidently been going from strength to strength, he has also enjoyed a healthy courtship with research in other legumes: by engaging in a Pan-African Bean Research Alliance (PABRA) bean project coordinated by the International Center for Tropical Agriculture (CIAT), Paul and his team were able to release and commercialise three bean varieties which are currently in farmers’ fields in Kenya.

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Paul (left) in the field. The crop is chickpeas of course!

With so many pots on the boil, the heat is certainly on in Paul’s research kitchen, yet he continues to navigate such daily challenges with characteristic aplomb. As a proven leader of change in his community and a ‘ can-do, make-it-happen’ kind of guy, he is driving research forward to ensure that both his school and discipline remain fresh and relevant – and he’s taking his colleagues, students and local community along with him every step of  the way.

Indeed, rallying the troops for the greater good is an achievement he values dearly: “By coming together, pooling skills from biotechnology, agronomy, breeding, statistics and other disciplines, we are stronger as a unit and better equipped to offer solutions to African agriculture and to the current challenges we face,” he affirms. This is a crusade he has no plans to abandon any time soon, as revealed when quizzed on his future aspirations and career plans: “My aim is to continue nurturing my current achievements, and to work harder to improve my abilities and provide opportunities for my institution, colleagues, students, friends and people within the region.”

With the chickpea research community thriving, resulting in concrete food-security alternatives, we raise a toast to Paul Kimurto and his chickpea champions!

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Mission possible for ‘Generation Open’: open access and open attitudes for Open Access Week

 Africa, Asia, Cassava, Crop breeding, Crop information and data management, Open Access  No Responses »
Oct 242014
 

OAweek2014By Eloise Phipps

Imagine the scene: it is the dead of night, and you are engaged on a dangerous mission. You are tense, alert for any noise. You must complete your task without being seen, or risk the shame and humiliation of failure… but it is not a pleasant undertaking!

Your mission? A critical matter of honour. To dispose of your family’s cassava peelings – not with the rest of your household waste, but smuggled into the murky depths of the pit latrine. Why?

“The stigma about cassava is mostly among the Kikuyu people of central Kenya,” explains Henry Ngugi, Kenyan scientist and former Maize Pathologist for Latin America at the International Maize and Wheat Improvement Center (CIMMYT). “Traditionally, the Kikuyu are very proud, and self-sufficiency in basic needs such as food is an important factor in this. That is, you cannot be proud if you cannot feed yourself and your family. Now, the other part of the equation regarding cassava is that, traditionally, cassava was eaten during seasons of severe food shortages. It is a hardy and drought-tolerant crop so it would be available when the ‘good food’ was not. This also meant that it was associated with hunger and poverty – inability to feed oneself.”

“Another factor that may have played a role in the way the Kikuyu view cassava is that some of the traditional cultivars produced high levels of cyanide and were toxic [if not properly cooked], so as a crop it was not very highly regarded to start with. Improved cultivars have been bred to remove this problem. But because of these issues, many people would not want their neighbours to know they were so hungry they had to rely on cassava, and would go to great lengths to conceal any evidence!”

The story is not the same everywhere: graceful and strong, this farmer tends her field of cassava, in the village of Tiniu, near Mwanza, northern Tanzania.

Opening up for Open Access Week

This year, 20–26 October is Open Access Week, a global event celebrating, promoting and sharing ideas on open access – that is, making research results, including both publications and data, freely and publicly available for anyone to read, use and build upon. Even more exciting for us, this year’s theme is ‘Generation Open’, reflecting the importance of students and researchers as advocates for open access – a call that falls on fertile ground at the Generation Challenge Programme  (video below courtesy of UCMerced on YouTube).

We at GCP have been reflecting this week on different virtues of openness and transparency, and the perils of shame and secrecy. But before we go on, we’re sticking with cassava (carrying over from World Food Week!) but crossing the globe to China to celebrate the latest open-access publication to join the GCP parade. ‘Cassava genome from a wild ancestor to cultivated varieties’ by Wang et al is still practically a newborn, published on the 10th of October 2014.

The article presents draft genome sequences of a wild ancestor and a domesticated variety of cassava, with additional comparative analyses with other lines. It shows, for example, that genes involved in starch accumulation have been positively selected in cultivated cassava, and those involved in cyanogenic (ie, cyanide-producing) glucoside formation have been negatively selected. The authors hope that their results will contribute to better understanding of cassava biology, and provide a platform for marker-assisted breeding of better cassava varieties for farmers.

The research was carried out by a truly international team, led by scientists from the Chinese Academy of Tropical Agriculture Sciences (CATAS) and Chinese Academy of Sciences (CAS). Authors Wenquan Wang of CATAS and Bin Liu of CAS are delighted that their publication will be freely available, particularly in a journal with the prestige and high impact of the Nature family. As they observe, the open access to the paper will spread their experience and knowledge quickly to every corner of China and of the world where people have internet connections.

The work incorporated and partially built upon previous work mapping the cassava genome, which was funded by GCP in our project on Development of genomic resources for molecular breeding of drought tolerance in cassava (G3007.03), led by Pablo Rabinowicz, then with the University of Maryland, USA. This provides a perfect example of the kind of constructive collaboration and continuation that open access and sharing of research results can facilitate: by building on what has already been done, rather than re-inventing the wheel or working in isolation, we share, disseminate and amplify knowledge more rapidly and efficiently, with win–win outcomes for all involved.

Cassava farmers in Vietnam.

One thing that makes the latest research even more special is that it was published in Nature Communications, which marked Open Access Week by going 100 percent open access from the 20th of October, making it an open-access flagship within the Nature Publishing Group – a clear indicator of the ever-increasing demand for and credibility of open-access publishing. We congratulate all of our open-access authors for making their work publicly available, and Nature Communications for its bold decision!

A matter of perspective: turning shame to pride and fears to opportunities

No shame here: a little girl clutches a cassava root in Kenya.

Of course, human beings worrying about their social status is old as humanity itself and nothing new. Food has never been an exception as an indicator. Back in mediaeval Europe, food was a hugely important status symbol: the poor ate barley, oats and rye, while only the rich enjoyed expensive and prestigious wheat. Although our ideas about what is luxurious have changed – for example, sugar was considered a spice thanks to its high cost – rare imported foods were something to boast about just as they might be today.

But why are we ashamed of eating the ‘wrong foods’ – like cassava – when we could take pride in successfully feeding our families? Many of the things we tend to try to hide are really nothing to be ashamed of, and a simple change in perspective can turn what at first seem like weaknesses into sources of pride (and there are two sides to the cassava saga, as we shall see later).

Throughout its existence, GCP has been characterised by its openness and transparency. We have worked hard to be honest about our mistakes as well as our successes, so that both we and others can learn from them. The rewards of this clear-eyed approach are clearly noted in our Final External Review: “GCP has taken an open and pro-active attitude towards external reviews – commissioning their own independent reviews (the case of the current one) as well as welcoming a number of donor reviews. There have been clear benefits, such as the major governance and research reforms that followed the EPMR [External Programme and Management Review] and EC [European Commission] Reviews of 2008. These changes sharply increased the efficiency of GCP in delivering benefits to the poor.”

Transparent decision-making processes for determining choices of methods have also improved the quality of our science, while open, mutually respectful relationships – including open data-sharing – have underpinned our rich network of partnerships.

One aspect of this open approach is, of course, our commitment to open access. All of our own publications are released under Creative Commons licences, and we encourage all GCP grant recipients to do the same, or to pursue other open-access options. When exploring our research publications you will note that many are directly available to download. Our website will act as an archive for the future, ensuring that GCP publications remain online in one place after GCP’s closure in December this year. See our Global Access Policy and our policy on data-sharing.

“Open access journals are just terrific,” says Jean-Marcel Ribault, Director of GCP. “It’s great to enable access to publications, and it’s important to promote sharing of data and open up analysis too. The next big challenge is data management, and assuring the quality of that data. At the end of the day, the quality of the information that we share with others is fundamental.”

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

That’s a challenge that many other organisations are also grappling with. Richard Fulss, Head of Knowledge Management at our host CIMMYT is currently working on standards and approaches for the quality and structure of data, with the aim of implementing open access to all data within five years, meeting guidelines being put in place across CGIAR. “The issues to resolve are threefold,” he explains. “You have a licence issue, a technology issue – including building the right platform – and a cultural issue, where you need to build a culture of knowledge sharing and make open access publishing the norm rather than the exception.”

Our partners at the International Center for Tropical Agriculture (CIAT) already have a strong open-access policy, and are debunking some cherished open-access myths.

It’s good to talk: saying no to secrecy

Back to cassava, and of course not everyone feels the same way about the same crop, as there are many sides to any story. In China, demand for cassava is soaring – for food, for animal feed and most of all as a raw material for starch and biofuel production – making breeding of resilient, productive cassava varieties even more important. Even within Kenya, there are those who are quicker to see the crop’s virtues. The Luhya people of western Kenya often mix cassava with finger millet or sorghum to make flour for ugali (a stiff porridge or dough eaten as a staple food in vast swathes of Eastern and Southern Africa). As Henry explains “one reason was that such ugali ‘stayed longer in the stomach’ in literal translation from local parlance meaning it kept you full for longer – which is scientifically sound because cassava has a crude starch that takes longer to digest, and lots of fibre!”

Meanwhile, watch the delightful Chiedozie Egesi, Nigerian plant breeder and molecular geneticist, in the video below to hear all about the high potential of cassava, both as a food in itself and as a raw material to make flour and other products – something some farmers have already spotted. “Cassava can really sustain a nation… we’ve seen that it can,” he says. “You have in Nigeria now some of the Zimbabwean farmers who left Zimbabwe, got to Nigeria, and they changed from corn [maize] to cassava, because they see the potential that it has.”

The power of openness is already showing itself in the case of cassava, as well as other root, tuber and banana crops. Check out RTBMaps, an online atlas developed by the CGIAR Research Program on Roots, Tubers and Bananas (RTB), using ‘scientific crowdsourcing’ to combine data on a wide range of variables, shared by many researchers, in a single map. Putting all that information together can help people make better decisions, for example on how to target breeding, or where disease threats are likely to be strongest. And for a sweet serving, here’s our humble contribution from Phase I to a world-favourite dessert!

We leave you with one final thought. It is not just cassava that is plagued with pride and prejudice; many foods attract high or low statuses in different regions – or even just variations of the same food. People in Asia and North America, for example, tend to prefer yellow maize, while Africans like their maize white. In fact, yellow maize still carries a powerful stigma in many parts of Africa, as this was the colour of the maize that arrived as external  aid in periods of famine, oftentimes perceived in Africa as animal fodder and not human food in the countries it was sourced from. And thus yellow maize became synonymous with terrible times and the suffering and indignity of being unable to feed oneself and one’s family. Consequently, some of the famine-stricken families would only cook the yellow ‘animal-fodder’  maize in the dead of night, to avoid ‘detection’ and preserve family pride and honour.

This might at first blush appear to be a minor curiosity on colour and coloured thinking, were it not for the fact that when crops – such as sweet potato, cassava, or indeed maize – are bred to be rich in pro-vitamin A, and so provide plenty of the vitamin A that is particularly crucial for young children and pregnant women, they take on a golden yellow-orange hue. When promoting the virtues of this enriched maize in parts of Africa, it’s vital to know that as ‘yellow maize’ it would fall flat on its face, but as ‘orange maize’ or ‘golden maize’ it is a roaring success. A tiny difference in approach and label, perhaps, but one that is a quantum leap in nutritional improvement, and in ‘de-stigmatisation’ and accelerating adoption. Ample proof then that sharing details matters, and that it’s good to talk – even about the things we are a little ashamed of, thereby breathing substance into the spirit of the theme ‘Generation Open’.

Do have some of these uncomfortable but candid conversations this Open Access Week and live its spirit to the fullest every day after that! As for us here at GCP, we shall continue to sow and cultivate the seeds of Generation next for plant breeding into the future, through our Integrated Breeding Platform which will outlive GCP.

A little girl in Zambia gets a valuable dose of vitamin A as she eats her orange maize.

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.

Links:

2 – 1 = 3: Seeking sorghum solutions, breeding for more yield with less water

 Africa, Crop breeding, Genetics, Genomics, Sorghum  No Responses »
Aug 292014
 
One of the greatest challenges of our time is growing more crops to feed more people, but using less water

Sorghum is one of the most ‘efficient’ crops in terms of needing less water and nutrients to grow. And although it is naturally well-adapted to sun-scorched drylands, there is still a need to improve its yield and broad adaptability in these harsh environments. In West Africa, for example, while sorghum production has doubled in the last 20 years, its yield has remained stagnant – and low.

The GCP Sorghum Research Initiative comprises several projects, which are exploring ways to use molecular-breeding techniques to improve sorghum yields, particularly in drylands. All projects are interdisciplinary international collaborations with an original focus on Mali, where sorghum-growing areas are large and rainfall is getting more erratic and variable. Through the stay-green project, the research has since broadened to also cover Burkina Faso, Ethiopia, Kenya, Niger and Sudan.

Using molecular markers is new and exciting for us as it will speed up the breeding process. With molecular markers, you can easily see if the plant you’ve bred has the desired characteristics without having to grow the plant and or risk missing the trait through visual inspection.”

What’s MARS got to do with it?

Niaba Témé is a local plant breeder and researcher at Mali’s L’Institut d’économie rurale (IER). He grew up in a farming community on the southern edge of the Sahara Desert, where crops would constantly fail during drier-than-normal seasons.

Niaba Teme

Niaba Témé

Niaba says these crop failures were in part his inspiration for a career where he could help farmers like his parents and siblings protect themselves from the risks of drought and extreme temperatures.

For the past four years, Niaba and his team at IER have been collaborating with Jean-François Rami and his team at France’s Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), to improve sorghum grain yield and quality for West African farmers. The work is funded by the Syngenta Foundation for Sustainable Agriculture.

“With the help of CIRAD and Syngenta, we have been learning how to use molecular markers to improve breeding efficiency of sorghum varieties more adapted to the variable environment of Mali and surrounding areas which receive less than 600 millimetres of rainfall per year,” he says.

Jean-François Rami

Jean-François Rami

“Using molecular markers is new and exciting for us as it will speed up the breeding process. With molecular markers, you can easily see if the plant you’ve bred has the desired characteristics without having to grow the plant and or risk missing the trait through visual inspection.”

Jean-François Rami, who is the project’s Principal Investigator, has been impressed by the progress made so far. Jean-François is also GCP’s Product Delivery Coordinator for sorghum.

“Since its inception, the project has progressed very well,” says Jean-François. “With the help of the IER team, we’ve been able to develop two bi-parental populations from elite local varieties, targeting two different environments of sorghum cropping areas in Mali. We’ve then been able to use molecular markers through a process called marker-assisted recurrent selection [MARS] to identify and monitor key regions of the genome in consecutive breeding generations.”

The collaboration with Syngenta came from a common perspective and understanding of what approach could be effectively deployed to rapidly deliver varieties with the desired characteristics.

“Syngenta came with their long experience in implementing MARS in maize. They advised on how to execute the programme and avoid critical pitfalls. They offered to us the software they have developed for the analysis of data which allowed the project team to start the programme immediately,” says Jean-François.

Like all GCP projects, capacity building is a large part of the MARS project. Jean-François says GCP has invested a lot to strengthen IER’s infrastructure and train field technicians, researchers and young scientists. But GCP is not the only player in this: “CIRAD has had a long collaboration in sorghum research in Mali and training young scientists has always been part of our mission. We’ve hosted several IER students here in France and we are interacting with our colleagues in Mali either over the phone or travelling to Mali to give technical workshops in molecular breeding. The Integrated Breeding Platform [IBP] has also been a breakthrough for the project, providing to the project team breeding services, data management tools, and a training programme – the Integrated Breeding Multiyear Course [IB–MYC].”

We don’t have these types of molecular-breeding resources available in Mali, so it’s really exciting to be a part of this project… the approach has the potential to halve the time it takes to develop local sorghum varieties with improved yield and adaptability to drought… one of the great successes of the project has been to bring together sorghum research groups in Mali in a common effort to develop new genetic resources for sorghum breeding.”

Back-to-back: more for Mali’s national breeding programme

On the back of the MARS project, Niaba successfully obtained GCP funding in 2010 to carry out similar research with CIRAD and collaborators in Africa at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT).

“In this project, we are trying to enhance sorghum grain yield and quality for the Sudano-Sahelian zone of West Africa using the backcross nested association mapping (BCNAM) approach,” explains Niaba, who is the Principal Investigator of the BCNAM project. “This involves using an elite recurrent parent that is already adapted to local drought conditions. The benefit of this approach is that it can lead to detecting elite varieties much faster.”

Kirsten Vom Brocke (CIRAD) Michel Vaksmann (CIRAD) Mamoutou Kouressy (IER) Eva Weltzien (ICRISAT) Jean-Francois Rami (CIRAD) Denis Lespinasse (Syngenta) Niaba Teme (IER) Ndeye Ndack Diop (GCP) Ibrahima Sissoko (Icrisat) Fred Rattunde (Icrisat)

A ‘sample’ of the rich mix of international partners in sorghum research: Left to right – Kirsten Vom Brocke (CIRAD), Michel Vaksmann (CIRAD), Mamoutou Kouressy (IER), Eva Weltzien (ICRISAT), Jean-François Rami (CIRAD), Denis Lespinasse (Syngenta), Niaba Teme (IER), Ndeye Ndack Diop (GCP Capacity Building Leader), Ibrahima Sissoko and Fred Rattunde (both from ICRISAT).

Eva Weltzien has been the Principal Scientist for ICRISAT’s sorghum breeding programme in Mali since 1998. She says the project aligned with much of the work her team had been doing, so it made sense to collaborate considering the new range of sorghum genetic diversity that this approach aims to use.

“We’ve been working with Niaba’s team to develop 100 lines for 50 populations from backcrosses carried out with 30 recurrent parents,” explains Eva. “These lines are being genotyped by CIRAD. We will then be able to use molecular markers to determine if any of these lines have the traits we want. We don’t have these types of molecular-breeding resources available in Mali, so it’s really exciting to be a part of this project.”

Eva Weltzien (holding sheet of paper) presenting to Mali's Minister of Agriculture (in white cap) a graph on the superiority of new guinea race hybrids. Also on display are panicles and seed of the huybrids and released varieties of sorghum in Mali. The occasion was an annual field day at ICRISAT's research station at Samanko, Mali.

An annual field day at ICRISAT’s research station at Samanko, Mali. Eva Weltzien (holding sheet of paper) showing Mali’s Minister of Agriculture, Tiemoko Sangare, (in white cap) a graph on the superiority of new guinea race hybrids. Also on display are panicles and seed of the hybrids and released varieties of sorghum in Mali.

Eva says that the approach has the potential to halve the time it takes to develop local sorghum varieties with improved yield and adaptability to drought.

For Jean-François, one of the great successes of the project has been to bring together sorghum research groups in Mali in a common effort to develop new genetic resources for sorghum breeding.

“This project has strengthened the IER and ICRISAT partnerships around a common resource. The large multiparent population that has been developed is analysed collectively to decipher the genetic control of important traits for sorghum breeding in Mali,” says Jean-François.

 Plants with this ‘stay-green’ trait keep their leaves and stems green during the grain-filling period. Typically, these plants have stronger stems, higher grain yield and larger grain.”

Sorghum staying green and strong, with less water

In February 2012, Niaba and his colleague, Sidi B Coulibaly, were invited to Australia as part of another Sorghum Research Initiative project they had been collaborating on with CIRAD, Australia’s University of Queensland and the Queensland Department of Agriculture, Fisheries and Forestry (QDAFF).

“We were invited to Australia for training by Andrew Borrell and David Jordan, who are co-Principal Investigators of the GCP stay-green sorghum project,” says Niaba.

Left to right: Niaba Teme (Mali), David Jordan (Australia), Sidi Coulibaly (Mali) and Andrew Borrell (Australia) visiting an experiment at Hermitage Research Facility in Queensland, Australia.

Left to right: Niaba Témé (Mali), David Jordan (Australia), Sidi Coulibaly (Mali) and Andrew Borrell (Australia) visiting an experiment at Hermitage Research Facility in Queensland, Australia.

“We learnt about association mapping, population genetics and diversity, molecular breeding, crop modelling using climate forecasts, and sorghum physiology, plus a lot more. It was intense but rewarding – more so the fact that we understood the mechanics of these new stay-green crops we were evaluating back in Mali.”

It wasn't all work and there was clearly also time to play, as we can see her., Sidi Coulibaly and Niaba Teme visiting with the Borrell family in Queensland, Australia.

It wasn’t all work and there was clearly also time to play, as we can see here., where Sidi Coulibaly and Niaba Témé are visiting the Borrell family in Queensland, Australia.

Stay-green is a post-flowering drought adaptation trait that has contributed significantly to sorghum yield stability in northeastern Australia and southern USA over the last two decades.

Andrew has been researching how the drought-resistant trait functions for almost 20 years, including gene discovery. In 2010, he and his colleague, David Jordan, successfully obtained funding from GCP to collaborate with IER and CIRAD to develop and evaluate drought-adapted stay-green sorghum germplasm for Africa and Australia.

“Stay-green sorghum grows a canopy that is about 10 per cent smaller than other lines. So it uses less water before flowering,” explains Andrew. “More water is then available during the grain-filling period. Plants with this ‘stay-green’ trait keep their leaves and stems green during the grain-filling period. Typically, these plants have stronger stems, higher grain yield and larger grain.”

Andrew says the project is not about introducing stay-green into African germplasm, but rather, enriching the pre-breeding material in Mali for this drought-adaptive trait.

The project has three objectives:

  1. To evaluate the stay-green drought-resistance mechanism in plant architecture and genetic backgrounds appropriate to Mali.
  2. To develop sorghum germplasm populations enriched for stay-green genes that also carry genes for adaptation to cropping environments in Mali.
  3. To improve the capacity of Malian researchers by carrying out training activities for African sorghum researchers in drought physiology and selection for drought adaptation in sorghum.

…we have found that the stay-green trait can improve yields by up to 30 percent in drought conditions with very little downside during a good year, so we are hoping that these new lines will display similar characteristics”

Expansion and extension:  beyond Mali to the world

Andrew explains that there are two phases to the stay-green project. The project team first focused on Mali. During this phase, the Australian team enriched Malian germplasm with stay-green, developing introgression lines, recombinant inbred lines and hybrids. Some of this material was field-tested by Sidi and his team in Mali.

“In the past, we have found that the stay-green trait can improve yields by up to 30 percent in drought conditions with very little downside during a good year, so we are hoping that these new lines will display similar characteristics,” says Andrew. “During the second phase we are also collaborating with ICRISAT in India and now expanding to five other African countries – Niger and Burkina Faso in West Africa; and Kenya, Sudan and Ethiopia in East Africa. During 2013, we grew our stay-green enriched germplasm at two sites in all these countries. We also hosted scientists from Burkina Faso, Sudan and Kenya to undertake training in Queensland in February 2014.”

 

A sampling of some of stay-green sorghum partnerships in Africa. (1) Asfaw Adugna assessing the genetic diversity of sorghum panicles produced from the GCP collaboration at Melkassa, Ethiopia. (2) Clarisse Barro-Kondombo (Burkina Faso) and Andrew Borrell (Australia) visiting a lysimeter facility in Hyderabad, India, as part of GCP training. (3) Clement Kamau (Kenya, left) and Andrew Borrell (Australia, right) visiting the seed store at the Kenya Agricultural Research Institute (KARI) in Katumani, Kenya.

A sampling of some of stay-green sorghum partnerships in Africa. (1) Asfaw Adugna of the Ethiopian Institute of Agricultural Research (EIAR)  assessing the genetic diversity of sorghum panicles produced from the GCP collaboration at Melkassa, Ethiopia. (2) Clarisse Barro-Kondombo (left, INERA – Institut de l’environnement et de recherches agricoles , Burkina Faso) and Andrew Borrell (right) visiting a lysimetre facility at ICRISAT’s headquarters in Hyderabad, India, as part of GCP training, in February 2013. (3) Clement Kamau (left, Kenya Agricultural Research Institute [KARI] ) and Andrew Borrell (right) visiting the seed store at KARI, Katumani, Kenya.

Andrew says that the collaboration with international researchers has given them a better understanding of how stay-green works in different genetic backgrounds and in different environments, and the applicability is broad. Using these trial data will help provide farmers with better information on growing sorghum, not just in Africa and Australia, but also all over the world.

“Both David and I consider it a privilege to work in this area with these international institutes. We love our science and we are really passionate to make a difference in the world with the science we are doing. GCP gives us the opportunity to expand on what we do in Australia and to have much more of a global impact.”

We’ll likely be hearing more from Andrew on the future of this work at GCP’s General Research Meeting (GRM) in October this year, so watch this space! Meantime, see slides below from GRM 2013 by the Sorghum Research Initiative team. We also invite you to visit the links below the slides for more information.

Links

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

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.

Sam in a maize field in Kenya.

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 (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:

 

Sugarcane, sorghum, students and maize: Claudia’s colourful and contrasting crop science career

 Comparative genomics in cereals, Genomics, Latin America, Maize, Researchers, Women in science  No Responses »
Jul 242014
 

Read how this cocktail blends in a comparative genomics crucible, where both family genes and crop genes come into play in Brazil. Nothing whatsoever to do with the World Cup. It’s all about a passionate love affair with plant science – specifically a quest for aluminium-resilient maize – spanning a decade-and-a-half, and still counting…

Claudia

Claudia Guimarães

 

“I love the whole process of science; from identifying a problem, developing a method, conducting the experiments, analysing the data and evaluating the findings.” – Claudia Guimarães (pictured), Researcher at EMBRAPA Milho e Sorgo, Sete Lagoas, Brazil

I always enjoyed looking after the cattle and horses as well as planting and harvesting different crops.”

Forged on family farm, federal institute and foreign land
Claudia Guimarães is a plant molecular geneticist, with a pronounced passion for science. At the Federal University of Viçosa, Claudia studied agronomy because it provided a wide range of possibilities career-wise. She also believes her family’s farming background too had a part to play in her study and career choice. “My father has a farm in a small village 200 km north of Sete Lagoas. My whole family used to go there during our school holidays. I always enjoyed looking after the cattle and horses as well as planting and harvesting different crops.”

During her bachelor’s degrees, Claudia was increasingly drawn to plant genetics. She decided to pursue this field further and completed a Master’s degree in Genetics and Breeding, focusing on maize. She then completed a PhD in Comparative Genomics where she split her time between California and Brazil. “For my PhD, I got a scholarship from the Brazilian Council for Scientific and Technological Development which included international training in San Diego, California. During my PhD, I focused on comparative genomics for sugarcane, maize and sorghum, which involved genetic mapping and markers,” Claudia reveals.

Returning to Brazil after two years in California, Claudia joined the Brazilian Agricultural Research Corporation, commonly referred to as EMBRAPA (Empresa Brasileira de Pesquisa Agropecuária), where she has worked for the last 15 years, since 1999.

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Preparing to put her shoulder to the wheel, literally? Claudia in a maize field at the International Maize and Wheat Improvement Center (CIMMYT), Tlaltizapan, Mexico, in January 2010.

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Maize plantlets cultivated in nutrient solution, the methodology Claudia and her team use to evaluate aluminium tolerance.

Our next challenge is to develop specific markers for a wider marker-assisted selection of aluminium tolerance in maize.”

Long-term allies in aluminium tolerance
EMBRAPA first became involved with GCP through one of its foundation programmes headed by Leon Kochian and his former PhD student Jurandir Magalhães. “Jura has been a really close friend for a long time,” explains Claudia. “We went to university together and have ended up working together here at EMBRAPA. I was involved in Jura’s project, which sought to clone a sorghum aluminium-tolerance gene.”

This gene is called SbMATE. Claudia continues, “EMBRAPA had a long-term aluminium-tolerance programme on maize and sorghum, within which there was a QTL mapping project for aluminium tolerance in maize, in which we started to look for a similar gene as the sorghum team.”

[Editor’s note: QTL stands for quantitative trait locus or loci – gene loci where allelic variation is associated with variation in a quantitative trait. An allele is a variant (different version) of a gene, that leads to variation in a trait, eg different colour for hair and eyes in human beings.]

Working with Leon Kochian at Cornell University, USA, Claudia and her team were able to find an important aluminium-tolerance gene homologue (loosely meaning a relative or counterpart) to the sorghum SbMATE, which they named ZmMATE. This gene is responsible for a major aluminium tolerance QTL that improves yield in acidic soil in maize breeding lines and hybrids. (see why scientists work jointly on closely related cereals)

“Identifying and then validating ZmMATE as the primary aluminium tolerance QTL in maize was a great project,” says Claudia. “Our next challenge is to develop specific markers for a wider marker-assisted selection of aluminium tolerance in maize.”

1: Rhyzobox containing two layers of Cerrado soil – a corrected top-soil and lower soils with 15 percent of aluminium saturation. We can see that near-isogenic lines (NILs) introgressed with the Al tolerance QTL (qALT6) that encompasses ZmMATE1 show deeper roots and longer secondary roots in acid soils, whereas the roots of L53 are mainly confined in the corrected top soil. 2: Maize ears, representing the improved yield stability in acid soils of a NIL per se and crossed with L3. NILs have the genetic background of L53 introgressed with qALT6, the major aluminium-tolerance QTL.

March 2014. Photo 1: Rhyzobox containing two layers of Cerrado soil – a corrected top-soil and lower soils with 15 percent aluminium saturation. We can see that near-isogenic lines (NILs) introgressed with the aluminium-tolerance QTL (qALT6) that encompasses ZmMATE1 show deeper roots and longer secondary roots in acidic soils, whereas the roots of L53 are mainly confined in the corrected top soil. Photo 2: Maize ears, representing the improved yield stability in acidic soils of a NIL per se and crossed with L3. NILs have the genetic background of L53 introgressed with qALT6, the major aluminium-tolerance QTL.

 

 …the students have really become my arms…  helping me a lot with the experiments…

Giving and receiving: students step in, partners in print
Supervising students has become a larger part of Claudia’s life since becoming a member of the Genetics Graduate Programme at Universidade Federal de Minas Gerais, in 2004. Because of this, she credits the students for helping her with her research. “I don’t have as much time as I used to in the lab, so the students have really become my arms in that area, helping me a lot with the experiments,” Claudia reveals. “This isn’t to say that they don’t have to think about what they are doing. I encourage them to always be thinking about why they are doing an experiment and what the result means. At the end of the day, they need to know more about what they are doing than I do, so they can identify indiscretions and successes.”

Claudia says she is always preaching three simple instructions to her students – work hard, always continue to learn and like what you do. “The last instruction is particularly important because as a scientist you need to dedicate a lot of time to what you do, so it helps if you like it. If you don’t like it then it becomes frustrating and no fun at all. I don’t think of my work as a job, rather as a passion. I just enjoy it so much!”

Claudia’s passion is not just a matter of the heart but also of the head, expressing itself in print. Her latest publication reflects the most current results on maize aluminium tolerance, highlighting GCP support, partnerships within and beyond EMBRAPA embracing Cornell University and the Agricultural Research Services of the United States Department of Agriculture (USDA–ARS) , as well as the strong presence of students. Check it out

Links:

SLIDES

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

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.

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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 AltSB 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 AltSB 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.

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

… identifying the AltSB 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 AltSB
For 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

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 AltSB 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, AltSB 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 AltSB 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.

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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 AltSB met Pup1…
Having spent more than a decade identifying and cloning AltSB, 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 AltSB 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

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

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 AltSB projects 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 AltSB gene to maize
Claudia Guimarães (pictured) is a maize geneticist at EMBRAPA. But unlike Jura, her interest lies in maize.

Claudia

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 AltSBprojects 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 AltSB 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 AltSB.”

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 in Kenya.

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.

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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’Cassava leaf. Photo: N Palmer/CIAT

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 16th 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.

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.

erect cass1_LS 4 web

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

 

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‘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

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.

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.

Photo: UEM

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.

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

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