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Sororal science and a mentor on a mission – why cassava and capacity building are closely coupled

 Africa, Capacity building, Cassava, Crop breeding, Researchers, Women in science  No Responses »
Mar 052014
 
Two peas in a pod, hand in hand, 

Elizabeth Parkes

“In the past, the assumption was always that ‘Africa can’t do this.’ Now, people see that when given a chance to get round circumstances – as GCP has done for us through the provision of resources, motivation, encouragement and training – Africa can achieve so much!…GCP has made us visible and attractive to others; we are now setting the pace and doing science in a more refined and effective manner…Building human capacity is my greatest joy….I’ve pushed to make people recognise that women can do advanced agricultural science, and do it well. To see a talented woman researcher firmly established in her career and with her kids around her is thrilling….Rural families are held together by women, so if you are able to change their lot, you can make a real mark…” –  Elizabeth Parkes, cassava researcher, Ghana

Elizabeth’s PhD is on cassava genetic diversity, combining ability, stability and farmer preference in Ghana. But for Elizabeth, it is not the academic laurels and limelight but rather, a broader vision of social justice which really drives her: “I see African communities where poverty and hunger are seemingly huge problems with no way out; I’m fortunate to be working on a crop whereby, if I put in enough effort, I can bring some solutions. My primary target group in my research is the less privileged, and women in particular have been my friends throughout. Rural families are held together by women, so if you are able to change their lot, you can make a real mark.”

 

…agricultural research was a man’s job!”

A perennial passion for cassava, and walking with giants: Elizabeth with the pick of the crop for the 2014 cassava harvest season at IITA, Ibadan, Nigeria.

A perennial passion for cassava, and walking with giants: Elizabeth with the pick of the crop for the 2014 cassava harvest season at IITA, Ibadan, Nigeria.

Prowess and prejudice: Breaking the mould and pioneering into pastures new
On first tentatively dipping her toe into the professional waters of crop science when growing up in her native Ghana, initial reactions from her nearest and dearest suggested that carving out a name for herself in her career of choice was never going to be a walk in the park: “As an only girl among eight  boys of whom three were half-siblings, and the youngest child, my father was not very amused; he thought agricultural research was a man’s job!” she recalls. Undeterred and ever more determined to turn this commonly held canard on its head, Elizabeth went on to bag a Bachelor’s degree in Agriculture, a diploma in Education, and an MPhil degree in Crop Science. During a stint of national service between academic degrees, she approached a scientist engaged in root and tuber projects at Ghana’s Council for Scientific and Industrial Research (CSIR) Crops Research Institute (CRI), offering to carry out some research on cassava, and soon establishing the institute’s first trials in Techiman, in the Brong Ahafo Region,where she was doing her national service. Recognising all the hallmarks of a great scientist, nurturer and leader, her CRI colleagues were quick to welcome this fresh talent into the fold as an Assistant Research Officer, with the full treasure trove of root tuber crops – from cassava to sweet potato to yam and cocoyam, among others – all falling under her remit. Not a bad start for the first woman to be assigned to the project!

Quickly proving herself as a fiercely cerebral researcher with a natural knack for the plant sciences, Elizabeth was encouraged by seasoned (then) GCP scientist, Martin Fregene (their paths had crossed during Elizabeth’s master’s degree thanks to research collaboration with the International Institute of Tropical Agriculture – IITA), to embark on a PhD degree with a focus on cassava. Coinciding with an era when links between Martin’s then home institute, the International Center for Tropical Agriculture (CIAT) and GCP were beginning to really take off the ground, it was a move that proved timely, and a path which Elizabeth pursued with her characteristic vigour and aplomb, climbing the GCP research ranks from multiple travel-grant recipient to a research fellow, and, more recently, to Lead Researcher for GCP’s cassava work in Ghana. Now a well established cassava connoisseur who regularly rubs shoulders with the crème de la crème of the global crop science community, Elizabeth specialises in drought tolerance and disease resistance in the GCP-related aspects of her work, whilst also turning her hand to biofortification research for GCP sister CGIAR Challenge Programme, HarvestPlus.

… it [biotechnology] was a breakthrough which Elizabeth spearheaded…”

Up, up and away! How a helping hand has led Elizabeth & Co to new professional and research heights
Life aboard the GCP ship, Elizabeth reveals, has offered a wealth of professional opportunities, both on personal and institutional levels. GCP-funded infrastructure, such as weather stations and irrigation systems, has helped to boost yields and enhance the efficiency of CRI trials, she observes. Professional development for herself and her team, she says, has been multifold: “Through our GCP work, we were able to build a lab and kick-start marker-assisted breeding – that ignited the beginning of biotechnology activities in CRI,” Elizabeth asserts.  It was a breakthrough which Elizabeth spearheaded, and which, happily, has since become run-of-the mill practice for the institute: “Now CRI scientists are regularly using molecular tools to do their work and are making cassava crosses on their own.” The positive domino effect of this change in tide cannot be underestimated: “Our once small biotechnology laboratory has evolved into a Centre of Excellence under the West Africa Agricultural Productivity Programme. Its first-class facilities, training courses and guiding hand in finding solutions have attracted countless visiting scientists, both from Ghana and internationally – this means that the subregion is also benefitting enormously.” The GCP’s Genotyping Support Service (GSS), Elizabeth affirms, has also proved an invaluable sidekick to these developments: “Through the GSS, our team learnt how to extract DNA as a first step, and later to re-enact all the activities that were initially done for us externally – data sequencing, interpretation and analysis for example – on a smaller scale in our own lab.” The collection and crunching of data has also become a breeze: “Thanks to GCP’s support, we have become a pace-setter for electronic data gathering using tablets, field notebooks and hand-held devices,” she adds.

….GCP gives you the keys to solving your own problems, and puts structures in place so that knowledge learnt abroad can be transferred and applied at home – it’s been an amazing journey!”

Ruth Prempeh, one of Elizabeth's charges, collecting data for her GCP-funded PhD on cassava post-harvest physiological deterioration. Ruth is one of those whose work–family balance Elizabeth celebrates. Ruth has since submitted her thesis awaiting results. As you'll hear in the accompanying podcast, both of Ruth's young children have each, er, sort of 'attended' two big GCP events!

Ruth Prempeh, one of Elizabeth’s charges, collecting data for her GCP-funded PhD on cassava post-harvest physiological deterioration. Ruth is one of those whose work–family balance Elizabeth celebrates. Ruth has since submitted her thesis awaiting results. As you’ll hear in the podcast below, both of Ruth’s young children have each, er, sort of ‘attended’ two big GCP events!

People power: capacity building and work–life balance
Elizabeth lights up most when waxing lyrical about the leaps and bounds made by her many students and charges through the years, who – in reaping some of the benefits offered by GCP, such as access to improved genetic materials; forging links with like-minded colleagues near and far, and, critically, capacity building – have gone on to become established and often internationally recognised breeders or researchers, with the impacts of their work posting visible scores in the fight against global food insecurity. On the primordial role of capacity building, she says: “GCP gives you the keys to solving your own problems, and puts structures in place so that knowledge learnt abroad can be transferred and applied at home – it’s been an amazing journey!” Of her female students who’ve surmounted the work–family pendulum challenge, she says: “I’ve pushed to make people recognise that women can do advanced agricultural science, and do it well. To see a talented woman researcher firmly established in her career and with her kids around her is thrilling.”

At IITA, Elizabeth continues to be an inspiration on work–life balance for women working on their PhDs, and more so for young women whose work is on cassava. In a male-dominated environment (global statistics report that women researchers are a meagre 30 percent), this inspiration is critical. .

No ‘I’ in team: tight-knit community a must for kick-starting real and sustainable solutions
As Elizabeth well knows, one swallow does not a summer make: as demonstrated by the GCP’s Communities of Practice (CoPs), she says, strength really does come in numbers: “The GCP Cassava CoP has brought unity amongst cassava breeders worldwide; it’s about really understanding and tackling cassava challenges together, and bringing solutions home.” Bolstering this unified spirit, Elizabeth continues, is the GCP’s Integrated Breeding Platform (IBP): “With the initial teething problems mainly behind us, IBP is now creating a global community and is an excellent way of managing limited resources, reducing duplication of efforts and allowing people to be more focused.” On helping scientists inundated with information to spot the wood from the trees, she says: “Over the years, lots of data have been generated, but you couldn’t find them! Now, thanks to IBP, you have sequencing information that you can tap into and utilise as and where you need to. It’s very laudable achievement!”

In the past, the assumption was always that ‘Africa can’t do this.’…GCP has made us visible and attractive to others; we are now setting the pace and doing science in a more refined and effective manner.” 

Clearly, keeping the company of giants is not new for Elizabeth (right). This giant cassava tuber is from a 2010 CRI trial crossing improved CIAT material with CRI landraces (traditional farmer varieties. The trial was part of Bright Boakye Peprah’s postgraduate work. Bright has since completed his GCP-funded masters on cassava breeding, and now a full time cassava breeder with CSIR–CRI. He is currently on study leave pursuing a PhD on cassava biofortification in South Africa. On the left is Joseph Adjebeng-Danquah, a GCP-funded PhD student whose work centres on cassava drought tolerance. Our best quote from Joseph: “It is important to move away from the all too common notion that cassava is an ‘anywhere, anyhow’ crop.”

Clearly, keeping the company of giants is not new for Elizabeth (right). This giant cassava tuber is from a 2010 CRI trial crossing improved CIAT material with CRI landraces (traditional farmer varieties. The trial was part of Bright Boakye Peprah’s postgraduate work. Bright has since completed his GCP-funded master’s  degree on cassava breeding, and now a full time cassava breeder with CSIR–CRI. He is currently on study leave pursuing a PhD on cassava biofortification in South Africa. On the left is Joseph Adjebeng-Danquah, a GCP-funded PhD student whose work centres on cassava drought tolerance. Our best quote from Joseph: “It is important to move away from the all too common notion that cassava is an ‘anywhere, anyhow’ crop.”

Empowered and engaged: African cassava researchers reclaim the driving seat
The bedrock of GCP’s approach, Elizabeth suggests, is the facilitation of that magical much sought-after Holy Grail: self-empowerment. “When I first joined GCP,” she recalls, “I saw myself as somebody from a country programme being given a place at the table; my inputs were recognised and what I said would carry weight in decision-making.” It’s a switch she has seen gain traction at national and indeed regional levels: “In the past, the assumption was always that ‘Africa can’t do this.’ Now, people see that when given a chance to get round circumstances – as GCP has done for us through the provision of resources, motivation, encouragement and training – Africa can achieve so much!” Reflecting on the knock-on effect for African cassava researchers particularly, she concludes: “GCP has made us visible and attractive to others; we are now setting the pace and doing science in a more refined and effective manner.”

Paying it forward and sharing: Helping women, and thereby, communities
Armed with bundles of knowledge as she is, Elizabeth is a firm believer in paying it forward and sharing: “Building human capacity is my greatest joy,” she affirms, citing farmers, breeders, and a Ghanaian private-sector company as just a few of the fortunate beneficiaries of her expertise over recent years. And on sources of motivation, it is not the academic laurels or limelight but rather a broader vision of social justice which really drives her: “I see African communities where poverty and hunger are seemingly huge problems with no way out; I’m fortunate to be working on a crop whereby, if I put in enough effort, I can bring some solutions.” They are solutions which she hopes will be of lasting service to those closest to her heart: “My primary target group in my research is the less privileged, and women in particular have been my friends throughout. Rural families are held together by women, so if you are able to change their lot, you can make a real mark.”

We’re in a blessed and privileged era where cassava, an ancient and once orphan crop, is now receiving lots of attention… I encourage young scientists to come on board!”

Inspired, and inspiring: nurturing budding cassava converts, and seizing opportunities for impact
In terms of future horizons, Elizabeth – who after more than two decades of service at CRI is currently on leave of absence at IITA where she’s working on biofortification of cassava – hopes to thereby further advance her work on cassava biofortification, and perhaps later move into a management role, focusing on decision-making and leading agricultural research leaders with monitoring and evaluation specifically to “ensure that the right people are being equipped with skills and knowledge, and that those people are in turn teaching others.” She is also confident that any young, gifted researcher with an eye on the prize would be foolhardy to overlook what Elizabeth views as a golden opportunity for creating meaningful and lasting impacts: “We’re in a blessed and privileged era where cassava, an ancient and once orphan crop, is now receiving lots of attention. Every agricultural research lead we have in Africa is there to be seized – I encourage young scientists to come on board!” A clear and convincing clarion call to budding breeders or potential cassava converts if ever there was one…. who wants in, in this love-match where cassava and capacity building are truly two peas in a pod?

Like meets like in a fair match: Our cassava champion in a male-dominated environment, Elizabeth, meets her match in Farmer Beatrice who refused to take no for an answer, and beat Elizabeth hands down. Listen to this! 

 

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Cassava on the catwalk: Ghanaian ‘make-over’ for crop-science underdog

 Africa, Cassava, Crop breeding, Women in science  No Responses »
Mar 042014
 
‘Made (up) in Ghana’

In the world of crop research as in the fashion industry, there are super-models, mere models, spectators and rank outsiders. Make no bones about it, trusty old cassava (Manihot esculenta) is a crop of very modest beginnings, but now finally strutting the research catwalk alongside the biggest and the best.

Elizabeth Parkes

Elizabeth Parkes

An ancient crop thought to have been first domesticated in Latin America more than 10,000 years ago, it was exported by Portuguese slave traders from Brazil to Africa in the 16th century as a cheap source of carbohydrates. From there, today we travel half a millennium forward in time – and in space, on to Ghana – to catch up with the latest on cassava in the 21st century.

Come on a guided tour with Elizabeth Parkes (pictured), of Ghana’s Crops Research Institute (CRI, of the Council for Scientific and Industrial Research, CSIR), currently on leave of absence at the International Institute of Tropical Agriculture (IITA).

A hard-knock life, but still going strong
In keeping with its humble heritage, cassava is a crop which has long been reputed for being more than a little worn through at the elbows, commonly known as a “poor man’s crop” according to GCP cassava breeder and researcher, Elizabeth Parkes. However, much like a dishevelled duffle coat, what the crop lacks in shimmer and shine, it makes up for in sturdiness and dependability, rising to the occasion time and again by filling a critical gap – that of putting food in bellies – with a readiness and ease that its more sophisticated crop relatives have often struggled to keep up with. Elizabeth explains:  “It has kept people alive over the years.” By the same token, the crop – now one of Africa’s most important staples – is fondly known in Ghana as bankye, meaning a ‘gift from the government’, thanks to its reliability and capacity to meet needs that other crops cannot. There is even a popular song in the country which pays homage to the crop as an indefatigable evergreen, conquering even the most willful and wily of weeds!

However, as cassava experts such as Elizabeth know only too well, behind this well-intentioned lyrical window dressing is the poignant story of a crop badly in need of a pressing pick-me-up. Hardy as it may seem on the surface, cassava is riddled with myriad problems of a political, physiological, environmental and socioeconomic nature, further compounded by the interactions between these. For starters, while it may be a timeless classic and a must-have item at the family table for a good part of Africa, à la mode it is not, or at least not for short-sighted policy-makers looking first and foremost to tighten their purse strings in straitened times, or for quick-fix, rapid-impact,  silver-bullet solutions: “African governments don’t invest many resources in research. Money is so meager, and funds have mostly come from external agencies looking to develop major cereals such as rice. Cassava has been ignored and has suffered a handicap as a result – it’s more or less an orphan crop now,” Elizabeth laments. Besides having to bear witness to their favourite outfit being left on the funding shelf, cassava breeders such as Elizabeth are also faced with a hotchpotch of hurdles in the field: “In addition to factors such as pests and disease, cassava is a long-season and very labour-intensive crop. It can take a whole year before you can expect to reap any rewards, and if you don’t have a strong team who can step in at different points throughout the breeding  process, you can often find unexpected results at the end of it, and then you have to start all over again,” Elizabeth reveals. Robust as it may be, then, cassava is no easy customer in the field: “After making crosses, you don’t have many seeds to move you to the next level, simply because with cassava, you just don’t get the numbers: some are not compatible, some are not flowering; it’s a real bottleneck that needs to be overcome,” she affirms.

No time for skirting the issue
And at the ready to flex their research muscles and rise to these considerable challenges was Elizabeth and her Ghanaian CRI  team, who – with GCP support and in unison with colleagues from across Africa and the wider GCP cassava community – have been working flat out to put cassava firmly back on the research runway.

Thanks to funders such as GCP, who recognised that we couldn’t afford to turn a blind eye to the plight of this struggling crop, cassava has been given a voice…cassava is no longer just a poor man’s staple” 

A cassava farmer in Northern Ghana.

A  cassava farmer in Northern Ghana.

Elizabeth walks us through the team’s game plan: “GCP socioeconomist Glenn Hyman and team undertook a study to identify the best area in Ghana for supporting cassava flowering [Editor’s note: Glenn works at the International Center for Tropical Agriculture, CIAT]. Armed with that information, we have been applying grafting techniques, using hormones to induce flowering in Ghana and beyond.” The initiative is starting to bear fruit: “At the IITA–Nigeria Ubiaja site, for example, flowering is underway at factory-like efficiency – it’s a great asset. The soil has also greatly improved – we haven’t been able to pinpoint the exact cause yet, but what we’ve seen is that all cultivars there will now flower,” she reveals. Elizabeth’s team has been making steady progress in biotechnological techniques such as DNA extraction: thanks to work led by then GCP cassava comrade Martin Fregene (then with the International Center for Tropical Agriculture, CIAT, and now with the Donald Danforth Plant Science Center) and colleagues, focusing on the development of more reliable and robust simple sequence repeat (SSR) markers, Elizabeth was able to carry out genetic diversity diagnosis work on cassava, collecting germplasm from all over Ghana for the global GCP cassava reference set. [Editor’s note: 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]

Similar work was also conducted in Nigeria and Guatemala. So has this tremendous and tenacious teamwork proved strong enough to drag cassava out of the doldrums? Elizabeth certainly seems to think so: “Thanks to funders such as GCP, who recognised that we couldn’t afford to turn a blind eye to the plight of this struggling crop, cassava has been given a voice. Having worked together to understand the peculiarities of this crop, cassava is no longer just a poor man’s staple: beyond subsistence, it is becoming a crop of high starch quality, and of real use for industry, confectionary and even biofuels,” she enthuses.

Thankfully, it’s a most welcome change of tide that shows no sign of abating any time soon.  Human capacity, Elizabeth says, is going from strength to strength, with three GCP-funded Ghanaian postgraduate students advancing well, two of them working on PhDs in what would normally be considered, according to Elizabeth, a ‘no-go area’ of cassava research – that is, cassava drought tolerance and post-harvest physiological deterioration (PPD), as well as bio-fortification. Efforts by the CRI team have resulted in the release of some 14–15 new drought-tolerant and PPD-resistant varieties in Ghana to date; all are anticipated to have a long shelf-life, and other varieties are also in the pipeline. Biofortified seeds are in the making, with a view to soon mainstream biofortification in the team’s breeding activities. The biofortification work is in collaboration with a sister CGIAR Challenge Programme, HarvestPlus.

The impact of our GCP-supported research on cassava has been remarkable. Above all, it’s been the community spirit which has moved things forward so effectively; in this respect, I think researchers working on other crops might want to borrow a leaf from the cassava book!”

Molecular masterstrokes, a leaf to lend despite cold shoulder, and a ‘challenge crop’ befitting Challenge Programmes
Forthcoming plans for Elizabeth and her cassava companions in Ghana include a GCP Cassava Challenge Initiative project which will seek to unearth new marker populations and materials which are drought-tolerant and resistant to cassava mosaic virus and cassava bacterial blight. The team has successfully introgressed materials from CIAT into their landraces, and the next step will be to gauge how best the new genes will react to these traits of interest. In terms of people power, the CRI biotechnology laboratory built with GCP support – and now a regionally accredited ‘Centre of Excellence’ – is a hive of activity for local and international scientists alike, and is consequently bolstering cassava research efforts in the wider subregion. “The impact of our GCP-supported research on cassava has been remarkable. Above all, it’s been the community spirit which has moved things forward so effectively; in this respect, I think researchers working on other crops might want to borrow a leaf from the cassava book!” Elizabeth ventures.

Reflecting back on the conspicuous cocktail of constraints which mired the crop in the early days of her research career – challenges which often resulted in a cold shoulder from many of her research peers over the years – Elizabeth recalls affectionately: “At first, people didn’t want to work on cassava since it’s truly a challenge crop: the genetics of cassava are really tricky. Colleagues from around the globe often asked me: ‘Why not go for a smooth crop which is friendly and easy?’” Her commitment, however, has been unfaltering throughout: “I’ve stuck with cassava because that’s my destiny! And now I see SNPs being developed, as well as numerous other resources. Once you clean something up it becomes more attractive, and my thanks go out to all those who’ve remained dedicated and helped us to achieve this.”

Thus, dusted down and  ‘marked-up’ with a molecular make-over well underway, all evidence now suggests that this once old-hat subsistence crop is en route to becoming the next season’s big research hit, with shiny new cassava varieties soon to be released at a field station near you! Go, Ghana, go!

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Wherefore art thou Integrated Breeding Platform?

 Crop breeding, Crop information and data management, Integrated Breeding Platform  Comments Off on Wherefore art thou Integrated Breeding Platform?
Feb 262014
 
Something old, something new; Plenty borrowed, and just a bit of  blue…

Why did the Integrated Breeding Platform (IBP) come to be, and what’s the latest offer from the five-year-old Platform? The answers are in this tell-all post on the bright and the bleak in IBP – beauty spots, blues, warts and all! Having heard on data management, breeding, and putting IBP tools, tips and services into use, let’s now take a couple of steps back and appraise the big picture: the IBP concept itself, candidly retold by an IBP old hand, in a captivating chronicle capturing the highs and lows, the drama and the humdrum, and befittingly capping our current season of IBP stories. Do read on…

We want to put informatics tools in the hands of breeders, be they in the public or private sector including small- and medium-scale enterprises, because we know they can make a huge difference”

Graham McLaren

Graham McLaren

Curtain up on BMS version 2, and back to basics on why IBP
January 2014 was a momentous month for our Integrated Breeding Platform, marking the release of version 2 of the Breeding Management System (BMS). After the flurry and fanfare of this special event, we caught up with Graham McLaren (pictured), GCP’s Bioinformatics and Crop Information Leader, Chair of the IBP Workbench Implementation Team and a member of the IBP Development Team. Graham has been intimately involved in taking IBP from an idea in 2008‒2009 to its initial launch in late 2009.

But what’s the background to all this, and why the need for IBP? Graham fills us in, explaining that in the 1980s and 1990s, informatics was the major contributor to successful plant breeding in large companies like Pioneer and Monsanto. After that, molecular technologies became the main contributors. “But to advance with molecular technologies, you need to have the informatics systems in place,” he says. “One of the biggest constraints to the successful deployment of molecular technologies in public plant breeding, especially in the developing world, is a lack of access to informatics tools to track samples, manage breeding logistics and data, and analyse and support breeding decisions.”

This is why IBP was set up. “We want to put informatics tools in the hands of breeders, be they in the public or private sector including small- and medium-scale enterprises, because we know they can make a huge difference.”

…breeders will not only find… information, but also the tools, services and support to put this information into use, in the context of their local crop-breeding projects…  [the information breeders] have accumulated over the years is mostly held in their heads, in institutional repositories, or in books and published papers. There are few common places for them to share these riches and tap into those of others… IBP  provides one such place.”

Breeding rice with optimised phosphorus uptake in The Philippines. See post: http://bit.ly/NgIH9C

The script: common sense, and working wonders
Plant breeders throughout the developing world have a wealth of information on adapting crops to the challenges of their particular environments. They work wonders in their experimental fields to develop crops that help local farmers deal with pests, diseases and less-than-ideal conditions such as drought, floods and poor soils. But this valuable information they have accumulated over the years is mostly held in their heads, in institutional repositories, or in books and published papers. There are few common places for them to share these riches and tap into those of others. The Integrated Breeding Platform (IBP) provides one such place, where breeders will not only find this information, but also the tools, services and support to put this information into use, in the context of their local crop-breeding projects.

Action! Setting the stage for a forward spring, and taking a leap of faith
IBP tackles the information management issues that are at the heart of many breeding processes, goals, pursuits and problems. “Informatics problems are not crop-specific” Graham says. “What GCP is doing is to put in place a generic system for plant breeders to manage and share information. This means they can collaborate and make better decisions about strains of the crops they are breeding and that they use in their programmes. It’s setting the stage for a big leap forward in plant breeding in developing countries.”

The proposal for a crop information system applicable to a wide range of crops attracted the attention of the Bill & Melinda Gates Foundation, which provided core funding for IBP.

According to Graham, the initial five-year USD 12 million grant from the Foundation was “the biggest single investment in an informatics project in CGIAR. It was half of what was needed, and other funders joined in with the other half.” These are the European Commission and the UK’s Department for International Development.

It’s been harder than we imagined… we really needed to employ the strategies used to build aeroplanes! … some of our partners are good at solving research problems but not at developing informatics tools… Our partnership with the software company was pretty unusual…Usually, you draw up the specifications for what you want and the company comes back with the product, like giving a builder an architect’s plans and getting the keys when the building is completed. But it wasn’t like that at all…”

Collaborative construction and conundrum – going off the script, winging it and winning it
Graham describes the hurdles that the team had to overcome along the way. “It’s been harder than we imagined because of the number of partners to coordinate. It’s like building a complicated machine with many parts. The parts built by different people in different places all need to fit when they are put together. It’s so complex, we really needed to employ the strategies used to build aeroplanes!”

It’s been a matter of encouraging all those involved to do what they do best. “I’ve learnt that some of our partners are good at solving research problems but not at developing informatics tools. We were fortunate to find a private company partner to do the software engineering and to have the backing of the Gates Foundation to change our strategy along the way.”

Working with a private-sector company was a first on both sides. “Our partnership with the software company was pretty unusual,” Graham recalls. “Usually, you draw up the specifications for what you want and the company comes back with the product, like giving a builder an architect’s plans and getting the keys when the building is completed. But it wasn’t like that at all. We didn’t know exactly what we wanted in terms of the final system, learning and adapting as we went along. Fortunately, the company was flexible and worked with us step by step. We would describe to them what we wanted, they would go off and work something up, then they would come back and we would dissect it and then they would go away again and rework. This way, they produced the system we wanted. Involving a private company brought us very handsome returns for money: it meant the project could deliver on time, and on budget.”

Breeders in developing countries and small- and medium-sized companies are looking at it… a revenue stream could be secured in a win–win relationship with companies also working to develop agriculture in the developing world”

Act II: going global, and continuous improvement
Now that the alpha version of BMS has been launched, the Bill & Melinda Gates Foundation is encouraging GCP to deploy the Platform more broadly. Graham explains, “Breeders in developing countries and small- and medium-sized companies are looking at it and, of course, they are coming up with ideas of their own. We’ve taken these on board in developing BMS version 2. In anticipation of yet more user feedback on version 2, we anticipate the third version will be released in June 2014.”

Electronic data collection for cassava breeding at Nigeria's National Root Crops Research Institute. GCP is promoting the use of digital tablets for data collection. See story: http://bit.ly/1fpeJON

Electronic data collection at Nigeria’s National Root Crops Research Institute. GCP is promoting the use of digital tablets for data collection. See story: http://bit.ly/1fpeJON

He continues: “Deployment will involve training people to use IBP, maintaining the system and developing new tools. We’re talking to the Gates Foundation, and others, about funding for IBP Phase II. While our primary objective is to make the Platform affordable – even free – for public-sector plant breeders in developing countries, we recognise that the system needs to be maintained, supported and upgraded over the years. The question is, will small- and medium-sized plant-breeding enterprises be willing to pay for the system so that some of this maintenance and support can be recovered and the system can become sustainable in the long run? In our GoToMarket Plan, the Marketing Director is canvassing a range of companies asking what services they need and how much they would pay for them. There is a strong need for such a system in this sector and it is clear that a revenue stream could be secured in a win–win relationship with companies also working to develop agriculture in the developing world.”

Graham is convinced that rolling out IBP will have a significant impact on plant breeding in developing countries. “Because IBP has a very wide application, it will speed up crop improvement in many parts of the world and in many different environments. What this means is that new crop varieties will be developed in a more rapid and therefore more efficient manner.”

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The Integrated Breeding FieldBook – An African agronomist’s perspective

 Africa, Capacity building, Cassava, Crop information and data management, Integrated Breeding Platform  No Responses »
Feb 242014
 
For this ‘IBP story-telling season’, our next stop is  very fittingly Africa, and her most populous nation, Nigeria. Travel with us!

Having already heard the Integrated Breeding Platform (IBP) story on data from Arllet (spiced with a brief detour through Asia’s sun-splashed rice paddies), and on IBP’s Breeding Management System from Mark (where we perched on a corner on his Toulouse workbench of tools and data), we next set out to get an external narrative on IBP, and specifically, one from an IBP user. Well, we got more than we had bargained for from our African safari…

Yemi Olojede

Yemi Olojede

Yemi Olojede (pictured) is much more than a standard IBP user. An agronomist by training with a couple of decades-plus experience, he not only works closely with breeders and other crop scientitsts, but is also a research coordinator and data manager. As you can imagine, this made for a rich and insightful conversation, ferrying us far beyond the frontiers of Yemi’s base in Nigeria, to the rest of West Africa,  further out to Africa , and as far afield as Mexico, in his travels and travails with partners. We now bring to you some of this captivating conversation…

Yemi  has been working for the last 23 years (since 1991) at Nigeria’s National Root Crops Research Institute (NRCRI) at Umudike in various capacities. After heading NRCRI’s Minor Root Crops Programme for 13 years, he was last year appointed Coordinator-in-Charge of the Cassava Research Programme.

But his involvement in agriculture goes much further back than NRCRI: Yemi says he “was born into farming”. His father, to whom he credits his love for agriculture, was a cocoa farmer. “I enjoy seeing things grow. When I see a field of crops …what a view!” Yemi declares.

Yemi is also the Crop Database Manager for NRCRI’s GCP-funded projects. He spent time at GCP headquarters in Mexico in February 2012 to sharpen his skills and provide user insights to the IBP team on the cassava database, on the then nascent Integrated Breeding Fieldbook, and on the tablet that GCP was considering for electronic field data collection and management.

To meet the farmers’ growing need for improved higher-yielding and stress-tolerant varieties, plant breeders are starting to incorporate molecular-breeding techniques to speed up conventional breeding.

Flashback to 2010: GCP was then piloting and testing small handheld devices for data collection. Field staff going through a training session for these under Yemi's watchful eye (right).

Flashback to 2010: GCP was then piloting and testing small handheld devices for data collection. Field staff going through a training session for these under Yemi’s watchful eye (right).

But for this to happen effectively, cassava breeders require consistent and precise means to collect and upload research and breeding data, and secure facilities to upload that data into the requisite databases and share it with their peers. Eighty percent of farmers in Africa have less than a hectare of land – that’s roughly two football fields! With so little space, they need high-value crops that consistently provide them with viable yields, particularly during drought. For this reason, an increasing number of Nigerian farmers are adopting cassava. It is not as profitable as, say, wheat, but it has the advantage of being less risky. The Nigerian government is encouraging this change and is implementing a Cassava Transformation Agenda, which will improve cassava markets and value chains locally and create a sustainable export market. All this is designed to encourage farmers to grow more cassava.

Enter GCP’s Integrated Breeding Platform (IBP), which has been working closely with NRCRI and other national breeding programmes to develop the right informatic tools and support services for the job. The International Cassava Information System (ICASS), the Integrated Breeding Fieldbook and the tablet are all part of the solution, backed up by a variety of bioinformatic tools for data management, data analysis and breeding decision support that have been developed to meet the specific needs of the users.

I enjoy working with the team. They pay attention to what we as breeders want and are determined to resolve the issues we raise”

Fastfoward to 2012: Based on feedback, a larger electronic tablet was favoured over the smaller handheld device. Yemi (centre) takes field staff through the paces in tablet use.

Fastfoward to 2012: Based on feedback, a larger electronic tablet was favoured over the smaller handheld device. Yemi (centre) takes field staff through the paces in tablet use.

The database and IB Fieldbook
“When I received the tablet I was excited! I had heard so much about it but only contributed ideas for its use through Skype and email,” Yemi remembers, echoing a sentiment that is frequently expressed by many partners who have been introduced to the device. “I experimented with the Integrated Breeding Fieldbook software focusing on pedigree management, trait ontology management, template design ‒ testing how easy it was to input data into the program and database.”  Yemi noted a few problems with layout and data uploading and suggested a number of additional features. The IBP Team found these insights particularly useful and worked hard to implement them in time for the 2nd Scientific Conference of the Global Cassava Partnership for the 21st Century (GCP21 II), held in Kampala, Uganda, in June, 2012.

“I enjoy working with the team. They pay attention to what we as breeders want and are determined to resolve the issues we raise,” says Yemi. He believes the IB FieldBook and the tablet, on which it runs, will greatly benefit breeders all over the world, but particularly in Africa. “At the moment, our breeders and researchers have to write down their observations in a paper field book, take that book back to their computer, and enter the data into an Excel spreadsheet,” he notes. “We have to double-handle the data and this increases the possibility of mistakes, especially when we are transferring it to our computers. The IB Fieldbook will streamline this process, minimising the risk of making mistakes, as we enter our observations straight into the tablet, using specified terms and parameters, which will upload all the data to the shared central database when it’s connected to the internet.”

The whole room was wide-eyed and excited when they first saw the tablets”

Bringing the tablet to Africa
After his trip to Mexico, Yemi was concerned that some African breeders would be put off using the IB Fieldbook and accompanying electronic tablet because both require some experience with computers. “I found the tablet and the FieldBook quite easy to use because I’m relatively comfortable with computers,” says Yemi. “The program is very similar to MS-Excel, which many breeders are comfortable with, but I still thought it would be difficult to introduce it given that computer literacy across the continent is very uneven.”

Slim, portable and nearly invisible. A junior scientist at NRCRI Umudike tries out the tablet during the 2012 training session.

Slim, elegant, portable and nearly invisible is this versatile tool. A junior scientist at NRCRI Umudike tries out the tablet during the 2012 training session.

At the GCP21 II meeting in Uganda, Yemi helped the IBP team run IB Fieldbook workshops for plant breeders from developing countries, with an emphasis on data quality and sharing. “The whole room was wide-eyed and excited when they first saw the tablets. They initially had trouble using them and I thought it was going to be a very difficult workshop, but by the end they all felt confident enough to use them by themselves and were sad to have to give them back!”

They … go back to their research institutes and train their colleagues, who are more likely to listen and learn from them than from someone else.”

Providing extra support, cultivating trust
Yemi recounts that attendees were particularly pleased when they received a step-by-step ‘how-to’ manual to help them train other breeders in their institutes, with additional support to be provided by the IBP or Yemi’s team in Nigeria. “They were worried about post-training support,” says Yemi. “We told them if they had any challenges, they could call us and we would help them. I feel this extra support is a good thing for the future of this project, as it will build confidence in the people we teach. They can then go back to their research institutes and train their colleagues, who are more likely to listen and learn from them than from someone else.”

In developing nations, it is important that we share data, because we don’t all have the capacity to carry out molecular breeding at this time, and data sharing would facilitate the dissemination of the benefits to a wider group”

Sharing data to utilise molecular breeding
Yemi asserts that incorporating elements of molecular breeding has helped NRCRI a great deal. With conventional breeding, it would take six to 10 years to develop a variety before release, but with integrated breeding (conventional breeding that incorporates molecular breeding elements) it is possible to develop and release new varieties in three to four years ‒ half the time. Farmers would hence be getting new varieties of cassava that will yield 20‒30 percent more than the lines they are currently using in a much shorter time.

“In developing nations, it is important that we share data, because we don’t all have the capacity to carry out molecular breeding at this time, and data sharing would facilitate the dissemination of the benefits to a wider group,” says Yemi. “I enjoy helping people with this technology because I know how much it will make their job easier.”

Links

Food for thought on video: a ‘rice-bowl of research’ spiced with flavours from Africa and Asia

 Africa, Asia, Capacity building, Crop breeding, Rice, Women in science  2 Responses »
Feb 212014
 

 

Steaming rice bowl

Steaming rice bowl

What’s the latest from ‘GCP TV’? Plenty! With a world-favourite – rice – featuring high and hot on the menu.

Now serving our latest news, to tease your taste-buds with a tantalising and tingling potpourri of memorable cross-continental rice flavours, all captured on camera for our viewers…

Our brand-new series on YouTube serves up a healthy seven-course video feast inviting our viewers to sink their teeth into rice research at GCP.

First, we settle down for a tête-a-tête in the rice research kitchen with chef extraordinaire, Marie-Noëlle Ndjiondjop, Principal Investigator (PI) of GCP’s Rice Research Initiative in Africa, and Senior Molecular Scientist at Africa Rice Center. Target countries are Burkina Faso, Mali and Nigeria.

Photo: A Okono/GCP

Marie-Noëlle Ndjiondjop

Starters, palate and pocket
Marie-Noëlle opens the feast with a short but succulent starter, as she explains succinctly in 30 seconds just how rice is becoming a staple in Africa. In the second course, Marie-Noëlle chews over the questions concerning combatting constraints and boosting capacity in rice research in Africa.

The third course is pleasing to the eye, the palate and the pocket! Marie-Noëlle truly sells us the benefits of molecular breeding, as she extolls the virtues of the “beauty of the marker”. Why should you use molecular tools? They’ll save you time and money!

Rice as beautiful as the markers Marie-Noëlle uses in molecular breeding

Wherefore art thou, capacity building in rice research in Africa?
The Shakespearean language alludes to the why of capacity building in Africa, as does video episode number four, which also tackles the what of this fourth dish in our banquet. Course number five offers the viewer a light look at how capacity building in Africa is carried out.

In the 6th course, Marie-Noëlle takes us out of this world and into MARS: she teaches us that ‘two are better than three’, as she explains how the novel bi-parental marker-assisted recurrent selection (MARS) method is proving effective when it comes to duelling with drought, the tricky three-headed monster comprising physiological, genetic and environmental components.

Blooming rice in the field

Of stars and scoundrels
The 7th and final course offers us a riveting tale of heroes and villains, that is, many heroes and a single villain! Our rice raconteuse, Marie-Noëlle, praises the power of the team, as a crew from cross-continental countries come together, carefully characterise their combatant (drought), before striking with environment-specific drought-tolerant varieties! AfricaRice’s project partners are Burkina Faso’s Institut de l’environnement et de recherches agricoles (INERA); Mali’s Institut d’économie rurale (IER); and Nigeria’s National Cereals Research Institute (NCRI). Collaborators are France’s Centre de coopération internationale en recherche agronomique (CIRAD); the International Center for Tropical Agriculture (CIAT); and the International Rice Research Institute (IRRI).

We hope these tasty teasers are enough to whet your appetite – you can savour each of the courses individually à la carte, or, for those with a daring desire to try the ‘all you can eat’ buffet for true rice gourmets, all seven courses are presented as a single serving on our YouTube channel.

Jonaliza Lanceras-Siangliw

Jonaliza Lanceras-Siangliw

Tastes from Asia
To further please your palate with our rice bowl of delights, our next stop is Asia. We are  pleased to offer you the Asian flavour through a peek into the world of molecular rice breeding in the Mekong region. Our connection to this project is through a GCP-funded capacity-building project entitled A Community of Practice for strengthening rice breeding programmes by using genotyping building strategy and improving phenotyping capacity for biotic and abiotic stresses in the Mekong region led by PI Jonaliza Lanceras-Siangliw, of the National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand (see project poster, and slides on a related drought-tolerance project led by Boonrat Jongdee). BIOTEC’s partners in the Mekong rice breeding CoP are the Cambodian Agricultural Research and Development Institute (CARDI); LAO PDR’s National Agricultural and Forestry Research Institute (NAFRI);  Myanmar’s Department of Agricultural Research (DAR); and Thailand’s Kasetsart University and Ubon Ratchathani University). The video also features former GCP PI, Theerayut Toojinda (BIOTEC) whose project was similarly entitled The ‘Community of Practices’ concept applied to rice production in the Mekong region: Quick conversion of popular rice varieties with emphasis on drought, salinity and grain quality improvement.

BIOTEC

Boonrat Jongdee

Shifting gears: golden oldie
If all of this talk of eating has been a little overwhelming, we also offer you the perfect digestif: a ‘golden oldie’ in terms of GCP video history showing a 2012 BBC interview with former GCP PI, Sigrid Heuer, then at the International Rice Research Institute (IRRI), who explains how her project isolated the rice root-enhancing gene PSTOL1. Bon appétit!

 

Might you still have a corner of your mind yearning for more material on rice research? If so, check out the following:

  • Our lip-smacking selection of rice-related blogposts
  • A gorgeous gallery of PowerPoint presentations on rice research (SlideShare)
  • Check out our one-stop Rice InfoCentre for all things rice and nice, that we have online!

 

A new breed of Workbench – Introducing the Breeding Management System

 Crop breeding, Crop information and data management, Integrated Breeding Platform  2 Responses »
Feb 182014
 

Mark Sawkins

Mark Sawkins

Mark the man in the middle, and of the markers…

Today, we talk to Mark Sawkins (pictured), the ‘middleware’ man in our Integrated Breeding Platform (IBP) so to speak, seeing as he is the human ‘interface’ between crop breeders on the one hand, and the developers of our Integrated Breeding Platform (IBP) on the other hand. Mark is the ‘bridge’ that connects IBP users and IBP developers – a special position which gives him a privileged and fascinating perspective on both sides of the coin, with a dash of public–private sector pragmatic partnership thrown in too. Here’s more on Mark, in this dispatch from and on his special perch on the bench…

Bridge to bench, abuzz on BMS: A ‘tinker’ at Toulouse…
Mark Sawkins is always busy tinkering away on his Workbench at his base in Toulouse in southern France. It’s not your traditional wooden workbench, covered in sawdust, soil or splattering of paint. Nor is it one carpeted in documents lit by the warm glow of a computer monitor. In fact, the workbench Mark is working on is virtual, having no physical form and residing solely online, or on a user’s computer, once downloaded.

Known as the Breeding Management System (BMS) the Workbench, comprising software tools linked to a database for access to pedigree, phenotypic and genotypic data, has been developed by GCP’s Integrated Breeding Platform. The BMS has what a crop breeder would require to conduct an analysis of phenotypic and genotypic data generated as part of a crop-breeding or evaluation experiment, covering a broad spectrum of needs from conventional breeding to advanced molecular breeding applications. Version 2 of the Breeding Management System was released just last month.

… it [BMS] will be of most help to breeders both in the public and private sector in Africa and Asia who, up to now, have had little or no access to tools and data to allow them to shift gears in their breeding programme…The BMS has a lot of tools and all the foundational data necessary for a breeder’s routine day-to-day activities…The BMS is also anticipated to have enormous positive impact on food security in developing countries in the years ahead, enabling crop breeders to evaluate their progenies using the most sophisticated statistical methods available”

A hands-on BMS orientation workshop underway for breeders in Africa, held in Ethiopia in July 2013 under the auspices of the GCP-funded cassava breeding community of practice. Standing, Yemi Olojode, of Nigeria’s National Root Crops Research Institute (NRCRI), Umidike, who was one of the trainers.

Previously known as the Integrated Breeding Workflow System (IBWS), the BMS incorporates both statistical analysis tools and decision-support tools. The tools are assembled in a way that data can flow seamlessly from one application to the next in tandem with the various stages of the crop-breeding process. It allows the breeder to accurately collect, securely store and efficiently analyse and synthesise their data on a local private database, and also share, or compare, their data with other breeders via a central public crop database.

“The BMS has a lot of tools and all the foundational data necessary for a breeder’s routine day-to-day activities,” explains Mark, a plant geneticist who joined IBP in 2011. “Any breeder can use it, but it will be of most help to breeders both in the public and private sector in Africa and Asia who, up to now, have had little or no access to tools and data to allow them to shift gears in their breeding programme, particularly in adopting modern breeding practices, including the use of molecular markers.”

The BMS is also anticipated to have enormous positive impact on food security in developing countries in the years ahead, enabling crop breeders to evaluate their progenies using the most sophisticated statistical methods available, and make selections on which lines to advance to the next phase of development in the progression towards more productive and resilient crop varieties.

Phenotyping and field trials are becoming the most expensive part of the breeding process… The biggest hurdle in the public sector in the past was the massive investment required to set up genotyping laboratory facilities… outsourcing, we believe, will help convince breeders to consider integrating molecular techniques into their breeding programmes”

Why integrated breeding?
For almost 30 years, the private sector has been implementing molecular-breeding approaches in developing more productive and resilient crops. These approaches allow breeders to select for plant characteristics (traits) early in the breeding process and then test whether a plant has the targeted trait, which they cannot visually identify.

“Phenotyping and field trials are becoming the most expensive part of the breeding process,” says Mark. “Using molecular markers is a way to reduce the investment in that process. By using markers, early in the development of a given crop line, you can reduce the number of plants you need to grow and test, reducing the time and cost associated with field trials.”

Mark hopes that the Workbench will in time enable breeders, in under-resourced public breeding institutes to access some of the leading molecular-marker databases, and make use of the markers therein for the desired traits they are breeding for, along with technical support from molecular breeders to guide them in making their breeding decisions.

“The biggest hurdle in the public sector in the past was the massive investment required to set up genotyping laboratory facilities,” explains Mark “but now there are plenty of professional service providers that people can send their samples to and get back good results at a very reasonable cost. This time- and cost-saving reality of outsourcing, we believe, will help convince breeders to consider integrating molecular techniques into their breeding programmes.”

We are currently conducting a three-year course to train scientists from national programmes in West and Central Africa, East and Southern Africa and South and Southeast Asia, who we hope will promote and support the adoption of modern breeding in their institutes and countries.”

An IB-MYC training course in session in April 2013 for the West and Central Africa group. Clarissa Pimentel, IBP's Data Manager/Training Specialist, at the front, traching trainees tricks on using Fieldlab in the tablet for data collection.

An Integrated Breeding Multiyear Course (IB-MYC) training course in session in April 2013 for the West and Central Africa group. Clarissa Pimentel, IBP’s Data Manager/Training Specialist, at the front, giving trainees tricks and tips on using FieldLab on the electronic tablet for field data collection.

Running with champions
Mark knows that giving breeders the tools and means to integrate molecular breeding into their programmes is one thing. To actually have them adopt them is another. But he has a plan.

In keeping with the core mission of GCP, which is to build sustainable capacity in developing-country breeding programmes, Mark proposes to recruit and train selected breeders in molecular-breeding techniques and set them up as champions and advocates for their particular crop or region.

Marker implementation methods can be varied but the tools required need to help the breeder make a quick informed decision on what to take forward to the next generation: What plants need to be crossed? Which plants should be kept and which ones discarded? The decision-support tools provided by the IB Workbench will help the breeder make these decisions.

“We are currently conducting a three-year course to train scientists from national programmes in West and Central Africa, East and Southern Africa and South and Southeast Asia, who we hope will promote and support the adoption of modern breeding in their institutes and countries,” Mark enthusiastically explains. The three-year training programme is known as the Integrated Breeding Multiyear Course (IB–MYC). Mark continues, “We believe that people will be more willing to listen to someone who is right there on the ground, whom they know and trust and can easily get in contact with if they need help.”

While the champions concept is still in its infancy, Mark believes it has real merit but must overcome two major barriers – time and confidence. “Identifying the champions won’t be hard,” he observes, “What will be hard is getting them to add this extra task to their already busy agenda. It will require buy-in from management at the institutional level to enable the champions to carry out their mission. It will also be individually hard for each champion, who will only be successful when they have the confidence in their own integrated breeding and extension skills. This confidence would be the thing that would really help sell the message.”

Engaging the private sector
Mark oversees the design, testing and deployment of the system that underpins the BMS, ensuring that both the system and the tools embedded in it are easy to use and meet the needs and expectations of the breeders. However, he and his team have had some trouble getting feedback on the system from the breeders it is intended for, due to their inexperience with such tools and systems. That is why he has called on his private-sector contacts, developed when he was at Syngenta where he worked for five years prior to his current assignment.

“We hope to show them what we’ve been doing in IBP with the Workbench, and hopefully get some private-sector buy-in and see how they can help us – not in developing tools, but with feedback on functionality and usability of the tools we are developing,” he explains. “We don’t have a core set of breeders who are routinely using markers in their breeding programme amongst the partners we are working with on the IBP project. So we are tapping into the private sector which has teams of molecular breeders who are more familiar with the types of breeding workflows and tools we are developing. We’re hoping that we can take advantage of their knowledge and experience to get some really useful feedback, which we will use to improve the usability and effectiveness of our tools.”

To maximise adoption and use, GCP has been actively engaged in extensive capacity building, and this will be reinforced with a comprehensive awareness-creation and communication effort immediately before and after a projected mid-year release of a newer BMS version incorporating the all-essential user feedback. The impact of the analytical pipeline in developing countries will be particularly enhanced with the availability of efficient user support services, which Mark will be overseeing.

Access the Breeding Management System (no-cost registration required)

More information

VIDEO: IBP’s comparative advantage for developed countries, while also relevant for developed countries.

SLIDES: IBP’s Breeding Management System

 

Cultivating a culture of change – Tools and tips for ‘SHARP’ data management, in and for the Information Age

 Crop breeding, Crop information and data management, Integrated Breeding Platform, Researchers, Women in science  No Responses »
Jan 312014
 
Arllet Portugal

Arllet Portugal

Today, we chit-chat with Arllet Portugal (pictured) on crop research data management. Arllet’s greatest daily challenge is convincing crop breeders and other crop researchers that their research data are just as important as their core research work. She also educates us on what she means by ‘SHARP’ data management. But first, a little background on Arllet…

Transitions, travels and tools
Plant breeding is in Arllet Portugal’s blood. Her father (now retired), one of the original field staff of the International Rice Research Institute (IRRI) at Los Baños in The Philippines, nurtured it in her from a tender age. It’s easy to picture him sharing fascinating tales daily with his family upon coming home, after a day of hard work in sun-splashed paddies where he nurtured mysterious and exotic new lines of rice which he was told may hold the solution to world hunger.

“He loved what IRRI stood for and admired the research they did,” reminisces Arllet. “I think he hoped one day he would have a son or daughter working alongside the researchers, so I guess I fulfilled that wish!” She adds “His IRRI stories still continue to this day, and I have learnt much from him which continues to give me deeper insights in my work and interactions with crop scientists.”

Having lived most of her life under the canopy of IRRI, including 12 years working as a database administrator at the Institute, she decided it was time for a change, and she spread her wings – an adventure that would take her across the oceans, pose new challenges, and plunge her deeper into agricultural research beyond IRRI’s mandate crop, rice. So, in 2009, she packed her bags and headed to Mexico, having accepted a position as a crop informatician for wheat at the International Maize and Wheat Improvement Center (CIMMYT), and then moving over to GCP the following year as Informatics Coordinator, and later on Data Management Leader of GCP’s Integrated Breeding Platform (IBP).

The Platform is a one-stop shop for crop information, informatics tools and services designed to propagate and support the application of modern approaches to crop breeding, particularly targeting developing countries.

We are trying to show breeders that their ‘system’ can be enhanced and streamlined if they enter data straight into a computer when they’re in the field and then upload them into an online database.” 

Gunning for a digital data revolution: The challenge of changing mindsets
Arllet’s greatest daily challenge is convincing crop breeders and other crop researchers that their research data are just as important as their core research work, and they should therefore dedicate as much time, energy and resources to managing data.

“Like everyone else, most plant breeders tend to be generally comfortable with the ‘systems’ that they and their predecessors have always used,” says Arllet. “For plant scientists, this often consists of recording results using pen and paper when they are out in the field, then coming back to their office and either filing those paper records as is, or re-entering the data into a basic Excel spreadsheet that is for their eyes only. They will then pull these data out when they want to compare them with their previous data.”

Arllet explains that this age-old system is not necessarily wrong, but it wastes valuable time, is insecure and limits the capacity of breeders to efficaciously reuse and also share their data with colleagues – a practice by which they would help each others’ work. “We are trying to show breeders that their ‘system’ can be enhanced and streamlined if they enter data straight into a computer when they’re in the field and then upload them into an online database,” she says.

Walking with giants…” 

Dealing with data: maximising efficiency, security, value and sharing
“These data can then be better secured and managed for their benefit and that of other researchers doing similar or related work, in essence increasing their working capacity. They would also have access to the most current analytical tools to verify their results and do their research more efficiently.”

Arllet explains that such improved systems have been in place for decades in the developed world, particularly within the private sector but not as prevalent in the developing world or public sector. This is largely attributable to the high cost of the equipment and informatics tools, and a lack of personnel with the appropriate skills to make use of the tools.

Through a collaborative effort bringing together a wide array of partners, with funding primarily from the Bill & Melinda Gates Foundation, supplemented by the European Commission and the United Kingdom’s Department for International Development, IBP is working to overcome some of these barriers. With the release of the Integrated Breeding (IB) FieldBook, the foundational informatics tool for the proposed system, Arllet believes a giant step has been made towards achieving this objective.

Breeders will be able to use it to plan their trials from start to finish”

What is the IB FieldBook?
The IB FieldBook is a user-friendly computer program that facilitates the design of field trials and produces electronic field-books, field plans and labels. It collects together – in a single application – all the basic tools that a plant breeder requires for these diverse but intertwined functions.

“Breeders will be able to use it to plan their trials from start to finish,” says Arllet. “This is important as it will, for example, keep track of all the identities of plant crosses, minimising the chance that the breeder, or assisting technician, will record the data incorrectly, while emphasising the importance of accurate data for correct crop-breeding decisions.”

Live demonstration: Taking the tablet through the paces at a training workshop for research technicians in January 2012. The regional workshop for West Africa (in French and English) was hosted by L’Institut d’économie rurale (IER) at Sotuba, Mali. A similar workshop was held in Ethiopia in English for the Eastern and Southern Africa region.

She and her team have been conducting training workshops on data management for breeders at which they demonstrate the IB FieldBook and the use of handheld electronic devices (such as tablets) for data collection, which breeders can conveniently take to the field with them and directly enter the phenotyping data they would normally capture in paper field-books.

Tablets and feedback
“The training has been challenging but fun,” says Arllet. “When we present the breeders with a tablet at the start of the exercise, they get really excited. It takes a while for them to learn how to use it, but once they do, they see how this technology could save them time and reduce the risk of mistakes. It’s a little sad for them and for us though when we have to take the tablets back at the end of the exercise, as demand always outstrips supply. We have however distributed around 200 tablets to breeders, university academic staff, researchers and postgraduate students of plant breeding. Majority of the recipients are from Africa and Asia. And the good news is that,  as a result, some of the institutes and programmes the recipients come from have gone ahead to purchase more units for themselves.”

Arllet observes that the workshops have not only allowed her team to educate breeders and build awareness, but also to receive valuable feedback on how the IB FieldBook could be improved to make it even better, and learn what other tools breeders need. “Based on this feedback, we worked on the IB FieldBook version 4, which was released in June 2013, as well as on a number phenotypic and genotypic data management tools to incorporate into both the FieldBook and the primary crop databases.”

‘SHARP’ data – shareable, available, reusable and preservable. 

Left to right: Diarah Guindo (IER), Ardaly Abdou Ousseini (L’Institut national de la recherche agronomique du Niger, INRAN) and Aoua Maiga (IER) at the January 2012 training at IER Sotuba, Mali.

SHARP and secure data management
Plant breeders are collaborating more often than they used to, and also drawing much more on specialised experts for each stage of the crop variety development chain. These experts are able to verify the data to make sure they are correct, do their job quickly and pass the data onto the next expert, an economical resource- and time-efficient process. However, as Arllet explains, consistent and secure data management is key to the success of these collaborations.

For Arllet, data that are properly managed are ‘SHARP’ – shareable, available, reusable and preservable. “By collecting data in a consistent format, uploading them to a secure database with easily identifiable tags, and making them available to other researchers, the data will be more accessible to partners, enable reliable analysis and conclusions, be more likely to be reused, and most importantly, save time and money. For example, breeders who share their data on the IBP database will receive support from researchers outside of their own breeding programme and enlist the help of experts and specialists  they require for particular tasks,” says Arllet. “This includes access to, say, a molecular biologist in Europe or Asia for the breeder in Africa or America who may need that kind of specialist help, for example.”

Arllet and her team of four consultants are currently helping breeders from all around the world upload their historical research data into the central crop databases of the Integrated Breeding Platform, a massive task given the issues of trust, language barriers, slow internet connections, inadequate computer skills and the sheer volumes of the data. However, these are challenges that are becoming easier to handle with greater awareness and the enthusiasm that comes with that.

What next, and what difference will it make?
Adoption and broad use of the FieldBook will of course also make the process easier in the future, enabling a single step uploading of phenotypic data – hence setting breeders free to get on with their work without the wastefulness of having to enter and re-check the data multiple times.

“What it all means is that we will facilitate the more rapid and efficient development of higher-yielding  more stress-tolerant crops that can benefit the farmers and the people they feed,” says Arllet, “and that is the ultimate goal of a plant breeder’s work.”

Links

See videos below: ‘ Masses of crop breeding information: How can it be handled?’ and “Why use IBP’s breeding and data management tools?“, which, in the view of one of our Australian partners, explains why IBP is particularly important for developing countries, and why they have a comparative advantage compared to the developed world.

Next video below:

PRIZE AND FUN! If you’ve survived this far, you deserve a prize, in the form of seeing Ms Portugal in party mode. To see what Arllet gets up to when she’s not crunching data, flip through this fun album

Making an indelible mark – Indonesia’s marathon Mother Nature, in science as in spirit

 Asia, Capacity building, Crop breeding, Researchers, Rice, Women in science  No Responses »
Dec 122013
 

Down memory lane with Masdiar Bustamam, from generation to generation

Masdiar Bustamam

In some circles, Masdiar Bustamam (pictured right) is a mother figure of molecular breeding in Indonesia. In a marathon career spanning 37 years as a horticulturist and agricultural researcher, she helped develop and nurture the practice at the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD).  Staying with the marathon metaphor, this quote from a celebrated middle- and long-distance Kenyan champion runner, Kipchoge Keino, is very apt: “This life we have is short, so let us leave a mark for people to remember.”

Back to Masdiar: having retired in early 2012, we were recently lucky enough to gain a rare insight into Masdiar’s life, and to witness the mark she has already made, by simply tagging along when she checked in on two of her ICABIOGRAD charges and mentees whose PhD studies were supported by GCP – Wening Enggarin and Joko Prasetiyono. At ICABIOGRAD, Wening and Joko have both taken the torch from Masdiar for GCP projects, as well as for other projects.

She was the best teacher for me … instilled in me a spirit to never lose hope in the research I’m doing – Joko

She was a great role model… Her persistence and positive can-do nature was exactly what I needed as a young researcher … to not just offer me assistance in my work but also in life and religion. For me, she has become a second mother  – Wening

… That project really helped us out a lot and we are grateful to GCP  for recognising the potential in us and supporting it – Masdiar

Here’s more of what Masdiar (and her charges) had to say as we tagged along, and chatted her up…

Tell us about your early life
I grew up and lived in West Java for most of my life. My father was a farmer and my mother a housewife. I was their first of five children.

I went to Andalas University in Padang and graduated with a Bachelor in Biology in 1974. After graduating, I worked as a staff researcher at a local horticulture research institute focusing on pests and diseases, particularly fungi in tomato soils. I was lucky early in my career to have opportunities to visit research institutes in The Netherlands, Japan and USA, all of which enhanced my skills. While in USA, I completed my Masters in rice blast disease – a fungus-related disease, which severely hampers rice yields in Indonesia, and all around the world.

After my time in USA, I accepted a position at the International Rice Research Institute (IRRI) in The Philippines. This was the start of the second phase of my career, in which I began to focus on molecular biology. When I returned from The Philippines, I realised that we needed to improve our capacity to use molecular markers for breeding, which led me to take a job at ICABIOGRAD.

Setting up a lab – GCP lends a hand
When I first started at ICABIOGRAD we had empty benches. It took a lot of time and money to fill them with the equipment we have today. Rebecca Nelson from Cornell University in USA provided us with a lot of support in getting us started. We were involved in one of her GCP projects for two years working on blast resistance in rice.

We were also working on another GCP project led by Abdelbagi Ismail studying phosphorus-deficiency tolerance in rice too, dubbed the Pup1 project. Joko was actually my PhD student for that project and did a lot of the work.

Selecting Pup1 lines in farmers' fields in Sukabumi, West Java, in 2010. L–R: Masdiar Bustamam, Tintin Suhartini and Ida Hanarida Sumantri.

Selecting Pup1 lines in farmers’ fields in Sukabumi, West Java, in 2010. L–R: Masdiar Bustamam, Tintin Suhartini and Ida Hanarida Sumantri.

Both Rebecca and Adbdelbagi helped me draft a proposal to GCP in 2007 for a project to enhance our capacity in phenotyping and molecular analysis to develop elite rice lines suitable for Indonesia’s upland regions. We had the understanding to do the science, but needed to enhance our facilities to carry it out.

That project really helped us out a lot and we are grateful to GCP  for recognising the potential in us and supporting it.”

GCP recognised the need for such a project as many of Indonesia’s brightest researchers were leaving the country because of the lack of suitable facilities, and so funded the two-year ICABIOGRAD-defined capacity-building project. The grant covered – among other areas – intensive residential staff training at IRRI; PhD student support, which allowed Wening to complete her PhD; infrastructure such as a moist room, temperature-controlled centrifuge apparatus, computers and appropriate specialised software; and blast and inoculation rooms.

Writer’s note: The tailor-made grantee-driven capacity-building project above was a cornerstone of  GCP Phase I’s capacity-building strategy, and was dubbed ‘Capacity building à la carte’. With this historical note, we take an interlude here, to tour the facilities Masdiar has mentioned above.

Our first stop is the Rice Blast Nursery…

....Front view...

….Front view…

...side view...

…side view…

 

 

 

 

 

 

 

 

... and a close-up on the sign in the side view.

… and a close-up on the sign in the side view.

 

Next, we visit the Inoculation and Moist Rooms…

 

Inoculation and Moist Rooms

Inoculation and Moist Rooms…

 

Close-up

…and a close-up on the sign at the front.

 

 

 

 

 

 

 

After our tour of the facilities, Masdiar resumes her story: “That project really helped us out a lot and we are grateful to GCP  for recognising the potential in us and supporting it so that researchers like Wening bloom and blossom, now and into the future,” says Masdiar glowingly of one of her mentees and successors.

I’m proud of how they have matured and I’m really looking forward to when they and their teams produce new rice varieties, from the facilities I helped establish, that will help the farmers…I sacrificed what I enjoyed doing for a challenge whose benefits I recognised for my country.”

Mission-driven researcher, nurturer and mentor, all rolled into one
For Masdiar, it wasn’t work, but rather a passion and a hobby. “Throughout my career, I always enjoyed research, especially in plant pathogens,” she remembers. “Working with biotechnology was difficult because I didn’t have a background in the area. I sacrificed what I enjoyed doing for a challenge whose benefits I recognised for my country.”

Photo: ICABIOGRAD

From generation to generation: Masdiar (2L) drops in on her charges and torch-bearers at ICABIOGRAD’s Molecular Biotechnology Lab. L–R: Wening Enggarini, Masdiar Bustamam, Tasliah Zulkarnaeni, Ahmad Dadang and Reflinur Basyirin.

In the later half of her career, Masdiar recollects how she enjoyed training and mentoring younger researchers like Joko and Wening. “I’m proud of how they have matured and I’m really looking forward to when they and their teams produce new rice varieties, from the facilities I helped establish, that will help the farmers.”

Both Joko and Wening attest that Masdiar’s support and supervision were vital for their professional development and consequent career advancement. “She was the best teacher for me. She taught me how to manage a project, how to forge international collaborations, and how to write a good publication,” remembers Joko. “She also instilled in me a spirit to never lose hope in the research I’m doing.”

“She was a great role model for me!” exclaims Wening proudly. “Her persistence and positive can-do nature was exactly what I needed as a young researcher who was just starting a career. Even more so was her ability to take time out of her busy day to not just offer me assistance in my work but also in life and religion. For me, she has become a second mother  in this life. I’m blessed to be so lucky!”

Clearly, Masdiar has made her mark, leaving a cross-generational living legacy in molecular breeding embodied in these young researchers.

Links

  • Masdiar’s project report, with a picture of the blast nursery under construction (p 156 in this PDF)
  • Photo-story on Facebook
  • Rebecca Nelson’s project, Targeted discovery of superior disease QTL alleles in the maize and rice genomes (p 16 in this PDF)
  • GCP’s capacity building

 

Cassava’s gain, and surgery’s ‘pain’: Career crossings and causerie with Chiedozie Egesi

 Africa, Capacity building, Cassava, Crop breeding, Researchers  No Responses »
Nov 202013
 
Chiedozie Egesi

Chiedozie Egesi

Despite the social injustice around me, I always thought there was opportunity to improve people’s lives…GCP helped us to build an image for ourselves in Nigeria and in Africa, and this created a confidence in other global actors, who, on seeing our ability to deliver results, are choosing to invest in us.”
 – Chiedozie Egesi, a would-have-been surgeon who switched sides to biology and crop genetics, and who got acquainted with GCP through the Internet.

Backdrop: A booming economy and a wealth of natural resources may be among some of the common preconceptions of the average Jane and Joe regarding Africa’s most populous nation. Lamentably, however, Nigeria, like numerous robust economies worldwide, is still finding its feet in addressing severe inequality and ensuring that the nation’s wealth also flows to the poorest and most marginalised communities.

It’s a problem Chiedozie Egesi (pictured above), a molecular plant breeder at Nigeria’s National Root Crops Research Institute (NRCRI), understands well: “Nigeria is an oil-producing country, but you still see grinding poverty in some cases. Coming from a small town in the Southeast of the country, I grew up in an environment where you see people who are struggling, weak from disease, poor, and with no opportunities to send their children to school,” he reveals. The poverty challenge, he explains, hits smallholder farmers particularly hard: “Urban ‘development’ caught up with them in the end: some of them don’t even have access to the land that they inherited, so they’re forced to farm along the street.”

Maturing cassava fruits.

Food first! A man with a mission and fire in his belly, determined to make a difference
For this gifted and socially conscious young man, however, the seemingly bleak picture only served to ignite a fierce determination and motivation to act: “Despite the social injustice around me, I always thought there was opportunity to improve people’s lives.” And thus, galvanised by the plight of the Nigerian smallholder, plans for a career in medical surgery were promptly shelved, and traded for biological sciences and a PhD in crop genetics, a course he interspersed with training stints at USA’s Cornell University and the University of Washington, Seattle, along the way, before returning to the motherland to accept a job as head of the cassava breeding team, and – following a promotion in 2010 – Assistant Director of the Biotechnology Department, at NRCRI.

As evident from the burgeoning treasure chest of research gems to his name, it was a professional detour which paid off, and which continues to bear fruit today.

Making a marked difference, cultivating new partnerships, and looking beyond subsistence
In 2010, work by Chiedozie and his NRCRI team resulted in the official release of Africa’s first molecular-bred cassava variety which was both disease-resistant and highly nutritious – an act they followed in 2012 with the release of a high-starch molecular-bred variety. The team’s astute navigation of molecular markers resulted in breeding Latin American cassava varieties resistant to cassava mosaic disease (CMD), leading to the release of CMD-resistant cassava varieties in the African continent for the first time. Genetic maps intended to enhance breeding accuracy for cassava – the first of their kind for the crop in Africa – have been produced, and quantitative trait loci (QTLs) for cassava breeding are in the making. In 2011, the team, together with their partners at the International Institute of Tropical Agriculture (IITA) and HarvestPlus (a CGIAR Challenge Programme), released three pro-vitamin A-rich varieties of cassava, which hold the potential to provide children under five and women of reproductive age with up to 25 percent of their daily vitamin A allowance – a figure Chiedozie and his team are now ambitiously striving to increase to 50 percent.

These new and improved varieties – all generated as a direct or indirect result of his engagement in GCP projects – are, Chiedozie says, worth their weight in gold: “Through these materials, people’s livelihoods can be improved. The food people grow should be nutritious, resistant and high-yielding enough to allow them sell some of it and make money for other things in life, such as building a house, getting a motorbike, or sending their kids to school.”

Prior to my GCP work, I was more or less a plant breeder, and a conventional one at that. Whilst I’d been exposed to molecular tools during my early work on yam and other crops, I was not applying them in my work back then…GCP was not only there to provide technology but also to guide you in how to operate that technology… Now all our staff understand what is meant by good breeding, data analysis or applying genotypic data. My whole team benefitted.”

A chance ‘meeting’, with momentous manifold connections
Having first stumbled across the GCP website by chance when casually surfing the internet one day in a cyber café back in 2004, Chiedozie’s attention was caught by an announcement for a plant breeders’ training course in South Africa, an opportunity which he applied for on the off chance…and for which, hey presto!, he was accepted! Thus, his GCP ‘adventure’ began!

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

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

Promptly revealing an exceptional craftsmanship for all things cassava, Chiedozie soon became engaged in subsequent opportunities, including a one-year GCP fellowship at the International Centre for Tropical Agriculture (CIAT) in Colombia, a number of GCP Capacity building à la carte-facilitated projects, and, more recently, a major role as a Principal Investigator in the GCP Cassava Research Initiative (RI), teaming up with NRCRI colleague and Cassava RI Product Delivery Coordinator, Emmanuel Okogbenin. The Cassava RI is where Chiedozie’s energies are primarily invested at present, with improving and deploying markers for biotic stresses in cassava being the name of the game.

The significance of his GCP engagements was, Chiedozie affirms, momentous: “Prior to my GCP work, I was more or less a plant breeder, and a conventional one at that. Whilst I’d been exposed to molecular tools during my early work on yam and other crops, I was not applying them in my work back then.”

Collaboration in a GCP-funded project with CIAT led to the development of a new laboratory space for NRCRI, bolstered by support for basic materials as well as training. “GCP was not only there to provide technology but also to guide you in how to operate that technology,” Chiedozie comments. (For more on how it all began, see At home and to go and Molecular bonds in pp 26–29 in this e-book)

GCP’s Integrated Breeding Platform (IBP), he says, has played a vital role in this regard: “By opening the door to training, generation of data, analysis of data, and by giving support in making decisions, GCP’s IBP serves as a one-stop shop for cassava breeding.” It’s a sentiment shared by his NRCRI colleagues, he says: “GCP is providing a comprehensive full-package deal. Besides myself, several colleagues have been trained at NRCRI. Now all our staff understand what is meant by good breeding, data analysis or applying genotypic data. My whole team benefitted.”

A real deal-breaker is the facilitation of self-empowerment amongst national programmes, and the new avenues unfolding for enhanced collaboration at the local, national and regional level…What we’re seeing is a paradigm shift. In the past there was a general belief that this kind of advanced molecular science was only feasible in the hands of CGIAR Centres or developed-country research institutes – the developing-country programmes were never taken seriously. When the GCP opportunity to change this came up we seized it, and now the developing-country programmes have the boldness and capacity to do molecular breeding and accurate phenotyping for themselves.”

Growth in numbers, capital, capacity, collaboration, reach and impact
Strength in numbers, Chiedozie says, is a vital lifeline for cassava, a crop which has suffered years of financial neglect. As such, a real deal-breaker in Chiedozie’s eyes is the facilitation of self-empowerment amongst national programmes, and the new avenues unfolding, thanks to his involvement in the GCP cassava breeding Community of Practice (CoP), for enhanced collaboration at the local, national and regional level: “We now have a network of cassava breeders that you can count on and relate with in different countries. This has really widened our horizons and also made work more visible,” he offers, citing effective links formed with Ghana, Sierra Leone, Liberia, Mozambique, Malawi and Côte d’Ivoire, amongst several other cassava-breeding neighbours near and far.

Cassava leaf

Cassava leaf

The achievements amongst this mushrooming community are, he stresses, unprecedented: “Participation in the CoP means many countries can now create their own hybrids and carry out their own selection, which they could not do before,” he affirms.

And it’s a milestone Chiedozie and colleagues are justifiably proud of: “What we’re seeing is a paradigm shift. In the past there was a general belief that this kind of advanced molecular science was only feasible in the hands of CGIAR Centres or developed-country research institutes – the developing-country programmes were never taken seriously. When the GCP opportunity to change this came up we seized it, and now the developing-country programmes have the boldness and capacity to do molecular breeding and accurate phenotyping for themselves,” Chiedozie confirms.

GCP helped us to build an image for ourselves in Nigeria and in Africa, and this created a confidence in other global actors, who, on seeing our ability to deliver results, are choosing to invest in us.” 

Building on success, going from strength to strength as the sands shift

With internal capacity now blossoming of its own accord – in no small measure due to the leading role played by NRCRI in the sensitisation of cassava plant breeders throughout Nigeria and beyond – the sands are certainly shifting: “GCP helped us to build an image for ourselves in Nigeria and in Africa, and this created a confidence in other global actors, who, on seeing our ability to deliver results, are choosing to invest in us.”

Anthony Pariyo (left) of NaCRRI, Uganda

Visitors with working clothes on: NaCRRI Uganda’s Anthony Pariyo (left) and Williams Esuma (right) visiting NRCRI Umudike on a breeder-to-breeder visit in July 2012. Williams’ postgraduate studies were funded by GCP through the cassava CoP.

And the beauty of it, Chiedozie continues, is that the cassava crew is going from strength to strength: “Nigeria is seen as a really strong cassava-breeding team, not only within Africa but also globally. And we have not yet realised all the benefits and potential – these are still unfolding,” he enthuses.

Also yet to unfold are Chiedozie’s upcoming professional plans, which, he reveals, will soon see him engaging with the USA’s Cornell University, the Bill & Melinda Gates Foundation, the International Institute of Tropical Agriculture (IITA) and Uganda’s National Crop Resources Research Institute (NaCRRI) in an initiative which, through its focus on genomic selection in cassava breeding, promises to be, Chiedozie reveals, “at the frontier of cutting-edge technology.” Genomic selection for this initiative is already underway.

Readers intrigued by this tantalising taster of what to expect in Chiedozie’s next professional chapter are encouraged to watch this space over the coming years…Judging by his remarkable research record to date, we feel confident that future installments will not disappoint!

Meantime, here’s Chiedozie’s presentation at the GCP General Research Meeting in September 2013. We are also working on videos of Chiedozie and his work. Yet more reason to watch this space!

Links
  • For a picture of Chiedozie’s work near the beginning in 2006, see pp 26–29 here (At home and to go and Molecular bonds)
  • More recent updates are on the Cassava InfoCentre

 

A bout with drought and disease: Beans that beat the heat and odds in Zimbabwe

 Africa, Beans, Capacity building, Genomics, Legumes  2 Responses »
Feb 282013
 

Drought stalks, some die
Despite the widespread cultivation of beans in Africa, yields are low, stagnating at between 20 and 30 percent of their potential. Drought brought about by climate change is the main culprit, afflicting 70 percent of Africa’s major bean-producing regions in Southern and Eastern Africa.Bean plant by R Okono

Today we turn the spotlight on Zimbabwe, where drought is a serious and recurrent problem. Crop failure is common at altitudes below 800 meters, and livestock death from shortage of fodder and water are all too common. In recent history, nearly every year is a drought year in these low-lying regions frequently plagued by delayed rains, as well as by intermittent and terminal drought.

The ‘battleground’ and ‘blend’
Zimbabwe is divided into five Natural Regions or agroecological zones. More than 70 percent of smallholder farmers live in Natural Region 3, 4 and 5, which jointly account for 65 percent of Zimbabwe’s total land area (293,000 km2). It is also here that the searing dual forces of drought and heat combine to ‘sizzle’  and whittle bean production.

The rains are insufficient for staple foods such as maize, and some of their complementary legumes such as groundnuts. In some areas where temperatures do not soar too high (less than 30oC), beans blend perfectly into the reduced rainfall regime that reigns during the growing season.

A deeper dig: the root of the matter

Godwill Makunde

Godwill Makunde

Research from Phase I of the Tropical Legumes I (TLI) project under GCP’s Legume Research Initiative showed that deep rooting is one of the ways to confer drought tolerance in common beans. High plant biomass at pod-filling stage also confers drought tolerance. “These important findings from TLI refined our breeding objectives, as we now focus on developing varieties combining deep roots and high plant biomass,” reveals Godwill Makunde (pictured), a bean breeder at Zimbabwe’s Crop Breeding Institute (CBI), which falls under the under the country’s Department of Research & Specialist Services. Zimbabwe is one the four target countries in Eastern and Southern Africa for GCP’s bean research (the other three being Ethiopia, Kenya and Malawi).

From America to Africa…the heat is on, so is the battle…

The battle is on to beat the heat: through the project, CBI received 202 Mesoamerican and Andean bean breeding lines from the reference set collection held by the International Center for Tropical Agriculture (CIAT, by its Spanish acronym). 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. The Institute also embarked on bringing in more techniques to breed for heat tolerance.

Kennedy Simango

Kennedy Simango

Drought, pests and disease
“We embraced mutation breeding in collaboration with the International Atomic Energy Agency, and we primarily look for heat tolerance in small-seeded beans,” says Kennedy Simango (pictured right and below), a plant breeder at CBI. “Preliminary results suggested that just like drought, the reproductive stages of common bean are when the crop is most sensitive to heat. Flower- and pod-drop are common. Yield components and yields are severely reduced. In addition, we also focus on developing pest- and disease-resistant varieties.”

 

Kennedy Simango at work a the Crop Breeding Institute.
Kennedy Simango at work a the Crop Breeding Institute.

The CBI project’s primary diseases and pests of focus are angular leaf spot (ALS), common bacterial blight (CBB), rust and bean stem maggot, and aphids. “This came from our realisation that drought co-exists with heat, diseases and pests,” Kennedy adds. “So, a variety combining drought, heat, disease and pest tolerance all together would increase common bean productivity under harsh environments or drought-prone areas.”

At first glance, piling up all these vital survival traits may appear insurmountable, but it is all feasible, thanks to advances in plant science. “Breeding methods are changing rapidly, and it is vital that we keep up with the technology,” says Kennedy.

The CBI team is using molecular breeding to identify drought-tolerant parents, and then cross them into preferred bean varieties to confer to the ‘offspring’ the best of both worlds – drought tolerance and market appeal.

All-round capacity and competence
GCP’s support does not stop at enabling access to breeding lines alone, or introduction to molecular breeding. “We got a lyophiliser, which is specialised equipment that enables us to extract DNA and send it for genotyping,” says Kennedy. “From the genotyping exercise, we hope to be able to trace the relationships among breeding lines so that we design better crossing programmes, and thereby maximise the diversity of our breeding lines. In addition, we hope to select recombinants carrying desirable genes in a short period of time, and at times without even needing to test them in the target environment.” GCP assists with genotyping through its Genotyping Support Service offered through the Integrated Breeding Platform.

For phenotyping, CBI has benefitted from a mobile weather station, a SPAD meter (for measuring chlorophyll content), a leaf porometer (for measuring leaf stomatal conductance) and water-marks (probes for measuring soil moisture).

Human resources have not been forgotten either. Godwill Makunde, a CBI bean breeder, is studying for a TLII-funded PhD in Plant Breeding at the University of the Free State, South Africa. A group of four scientists (Godwill and Kenedy,  plus Charles Mutimaamba, and Munyaradzi Mativavarira) are in GCP’s three-year Integrated Breeding Multi-Year Course (IB–MYC). The curriculum includes design of experiments, data collection, analysis and interpretation, molecular breeding and data management techniques. In addition, GCP also trains research technicians. For CBI, Clever Zvarova, Anthony Kaseke, Mudzamiri and Chikambure have attended this training. Their course also includes phenotyping protocols (data collection and use of electronic tablets in designing field-books). To date, CBI has received five tablets for digital data collection , of which two are outstanding.

Photo: CBI

Godwill doing what he does best: bean breeding.

Bringing it all together, and on to farms
But how relevant are all these breeder-focused R&D efforts to the farmer? Let’s review this in proper context: in the words of Mr Denis Mwashita, a small-scale farmer at the Chinyika Resettlement Scheme in Bingaguru, Zimbabwe, “Beans have always carried disease, but from the little we harvest and eat, we and our children have developed stomachs.”

“What Mr Mwashita means is that despite the meagre harvests, farm families fare better in terms of health and nutrition for having grown beans,” explains Godwill.

With this solid all-round support in science, working partnerships, skills and infrastructure, the CBI bean team is well-geared to breed beans that beat both heat and disease, thereby boosting yields, while also meeting farmer and market needs. Trials are currently underway to select lines that match these critical needs which are the clincher for food security.

“The Zimbabwe market is used to the sugar type, which is however susceptible to drought. We hope to popularise other more drought-tolerant types,” says Kennedy. “We plan to selected a few lines in the coming season and test them with farmers prior to their release. Our goal is to have at the very least one variety released to farmers by mid-2013.”

A noble goal indeed, and we wish our Zimbabwe bean team well in their efforts to improve local food security.

VIDEO: The ABCs of bean breeding in Africa and South America, with particular focus on Ethiopia, Kenya, Malawi and Zimbabwe

Related blogposts

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