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Chickpeas on the map of champions in the genome world: Challenges, rewards… and ‘Rajeevs’

 Africa, Asia, Chickpeas, Genomics, Legumes  No Responses »
Jan 282013
 

Today, Nature Biotechnology published the first-ever draft genome sequence map for a chickpea variety (PDF). The map will help researchers and breeders the world over to – through molecular breeding methods – deliver to growers higher-yielding more resilient varieties of chickpeas. 

Now that we have the rewards in a nutshell, and we choose to chew the chestnut of challenges later in the story, let’s next decipher the ‘Rajeevs’ part in the title: introducing Rajeev K Varshney, our very own Leader of Comparative and Applied Genomics, who also led and coordinated the transnational collaboration that developed this map.

We had the pleasure of talking to the gently-spoken Indian, a week before the release of the paper, asking him to recount how the project began, and the challenges and success they faced along the way. We’ll soon get to what Rajeev had to say, but first, a rapid rewind for backgrounding before Rajeev tells us the rest of the story…

… we have the ‘borders’ done… a good idea of what the picture is, and where the rest of the pieces will fit.”

Rajeev in the lab.

Reality check from the Genomics Gnome of Good News: two is but the twinkling of an eye…
The sequence map of the genotype CDC Frontier – a Canadian kabuli chickpea variety – took about two years to construct.”

No, the time taken is not the challenge since we’re yet to get to that part. In fact, in the world of genomics , two years is fairly fast, compared to, say, the time taken for sequencing other grain genomes such as maize, rice and wheat.

Rajeev attributes this to the interdisciplinary expertise of his team, most of whom are world leaders in their field, and to the enthusiasm and generosity of all partner institutes who funded the collaboration.

And with that background, on to our chat with Rajeev!

Sandwiches in the Sunshine State, and a search starts for the then unattainable holy grail

Q: Is it correct that this project started over sandwiches under a sunny sky in California?
Funnily enough, yes. We had the preliminary discussion during a lunchtime break at the fifth International Congress on Legume Genetics and Genomics back in July 2010. Doug Cook, from the University of California, Davis, and I, organised the meeting for select attendees to discuss the idea.

With daughter, Nanz. Rajeev in ‘Daddy-mode’, a galaxy away from genomic research.

Many researchers at the time had, or were toying with, sequencing parts of the chickpea genome to discover genes that helped plants tolerate salinity, drought, disease, and so on. The idea of mapping the whole genome, however, was thought to be unachievable given the cost and resources required. What Doug and I proposed to the 10-odd senior researchers that day was that we form an alliance to pool together our knowledge, funds and resources.

When we returned to our home institutes, we all approached our institutes or funding agencies in respective countries, to propose they consider funding the collaborative project. To be honest, this was probably the most challenging task of the project, as it often is with other projects, as they had a hard time recognising the benefits. However, we finally got there, and with the help of more than 20 institutes from North and Central America, Asia, Australia and Europe, we have successfully assembled 74 percent of the genome within two years.

Pieces fall into place for mix-and-match combinations

Now, you may say that 74 percent doesn’t equal the whole genome, but it does provide us with a map and pointers we’d never had before. Imagine doing a jigsaw without a picture to guide you – that’s how hard it was for us at the start. Now at least we have the ‘borders’ done, and we have a good idea of what the picture is, and where the rest of the pieces will fit.

Q:Why is mapping the chickpea genome so important?
Having the genome mapped is going to benefit all chickpea breeders, researchers and growers.

Say a conventional breeder wanted to create a new breed of chickpeas with drought tolerance. They would cross a domesticated, high-yielding variety of chickpeas, with a variety that tolerates dry conditions – most likely, lower-yielding – and then grow the progeny in the field. They wait for these progenies to grow, then visually select the best lines and make crosses with these. They keep doing this process over and over again for six to seven years until they’ve generated a new variety with the desired trait.

Different breed, mould and mode

Molecular breeders do it differently: instead of selecting the lines by visual inspection, they select lines based on their genes. This means they can correctly trace whether the progeny has received the genes which help the plant tolerate drought and only grow, test and cross with these plants, almost halving the time it would take through conventional methods.

With the map, researchers will be able to more rapidly identify genes of interest, and work with breeders to select for plants that display the favourable traits of these genes, whether this be for drought tolerance, pest resistance or for any other trait they are interested in.

Q: Good for researchers and breeders, but how is that going to benefit growers though?
Knowing which plant is more tolerant of drought from the start of the breeding process is going to significantly reduce the time it takes for breeders to develop these types of chickpea cultivars. So, growers will have new breeds of higher-yielding more resilient chickpeas available sooner.

Ethiopian farmer, Temegnush, and her chickpea harvest.

Remember also that chickpeas are a very important crop for smallholders in the resource-poor harsh environments of sub-Saharan Africa, India and Southeast Asia. Not only do they grow it for food and to replenish soil nitrogen, they also export to India, the world’s largest consumer of chickpeas. Most of these farmers would be lucky to harvest one tonne per hectare, so any yield advantage means extra income.

This point is particularly relevant for GCP’s goal, which is to improve the livelihoods of such farmers.

Q: This was one of the largest collaborative projects you’ve coordinated in your relatively short career. What was the most challenging aspect?
Short answer is….many!  With it being a collaborative project, bringing together researchers from all around the world, it was always difficult to coordinate suitable times for Skype and phone meetings.

Personally though, my biggest challenge was trying to coordinate so many esteemed researchers. We all had great ideas and we all thought each of our ideas was the right one. I had to resolve all issues amicably and find a solution to move forward.

Luckily I have surrounded myself over the years with some good colleagues to whom I’ve always been able to turn to discuss any problems. Jean-Marcel Ribaut, who is the Director of GCP, was one particular colleague to whom I often turned to for advice, given his experience with coordinating all of GCP’s collaborative interdisciplinary projects. He also helped source much-needed funds and suggested several useful partnerships, which were vital in carrying out the project.

My boss at ICRISAT, William Dar, the Director General, has always been very supportive, and time and again went out of his way to make sure I had the funds, capacity and sanity to keep the project going! I am deeply indebted to him.

The future

Q: How will the research continue?
Researchers and breeders will be able to customise the genome map to fit their particular purposes. Most will be interested in using it to develop molecular markers, which breeders can use to highlight specific genes of interest for molecular breeding. As I mentioned earlier, this could realistically halve the time it takes to breed new varieties from six to10 years to four to five years.

One outcome of the project, which I’m particularly interested in exploring further, relates to chickpea diversity. When we compared the 90 chickpea genomes, we realised that that diversity in the elite varieties was very low, meaning they all had very similar alleles (form of genes).

This has come about because over the years, breeders and growers have continually chosen only a handful of chickpea varieties to continually breed with. This is because these breeds tend to produce higher yields, something which all growers want.

The drawback of this, however, is that if all the popular breeds are too similar, then they could all be susceptible to a particular disease. If this particular disease were to strike, then chickpeas could be wiped out – globally.

So this map will be a valuable tool to use to enhance genetic diversity in the elite gene pool, thus safeguarding the world’s supply of chickpeas.

 

Links

Chickpea research in Ethiopia – A major boost for food security

 Africa, Chickpeas, Crop breeding  No Responses »
Jun 302012
 

Fikre Asnake (pictured)  is a researcher and breeder in both Tropical Legumes I and II projects (TLI and TLII), working at the Ethiopian Institute of Agricultural Research (EIAR).

He has been leading the project activities since 2008. Through the project, EIAR has obtained diverse chickpea germplasm from ICRISAT. This germplasm is undergoing different breeding schemes using marker-assisted recurrent selection (MARS) and marker-assisted backcrossing (MABC) for evaluation.

The germplasm is now in the pre-release testing phase. Some of the work is being done by postgraduate students trained by TLI (two PhDs and 1 MSc). The project is using MABC to introduce drought-resistant traits into proven superior cultivars. “We expect good gains in productivity for drought-prone environments, which will make a huge difference. The varieties we hope to release will increase not only quantity, but also quality,” says Fikre. “We anticipate some of these improved chickpea varieties will be released in the course of Phase II of the TLI project, based on work that began in Phase I.”

Building capacity
Capacity-building is a crucial cornerstone. “In addition to our three postgraduate students, about five or six of our researchers and technicians have been trained in molecular breeding and related areas, mostly at ICRISAT in India ,” reports Fikre. And that is not all: “We have also benefited from infrastructure improvements, including construction of a rainout shelter for our drought trials and coldrooms for seed preservation. A glasshouse will also be built for trials under controlled conditions.”

Fikre further notes, “These facilities and staff development will make us more effective in achieving the objectives we have set in the project. In addition, because the infrastructure is shared with other colleagues not directly involved in the TLI project, it is also an indirect conduit for further cementing synergies and collaboration, even as we already have good synergies with the national programme’s breeding scheme.”

Fikre is keen to see the capacity building translate into a larger critical mass of breeders conversant with molecular breeding, as well as an increase in the information on chickpeas, an area in which students have been extremely instrumental in eriching. “We are all learning a lot from molecular technologies through TLI, and beyond that, how to actually apply these technologies in a breeding programme.”

VIDEO: Fikre discusses capacity-building with other TLI colleagues

What next?
Looking into the future, what are Fikre’s projections and aspirations regarding TLI Phase II? “It is now time to test the drought-tolerant breeding lines already processed and tested through MARS. We will be undertaking this testing over the next two to three years or so, to see what gains have been made towards improving chickpeas.”

This testing will be done through multilocation trials both in research stations as well as on farmers’ fields, and will include a parallel evaluation and validation by colleagues outside the project.

“By the end of TLI Phase II, our goal is to have varieties that will go to farmers’ fields that will make a clearly discernible difference,” concludes Fikre.

VIDEO: Involving farmers in selecting varieties – Fikre and other TLI colleagues

Related links

 

Chickpea research in Kenya – A boon for the fallow period

 Africa, Chickpeas, Crop breeding, Legumes  No Responses »
Jun 302012
 

“When we first started working on this project in mid-2007, our breeding programme was very weak,” says Paul Kimurto (pictured), Lead Scientist for chickpea research in the Tropical Legumes I (TLI) project, Kenya, and a lecturer in Crop Science at Egerton University.

“We have since accumulated a lot of germplasm, a chickpea reference set, and a mapping population, all of which have greatly boosted our breeding programme. From these, we have been able to select appropriate genotypes, and we obtained 400 breeding lines. None of this would have been directly possible without GCP’s support,” adds Paul. [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]

Due to their hardiness against drought, chickpeas have been steadily gaining popularity in Kenyan drylands – including the dry highlands – where they are grown as a ‘relay’ crop after wheat and maize harvests during the short rains, when the land would otherwise lie fallow. “Chickpeas have therefore increased food security and nutritional status of more than 27,000 households living in Baringo, Koibatek, Kerio Valley and Bomet Districts in Kenya, who frequently face hunger due to frequent crop failure of main staples such as maize and beans owing to climate change,” says Paul.

Chickpea adoption in these areas has increased due to close collaboration between GCP, ICRISAT and Egerton University through funding, training, resources and germplasm facilitated by GCP.

Exposure and capacity building
Through the project, various members of the Egerton research team have benefited from training in Europe, Africa and Asia on wide-ranging aspects of modern breeding, including data management. The learning resources that the team accesses through GCP are also shared widely and used as teaching materials and resources for faculty staff and postgraduate students not directly involved in the project.

“We have also benefitted from physical infrastructure such as a rain-shelter, irrigation system, laboratory equipment and a greenhouse. We didn’t have these, and probably couldn’t have had them, because all these are costly investments. This has greatly improved the efficiency of not only our research, but also our teaching,” says Paul. In addition, three postgraduate students are supported by GCP – two are pursuing PhDs and one a Masters, all using modern molecular breeding methods in their studies.

VIDEO: Paul discusses capacity building in Kenya, alongside other TLI colleagues


Community gains

Besides the university, capacity building has benefited the broader community: agricultural extension staff from the Ministry of Agriculture and from Koibatek Farmers Training Centre (one of the project’s research site), have been trained in various fields. The Centre manager attended a GCP course in Ghana tailored for research station staff (link below), as did an Egerton University technician.

In addition to aiding research trials, the irrigation system and weather station installed at Koibatek help with teaching and producing crop seed and planting materials as well as pasture for the community, since the Centre has a mandate to provide high-quality seed and livestock breeds to the community.

According to Beatrice Komen, a farmer in Koibatek, the irrigation system “has enabled the Agricultural Training Centre supply us with high-quality pasture and crop seeds for planting during the right time because Egerton University uses it to produce sufficient seed without having to rely on seasonal conditions.”

Paul adds, “The automated weather station is a first in the region.” The weather station also feeds regional data into the national meteorological database and is used for teaching by secondary schools in the community.

Going further, faster
Paul observes “With the direct funding we obtain through the project, we are able to expand into other areas of dryland research such as soil science and nitrogen fixation for chickpeas. Our efficiency has also increased: with the greenhouse and rainout shelter, we can now rapidly obtain generation crosses. And the irrigation system means we can now do off-season trials without having to wait for seasonal changes.”

“We have learnt a lot through our involvement with the Programme, including outsourcing of genotyping services which GCP fully supports, the advanced tools and wide range of services offered by the Integrated Breeding Platform for both breeding and data management,” says Paul. “We have also received digital tablet for electronic field data collection in a more efficient and accurate manner compared to the traditional pen and paper.”

The goal
“Our goal is to apply the modern breeding methods we have learnt to release new improved drought- and disease-resistant varieties before the project closes in mid-2014.” Some of these new methods include using quantitative trait loci (QTLs) through marker-assisted selection (MAS) and marker-assisted backcrossing (MABC).

“The results we obtain will provide foundation seed that can then be used for mass production through the Tropical Legumes II project,” says Paul.

“Our task is not complete until we have improved varieties in the hands of farmers,” he concludes.

VIDEO on farmer participation, and the relevance of genomics – Paul and TLI colleagues

Related links

Chickpea research in India – Getting to the root of the matter to enhance drought tolerance

 Asia, Chickpeas, Crop breeding, Legumes  No Responses »
Jun 272012
 

India is the world’s largest producer and consumer of chickpea, accounting for more than a third (66 percent) of world production.

The Indian Agricultural Research Institute (IARI) and the Indian Institute of Pulses Research (IIPR) are collaborating with the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) on marker-assisted backcrossing (MABC), to improve chickpeas for drought tolerance.

This complementary activity in the Tropical Legumes I project (TLI) Phase II is being funded by the Department of Biotechnology, Government of India.

Dr N Nadrajan (pictured left), IIPR Director, adds “We have been trained on the breeding tools offered by the Integrated Breeding Platform, including data management, and on electronic data collection using a handheld device.”

Shailesh Tripathi (pictured right) is a Senior Scientist working on chickpea breeding at IARI. “During Phase I of TLI, ICRISAT and its partners identified a root-trait QTL region which confers drought tolerance in chickpeas, and the markers by which to transfer this QTL region. By evaluating the chickpea reference set, ICRISAT and its partners in Africa identified about 40 lines for drought tolerance, and these lines are being used in Phase II of the project,” says Shailesh. [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]

“Through GCP, we have benefitted from training in molecular breeding. The benefits of this go beyond this project,” he adds.

The Indian scientists are using MABC as well as marker-assisted recurrent selection (MARS) in Phase II, applying genomic resources that came from Phase I of the project.

“Our goal is to obtain lines with good root traits for drought tolerance,” says Shailesh, realistically adding that “Variety release will take time, but the good news is that we already have the pre-release materials to identify donors for specific traits, like root biomass.”

Progress in chickpea research in Africa and Asia

Related links

Chickpeas: Toughening a tough crop for tougher times by healing its Achilles’ heel

 Africa, Chickpeas, Crop breeding, Legumes  No Responses »
Jun 262012
 

It’s all about water and weakness – or strength. The Greek legend has it that Achilles was dipped into River Styx by his mother, Thetis, in order to make him invulnerable. His heel wasn’t covered by the water and he later died of the wound from an arrow that struck his heel.

In our times, this analogy can be applied to chickpeas, where this streetwise tough customer in the crop kingdom that thrives on the most rugged terrains is hamstrung if there is no rain at the critical grain-filling period – its sole Achilles’ heel, when it cannot take the searing heat in the drylands it otherwise thrives in.

But before you read on about the latter-day borrowing of this ancient legend, and science’s quest to heal the hit from heat and to cure the crop’s fatal flaw on water, first, an important aside…

Who’s now calling the shots in chickpea research?

Molecular breeding in Phase I was led by ICRISAT, with country partners in a supporting role. In Phase II, activities are being led by country partners, which also assures sustainability and continuity of the work. ICRISAT is now in a facilitating role, providing training and data, while the research work is now in the hands of country partners.” – Pooran Gaur, Principal Scientist: Chickpea Breeding,  ICRISAT.

The facts
Chickpeas are an ancient crop that was first domesticated in central and western Asia. Today, this crop is cultivated in 40 countries and is second only to common beans as the food legume most widely grown by smallholders. The two main types of chickpeas – desi and kabuli – are valuable for both subsistence and cash.

Even for the hardy, times are tough
“Chickpeas are well-known to be drought-tolerant,” says Rajeev K Varshney, Principal Investigator of the project to improve chickpeas work in the Tropical Legumes I Project (TLI). He explains, “The plants are very efficient in using water and possess roots that seek out residual moisture in deeper soil layers.” However, he points out that, with changing climatic conditions, especially in drier areas, terminal drought – when rain does not fall during grain-filling – is the crop’s Achilles’ heel, and principal production constraint.

“Chickpeas are such tough plants that, even for conditions of terminal drought, yields can be increased by improving root characteristics and water-use efficiency,” says Rajeev. The research team has identified several lines with superior traits such as drought tolerance, after screening a set of 300 diverse lines selected based on molecular diversity of large germplasm collections.

VIDEO CLIP: Recipe for chickpea success

Enhancing the genetic makeup to beat the heat
The team went on to develop genomic resources such as molecular markers. With these markers, the team developed a high-density genetic map, and identified a genomic region containing several quantitative trait loci (QTLs), conferring drought tolerance. “QTLs help pinpoint, more specifically, the location of genes that govern particular traits like root length” explains Rajeev.

Longer roots will naturally give the plants a deeper reach into the water table. Root length is the difference between survival and perishing, which is why trees will be left standing on a landscape otherwise laid bare by prolonged drought.

Q for ‘quick’: QTLs speed things along from lab to field, and running with the winners
The discovery of QTLs makes identifying tolerant plants not only easier, but also cheaper and faster. “This means that better-adapted varieties will reach farmers faster, improving food security,” says Rajeev.

Pooran Gaur, GCP’s Product Delivery Coordinator for chickpeas, Principal Scientist for Chickpea Breeding at ICRISAT, and an important collaborator on the TLI project, adds, “We began marker-assisted selection backcrossing (MABC) in Phase I. By 2011, lines were already being evaluated in Ethiopia, India and Kenya. We are now at the stage of singling out the most promising lines.”

Putting chickpeas to the test: Rajeev Varshney (left) and Pooran Gaur (right) inspecting a chickpea field trial.

What was achieved in Phase I, and what outcomes are expected?
Phase I run from mid-2007 to mid-2010, during which time 10 superior lines for improved drought tolerance and insect resistance were identified for Ethiopia, Kenya and India. As well, a total of 1,600 SSR markers and 768 SNPs on GoldenGate assays were developed, along with an expanded DArT array with more than 15,000 features. A high-density reference genetic map and two intraspecific genetic maps were developed.

“We now have materials from marker-assisted backcrossing by using the genomic resources we produced in Phase I. These materials were sent to partners last year [2011]. And because in most cases we have the same people working in TLI as in TLII, this material is being simultaneously evaluated across six to seven locations by all TLI and TLII partners,” says Pooran.

“Preliminary analysis of data is quite encouraging and it seems that we will have drought-tolerant lines soon,” adds Rajeev.

Future work, and who’s now calling the shots in the field
In Phase II, 1,500 SNPs on cost-effective KASPar assays have been developed that have been useful to develop a denser genetic map. In collaboration with University of California–Davis (USA) and the National Institute of Plant Genome Research (India), a physical map has been developed that will help to isolate the genes underlying the QTL region for drought tolerance. A novel molecular breeding approach called marker-assisted recurrent selection (MARS) has been adopted. Over the remaining two years of Phase II, the chickpea work will focus on developing chickpea populations with superior genotypes for drought tolerance through MABC and MARS.

Pooran adds, “Molecular breeding in Phase I was led by ICRISAT, with country partners in a supporting role. In Phase II, activities are being led by country partners, which also assures sustainability and continuity of the work. ICRISAT is now in a facilitating role, providing training and data, while the MABC and MARS aspects are both in the hands of country partners.”

“Another important activity in Phase II is development of multi-parents advanced generation intercross (MAGIC) population that will help generation of genetic populations with enhanced genetic diversity,” says Rajeev.

Partnerships
The chickpea work is led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), working with partners at the Ethiopian Institute of Agricultural Research, Egerton University in Kenya, and the Indian Agricultural Research Institute. Additional collaborators in Phase I included the University of California–Davis (USA), the National Center for Genome Resources (USA) and DArT P/L (Australia).

For more information on the overall work in chickpeas, please contact Rajeev K Varshney, Principal Investigator of the chickpea work.

Video: Featuring Rajeev and partners Fikre Asnake (Ethiopia) and Paul Kimurto (Kenya)

Related links

 

 

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

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

Beyond chickpeas to embrace beans, chickpeas, groundnuts and pigeonpeas

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

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

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

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

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

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

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

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

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

Inspecting maturity, Koibatek FTC, Bomet_R Mulwa_Sep'12_w

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Links

 

Thank you from GCP, and fare thee well

 Closing GCP  No Responses »
Dec 312014
 

sunset-taskforce-130Our sunset is finally here: the Generation Challenge Programme officially closes today, Wednesday the 31st of December 2014. It is with great sadness, but with even more joy and pride, that we say our farewells, look back on all that GCP has achieved in its decade of existence, and look forward to GCP’s legacy to the researchers, farmers and hungry consumers of the future.

As GCP reaches its end, we would very much like to thank all those who have been part of the GCP journey, whether as active participants or simply cheering us on. This card is for you, with our heartfelt gratitude (and please keep reading, as we have more to say below!).

thank you from gcp

The GCP family is both mighty and numerous, and we cannot hope to name all those whose invaluable contributions have helped make GCP what it is.

First and foremost, we thank the Product Delivery Coordinators past and present who have provided essential leadership and vision to each of our Research Initiatives, and the Principal Investigators who have shepherded each of GCP’s projects – sometimes through green pastures and sometimes along stony paths – to their triumphant conclusions. Our sincere thanks also go to all the hundreds of researchers who have worked with them, and whose efforts have been instrumental in the results and impacts that GCP has achieved.

A body is nothing without its head, and so we offer our profound thanks to the members of our Executive Board, and its predecessor the Programme Steering Committee. Defying anatomy, they have furnished GCP with not only brains but also a heart and firm hands to steer the GCP ship deftly on its course. We further thank all the members of the Consortium Committee, the Intellectual Property Advisory Committee, the now defunct Review and Advisory Panel and Programme Advisory Committee, and the Integrated Breeding Platform’s Scientific and Management Advisory Committee, for their indispensable advice and guidance. (See our current governance and advisory bodies)

We are deeply grateful to all of our funders, whose steadfast faith in GCP enabled this remarkable decade of collaboration and discovery. And last but not least, we thank all of GCP’s staff, both past and present, as well as consultants and others who have worked with us, for their incredible hard work, loyalty and habitual miracle-working.

We would also like to offer a special and thankful mention to our esteemed 3,000-plus readers of GCP News who have faithfully stayed with us through the years, as well as our friends, fans and followers on all our social-media accounts (see them all along the top and bottom of our website).

Together, we have created something remarkable (as our external reviews attest), and none of us will continue in our lives untouched by the GCP spirit. To all those listed above, and to all our other friends who have collaborated, contributed and cheered us on our way – THANK YOU!

Sunset_PPT

Just as it would be impossible to name each and every person who has been part of GCP, we also could not possibly list all the ways in which GCP will live on. GCP’s legacy takes many forms: new crop varieties for farmers, scientific knowledge, relationships between researchers, both young and senior scientists trained in the latest tools and techniques, new ways of working together… we could go on and on!

However, there are a few things we would particularly like to mention. The Integrated Breeding Platform (IBP) is one of GCP’s most important offspring, and in many ways its heir. IBP is a one-stop shop for both conventional and molecular breeding activities, making the latest tools and knowledge available to breeders across the world. Its Breeding Management System (BMS) offers a suite of interconnected software designed to help breeders manage their day-to-day work at all stages of the routine breeding process. IBP has also taken over the hosting of certain GCP activities, such as the crop-specific communities of practice fostered by GCP, so that these will continue to go from strength to strength.

Many other GCP projects are also continuing in new phases and forms – their success at securing funding from new sources a validation of their accomplishments so far. For example, Tropical Legumes I and II projects, respectively led by GCP and ICRISAT, will be merging into a new incarnation, Tropical Legumes III, to be led by ICRISAT. In general, the work in GCP’s key Phase II crops – cassava, legumes (beans, chickpeas, cowpeas and groundnuts), maize, rice, sorghum and wheat – will continue under the umbrellas of the CGIAR Research Programmes, as we had hoped and envisaged in our 2010 Transition Strategy.

Meanwhile, you can expect a few final news posts from us in the New Year, as we wrap up the Programme and its communications. It’s our pleasure to announce that, thanks to your demonstrated interest, the GCP website will continue to be online (albeit as an archive), so you will still be able to call in for any GCP information you need – or purely for nostalgia. And we will continue to publish our collection of closing stories on our Sunset Blog, so keep visiting for upbeat and comprehensive journeys through GCP’s achievements, including how GCP has done things differently, our impacts, what we have learnt, and how these will carry on into the future.

Finally, we have one more special thank you to give: to our GCP artists Durga Bernhard and Rhoda Okono, to CIMMYT designers Miguel Mellado, Marcelo Ortiz and Eliot Sánchez for incorporating their beautiful artworks into so many gorgeous designs over the years, and to our web developer and designer Brandon Tooke for stunning concepts. Without Rhoda and Durga to give us our signature look, GCP would hardly be so colourful or distinctive. If you enjoyed the glimpses of their paintings in the thank you card above, why not sample the full works in our online galleries? The first exhibit is fittingly a ‘decoding’ of the lovely logo that Marcelo designed for us in 2004, and the sunset twist Brandon has added to it since (see below).

On that joyful artistic note, from us here at GCP, fare thee well, thank you, and long live the GCP spirit!

gcp-logo-sunset_small

P.S. Hold on! We’re not done just yet with our roll of honour. Please step forward, Vincent Vadez, groundnut researcher, for giving substance, form and name to that which most of us felt and loved, but could not put a name to – the GCP spirit. Here’s what Vincent said in a survey response in September 2011: “I feel that GCP is not a consortium, or an institution. It is a spirit.” And thus, a handy and legendary moniker was born, that served us well in the years that followed, and that will hopefully live on into the future. Thank you Vincent for that down-to-earth gem of groundtruth from our main groundnut researcher!

 Posted by at 4:12 pm

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

 Africa, Genetics, Genomics, Groundnuts, Legumes  2 Responses »
Mar 312014
 
Vincent Vadez

Vincent Vadez

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

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

In Africa, groundnuts are typically cultivated in moderate rainfall areas across the continent, usually by women.

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

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

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

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

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

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

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

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

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

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

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

Groundnut flower

Groundnut flower

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

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

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

Freshly dug-up groundnuts.

Freshly dug-up groundnuts.

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

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

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

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

Youngster bearing fresh groundnuts along River Gambia in Senegal.

Youngster bearing fresh groundnuts along River Gambia in Senegal.

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

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

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

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

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

Groundnut drawing

Groundnut drawing

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

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

Links

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

California’s ‘Constant Gardener’, cowpea crusader and catapult constructor

 Africa, Capacity building, Cowpeas, Genetics, Genomics, Legumes, Researchers  2 Responses »
Mar 202014
 

 

Jeff Ehlers

Jeff Ehlers

Our guest today is Jeff Ehlers (pictured), Programme Officer at the Bill & Melinda Gates Foundation. Jeff’s an old friend of GCP, most familiar to the GCP community in his immediate past stomping grounds at the University of California, Riverside (UCR), USA, leading our research to improve cowpea production in the tropics, for which sunny California offers a perfect spot for effective phenotyping. Even then, Jeff was not new to CGIAR, as we’ll see from his career crossings. But let’s not get ahead of ourselves in narrating Jeff’s tale. First, what would high-end cowpea research have to do with crusading and catapults? Only Jeff can tell us, so please do read on!

The GCP model was a very important way of doing business for CGIAR and the broader development community, enabling partnerships between international research institutes, country programmes and CGIAR. This is particularly important as the possibilities of genomics-led breeding become even greater…If anything, we need to see more of this collaborative model.”

Growing green, sowing the seed, trading glory for grassroots
Growing up in USA’s Golden State of California, green-fingered Jeff had a passion for cultivating the land rather than laboratory samples, harbouring keen ambitions to become a farmer. This did not change with the years as he transited from childhood to adolescence. The child grew into a youth who was an avid gardener: in his student days, Jeff threw his energy into creating a community garden project ‒ an initiative which promptly caught the eye of his high school counsellor, who suggested Jeff give the Plant Science Department at UCR a go for undergraduate studies.

And thus the seeds of a positively blooming career in crop research were sown. However, remaining true to the mission inspired by his former community-centred stomping grounds, a grassroots focus triumphed over glory-hunting for Jeff, who – no stranger to rolling his sleeves up and getting his fingers into the sod – found himself, when at the University of California, Davis, for his advanced studies, embarking on what was to become a lifelong undertaking, first at the International Institute of Tropical Agriculture (IITA) and then at UCR, dedicated to a then under-invested plant species straggler threatening to fall by the research world’s wayside. With a plethora of potential genomic resources and modern breeding tools yet to be tapped into, Jeff’s cowpea crusade had begun in earnest…

GCP’s TLI was essential in opening that door and putting us on the path to increased capability – both for cowpea research enablement and human capacity”

Straggler no more: stardom beckons, and a place at the table for the ‘orphan’
And waiting in the wings to help Jeff along his chosen path was the Generation Challenge Programme (GCP), which, in 2007, commissioned Jeff’s team to tackle the cowpea component of the flagship Tropical Legumes I (TLI) project, implemented by GCP under the Legumes Research Initiative. TLI is mainly funded by the Bill & Melinda Gates Foundation. The significance of this project, Jeff explains, was considerable: “The investment came at a very opportune time, and demonstrated great foresight on the part of both GCP and the Foundation.” Prior to this initiative, he further explains, “there had been no investment by anyone else to allow these orphan crops to participate in the feast of technologies and tools suddenly available and that other major crops were aggressively getting into. Before GCP and Gates funding for TLI came along, it was impossible to think about doing any kind of modern breeding in the orphan grain legume crops. GCP’s TLI was essential in opening that door and putting us on the path to increased capability – both for cowpea research enablement and human capacity.”

Flashback: UCR cowpea team in 2009. Left to right: Wellington Muchero, Ndeye Ndack Diop (familiar, right?!), Raymond Fenton, Jeff Ehlers, Philip Roberts and Timothy Close in a greenhouse on the UCR campus, with cowpeas in the background. Ndeye Ndack and Jeff seem to love upstaging each other. She came to UCR as a postdoc working under Jeff, then she moved to GCP, with oversight over the TLI project, thereby becoming Jeff's boss, then he moved to the Foundation with oversight over TLI. So, what do you think might be our Ndeye Ndack's next stop once GCP winds up in 2014? One can reasonably speculate....!

Flashback: UCR cowpea team in 2009. Left to right: Wellington Muchero, Ndeye Ndack Diop (familiar, right?!), Raymond Fenton, Jeff Ehlers, Philip Roberts and Timothy Close in a greenhouse on the UCR campus, with cowpeas in the background. Ndeye Ndack and Jeff seem to love upstaging each other. She came to UCR as a postdoc working under Jeff, then she moved to GCP, with oversight over the TLI project, thereby becoming Jeff’s boss, then he moved to the Foundation with oversight over TLI. So, what do you think might be our Ndeye Ndack’s next stop once GCP winds up in 2014? One can reasonably speculate….!

Of capacity building, genomics and ‘X-ray’ eyes
This capacity-building cornerstone – which, in the case of the TLI project, is mainly funded by the European Commission – is, says Jeff, a crucial key to unlocking the potential of plant science globally. “The next generation of crop scientists ‒ particularly breeders ‒ need to be educated in the area of genomics and genomics-led breeding.”

While stressing the need for robust conventional breeding efforts, Jeff continues: ”Genomics gives the breeder X-ray eyes into the breeding programme, bringing new insights and precision that were previously unavailable.”

In this regard, Jeff has played a leading role in supporting skill development and organising training for his team members and colleagues across sub-Saharan Africa, meaning that partners from Mozambique, Burkina Faso and Senegal, among others, are now, in Phase II of the TLI project, moving full steam ahead with marker-assisted and backcross legume breeding at national level, thanks to the genotyping platform and genetic fingerprints from Phase I of the project. The genotyping platform, which is now publicly available to anyone looking to undertake marker-assisted breeding for cowpeas, is being widely used by research teams not only in Africa but also in China. Thanks in part then to Jeff and his team, the wheels of the genomics revolution for cowpeas are well and truly in motion.

Undergoing the transition from phenotypic old-school plant breeder to modern breeder with all the skills required was a struggle…it was challenging to teach others the tools when I didn’t know them myself!…without GCP, I would not have been able to grow in this way.”

Talking about a revolution, comrades-in-arms, and a master mastering some more
But as would be expected, the road to revolution has not always been entirely smooth. Reflecting on some of the challenges he encountered in the early TLI days, and highlighting the need to invest not only in new students, but also in upgrading the existing skills of older scientists, Jeff tells of a personal frustration that had him battling it out alongside the best of them: “Undergoing the transition from phenotypic old-school plant breeder to modern breeder with all the skills required was a struggle,” he confides, continuing: “It was challenging to teach others the tools when I didn’t know them myself!”

Thus, in collaboration with his cowpea comrades from the global North and South, Jeff braved the steep learning curve before him, and came out on the other side smiling – an accomplishment he is quick to credit to GCP: “It was a very interesting and fruitful experience, and without GCP, I would not have been able to grow in this way,” he reveals. Holding the collaborative efforts facilitated by the broad GCP network particularly dear, Jeff continues: “The GCP model was a very important way of doing business for CGIAR and the broader development community, enabling partnerships between international research institutes, country programmes and CGIAR. This is particularly important as the possibilities of genomics-led breeding become even greater…If anything, we need to see more of this collaborative model.”

GCP’s Integrated Breeding Platform addresses the lack of modern breeding skills in the breeding community as a whole, globally…The Platform provides extremely valuable and much-needed resources for many public peers around the world, especially in Africa…”

One initiative which has proved especially useful in giving researchers a leg up in the mastery of modern breeding tools, Jeff asserts, is GCP’s Integrated Breeding Platform (IBP): “IBP addresses the lack of modern breeding skills in the breeding community as a whole, globally. By providing training in the use of genomic tools that are becoming available, from electronic capture of data through to genotyping, phenotyping, and all the way to selective decision-making and analysis of results, IBP will play a critical role in helping folks to leverage on the genomics revolution that’s currently unfolding,” Jeff enthuses, expanding: “The Platform provides extremely valuable and much-needed resources for many public peers around the world, especially in Africa where such one-off tools that are available commercially would be otherwise out of reach.”

Conqueror caparisoned to catapult: life on the fast lane and aiming higher
Well-versed in conquering the seemingly unobtainable, Jeff shares some pearls of wisdom for young budding crop scientists:”Be motivated by the mission, and the ideas and the science, and not by what’s easy, or by what brings you the most immediate gratification,” he advises, going on to explain: “Cowpeas have been through some really tough times. Yet, my partners and I stuck it out, remained dedicated and kept working.” And the proof of Jeff’s persistence is very much in the pudding, with his team at UCR having become widely acclaimed for their success in catapulting cowpeas into the fast lane of crop research.

It was a success that led him to the hallways of the Bill & Melinda Gates Foundation, where, after two decades at UCR, Jeff is currently broadening his legume love affair to also embrace beans, groundnuts, chickpeas, pigeonpeas and soya beans.

February 2014: Jeff donning his new Gates hat (albeit with a literal ICRISAT cap on). Behind him is a field of early maturing pigeonpea experiment at ICRISAT India.

February 2014: Jeff donning his (now-not-so-)new Gates hat and on the road, visiting ICRISAT in India. Behind him is an ICRISAT experimental field of early-maturing pigeonpeas. Here, our conquering crusader is ‘helmeted’ in an ICRISAT cap, even if not horsed and caparisoned for this ‘peacetime’ pigeonpea mission!

On his future professional aspirations, he says: “The funding cut-backs for agriculture which started before 1990 or so gutted a lot of the capacity in the public sector, both in the national programmes in Africa but also beyond. I hope to play a role in rebuilding some of the capacity to ensure that people take full advantage of the technical resources available, and to enable breeding programmes to function at a higher level than they do now.”

Jeff (foreground) inspecting soya bean trials in Kakamega, Kenya.

Jeff (foreground) inspecting soya bean trials in Kakamega, Kenya, in January 2013. Next to Jeff is Emmanuel Monyo, the coordinator of the Tropical Legumes II (TLII) project – TLI’s twin – whose brief is seed multiplication. TLII is therefore responsible for translating research outputs from TLI into tangible products in the form of improved legume varieties.

Whilst it’s been several years since he donned his wellington boots for the gardening project of his youth, what’s clear in this closing statement is an unremitting and deeply ingrained sense of community spirit – albeit with a global outlook – and a fight for the greater good that remain at the core of Jeff’s professional philosophy today.

No doubt, our cowpea champion and his colleagues have come a long way, with foundations now firmly laid for modern breeding in the crop on a global scale, and – thanks to channels now being established to achieve the same for close relatives of the species – all signs indicate that the best is yet to come!

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A grand gathering: General Research Meeting (GRM) 2013

 Closing GCP, Crop breeding, Events  No Responses »
Nov 122013
 

 

 

Participants at the 2013 GRM. High-resolution version on Flickr: http://bit.ly/1fxhkmQ

Participants at the 2013 GRM. High-resolution version on our Flickr account.

The General Research Meeting (GRM) is by far the largest and most important event on our calendar. This year’s GRM was held on September 27‒30 2013, with 135 people from 35 countries attending (see list).

Various presentations were made on progress and next steps on research in GCP projects, including for GCP’s Integrated Breeding Platform (IBP). Focus was on GCP’s nine focus crops in Phase II – beans, cassava, chickpeas, cowpeas, groundnuts, maize, rice, sorghum and wheat, with the poster sessions adding a couple more (see ‘sixty posters’ below). You can view the presentations made on our website  (to see them in the context of the overall agenda), or on SlideShare (all gathered in one place).  We have uploaded all but one presentation, where we’re still waiting for the presenter’s permission to publish. A comprehensive update on all GCP projects is here (PDF). The meeting was a blend of plenary sessions on core topics and research updates, and ‘drill-down’ breakouts on crops, data management and capacity building (the last two, in the context of IBP’s proposed Phase II, which had its own dedicated one-day stakeholder meeting after GRM, on 1st October).DSC07162_w

Social were we…but we also did some heavy lifting
We didn’t just talk to ourselves: we made a bit of noise on social media to also bring in other voices into the GRM discourse and chit-chat, using the hashtag #GRM13, creating a good buzz of conversations. Also linking in to GRM were our LinkedIn followers. And neither was it all business, science and rigid structure: there was free-flow too, with an open afternoon where participants could take a relaxing break, organise their own meetings, or take a tour to Lisbon. Some of the scenes from the tour are posted on Flickr, as are other snapshots from the meeting. We’ve since gathered up some of the social media posts on Storify.

GRM was far from its grim-sounding  abbreviation and hashtag on social media:  exemplifying the best of the ‘GCP spirit’,  the sessions were engaging, relaxed, conversational and spiced with humour and a light touch, despite the ‘heavy’ topics under discussion (see agenda). But the topic at hand was grim, since the situation is dire – drought affects almost all crops and all regions worldwide. As drought tolerance is our key focus since inception, most of the discussions naturally centred on this topic. Equally important is the scourge wrought by pests and disease, which afflict some crops more than others. For example, under most circumstance, cassava is naturally very drought-tolerant, but what good will this do if cassava survives drought only to succumb to the deadly pests and diseases that stalk this drought champion?

Sunset and ‘moon-rise’
GRM was also a time for both stocktaking and mapping the future  given GCP’s sunset in 2014.  A central and recurring theme was GCP’s transition strategy, and how – and where – to embed GCP-initiated projects that will extend beyond the Programme’s lifetime. For this, the CGIAR Research Programs (CRPs) are a natural first choice. GRM enjoyed a very good representation of the CRPs, with all six crop CRPs represented, some at the highest level.

A few members of our Executive Board also attended. Board Chair, Andrew Bennett, set the right tone for the meeting. In his remarks at the opening session, he emphasised that this was not a time for sadness, swan songs and moping as GCP approaches sunset.  Rather, it was a time to appreciate the beauty of sunsets, in the sure knowledge that sunsets give rise to  moon-rise!

A section of Poster Session II presenters. IN the foreground, Andrew Bennett, Chair, GCP Excecutive Board.

A section of Poster Session II presenters. In the foreground, Andrew Bennett, Chair, GCP Executive Board.

“Say it succinctly in sixty seconds!”
The poster session was as lively as always, with a record of… (hold your breath!) 60 posters presented, surpassing the previous GRM in 2011 which attracted 53 posters.

Perfection!  Sixty posters for sixty seconds
Sixty was a PERFECT number for the 60-second sizzle, where each poster presenter had a maximum of 60 seconds (and not a second more!) to present at plenary, devising whichever means necessary to attract the audience to their poster. It was easy to discern the brash ‘old hands’ who had perfected their art after several GRMs; the tricksters and various reincarnations of The Artful Dodger amongst them, trying to beat the clock; new and slightly jittery presenters who were more than just a little bewildered but still proved their mettle; and the new, sassy and confident. This beautiful blend apart, the poster session brought in not only new faces to add to the familiar ones, but also refreshing new tastes to diversify and sweeten our Staple of Nine crops. To our diet of cereals, legumes and tubers, poster presenters from The Philippines added eggplants, rounded off with bananas for dessert.

"Definitely time for dessert, and do not disturb!" they seem to be saying. Jean-Christophe Glaszmann (left) and Hei Leung (right), who played ace roles on a multi-partner GCP project on bananas.

“Definitely time for dessert, and do not disturb!” they seem to be saying. Jean-Christophe Glaszmann (left) and Hei Leung (right), who played ace roles on a multi-partner GCP project on bananas.

♫ Welcome to the Hotel California! ♫…
As always, GRM was a mingling of old and new friends, a time for some paths to meet and for new forks to branch out, a season to reflectively look back and progressively face forwards. In keeping with Andrew’s continuity of sunsets giving way to moonrise, we said a group goodbye to Rajeev Varshney, former Genomics Theme Leader, who left the GCP Management Team in August. And we were happy to once again welcome, embrace and recognise two old friends – Jean Christophe Glaszmann (CIRAD) and Hei Leung (IRRI), who were, respectively ex-Subprogramme Leaders for genetic diversity and genomics in GCP Phase I, and continue to be involved with GCP as researchers, as will Rajeev.

In this picture, we caught up with them at a very appropriate moment: dessert during the Gala Dinner. Take it from us, these two guys are well versed in matters dessert, with a dash of science, as this blast from the past on bananas attests, also summarised in a Facebook photo-story here.

We are indeed a Hotel California of sorts – always open for check-in and checkout. As for leaving…we’re still working on the modalities of that!

And despite the fond farewell, truth is Rajeev is not going anywhere either, as far as GCP is concerned. You only needed to have been at GRM or following the conversations on Facebook and Twitter, especially the photos, to witness this. He was (delightfully!) all over the place, passing on his ‘positive epidemic’ of highly infectious enthusiasm and incredible energy. Here he is in action at the Gala Dinner in the photos below, which really need no caption. We’re sure you’ll be able to easily spot Rajeev, ‘high-fivin’ and ‘rapping’, eclipsing the GCP Director, who however appears quite pleased in his lower perch with Rajeev on the platform. But if you’re truly lost and can’t spot the super-charged high-energy guy in the photos, no worries! Here are some handy clues.

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In distinguished company
Rajeev’s energy goes beyond GRM and GCP; this year as in previous ones, he received several awards, among them, the Young Crop Scientist Award by Crop Science Society of America, and the Illumina Agriculture Greater Good Initiative Award.

Hari Upadhyaya

Hari Upadhyaya

Prior to these recognitions during the Gala Dinner, Jean-Marcel formally honoured ICRISAT’s Hari Upadhyaya (pictured) during plenary for two awards Hari had received in the course of the year, also from the Crop Science Society of America. These awards were for Hari’s notable contributions – at international level – to crop science, and to plant genetic resources.

Hari is a long-term GCP Principal Investigator, working primarily on sorghum. But that is not the only crop he works on. Hari was the lead author of the joint chickpea and pigeonpea chapter in our book on drought phenotyping.

Evaluation
Unlike other GRMs where we’ve requested participants to evaluate the meeting, we did not do so this year, since this is very likely the last meeting of its kind, and the goal of the evaluation is to use participant feedback to improve future meetings. With the help of our participants, we’ve applied the lessons we’ve learnt from them through the years to arrive at what we believe to be a winning combination, balancing the diverse interests of our participants for overall improvement of their GRM experience.

 

 

 

 

 

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