Generation Challenge Programme
GCP website		Integrated Breeding
IBP website		Sunset Blog
Sunset blog		   Connect with us GCP on Facebook GCP on Twitter GCP on LinkedIn Subscribe to GCP Newsletter Subscribe to GCP RSS feeds

Rooting for the key to more phosphorus for rice

 Comparative genomics in cereals, Crop breeding, Genetics, Genomics, Rice  3 Responses »
Sep 072012
 

Preparing rice root samples (Photo: IRRI)ALL IN THE ROOTS: A plant’s roots are a marvellously multitalented organ. They act as fingers and mouths helping plants forage and absorb water and nutrients. They act like arms and legs offering a sturdy base of support so a plant doesn’t keel over. They help store food and water, like our stomach and fat cells. And in some plants, can spawn new life – we leave that to your imagination!

That is why it is of little surprise that this multitalented organ was the key to discovering why some rice lines yield better in phosphorus-poor soils, a puzzle whose answer has eluded farmers and researchers… until now.  And even better, the findings hold promise for sorghum, maize and wheat too. Please read on!

 In search of the key – The Gene Trackers
In 1999, Dr Matthias Wissuwa, now with the Japan International Research Centre for Agricultural Sciences (JIRCAS), deduced that Kasalath, a northern Indian rice variety, contained one or more genes that allowed it to grow successfully in low-phosphorus conditions.

For years, Matthias made it his mission to find these genes, only to find it was as easy as finding a needle in a genetic haystack. He teamed up with the International Rice Research Institute (IRRI), and with GCP’s support, the gene trackers were able to narrow the search down to five genes of interest.

“We had started with 68 genes and within three years, we had narrowed in on these five candidate genes. And then, one-by-one, we checked whether they were related to phosphorous uptake,” recollects Dr Sigrid Heuer, senior scientist at IRRI and leader of the team that published the discovery in Nature in August 2012.

Sigrid Heuer at a rice phosphorus uptake demonstration field in The Philippines.

“In the end we found that if a certain protein kinase gene was turned on in tolerant plants like Kasalath, then those plants would perform better in phosphorus-deficient soils.”

They named this protein kinase gene PSTOL1, which stands for Phosphorus Starvation Tolerance. “When we put this gene into intolerant rice varieties that did not have this gene, they performed better in phosphorus-deficient soils.”

The importance of phosphorus
Rice, like all plants, needs phosphorus to survive and thrive. It’s a key element in plant metabolism, root growth, maturity and yield. Plants deficient in phosphorus are often stunted.

Sigrid explains that whereas phosphorus is abundant in most soils, it is however not always easily accessible by plants. “Many soil types bond tightly to phosphorus, surrendering only a tiny amount to plant roots. This is why more than half of the world’s rice lands are phosphorus-deficient.”

Farmers can get around this by applying phosphate fertilisers. However this is a very expensive exercise and is not an option for the majority of the world’s rice growers, especially the poorer ones –the price of rock phosphate has more than doubled since 2007. The practice is also not sustainable since it is a finite resource.

By selecting for rice varieties with PSTOL1, growers will be less reliant on phosphate fertilisers.

How it works: unravelling PSTOL1 mechanics
In phosphorus-poor soils, PSTOL1 switches on during the early stage of root development. The gene tells the plant to grow larger longer roots, which are able to forage through more soil to absorb and store more nutrients.

“By having a larger root surface area, plants can explore a greater area in the soil and find more phosphorus than usual,” says Sigrid. “It’s like having a larger sponge to absorb more water.”

A rice variety — IR-74 — with Pup1 (left) and without Pup1 (right).

Although the researchers focussed on this one key nutrient, they found the extra root growth helped with other vital elements like nitrogen and potassium.

Another by-chance discovery was that phosphorus uptake 1 (Pup1), the collection of genes (locus) where PSTOL1 is found, is present within a large group of rice varieties.

“We found that in upland rice varieties – those bred for drought-prone environments – most have Pup1,” says Sigrid. “So the breeders in these regions have, without knowing it, been selecting for phosphorus tolerance.”

“When thinking about it, it makes sense as phosphorus is very immobile in dry soils, therefore these plants would have had to adapt to grow longer roots to reach water deeper in the soil and this, at the same time, helps to access more reservoirs of phosphorous .”

Breeding for phosphorus tolerance, and going beyond rice
Using conventional breeding methods, Sigrid says that her team introduced PSTOL1 into two irrigated rice varieties and three Indonesian upland varieties, and found that this increased yields by up to 20 percent.

“In our pot experiments,” she added, “when we use soil that is really low in phosphorus, we see yield increases of 60 percent and more. This will mean growers of upland rice varieties will probably benefit the most from these new lines, which is pleasing given they are among the poorest rice growers in the world.”

Read how Indonesian researchers are developing their own breeds of upland rice with the PSTOL1 gene

Sigrid also sheds light on broadening the research to other crop varieties: “The project team is currently looking at Pup1 in sorghum and maize and we are just about to start on wheat.”

Building capacity and ensuring impact
Like all GCP projects, this one invests as much time in building capacity for country breeding programmes as on research.

Sigrid and her team are currently conducting the first Pup1 workshop to train researchers from Bangladesh, India, Indonesia, Nepal, Philippines, Thailand and Vietnam. They will share molecular markers that indicate the presence of PSTOL1, techniques to select for the gene, as well as for new phosphorus-efficient varieties.

Breeding for phosphorus-efficient rice in the Philippines.

“The aim of these workshops is to take these important tools to where they are most needed and allow them to evolve according to the needs and requirements of each country,” says Dr Rajeev Varshney, GCP’s Comparative and Applied Genomics Leader. “Breeders will be able to breed new rice varieties faster and more easily, and with 100 percent certainty that their rice plants will have the gene. Within three to five years, each country will be able to breed varieties identical to those that growers know and trust except that they will now have the Pup1 gene and an improved ability to unlock and take up soil phosphorus.”

Joining hands in collaboration
This IRRI-led project was conducted in collaboration with JIRCAS and the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD) working with the Indonesian Centre for Rice Research. Other partners included: Italy’s University of Milano, Germany’s Max Planck Institute in Golm, the University of The Philippines at Los Baños, USA’s Cornell University and University of California (Davis and Riverside), Brazil’s EMBRAPA, Africa Rice Center, Iran’s Agricultural Biotechnology Research Institute, Australia’s Commonwealth Scientific and Industrial Research Organisation (CSIRO) and University of Dhaka in Bangladesh.

Links

Sigrid’s presentation at the GCP General Research Meeting 2011

GCP now, then, and after

 Closing GCP, GCP, History  No Responses »
Jul 032012
 

Where we’ve come from, where we are, and where we’re going

Travel with Dave from the beginning – and before the beginning – of GCP, and how the Programme will be brought to an orderly close. Dave also elaborates on the role of the Consortium Committee.

There’s no doubt that the Programme has enabled new partnerships and rekindled and rejuvenated old or existing partnerships amongst the different partners. Some of these are between the different CGIAR Centres and others are between these Centres and partners outside the CGIAR. These partnerships have been very fruitful.

People speak of GCP almost as if it were the 16th Centre. They speak of it with pride and respect. They understand the important role it can play.

GCP has a lot of credibility with national programmes. When you go to GCP’s General Research Meetings, there’s clearly a feeling of being part of the community, and that we are all improving our efficiency because of the Programme.

…I think it’s been one of the more successful Challenge Programmes.

Dave Hoisington (pictured)  is the Chair of GCP’s Consortium Committee, and currently ICRISAT’s Director of Research. Dave was previously with CIMMYT, GCP’s host Centre. He has therefore been involved with GCP “since day minus one” in his words. “It’s equally exciting to be involved in the Programme’s closure, because I think that is even more important with regard to keeping its legacy alive.” Dave now walks us through the workings of the Programme today, its achievements and challenges, and what the early formative years were like….

What is the role of the GCP Consortium Committee?
GCP was set up as a multi-institutional endeavour. As an elaborate and broad partnership representing various interests, the decision at the Programme’s inception was to set up a committee representing all the key members from CGIAR Centres, developing-country programmes and advanced research institutes.

This Consortium Committee is ultimately the one that ‘owns’ GCP and oversees the basic functioning of the Programme to make sure that it is going in the right direction. We have an Executive Board which the Consortium appointed and it’s that Executive Board that Jean-Marcel [GCP Director] reports to. Because we set up the Board, they actually report to us.

…by having this Committee of the key players in research as well as an independent Board, we can all make sure GCP is going in the right direction, by giving voice to both the ‘players’ and ‘referees’.

Why have a Committee as well as a Board, and why seek broad partnerships?
During a mid-term review of GCP, the need for both a Committee and an independent Executive Board was recognised to give the Programme more structure and guidance. The Consortium Committee was established in 2008, and its precursor was the Programme Steering Committee.

GCP is not a research programme run by a single institute but really a consortium to enhance effectiveness. So, by having this Committee of the key players in research as well as an independent Board, we can all make sure GCP is going in the right direction, by giving voice to both the ‘players’ and ‘referees’.

There’s no doubt that the Programme has enabled new partnerships and rekindled and rejuvenated old or existing partnerships amongst the different partners. Some of these are between the different CGIAR Centres and others are between these Centres and partners outside the CGIAR. These partnerships have been very fruitful.

GCP’s tagline – ‘Partnerships in modern crop breeding for food security’ – what does this mean for you?
It really captures the essence of GCP – GCP is about creating opportunities for these partnerships. It’s about using a modern approach, a more integrated approach to breeding, to aid food security in the developing world.

Why is GCP’s work important?
The whole premise of setting up GCP 10 years ago was really the fact that our major crops were not registering the necessary increases in yield to meet food needs in developing countries. There are many reasons for that. The reason that became the main driving force for GCP was that we had not been able to tap the rich genetic diversity that exists for almost all of these crops. So the idea was to come up with mechanisms, methods, examples and proofs-of-concept that tap into this genetic diversity, and package it such that breeding programmes can integrate it into their operations. By so doing, we would broaden the horizon of breeding programmes for more rapid gains in yields and productivity in farmers’ fields.

Originally, the whole idea was mostly a proof-of-concept. Once we realised it could work, we realised that capacity needed to be built within national programmes since GCP’s scope was 10 years. So, the emphasis began to rightly shift from exploration and discovery to application and impact, buttressed by more training and capacity building within national programmes for sustainability. Genetic research was – and still remains – the backbone, but there has been a growing reliance on other tools including IT and molecular breeding. Now the technology has matured, costs have decreased, making it more viable for public research.

Unfortunately, we don’t have the alternative case of what it would have been like without GCP… but I think that many institutes within and outside CGIAR are trying to use genomics as a technology, and I think a lot of that can be traced back to projects that GCP supported.

What have been the major outcomes of GCP so far?
The greatest overall outcome is a stronger awareness and use of genomics in our research programmes across the board.

Unfortunately, we don’t have the alternative case of what it would have been like without GCP, which we could compare to, but I think that many institutes within and outside CGIAR are trying to use genomics as a technology, and I think a lot of that can be traced back to projects that GCP supported and encouraged.

In the early years, characterisation of genetic resources was very beneficial and it’s encouraging to see it still continues, with characterising genetic resources now considered routine.

What outcomes are you most looking forward to?
I think one of the most promising, and potentially important outcomes will be the adoption of GCP’s Integrating Breeding Platform.

‘Challenge’ is in GCP’s name. What are the major challenges that the Programme has so far overcome?
When GCP was being designed, there was no definition or case study for what a Challenge Programme had to do. The preliminary idea was that for projects to succeed and overcome major challenges, partnerships were key and no single institute could do it alone: they needed to do business differently, whether among the CGIAR Centres, or with partners outside the CGIAR. We had all these genebanks, all this diversity, genetic and genomic tools for some crops but not all crops. So, we put our heads together and asked ourselves, “What if we combine these modern molecular approaches used in one crop and apply them to another crop? Can we unlock the genetic diversity within it to improve quality and yield? How do we get all partners to work together towards a common goal?”

At the beginning, GCP had probably way too many facets and we were trying to move ahead on all the different fronts, so I think the mid-term reshaping and redefinition of the Programme helped it gain more focus to actually do what it set out to do.

GCP has built capacity, tools, methodologies and technologies. All these need to continue so as to increase and improve outputs and enhance outcomes.

What future challenges must the Programme overcome to remain sustainable?
Ensuring its achievements are sustained. While it was a time-bound programme from day one, the results and successes are not time-bound. They should be sustained and continued in other shapes and forms.

The challenge now is filtering these successes and figuring out how best to continue them. GCP has built capacity, tools, methodologies and technologies. All these need to continue so as to increase and improve outputs and enhance outcomes.

What are the main lessons learnt so far?
Partnerships are not easy. They take a lot of time. It’s one thing to write a proposal and say we will work together but it’s another thing to make that work effectively. I know GCP has had some instances where partners brought in have not been effective. I’m sure the GCP management has learnt lessons on how to deal with that.

People work together because they trust and respect one another and recognise and understand each other’s roles. They don’t view it as a competition. Some partnerships occur spontaneously, while others take time. They have to build trust, understanding and communication.

We’ve all learnt lessons from the research side, such as what does and doesn’t work. Focussing was a good lesson that GCP and all of us have learnt. At the beginning, we just spread ourselves too thin, trying to do too many things, making it very difficult to measure progress.

What is the most enjoyable aspect of your involvement with GCP?
I’ve been involved in GCP from day minus one. I used to be at CIMMYT and was involved in the ‘pre-pre-birth’ of the Programme, even before it had been conceptualised. Through the years since then, I’ve had different levels of engagement – and even periods of disengagement – but have always enjoyed my involvement.

It’s always been a good group of people working together, even when there have been problems. I think the Programme has scored high on successes. Jean-Marcel and his team deserve a lot of credit. They’ve really been able to keep the momentum going.

It’s equally exciting to be involved in the Programme’s closure, because I think that is even more important with regard to keeping its legacy alive.

People speak of GCP almost as if it were the 16th Centre. They speak of it with pride and respect. They understand the important role it can play.

GCP has a lot of credibility with national programmes… Ithink it’s been one of the more successful Challenge Programmes.

Jean-Marcel talks of the ‘GCP spirit’ and how successful partners share this spirit. What are your thoughts on this?
GCP definitely has a strong ‘entity’, although I’m not sure if this is a spirit! People speak of GCP almost as if it were the 16th Centre. They speak of it with pride and respect. They understand the important role it can play.

GCP has a lot of credibility with national programmes. When you go to GCP’s General Research Meetings, there’s clearly a feeling of being part of the community, and that we are all improving our efficiency because of the Programme.

I think it’s been one of the more successful Challenge Programmes.

Relevant 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

 

 

Hitting the nail on the head: A nuts-and-bolts approach to local capacity empowerment (short version)

 Capacity building, Closing GCP  No Responses »
Jun 202012
 

Breathing life into support services

By addressing the needs at the heart of quality agricultural research, right there on the station, GCP was the first to cotton on to a crucial missing link between researcher, research station, and support services.” – Hannibal Muhtar (pictured)

“One thing that really energises me,“ enthuses GCP Consultant Hannibal Muhtar, “is seeing people understand why they need to do the work, and being given the chance to do the how.”

And so was born another wonderfully fruitful GCP collaboration. Hannibal, who describes the assignment as “a breath of fresh air,” was asked to identify, together with GCP project Principal Investigators, African research sites of ongoing or potential GCP Research Initiative projects where effective scientific research might be hampered by significant gaps in one fundamental area: infrastructure, equipment and support services. As at June 2012, 19 sites had been selected.

Meet Hannibal Muhtar (audio clip)

Embarking on the voyage to change, storms ‘n’ all
In 2010 and 2011, Hannibal visited these stations, meeting staff at all levels and functions, for an in-depth analyses and appropriate recommendations to assure high-quality field evaluations for GCP-funded projects. With funding from GCP’s Integrated Breeding Platform (IBP), and with the openness, commitment and energy of station staff to implement these recommendations, the efforts are, starting to bear fruit.

Photos: AgCommons

Flashback to 2010. Photo 1: Hannibal (centre) at a planning session at Sega, Western Kenya, with Samuel Gudu of Moi University  (right) and Onkware Augustino (left). Photo 2: Similarly, at Tanzania’s Agricultural Research Institute, Naliendele, with Omari Mponda (right).

But it has not all been smooth sailing, and the storms encountered along en route should not be underestimated.

Weeds, wear and tear, and a walk on the wild side
“The real challenge,” says GCP’s Director of Research, Xavier Delannay (pictured), “is not in the science, but rather in the real nuts-and-bolts of getting the work done in local field conditions.” The obstacles, are often mundane – missing or faulty, weather stations or irrigation systems; weed-infested fields ravaged, or poor drainage, for example. Yet such factors compromise brilliant research. Take unfenced plots for example – equipment gets stolen, and animals roam freely.

Getting down to the brass tacks of local empowerment, and aiming higher
The overarching objective is, in Xavier’s words, “The effective running of local stations, for facilitating local research, improving local crops, and ultimately leading to empowerment and self-reliance of local farming communities.”

In tackling the matter, Hannibal employed a multi-faceted customised approach, based on the needs of each site, for both equipment and training for technicians, tractor operators and station managers. The dedication of the managers to both learn and continue these efforts after the training was particularly gratifying, since it assures sustainability.

“At the end of the day, it’s about achieving food security and improving livelihoods… which pave the way for healthy families and profitable agriculture,” concludes Hannibal.

Lights, curtain… action!
Much like in theatre, with all the ‘props’ in place, field trials are now performing well, thanks to streamlined ‘backstage’ support. Hannibal likens the positive feedback from the partners he has worked with to “A glass of cold water, after a long day in the sun!”

“With proper infrastructure in place, and with research station staff duly equipped with the hands-on expertise and practical know-how to utilise and apply this infrastructure and training, we’re now seeing field experiments being conducted as they should be, and getting good-quality phenotyping data as a result,” says Xavier. “Moreover,” he continues, “by providing glass-houses or the capacity to irrigate in the dry season, we are enabling breeders to accelerate their breeding cycles, so that they can work all year round, rather than having to wait until the rain comes.”
Examples include sites in Kenya, Mali and Nigeria.

The missing link
As the nuts-and-bolts begin to fall in place for, Hannibal reveals: “By addressing the needs at the heart of quality agricultural research, right there on the station, GCP was the first to cotton on to a crucial missing link between researcher, research station, and support services.”

…and yet another missing link…
But the job is not quite done. One crucial gap is the sensitisation of upper management – those at the helm of national research institutes and research station Directors – to support and sustain infrastructure, training and related services. In some cases, costs could be easily met by utilising a priceless asset that most institutes already have, and which they could put to greater us – land and a controlled environment.

Upper management needs to be actively on board. “A research institute should work like a good sewing machine,” says Hannibal. “All well-oiled, all parts working well, and everybody knowing what they need to do.”

In the meantime, however, results from the field suggest that researchers in GCP projects are already reaping the benefits from improved infrastructure and support services, and are already off to a good start.

The ‘stage’ is therefore set: ‘backstage’ and ‘props’ are well primed, performance trials are acting like they should, and the ‘theatre directors’ have an eye on sustainability after GCP’s final curtain call in 2014.

So, long may the show go on, with a cautionary word, however, to continually seek ways to not only maintain but also enhance performance!

Want more details? Read the extended version of this story

Relevant links

  • PODCASTS: You can also listen to Hannibal, by tuning into Episode 2 for the entire interview, or zooming in on your particular area of interest in the mini-podcasts labelled Episodes 2.1 to 2.7 c here.
  • Capacity building
  • Research Initiatives
  • Integrated Breeding Platform website

Hitting the nail on the head: A nuts-and-bolts approach to local capacity empowerment (extended version)

 Capacity building, Closing GCP  No Responses »
Jun 202012
 

Breathing life into support services

By addressing the needs at the heart of quality agricultural research, right there on the station, GCP was the first to cotton on to a crucial missing link between researcher, research station, and support services.” – Hannibal Muhtar

Want to cut to the chase and only need the bare bones of this story? Skip over to the short version

“One thing that really energises me,” enthuses GCP Consultant Hannibal Muhtar, “is seeing people understand why they need to do the work, and being given the chance to do the how.” And so was born another wonderfully fruitful GCP collaboration. Hannibal, who describes the assignment as “a breath of fresh air,” was asked to identify, together with GCP project Principal Investigators, African research sites of ongoing or potential GCP Research Initiative projects where effective scientific research might be hampered by significant gaps in one fundamental area: infrastructure, equipment and support services.

Meet Hannibal Muhtar (Audio clip)

As at June 2012, the 19 sites selected were:

Burkina Faso – L’Institut de l’environnement et de recherches agricoles sites at :
1.  Banfora
2.  Farako-Bâ Regional Centre
Ethiopia
3.  Hawassa Agricultural Research Station
4.  The Southern Agricultural Research Institute
Ghana – Council for Scientific and Industrial Research, Crops Research Institute sites at:
5.  Kumasi
6.  Tamale
Kenya
7.    Moi University (site 1)
8.    Moi University (site 2)
9.    Egerton University (Njoro site)
10.    Egerton University (Koibatek Farmers Training Centre)
Mali – L’Institut d’Économie Rurale sites at:
11.    Sotuba
12.    Cinzana
13.    Longrola
Niger – ICRISAT site
14.    Sadore
Nigeria
15.    National Cereals Research Institute
National Root Crops Research Institute sites at:
16.    Umudike
17.    Kano
Tanzania – Agricultural Research Institute at:
18.    Naliendele
19.    Mtwara

Flashback to 2010. Picture on the left: Hannibal at a planning session at Sega, Western Kenya, with Samuel Gudu and  Onkware Augustino. Picture on the right: Similarly, at Naliendele, in Tanzania with Omari Mponda.

Flashback to 2010. Picture on the left: Hannibal at a planning session at Sega, Western Kenya, with Samuel Gudu and  Onkware Augustino. Picture on the right: Similarly, at Naliendele, in Tanzania with Omari Mponda.

Embarking on the voyage to change, storms ‘n’ all
Hannibal, armed with years of practical experience in the application of engineering sciences in agriculture and developing countries, as well as an attentive ear to the real needs of researchers, embarked on a series of visits to these research stations in 2010 and 2011, meeting with staff of all levels, departments and functions, carrying out in-depth analyses and draw up concrete recommendations for infrastructure and support service investments for each of the sites so that good-quality field evaluations (‘phenotyping’ in ‘breeder-speak) of GCP-funded projects could be conducted. Thanks to funding from GCP’s Integrated Breeding Platform (IBP), and to the openness, commitment and energy of research staff on the ground to implement these recommendations, the efforts of multiple cross-cutting partnerships across Sub-Saharan Africa are, in 2012, starting to bear fruit. But it has not all been smooth sailing, and the storms encountered along the way to reach this end goal should not be underestimated.

Weeds, wear and tear, and a walk on the wild side
The obstacles, says GCP’s Director of Research, Xavier Delannay (pictured, can often be mundane in nature – a  lack of or faulty weather stations or irrigation systems, or fields ravaged by weeds or drainage problems and in dire need of rehabilitation, for example. Yet such factors compromise brilliant research. A simple lack of fencing, Xavier and Hannibal expound, commonly results not only in equipment being stolen, but also in roaming cattle and wild animals – boars, monkeys, hippopotamus and hyena, to name but a few – stomping over precious experiment sites and posing serious threats to field staff safety. “The real challenge lies not in the science, but rather in the real nuts-and-bolts of getting the work done in local field conditions,” he explains.’’

Hannibal concurs: “If GCP had not invested in these research support infrastructure and services, then their investment in research would have been in vain. Tools and services must be in place as and when needed, and in good working order. Tractors must be able to plough when they should plough.’’

But a critical change is also needed in mindset and budgeting. ‘’The word ‘maintenance,’’’ a Senegalese partner commented to Hannibal, describing his institute, “does not exist in our vocabulary and is not a line-item on our budget.”

The problem then is not always about limited funds but rather much more on how the funds available are budgeted, excluding the all-essential support services.

Getting down to the brass tacks of local empowerment, and aiming higher
Multi-lingual and fluent in English, Arabic and French, Hannibal employed a multi-faceted customised approach, based on the needs of each site, be it sharing his tricks-of-the-trade and improvising local solutions, or guiding researchers in identifying their specific needs, as well as on where and how to request equipment, just to mention a few examples. In other cases he would teach local station managers to build and apply simple yet revolutionary tools such as land-levellers (referred to as ‘floats’ in industrial-speak), as well as row-markers for more uniform spacing between rows and plants in the field.

In addition, he would organise a training workshops in either English or French, with different content for technicians, machine operators and station managers. The dedication demonstrated by this latter group to both learn and continue these efforts after the training was particularly pertinent for ensuring the long-term sustainability of the investments.

A colourful menu of options, then, for achieving one common overarching objective, which, as summarised neatly by Xavier, is: “The effective running of local experiment stations, for facilitating local research, improving local crops, and ultimately leading to empowerment and self-reliance of local farming communities.”

“At the end of the day, it’s about achieving food security and improving livelihoods,” Hannibal emphasises. Looking back at some of the research stations that are now well-equipped and are being managed well, and the improved crop varieties being produced and projected, Hannibal highlights the “harmonious chain” triggered as a result: “Food security and better livelihoods pave way for healthy, well-fed families, and agriculture growing beyond subsistence into an economic activity,” Hannibal concludes.

Lights, curtain… ACTION!
Much like in theatre, with all the ‘props’ in place, Hannibal reports that field trials are now performing well, thanks to the all-important ‘backstage’ support service elements being in good shape. Hannibal likens the positive feedback from the partners he has worked with to “A glass of cold water, after a long day in the sun!”

And there’s a beautiful simplicity to the impacts described: “With proper infrastructure in place, and with research station staff duly equipped with the hands-on expertise and practical know-how to utilise and apply this infrastructure and training, we’re now seeing field experiments being conducted as they should be, and getting good-quality phenotyping data as a result,” says Xavier. “Moreover,” he continues, “by providing glass-houses or the capacity to irrigate in the dry season, we are enabling breeders to accelerate their breeding cycles, so that they can work all year round, rather than having to wait until the rain comes.” Sites hosting GCP projects on rice in Nigeria, as well as on sorghum and rice in Mali, are just a few examples of those enjoying off-season work thanks to new irrigation systems.

Similar good news is expected soon for cassava in Ghana and in northern Nigeria. And yet more good news: in some cases, the impacts have not been limited to the trials, or even to the research trials and stations alone, as Xavier highlights with an example from Kenya: “The establishment of an irrigation system on a plot at Koibatek Farmer Training Centre – a partner of Egerton University – yielded excellent results for chickpea experiments. We emphasised that we did not want the equipment to be ‘bracketed’ exclusively for science and experiments. So, it was also used to train staff and farmers from the local community as well. This was greatly appreciated.”

Seeing the nuts-and-bolts now firmly in place for the majority of the sites visited, Hannibal believes GCP has facilitated a pioneering approach to local capacity building: “By addressing the needs at the heart of quality agricultural research, right there on the station, GCP was the first to cotton on to a crucial missing link between researcher, research station, and support services,” he reveals.

…Another missing link…
But the job is not quite done. One crucial gap is the sensitisation of upper management – those at the helm of national research institutes and research station Directors – to support and sustain infrastructure, training and related services. In some cases, costs could be easily met by utilising a priceless asset that most institutes already have, and which they could put to greater us – land and a controlled environment.

Upper management needs to be actively on board. “A research institute should work like a good sewing machine,” says Hannibal. “All well-oiled, all parts working well, and everybody knowing what they need to do.”

In the meantime, however, results from the field suggest that researchers in GCP projects are already reaping the benefits from improved infrastructure and support services, and are already off to a good start.

The stage is therefore set: backstage and props are well primed, performance trials are acting like they should, and the ‘theatre directors’ have an eye on sustainability after GCP’s final curtain call in 2014.

So, long may the show go on, with a cautionary word, however, to continually seek ways to not only maintain but also enhance performance!

Relevant links

  • PODCASTS: You can also listen to Hannibal, by tuning into Episode 2 for the entire interview, or zooming in on your particular area of interest in the mini-podcasts labelled Episodes 2.1 to 2.7 c here.
  • Capacity building
  • Research Initiatives
  • Integrated Breeding Platform website

 

 Newer Entries
cheap ghd australia