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

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

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

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

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

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

A deeper dig: the root of the matter

Godwill Makunde

Godwill Makunde

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

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

The battle is on to beat the heat: through the project, CBI received 202 Mesoamerican and Andean bean breeding lines from the reference set collection held by the International Center for Tropical Agriculture (CIAT, by its Spanish acronym). A ‘reference set’ is a sub-sample of existing germplasm collections that facilitates and enables access to existing crop diversity for desired traits, such as drought tolerance or resistance to disease or pests. The Institute also embarked on bringing in more techniques to breed for heat tolerance.

Kennedy Simango

Kennedy Simango

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

 

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

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

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

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

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

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

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

Photo: CBI

Godwill doing what he does best: bean breeding.

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

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

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

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

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

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

Related blogposts

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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

Breeding beans to better battle drought and disease in Ethiopia

 Africa, Beans, Crop breeding, Genetics, Genomics, Legumes  No Responses »
Nov 132012
 

Bean breeding in his bones: Asrat A Amele

For our bean team, we already see the benefits of being in the Tropical Legumes I  project. We now understand molecular breeding, and we are able to apply molecular breeding techniques.” – Asrat A Amele (pictured)

Asrat is a bean breeder at Ethiopia’s South Agricultural Research Institute (SARI) at the Awassa Research Centre.

Besides breeding beans that will better battle drought, Asrat’s team combines drought tolerance with resistance to the bean stem maggot (BSM) – a pest that afflicts all bean-growing zones in Ethiopia.

Connections, continuity and capacity building
The Tropical Legumes I (TLI) was not an entirely new connection, as Asrat’s involvement with GCP predates this particular project. He started off as a GCP-funded fellow in 2007, investigating bean genetics for drought tolerance. The fellowship would also seem him do a stint in Colombia at the International Center for Tropical Agriculture  (CIAT, by its Spanish acronym). His work at the time on root phenotyping and quantitative trait loci (QTL) analysis has since been published.

At that time, Asrat remarked:

The GCP fellowships programme is great for a person like me, working in a developing-country research institute. I can say it potentially provides researchers with up-to-date scientific knowledge in areas of specialisation. It provides better contact with scientists in other parts of the world and opens a wider window to think on problems and deliver better research products.”

Thorugh GCP, Asrat also attended a molecular breeding course at Wageningen University and Research Centre in The Netherlands. Wageningen is a GCP Consortium member.

The ravages wrought by bean stem maggot.

Having passed through that door of opportunity and looking back now, what does Asrat say? “Through TLI, we were able to access new parental sources of germplasm recommended for release and use for breeding. For instance, we’ve received more than 200 lines from CIAT, from which 10 have been selected to be used as parents. We plan to do crosses with these parents to develop a marker-assisted recurrent selection [MARS] population, based on the problems plaguing beans in Africa.”

And it’s not all about material but also matters cerebral (and matters manual, as we shall see further on): “From the science meetings we attend, we’ve also gained valuable new contacts and acquired new knowledge.” Asrat reveals.

Two…and two

Fitsum Alemayehu

Daniel Ambachew

The next step is to validate the workability of MARS, and SARI has a GCP-funded PhD student, Fistum Alemayehu (pictured right), registered at the South Africa’s Free State University and conducting his phenotyping in Ethiopia, alongside other well-trained staff that SARI now has. Fistum is working on marker-assisted recurrent selection for drought tolerance in beans, while Daniel Ambachew (pictured left), another GCP-funded MSc student enrolled at Haramaya University, Ethiopia, is evaluating recombinant inbred line populations and varieties for combined dual tolerance of drought and bean stem maggot.

Both students are using molecular breeding: “For this work, we’ll be using SNP* markers. It is probably the first use of bean SNPs in sub-Saharan Africa. We will now do QTL analysis with the bean population we have from CIAT,” reveals Asrat.

* SNP: (pronounced ‘snips’) is a technical term, and the abbreviation is derived from ‘single nucleotide polymorphism’ – an advanced molecular-marker system widely used in genetic science. You can read more about SNPs in this press release.

Of humans and machines

A training session on maintaining farm machinery.

Moving on to matters manual and mechanical, besides enhanced human resources, SARI has benefited from infrastructure support as part of GCP’s comprehensive capacity-building package: the Institute now has an irrigation system to enable them conduct drought trials, and SARI technicians from more than 20 different SARI stations have been trained in proper use and routine maintenance of farm machinery. SARI also received two automatic weather stations from GCP for high-precision climatic data capture, with automated data loading and sharing with other partners in the network.

Through this project, SARI is now well tuned into the international arena of bean research and development, and profiting in new ways from this exposure to growing international connections.

Water drilling to install irrigation equipment at SARI.

Institutional revolution and rebirth
The engagement with GCP has revolutionised bean breeding at SARI and institutionalised marker-assisted selection. As a result, SARI will soon have a small molecular breeding laboratory funded by another agency. This lab will support one more PhD student and an additional MSc student, both registered in Ethiopian universities and working on marker-assisted selection for beans.

Thus, in this southern corner of Ethiopia, bean breeders conversant in molecular methods will continue to be ‘born’, better-prepared and well-equipped to meet the challenges facing bean breeding today.

 

 

 

Asrat on video

Links

SLIDES: Phenotyping common beans for tolerance of drought and bean stem maggots in Ethiopia

 

Beans: Sidestepping variety… to create varieties to combat drought, disease and pests

 Africa, Beans, Crop breeding, Genetics, Genomics, Legumes  No Responses »
Oct 302012
 

BREAK-TIME AND BRAKE-TIME from beans for a bit: Steve Beebe takes a pause to strike a pose in a bean field.

“These [molecular breeding] techniques, combined with conventional methods, shorten the time it takes to breed improved varieties  that simultaneoulsy combine several traits.

And this means that we also get them out to farmers more quickly compared to phenotypic selection alone.”
– Steve Beebe

THE NEAR-PERFECT FOOD: Common beans (Phaseolus vulgaris L) comprise the world’s most important food legume, feeding about 200 million people in sub-Saharan Africa alone. Their nutritional value is so high, they have been termed ‘a near-perfect food’. They are also easy to grow, adapting readily to different cropping systems and maturing quickly.

That said, this otherwise versatile, adaptable and dapper dicotyledon does have some inherent drawbacks and ailments that crop science seeks to cure….

Rains are rapidly retreating, and drought doggedly advancing
Despite the crop’s widespread cultivation in Africa, “yields are low, stagnating at between 20 and 30 percent of their potential,” remarks Steve Beebe, GCP’s Product Delivery Coordinator for beans, and a researcher at the International Center for Tropical Agriculture (CIAT, by its Spanish acronym).

“The main problem is drought, brought about by climate change,” he says. “And it’s spreading – it already affects 70 percent of Africa’s major bean-producing regions.”  Drought decimates bean harvests in most of Eastern Africa, but is particularly severe in the mid-altitudes of Ethiopia, Kenya, Tanzania, Malawi and Zimbabwe, as well as in southern Africa as a whole.

A myriad of forms and hues: bean diversity eloquently speaks for itself in this riot of colours.

Drought, doubt and duality − Diversity a double-edged sword
“Common beans can tolerate drought to some extent, using various mechanisms that differ from variety to variety,” explains Steve. But breeding for drought resistance is complicated by the thousands of bean varieties that are available. They differ considerably according to growth habit, seed colour, shape, size and cooking qualities, and cultivation characteristics.

“A variety might be fantastic in resisting drought,” says Steve, ‘but if its plant type demands extra work, the farmers won’t grow it,” he explains. “Likewise, if consumers don’t like the seed colour, or the beans take too long to cook, then they won’t buy.”

Molecular breeding deals a hand, waves a wand, and weaves a band
This is where molecular breeding techniques come in handy, deftly dealing with the complexities of breeding drought-resistant beans that also meet farmer and consumer preferences. No guesswork about it: molecular breeding rapidly and precisely gets to the heart of the matter, and helps weave all these different ‘strands’ together.

The bean research team has developed ‘genetic stocks’, or strains of beans that are crossed with the varieties favoured by farmers and consumers. The ‘crosses’ are made so that the gene or genes with the desired trait are incorporated into the preferred varieties.

The resulting new varieties are then evaluated for their performance in different environments throughout eastern and southern Africa, with particular focus on Ethiopia, Kenya, Malawi and Zimbabwe which are the target countries of the Tropical Legumes I (TLI) project.

Propping up the plant protein: a veritable tapestry of terraces of climbing beans.

GCP supported this foundation work to develop these molecular markers. This type of breeding – known in breeder parlance as marker-assisted selection (MAS) – was also successfully used to combine and aggregate resistance to drought; to pests such as bean stem maggot (BSM); and to diseases such as bean common mosaic necrosis potyvirus (BCNMV) and to bruchid or common bacterial blight (CBB). The resulting ‘combinations’ laden with all this good stuff were then bred into commercial-type bean lines.

“These techniques, combined with conventional methods, shorten the time it takes to breed improved varieties that simultaneoulsy combine several traits,” comments Steve. “This means that we also get them out to farmers more quickly compared to phenotypic selection alone.”

Informed by history and reality
Breeding new useful varieties is greatly aided by first understanding the crop’s genetic diversity, and by always staying connected with the reality on the ground: earlier foundation work facilitated by GCP surfaced the diversity in the bean varieties that farmers grow, and how that diversity could then be broadened with genes to resist drought, pests and disease.

What next?
Over the remaining two years of Phase II of the Tropical Legumes I (TLI) project, the bean team will use the genetic tools and breeding populations to incorporate drought tolerance into farmer- and market-preferred varieties. “Hence, productivity levels on smallholder farms are expected to increase significantly,” says Steve.

Partnerships
The work on beans is led by CIAT, working in partnership with Ethiopia’s South Agricultural Research Institute (SARI),  the Kenya Agricultural Research Institute (KARI),  Malawi’s Department of Agricultural Research and Technical Services (DARTS) and  Zimbabwe’s Crop Breeding Institute (CBI) of the Department of Research and Specialist Services (DR&SS).

Other close collaborators include the eastern, central and southern Africa regional bean research networks (ECABREN and SABRN, their acronyms) which are components of the Pan-African Bean Research Alliance (PABRA). Cornell University (USA) is also involved.

VIDEO: Steve talks about what has been achieved so far in bean research, and what remains to be done

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

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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

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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)

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