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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

Paradise left… then regained: A lifelong passion for plants, and plant science

 Asia, Crop breeding, Genetics, Genomics, Researchers, Rice  No Responses »
Jan 232013
 

Abdelbagi Ismail

 I was forever inquisitive as to how things grew, and questioning when they didn’t grow well. I think it’s what got me interested in plant science.”
– Abdelbagi Ismail, Plant Physiologist and Principal Scientist, International Rice Research Institute.

Today, we talk to Abdel. His riveting voyage in plant science starts on the bountiful banks of the Nile, before we sail on to Asia’s ricelands.  We’ll make a short stopover in USA for cowpeas and drought in between,  then proceed to to our main meal of rice, spiced and seasoned with a strong dash of salt-and-P.

It’s not just about food, but also family: you’ll  get to meet a sister Challenge Programme along the way. Intrigued? We hope so, so please do read on! 

‘A’ for Abdel and agriculture – an early passion for plants
From a tender age, Abdel was fascinated by agriculture.

Growing up on a small family farm backing onto the banks of the Nile in the Northern State of Sudan, he helped his parents in tilling the land, sowing and harvesting.

Abdel reminisces, “It was a relaxing paradise with all types of fruit growing around you year-round. Working and living on a farm, I was forever inquisitive as to how things grew, and questioning when they didn’t grow well. I think it’s what got me interested in plant science.”

Armed with a Bachelor’s and Master’s in Agricultural Sciences (agronomy, crop production, water relations) from the University of Khartoum, Sudan, Abdel moved to the University of California, Riverside, USA, for a PhD on drought tolerance in cowpeas.

“It was the first time I had ever left Africa, and it was a real eye-opener,” Abdel recalls. “It was a fantastic new page in my career too, as I was working with world-class professors and mentors. I chose to work on cowpeas because it is a hardy crop that can be grown in dry conditions which were – and still are – becoming more prevalent in sub-Saharan Africa.” (you can take a sidetrack here, to see our research on cowpeas)

 What interests me is how some societies have survived, and, in some cases, flourished because they invested in improving their plants and crops to adapt and adjust to weather adversities.”

Navigating away from the Nile, and discovering his niche
For this native son of the Nile, this move was a watershed. It marked the start of a dedicated – and still ongoing – career quest to understand how plants can adapt to better tolerate extreme environmental stresses such as higher and lower temperatures, too much or too little water, salinity, and nutrient imbalances.

“Abiotic stresses have had, and continue to have, a major impact on human life, with some societies disappearing altogether because of changes in soils or climate,” says Abdel. “What interests me is how some societies have survived, and, in some cases, flourished because they invested in improving their plants and crops to adapt and adjust to weather adversities.”

From time immemorial, the communities around the Nile where Abdel spent his childhood are a prime example of this flourishing against adversity.

IRRI beckons, and nurtures
In 2000, Abdel accepted a position at the International Rice Research Institute (IRRI) in The Philippines.

Abdel inspects cyclone-damaged rice in Isladi Village, southern Bangladesh.

“I saw it as an opportunity to convert knowledge and scientific discoveries into resources that could help needy farmers,” explains Abdel.

Abdel confesses that when he joined IRRI, his intention was to stay for a short stint and then move on. But as he became more involved in his work, he felt IRRI offered him the best opportunity to build his career, and to contribute to global food-security issues.

“I’ve been here for 12 years now. IRRI really is a great place to grow as a person and a researcher, and to learn how to become a leader.”

Having GCP provide ongoing funding and support for public institutions to conduct a long-term project has been pivotal to the success of the project. It has given us all the security we need to focus on conducting the complex research required…”

Trailblazing for GCP : a much-needed dash of ‘salt-and-P’
In 2004, Abdel proposed a collaborative project between nine different research organisations, across seven countries, to improve salt tolerance and phosphorus uptake efficiency in rice. The work was funded by a sister CGIAR Challenge Programme on Water and Food (CPWF).

This work caught – and held – GCP’s attention, because it sought to overcome a problem that negatively affects the lives of tens of thousands of rice growers around the world. The two resultant GCP-funded IRRI-led projects involved partners from Bangladesh, India, Indonesia, Vietnam and USA’s University of California, Davis. Globally, more than 15 million hectares of ricelands are saline, and more than one-third of all ricelands are phosphorus-deficient, hitting poor communities hardest.

In the nine years since, and together with his colleagues and partners, Abdel has developed the proposal into a productive and coherent suite of interconnected projects: he has managed and overseen most of the progress made during the discovery of the genes associated with salinity tolerance (Saltol) and phosphorus uptake (Pup1), and their insertion into well-known rice varieties that farmers in Bangladesh, Indonesia and The Philippines know and trust.

It’s all about rice: salt tolerance (Saltol) ‘meets’ phosphorus uptake (Pup1) in Bangladesh. Abdel is on the extreme right. Next to him is Sigrid Heuer, Principal Investigator of the ‘Pup1’ work.

Keeping the faith, and going where no rice has gone before…
A long-term horizon helps, since, just like art, science cannot be hurried: “Having GCP provide ongoing funding and support for public institutions to conduct a long-term project has been pivotal to the success of the project,” Abdel emphasises.

“It has given us all the security we need to focus on conducting the complex research required to advance our knowledge about these genes, then breed and develop popular varieties containing then. In some cases, we have developed lines with doubled yields, and grown rice in areas where it has never been grown before because the land was too saline.”

For Abdel, such achievements are heartening as they provide farmers with greater food and income security, which in turn improves their and their community’s livelihoods.

“It brings a smile to my face whenever I think about how our work helps to produce higher-yielding crops for poverty-stricken countries whose farmers often can only afford to grow one crop per year,” says Abdel sincerely.

Abdel continues to build upon, and has even employed, partners he has met through the GCP project…”We want to improve their capacity to take up new breeding techniques, such as the use of molecular markers, which can reduce the time it takes to breed new varieties from six to 10 years to two to three years…”

Continually building on the best
So what’s in store for the future?

Having discovered the Saltol gene and developed experimental lines, his team is now training breeders from country breeding programmes on how they can successfully breed for salt tolerance and tolerance of other abiotic stresses using their own popular varieties, thereby fortifying popular varieties with these much-needed tolerance traits.

“We want to improve their capacity to take up new breeding techniques, such as the use of molecular markers, which can reduce the time it takes to breed new varieties from six to 10 years to two to three years,” reveals Abdel. “This will allow them to breed for crops quicker, in response to ever-changing and extreme climate conditions.”

As for his other projects with IRRI, Abdel continues to build upon, and has even employed, partners he has met through the GCP project to help him with his Stress tolerant rice for Africa and South Asia (STRASA) project.

GCP helped IRRI attract support from other funders…”

Going further, faster, together… five and counting, still learning, and the future looks bright
STRASA is almost five years old and has another five years left to run.

“GCP helped IRRI to attract additional support from other funders, such as the Bill & Melinda Gates Foundation, to start STRASA, which seeks to support the development and distribution of stress-tolerant varieties in Africa and South Asia,” Abdel explains.

Abdel’s parting words? “I’m still committed to understand how plants can be manipulated to adapt to, and better tolerate, extreme environmental stresses, which seems  more feasible today than it has ever been before.”

Links

Science in her blood – Born into botany, bloomed into biochemistry and molecular biology, and now in applied science

 Asia, Capacity building, Genetics, Genomics, Researchers, Rice, Women in science  1 Response »
Dec 212012
 

I’ve always enjoyed my job, particularly teaching students and young researchers, but this project has made me think about how I can do more practical science.” – Zeba Seraj, Biochemistry and Molecular Biology Professor, University of Dhaka, Bangladesh

Zeba Seraj

Growing up with a botanist as a father, Zeba Seraj was nurtured to look at plants in a scientific light. But at one stage in her life, she took a different fork on the road: she was more interested in rat livers and cow eyes, before becoming a ‘late bloomer’ in applied science and molecular plant breeding, which is her current niche.

Taking that fork: rats seduced, cows made eyes, but both lost…
Having completed her Undergraduate and Master’s in Biochemistry at the University of Dhaka, Bangladesh, during the 70s and 80s, she moved to Scotland for a PhD at the University of Glasgow. After being persuaded that molecular biology and recombinant DNA technology were not likely to be too different in animals and plants, she focused on the separation of nuclear proteins involved in post-transcriptional processing in the rat liver system.

“I then went on to work as a postdoc at the University of Liverpool, UK, for 18 months, where I worked on a bovine retina cDNA [complementary DNA] library,” Zeba recalls. “I was exposed to a number of recombinant DNA techniques and was pleasantly surprised to find DNA much easier to work with compared to proteins! I enjoyed it, but when I returned to the Bangladesh, there was no work in that field, so I turned to plants.”

The rise of rice, propelled by ‘Petrra’ project and petri dish
Back at her old University, one of Zeba’s first projects was working on salt tolerance in rice which allowed her to set up plant tissue culture facilities and establish a modest molecular biology laboratory. Zeba thereafter worked with the International Rice Research Institute (IRRI) and the Bangladesh Rice Research Institute (BRRI) on the Petrra project (poverty elimination through rice research assistance). The project was funded by the Department for International Development, UK. Meanwhile, she also spent a couple of months in the laboratory of the illustrious Dr John Bennett at IRRI, learning the latest technology in DNA markers and polymerase chain reaction (PCR) technology. This inital work would, in a way, lead her to GCP.

Meeting GCP, and banking on potential
Zeba joined the GCP community in 2005, working on the rice Saltol (salt tolerance) project. She was a focal collaborator in Bangladesh for this IRRI-led project that aimed to revitalise marginal ricelands by discovering and breeding into popular rice varieties ‘survival’ genes to enable rice to not only survive but also thrive on saline or phosphorus-poor soils.

“We were introduced to the project through the Principal Investigator, Abdel Ismail,” recalls Zeba. “Our lab was not very modern, but we did have all the facilities to do marker work, as well as a firm grasp on the theory, so IRRI and GCP must have seen potential in us.”

 …doing the research helped me understand the practical application better… It was a real eye-opener.”

Transiting from theory to practice
After 15 years of working as an associate professor and professor at the University of Dhaka (DU), mainly nurturing young biochemists, Zeba was re-energised by the thought of working on such a practical project that would have a direct impact on her country’s food security, and on its farmers’ livelihoods.

In the background, genotyping in progress at the Department of Biochemistry and Molecular Biology, University of Dhaka. In thef oreground, student– supervisor consultations. Pictured (left to right) are: Zeba I Seraj, Roman, Adnan, Sarwar, Debashis,Rabin, Dost, Mishu, Shamim and Rejbana.

Nearly one million hectares along the Bangladesh coast are affected by varying degrees of salinity which has severely limited the introduction of modern high-yielding rice varieties, as few of these are saline-tolerant. Given Bangladesh’s high population, farmers need as bountiful yields as possible, and minimum risk of failure.

“After reading and teaching theory for so long, it was really exciting to actually put it into practice and work towards a practical outcome,” says Zeba.

“Actually doing the research helped me understand the practical application better too. It was a real eye-opener.”

 Using molecular markers allowed us to at least halve the time it would take to release stress-tolerant rice.” 

Gaining time: the ‘miracles’ and ‘magic’ of molecular makers
Zeba’s lab was responsible for the molecular evaluation and selection of rice lines bred by BRRI for insertion of the genomic region containing Saltol (discovered to confer salt toleranceby the previous IRRI-led GCP-funded project).

Md Sazzadur Rahman of BRRI assesses progress on a salt-tolerant rice variety in the field.

“We collected leaf samples from the BRRI-bred lines which were a combination of popular rice landraces and a Saltol donor.” explains Zeba ‘Landraces’ is ‘breeder-speak’ for varieties grown by, and popular with, farmers, but not necessarily improved by selective scientific breeding. Zeba continues, “We then used molecular markers which would indicate the presence of the Saltol genomic region.”

“The information we gathered guided the breeders at BRRI to select rice plants with the Saltol region. Selected plants were then further analysed with markers, to maximise the presence of popular alleles,” she adds. Allele is one of two, or more, forms of a gene – the alternative form of a gene responsible for a trait producing different effects.

“Using molecular markers allowed us to at least halve the time it would take to release stress-tolerant rice,” Zeba reveals.

 I will be the happiest person on earth the day they release the new lines, knowing that I’d helped to make a difference.”

Seven years on, what next?
Zeba is grateful that she and her lab were active partners in GCP projects for seven consecutive years: first in the IRRI-led project in 2005 to 2009, then in a follow-up supplementary capacity-building DU-led project from 2010 to 2011, for which Zeba was the Principal Investigator.

Nirmal Sharma and Jamal emasculate the first backcross population of a crosscombination for a second backcross at BRRI

“I don’t think we could have done the work without the various GCP networks. Several times in the project we would lag behind and they’d offer us support to get us back on track,” says Zeba. “They also instilled in us the importance of proper data management, and we have now implemented their system to collect, store and report data for all of our projects. We also now have all the equipment and processes in place, meaning that we’re now able to accommodate similar projects, now and into the future.”

Personally Zeba feels the project has given her a new direction in her career that she’s keen to further explore. “I’ve always enjoyed my job, particularly teaching students and young researchers, but this project has made me think about how I can do more practical science,” confides Zeba.

As for the Saltol project, she is keeping a close eye on the application waiting for the news of high-yield salt-tolerant lines becoming accessible to all Bangladeshi rice farmers.

“I will be the happiest person on earth the day they release the new lines, knowing that I’d helped to make a difference.”

Links

  • More on Zeba Seraj on page 40 here
  • The road behind us: read on the early days (2005/2006) of the rice salt-tolerance work:
    • on pages 36–39 here
    • on pages 28–30 here
    • on page 6 here
  • Profile: Abdel Ismail, Principal Investigator of the salt tolerance project

 

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

 

Banana genetics: (not-so-)Easy as ♫ABC, 123♫

 Bananas, Genetics, Genomics  No Responses »
Sep 202012
 

Getting to the core of a world-favourite dessert by unravelling banana’s origin and genealogy

GCP has enabled us to lay a credible foundation, which gave us a leg-up in the intense competition that typifies the genome sequencing arena” – Angélique D’Hont, CIRAD researcher

‘A’ is also for Angélique, as you will see once you read on…

An ‘A’ to our banana team for ushering in a new era in banana genetics. But let soup precede dessert, and don’t let this worry you: stay with us because we’re still very much on the topic and focused on bananas, which offer the whole range from soup and starters, to main course and dessert, plus everything else in between, being central for the food security of more than 400 million people in the tropics: around a third each is produced in Africa, Asia-Pacific and Latin America, and the Caribbean. About 87  percent of all the bananas produced worldwide are grown by small-scale farmers.

Moving back then to soup for starters, we’re serving up our own unique blend of alphanumeric banana ‘soup’, spiced with ABCs, a pinch of 123s, plus a dash of alpha and omega. Curious about the ABCs? Look no further:‘C’ for getting to the core of ‘B’ for bananas, and an ‘A’ score for our ace genomics team that did it.

Read how GCP seeded … and succeeded, in helping open a new era in banana genetics. An achievement by itself, and an important milestone on the road to unlocking genetic diversity for the resource-poor, which is GCP’s raison d’être.

So get your travelling gear please, for time travel with a ‘midspace checkpoint’ in Malaysia.

We start in 2004, when GCP commissioned a survey of diversity with microsatellites (or SSRs, simple sequence repeats) for all mandate food crops in the CGIAR crop research Centres. The objective of that study was to make new genetic diversity from genebank accessions available to breeders.

The endpoint is opening new research avenues to incorporate genes for disease resistance, with the added bonus of an article published in Nature online on July 11 2012, entitled The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.

It may not be quite as easy as the ABC and 123 that The Jacksons promise in song, but we promise you that the science is just as exciting, with practical implications for breeding hardy disease-resistant bananas. Onwards then to the first leg of this three-step journey!

(Prefer a shorter version of this story in pictures? We’ve got it! Choose your medium between Flickr and Facebook)

1) Let’s go Greek: the alpha and omega of it

Rewinding to the beginning

The proof of the pudding is in the eating: we imagine that Jean Christophe Glaszmann just has to be saying “Yummy!” as he samples this banana.

Start point, 2004: “At that time, several research groups had developed SSR markers for bananas, but there was no coordination and only sketchy germplasm studies,” recalls Jean Christophe Glaszmann (pictured), then the leader of what was GCP’s Subprogramme 1 (SP1) on Genetic Diversity on a joint appointment with CIRAD. He stepped down as SP1 Leader in March 2010, and is currently the Director of a multi-institutional research unit Genetic improvement and adaptation of Mediterranean and tropical plants (AGAP, by its French acronym) at France’s Centre de ccoopération internationale en recherche agronomique pour le développement (CIRAD) in Montpellier.

Jean Christophe continues, “The reference studies had been conducted with RFLP* markers, a very useful tool but far too cumbersome for undertaking large surveys. We mobilised Bioversity International, CIRAD and the International Institute of Tropical Agriculture for the project. The process took time, but delivered critical products.” [*RFLP stands for restriction fragmented length polymorphism]

Fastforward to 2012, and gets just a little geeky…

Eight years down the road in 2012, the list of achievements is impressive, as evidenced by a suite of published papers which provide the details of the analysis of SSR diversity and describe how the data enabled the researchers to unravel the origin and genealogy of the most important dessert bananas. The origin of the predominant variety – Cavendish – suggested by the markers, involves two rounds of spontaneous hybridisation between three markedly differentiated subspecies. This scheme has been marvellously corroborated by linguistic patterns found in banana variety names as revealed in a paper published in 2011 in the proceedings of USA’s National Academy of Sciences.

But what else happened in between the start- and end-point? We now get to the really ‘sweet’ part of this bonanza for banana breeding!

It is now possible to conduct research to identify and incorporate genes for disease resistance within fertile populations that are close to the early progenitors, and then inter-cross them to re-establish sterility and obtain vigorous, disease-resistant and seedless progenies.

 2) Of bits, bananas, breeding and breadcrumbs

Threading all these bits together for breeding better bananas is akin to following a trail of breadcrumbs, in which GCP played an important facilitating role: where in the germplasm to undertake genetic recombination is one key; and then, how to expedite incorporation of disease resistance and how to control sterility – so as to first suppress it, then re-establish it – is another set of keys that are necessary for proficient breeding.

Hei Leung in the lab at IRRI.

In 2005, Hei Leung (pictured), then Leader of GCP’s Subprogramme 2 on Comparative Genomics (until June 2007) on a dual appointment with the International Rice Research Institute (IRRI), recognised that with GCP’s main focus being drought tolerance in crops, Musa (the banana and plantain botanical genus) was somewhat on the fringe. However, it was still important that GCP support the emergence of banana genomics.

Hei is currently Programme Leader of Genetic Diversity and Gene Discovery at IRRI. He remembers, “We had a highly motivated group of researchers willing to devote their efforts to Musa. Nicolas Roux at Bioversity was a passionate advocate for the partnership. The GCP community could offer a framework for novel interactions among banana-related actors and players working on other crops, such as rice. The team led by Takuji Sasaki of Japan’s National Institute of Agrobiological Science, which had vast experience in rice genome sequencing, added the scientific power. So, living up to its name as a Challenge Programme, GCP decided to take the gamble on banana genomics and help it fly.”

Angélique D’Hont, CIRAD researcher and lead author of the article published in ‘Nature’.

Through several projects, GCP helped consolidate Musa genomic resources, contributed to the establishment of medium-throughput DArT markers as well as the construction of the first saturated genetic map. Additional contributions included the first round of sequencing of large chromosome segments (BAC clones) and its comparison with the rice sequence and a detailed analysis of resistance gene analogues. All these findings have now been published in peer-reviewed journals. And while publication takes time, it still remains a high-premium benchmark for quality and validation of results, and for efficient sharing of information. It reinforces the value of collaboration, builds capacity and gives visibility to all partners, thereby providing potential new avenues for funding.

Such was the case with bananas: using a collaborative partnership framework established with the Global Musa Genomics Consortium, animated by Nicolas Roux and now chaired by Chris Town, the community developed a case for sequencing the genome. With the mentorship of Francis Quétier, contacts were made with various major players in genomics, which in the end formalised a project between France’s CIRAD and CEA–Genoscope, funded by the Agence Nationale de la Recherche and led by Angélique D’Hont (pictured) and Patrick Wincker.

GCP contributed DArT analysis for anchoring the sequence to the genetic map. But, as stressed by Angélique, CIRAD researcher and lead author of the Nature paper: “Above all, GCP has enabled us to lay a credible foundation, which gave us a leg-up in the intense competition that typifies the genome sequencing arena. We were delighted that France rolled the dice in our favour by funding this work.”

3) Musa musings on the road to and from Malaysia checkpoint

Three years down the road, the team published a description of the genome of a wild banana from Malaysia.

Jean Christophe communes with a Musa plant, perhaps musing “What’s your family history and when will you be fully grown?”

Let’s drill down to some technical facts and figures here: the Musa genome has some 520 million nucleotides distributed across 11 chromosomes, revealing traces of past duplications and bearing some 36,000 genes. While most genes derived from duplication tend to lose their function, some develop novel functions that are essential for evolution; bananas seem to have an outstanding range of transcription factors that could be involved in fruit maturity.

And while the road ahead remains long, we now have a good understanding of banana’s genetic diversity, we have genomic templates for functional studies (a whole-gene repertoire) as well as for structural studies (the chromosome arrangement in one subspecies) aimed at unraveling the genomic translocations that could control sterility in the species complex.

It is now possible to conduct research to identify and incorporate genes for disease resistance within fertile populations that are close to the early progenitors, and then inter-cross them to re-establish sterility and obtain vigorous, disease-resistant and seedless progenies.

This is undoubtedly an inspiring challenge towards unlocking the genetic diversity in this crop, which is central to food security for more than 400 million people in the tropics.

Links

 

♫We’ll rock your world!♫

 Comparative genomics in cereals, Crop breeding, Genomics, Researchers, Rice  No Responses »
Sep 072012
 

“It is very rare that scientists can take their projects wherever they go. I’ve been very lucky to be able to do this, and much of this has to do with the support I’ve received from GCP.” – Matthias Wissuwa

In the world of phosphorus, Matthias (pictured) is somewhat of a ‘rock star, not that he would admit to it. We don’t understand why not, since to borrow his words, the project he’s involved has becoming something of a ‘celebrity project’ in the scientific community.

For  a decade-and-a-half, he has searched tirelessly for a rice gene that could improve the crop’s yield in phosphorus-deficient soils –which make up half of the world’s soils. Last month, his transnational team published in Nature that their 15-year quest had ended, having finally found the elusive gene – Pup1.

We celebrate this happy ending, especially as we had the added pleasure of talking to Matthias recently: it was delightful in listening to the modest German recount the long journey which has taken him from his home town of Hamburg, to USA, Japan, The Philippines and back to Japan, all this while,  faithfully ‘carrying’ Pup1 with him as he switched employers. As you’ve seen, Japan scores a double strike, so our ‘rock star’ is also ‘big on Japan’! 

Talking to Matthias, we could sense the achievement was only just sinking in – that he and his team’s years of laboratory work was becoming a practical reality that will aid rice-growing farmers from Africa to Asia,  and hopefully other grain growers in years to come. Here’s what Matthias had to say…

You started this project back in 1997. Tell us how you became interested in phosphorus deficiency and rice.

After completing my PhD in the United States, I accepted a postdoc position in Tsukuba, Japan, with the National Institute of Agro-Environmental Sciences (NIAES). It was an easy decision because my wife is Japanese.

My postdoc host, Dr Ae was interested in phosphorus, particularly in legumes. I originally started work on tolerance to phosphorus deficiency in groundnuts, but soon changed to rice to take advantage of the molecular tools available for rice.

Tsukuba is a very new city. It’s called The Science City in Japan because the Japanese government built it to house all the national research institutes. This was great for me as I became interested in QTL mapping, which was pioneered by scientists in Tsukuba. I got talking to people in the rice research community in Tsukuba and was introduced to Dr Yano, who was developing mapping populations for rice at the National Institute of Agrobiological Sciences. He kindly gave me his populations and that’s how I started to map QTL for phosphorus-deficiency tolerance in rice.

Dr Ae was perplexed by my decision, believing that studying legumes was far more challenging than rice. He always told me: “Rice is boring. They just make long, fine roots to capture phosphorus.” That was 15 years ago and he turned out to be right. Long roots are the secret for phosphorus uptake in rice, particular in Kasalath and varieties like that.

Field trials for phosporus-efficient rice in The Philippines.

Did you share Dr Ae’s hypothesis that longer roots were the secret to some rice varieties being able to tolerate phosphorus-deficient soils?

For a long time, I was not sure if it was just long roots. It was a real chicken-and-egg scenario – does strong phosphorus uptake spur root growth, or the other way around?

As it turns out, it is the latter – plants growing longer roots help with the uptake of more phosphorus – and Pup1 is responsible for this.

We have now shifted our aim and are looking for varieties of rice tolerant to phosphorus-deficient soils that either:

  • release organic acids, phosphatases or some other compound that makes phosphorus more readily available for the plant to absorb, or
  • manipulate soil microorganisms to favour those that can aid in making phosphorus more soluble, or
  • very efficiently utilise phosphorus once it is taken up.

All three mechanisms are found in legumes, so there is reason to believe that they exist in rice and we are now working on finding them.

GCP has been interested in the project since 2004 as its outcome aligns with GCP’s goals to improve crop yields and security in developing countries… It has become something of a ‘celebrity project’ in the scientific community, attracting researchers to work on the project or collaborate with us.

In 2002 you left NIAES and accepted a position with the International Rice Research Institute (IRRI), and were encouraged to continue your work on Pup1. When you moved back to Tsukuba in 2005 to accept the position you currently hold with the Japan International Research Center for Agricultural Sciences (JIRCAS), you were again encouraged to continue your Pup1 project, collaborating with your successor at IRRI, Dr Sigrid Heuer. How important has it been to you and the project to have the support of your institutes?

It is very rare that scientists can take their projects wherever they go. I’ve been very lucky to be able to do this, and much of this has to do with the support I’ve received from GCP. They’ve been interested in the project since 2004 as its outcome aligns with GCP’s goals to improve crop yields and security in developing countries.

When I left IRRI, Sigrid was just starting and was more or less free to take on the project, so I asked her if she’d be interested in continuing my work with Pup1 at IRRI and collaborate with me in Japan. She was actually the perfect person for the project because her background in molecular biology complemented my background as a plant breeder.

Over the past seven years, we have worked together very well, and with the addition of Rico Gamuyao, a PhD student supervised by Sigrid, things have recently progressed quite quickly to the point that we were able to pinpoint Pup1.

So GCP has played a major role along your journey?

Yes, definitely. The support from GCP on the Pup1 project, now in its 8th year, was instrumental at getting this project to where it is.

Quite simply, the funding from GCP allowed us to hire Rico as well as Juan Pariasca-Tanaka, a project scientist with me at JIRCAS. Neither Sigrid nor myself had the time to do all the hands-on work so having both Rico and Juan has been hugely helpful.

How important has the collaboration between IRRI and JIRCAS been for the project?

Are they playing with mud? Not at all! Working. Matthias (L) and Rico (R) have zipped up their boots and gone back to their bee…er…. we mean, roots, mucking mud here as they do some fieldwork related to the search for PSTOL1.

Tremendously important. Sigrid’s group at IRRI is relatively small as is mine in Japan, so we rely on each other’s complementary expertise when working on complicated projects.

We have also been fortunate to have constant interest in the project from the scientific community. It has become something of a ‘celebrity project’, and as such, attracted researchers to work on the project or collaborate with us.

For example, we are working with two US groups at Cornell University and Penn State, that are also funded by GCP, trying to track down Pup1 in other crops and identifying genes that control root architecture, and how different architectures may affect P uptake.

These collaborations are really exciting, and make it possible to answer questions that we could not answer ourselves, or that we would have overlooked, were it not for the partnerships.

It really has been a team effort and we wouldn’t have got to where we are now without all the help of everyone involved

You’ve been described as the Godfather and Guru of Pup1. How do compliments like this make you feel?

It makes me laugh but of course it’s a very well-meant comment, and to some extent, considering I’ve worked on it for 15 years, you could say that there is some truth to it.

I’ve done all the original work, but Sigrid has been just as instrumental. She did the part where my expertise was no longer adequate – the molecular side, looking at genes and thinking about the function of a gene and testing for its function.

It really has been a team effort and we wouldn’t have got to where we are now without all the help of everyone involved, which also includes the support of Dr Yano over the years.

…phosphorus deficiency is a worldwide problem that has recently gained public attention because of how expensive phosphate fertilisers have become…Farmers are always interested in saving money and improving yields and we believe this discovery will help with both.

Have you been surprised by the attention this project has received?

As I said, the project has always been in the scientific spotlight because it was the first to map a major QTL for phosphorus uptake.

We knew from the Sub1 story – the submergence tolerance gene, which was published in Nature 4–5 years ago – that the media would probably be interested in this similar discovery. I’m still very surprised that this unsexy story has caused such interest.

You have to remember though, phosphorus deficiency is a worldwide problem that has recently gained public attention because of how expensive phosphate fertilisers have become. About four years ago, the price almost tripled and continues to stay high.

Farmers are always interested in saving money and improving yields and we believe this discovery will help with both.

Phosphorus deficiency is probably even more critical in Africa than it is in Asia… This means Pup1 may have its biggest impact in Africa.

How will the research continue?

Having focused so much on the basic research, we now want to turn our attention to the application. IRRI and JIRCAS will train national breeding programmes to use marker-assisted selection and help them breed their own rice varieties with Pup1.

Sigrid and IRRI are mainly working with Asian national breeding programmes and we at JIRCAS focus more on African programmes such as the Africa Rice Center. Phosphorus deficiency is probably even more critical in Africa than it is in Asia, as phosphate fertilisers aren’t used nearly as much as they are in Asia. This means Pup1 may have its biggest impact in Africa.

We are also looking for new sources of tolerance to phosphorus-deficiency. One very exciting project involves West African rice (Oryza glaberrima) the father of the Nerica ™ (New Rice for Africa) varieties.

So far, we have found that this rice is very tolerant to phosphorus-deficient soils. It does have Pup1, but in addition harbours novel genes that also enhance performance on phosphorus-deficient soils.

We hope to discover a Pup2 in the years to come.

Links

 

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

Extract from a ‘genomicist’s’ diary: Excited in Seattle!

 Genomics, Integrated Breeding Platform  No Responses »
Aug 222012
 

Which we promise you is a much greater thriller than ‘Sleepless in Seattle’. We’d like to share with you an exciting day in the life of our Comparative Genomics Leader, Rajeev Varshney (pictured). And yes, we just made up the word ‘genomicist’ featuring in this blogpost’s title: if those who study economics are ‘economists’, then it’s logical that those who study genomics are…’genomicists’ of course!

Rewind to early July, and here’s the extract from Rajeev’s jottings in his diary on that day…

10 July 2012 – I had a wonderful day in Seattle today: I delivered a presentation on Genomics and informatics for digitalisation of crop breeding in the brainstorming session on A digital revolution in agriculture at the Bill & Melinda Gates Foundation.

The meeting was chaired by Bill Gates and attended by his former and present associates (high-level business executives, entrepreneurs, philanthropists) and selected officials from the Gates Foundation. Discussions centred on four main topics – architecture, genomics, ecological intensification and ICT for a digital revolution in agriculture.

I was privileged to be invited to the meeting as one of three specialists in genomics (the other two being Jun Wang, Executive Director of BGI [Beijing Genomics Institute in Shenzhen China]; and Bob Reiter, VP at Monsanto). In total, there were 10 external experts from all four core areas in the meeting. I never thought that I would have the opportunity to spend a day with such a group of eminent personalities!”

GCP’s work on the Integrated Breeding Platform and on crop ontology were of relevance at the meeting.

A couple of snapshots from that meeting follow, and do look at the links below the photos…

 

Rajeev (standing left) gives his presentation during the meeting

Rajeev on the left, and guess who’s on the right?….That’s right! Bill Gates!

 

 

 

 

 

 

 

 

Links: Rajeev’s profile | Comparative and Applied Genomics Theme | Comparative Genomics Research Initiative | Integrated Breeding Platform | Crop ontology (click on crop of interest from the menu along the top, then follow the ‘crop ontology’ link from the links in the box on the left)

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.

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