Jul 232014
 

 

DNA spiral

DNA spiral

Crop researchers including plant breeders across five continents are collaborating on several GCP projects to develop local varieties of sorghum, maize and rice, which can withstand phosphorus deficiency and aluminium toxicity – two of the most widespread constraints leading to poor crop productivity in acidic soils. These soils account for nearly half the world’s arable soils, with the problem particularly pronounced in the tropics, where few smallholder farmers can afford the costly farm inputs to mitigate the problems. Fortunately, science has a solution, working with nature and the plants’ own defences, and capitalising on cereal ‘family history’ from 65 million years ago. Read on in this riveting story related by scientists, that will carry you from USA to Africa and Asia with a critical stopover in Brazil and back again, so ….

… welcome to Brazil, where there is more going than the 2014 football World Cup! Turning from sports to matters cerebral and science, drive six hours northwest from Rio de Janeiro and you’ll arrive in Sete Lagoas, nerve centre of the EMBRAPA Maize and Sorghum Research Centre. EMBRAPA stands for Empresa Brasileira de Pesquisa Agropecuária  ‒  in  English, the Brazilian Agricultural Research Corporation.

Jura_w

Jurandir Magalhães

Jurandir Magalhães (pictured), or Jura as he prefers to be called, is a cereal molecular geneticist and principal scientist who’s been at EMBRAPA since 2002.

“EMBRAPA develops projects and research to produce, adapt and diffuse knowledge and technologies in maize and sorghum production by the efficient and rational use of natural resources,” Jura explains.

Such business is also GCP’s bread and butter. So when in 2004, Jura and his former PhD supervisor at Cornell University, Leon Kochian, submitted their first GCP project proposal to clone a major aluminium tolerance gene in sorghum they had been searching for, GCP approved the proposal.

“We were already in the process of cloning the AltSB gene,” remembers Jura, “So when this opportunity came along from GCP, we thought it would provide us with the appropriate conditions to carry this out and complete the work.”

Cloning the AltSB gene would prove to be one of the first steps in GCP’s foundation sorghum and maize projects, both of which seek to provide farmers in the developing world with crops that will not only survive but thrive in the acidic soils that make up more than half of the world’s arable soils (see map below).

More than half of world’s potentially arable soils are highly acidic.

More than half of world’s potentially arable soils are highly acidic.

… identifying the AltSB gene was a significant achievement which brought the project closer to their final objective, which is to breed aluminium-tolerant crops that will improve yields in harsh environments, in turn improving the quality of life for farmers.”

A star is born: identifying and cloning AltSB
For 30 years, Leon Kochian (pictured below) has combined lecturing and supervising duties at Cornell University and the United States Department of Agriculture, with his quest to understand the genetic and physiological mechanisms behind the ability of some cereals to withstand acidic soils. Leon is also the Product Delivery Coordinator for GCP’s Comparative Genomics Research Initiative.

Leon Kochian

Leon Kochian

Aluminium toxicity is associated with acidic soils and is the primary limitation on crop production for more than 30 percent of farmland in Southeast Asia and Latin America, and approximately 20 percent in East Asia, sub-Saharan Africa and North America. Aluminium ions damage roots and impair their growth and function. This results in reduced nutrient and water uptake, which in turn depresses yield.

“These effects can be limited by applying lime to increase the soil’s pH. However, this isn’t a viable option for farmers in developing countries,” says Leon, who was the Principal Investigator for the premier AltSB project and is currently involved in several off-shoot projects.

Working on the understanding that grasses like barley and wheat use membrane transporters to insulate themselves against subsoil aluminium, Leon and Jura searched for a similar transporter in sorghum varieties that were known to tolerate aluminium.

“In wheat, when aluminium levels are high, these membrane transporters prompt organic acid release from the tip of the root,” explains Leon. “The organic acid binds with the aluminium ion, preventing it from entering the root. We found that in certain sorghum varieties, AltSB is the gene that encodes a specialised organic acid transport protein – SbMATE*  –  which mediates the release of citric acid. From cloning the gene, we found it is highly expressed in aluminium-tolerant sorghum varieties. We also found that the expression increases the longer the plant is exposed to high levels of aluminium.”

[*Editor’s note: different from the gene with the same name, hence not in italics]

Leon says identifying the AltSB gene and then cloning it was a significant achievement and it brought the project closer to their final objective, which he says is “to breed aluminium-tolerant crops that will improve yields in harsh environments, in turn improving the quality of life for farmers.”

This research was long and intensive, but it set a firm foundation for the work in GCP Phase II, which seeks to use what we have learnt in the laboratory and apply it to breed crops that are tolerant to biotic or abiotic stress such as aluminium toxicity and phosphorus deficiency.”

Comparative genomics: finding similar genes in different crops
Wheat, maize, sorghum and rice are all part of the Poaceae (grasses) family, evolving from a common grass ancestor 65 million years ago. Over this time they have become very different from each other. However, at a genetic level they still have a lot in common.

Over the last 20 years, genetic researchers all over the world have been mapping these cereals’ genomes. These maps are now being used by geneticists and plant breeders to identify similarities and differences between the genes of different cereal species. This process is termed comparative genomics and is a fundamental research theme for GCP research as part of its second phase.

rajeev-varshney_1332450938

Rajeev Varshney

“The objective during GCP Phase I was to study the genomes of important crops and identify genes conferring resistance or tolerance to biotic or abiotic stresses,” says Rajeev Varshney (pictured), Director, Center of Excellence in Genomics and Principal Scientist in applied genomics at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). “This research was long and intensive, but it set a firm foundation for the work in GCP Phase II, which seeks to use what we have learnt in the laboratory and apply it to breed crops that are tolerant to biotic or abiotic stress such as aluminium toxicity and phosphorus deficiency.”

Until August 2013, Rajeev had oversight on GCP’s comparative genomics research projects on aluminium tolerance and phosphorus deficiency is sorghum, maize and rice, as part of his GCP role as Leader of the Comparative and Applied Genomics Theme.

“Phosphorus deficiency and aluminium toxicity are soil problems that typically coincide in acidic soils,” says Rajeev. “They are two of the most critical constraints responsible for low crop productivity on acid soils worldwide. These projects are combining the aluminium tolerance work done by EMBRAPA and Cornell University with the phosphorus efficiency work done by IRRI [International Rice Research Institute] and JIRCAS [Japan International Research Centre for Agricultural Sciences] to first identify and validate similar aluminium-tolerance and phosphorus-efficient genes in sorghum, maize and rice, and then, secondly, breed crops with these combined improvements.”

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

When AltSB met Pup1
Having spent more than a decade identifying and cloning AltSB, Jura and Leon have recently turned their attention to identifying and cloning the genes responsible for phosphorus efficiency in sorghum. Luckily, they weren’t starting from scratch this time, as another GCP project on the other side of the world was well on the way to identifying a phosphorus-efficiency gene in rice.

Led by Matthias Wissuwa at JIRCAS and Sigrid Heuer at IRRI, the Asian base GCP project had identified a gene locus, which encoded a particular protein kinase that allowed varieties with this gene to grow successfully in low-phosphorous conditions. They termed the region of the rice genome where this gene resides as ‘phosphorus uptake 1’ or Pup1 as it is commonly referred to in short.

“In phosphorus-poor soils, this protein kinase instructs the plant to grow larger, longer roots, which are able to forage through more soil to absorb and store more nutrients,” explains Sigrid. “By having a larger root surface area, plants can explore a greater area in the soil and find more phosphorus than usual. It’s like having a larger sponge to absorb more water!”

Read more about the mechanics of Pup-1 and the evolution of the project.

Jura and Leon are working on the same theory as IRRI and JIRCAS, that larger and longer roots enhance phosphorus efficiency. They are identifying sorghum with these traits, using comparative genomics to identify a locus similar to Pup1 in these low-phosphorus-tolerant varieties, and then verify whether the genes at this locus are responsible for the trait.

“So far, the results are promising and we have evidence that Pup1 homologues may underlie a major QTL for phosphorous uptake in sorghum,” says Jura who is leading the project to identify and validate Pup1 and other phosphorus-efficiency QTLs in sorghum.  QTL stands for ‘quantitative trait locus’ which refers to stretches of DNA containing ‒ or linked to ‒ the genes responsible for a quantitative trait  “What we have to do now is to see if this carries over in the field, leading to enhanced phosphorus uptake and grain yield in low-phosphorus soils,” he adds.

Jura and Leon are also returning the favour to IRRI and JIRCAS and are collaborating with both institutes to identify and clone in rice similar genes to the AltSB gene in sorghum.

“These collaborations are really exciting! They make it possible to answer questions that we could not answer ourselves, or that we would have overlooked, were it not for the partnerships,” says Sigrid.

To make a difference in rural development, to truly contribute to improved food security through crop improvement and incomes for poor farmers, we knew that capacity development had to be a continuing cornerstone in our strategy.”

Building capacity in Africa
In GCP Phase II which is more application oriented, projects must have objectives that deliver products and build capacity in developing-world breeding programmes.

Jean-Marcel Ribaut

Jean-Marcel Ribaut

“The thought behind the latter requirement is that GCP is not going to be around after 2014 so we need to facilitate these country breeding programmes to take ownership of the science and products so they can continue it locally,” says Jean-Marcel Ribaut, GCP Director (pictured). “To make a difference in rural development, to truly contribute to improved food security through crop improvement and incomes for poor farmers, we knew that capacity development had to be a continuing cornerstone in our strategy.”

Back to Brazil: Jura says this requirement is not uncommon for EMBRAPA projects as the Brazilian government seeks to become a world leader in science and agriculture. “Before GCP started, we had been working with African partners for five to six years through the McKnight Project. It was great when GCP came along as we were able to continue these collaborations.”

Samuel Gudu

Samuel Gudu

One collaboration Jura was most pleased to continue was with his colleague and friend, Sam Gudu (pictured), from Moi University, Kenya. Sam has been collaborating with Jura and Leon on several GCP projects and is the only African Principal Investigator in the Comparative Genomics Research Initiative.

“Our relationship with EMBRAPA and Cornell University has been very fruitful,” says Sam. “We wouldn’t have been able to do as much as we have done without these collaborations or without our other international collaborators at IRRI, JIRCAS, ICRISAT or Niger’s National Institute of Agricultural Research [INRAN].”

Sam is currently working on several projects with these partners looking at validating the genes underlying major aluminium-tolerance and phosphorus-efficiency traits in local sorghum and maize varieties in Kenya, as well as establishing a molecular breeding programme.

“The molecular-marker work has been very interesting. We have selected the best phosphorus-efficient lines from Brazil and Kenya, and have crossed them with local varieties to produce several really good hybrids which we are currently field-testing in Kenya,” explains Sam. “Learning and using these new breeding techniques will enable us to select for and breed new varieties faster.”

Sam is also grateful to both EMBRAPA and Cornell University for hosting several PhD students as part of the project. “This has been a significant outcome as these PhD students are returning to Kenya with a far greater understanding of molecular breeding which they are sharing with us to advance our national breeding programme.”

We’ve used the knowledge that Jura’s and Leon’s AltSB projects have produced to discover and validate similar genes in maize…We identified Kenyan lines carrying the superior allele of ZmMATE …This work will also improve our understanding of what other mechanisms may be working in the Brazilian lines too.” 

‘Everyone’ benefits! Applying the AltSB gene to maize
Claudia Guimarães (pictured) is a maize geneticist at EMBRAPA. But unlike Jura, her interest lies in maize.

Claudia

Claudia Guimarães

Working on the same comparative genomics principle used to identify Pup1 in sorghum, Claudia has been leading a GCP project replicating the sorghum aluminium tolerance work in maize.

“We’ve used the knowledge that Jura’s and Leon’s AltSBprojects have produced to discover and validate similar genes in maize,” explains Claudia. “From our mapping work we identified ZmMATE as the gene underlying a major aluminium tolerance QTL in maize. It has a similar sequence as the gene found in sorghum and it encodes a similar protein membrane transporter that is responsible for citrate extradition.”

A maize field at EMBRAPA. Maize on the left is aluminum-tolerant while the maize on the right is not.

A maize field at EMBRAPA. Maize on the left is aluminium-tolerant while the maize on the right is not.

Using molecular markers, Claudia and her team of researchers from EMBRAPA, Cornell University and Moi University have developed near-isogenic lines from Brazilian and Kenyan maize varieties that show aluminium tolerance, with ZmMATE present. From preliminary field tests, the Brazilian lines have had improved yields in acidic soils.

“We identified a few Kenyan lines carrying the superior allele of ZmMATE that can be used as donors to develop maize varieties with improved aluminium tolerance,” says Claudia.  “This work will also improve our understanding of what other mechanisms may be working in the Brazilian lines too.”

What has pleased Jura and other Principal Investigators the most is the leadership that African partners have taken in GCP projects.

Cherry on the cereal cake
With GCP coming to an end in December 2014, Jura is hopeful that his and other offshoot projects dealing with aluminium tolerance and phosphorus efficiency will deliver on what they set out to do.

“For me, the cherry on the cake for the aluminium-tolerance projects would be if we show that AltSB improves tolerance in acidic soils in Africa. If everything goes well, I think this will be possible as we have already developed molecular markers for AltSB.”

What has pleased Jura and other Principal Investigators the most is the leadership that African partners have taken in GCP projects.

“This has been a credit to them and all those involved to help build their capacity and encourage them to take the lead. I feel this will help sustain the projects into the future and one day help these developing countries produce varieties of sorghum and maize for their farmers that are able to yield just as well in acidic soils as they do in non-acidic soils.”

In the foreground, left to right, Leon, Jura and Sam in a maize field in Kenya.

In the foreground, left to right, Leon, Jura and Sam in a maize field at the Kenya Agricultural Research Institute (KARI), Kitale, in May 2010. They are examining crosses between Kenyan and Brazilian maize germplasm.

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Jul 082012
 

Inside GCP today

Do a deep dive with Jean-Marcel into GCP’s ‘engine room’. What makes the Programme work? How is it structured and governed? For a geographically dispersed Programme with multi-institutional teams, what’s the trick that keeps the different parts moving and well-oiled to maintain forward motion and minimise friction? Get acquainted (and hopefully ‘infected’) with the ‘GCP Spirit’…

Jean-Marcel Ribaut (pictured) is the GCP Director. His work involves coordinating the research activities and overseeing finances, ensuring that at the end of the day that the overall Programme objectives are met. This means much multitasking, a great asset in running a multi-institutional partnership-based Programme. Jean-Marcel comes from a research background, although the research team he led while at CIMMYT was nothing the size of GCP…

…we’ve moved from exploration to application…underpinned by services and capacity building. To make a difference in rural development, to truly contribute to improved food security through crop improvement and incomes for poor farmers, we knew that building capacity had to be a cornerstone in our strategy.”

How long have you been GCP Director?
Since 2005. My first two years were a steep learning curve!

The GCP tagline – ‘Partnerships in modern crop breeding for food security’  – what does this mean for you?
GCP is a very dynamic Programme. The kind of research that we were doing in 2005 is quite different from what we are doing today. As we implement our strategy, we’ve moved from exploration to application. We therefore revised our tagline to match this evolution, with the Programme now focussing much more on modern crop breeding and related aspects. We had naturally started by looking for diversity in the alleles, then evolved to gene discovery and developing supporting tools and markers alongside capacity building. Now, our focus is on application – using this diversity, markers and tools to progress to the next level, and boost the genetic gains for our nine key crops in challenging environments.

This application is underpinned by a service component through our Integrated Breeding Platform, as well as a strong capacity-building component for both human resources and infrastructure.

To make a difference in rural development, to truly contribute to improved food security through crop improvement and incomes for poor farmers, we knew that building capacity had to be a cornerstone in our strategy.

We take an integrated approach … exploring new avenues but exercising due caution …we are not promoting molecular breeding as the magic bullet and only solution – it’s an additional useful tool for arriving at educated breeding decisions.

One of our objectives was to bridge the gap between upstream and downstream research in the teams we brought together. While we did have some failures where groups worked together for the project duration alone and didn’t continue their collaboration, we have had other cases where the teams we forged then have not only grown but also continued to work together – with or without us.”

Why is GCP’s work important?
Through our Research Initiatives, we focus on several crops, with relatively limited funding for each of them compared, say, to other much larger crop-specific initiatives supported for example by the Bill & Melinda Gates Foundation. So,  we operate on a proof-of-concept model: our goal is to demonstrate the use of new technologies and the application of out-of- the-box strategies which – if proven effective – will be funded and expanded by other agencies, including governments.

We take an integrated approach to problem-solving, exploring new avenues but exercising due caution while so doing. For example, for modern crop breeding which is our current focus, we are not promoting molecular breeding as the magic bullet and only solution – it’s an additional useful tool for arriving at educated breeding decisions.

…more than half our projects are led by scientists in developing countries

…The ‘GCP Spirit’ is visible and palpable: you can recognise people working with us have a spirit that is typical of the Programme.”

For you, what have been the major outcomes of the Programme so far?
Seeing developing-country partners come to the fore, and take the reins of project leadership. During Phase I, most project leaders were from CGIAR and advanced research institutes. However, over time, there has been a major shift and we are proud that today, more than half our projects are led by scientists in developing countries. They’ve moved from the position of implementers to the role of leaders, while CGIAR Centres and universities have taken a back seat, being more in a supporting role as mentors or tutors.

We have created this amazing chain of people, stretching  from the labs to the fields. This ‘human’ component is a terrific living asset, but it is also very difficult to scientifically quantify. Perhaps the best way I can describe it is as a ‘GCP Spirit’ created by the researchers we work with. The Programme’s ‘environment’ is friendly, open to sharing and is marked by a strong sense of community and ‘belonging’. The ‘GCP Spirit’ is visible and palpable: you can recognise people working with us have a spirit that is typical of the Programme.

One of our objectives was to bridge the gap between upstream and downstream research in the teams we brought together. While we did have some failures where groups worked together for the project duration alone and didn’t continue their collaboration, we have had other cases where the teams we forged then have not only grown but also continued to work together – with or without us.

A number of the partnerships we’ve forged have had a win–win outcome for players at opposite ends of the research–development spectrum. For example, academia tends to place a high premium on publications and theory, and relatively lower value on application and the real-world context. GCP provides a window for academics to apply their expertise, which benefits developing-country partners.

GCP’s relationship with project ppartners goes beyond funding. We are not just giving money; we are engaged in partnership with our project teams. We in management consult with them, interact and grapple over the technical issues with them in candour, and we toast and celebrate the successes together. I see our management style as fairly ‘paternal’, particularly for projects led by scientists from developing countries, but paternal in the positive sense of wanting to see these groups of people succeed, and us helping them to do so.

If a research site needs a pump for fieldwork, we work with a local or international consultant who will visit the partner and evaluate their needs, advise them on what type of pump they need, as well as other infrastructure they’ll need for the whole system to be sustainable. We’ll then provide training on how to use the pump most effectively.

It’s an investment in the people as much as in the products they are working on because we are trying to change the system of how science within partnerships is conducted and supported, as much as we are trying tap genetic diversity and breed resilient crops for the developing world.

Our successes have only been possible because of our ‘slim’ structure and the structural support we have enjoyed. With governance and advisory roles vested in an Executive Board and Consortium Committee, and with CIMMYT providing us with a legal and administrative home, we have minimal overheads and much flexibility. This agility has allowed us to adjust rapidly to changes when needed than, say, a classic research institute which would – quite rightly – have more rigid and elaborate obligatory steps, over a much longer time horizon.

…advocacy, persuasion and presenting a compelling business case are all necessary ingredients. Because we cannot be ‘directive’ with our partners in the manner their own institutes can be since they don’t ‘belong’ to us, we need to demonstrate success and convince people to adopt new business models.

How will GCP ensure sustainability?
Through our project Delivery Plans which link up a chain of users of our research products, and our Transition Strategy which shows how our research activities are embedded in the new CGIAR Research Programmes. We also hope to see our nascent communities of practice confer a sense of ownership to community members, and therefore sustainability. All that is on the ‘systematic’ and ‘documentation’ side of things.

Even more compelling is something I mentioned earlier, on the ‘organic’ and community side of things. Although it is completely outside our control, so to speak, it is wonderful to see that some of the partnerships we brought together have acquired a life of their own, and the teams we constituted are working together in other areas that have nothing to do with their GCP projects.

What are some of the lessons learnt so far?
The first one was focus. It’s very difficult to coordinate too many tasks, carried out by too many partners. Midstream in 2008, we had to review the way we were working and change course.

People management is the other. Cultivating relationships with people is critical. The trick is in balancing: by being cordial and friendly managers, we perhaps erode some of our authority over some of our project partners!

Another big lesson is that if it’s not working, don’t push it. Learn the lesson, cut your losses, and move on. Two main lessons have come from both our research and service aspects. For research, we invested in a massive fingerprinting exercise to characterise reference sets for all our 18 mandate crops at the time. [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]

The results were not great, the documentation was poor, and it was very difficult reconciling the different datasets from the work. We ended up incurring extra costs for genotyping, to salvage the investment. Then for building the Integrated Breeding Platform, we’d initially involved all major actors in developing the ‘middleware’ – the ‘invisible’ part that links the tools, services and resources IBP provides to breeders, with the respective crop databases. This did not work, and we subcontracted the work to an external service provider.

In both cases, we erred on the side of inclusiveness since we wanted to have all the players on board, and to also facilitate their capacity-building-by-engagement. We have learnt the need to strike a balance between inclusiveness and capacity building on the one hand, and outsourcing to get the job done on the other.

Then there is behaviour change – changing people’s mindsets to adopt technology, since people tend to be naturally conservative. We’ve learnt that developing the tools and techniques is the easy part. The human component – changing how people do business, getting them to adopt a corporative and cooperative over an institutional focus – is a real challenge, and needs to be strongly demand-driven with clear short-term benefits.

Data management and quality control, their documentation, publication and sharing continue to dog us and it’s probably the greatest challenge, although not unique to GCP.

Finally, advocacy, persuasion and presenting a compelling business case are all necessary ingredients. Because we cannot be ‘directive’ with our partners in the manner their own institutes can be since they don’t ‘belong’ to us, we need to demonstrate success and convince people to adopt new business models.

What is the most enjoyable aspect of your position at GCP?
More than one, actually.

We enable people, research teams and institutes to grow, thrive and stand on their own, and this is deeply gratifying; it is very rewarding to see people from developing countries growing and becoming leaders.

Working on different crops, with different partners, in different circumstances, and of different capacities is highly stimulating and brings a lot of diversity. My job is anything but boring!

I also appreciate being sheltered from the administrative burden our multi-institutional approach carries. The administrative load is ably borne by CIMMYT. This allows me to dedicate more of my time to supporting our research partnerships, institutional relationships and services to researchers.

I work with a small and dedicated team. As you can imagine, things are not always rosy, since a small team also means we operate in a ‘tight’ space and occasionally knock knuckles, and we also come from different cultures, but all these work to the good. This cultural diversity is actually a big plus, bringing a broader array of perspectives to the table. And the benefit of the ‘tight’ space is that, when there is a task to be done, the team spirit is incredible – everyone in the group, from management to office assistants, apply themselves to the task at hand. This is a fantastic experience!

Beyond the management and staff group, there is also the real GCP that is out there, which is highly stimulating, and I will end by sharing an excerpt from the external mid-term review report:

“Perhaps the most important value of GCP thus far, is the opportunities it has provided for people of diverse backgrounds to think collectively about solutions to complex problems, and, in the process, to learn from one another.”

Related blogposts

GCP website

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