Jul 242014
 

Read how this cocktail blends in a comparative genomics crucible, where both family genes and crop genes come into play in Brazil. Nothing whatsoever to do with the World Cup. It’s all about a passionate love affair with plant science – specifically a quest for aluminium-resilient maize – spanning a decade-and-a-half, and still counting…

Claudia

Claudia Guimarães

 

“I love the whole process of science; from identifying a problem, developing a method, conducting the experiments, analysing the data and evaluating the findings.” – Claudia Guimarães (pictured), Researcher at EMBRAPA Milho e Sorgo, Sete Lagoas, Brazil

I always enjoyed looking after the cattle and horses as well as planting and harvesting different crops.”

Forged on family farm, federal institute and foreign land
Claudia Guimarães is a plant molecular geneticist, with a pronounced passion for science. At the Federal University of Viçosa, Claudia studied agronomy because it provided a wide range of possibilities career-wise. She also believes her family’s farming background too had a part to play in her study and career choice. “My father has a farm in a small village 200 km north of Sete Lagoas. My whole family used to go there during our school holidays. I always enjoyed looking after the cattle and horses as well as planting and harvesting different crops.”

During her bachelor’s degrees, Claudia was increasingly drawn to plant genetics. She decided to pursue this field further and completed a Master’s degree in Genetics and Breeding, focusing on maize. She then completed a PhD in Comparative Genomics where she split her time between California and Brazil. “For my PhD, I got a scholarship from the Brazilian Council for Scientific and Technological Development which included international training in San Diego, California. During my PhD, I focused on comparative genomics for sugarcane, maize and sorghum, which involved genetic mapping and markers,” Claudia reveals.

Returning to Brazil after two years in California, Claudia joined the Brazilian Agricultural Research Corporation, commonly referred to as EMBRAPA (Empresa Brasileira de Pesquisa Agropecuária), where she has worked for the last 15 years, since 1999.

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Preparing to put her shoulder to the wheel, literally? Claudia in a maize field at the International Maize and Wheat Improvement Center (CIMMYT), Tlaltizapan, Mexico, in January 2010.

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Maize plantlets cultivated in nutrient solution, the methodology Claudia and her team use to evaluate aluminium tolerance.

Our next challenge is to develop specific markers for a wider marker-assisted selection of aluminium tolerance in maize.”

Long-term allies in aluminium tolerance
EMBRAPA first became involved with GCP through one of its foundation programmes headed by Leon Kochian and his former PhD student Jurandir Magalhães. “Jura has been a really close friend for a long time,” explains Claudia. “We went to university together and have ended up working together here at EMBRAPA. I was involved in Jura’s project, which sought to clone a sorghum aluminium-tolerance gene.”

This gene is called SbMATE. Claudia continues, “EMBRAPA had a long-term aluminium-tolerance programme on maize and sorghum, within which there was a QTL mapping project for aluminium tolerance in maize, in which we started to look for a similar gene as the sorghum team.”

[Editor’s note: QTL stands for quantitative trait locus or loci – gene loci where allelic variation is associated with variation in a quantitative trait. An allele is a variant (different version) of a gene, that leads to variation in a trait, eg different colour for hair and eyes in human beings.]

Working with Leon Kochian at Cornell University, USA, Claudia and her team were able to find an important aluminium-tolerance gene homologue (loosely meaning a relative or counterpart) to the sorghum SbMATE, which they named ZmMATE. This gene is responsible for a major aluminium tolerance QTL that improves yield in acidic soil in maize breeding lines and hybrids. (see why scientists work jointly on closely related cereals)

“Identifying and then validating ZmMATE as the primary aluminium tolerance QTL in maize was a great project,” says Claudia. “Our next challenge is to develop specific markers for a wider marker-assisted selection of aluminium tolerance in maize.”

1: Rhyzobox containing two layers of Cerrado soil – a corrected top-soil and lower soils with 15 percent of aluminium saturation. We can see that near-isogenic lines (NILs) introgressed with the Al tolerance QTL (qALT6) that encompasses ZmMATE1 show deeper roots and longer secondary roots in acid soils, whereas the roots of L53 are mainly confined in the corrected top soil.  2: Maize ears, representing the improved yield stability in acid soils of a NIL per se and crossed with L3. NILs have the genetic background of L53 introgressed with qALT6, the major aluminium-tolerance QTL.

March 2014. Photo 1: Rhyzobox containing two layers of Cerrado soil – a corrected top-soil and lower soils with 15 percent aluminium saturation. We can see that near-isogenic lines (NILs) introgressed with the aluminium-tolerance QTL (qALT6) that encompasses ZmMATE1 show deeper roots and longer secondary roots in acidic soils, whereas the roots of L53 are mainly confined in the corrected top soil. Photo 2: Maize ears, representing the improved yield stability in acidic soils of a NIL per se and crossed with L3. NILs have the genetic background of L53 introgressed with qALT6, the major aluminium-tolerance QTL.

 

 …the students have really become my arms…  helping me a lot with the experiments…

Giving and receiving: students step in, partners in print
Supervising students has become a larger part of Claudia’s life since becoming a member of the Genetics Graduate Programme at Universidade Federal de Minas Gerais, in 2004. Because of this, she credits the students for helping her with her research. “I don’t have as much time as I used to in the lab, so the students have really become my arms in that area, helping me a lot with the experiments,” Claudia reveals. “This isn’t to say that they don’t have to think about what they are doing. I encourage them to always be thinking about why they are doing an experiment and what the result means. At the end of the day, they need to know more about what they are doing than I do, so they can identify indiscretions and successes.”

Claudia says she is always preaching three simple instructions to her students – work hard, always continue to learn and like what you do. “The last instruction is particularly important because as a scientist you need to dedicate a lot of time to what you do, so it helps if you like it. If you don’t like it then it becomes frustrating and no fun at all. I don’t think of my work as a job, rather as a passion. I just enjoy it so much!”

Claudia’s passion is not just a matter of the heart but also of the head, expressing itself in print. Her latest publication reflects the most current results on maize aluminium tolerance, highlighting GCP support, partnerships within and beyond EMBRAPA embracing Cornell University and the Agricultural Research Services of the United States Department of Agriculture (USDA–ARS) , as well as the strong presence of students. Check it out

Links:

SLIDES

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.

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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.

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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.

Links

 

 

Apr 042014
 

 

Phil Roberts

Phil Roberts

Like its legume relatives, cowpeas belong to a cluster of crops that are still referred to in some spheres of the crop-breeding world as ‘orphan crops’. This, because they have largely been bypassed by the unprecedented advances that have propelled ‘bigger’ crops into the world of molecular breeding, endowed as they are with the genomic resources necessary. But as we shall hear from Phil Roberts (pictured), of the University of California–Riverside, USA, and also the cowpea research leader for the Tropical Legumes I Project (TLI), despite the prefix in the  name, this ‘little kid’ in the ‘breeding block’ called cowpeas is uncowed and unbowed, confidently striding into the world of modern crop breeding, right alongside the ‘big boys’! What more on this new kid on the block of modern molecular breeding? Phil’s at hand to fill us in…

Vigna the VIP that shrinks with the violets
But is no shrinking violet, by any means, as we shall see. Also known  as niébé in francophone Africa, and in USA as black-eyed peas (no relation to the musical group, however, hence no capitals!), this drought-tolerant ancient crop (Vigna unguiculata [L] Walp) originated in West Africa. It is highly efficient in fixing nitrogen in the unforgiving and dry sandy soils of the drier tropics. And that is not all. This modest VIP is not addicted to the limelight and is in fact outright lowly and ultra-social: like their fetching African counterpart in the flower family, the African violet, cowpeas will contentedly thrive under the canopy of others, blooming in the shade and growing alongside various cereal and root crops, without going suicidal for lack of limelight and being in the crowd. With such an easy-going personality, added to their adaptability, cowpeas have sprinted ahead to become the most important grain legume in sub-Saharan Africa for both subsistence and cash. But – as always – there are two sides to every story, and sadly, not all about cowpeas is stellar…

Improved varieties are urgently needed to narrow the gap between actual and potential yields… modern breeding techniques… can play a vital role”

A cowpea experimental plot at IITA.

A cowpea experimental plot at IITA.

What could be, and what molecular breeding has to do with it
Yields are low, only reaching a mere 10 to 30 percent of their potential, primarily because of insect- and disease-attack, sometimes further compounded by chronic drought in the desiccated drylands cowpeas generally call home. “Improved varieties are urgently needed to narrow the gap between actual and potential yields,” says Phil. The cowpea project he leads in TLI is implemented through GCP’s Legume Research Initiative. Phil adds, “Such varieties are particularly valuable on small farms, where costly agricultural inputs are not an option. Modern breeding techniques, resulting from the genomics revolution, can play a vital role in improving cowpea materials.”

He and his research team are therefore developing genomic resources that country-based breeding programmes can use. Target-country partners are Institut de l’Environnement et de Recherches Agricoles (INERA) in Burkina Faso; Universidade Eduardo Mondlane in Mozambique; and Institut Sénégalais de Recherches Agricoles (ISRA) in Senegal. Other partners are the International Institute of Tropical Agriculture (IITA) headquartered in Nigeria and USA’s Feed the Future Innovation Labs for Collaborative Research on Grain Legumes and for Climate Resilient Cowpeas.

It’s a lot easier and quicker, and certainly less hit-or-miss than traditional methods!… By eliminating some phenotyping steps and identifying plants carrying positive-trait alleles for use in crossing, they will also shorten the time needed to breed better-adapted cowpea varieties preferred by farmers and markets.”

Cowpea seller at Bodija Market, Ibadan, Nigeria.

Cowpea seller at Bodija Market, Ibadan, Nigeria.

 

On target, and multiplying the score
[First, a rapid lesson on plant-genetics jargon so we can continue our story uninterrupted: ‘QTLs’ stands for quantitative trait loci, a technical term in quantitative genetics to describe the locations where genetic variation is associated with variation in a quantitative trait. QTL analysis estimates how many genes control a particular trait. ‘Allele’ means an alternative form of a the same gene. Continuing with the story…]

The curved shape means that these cowpea pods are mature and ready for harvesting.

Culinary curves and curls: the curved shape means that these cowpea pods are mature and ripe for harvesting.

“We first verified 30 cowpea lines as sources of drought tolerance and pest resistance,” Phil recalls. “Using molecular markers, we can identify the genomic regions of the QTLs that are responsible for the desired target phenotype, and stack those QTLs to improve germplasm resistance to drought or pests. It’s a lot easier and quicker, and certainly less hit-or-miss than traditional methods! However, standing alone, QTLs are not the silver bullet in plant breeding. What happens is that QTL information complements visual selection. Moreover, QTL discovery must be based on accurate phenotyping information, which is the starting point, providing pointers on where to look within the cowpea genome. Molecular breeding can improve varieties for several traits in tandem,” suggests Phil. “Hence, farmers can expect a more rapid delivery of cowpea varieties that are not only higher-yielding, but also resistant to several stresses at once.”

And what are Phil and team doing to contribute to making this happen?

The genomic resources from Phase I – especially genotyping platforms and QTL knowledge – are being used in Phase II of the TLI Project to establish breeding paradigms, using molecular breeding approaches,” Phil reveals. He adds that these approaches include marker-assisted recurrent selection (MARS) and marker assisted back-crossing (MABC). “These paradigms were tested in the cowpea target countries in Africa,” Phil continues. “By eliminating some phenotyping steps and identifying plants carrying positive-trait alleles for use in crossing, they will also shorten the time needed to breed better-adapted cowpea varieties preferred by farmers and markets.”

… best-yielding lines will be released as improved varieties… others will be used…as elite parents…”

Future work
What of the future? Phil fills us in: “The advanced breeding lines developed in TLI Phase II are now entering multi-location performance testing in the target African countries. It is expected that best-yielding lines will be released as improved varieties, while others will be used in the breeding programmes as elite parents for generating new breeding lines for cowpeas.”

Clearly then, the job is not yet done, as the ultimate goal is to deliver better cowpeas to farmers. But while this goal is yet to be attained and – realistically – can only be some more years down the road, it is also equally clear that Phil and his team have already chalked up remarkable achievements in the quest to improve cowpeas. They hope to continue pressing onwards and upwards in the proposed Tropical Legumes III Project, the anticipated successor to TLI and its twin project TLII – Tropical Legumes II.

Links

Jul 012012
 

A shared vision

What is GCP all about and why is its work important? Why was GCP created? Read recollections from key people involved in GCP’s conceptualisation, and find out how realisation of the shared vision continues today. Featuring candid conversations with Masa Iwanaga, former Director General, CIMMYT; Dave Hoisington, Consortium Committee Chair; Andrew Bennett, Executive Board member; and Jean-Marcel Ribaut, GCP Director.

When was the last time you went to your local shop to buy something only to be told they’ve run out of it? How did you react? Like most of us, did you question how they could have run out – after all, isn’t it their business to adequately supply the demand?

Most likely you just went to another store. But what if there wasn’t another store around that had your product, or worse, there was actually a national shortage of your product? This is the reality that faces not just those after the latest iPad, but billions of people who just want something, anything, to eat.

With less productive land on which to grow crops, a more variable climate and more extreme weather events, farmers across all continents are struggling to produce crops, let alone increase yields to meet an ever-growing demand.

This scenario has continually raised its ugly head over the last 200 years as the world’s population has grown exponentially and shifted to urban surroundings. If not for the Green Revolution, inspired by the late Norman Borlaug’s agricultural development research within the Office of Special Studies in Mexico (now the International Maize and Wheat Improvement Center, more commonly known as CIMMYT, its Spanish acronym), the world population would have already suffered losses into the billions.

Even so, food insecurity is still recognised as a global challenge by the UN’s Food and Agriculture Organization (FAO). While there is debate over the cause for such insecurity, the advances of agricultural technology born from a Mexican-flavoured research programme are once again coming to the fore to meet the challenge.

Genebanks are not limited to conservation but are also a source of new alleles for crop improvement.

The genies in the genebank
Seedbank collections serve as insurance against unanticipated future threats to food security, the degradation of our environment and the loss of plant biodiversity.

But that is not all: the banks are not limited to conservation but are also a source of new alleles for crop improvement. The temperature-controlled CGIAR genebanks are a veritable treasure trove for plant breeding. Over the past four decades, their curators have scoured the planet, collecting, categorising and conserving more than 650,000 samples of crop, forage and agroforestry genetic resources, held in trust on behalf of humanity.

One such temperature-controlled genebank is located just outside the sweltering Mexico City: the CIMMYT genebank holds more than 150,000 unique samples of wheat and its relatives from more than 100 countries – said to be the largest collection of a single crop.

While genebank ‘stocks’ have always been open to plant breeders, it wasn’t until 2002 that CGIAR researchers embarked on a more structured and systematic approach using modern technologies to tap their breeding potential, thereby elevating the genebanks beyond their traditional collection and conservation role. Prior to that, far-sighted individual pioneering researchers had been studying (termed ‘screening’ in breeder-speak) the stocks for solutions to breeding problems and to improve crops, but the turning point for a concerted ‘institutional’ effort, would come in the early noughties.

By studying the genes of wild versions of, let’s say, wheat, researchers can find genes that could help cultivated wheat to better battle drought.

The dawn of a new generation
One of these researchers was Dave Hoisington (pictured), then with CIMMYT, and now Chair of GCP’s Consortium Committee, and ICRISAT’s Director of Research. Dave worked with the then newly appointed CIMMYT Director General, Masa Iwanaga, and helped draft a joint proposal with other institutes to CGIAR to form a Challenge Programme that could use the recent advances in molecular biology to harness their rich global stocks of crop genetic resources to create and provide a new generation of plants to meet farmers’ needs. This successfully gave rise to the CGIAR Generation Challenge Programme.

“GCP’s first task was to go in and identify the genetic wealth held within the CGIAR banks,” says Dave.

“To do this, we wanted to use the most recent molecular tools, like molecular markers, to help scan the genomes and discover genes in species related to crops of interest that could help increase yield.”

Let’s use an analogy from a familiar medium – text: think of this story you are now reading as the plant’s genome, its words as its genes and a molecular marker as a text highlighter. You can use different markers to highlight different keywords in this story. Once you can see these keywords, you can then study them in more detail, and, in the case of genes, see what they control in the plant, and how they affect its different aspects.

Photo: JIRCASBy studying the genes of wild versions of, let’s say, wheat, researchers can find genes that could help cultivated wheat to better battle drought.

“At that time, we recognised that a Centre like CIMMYT could no longer undertake this tremendously complex task on its own,” recounts Masa (pictured).”We needed to work within a programme that could concentrate on the task and that rallied together various CGIAR Centres as well as research institutes outside CGIAR, especially in developing countries.”

Partnerships with spirit
Partnerships have always been a key ingredient to success. At the same time, they have led to the downfall of many projects.

Back in the early noughties, CGIAR recognised their business model and research system were not actively fostering partnerships between their different research Centres as much as they should have been, nor were they vigorously encouraging Centres to seek collaboration outside CGIAR.

This was one of the fundamental reasons for establishing the Challenge Programmes, says Jean-Marcel Ribaut (pictured), who, in his role as GCP Director, has been credited by the Board and Committee for the significant time he has taken to broker, nurture and manage GCP’s partnerships.

“One of our major outputs has been the human assets,” says Jean-Marcel with great pride. “We have created this amazing chain of people from the lab to the field.”

In fact, GCPs greatest asset – its ‘crown jewel’ – is its network of people and the capacity the Programme provides them with to buttress all the hard work, particularly in countries where the end products (crops) will be of most benefit.

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

“To make a difference in rural development, to truly contribute to improved food security through crop improvement and income for poor farmers, we knew we had to build capacity in these areas,” observes Jean-Marcel.

“I see our management style as fairly ‘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.”

We were attracted to GCP because of its strong facilitating role, which offered considerable support to addressing the bottlenecks associated with research programmes that researchers and CGIAR identified.”

This support and change have been major selling points for potential partners who have resonated with what Jean-Marcel calls ‘the GCP Spirit’ – partners open to sharing their skills, tools and knowledge, willing to sacrifice their views and leadership and, most importantly, support one another.

“It is visible and palpable: you can recognise people working with us have a spirit that is typical of the Programme,” says Jean-Marcel.

Funders like the Swiss Agency for Development and Cooperation (SDC) are attracted to, and impressed by, GCP’s approach as an honest and impartial ‘broker’.

“We were attracted to GCP because of its strong facilitating role, which offered considerable support to addressing the bottlenecks associated with research programmes that researchers and CGIAR identified,” says Carmen Thönnissen (pictured), Senior Advisor at SDC.

“GCP is also in line with SDC’s internal guidelines on Green Biotechnology, where it is our aim not to support single-donor initiatives but to work in larger programmes that have a clear focus on strengthening the national partner capacities too.”

At the beginning, most project leaders were from developed nations and CGIAR Centres. … now more than half of our projects are led by scientists in developing countries.”

A structured revolution within an evolution: aiming for products and sustainable change
GCP was designed in two phases over its 10-year life. The first was about the research and using genetic plant breeding techniques. The second and current phase focuses more on accessing modern breeding technologies and building capacity in developing countries to do the research for themselves.

Within nine years, GCP has produced useful tools and products from its studies of genetic resources.
These products have contributed to advancing knowledge, and will continue to do so into the future, particularly in plant breeding.

“At the very beginning, most project leaders were from established universities and institutes  in developed nations, and CGIAR Centres. However, over time there has been a major shift and now we are proud that more than half of our projects are led by scientists in developing countries,” says Jean-Marcel. “They’ve moved from the position of implementers to the role of leaders, while the CGIAR Centres and institutes in developed countries have evolved more into mentors and teachers. We hope this empowerment will allow national programmes to grow and establish themselves to be sustainable when the funding dries up.”

Challenges within the Challenge Programme
All this talk about spirit, collaboration and partnerships does make it sound as if GCP has found the winning formula, but Jean-Marcel is quick to counter such notions, and there have been constant course corrections in charting the Programme’s path. “If anything, our strength comes from recognising our weaknesses, acknowledging that we don’t have it all worked out, and embracing change where it is needed.”

A mid-term external review was conducted in 2008 to audit the Programme’s weaknesses, strengths and lessons learnt from both. This review resulted in some governance reforming, bringing about the Consortium Committee and an independent Executive Board.

“It’s a major improvement that we have an independent Board, allowing for focus, and without any conflict of interest. I think they are doing a great job,” says Jean-Marcel. “They are monitoring and evaluating what we are doing, providing plenty of feedback and ideas on how to move forward, and contributing a lot to the success of the Programme.”

The Board’s focus now turns to auditing the Programme and mapping a strategy to sustain its successful partnerships and systems, so they can continue to deliver products and capacity to the developing world.

Bird’s eye view from the Board
With more than 45 years of experience in international development and disaster management and, having worked in development programmes in Africa, Asia, Latin America, the Pacific and the Caribbean, Andrew Bennett (pictured) was a perfect candidate for the Board Chair.

“We are committed to the role that can be played by science in development, and to the Programme,” says Andrew. “We have offered advice and helped the Programme’s Consortium Committee and management refocus the Programme. By all accounts, they seem happy with how things have evolved.”

Advice and helping aren’t normally the words associated with how a Board works but, like so much of the GCP family, this isn’t a classical board.

Andrew explains “Because GCP is hosted by CIMMYT, the Board does not have to deal with any policy issues. That is the responsibility of the Consortium Committee. Our role is more to provide advice and to help with decision-making and implementation, which is great as we’ve been able to focus on the Programme’s science and people.”

That focus now turns to auditing the Programme and mapping a strategy to sustain its successful partnerships and systems, so they can continue to deliver products and capacity to the developing world.

Turning sunset to sunrise
With only two-and-a-half years left to run, Jean-Marcel and his team are working just as passionately on sustaining the partnerships, projects and outputs that GCP has created.

“We knew we weren’t going to be around forever, so we had a plan from early on to hand over the managerial reins to other institutes, including CGIAR,” says Jean-Marcel, with the slight affliction of a parent helping their child move out of home.

“We have begun integrating projects into the CGIAR Research Programmes (CRPs) which we hope will allow them to continue to grow and work effectively towards the goals set.”

At the same time, the Management Team, Committee and Board are all busy auditing the successes and failures of the Programme to quantify the achievements of what has been termed as one of the CGIAR’s more successful Challenge Programmes, and on how to make GCP products freely accessible to other research institutes and programmes.

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