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Sugarcane, sorghum, students and maize: Claudia’s colourful and contrasting crop science career

Comparative genomics in cereals, Genomics, Latin America, Maize, Researchers, Women in science No Responses »

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 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.

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.

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:

Claudia’s maize project
Comparative Genomics Research Initiative – Blogpost | Project | InfoCentre

SLIDES

GRM 2013: Validation of ZmMATEs as Genes Underlying Major Al Tolerance QTLs in Maize — C Guimarães (redacted) from CGIAR Generation Challenge Programme

Science enlists nature and collaboration to ‘neutralise’ acidic soils

Africa, Asia, Comparative genomics in cereals, Genomics, Latin America, Maize, Rice, Sorghum No Responses »

Jul 232014

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.

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 Alt_SB 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 Alt_SB 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.

… identifying the Alt_SB 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 Alt_SBFor 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

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 Alt_SB 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, Alt_SB 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 Alt_SB 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

“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 Alt_SB met Pup1…
Having spent more than a decade identifying and cloning Alt_SB, 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 Alt_SB 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

“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

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 Alt_SBprojects 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 Alt_SB gene to maize
Claudia Guimarães (pictured) is a maize geneticist at EMBRAPA. But unlike Jura, her interest lies in maize.

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 Alt_SBprojects 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 Alt_SB 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 Alt_SB.”

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

Comparative Genomics Research Initiative on cereals
Comparative and Applied Genomics Theme
Comparative Genomics InfoCentre: for genomic resources, slides, news articles, press releases, videos, podcasts, blogposts, community of researchers, crop databases, and more
Researcher profiles – Claudia Guimarães | Sam Gudu |Leon Kochian | Niaba Témé | Jurandir Magalhães
Selected slides below:

GRM 2013: Cloning, characterization and validation of AltSB/Al tolerance in rice — L Kochian from CGIAR Generation Challenge Programme

GRM 2013: Cloning, characterization and validation of PUP1/P efficiency in maize — L Kochian from CGIAR Generation Challenge Programme

The curious case of cassava’s quirks, narrated in Nigeria

Africa, Cassava 4 Responses »

Jun 242014

Triumphs and tragedies, pitfalls and potential of the ‘camel crop’

We travel through space and time, with a pair of researchers who have a pronounced passion for a plant brought to Africa by seafaring Portuguese traders in the 16^th century. Fastforwarding to today, half a millennium later, the plant is widespread and deep inland, and is the staple food for Africa’s most populous nation – Nigeria.

Meet cassava, the survivor. After rice and maize, cassava is the third-largest source of carbohydrate in the tropics. Surviving, nay thriving, in poor soils and shaking off the vagaries of weather – including an exceptionally high threshold for drought – little wonder that cassava, the ‘camel’ of crops is naturally the main staple in Nigeria. And with that, it has propelled Nigeria to the very top of the cassava totem pole as the world’s leading cassava producer, and consumer: most Nigerians eat cassava in one form or another practically every day.

Great, huh? But there’s also a darker side to cassava, as we will soon find out from our two cassava experts. For starters, the undisputed global cassava giant, Nigeria, produces just enough to feed herself. Even if there were a surplus for the external demand, farming families, which make up 70 percent of the Nigerian population, have limited access to these lucrative external markets. Secondly, cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) are deadly in Africa. Plus, cassava is a late bloomer (up to two years growth cycle, typically one year), so breeding and testing improved varieties takes time. Finally, cassava is most definitely not à la mode at all in modern crop breeding: the crop is an unfashionably late entrant into the world of molecular breeding, owing to its complex genetics which denied cassava the molecular tools that open the door to this glamour world of ‘crop supermodels’.

Emmanuel Okogbenin (left) and Chiedozie Egesi (right) in a cassava field.

But all is not doom and gloom, which inexorably dissolve in the face of dogged determination. All the above notwithstanding, cassava’s green revolution seems to be decidedly on the way in Nigeria, ably led by born-and-bred sons of the soil: Chiedozie Egesi and Emmanuel Okogbenin (pictured right) are plant breeders and geneticists at the National Root Crops Research Institute (NRCRI). With 36 years’ collective cassava research experience between them, the two men are passionate about getting the best out of Nigeria’s main staple crop, and getting their hands into the sod while about it: “I’m a plant breeder,” says Chiedozie, with pride. “I don’t just work in a laboratory. I am also in the field to experience the realities.”

Hitting two birds with one stone…two stones are even better!
As Principal Investigators (PIs) leading three different projects in the GCP-funded Cassava Research Initiative, Chiedozie and Emmanuel, together with other colleagues from across Africa, form a formidable team. They also share a vision to enable farmers increase cassava production for cash, beyond subsistence. This means ensuring farmers have new varieties of cassava that guarantee high starch-rich yields in the face of evolving diseases and capricious weather.

Chiedozie is one of cassava’s biggest fans. His affection for, and connection to, cassava is almost personal and definitely paternal. He is determined to deploy the best plant-breeding techniques to not only enhance cassava’s commercial value, but to also protect the crop against future disease outbreaks, including ‘defensive‘ breading. But more on that later…

Emmanuel is equally committed to the cassava cause. As part of his brief, Emmanuel liaises with the Nigerian government, to develop for – and promote to – farmers high-starch cassava varieties. This ensures a carefully crafted multi-pronged strategy to revolutionise cassava: NRCRI develops and releases improved varieties, buttressed by financial incentives and marketing opportunities that encourage farmers to grow and sell more cassava, which spurs production, thereby simultaneously boosting food security while also improving livelihoods.

Standing tall. Disease resistance and high starch and yield aside, farmers also prefer an upright architecture, which not only significantly increases the number of plants per unit, but also favours intercropping, a perennial favourite for cassava farmers.

Cross-continental crosses and cousins, magic for making time, and clocking a first for cassava

No one has been able to manufacture time yet, so how can breeders get around cassava’s notoriously long breeding cycle? MAS (marker-assisted selection) is crop breeding’s magic key for making time. And just as humans can benefit from healthy donor organ replacement, so too does cassava, with cross-continental cousins donating genes to rescue the cousin in need. Latin American cassava is nutrient-rich, while African cassava is hardier, being more resilient to pests, disease and harsh environments.

Thanks to marker-assisted breeding, CMD resistance from African cassava can now be rapidly ‘injected’ much faster into Latin American cassava for release in Africa. Consequently, in just a three-year span (2010–2012), Chiedozie, Emmanuel, Martin Fregene of the Donald Danforth Plant Science Center (USA) and the NRCRI team, released two new cassava varieties from Latin American genetic backgrounds (CR41-10 and CR36-5). These varieties, developed with GCP funding, are the first molecular-bred cassava ever to be released, meaning they are a momentous milestone in cassava’s belated but steady march towards its own green revolution.

Marker-assisted selection is much cheaper, and more focused.”

On the cusp of a collaborative cassava revolution: on your marks…
With GCP funding, Chiedozie and Emmanuel have been able to use the latest molecular-breeding techniques to speed up CMD resistance. Using marker-assisted selection (MAS) which is much more efficient, the scientists identified plants combining CMD resistance with desirable genetic traits.

“MAS for CMD resistance from Latin American germplasm is much cheaper, and more focused,” explains Emmanuel. “There is no longer any need to ship in tonnes of plant material to Africa. We can narrow down our search at an early stage by selecting only material that displays markers for the genetic traits we’re looking for.” Using markers, combining traits (known as ‘gene pyramiding’) for CMD resistance is faster and more efficient, as it is difficult to distinguish phenotypes with multiple resistance in the field by just observing with the naked eye. This is what makes marker-assisted breeding so effective and desirable in Africa.

GCP’s mode of doing business coupled with its community spirit has spurred the NRCRI scientists to cast their eyes further out to the wider horizon beyond their own borders.

By collaborating with research centres in other parts of the world, Emmanuel and Chiedozie have made remarkable strides in cassava breeding. According to Emmanuel, “GCP helped us make links with advanced laboratories and service providers like LGC Genomics. The outsourcing of genotyping activities for molecular breeding initiatives is very significant, as it enables us to carry out analyses not otherwise possible.”

We can’t afford to sit idle until it comes – we need to be armed and on the ready.”

‘Defensive’ breeding: partnerships to pre-empt catastrophe and combat disease
Closer home in Africa, as PI of the corollary African breeders community of practice (CoP) project, Emmanuel co-organises regular workshops with plant breeders from a dozen other countries (Côte d’Ivoire, DR Congo, Ethiopia, Ghana, Kenya, Liberia, Malawi, Mozambique, Sierra Leone, Tanzania, Uganda and South Sudan). These events are an opportunity to share knowledge on molecular breeding and compare notes.

Of the diseases that afflict cassava, CBSD is the most devastating. Mercifully, in Nigeria, the disease is non-existent, but Chiedozie is emphatic that this is by no means cause for complacency. “If CBSD gets to Nigeria, it would be a monumental catastrophe!” he cautions. “We can’t afford to sit idle until it comes – we need to be armed and on the ready.”

Putting words to action, though this work on CBSD resistance is still in its early stages, more than 1,000 cassava genotypes (different genetic combinations) have already have been screened in the course of just one year. Chiedozie hopes that the team will be able to identify key genetic markers, and validate these in field trials in Tanzania, where CBSD is widespread. This East African stopover, Chiedozie emphasises, is a crucial checkpoint in the West African process. So the cassava CoP not only provides moral but also material support.

And Africa is not the limit. GCP-funded work on CMD resistance is more advanced than the CBSD work, though the real breakthrough in CMD only happened recently, on the international arena within which the African breeders now operate. According to Chiedozie, two entire decades of screening cassava genotypes from Latin America yielded no resistance to CMD. The reason for this is that although it is widespread in Africa, CMD is non-existent in Latin America.

Through international collaborative efforts, cassava scientists, led by Martin Fregene (now based in USA), screened plants from Nigeria and discovered markers for the CMD2 gene, indicating resistance to CMD. Once they had found these markers, the scientists were off and away! By taking the best of the Latin American material and crossing it with Nigerian genotypes that have CMD resistance, promising lines were developed from which the Nigerian team produced two new varieties. These varieties, CR41-10 and CR36-5, have already been released to farmers, and that is not all. More varieties bred using these two as parents are in the pipeline.

“GCP funding has given us the opportunity to show that a national organisation can do the job and deliver.”

Delivery attracts
The success of the CGP-funded cassava research in Nigeria lies in its in-country leadership. Chiedozie, Emmanuel and Martin are native Nigerian scientists and as such are – in many ways – best placed to drive a research collaboration to benefit the country’s farmers and boost food security. “GCP funding has given us the opportunity to show that a national organisation can do the job and deliver,” says Chiedozie.

This proven expertise has helped NRCRI forge other partnerships and attract more financial support, for example from the Bill & Melinda Gates Foundation for a project on genomic selection. GCP support has also bolstered communications with the Nigerian government, which has launched financial instruments, such as a wheat tariff,* to boost cassava production and use.

[Editors note: * wheat tariff: The Nigerian government is trying to reduce wheat import bills and also boost cassava commercialisation by promoting 20 percent wheat substitution in bread-making. Tariffs are being imposed on wheat to dissuade heavy imports and encourage utilisation of high-quality cassava flour for bread.]

“The government feels that to quickly change the fortunes of farmers, cassava is the way to go,” explains Emmanuel. He clarifies, “The tariff from wheat is expected to be ploughed back to support agricultural development – especially the cassava sector – as the government seeks to increase cassava production to support flour mills. Cassava offers a huge opportunity to transform the agricultural economy and stimulate rural development, including rapid creation of employment for youth.”

The Nigerian government is right in step aiding cassava’s march towards the crop’s own green revolution, as is evident in the the Minister of Agriculture’s tweet earlier this year, and in his video interview below. See also related media story, ‘Long wait for cassava bread’.

Clearly, the ‘camel’ crop – once considered an ‘orphan’ in research – has travelled as far in science as in geography, and it is a precious asset to deploy for food production in a climate-change-prone world. As Emmanuel observes, cassava’s future can only be brighter!

Slides by Chiedozie and Emmanuel

GRM 2013: Improving and deploying markers for biotic stresses in cassava — C Egesi from CGIAR Generation Challenge Programme

GRM 2013: Implementing MARS Project for drought tolerance and the Cassava Breeding Community of Practice: Accomplishments in the GCP and the Years Ahead — E Okogbenin from CGIAR Generation Challenge Programme

More links

Chiedozie’s profile
Cassava – Research | Community of practice | InfoCentre | Podcasts | Videos | Data management | Blogposts |Slides
Integrated Breeding Platform (IBP)

‘Milking’ cowpeas in Mozambique for protein and profit… plus a pox upon pests!

Africa, Capacity building, Cowpeas, Crop breeding, Genomics, Legumes No Responses »

May 302014

Rogério Chiulele

Today, we travel the Milky Way on a voyage to Mozambique. Our man along the Milky Way is Rogério Marcos Chiulele (pictured), a lecturer at Mozambique’s Universidade Eduardo Mondlane’s Crop Science Department. He is also the lead scientist for cowpea research in Mozambique for the Tropical Legumes I (TLI) project. This gives Rogério a crucial tri-focal down-to-earth and away-from-the-clouds perspective on cowpea pedagogy, research and development. It is through this pragmatic triple-lens prism that Rogerio speaks to us today, once he’s captained us safely back from the stars to Planet Earth, Southeast Africa. After the protein and profit, next stop for him and team is ridding cowpeas of pod-sucking pests, among other things slated for the future. But back from the future to the present and its rooted realities…Problems, yes, but also lots of good scores, plus a deft sleight of hand that are bound to have you starry-eyed, we bet.

…cowpeas rank fourth as the most cultivated crop…”

Q: Tell us about Mozambique and cowpeas: are they important?

The devastating effects of nematodes on cowpea roots.

In Mozambique, cowpeas are an important source of food, for both protein and profit, particularly for the resource-poor households that benefit from cowpea income and nutrition. In terms of cultivation, cowpeas rank fourth as the most cultivated crop after maize, cassava and groundnuts, accounting for about 9 percent of the total cultivated area, and estimated at nearly four million hectares of smallholder farms. The crop is produced for grain and leaves, mostly for household consumption but it is becoming increasingly important as a supplement for household income.

But while its potential for food, protein and income is recognised, the realisation of such potential is still limited by drought due to irregular and insufficient rain; affliction by pests such as aphids, flower thrips and nematodes; diseases such as cowpea aphid mosaic virus and cowpea golden mosaic virus; and cultivation of low-yielding and non-improved varieties.

…we backcross to varieties with traits that farmers prefer…”

Q: And on cowpea research and breeding?
Since 2008, Universidade Eduardo Mondlane [UEM] established a cowpea-breeding programme for addressing some of the limiting constraints affecting cowpea production and productivity. This has been possible through collaboration with different funding institutions such as the Generation Challenge Programme.

2008: Screening of the 300 genotypes.

That same year [2008], a UEM research team that I coordinate qualified for a GCP capacity-building à la carte grant. In this project, we screened 300 Mozambican cowpea lines for drought tolerance. From these, we identified 84 genotypes that were either high-yielding or drought-tolerant. We further evaluated the 84 genotypes for another three seasons in two locations. From the 84, we identified six genotypes that not only had the two sought-after traits, but were also adapted to different environments.

In 2010, the UEM team joined the TLI project. For the six pre-identified genotypes, the UEM breeding programme is using marker-assisted recurrent selection [MARS] and marker-assisted backcrossing [MABC], combining drought tolerance and resistance to major biotic stresses occurring in Mozambique. In MABC, we are conducting a backcross to varieties with traits that farmers prefer, which includes aspects such as large seeds, early maturity and high leaf production.

…we conducted a farmers’ participatory varietal selection to glean farmers’ perceptions and preferences on cowpea varieties and traits…”

Q: What is the main focus in your work, and how and when do farmers come in?
The breeding work conducted by UEM is targeting all Mozambican agroecologies, but with particular focus on southern Mozambique which is drought-prone. In addition to drought, the area is plagued by many pests such as aphids, flower thrips, nematodes and pod-sucking pests. So, in addition to drought tolerance, we are conducting screening and selection for resistance to aphids, flower thrips and nematodes. In the near future, we will start screening for resistance to pod-sucking pests.

2009: field screening of the 84 genotypes in diff locations.

2009: Rogério during field screening of the 84 genotypes in different locations.

In 2009, we conducted a farmers’ participatory varietal selection to glean farmers’ perceptions and preferences on cowpea varieties and traits. From the study, six of the lines passed participatory variety selection with farmers, as they were large-seeded with good leaf production which provides additional food.

we hope to release three varieties in 2015…Our involvement with GCP has not only increased our exposure, but also brought along tangible benefits… I firmly believe black-eyed peas can really make a difference.”

Q: To what would you attribute the successes your team is scoring, and what are your goals for the future, besides screening for pod-sucking pests?
The success of the work that the Eduardo Mondlane team is doing is partly due to the collaboration and partnership with USA’s University of California, Riverside [UCR]. UCR sent us 60 lines from the GCP cowpea reference set* [Editorial note: see explanation at the bottom], which we evaluated for drought tolerance for four seasons in two locations – one with average rainfall and the other drought-prone. As these lines were already drought-tolerant, we tested them for adaptation to the local environment, and for high yield. From the set, we hope to release three varieties in 2015. In addition, for evaluating the different varieties, we also crossed the local varieties with black-eyed peas, which have a huge market appeal: local varieties fetch roughly half a US dollar per kilo, compared to black-eyed peas whose price is in the region of four to five US dollars.

2013: multilocation trials.

Our involvement with GCP has not only increased our exposure, but also brought along tangible benefits. For example, previously, nothing was being done on drought tolerance for cowpeas. But now we receive and exchange material, for example, the black-eyed peas from UCR that we received through GCP, which are set to boost production and markets, thereby improving lives and livelihoods. Amongst the varieties we are proposing to release is one black-eye type. I firmly believe black-eyed peas can really make a difference.

In addition, besides funding a PhD for one of our researchers, Arsenio Ndeve, who is currently at UCR, the Generation Challenge Programme, contributed to improvement on storage and irrigation facilities. We purchased five deep freezers for seed storage and one irrigation pump. Presently, we have adequate storage facilities and we conduct trials even during the off-season, thanks to the irrigation pump provided by GCP.

****

And on that upbeat note even as the challenge ahead is immense, today’s chat with Rogério ends here. To both pod-sucking pests and all manner of plagues on cowpeas, beware, as thy days are numbered: it would seem that Rogério and team firmly say: “A pox on both your houses!”

*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

Links

REPORT on Rogério’s groundbreaking cowpea research capacity-building project on pp 130–132 in this PDF. Excerpt: “This project was the first of this nature in the country.”
BLOGPOST: Cowpeas – uncowed and unbowed: believing that what could be can be, in breeding
BLOGPOST: Profile on Jeff Ehlers, previously TLI cowpea research leader, he talks of his past but also his TLI work in this post
Cowpea research | research products | blogposts
Legumes Research initiative | InfoCentre | blogposts
Capacity building

Tanzanian groundnut researchers breaking new ground…and carrying their own crosses!

Africa, Capacity building, Groundnuts, Legumes No Responses »

May 122014

Omari Mponda

After getting a good grounding on the realities of groundnut research from Vincent, our next stop is East Africa, Tanzania, where we meet Omari Mponda (pictured). Omari is a Principal Agricultural Officer and plant breeder at Tanzania’s Agricultural Research Institute (ARI), Naliendele, and country groundnut research leader for the Tropical Legumes I (TLI) project, implemented through our Legumes Research Initiative. Groundnut production in Tanzania is hampered by drought in the central region and by rosette and other foliar diseases in all regions. But all is not bleak, and there is a ray of hope: “We’ve been able to identify good groundnut-breeding material for Tanzania for both drought tolerance as well as disease resistance,” says Omari. Omari’s team are also now carrying their own crosses, and happy about it. Read on to find out why they are not labouring under the weight of the crosses they carry…

…we have already released five varieties…TLI’s major investment in Tanzania’s groundnut breeding has been the irrigation system… Frankly, we were not used to being so well-equipped!”

Q: How did you go about identifying appropriate groundnut-breeding material for Tanzania?
A: We received 300 reference-set lines from ICRISAT [International Crops Research Institute for the Semi-Arid Tropics], which we then genotyped over three years [2008– 2010] for both drought tolerance and disease resistance. After we identified the best varieties, these were advanced to TLII [TLI’s sister project] for participatory variety selection with farmers in 2011–2012, followed by seed multiplication. From our work with ICRISAT, we have already released five varieties.

Harvesting ref set collection at Naliendele_w

Harvesting the groundnut reference-set collection at Naliendele. 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.

ARI–Naliendele has also benefitted from both human and infrastructure capacity building. Our scientists and technicians were trained in drought phenotyping at ICRISAT Headquarters in India. One of our research assistants, Mashamba Philipo, benefitted from six-month training, following which he advanced to an MSc specialising in drought phenotpying using molecular breeding. In his work, he is now using drought germplasm received from ICRISAT. In terms of laboratory and field infrastructure, the station got irrigation equipment to optimise drought-phenotyping trials. Precision phenotyping and accurate phenotypic data are indispensable for effective molecular breeding. To facilitate this, ARI–Naliendele benefitted from computers, measuring scales, laboratory ware and a portable weather station, all in a bid to assure good information on phenotyping. But by far, TLI’s major investment in Tanzania’s groundnut breeding has been the irrigation system which is about to be completed. This will be very useful as we enter TLIII for drought phenotyping.

For us, this is a big achievement to be able to do national crosses. Previously, we relied on ICRISAT…we are advancing to a functional breeding programme in Tanzania… gains made are not only sustainable, but also give us independence and autonomy to operate..We developing-country scientists are used to applied research and conventional breeding, but we now see the value and the need for adjusting ourselves to understand the use of molecular markers in groundnut breeding.”

Omari (right), with Hannibal Muhtar (left), who was contracted by GCP to implement infrastructure improvement for ARI Naliendele. See http://bit.ly/1hriGRp

Flashback to 2010: Omari (right), with Hannibal Muhtar (left), who was contracted by GCP to implement infrastructure improvement for ARI Naliendele, and other institutes. See http://bit.ly/1hriGRp

Q: What difference has participating in TLI made?
A: Frankly, we were not used to being so well-equipped, neither with dealing with such a large volume as 300 lines! But we filtered down and selected the well-performing lines which had the desired traits, and we built on these good lines. The equipment purchased through the project not only helped us with the actual phenotyping and being able to accurately confirm selected lines, but also made it possible for us to conduct off-season trials.

We’re learning hybridisation skills so that we can use TLI donors to improve local varieties, and our technicians have been specifically trained in this area. For us, this is a big achievement to be able to do national crosses. Previously, we relied on ICRISAT doing the crosses for us, but we can now do our own crosses. The difference this makes is that we are advancing to a functional breeding programme in Tanzania, meaning the gains made are not only sustainable, but also give us independence and autonomy to operate. Consequently, we are coming up with other segregating material from what we’ve already obtained, depending on the trait of interest we are after.

Another big benefit is directly interacting with world-class scientists in the international arena through the GCP community and connections – top-rated experts not just from ICRISAT, but also from IITA, CIAT, EMBRAPA [Brazil], and China’s DNA Research Institute. We have learnt a lot from them, especially during our annual review meetings. We developing-country scientists are used to applied research and conventional breeding, but we now see the value and the need for adjusting ourselves to understand the use of molecular markers in groundnut breeding. We now look forward to TLIII where we expect to make impact by practically applying our knowledge to groundnut production in Tanzania.

Interesting! And this gets us squarely back to capacity building. What are your goals or aspirations in this area?
A: Let us not forget that TLI is implemented by the national programmes. In Africa, capacity building is critical, and people want to be trained. I would love to see fulltime scientists advance to PhD level in these areas which are a new way of doing business for us. I would love for us to have the capacity to adapt to our own environment for QTLs [quantitative trait loci], QTL mapping, and marker-assisted selection. Such capacity at national level would be very welcome. We also hope to link with advanced labs such as BecA [Biosciences eastern and southern Africa] for TLI activities, and to go beyond service provision with them so that our scientists can go to these labs and learn.

There should also be exchange visits between scientists for learning and sharing, to get up to date on the latest methods and technologies out there. For GCP’s Integrated Breeding Platform [IBP], this would help IBP developers to design reality-based tools, and also to benefit from user input in refining the tools.

Links

Groundnuts – Research | Research products | Videos | Blogposts | InfoCentre | Slides
Legumes – Research Initiative | InfoCentre (including for groundnuts)
Integrated Breeding Platform (IBP) – What’s it all about? | Introduction blogpost | Other IBP blogposts
TLIII – Tropical Legumes III Project
‘Naliendele’ demystified: what does the name mean?

SLIDES by Omari on groundnut research and research data management in Tanzania

TLI 2012: Groundnut breeding – Tanzania from CGIAR Generation Challenge Programme

TLI 2012: Data management for groundnut breeding – Tanzania from CGIAR Generation Challenge Programme

A grounding in the reality of groundnut research in Africa, and why blood is thicker than water

Africa, Genetics, Genomics, Groundnuts, Legumes 2 Responses »

Mar 312014

Vincent Vadez

Today, we travel to yet another sun-kissed spot, leaving California behind but keeping it legumes. We land in Africa for some ground truths on groundnuts with Vincent Vadez (pictured), groundnut research leader for the Tropical Legumes I (TLI) Project. Vincent fills us in on facts and figures on groundnuts and Africa – a tale of ups and downs, triumphs and trials, but also of ‘family’ alliances not feuds, and of problems, yes, but also their present or potential solutions. On to the story then! Read on to find out why groundnuts are…

….A very mixed bag in Africa
Groundnuts (Arachis hypogaea L), also called peanuts, are a significant subsistence and food crop in sub-Saharan Africa. There, groundnuts are grown in practically every country, with the continent accounting for roughly a quarter of the world’s production. Despite this rosy African statistic, problems abound: for example, nearly half (40 percent) of the of the world’s total acreage for groundnuts is in Africa, which dramatically dims the 25 percent global production quota.

In Africa, groundnuts are typically cultivated in moderate rainfall areas across the continent, usually by women. (See editorial note* at the end of the story)

Clearly then, Africa’s yields are low, borne out by telling statistics which show African production at 950 kilos per hectare, in acute contrast to 1.8 tonnes per hectare in Asia.

…every year, yields worth about USD 500 million are lost”

What ails Africa’s production?
The main constraints hampering higher yields and quality in Africa are intermittent drought due to erratic rainfall, as well as terminal drought during maturation. And that is not all, because foliar (leaf) diseases such as the late leaf spot (LLS) or groundnut rosette are also taking their toll. Economically speaking, every year, yields worth about USD 500 million are lost to drought, diseases and pests. Plus, the seeding rates for predominantly bushy groundnut types are low, and therefore insufficient to achieve optimal ground cover. Thus, genetic limitations meet and mingle with major agronomic shortcomings in the cultivation of groundnuts, making it…

…. A tough nut to crack
Groundnuts are mostly cultivated by impoverished farmers living in the semi-arid tropics where rainfall is both low and erratic.

. Tough it may be for crop scientists, but clearly not too tough for these two youngsters shelling groundnuts at Mhperembe Market, Malawi.

“To help double the productivity of this crop over the next 10 years, we need to improve groundnuts’ ability to resist drought and diseases without farmers needing to purchase costly agricultural inputs,” says Vincent.

But the crop’s genetic structure is complex, plus, for resistance to these stresses, its genetic diversity is narrow. “Groundnuts are therefore difficult and slow to breed using conventional methods,” says Vincent. And yet, as we shall see later, groundnuts are distinctly disadvantaged when it comes to molecular breeding. But first, the good news!

…wild relatives have genes for resisting the stresses… molecular markers can play a critical role”

Why blood is thicker than water, and family black sheep are valued
Kith and kin are key in groundnut science. Vincent points out that groundnuts have several wild relatives that carry the necessary genes for resisting the stresses – especially leaf diseases – to which the crop is susceptible. These genes can be transferred from the wild cousins to the cultivated crop by blending conventional and molecular breeding techniques. But that is easier said than done, because cultivated groundnuts can’t cross naturally with their wild relatives owing to chromosomic differences.

Groundnut flower

“In modern breeding, molecular markers can play a critical role,” says Vincent. “Using markers, one can know the locations of genes of interest from an agronomic perspective, and we can then transfer these genes from the wild relatives into the groundnut varieties preferred by farmers and their markets.”

[The] ‘variegated’ partnership has been essential for unlocking wild groundnut diversity…”

Partnerships in and out of Africa, core capacities
“Partners are key to this work,” says Vincent. The groundnut work is led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), with collaborators in the target countries, which are Malawi (Chitedze Agricultural Research Centre), Senegal (Institut sénégalais de recherches agricoles ‒ ISRA) and Tanzania (Agricultural Research Institute, Naliendele), Moving forward together, continuous capacity building for partners in Africa is part and parcel of the project. To this end, there have been several training workshops in core areas such as molecular breeding and phenotyping, farmer field days in the context of participatory varietal selection, as well as longer-term training on more complex topics such as drought, in addition to equipping the partners with the critical infrastructure needed for effective phenotyping.

Freshly dug-up groundnuts.

Further afield out of Africa, Vincent’s team also collaborates with the Brazilian Agricultural Research Corporation (EMBRAPA), France’s Centre de coopération internationale en recherche agronomique pour le développement ‒ CIRAD, and USA’s University of Georgia.

This ‘variegated’ partnership has been essential for unlocking the wild groundnut diversity when about 12 years ago the EMBRAPA team successfully generated a number of ‘synthetic’ groundnuts from their wild relatives. Unlike the wild groundnuts, these synthetic groundnuts can be crossed to the cultivated type, bringing with them treasure troves of beneficial genes pertaining to the wild that would be otherwise unreachable for the cultivated varieties. Taking this one step further, the CIRAD‒ISRA team, in a close North‒South partnership, has used one of the synthetics from the Brazilian programme to generate new genetic diversity in the groundnut cultivar Fleur11. They are using additional synthetics from ICRISAT to further enlarge this genetic diversity in cultivated groundnuts.

These techniques and tools provide signposts on the genome of varieties for characteristics of importance”

A world first for an ‘orphan’, goals achieved, and what next
Among other goals, the team notably achieved a world first: “To produce the first SSR-based genetic linkage map for cultivated groundnuts!” declares Vincent. SSR stands for simple sequence repeat. The map was published in 2009, followed later on by a groundnut consensus map in 2012.

Youngster bearing fresh groundnuts along River Gambia in Senegal.

But what do these maps and their publication mean for groundnut production? Vincent explains: “These techniques and tools provide signposts on the genome of varieties for characteristics of importance ‒ for instance, resistance to a disease ‒ and these are used in combination to speed up the development of groundnut varieties that are more resistant to the stresses found in the harsh environments where most of the tropical world’s poor farmers live. Accelerating development means quicker delivery to farmers who are at high risk of going hungry. TLI Phase I produced synthetic groundnuts with new genes for disease resistance.”

In Phase II of the TLI Project which terminates in mid-2014, the team has continued to identify new genetic and genomic resources, for instance new sources of drought resistance from the germplasm and which are currently being used in the development of new breeding stocks. What is significant about this is that groundnuts ‒ like most other members of the legume family ‒ do not have much in the way of genomic and molecular-genetic resources, and are in fact consequently referred to in some circles as ‘orphans’ of the genome revolution. The focus has also been on resistance to rust, early and late leaf spot, and rosette – all economically critical diseases – by tapping the resilience of GBPD4, a cultivar resistant to rust and leaf spot, and introducing its dual resistance to fortify the most popular varieties against these diseases. The team also hopes to scale up these promising examples.

We believe this team is firmly on the way to fulfilling their two-fold project objectives which were: (1) to develop genomic resources and produce the first molecular-breeding products of the crop by injecting disease resistance (from TLI Phase I work) into farmer- and market-preferred varieties; and, (2) to lay the foundation for future marker-assisted recurrent selection (MARS) breeding by tapping on newly identified sources of drought tolerance.

the genetic stocks that hold the most promise to overcome leaf disease are found in the wild relatives… A thorough reflection is needed to combine good genetics with sound agronomic management”

The future
But the team is not resting on their laurels, as the work will not stop with the fulfillment of project objectives. In many ways, their achievements are in fact just the beginning. The new breeding stocks developed during TLI Phase II need to be evaluated further for their drought tolerance and disease resistance prior to their deployment in breeding programmes, and this activity ‒ among others ‒ is included for the next phase of the work in the proposed Tropical Legumes III project. In particular, the genetic stocks that hold the most promise to overcome leaf disease are found in the wild relatives. Thus, the existing materials need to be fully exploited and more need to be produced to cover the full breadth of potential stresses. Vincent adds “Of course an increasing part of the efforts will be about assuring quality evaluation data, meaning we must continue to significantly enhance the capacity ‒ both human and physical ‒ of our partners in target countries. Last but not least, the good wheat and rice cultivars that directly arose from the green revolution would have been nothing without nitrogen fertiliser and irrigation.” Vincent adds that the same applies to groundnuts: they are cultivated in infertile soil, at seeding rates that are unlikely to optimise productivity.

Groundnut drawing

For this reason, and others explained above, “A thorough reflection is needed to combine good genetics with sound agronomic management,” Vincent concludes, stressing the importance of what he terms as ‘looking beyond the fence’. Vincent’s parting shot, as our conversation draws to close: “In fact, I have grown increasingly convinced over the past year that we probably overlook those agronomic aspects in our genetic improvements at our peril, and we clearly need a re-think of how to better combine genetic improvement with the most suitable and farmer-acceptable agronomic management of the crop.”

Much food for thought there! And probably the beginnings of an animated conversation to which a groundnut crop model, on which Vincent and team are currently working, could soon yield some interesting answers on the most suitable genetic-by-management packages, and therefore guide the most adequate targets for crop improvement.

Links

Photo-story on Flickr
Groundnut research in Africa
Groundnut research Videos | Slides | in Tanzania
Legumes Research Initiative | InfoCentre
Journal articles: advances in groundnut genomics (2012) | Orphan legume crops enter the genomics era! (2009)
Ever wondered why the name groundnuts? Wonder no more, with this answer from the underground

*Editorial note: Erratum – Photo changed on April 8 2014, as the previous one depicted chickpeas, not groundnuts. We apologise to our readers for the error.

California’s ‘Constant Gardener’, cowpea crusader and catapult constructor

Africa, Capacity building, Cowpeas, Genetics, Genomics, Legumes, Researchers 2 Responses »

Mar 202014

Jeff Ehlers

Our guest today is Jeff Ehlers (pictured), Programme Officer at the Bill & Melinda Gates Foundation. Jeff’s an old friend of GCP, most familiar to the GCP community in his immediate past stomping grounds at the University of California, Riverside (UCR), USA, leading our research to improve cowpea production in the tropics, for which sunny California offers a perfect spot for effective phenotyping. Even then, Jeff was not new to CGIAR, as we’ll see from his career crossings. But let’s not get ahead of ourselves in narrating Jeff’s tale. First, what would high-end cowpea research have to do with crusading and catapults? Only Jeff can tell us, so please do read on!

The GCP model was a very important way of doing business for CGIAR and the broader development community, enabling partnerships between international research institutes, country programmes and CGIAR. This is particularly important as the possibilities of genomics-led breeding become even greater…If anything, we need to see more of this collaborative model.”

Growing green, sowing the seed, trading glory for grassroots
Growing up in USA’s Golden State of California, green-fingered Jeff had a passion for cultivating the land rather than laboratory samples, harbouring keen ambitions to become a farmer. This did not change with the years as he transited from childhood to adolescence. The child grew into a youth who was an avid gardener: in his student days, Jeff threw his energy into creating a community garden project ‒ an initiative which promptly caught the eye of his high school counsellor, who suggested Jeff give the Plant Science Department at UCR a go for undergraduate studies.

And thus the seeds of a positively blooming career in crop research were sown. However, remaining true to the mission inspired by his former community-centred stomping grounds, a grassroots focus triumphed over glory-hunting for Jeff, who – no stranger to rolling his sleeves up and getting his fingers into the sod – found himself, when at the University of California, Davis, for his advanced studies, embarking on what was to become a lifelong undertaking, first at the International Institute of Tropical Agriculture (IITA) and then at UCR, dedicated to a then under-invested plant species straggler threatening to fall by the research world’s wayside. With a plethora of potential genomic resources and modern breeding tools yet to be tapped into, Jeff’s cowpea crusade had begun in earnest…

GCP’s TLI was essential in opening that door and putting us on the path to increased capability – both for cowpea research enablement and human capacity”

Straggler no more: stardom beckons, and a place at the table for the ‘orphan’
And waiting in the wings to help Jeff along his chosen path was the Generation Challenge Programme (GCP), which, in 2007, commissioned Jeff’s team to tackle the cowpea component of the flagship Tropical Legumes I (TLI) project, implemented by GCP under the Legumes Research Initiative. TLI is mainly funded by the Bill & Melinda Gates Foundation. The significance of this project, Jeff explains, was considerable: “The investment came at a very opportune time, and demonstrated great foresight on the part of both GCP and the Foundation.” Prior to this initiative, he further explains, “there had been no investment by anyone else to allow these orphan crops to participate in the feast of technologies and tools suddenly available and that other major crops were aggressively getting into. Before GCP and Gates funding for TLI came along, it was impossible to think about doing any kind of modern breeding in the orphan grain legume crops. GCP’s TLI was essential in opening that door and putting us on the path to increased capability – both for cowpea research enablement and human capacity.”

Flashback: UCR cowpea team in 2009. Left to right: Wellington Muchero, Ndeye Ndack Diop (familiar, right?!), Raymond Fenton, Jeff Ehlers, Philip Roberts and Timothy Close in a greenhouse on the UCR campus, with cowpeas in the background. Ndeye Ndack and Jeff seem to love upstaging each other. She came to UCR as a postdoc working under Jeff, then she moved to GCP, with oversight over the TLI project, thereby becoming Jeff’s boss, then he moved to the Foundation with oversight over TLI. So, what do you think might be our Ndeye Ndack’s next stop once GCP winds up in 2014? One can reasonably speculate….!

Of capacity building, genomics and ‘X-ray’ eyes
This capacity-building cornerstone – which, in the case of the TLI project, is mainly funded by the European Commission – is, says Jeff, a crucial key to unlocking the potential of plant science globally. “The next generation of crop scientists ‒ particularly breeders ‒ need to be educated in the area of genomics and genomics-led breeding.”

While stressing the need for robust conventional breeding efforts, Jeff continues: ”Genomics gives the breeder X-ray eyes into the breeding programme, bringing new insights and precision that were previously unavailable.”

In this regard, Jeff has played a leading role in supporting skill development and organising training for his team members and colleagues across sub-Saharan Africa, meaning that partners from Mozambique, Burkina Faso and Senegal, among others, are now, in Phase II of the TLI project, moving full steam ahead with marker-assisted and backcross legume breeding at national level, thanks to the genotyping platform and genetic fingerprints from Phase I of the project. The genotyping platform, which is now publicly available to anyone looking to undertake marker-assisted breeding for cowpeas, is being widely used by research teams not only in Africa but also in China. Thanks in part then to Jeff and his team, the wheels of the genomics revolution for cowpeas are well and truly in motion.

Undergoing the transition from phenotypic old-school plant breeder to modern breeder with all the skills required was a struggle…it was challenging to teach others the tools when I didn’t know them myself!…without GCP, I would not have been able to grow in this way.”

Talking about a revolution, comrades-in-arms, and a master mastering some more
But as would be expected, the road to revolution has not always been entirely smooth. Reflecting on some of the challenges he encountered in the early TLI days, and highlighting the need to invest not only in new students, but also in upgrading the existing skills of older scientists, Jeff tells of a personal frustration that had him battling it out alongside the best of them: “Undergoing the transition from phenotypic old-school plant breeder to modern breeder with all the skills required was a struggle,” he confides, continuing: “It was challenging to teach others the tools when I didn’t know them myself!”

Thus, in collaboration with his cowpea comrades from the global North and South, Jeff braved the steep learning curve before him, and came out on the other side smiling – an accomplishment he is quick to credit to GCP: “It was a very interesting and fruitful experience, and without GCP, I would not have been able to grow in this way,” he reveals. Holding the collaborative efforts facilitated by the broad GCP network particularly dear, Jeff continues: “The GCP model was a very important way of doing business for CGIAR and the broader development community, enabling partnerships between international research institutes, country programmes and CGIAR. This is particularly important as the possibilities of genomics-led breeding become even greater…If anything, we need to see more of this collaborative model.”

GCP’s Integrated Breeding Platform addresses the lack of modern breeding skills in the breeding community as a whole, globally…The Platform provides extremely valuable and much-needed resources for many public peers around the world, especially in Africa…”

One initiative which has proved especially useful in giving researchers a leg up in the mastery of modern breeding tools, Jeff asserts, is GCP’s Integrated Breeding Platform (IBP): “IBP addresses the lack of modern breeding skills in the breeding community as a whole, globally. By providing training in the use of genomic tools that are becoming available, from electronic capture of data through to genotyping, phenotyping, and all the way to selective decision-making and analysis of results, IBP will play a critical role in helping folks to leverage on the genomics revolution that’s currently unfolding,” Jeff enthuses, expanding: “The Platform provides extremely valuable and much-needed resources for many public peers around the world, especially in Africa where such one-off tools that are available commercially would be otherwise out of reach.”

Conqueror caparisoned to catapult: life on the fast lane and aiming higher
Well-versed in conquering the seemingly unobtainable, Jeff shares some pearls of wisdom for young budding crop scientists:”Be motivated by the mission, and the ideas and the science, and not by what’s easy, or by what brings you the most immediate gratification,” he advises, going on to explain: “Cowpeas have been through some really tough times. Yet, my partners and I stuck it out, remained dedicated and kept working.” And the proof of Jeff’s persistence is very much in the pudding, with his team at UCR having become widely acclaimed for their success in catapulting cowpeas into the fast lane of crop research.

It was a success that led him to the hallways of the Bill & Melinda Gates Foundation, where, after two decades at UCR, Jeff is currently broadening his legume love affair to also embrace beans, groundnuts, chickpeas, pigeonpeas and soya beans.

February 2014: Jeff donning his new Gates hat (albeit with a literal ICRISAT cap on). Behind him is a field of early maturing pigeonpea experiment at ICRISAT India.

February 2014: Jeff donning his (now-not-so-)new Gates hat and on the road, visiting ICRISAT in India. Behind him is an ICRISAT experimental field of early-maturing pigeonpeas. Here, our conquering crusader is ‘helmeted’ in an ICRISAT cap, even if not horsed and caparisoned for this ‘peacetime’ pigeonpea mission!

On his future professional aspirations, he says: “The funding cut-backs for agriculture which started before 1990 or so gutted a lot of the capacity in the public sector, both in the national programmes in Africa but also beyond. I hope to play a role in rebuilding some of the capacity to ensure that people take full advantage of the technical resources available, and to enable breeding programmes to function at a higher level than they do now.”

Jeff (foreground) inspecting soya bean trials in Kakamega, Kenya, in January 2013. Next to Jeff is Emmanuel Monyo, the coordinator of the Tropical Legumes II (TLII) project – TLI’s twin – whose brief is seed multiplication. TLII is therefore responsible for translating research outputs from TLI into tangible products in the form of improved legume varieties.

Whilst it’s been several years since he donned his wellington boots for the gardening project of his youth, what’s clear in this closing statement is an unremitting and deeply ingrained sense of community spirit – albeit with a global outlook – and a fight for the greater good that remain at the core of Jeff’s professional philosophy today.

No doubt, our cowpea champion and his colleagues have come a long way, with foundations now firmly laid for modern breeding in the crop on a global scale, and – thanks to channels now being established to achieve the same for close relatives of the species – all signs indicate that the best is yet to come!

Links

Cowpea research
Cowpea research products
Legume Research Initiative
Legumes InfoCentre
At the time we published this post, this is where Jeff was
Check out Jeff’s new perch: see more of what he’s been up to – and with whom he’s been hobnobbing – through these thousand-words-worth photos.

Inspiring change: GCP celebrates sisters in science on International Women’s Day

Africa, Asia, Capacity building, Crop breeding, Events, Researchers, Women in science No Responses »

Mar 072014

“Women can do advanced agricultural science, and do it well!” Elizabeth Parkes, cassava researcher, Ghana

Being a woman scientist in today’s world (or at any time in history!) is no mean feat, science traditionally having been the domain of men. We are therefore drawn to this sub-theme: Inspiring change, in addition to the global theme Equality for women is progress for all, To mark International Women’s Day tomorrow, UNESCO has developed an interactive tool which collates facts and figures from across the world on women in science. The cold scientific truth displayed in the attractive petri dish design shows that only 30 percent of researchers worldwide are women.

At GCP, we have been fortunate enough to have a cross-generational spectrum of, not only women scientists, but that even rarer species, women science leaders – who head a project or suite of projects and activities, and who actively nurture and mentor future science leaders – to ultimately contribute to the fulfilment of our mission: Using genetic diversity and advanced plant science to improve crops for greater food security in the developing world. The United Nations has designated 2014 as the Year of Family Farming. GCP’s women researchers have contributed to improving the lives of their farming counterparts the world over, especially in the developing world where on average, 43 percent of the agricultural labour force are women, rising to 60 percent and 70 percent in some regions. (FAO)

Please mind the gap…to leap to that all-important initiation into science

UNESCO’s Women in Science interactive tool

The UNESCO tool mentioned above and embedded to the left allows users to “explore and visualise gender gaps in the pipeline leading to a research career, from the decision to get a doctorate degree to the fields of science that women pursue and the sectors in which they work” with this affirmation: “Perhaps most importantly, the data tool shows just how important it is to encourage girls to pursue mathematics and science at a young age.”

In our International Women’s Day multimedia expo, we profile the life and work of a selection of our smart scientific sisters through words, pictures and sound, to explain just how they overcame obstacles, from taking that first hurdle to study science at an early age, to mobility up the research rungs to reach the very top of their game, all the while balancing work, life and family.

A blogpost fest to introduce our first special guests

Masdiar Bustamam

We begin our show with a blogpost fest, and first up is GCP’s original Mother Nature, renowned scientist and constant gardener of the molecular breeding plot, Masdiar Bustamam. After a virtual world-tour of research institutes early on in her career, Masdiar took the knowledge of molecular breeding back home, to the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD), where she personally took up the challenge to work with the fledgling world of biotechnology, set up a lab, and helped establish molecular breeding in her country. In an amazing 37-years-odd research career, Masdiar tended not only tender rice shoots, but also budding blossoms in the form of her many students, whom she nurtured and mentored throughout their studies, and who have now seamlessly inherited her mantle to carry on the mission with the same ever-bright spirit. More

Rebecca Nelson

We now skip continents and oceans to meet the feisty, continent- and crop-hopping scientist, Rebecca Nelson (Cornell University, USA). “I wanted to get out into the world and try and have a practical impact instead of doing research for the sake of research,” Rebecca says – and that she did, first leaving her native USA to work in the International Rice Research Institute (IRRI) in the Philippines. There she teamed up with friend and colleague, Masdiar Bustamam, to establish Masdiar’s laboratory at ICABIOGRAD, Indonesia. The American continent then called her back, where she moved countries and institutes, and switched from rice to maize research, marking the launch of her GCP experience – which simultaneously introduced her to her a whole new network of international crop researchers. This rich research tapestry was woven together by a poignant pain deep in her heart, as a mother herself, of “so many mothers not being able to feed their families.” Rebecca wanted to combat this problem, and crop science is her weapon. More

Zeba Seraj

Next, we meet another true mother of molecular plant breeding, Zeba Seraj (University of Dhaka, Bangladesh). Zeba, whose mind is perpetually on call in the pursuit of science, has been around the world, and from plants to animals and back again in the course of her multifaceted science career. During her PhD and postdoc experience in the UK, still with fauna, she cultivated her expertise in molecular biology and recombinant DNA technology, but a lack of opportunities in that field back in Bangladesh saw her enter the world of crop science, where she has remained ever since. Back at her alma mater, the University of Dhaka, she founded a molecular biology lab, and has nurtured and inspired generations of young biochemists. Her GCP project, using molecular markers to develop salt-tolerant rice, was a real eye-opener for her, and allowed her to truly ‘see’ how applied science and such a practical project would have a direct impact on her country’s food security, now and in the future. More

Sigrid Heuer

Our next scientist is also truly motivated by putting theory into practice through the application of upstream research all the way down the river, and directly into farmers’ fields. Sigrid Heuer (now with the Australian Centre for Plant Functional Genomics), a German national, has pursued her scientific ventures in Europe, Africa, Asia, and now Oceania, with many challenges along the way. Enter the Generation Challenge Programme, and the chance for Sigrid (then at IRRI) to lead a major project, the Pup1 rice phosphorus uptake project, which taught Sigrid the A–Z of project management, and gave her ample scope for professional growth. Her team made a major scientific breakthrough, which was not only documented in international journals, but was also widely covered by global media. From this pinnacle, Sigrid passed on the baton to other scientists and moved on to new conquests. More

Arllet Portugal

Now, all this research we’ve been celebrating generates a massive amount of data, as you can well imagine. What exactly can our scientists do with all that data, and how can they organise them? GCP’s Arllet Portugal, hailing from The Philippines, gives us the lowdown on smart and SHARP data management whilst also giving us some insights into how she started out on the long and winding road to leading data management for GCP’s Integrated Breeding Platform. In particular, Arllet describes the considerable challenge of changing researchers’ mindsets regarding the importance of effective data management in the context of their research, and enthuses over the excitement with which developing-country researchers welcome the GCP-funded electronic tablets they now use to collect and record data directly in the field. More

Armin Bhuiya

If there were a muse for young women scientists, it might very well be the subject of our next blogpost profile, Armin Bhuiya (Bangladesh Rice Research Institute). After completing her master’s degree on hybrid rice in her native Bangladesh, Armin was already thinking like a true change-catalyst scientist, trying to discover what line of research would be the most useful for her country and the world. After much deliberation, she embarked on a PhD focusing on developing salt- and submergence-tolerant rice. This wise choice would take her to study under the expert eye of Abdelbagi Ismail at IRRI, in The Philippines, with the helping hand of a GCP–DuPont postgraduate fellowship. There, she learnt much in the way of precise and meticulous research, while also taking advantage to self-train in modern molecular plant breeding methods. Our bright resourceful student has now advanced to the patient erudite teacher – as she takes home her knowledge of high-tech research methods to share with her colleagues and students in Bangladesh. More

Elizabeth Parkes

Hello Africa! Switching continents and media, we now we move from the written medium to tune in to the melodic tones of Elizabeth Parkes (Crops Research Institute [CRI] of Ghana’s Council for Scientific and Industrial Research [CSIR], currently on leave of absence at the International Institute of Tropical Agriculture [ IITA]). We’re now at profile number seven in GCP’s gallery of women in science. Elizabeth, who is GCP’s Lead Cassava Researcher in Ghana, narrates an all-inclusive engaging story on the importance to agriculture of women scientists, women farmers, and cassava the wonder crop – all captured on memorable sound waves in this podcast.

If the gravity of words inscribed holds more weight, you can also read in depth about Elizabeth in a blogpost on this outstanding sister of science. Witness the full radiance of Elizabeth’s work in the life-changing world in which she operates; as she characteristically says, “I’ve pushed to make people recognise that women can do advanced agricultural science, and do it well.” And she is no exception to her own rule, as she grew professionally, apparently keeping pace with some of the giant cassava she has helped to develop through the years. But it is her role as nurturer, mentor and teacher that really raises her head-and-shoulders above the rest, from setting up a pioneering biotech lab at CRI–CSIR to conscientiously mentoring her many students and charges in work as in life, because, for Elizabeth, capacity building and cassava are inextricably coupled! More

Marie-Noëlle Ndjiondjop

In the wake of some recent high-profile screen awards, we close our multimedia expo with impressions of our science sisterhood through the medium of the seventh art: the magic visual world of the movies! A good fit for a Friday!

The following tasteful and tasty (you’ll see why!) blogpost takes our film fans right onto the red carpet to rub shoulders with our scientific screen stars!

The first screen star you’ll meet is Marie-Noëlle Ndjiondjop (Africa Rice Center), Principal Investigator (PI) of GCP’s Rice Research Initiative, who opens the video-viewing session with seven succulent slices of rice research delight. Her movies are set in the rice-growing lands of Africa, where this savoury cereal is fast becoming a staple, and tackles the tricky topics of rice-growing constraints, capacity building, molecular breeding methods, and the colossal capacity of community in collaborative research projects.

Jonaliza Lanceras-Siangliw

The following feature introduces the talented GCP PI Jonaliza Lanceras-Siangliw (BIOTEC, Thailand), whose community-minded project, set in the Mekong region, focused on strengthening rice breeding programmes by using a genotyping building strategy and improving phenotyping capacity for biotic and abiotic stresses. Though this title is something of a spoiler alert, we hope you tune in to this comprehensive reel to see the reality of molecular rice breeding in the Mekong. More

Soraya Leal-Bertioli

Last, and by no means least, is a captivating collage of clips featuring GCP researcher, Soraya Leal-Bertioli (EMBRAPA, Brazil) waxing lyrical about that hard genetic nut to crack: the groundnut, and how GCP’s Tropical Legumes I (TLI) project was crucial in getting the crop breeding community to share genetic resources, molecular markers, knowledge, and tools on a cross-continental initiative breaking boundaries in multiple ways. Video collage

Links

See what we’ve been up to on some of the social media streets, in this continuing collage of our International Women’s Day tweets in Storify. More #IWD2014 posts on our Facebook page
From our Integrated Breeding Platform (IBP), more portraits of women in science, who are keen users of IBP tools and beneficiaries of the Platform’s capacity-building opportunities.
International Women’s Day at CGIAR in text and in pictures

Made in Bangladesh: 2-in-1 salt-and-water rice ‘sandwich’ with Filipino filling and Atlantis touch

Asia, Capacity building, Genetics, Genomics, Researchers, Rice, Women in science No Responses »

Mar 072014

Two in one, in more ways than one

Armin Bhuiya

Armin Bhuiya (pictured) is a dynamic and lively young geneticist and plant breeder, who has made huge strides in tracking crucial genes in Bangladeshi rice landraces (or traditional farmer varieties). Armin took a ‘sandwich’ approach twinning two traits – salt and submergence tolerance – in order to boost farmers’ yields. Her quest for salt-impervious ‘amphibian’ rice has seen her cross frontiers to The Philippines, and back to her native Bangladesh with solutions that will make a difference, borrowing a leaf along the way from the mythical submarine world of Atlantis for life under water. Using cutting-edge crop science, Armin is literally recreating out-of-this-world stuff working two elements of the ancient world – earth and water – plus that commodity that was then so prized enjoying a premium comparable to gems: salt. Read on!

A rice heritage, and the ‘sandwich’ saga and submarine search both begin…

“My father worked at the Bangladesh Rice Research Institute (BRRI), which basically means I grew up in rice research. You could say that I was born and bred in agriculture and this inspired me to study agriculture myself,” says Armin. As a result of these early experiences, Armin started a master’s degree in 2006 on genetics and plant breeding, specialising in hybrid rice. Ever since, rice has been her religion, following in the footsteps of her father to join the Bangladesh Rice Research Institute (BRRI).

Her other defining hallmark is her two-in-one approach. Sample this: once she completed her two-in-one master’s, Armin went on to study for a PhD in the same twin areas at Bangladesh Agricultural University. Pondering long and hard on what research would be of most practical use, she asked herself “What is the need? What research will be useful for my country and for the world?” (Editorial aside: out of this world work, apparently…)

Not content pondering over the question by herself, her natural two-track approach kicked in. Mulling with her colleagues from BRRI, the answer, it first seemed, was to find ways to produce salt-tolerant high-yielding rice. In Bangladesh and many other parts of South and Southeast Asia, climate change is driving up the sea level, spreading salinity further and deeper across low-lying coastal rice-fields, beyond the bounds where salt-drenched terrain has long been a perennial problem. Modern rice varieties are highly sensitive to salt. So, despite the low yields and quality, farmers continue to favour hardy traditional rice landraces that can take the heat and hit from the salt. Proceeding from this earthy farmer reality and inverting the research–development continuum, Armin needed no further thinking as the farmers showed the way to go. Her role and the difference she could make was to track the ‘treasure’ genes locked in these landraces that were transferred to high-yielding but salt-sensitive rice varieties, to fortify them against salt.

But that was not all. There’s power in numbers and consulting others, harnessing the best in diversity. In comes the two-track approach again, with Armin now turning to fellow scientists again, with the reality from farmers. Upon further consultations with colleagues, yet another fundamental facet emerged that could not be ignored. Apparently, salt-impervious rice alone would not be not enough, and here’s why. Salt and tides aside, during the rainy season inland, flash floods regularly submerge the fields, literally drowning the crop. More than 20 million hectares in South and Southeast Asia are affected – including two million hectares in coastal Bangladesh alone. The southern belt of Bangladesh is particularly affected, as modern varieties are sensitive to not only submergence but also salinity. So Armin had her work cut out for her, and she now knew that for the fruit of her labour to boost rice production in coastal regions as well (two tracks again! Inland and coastal low-lying rice-lands), what she needed to do was to work on producing high-yielding, salt-impervious, ‘amphibian’ rice that could withstand not only salinity but also submarine life. In other words, pretty much rice for a latter-day real-life rendition of the mythical Atlantis.

Armin has successfully incorporated dual tolerance to salinity and submergence in the popular Bangladeshi mega-variety BR11. This will provide the ideal salt-tolerant ‘amphibian’ rice suitable for farmers in the flood-prone salty-water-drenched swaths of southern Bangladesh.”

Through the door of opportunity
The opportunity that opened the door for Armin to fulfil her dream was a DuPont Pioneer postgraduate fellowship implemented by GCP. The competitive programme provides grants for postgraduate study in plant breeding and genetics to boost the yields of staple food crops. This fellowship took Armin to Filipino shores and the molecular breeding labs at the International Rice Research Institute (IRRI). Here she got what she terms a golden opportunity to work under the tutelage of Abdelbagi Ismail, a leading plant physiologist focusing on overcoming abiotic stresses. From him, Armin learnt how carry out the precise meticulous research required for identifying quantitative trait loci (QTLs).

Armin at work at the IRRI greenhouse in 2011.

Armin conducted her research with two different mapping populations, both derived from Bangladeshi landraces (Kutipatnai and Ashfal). She found a total of nine quantitative trait loci (QTLs) from one mapping population and 82 QTLs from another for tolerance to salinity stress at seedling stage (QTL is a gene locus where allelic variation is associated with variation in a quantitative trait). Incorporating these additional genes into a high-yielding variety will help to develop promising salt-tolerant varieties in future. She has also successfully incorporated QTLs for dual tolerance to salinity (Saltol) and submergence (Sub1) in the popular Bangladeshi mega-variety, BR11. Stacking (or ‘pyramiding’ in technical terms) Saltol and Sub1 QTLs in BR11 will provide the ideal salt-tolerant ‘amphibian’ rice suitable for farmers in the flood-prone salty-water-drenched swaths of southern Bangladesh.

I know what to do and what is needed… I am going to share what I learned with my colleagues at BRRI and agricultural universities, as well as teach these techniques to students”

Dream achiever and sharer: aspiring leader inspiring change
The Pioneer–GCP fellowship has given Armin the opportunity to progress professionally. But, more than that, it means that through this remarkable young scientist, others from BRRI will benefit – as will her country and region. “While I was at IRRI,” Armin says, “I trained myself in modern molecular plant-breeding methods, as I knew that this practical experience in high-tech research methods would definitely help Bangladesh. I know what to do and what is needed. I am going to share what I learned with my colleagues at BRRI and agricultural universities, as well as teach these techniques to students. It makes me very happy and my parents very proud that the fellowship has helped me to make my dream come true.”

Away from professional life, there have been benefits at home too, with these benefits delivered with Armin’s aplomb and signature style in science – doing two in one, in more ways than one. This time around, the approach has led to dual doctorates for a dual-career couple in different disciplines: “When I went to The Philippines” Armin reveals, “my husband decided to come with me, and took the opportunity to study for a PhD in development communications. So we were both doing research at the same time!”

While Armin’s research promises to make a real difference in coastal rice-growing areas, Armin herself has the potential to lead modern plant breeding at her institute, carry GCP work forward in the long term, post-GCP, and to inspire others as she herself was inspired – to make dreams come true and stimulate change. An inspired rice scientist is herself an inspiration. You will agree with us that Armin personifies Inspiring change, our favoured sub-theme for International Women’s Day this year.

Go, Armin, Go! We’re mighty proud of what you’ve achieved, which we have no doubt serves as inspiration for others!

Links

Poster and poster abstract (p 32) on Armin’s work
PHOTO: Armin at GCP’s General Research Meeting 2013. Photo-story coming soon!
Profiles: Zeba Seraj (University of Dhaka, Bangladesh) and Abdelbagi Ismail (IRRI)

‘Frontier’ science and Rebecca’s ‘fire’ – enlisting nature to fortify crops against disease

Genetics, Genomics, Maize, Researchers, Rice, Women in science No Responses »

Mar 062014

Restless Rebecca

Rebecca Nelson

I’m a mother and a wife. The idea of so many mothers not being able to feed their families, and so many children not getting the nutrients they need to reach their potential, has always pained me.” – Rebecca Nelson (pictured), Professor, Plant Pathology and Plant-Microbe Biology, Cornell University, USA

In this dispatch from the ‘frontline’, fired up and leading the charge against crop disease is ‘frontier’ scientist, restless Rebecca Nelson. Where does Rebecca’s restlessness and consequent fire come from? She says it has always bothered her that a billion people go hungry every single day…

Wrestling Rebecca: feeding families one disease-resistant crop at a time
Wanting to remedy this billion-strong calamity, Rebecca has spent the last quarter century working with national and international institutes in Asia, Africa and the Americas. During this time, she has focused on understanding the ways in which plants defend themselves against diseases.

“An amazing percentage of crops are lost to pests and diseases in the developing world each year, which in turn leads to lack of food and impoverishes local economies,” she says. “These farmers can’t afford the herbicides and pesticides that developed-world farmers use to protect their crops, and those are not great solutions to the problems anyway. So it’s important to find ways to help these crops defend themselves.”

This means identifying crops with disease-resistant traits and using them to breed disease-resistant crops with long-lasting protection from a multitude of diseases.

We were really grateful that the GCP funded us so we could continue to understand and build resistance to rice blast and bacterial blight, and to connect the work on rice and maize”

Travels and travails to make a difference
After completing a PhD in zoology at the University of Washington, USA, in 1988, Rebecca spent eight years in The Philippines at the International Rice Research Institute (IRRI) and then five years at the International Potato Center in Peru. “I wanted to get out into the world and try and have a practical impact instead of doing research for the sake of research,” she says.

During her time in The Philippines, Rebecca worked on several rice disease-resistance projects. She was to continue many of these projects nine years later, as part of her GCP project – Targeted discovery of superior disease QTL alleles in the maize and rice. “We were really grateful that GCP funded us so we could continue to understand and build resistance to rice blast and bacterial blight, and to connect the work on rice and maize,” she says.

Rebecca was also delighted to involve her IRRI mentor, Hei Leung (then a GCP Subprogramme Leader for genomics), and friend, Masdiar Bustamam, of the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD). During her time at IRRI, Rebecca and her IRRI team had worked with Masdiar to establish her laboratory. “It was really pleasing to have Masdiar participate in the project and to see how far she and her lab had come since our earlier collaboration. The difference is that they now made a markedly significant contribution to the project in advancing the understanding of inheritance of rice blast and sheath blast resistance, and they developed germplasm that has really good resistance to these diseases.”

I’ve always been grateful to GCP for supporting me at that transitional stage in my career…. [I] was a relative newbie when it came to working with maize. However, I was lucky to have some really great collaborators…James helped me a lot at the start of the project and throughout. Even though our project is finished, we have teamed up on a number of other projects to continue what we started.“

Tentative transition from rice to maize; shunting between class and grant-giving
Despite winning a merit-based competitive grant, Rebecca confesses she wasn’t sure GCP would accept her proposal, owing to her then limited experience in maize research. “I’ve always been grateful to GCP for supporting me at that transitional stage in my career. I’d just returned from Peru and taken up a position at Cornell and was at that time a relative newbie when it came to working with maize. However, I was lucky to have some really great collaborators.”

Rebecca (left) on a field visit to Kenya in September 2006. On the left is John Okalembo of Moi University, with James Gethi behind the camera.

One such collaborator, who Rebecca is thankful to have had on her project, was James Gethi, of the Kenya Agricultural Research Institute (KARI), and a leading researcher in Kenya. At the time, James was a recent Cornell graduate who was returning home to help bolster his nation’s crop-research capabilities. “James helped me a lot at the start of the project and throughout. Even though our project is finished, we have teamed up on a number of other projects to continue what we started.”

At Cornell, Rebecca oversees her own laboratory and still finds time to teach a class on international agriculture and rural development. She also serves as scientific director for the McKnight Foundation’s Collaborative Crop Research Program (CCRP), a grants programme funding agricultural research in developing countries.

Growing up with science…and a moderate Rebecca rebellion!
As our conversation draws to a close, Rebecca reveals she is currently skyping from the bedroom she grew up in, in Bethesda, Maryland, half an hour from downtown Washington DC, USA. “I’m down visiting my parents before I jet off to West Africa tomorrow,” she says where she is carrying out her CCRP commitments.

Rebecca credits her parents for encouraging her scientific inquisitiveness and determination to aid those in need. “Both of my parents are physicians, as is my younger brother. I thought I was a rebel with my interest in agriculture, but my younger sister is a farmer and agroecologist, so I guess we’re both straddling agriculture and science,” Rebecca says with a laugh.

“In all honesty though, my parents encouraged all of us to follow what we were fascinated by and passionate about, and for me and my sister, that was agriculture. We reared goats in our suburban backyard, dissected animal road-kills on the kitchen table and even turned the family swimming pool into a fish-pond because we wanted to learn about fish farming!” Rebecca recollects with great fondness.

I still get a kick out of trying to understand the biology of disease resistance and to try to help develop disease-resistant crops, which will help alleviate the fallout from crop failure and subsequent food shortages in developing nations”

Wife and mum, manager and mentor, and what gives Rebecca a kick
Rebecca says she and her journalist husband, Jonathan Miller, try to encourage their two sons, William and Benjamin, in the same manner. She also says she uses a similar theory as a mentor. “I love interacting with the young talent and I like to think I’ve grown as a person the more that I’ve evolved as a manager and mentor.”

Although she spends most of her time at her desk or on a plane or in a meeting room, Rebecca is always keen to jump back into the field and familiarise herself with the science she is overseeing. “I still get a kick out of trying to understand the biology of disease resistance and to try to help develop disease-resistant crops, which will help alleviate the fallout from crop failure and subsequent food shortages in developing nations.”

Links

Rebecca’s project, Targeted discovery of superior disease QTL alleles in the maize and rice genomes
- Blogpost
- p 16 in this PDF
Rebecca at Cornell University
Our current work on maize and rice
Crop genomics at GCP
GCP capacity building

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