Genomics » GCP Blog

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.

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

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

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

Feb 282013

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

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

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

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

A deeper dig: the root of the matter

Godwill Makunde

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

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

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

Kennedy Simango

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

Kennedy Simango at work a the Crop Breeding Institute.

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

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

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

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

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

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

Godwill doing what he does best: bean breeding.

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

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

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

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

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

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

Related blogposts

Other links

Bean research with the Legumes Research Initiative
OPEN ACCESS BOOK CHAPTER: How to phenotype beans for drought

TLI 2012: Data management for bean breeding – Zimbabwe from CGIAR Generation Challenge Programme

Chickpeas on the map of champions in the genome world: Challenges, rewards… and ‘Rajeevs’

Africa, Asia, Chickpeas, Genomics, Legumes No Responses »

Jan 282013

Today, Nature Biotechnology published the first-ever draft genome sequence map for a chickpea variety (PDF). The map will help researchers and breeders the world over to – through molecular breeding methods – deliver to growers higher-yielding more resilient varieties of chickpeas.

Now that we have the rewards in a nutshell, and we choose to chew the chestnut of challenges later in the story, let’s next decipher the ‘Rajeevs’ part in the title: introducing Rajeev K Varshney, our very own Leader of Comparative and Applied Genomics, who also led and coordinated the transnational collaboration that developed this map.

We had the pleasure of talking to the gently-spoken Indian, a week before the release of the paper, asking him to recount how the project began, and the challenges and success they faced along the way. We’ll soon get to what Rajeev had to say, but first, a rapid rewind for backgrounding before Rajeev tells us the rest of the story…

… we have the ‘borders’ done… a good idea of what the picture is, and where the rest of the pieces will fit.”

Rajeev in the lab.

Reality check from the Genomics Gnome of Good News: two is but the twinkling of an eye…
The sequence map of the genotype CDC Frontier – a Canadian kabuli chickpea variety – took about two years to construct.”

No, the time taken is not the challenge since we’re yet to get to that part. In fact, in the world of genomics , two years is fairly fast, compared to, say, the time taken for sequencing other grain genomes such as maize, rice and wheat.

Rajeev attributes this to the interdisciplinary expertise of his team, most of whom are world leaders in their field, and to the enthusiasm and generosity of all partner institutes who funded the collaboration.

And with that background, on to our chat with Rajeev!

Sandwiches in the Sunshine State, and a search starts for the then unattainable holy grail

Q: Is it correct that this project started over sandwiches under a sunny sky in California?
Funnily enough, yes. We had the preliminary discussion during a lunchtime break at the fifth International Congress on Legume Genetics and Genomics back in July 2010. Doug Cook, from the University of California, Davis, and I, organised the meeting for select attendees to discuss the idea.

With daughter, Nanz. Rajeev in ‘Daddy-mode’, a galaxy away from genomic research.

Many researchers at the time had, or were toying with, sequencing parts of the chickpea genome to discover genes that helped plants tolerate salinity, drought, disease, and so on. The idea of mapping the whole genome, however, was thought to be unachievable given the cost and resources required. What Doug and I proposed to the 10-odd senior researchers that day was that we form an alliance to pool together our knowledge, funds and resources.

When we returned to our home institutes, we all approached our institutes or funding agencies in respective countries, to propose they consider funding the collaborative project. To be honest, this was probably the most challenging task of the project, as it often is with other projects, as they had a hard time recognising the benefits. However, we finally got there, and with the help of more than 20 institutes from North and Central America, Asia, Australia and Europe, we have successfully assembled 74 percent of the genome within two years.

Pieces fall into place for mix-and-match combinations

Now, you may say that 74 percent doesn’t equal the whole genome, but it does provide us with a map and pointers we’d never had before. Imagine doing a jigsaw without a picture to guide you – that’s how hard it was for us at the start. Now at least we have the ‘borders’ done, and we have a good idea of what the picture is, and where the rest of the pieces will fit.

Q:Why is mapping the chickpea genome so important?
Having the genome mapped is going to benefit all chickpea breeders, researchers and growers.

Say a conventional breeder wanted to create a new breed of chickpeas with drought tolerance. They would cross a domesticated, high-yielding variety of chickpeas, with a variety that tolerates dry conditions – most likely, lower-yielding – and then grow the progeny in the field. They wait for these progenies to grow, then visually select the best lines and make crosses with these. They keep doing this process over and over again for six to seven years until they’ve generated a new variety with the desired trait.

Different breed, mould and mode

Molecular breeders do it differently: instead of selecting the lines by visual inspection, they select lines based on their genes. This means they can correctly trace whether the progeny has received the genes which help the plant tolerate drought and only grow, test and cross with these plants, almost halving the time it would take through conventional methods.

With the map, researchers will be able to more rapidly identify genes of interest, and work with breeders to select for plants that display the favourable traits of these genes, whether this be for drought tolerance, pest resistance or for any other trait they are interested in.

Q: Good for researchers and breeders, but how is that going to benefit growers though?
Knowing which plant is more tolerant of drought from the start of the breeding process is going to significantly reduce the time it takes for breeders to develop these types of chickpea cultivars. So, growers will have new breeds of higher-yielding more resilient chickpeas available sooner.

Ethiopian farmer, Temegnush, and her chickpea harvest.

Remember also that chickpeas are a very important crop for smallholders in the resource-poor harsh environments of sub-Saharan Africa, India and Southeast Asia. Not only do they grow it for food and to replenish soil nitrogen, they also export to India, the world’s largest consumer of chickpeas. Most of these farmers would be lucky to harvest one tonne per hectare, so any yield advantage means extra income.

This point is particularly relevant for GCP’s goal, which is to improve the livelihoods of such farmers.

Q: This was one of the largest collaborative projects you’ve coordinated in your relatively short career. What was the most challenging aspect?
Short answer is….many! With it being a collaborative project, bringing together researchers from all around the world, it was always difficult to coordinate suitable times for Skype and phone meetings.

Personally though, my biggest challenge was trying to coordinate so many esteemed researchers. We all had great ideas and we all thought each of our ideas was the right one. I had to resolve all issues amicably and find a solution to move forward.

Luckily I have surrounded myself over the years with some good colleagues to whom I’ve always been able to turn to discuss any problems. Jean-Marcel Ribaut, who is the Director of GCP, was one particular colleague to whom I often turned to for advice, given his experience with coordinating all of GCP’s collaborative interdisciplinary projects. He also helped source much-needed funds and suggested several useful partnerships, which were vital in carrying out the project.

My boss at ICRISAT, William Dar, the Director General, has always been very supportive, and time and again went out of his way to make sure I had the funds, capacity and sanity to keep the project going! I am deeply indebted to him.

The future

Q: How will the research continue?
Researchers and breeders will be able to customise the genome map to fit their particular purposes. Most will be interested in using it to develop molecular markers, which breeders can use to highlight specific genes of interest for molecular breeding. As I mentioned earlier, this could realistically halve the time it takes to breed new varieties from six to10 years to four to five years.

One outcome of the project, which I’m particularly interested in exploring further, relates to chickpea diversity. When we compared the 90 chickpea genomes, we realised that that diversity in the elite varieties was very low, meaning they all had very similar alleles (form of genes).

This has come about because over the years, breeders and growers have continually chosen only a handful of chickpea varieties to continually breed with. This is because these breeds tend to produce higher yields, something which all growers want.

The drawback of this, however, is that if all the popular breeds are too similar, then they could all be susceptible to a particular disease. If this particular disease were to strike, then chickpeas could be wiped out – globally.

So this map will be a valuable tool to use to enhance genetic diversity in the elite gene pool, thus safeguarding the world’s supply of chickpeas.

Links

Press release | Photos on Flickr
Download the Nature Biotechnology article in PDF
GCP’s reseach to improve chickpeas
Rajeev’s profile
ICRISAT Video
GCP videos on chickpea research (4-part series)
Opinion piece: Can genomics boost productivity of orphan crops? (co-authored by Rajeev and Jean-Marcel Ribaut, GCP Director)
Blogposts on chickpea research in Ethiopia, India and Kenya

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

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

Jan 232013

Abdelbagi Ismail

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

GCP helped IRRI attract support from other funders…”

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

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

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

Links

For an early history of Abdel’s work (2005–2006) see pp 36–40 here, and pp 26–28 here
Abdel’s research partners in Bangladesh and Indonesia
Complementary research and findings on improving rice phosphorus uptake

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

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

Dec 212012

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

Zeba Seraj

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Links

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

Born in Africa: A lifelong cross-continental love affair with science

Africa, Asia, Crop breeding, Genetics, Genomics, Researchers, Rice, Women in science 2 Responses »

Nov 302012

Sigrid Heuer

Meet Sigrid Heuer (pictured), a Molecular Biologist and Senior Scientist at the International Rice Research Institute (IRRI). Her lively and riveting story will take us from Africa through her native Europe and on to Asia, and finally Down Under to Australia.

Origins – the African chapter
Africa holds a special and soft spot in Sigrid’s love affair with science: it was while on this continent that she realised her calling in life as a scientist – linking people doing pure research on plant genes to help plants survive and even thrive in harsh environments, with people who want to apply that knowledge to breed crops that can change the lives of millions of farmers who constantly compromise with nature to make a living.

Fieldwork: Sigrid at a field trial for rice phosphorus uptake.

“Working as a postdoc at the Africa Rice Center in Senegal was a real life-changing experience,” Sigrid recollects with great fondness. “It’s where I found my niche, using my background in theoretical science and applying it to developing crops that could overcome abiotic stresses, and in doing so, make a real impact on people’s lives.”

Rowing further down the river: from upstream to downstream science
Sigrid was born and raised in Hamburg, Germany. She remembers wanting to be a psychologist and didn’t consider science until a few years after finishing school. After completing a biology undergraduate at Phillips University, Marburg, Germany, she returned to her home city of Hamburg to complete a Masters and PhD in plant physiology and molecular biology respectively.

“Back then, I was really involved in upstream science, fascinated in the fine details without much consideration of how such research could benefit society,” says Sigrid. “I still enjoy this form of science and really do value its purpose, but putting it into practice and focusing on the impact that it can have is what really motivates me now.”

Moving to IRRI, and meeting Pup1 and GCP
After three years in Senegal, Sigrid moved to the Philippines to join IRRI in 2003, first as a consultant then as a part-time scientist. In these early years, she was working on several projects, one of which was the GCP-funded Pup1 (rice phosphorus uptake) project.

“The project sought to identify the genes associated with phosphorus uptake in rice lines that could tolerate phosphorus-deficient soils,” says Sigrid. “It was an interesting project in which I was able to use my background in molecular biology. Little by little, I got more and more involved in the Pup1 project and after a year I was asked by Matthias Wissuwa, who was leading the project at the time, if I wanted to take it over. It was a great opportunity which I jumped at, not knowing then how challenging it would prove.”

Pup1 was the first major project I had managed. It was a playground of sorts that allowed me to learn what I needed to know about managing a project – writing proposals and reports, managing budgets and people’s time, and everything else that comes with leading a team.

The ‘root’ and ‘command post’ where it all happens: Sigrid in the office. For the benefit of our readers, we would have credited the young artist whose colourful work graces the background below the bookshelf, but we were too polite to pry and prise out the young talent’s name, having hogged too much of Sigrid’s time already!

Learning to lead – both work and play

Over the last seven years, Sigrid has been a Principal Investigator and joint leader of the project, which has given her latitude to mature professionally, and not just in science alone. “It’s been tough but personally fulfilling,” Sigrid says, with just a touch of exhaustion.

“Pup1 was the first major project I had managed. It was a playground of sorts that allowed me to learn what I needed to know about managing a project – writing proposals and reports, managing budgets and people’s time, and everything else that comes with leading a team. I was really lucky to have Matthias’ help as well as the other experienced collaborators and networks. However, the main factor that made my job a lot less stressful, was the benefit of long-term funding and support from GCP. GCP was always there, supporting us and giving us confidence even when we weren’t sure we were going to succeed.”

Persistence pays: tangible products, plus publication in Nature
In August 2012, Sigrid and her team achieved what they had set out to do seven years ago, through what Sigrid puts down to sheer persistence: their discovery of the Pup1 gene was recognised by their scientific peers and published in the highly renowned journal, Nature.

Sigrid (3rd left) at the lab with other colleagues in the phosphorus uptake team.

“Having our paper published is really something special and personally my greatest achievement to date,” says Sigrid, but she is also quick to add that it was a team achievement, and that the achievement was in itself humbling.

“It was a double reward for persisting with the research, and with getting it into Nature. We wanted it in Nature for several reasons. To raise awareness on phosphorus deficiency and phosphorus being a limited resource, especially in poorer countries; and to draw attention to how we do molecular breeding these days, which is a speedier, easier and cost-effective approach to developing crops that have the potential to alleviate such problems.”

Sigrid hopes the article will have a lasting impression on readers, and encourage funders to continue to support projects that have such impact on the lives of end-users.

What next? Technology transfer, transitions and torch smoothly passing on…
With the Pup1 gene now found, IRRI researchers are working with breeders from country-based breeding programmes around the world to help them understand the techniques to breed local varieties of rice that can grow in phosphorus-deficient soils. They are also collaborating with other projects that wish to use the Pup1 project as a case study for phosphorous deficiency tolerance in other crops like maize, sorghum, and wheat (see an example here, that includes partners from Africa and Latin America).

Sigrid sees this next stage as a perfect time to step down from the project: she plans to move to Adelaide, Australia at the end of 2012 to lead a new project that is looking at drought and nitrogen deficiency tolerance in wheat.

“Matthias passed the baton on to me, and now I get to pass the baton on to someone else, so it’s nice. And I’ll be sure to always be around to help them too.”

Links

VIDEO: Sigrid’s interview on BBC News, August 2012, on the discovery of the rice gene that boosts phosphorus uptake
PHOTO STORIES − Choose your favourite medium! We post to both Flickr and Facebook
- Meet the rice phosphorus uptake team and their work Flickr | Facebook
- Training breeders from developing countries Flickr | Facebook

Sigrid’s presentation at the GCP General Research Meeting 2011

GRM 2011: Rice with dual strength — Phosphorus uptake efficiency and alumunium tolerance from CGIAR Generation Challenge Programme

Breeding beans to better battle drought and disease in Ethiopia

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

Nov 132012

Bean breeding in his bones: Asrat A Amele

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

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

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

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

At that time, Asrat remarked:

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

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

The ravages wrought by bean stem maggot.

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

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

Two…and two

Fitsum Alemayehu

Daniel Ambachew

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

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

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

Of humans and machines

A training session on maintaining farm machinery.

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

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

Water drilling to install irrigation equipment at SARI.

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

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

Asrat on video