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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

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

Of magic beans and giant beanstalks: A legume fairy tale coming true in Ethiopia

Africa, Beans, Legumes No Responses »

Nov 292012

By Gillian Summers

The TLI project lets us know about molecular breeding, so it’s exposed us to new developments in science, especially in the application of molecular techniques and plant breeding.” – Asrat Asfaw Amele, Southern Agricultural Research Institute, Ethiopia

Many a tale about Ethiopia will regale the reader with details of its contrasting landscape, numerous rivers, searing regional temperatures, the multicultural makeup of its society, its world-famous, unbeatable long-distance and high-altitude runners, its rich history and culture; a sweet producer of honey, the home of coffee, and origin of all mankind…

Seeing red… but no blood
…I found a land of incurably hospitable and kind people, proud of their country and culture; infectiously good music, incredibly strong coffee, where they love both bloody raw meat and protein-rich red beans, dubbed ‘bloodless meat’ in this part of the world.

Cool early morning departure

Out & about
My first real taste of Ethiopia was out in the countryside where I visited the work of GCP’s Tropical Legumes I (TLI) project in the field, on a trip to the bean fields at the Southern Agricultural Research Institute’s (SARI) research stations at Areka and Hawassa, which took us on a 600-km round tour, out of the capital Addis Ababa and into the Great Rift Valley beyond.

We set off early that cool morning, and as we headed into the countryside, I glimpsed many a local taking their first breath of morning air as they stepped outside from their decoratively-painted, round, thatched-roof homes, and shook the night’s sleep from their shoulders.

Traditional thatched living rooms

So their day began – already there was smoke coming from the chimneys, and I imagined the lady of the house beginning to prepare for the first coffee ceremony of the day. Coffee is often accompanied by a dish of boiled red beans. Or maybe she was warming the pan for the morning injera – a kind of ‘teff tortilla’: a sour-dough thin pancake made of the local cereal, teff. Injera is an iconic ubiquitous component of Ethiopian cuisine, with which diners take all manner of wat, or stew made from a rich variety of ingredients – from legumes to raw meat, carefully rolling the spongy crepe around the filling twice, making sure no food falls onto the fingers, for dining etiquette strictly dictates against the licking of fingers.

Ensete plantations

Living landscape

We pass score upon score of the gently-smoking thatched round huts – the traditional ‘living rooms’ in these parts; most dwellings are accompanied by modest smallholdings, with maybe a grazing goat or two, and many more with plantations of ensete – a banana-like plant, which, in spite of its inedible fruit, has long been a staple in Ethiopia. It is used for its root, which is mashed to make a tasty, stodgy, bread-like food called kocho, used to accompany meals, a denser cousin of the favourite injera. These smallholdings would also be the perfect size for cultivating beans, as they are not an acre-hungry crop, but grow happily on small plots of land, and in some areas are intercropped with ensete to maximise the space.

Dromedaries, drought and beans

Our common legume: the bean, Phaseolus vulgaris L

Into this landscape we pass the incongruous addition of a herd or two of camels with their owners…significantly peculiar as these aren’t desert lands, but the edge of the Ethiopian highlands, gradually and graciously giving way to the majestic Great Rift Valley below. I ask my guide about the addition of camel hands to this highland scenery: he explains their strange presence is due to a growing food shortage which has forced these nomadic peoples further afield to find their fare. The appearance of these dromedaries and their human partners brings harshly to mind Ethiopia’s most notorious claim to fame – especially for anyone who recalls the mid-1980s – for whom Ethiopia will always be indelibly synonymous with famine. It also throws the work of GCP, and specifically TLI, sharply into the spotlight, for the over-arching objective of this project is to improve legume productivity in environments considered marginal for agriculture, due to heat and other stresses. Somehow, it seems that more of the world’s environment is becoming ‘stressed’ by the day, though luckily the giant beanstalk of our story is a hardy crop which can be grown on the poor soils and fragmented plots of these challenged lands.

L–R: Asrat Asfaw Amele (SARI), Bodo Raatz (CIAT), Daniel A Demissie

L–R: Asrat Asfaw Amele (SARI), Bodo Raatz (CIAT) and Daniel A Demissie (Areka Research Station) discuss the A–Z of beans at Areka Research Station.

So the legume of choice for this most uncommon road trip is the common bean, Phaseolus vulgaris L, and our Ethiopian bean breeding expert is Asrat Asfaw Amele of the Southern Agricultural Research Institute (SARI), who is the Lead Scientist of the TLI beans component in Ethiopia. Asrat is our friendly guide and fount of knowledge of all things Ethiopian throughout this impassioned passage into the ‘bean valley’, and we are accompanied by Bodo Raatz of the Centro Internacional de Agricultura Tropical (CIAT), recently appointed Principal Investigator of TLI’s bean research. At Areka research station we are joined on our journey by Daniel A Demissie, who, along the way, shares his many insights on beans, diseases such as bean stem maggot (BSM), and on drought . We are chaperoned throughout by our courageous driver, Mr Abebe, who at times resembles a pilot as we seem to fly over the bumpy terrain in the plucky pick-up that is our steed for the day.

Courageous steeds: our driver, Mr Abebe (foreground and far right) and the intrepid pickup are joined by workers from Areka station

Impact

Asrat Afaw Amele

Against the scenic backdrop of the Ethiopian landscape racing by, with background music courtesy of Teddy Afro (whose politically charged songs, sweet voice and infectious rhythm have made him nothing short of a legend in his homeland), I take advantage of this long and winding road trip to interview Asrat, where his answers echo the whirlwind tour rushing by outside – from a description of the landscape he knows so well, and toils in every day – to the impact that this project has had on national scientists, the impacts on farmers’ lives, as well as impacts that are likely to come in the not-too-distant future.

We consider farmers our partners. We try to understand what farmers are looking for, what they like, and we try to include their interests in our breeding materials so that the breeding materials released by our institution start to get wider adoption.” – Asrat Asfaw Amele (pictured).

The rich Ethiopian landscape

Revolution, alliances & partnerships

Ethiopia’s rich history, as varied as its topographical landscape, has known its fair share of extreme rulers. Now it seems the new ‘regime’ calling the shots is climate change, whose ravaging effects are seen worldwide, and no less in the bean fields of Ethiopia. Asrat even pinpoints climate change as the greatest challenge for the next generation of bean researchers, saying, “The farmers’ growing environment may be modified or a new environment may be created. That could also be a challenge – a new pest population or new disease may come; so the challenge in the future may be to breed or develop varieties which adapt to the changing environment.”

Beans line up at Awassa Research Station

The revolutionaries needed to overthrow this ‘tyrant’, it seems, are those of the ‘triple alliance’ partnership, comprising: Ethiopia’s national scientists, researchers from the international science community including CGIAR Centres, and farmers. Firstly, with this approach, the science sector can understand farmers’ needs, which also has a reciprocal effect, as Asrat explains, “We consider farmers our partners. We try to understand what farmers are looking for, what they like, and we try to include their interests in our breeding materials so that the breeding materials released by our institution start are widely adopted.” Secondly, national and international science systems come together to work for a common goal – in Asrat’s words: “Now we’ve got the knowledge and we can speak a common language with people from advanced laboratories. It’s also brought us closer to international institutes like CIAT and other CG Centres – we work together, so they understand our system better and we understand how they function.” He adds, “We are getting technical backstopping from CGIAR Centres, so as a national partner we are doing work, and they are supplying germplasm. That’s the partnership that will continue in the future.”

The weapon used by this ‘revolutionary army’ is GCP’s double-barrelled approach which combines both traditional and molecular breeding practices and is proving to be effective in developing new, more productive bean varieties to combat drought and disease. Specifically of the TLI project, Asrat says, “It lets us know about molecular breeding, so it’s exposed us to new developments in science, especially in the application of molecular techniques and plant breeding.”

Daniel A Demissie contemplates looming rain clouds across the parched terrain

The ‘monster’, climate change, rears its ugly head only to be shot down expertly by Asrat and the mighty beans as he reveals, “A lot of farmers are growing our varieties, and, because of changing weather or instability, many people are starting to grow beans; beans are now becoming a major crop, especially in our mandate area.”

Capacity building …
At this stage, the major impact of the TLI beans component in Ethiopia has been on capacity building – both in terms of human resources and physical infrastructure, as Asrat illustrates, “In our breeding programme, capacity building has been an important aspect: scientists in our national system are being exposed to new technology, information, and training; we also have a full irrigation system in about 10 hectares of land, which will revolutionise our work.”

Magical bean diversity

… and on to farmers
By building on lessons learnt throughout this project, current impacts for the national science system will be translated into ‘real impacts’ in farmers’ fields in the near future. Indeed, Asrat hopes his future work will involve “getting the material into the hands of farmers, to see some impact or change, and to modernise and speed up breeding processes using markers developed by this project.”

Beanstalks: giant potential in Ethiopia

So the ‘magic beans’ of our story tell of a rich brew brimming with such potent ingredients as molecular breeding, capacity building, partnerships spanning continents and research systems, true teamwork with the farmers in the fields, and the drive to conquer the new challenge of a changing climate.

The impacts from the TLI project are the pot of gold at this rainbow’s end, showing that fairy tales do come true, where ‘magic beans’ put down roots and grow real shoots, and are not just ‘castles in the air’.

Links

Bean research in Ethiopia
OPEN ACCESS BOOK CHAPTER: How to phenotype beans for drought
Video featuring Asrat A Amele

Chickpeas: Toughening a tough crop for tougher times by healing its Achilles’ heel

Africa, Chickpeas, Crop breeding, Legumes No Responses »

Jun 262012

It’s all about water and weakness – or strength. The Greek legend has it that Achilles was dipped into River Styx by his mother, Thetis, in order to make him invulnerable. His heel wasn’t covered by the water and he later died of the wound from an arrow that struck his heel.

In our times, this analogy can be applied to chickpeas, where this streetwise tough customer in the crop kingdom that thrives on the most rugged terrains is hamstrung if there is no rain at the critical grain-filling period – its sole Achilles’ heel, when it cannot take the searing heat in the drylands it otherwise thrives in.

But before you read on about the latter-day borrowing of this ancient legend, and science’s quest to heal the hit from heat and to cure the crop’s fatal flaw on water, first, an important aside…

Who’s now calling the shots in chickpea research?

Molecular breeding in Phase I was led by ICRISAT, with country partners in a supporting role. In Phase II, activities are being led by country partners, which also assures sustainability and continuity of the work. ICRISAT is now in a facilitating role, providing training and data, while the research work is now in the hands of country partners.” – Pooran Gaur, Principal Scientist: Chickpea Breeding, ICRISAT.

The facts
Chickpeas are an ancient crop that was first domesticated in central and western Asia. Today, this crop is cultivated in 40 countries and is second only to common beans as the food legume most widely grown by smallholders. The two main types of chickpeas – desi and kabuli – are valuable for both subsistence and cash.

Even for the hardy, times are tough
“Chickpeas are well-known to be drought-tolerant,” says Rajeev K Varshney, Principal Investigator of the project to improve chickpeas work in the Tropical Legumes I Project (TLI). He explains, “The plants are very efficient in using water and possess roots that seek out residual moisture in deeper soil layers.” However, he points out that, with changing climatic conditions, especially in drier areas, terminal drought – when rain does not fall during grain-filling – is the crop’s Achilles’ heel, and principal production constraint.

“Chickpeas are such tough plants that, even for conditions of terminal drought, yields can be increased by improving root characteristics and water-use efficiency,” says Rajeev. The research team has identified several lines with superior traits such as drought tolerance, after screening a set of 300 diverse lines selected based on molecular diversity of large germplasm collections.

VIDEO CLIP: Recipe for chickpea success

Enhancing the genetic makeup to beat the heat
The team went on to develop genomic resources such as molecular markers. With these markers, the team developed a high-density genetic map, and identified a genomic region containing several quantitative trait loci (QTLs), conferring drought tolerance. “QTLs help pinpoint, more specifically, the location of genes that govern particular traits like root length” explains Rajeev.

Longer roots will naturally give the plants a deeper reach into the water table. Root length is the difference between survival and perishing, which is why trees will be left standing on a landscape otherwise laid bare by prolonged drought.

Q for ‘quick’: QTLs speed things along from lab to field, and running with the winners
The discovery of QTLs makes identifying tolerant plants not only easier, but also cheaper and faster. “This means that better-adapted varieties will reach farmers faster, improving food security,” says Rajeev.

Pooran Gaur, GCP’s Product Delivery Coordinator for chickpeas, Principal Scientist for Chickpea Breeding at ICRISAT, and an important collaborator on the TLI project, adds, “We began marker-assisted selection backcrossing (MABC) in Phase I. By 2011, lines were already being evaluated in Ethiopia, India and Kenya. We are now at the stage of singling out the most promising lines.”

Putting chickpeas to the test: Rajeev Varshney (left) and Pooran Gaur (right) inspecting a chickpea field trial.

What was achieved in Phase I, and what outcomes are expected?
Phase I run from mid-2007 to mid-2010, during which time 10 superior lines for improved drought tolerance and insect resistance were identified for Ethiopia, Kenya and India. As well, a total of 1,600 SSR markers and 768 SNPs on GoldenGate assays were developed, along with an expanded DArT array with more than 15,000 features. A high-density reference genetic map and two intraspecific genetic maps were developed.

“We now have materials from marker-assisted backcrossing by using the genomic resources we produced in Phase I. These materials were sent to partners last year [2011]. And because in most cases we have the same people working in TLI as in TLII, this material is being simultaneously evaluated across six to seven locations by all TLI and TLII partners,” says Pooran.

“Preliminary analysis of data is quite encouraging and it seems that we will have drought-tolerant lines soon,” adds Rajeev.

Future work, and who’s now calling the shots in the field
In Phase II, 1,500 SNPs on cost-effective KASPar assays have been developed that have been useful to develop a denser genetic map. In collaboration with University of California–Davis (USA) and the National Institute of Plant Genome Research (India), a physical map has been developed that will help to isolate the genes underlying the QTL region for drought tolerance. A novel molecular breeding approach called marker-assisted recurrent selection (MARS) has been adopted. Over the remaining two years of Phase II, the chickpea work will focus on developing chickpea populations with superior genotypes for drought tolerance through MABC and MARS.

Pooran adds, “Molecular breeding in Phase I was led by ICRISAT, with country partners in a supporting role. In Phase II, activities are being led by country partners, which also assures sustainability and continuity of the work. ICRISAT is now in a facilitating role, providing training and data, while the MABC and MARS aspects are both in the hands of country partners.”

“Another important activity in Phase II is development of multi-parents advanced generation intercross (MAGIC) population that will help generation of genetic populations with enhanced genetic diversity,” says Rajeev.

Partnerships
The chickpea work is led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), working with partners at the Ethiopian Institute of Agricultural Research, Egerton University in Kenya, and the Indian Agricultural Research Institute. Additional collaborators in Phase I included the University of California–Davis (USA), the National Center for Genome Resources (USA) and DArT P/L (Australia).

For more information on the overall work in chickpeas, please contact Rajeev K Varshney, Principal Investigator of the chickpea work.

Video: Featuring Rajeev and partners Fikre Asnake (Ethiopia) and Paul Kimurto (Kenya)