2014 December » GCP Blog

Thank you from GCP, and fare thee well

Dec 312014

Our sunset is finally here: the Generation Challenge Programme officially closes today, Wednesday the 31^st of December 2014. It is with great sadness, but with even more joy and pride, that we say our farewells, look back on all that GCP has achieved in its decade of existence, and look forward to GCP’s legacy to the researchers, farmers and hungry consumers of the future.

As GCP reaches its end, we would very much like to thank all those who have been part of the GCP journey, whether as active participants or simply cheering us on. This card is for you, with our heartfelt gratitude (and please keep reading, as we have more to say below!).

The GCP family is both mighty and numerous, and we cannot hope to name all those whose invaluable contributions have helped make GCP what it is.

First and foremost, we thank the Product Delivery Coordinators past and present who have provided essential leadership and vision to each of our Research Initiatives, and the Principal Investigators who have shepherded each of GCP’s projects – sometimes through green pastures and sometimes along stony paths – to their triumphant conclusions. Our sincere thanks also go to all the hundreds of researchers who have worked with them, and whose efforts have been instrumental in the results and impacts that GCP has achieved.

A body is nothing without its head, and so we offer our profound thanks to the members of our Executive Board, and its predecessor the Programme Steering Committee. Defying anatomy, they have furnished GCP with not only brains but also a heart and firm hands to steer the GCP ship deftly on its course. We further thank all the members of the Consortium Committee, the Intellectual Property Advisory Committee, the now defunct Review and Advisory Panel and Programme Advisory Committee, and the Integrated Breeding Platform’s Scientific and Management Advisory Committee, for their indispensable advice and guidance. (See our current governance and advisory bodies)

We are deeply grateful to all of our funders, whose steadfast faith in GCP enabled this remarkable decade of collaboration and discovery. And last but not least, we thank all of GCP’s staff, both past and present, as well as consultants and others who have worked with us, for their incredible hard work, loyalty and habitual miracle-working.

We would also like to offer a special and thankful mention to our esteemed 3,000-plus readers of GCP News who have faithfully stayed with us through the years, as well as our friends, fans and followers on all our social-media accounts (see them all along the top and bottom of our website).

Together, we have created something remarkable (as our external reviews attest), and none of us will continue in our lives untouched by the GCP spirit. To all those listed above, and to all our other friends who have collaborated, contributed and cheered us on our way – THANK YOU!

Just as it would be impossible to name each and every person who has been part of GCP, we also could not possibly list all the ways in which GCP will live on. GCP’s legacy takes many forms: new crop varieties for farmers, scientific knowledge, relationships between researchers, both young and senior scientists trained in the latest tools and techniques, new ways of working together… we could go on and on!

However, there are a few things we would particularly like to mention. The Integrated Breeding Platform (IBP) is one of GCP’s most important offspring, and in many ways its heir. IBP is a one-stop shop for both conventional and molecular breeding activities, making the latest tools and knowledge available to breeders across the world. Its Breeding Management System (BMS) offers a suite of interconnected software designed to help breeders manage their day-to-day work at all stages of the routine breeding process. IBP has also taken over the hosting of certain GCP activities, such as the crop-specific communities of practice fostered by GCP, so that these will continue to go from strength to strength.

Many other GCP projects are also continuing in new phases and forms – their success at securing funding from new sources a validation of their accomplishments so far. For example, Tropical Legumes I and II projects, respectively led by GCP and ICRISAT, will be merging into a new incarnation, Tropical Legumes III, to be led by ICRISAT. In general, the work in GCP’s key Phase II crops – cassava, legumes (beans, chickpeas, cowpeas and groundnuts), maize, rice, sorghum and wheat – will continue under the umbrellas of the CGIAR Research Programmes, as we had hoped and envisaged in our 2010 Transition Strategy.

Meanwhile, you can expect a few final news posts from us in the New Year, as we wrap up the Programme and its communications. It’s our pleasure to announce that, thanks to your demonstrated interest, the GCP website will continue to be online (albeit as an archive), so you will still be able to call in for any GCP information you need – or purely for nostalgia. And we will continue to publish our collection of closing stories on our Sunset Blog, so keep visiting for upbeat and comprehensive journeys through GCP’s achievements, including how GCP has done things differently, our impacts, what we have learnt, and how these will carry on into the future.

Finally, we have one more special thank you to give: to our GCP artists Durga Bernhard and Rhoda Okono, to CIMMYT designers Miguel Mellado, Marcelo Ortiz and Eliot Sánchez for incorporating their beautiful artworks into so many gorgeous designs over the years, and to our web developer and designer Brandon Tooke for stunning concepts. Without Rhoda and Durga to give us our signature look, GCP would hardly be so colourful or distinctive. If you enjoyed the glimpses of their paintings in the thank you card above, why not sample the full works in our online galleries? The first exhibit is fittingly a ‘decoding’ of the lovely logo that Marcelo designed for us in 2004, and the sunset twist Brandon has added to it since (see below).

On that joyful artistic note, from us here at GCP, fare thee well, thank you, and long live the GCP spirit!

P.S. Hold on! We’re not done just yet with our roll of honour. Please step forward, Vincent Vadez, groundnut researcher, for giving substance, form and name to that which most of us felt and loved, but could not put a name to – the GCP spirit. Here’s what Vincent said in a survey response in September 2011: “I feel that GCP is not a consortium, or an institution. It is a spirit.” And thus, a handy and legendary moniker was born, that served us well in the years that followed, and that will hopefully live on into the future. Thank you Vincent for that down-to-earth gem of groundtruth from our main groundnut researcher!

‘Jurassic’ genes make tricky soils a walk in the park for crop cousins

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

Dec 042014

By Eloise Phipps

Think of something acid.

What came to mind… vinegar? Lemon juice? An acid remark? Chances are that you did not think of soil – the humble sods and clods we rely on to produce our food – unless, perhaps, you grow or breed crops.

It is a cruel and surprising fact that acid soils cover almost half the land that the world uses to grow food. They can be a natural result of rainfall and soil type, but are also made worse by overuse of nitrogen fertilisers. The negative impact of acid soils on annual global harvests is second only to that of drought.

We’re getting down to earth in celebration of World Soil Day, the 5^th of December – and looking forward to 2015, the International Year of Soils – as we get our teeth into this Diplodocus-sized problem, and examine how research into genes shared between different species is helping plant breeders provide farmers with crops that thrive even as the pH drops.

More than half of the world’s potential crop-growing land is highly acidic. Map courtesy of Leon Kochian.

Cretaceous crop split leaves common heritage – helping plants pass the acid test when soil dosages get dramatic

Did Triceratops, just like us, enjoy its daily morning breakfast cereal?

The cereal crops that we rely on for our staple foods are relative newcomers in evolutionary terms – just like humans ourselves. The species that are now maize, rice and sorghum all belong to the Poaceae family, or true grasses. They separated out and began to take their own evolutionary pathways roughly 65 million years ago – around the time the dinosaurs were going extinct. Before this, they had a single common ancestor, getting munched on by hungry Triceratops.

Because of this family relationship, maize, rice and sorghum still have many similar genes in common, often carrying out the same or similar functions in the different crops. And some of these functions can help plants do well when faced with the acid test.

The trouble with acid soils is not so much the pH itself, but the way it affects the availability of important nutrients. As acidity increases, aluminium becomes more soluble, giving plants an overdose that causes aluminium toxicity. One of the symptoms is stunted root growth – making it even harder for plants to reach other nutrients. Meanwhile, nutrients such as phosphorus become less available, stuck in forms that plants can’t absorb, making phosphorus deficiency another huge issue.

The consequences of subpar soils are far-reaching. A new report from the Montpellier Panel, ‘No Ordinary Matter: Conserving, Restoring and Enhancing Africa’s Soils’, finds that soil degradation affects two-thirds of arable land in Africa, and that without action it is likely to lock the continent into cycles of food insecurity for generations to come, and hamper both agricultural and economic development. Widespread soil acidity and its effect on nutrient availability are a key piece of the jigsaw; as the report observes, “In the more humid lowland areas [of Africa], soils are typically highly weathered, acidic and nutrient deficient.”

A Kenyan farmer prepares her maize plot for planting. Acid soils cover almost 90 percent of Kenya’s maize-growing area, and can more than halve yields.

Collaboration and gene comparison for crops that thrive when pH dives

Fortunately, our scientists are no dinosaurs. Since 2004, crop researchers and plant breeders across the world – collaborating in several GCP projects within the Comparative Genomics Research Initiative – have been using genetic knowledge at the cutting edge of science to develop local varieties of maize, rice and sorghum which can withstand acid soils’ topsy-turvy nutrient levels. Explore our comparative genomics-themed blogposts to meet our heroes Claudia, Eva, Jura, Leon, Matthias, Rajeev, Sam, and others.

Left to right (foreground): Leon Kochian, Jurandir Magalhães (both EMBRAPA) and Sam Gudu (Moi University) examine crosses between Kenyan and Brazilian maize, at the Kenya Agricultural Research Institute (KARI), Kitale, in May 2010.

What is the advantage for breeders of knowing about a gene like PSTOL1 (in the locus Pup1), which helps rice do well under low-phosphorus conditions by encouraging it to grow longer roots? Simple. Unlike the scientists in Jurassic Park, our breeders don’t need to resurrect long-dead species to get their kicks (and fortunately, they are at lower risk of being eaten by their work!). The crops they are interested already have all kinds of useful genes hidden within them, but, as with all living things, each species is tremendously varied and diverse.

This is where genomics comes in. Instead of growing many thousands of seeds to see which plants thrive, breeders can use genetic markers to look inside the seeds to see which ones have, say, Pup1. Then they only need to grow those seeds, in order to cross-pollinate them with plants with other useful traits, making the breeding process much faster and more efficient.

Screening for phosphorus-efficient rice, able to make the best of low levels of available phosphorus, on an International Rice Research Institute (IRRI) experimental plot in the Philippines. Some types of rice have visibly done much better than others.

Women farmers in India bring home their sorghum harvest.

And what makes the Comparative Genomics Research Initiative even more powerful is that it looks across related crops. Once researchers have found an acid-beating gene in one crop, they can look for similar genes in the others – turning knowledge of a single gene into multi-impact dino-mite. For example, the discovery of the SbMATE gene, behind aluminium tolerance in sorghum, spurred researchers to seek and find a similar gene in maize – which they named ZmMATE. This knowledge is now being used to breed aluminium-tolerant varieties of both sorghum and maize for Africa – and is being applied to rice too.

Maize trials in the field at our partners EMBRAPA, the Brazilian Agricultural Research Corporation. The maize plants on the left are aluminium-tolerant while those on the right are not.

There are many more examples of the power of comparative genomics, but the real proof will be soon to come in farmers’ fields as these new, anti-acid varieties are tested and released. The world’s poorest farmers generally cannot afford other approaches to dealing with soil acidity, such as treating soil with lime or applying extra phosphorus to their fields, so the comparative approach to cousin crops promises to be a king (or should that be Tyrannosaurus rex?) among soil solutions.

A boy rides his bicycle next to a rice field in the Philippines. With acid soils affecting half the world’s arable fields, acid-beating crop varieties will help farmers feed their families – and the world – into the future.

Links

Explore our Comparative Genomics Research Initiative
Meet our partners and their projects in our Comparative Genomics-themed blogposts
Get your info straight from the horse’s (definitely not dinosaur’s!) mouth with presentations galore on SlideShare:

GRM 2013: Marker-assisted breeding for improving phosphorus-use efficiency and tolerance to aluminum toxicity in maize — S Gudu from CGIAR Generation Challenge Programme

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

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

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

GRM 2013: Status of maize projects in the Comparative Genomics Research Initiative: Products and the future — L Kochian from CGIAR Generation Challenge Programme

GRM2013: Establishing a molecular breeding program based on the aluminum tolerance gene AltSB and the P efficiency QTL Pup-1, for increasing sorghum production in Sub-Saharan Africa — F Rattunde from CGIAR Generation Challenge Programme

‘Dosing’ the digital divide: A tablet for that field-to-desk headache

Uncategorized No Responses »

Dec 032014

The latest – and most readily available – tools for breeders are often intangible things, such as ideas, approaches and even software. But they also include new physical tools, such as electronic tablets to make data collection more efficient. Read on to discover how structured user testing paved a path from pioneer to perfection.

This article was first published on the Integrated Breeding Platform (IBP) website on the 17^th of October 2011, and is republished here as a complement to our last blogpost on the Integrated Breeding Multiyear Course (IB–MYC), illustrating yet another facet of our multi-pronged approach to capacity building.

From small and sweet to bigger and better, this ‘cure’ might just do the trick… After initial testing of small electronic handheld devices for field data collection, followed by extensive testing of alternative options on the market, an appropriate digital tablet was identified. Last month (September 2011), 20 tablets were distributed to IBP users from research programmes in Africa and Asia for pre-test. Should this user evaluation be positive, the plan is to distribute more of these tablets in the future, to a total ‘dosage’ of between 100–200 tablets in all, in the course of the next 12 months.

Flashback to February 2011: Pioneer handheld devices

The road behind us

We initially started by piloting smaller handheld devices (Honeywell and HP iPaq) among a small set of selected users, to get feedback from them, and collectively see what would work best to meet their needs. The smaller, handheld devices were piloted in late 2009 into early 2010 for evaluation by users.

Significantly, some institutes such as AfricaRice and IITA even procured additional units at their own cost – an act which speaks for itself. Most of our users reported finding the devices easy to use, simple and straight forward. Plus, they reported that it increases efficiency, saves time and minimises data error because data are recorded in a ready-for-use format. But it wasn’t all a bed of roses and there a few thorns as well: users encountered difficulties in synchronisation between the handheld and their computer due to configuration conflicts. The small screen and keyboard and short battery life also brought no joy, and data collection for multiple samples was a problem.

But enough from us on the pros and cons! Here is what some of the users from the rice and sorghum Research Initiatives (RIs) had to say way back in February 2011. As you will see, almost all of them got incurably ‘digitally infected’ despite the cons reported with the small portable devices.

In their own words: Users speak

Akinwale Gbenga of AfricaRice, Ibadan, Nigeria, pictured in the field recording data using the handheld device

Q: What has been your experience with the handheld device?

Akinwale: This device was very timely for us because we were already exploring and experiment with ways to improve the way data were being collected. The handheld device has greatly improved our efficiency. Previously, we’d collect data in a physical workbook then the data would be transferred manually to the computer. The handheld device saves time, guarantees accurate entries with no proofreading required, and safeguards the data: there is no risk of datasheets being lost or misplaced. With this device, what is recorded in the field is what is transferred into the computer without any errors. Whereas when deciphering handwriting, it’s very easy to confuse 3 for 8, 7 for 9, and so on, even when it is your own writing. Also, when working in the lowlands, mud smears and water smudges on the paper sometimes mean that handwritten data cannot be read. In a timed exercise to compare this new method and the usual methods, it took me 35 minutes to enter one trait and the job was fully done. With the usual methods, it would have taken me double the time since I would have had to manually collect and enter data then proofread entries.

Q: What drawbacks or concerns might you have observed about the device, and what would you advise?

Akinwale: The battery lasts four hours, so it is important to ensure it is fully charged before going to the field. Data collection is best done in the morning to avoid reflection and glare from the screen. I’m not sure how long the device will last, but I have no doubt that it is good value for money. Some programming work will also be needed to cater for traits that need multiple measurements.

Ibonou Dieng, a biometrician, AfricaRice, commented, “The only dataset that is complete at this time is for the station that had the handheld device. This underscores the efficiency of the handheld device. We therefore plan to disseminate the handheld device to all our rice RI partners in Burkina Faso, Mali and Nigeria. Significantly, management at AfricaRice has committed to buy the device for other projects as well for use in recording dry-season data in March.” Ibnou is one of the Joint Co-ordinators of the of the Data Managers Community of Practice with specific responsibility for Africa.

Bashir Mohamed, a researcher and data manager at Nigeria’s National Cereal Research Institute at Badeggi, was impatiently waiting for the handheld device and observed, “Manual data collection and entry is extremely laborious. It generally involves three people – a field technician to do the counting, a data manager to do the recording and the breeder. With the handheld device, this job can be done by the data manager singlehandedly.”

Aboubacar Diarra, an Assistant Rice Breeder at l’Institut d’economie rurale in Mail noted, “The handheld device promises many advantages, and eases the task of data collection. Generally, it is rare to collect, enter and verify data all on the same day, meaning that should anomalies be noted at verification, the reality in the field may have significantly changed by the time one returns to the site to take a new reading. By easing the job, the handheld device makes it possible to do all three steps in a single day, and therefore to return to the field if need be for verification in good time.”

Alexis Traore, Institut de l’environnement et de recherche agricole (INERA), Burkina Faso, said, “Data management is indispensable for molecular breeding, and therefore an understanding of data management is absolutely essential. We need training in data management and on new tools such as the handheld device that can help us manage data better. That way, we not only learn but we’ll also train other scientists as well as students who come to our institutes.”

Marie-Noëlle Ndjiondjop of AfricaRice, and the Rice Research Initiative Principal Investigator, summed it up thus:“Our riceproject has and will continue to produce a lot of data. The time to think about data management is now. We will ensure that all our rice RI partners receive the handheld device, and we are glad to note that the management at AfricaRice is actively promoting the device and recommending it for all breeding programmes at the Centre.”

But not all the users were complimentary, convinced and converted…

Niaba Teme, a sorghum breeder at L’Institut d’économie rurale, Mali, complained, “The handheld device is difficult to use. For traits like flowering which occurs at different times, you have to scroll to find the plot and flower which is time-consuming. It’s also difficult to work with it outdoors in the sunshine. Pen and paper are easier to use.” Niaba Teme is co-PI for the BCNAM project of the Sorghum Research Initiative.

On balance though, the concept of electronic data collection was clearly appreciated and was creating a ‘positive epidemic’, but clearly, a better tool was needed. Users recommended that IBP explore alternative mobile devices such as the tablet, to address the cons and drawbacks reported by Niaba and others on the small handheld devices. We listened and acted…

Fastforward to September 2011

Taking into account the comprehensive feedback received from users, the IBP team, led by Arllet Portugal, the Informatics Coordinator, set out to identify an appropriate handheld device that would meet the needs of users. They settled on a Samsung Galaxy 10.1-inch digital tablet (pictured) because it uses a common and open Honeycomb Android operating system specially designed for tablets, it has a large clear screen for easy viewing, good battery life and is lightweight and relatively robust. It can also communicate with a bar-code reader.

The 20 partners who received the tablet in September 2011 appeared very pleased with it, and committed to provide systematic and structured feedback over a one-year test period. Terms and conditions apply for this receipt: tablet recipients signed formal contracts whereby they will have to demonstrate that they indeed used the tablet to capture field data. Once preliminary feedback is received from this pioneer set of tablet users and analysed, the circle of evaluators will be expanded by contacting other users interested in trying out digital data-collection devices. And to maximise benefit and mutual learning, the IBP team will organise a forum for tablet users – probably around the next IBP annual meeting – to share experiences and tips, including a data clinic, should there be need.

We shall be following their experience with the tablet, so please watch this space to stay with the story, and travel with our users on what we trust will be a very momentous road ahead!