Nov 122013
 

 

 

Participants at the 2013 GRM. High-resolution version on Flickr: http://bit.ly/1fxhkmQ

Participants at the 2013 GRM. High-resolution version on our Flickr account.

The General Research Meeting (GRM) is by far the largest and most important event on our calendar. This year’s GRM was held on September 27‒30 2013, with 135 people from 35 countries attending (see list).

Various presentations were made on progress and next steps on research in GCP projects, including for GCP’s Integrated Breeding Platform (IBP). Focus was on GCP’s nine focus crops in Phase II – beans, cassava, chickpeas, cowpeas, groundnuts, maize, rice, sorghum and wheat, with the poster sessions adding a couple more (see ‘sixty posters’ below). You can view the presentations made on our website  (to see them in the context of the overall agenda), or on SlideShare (all gathered in one place).  We have uploaded all but one presentation, where we’re still waiting for the presenter’s permission to publish. A comprehensive update on all GCP projects is here (PDF). The meeting was a blend of plenary sessions on core topics and research updates, and ‘drill-down’ breakouts on crops, data management and capacity building (the last two, in the context of IBP’s proposed Phase II, which had its own dedicated one-day stakeholder meeting after GRM, on 1st October).DSC07162_w

Social were we…but we also did some heavy lifting
We didn’t just talk to ourselves: we made a bit of noise on social media to also bring in other voices into the GRM discourse and chit-chat, using the hashtag #GRM13, creating a good buzz of conversations. Also linking in to GRM were our LinkedIn followers. And neither was it all business, science and rigid structure: there was free-flow too, with an open afternoon where participants could take a relaxing break, organise their own meetings, or take a tour to Lisbon. Some of the scenes from the tour are posted on Flickr, as are other snapshots from the meeting. We’ve since gathered up some of the social media posts on Storify.

GRM was far from its grim-sounding  abbreviation and hashtag on social media:  exemplifying the best of the ‘GCP spirit’,  the sessions were engaging, relaxed, conversational and spiced with humour and a light touch, despite the ‘heavy’ topics under discussion (see agenda). But the topic at hand was grim, since the situation is dire – drought affects almost all crops and all regions worldwide. As drought tolerance is our key focus since inception, most of the discussions naturally centred on this topic. Equally important is the scourge wrought by pests and disease, which afflict some crops more than others. For example, under most circumstance, cassava is naturally very drought-tolerant, but what good will this do if cassava survives drought only to succumb to the deadly pests and diseases that stalk this drought champion?

Sunset and ‘moon-rise’
GRM was also a time for both stocktaking and mapping the future  given GCP’s sunset in 2014.  A central and recurring theme was GCP’s transition strategy, and how – and where – to embed GCP-initiated projects that will extend beyond the Programme’s lifetime. For this, the CGIAR Research Programs (CRPs) are a natural first choice. GRM enjoyed a very good representation of the CRPs, with all six crop CRPs represented, some at the highest level.

A few members of our Executive Board also attended. Board Chair, Andrew Bennett, set the right tone for the meeting. In his remarks at the opening session, he emphasised that this was not a time for sadness, swan songs and moping as GCP approaches sunset.  Rather, it was a time to appreciate the beauty of sunsets, in the sure knowledge that sunsets give rise to  moon-rise!

A section of Poster Session II presenters. IN the foreground, Andrew Bennett, Chair, GCP Excecutive Board.

A section of Poster Session II presenters. In the foreground, Andrew Bennett, Chair, GCP Executive Board.

“Say it succinctly in sixty seconds!”
The poster session was as lively as always, with a record of… (hold your breath!) 60 posters presented, surpassing the previous GRM in 2011 which attracted 53 posters.

Perfection!  Sixty posters for sixty seconds
Sixty was a PERFECT number for the 60-second sizzle, where each poster presenter had a maximum of 60 seconds (and not a second more!) to present at plenary, devising whichever means necessary to attract the audience to their poster. It was easy to discern the brash ‘old hands’ who had perfected their art after several GRMs; the tricksters and various reincarnations of The Artful Dodger amongst them, trying to beat the clock; new and slightly jittery presenters who were more than just a little bewildered but still proved their mettle; and the new, sassy and confident. This beautiful blend apart, the poster session brought in not only new faces to add to the familiar ones, but also refreshing new tastes to diversify and sweeten our Staple of Nine crops. To our diet of cereals, legumes and tubers, poster presenters from The Philippines added eggplants, rounded off with bananas for dessert.

"Definitely time for dessert, and do not disturb!" they seem to be saying. Jean-Christophe Glaszmann (left) and Hei Leung (right), who played ace roles on a multi-partner GCP project on bananas.

“Definitely time for dessert, and do not disturb!” they seem to be saying. Jean-Christophe Glaszmann (left) and Hei Leung (right), who played ace roles on a multi-partner GCP project on bananas.

♫ Welcome to the Hotel California! ♫…
As always, GRM was a mingling of old and new friends, a time for some paths to meet and for new forks to branch out, a season to reflectively look back and progressively face forwards. In keeping with Andrew’s continuity of sunsets giving way to moonrise, we said a group goodbye to Rajeev Varshney, former Genomics Theme Leader, who left the GCP Management Team in August. And we were happy to once again welcome, embrace and recognise two old friends – Jean Christophe Glaszmann (CIRAD) and Hei Leung (IRRI), who were, respectively ex-Subprogramme Leaders for genetic diversity and genomics in GCP Phase I, and continue to be involved with GCP as researchers, as will Rajeev.

In this picture, we caught up with them at a very appropriate moment: dessert during the Gala Dinner. Take it from us, these two guys are well versed in matters dessert, with a dash of science, as this blast from the past on bananas attests, also summarised in a Facebook photo-story here.

We are indeed a Hotel California of sorts – always open for check-in and checkout. As for leaving…we’re still working on the modalities of that!

And despite the fond farewell, truth is Rajeev is not going anywhere either, as far as GCP is concerned. You only needed to have been at GRM or following the conversations on Facebook and Twitter, especially the photos, to witness this. He was (delightfully!) all over the place, passing on his ‘positive epidemic’ of highly infectious enthusiasm and incredible energy. Here he is in action at the Gala Dinner in the photos below, which really need no caption. We’re sure you’ll be able to easily spot Rajeev, ‘high-fivin’ and ‘rapping’, eclipsing the GCP Director, who however appears quite pleased in his lower perch with Rajeev on the platform. But if you’re truly lost and can’t spot the super-charged high-energy guy in the photos, no worries! Here are some handy clues.

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In distinguished company
Rajeev’s energy goes beyond GRM and GCP; this year as in previous ones, he received several awards, among them, the Young Crop Scientist Award by Crop Science Society of America, and the Illumina Agriculture Greater Good Initiative Award.

Hari Upadhyaya

Hari Upadhyaya

Prior to these recognitions during the Gala Dinner, Jean-Marcel formally honoured ICRISAT’s Hari Upadhyaya (pictured) during plenary for two awards Hari had received in the course of the year, also from the Crop Science Society of America. These awards were for Hari’s notable contributions – at international level – to crop science, and to plant genetic resources.

Hari is a long-term GCP Principal Investigator, working primarily on sorghum. But that is not the only crop he works on. Hari was the lead author of the joint chickpea and pigeonpea chapter in our book on drought phenotyping.

Evaluation
Unlike other GRMs where we’ve requested participants to evaluate the meeting, we did not do so this year, since this is very likely the last meeting of its kind, and the goal of the evaluation is to use participant feedback to improve future meetings. With the help of our participants, we’ve applied the lessons we’ve learnt from them through the years to arrive at what we believe to be a winning combination, balancing the diverse interests of our participants for overall improvement of their GRM experience.

 

 

 

 

 

Dec 212012
 

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

Zeba Seraj

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Links

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

 

Nov 302012
 
Photo: IRRI

Sigrid Heuer

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

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

Photo: IRRI

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

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

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

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

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

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

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

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

Learning to lead – both work and play

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

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

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

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

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

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

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

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

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

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

Links

Sigrid’s presentation at the GCP General Research Meeting 2011

 

 

Sep 202012
 

Getting to the core of a world-favourite dessert by unravelling banana’s origin and genealogy

GCP has enabled us to lay a credible foundation, which gave us a leg-up in the intense competition that typifies the genome sequencing arena” – Angélique D’Hont, CIRAD researcher

‘A’ is also for Angélique, as you will see once you read on…

An ‘A’ to our banana team for ushering in a new era in banana genetics. But let soup precede dessert, and don’t let this worry you: stay with us because we’re still very much on the topic and focused on bananas, which offer the whole range from soup and starters, to main course and dessert, plus everything else in between, being central for the food security of more than 400 million people in the tropics: around a third each is produced in Africa, Asia-Pacific and Latin America, and the Caribbean. About 87  percent of all the bananas produced worldwide are grown by small-scale farmers.

Moving back then to soup for starters, we’re serving up our own unique blend of alphanumeric banana ‘soup’, spiced with ABCs, a pinch of 123s, plus a dash of alpha and omega. Curious about the ABCs? Look no further:‘C’ for getting to the core of ‘B’ for bananas, and an ‘A’ score for our ace genomics team that did it.

Read how GCP seeded … and succeeded, in helping open a new era in banana genetics. An achievement by itself, and an important milestone on the road to unlocking genetic diversity for the resource-poor, which is GCP’s raison d’être.

So get your travelling gear please, for time travel with a ‘midspace checkpoint’ in Malaysia.

We start in 2004, when GCP commissioned a survey of diversity with microsatellites (or SSRs, simple sequence repeats) for all mandate food crops in the CGIAR crop research Centres. The objective of that study was to make new genetic diversity from genebank accessions available to breeders.

The endpoint is opening new research avenues to incorporate genes for disease resistance, with the added bonus of an article published in Nature online on July 11 2012, entitled The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.

It may not be quite as easy as the ABC and 123 that The Jacksons promise in song, but we promise you that the science is just as exciting, with practical implications for breeding hardy disease-resistant bananas. Onwards then to the first leg of this three-step journey!

(Prefer a shorter version of this story in pictures? We’ve got it! Choose your medium between Flickr and Facebook)

1) Let’s go Greek: the alpha and omega of it

Rewinding to the beginning

The proof of the pudding is in the eating: we imagine that Jean Christophe Glaszmann just has to be saying “Yummy!” as he samples this banana.

Start point, 2004: “At that time, several research groups had developed SSR markers for bananas, but there was no coordination and only sketchy germplasm studies,” recalls Jean Christophe Glaszmann (pictured), then the leader of what was GCP’s Subprogramme 1 (SP1) on Genetic Diversity on a joint appointment with CIRAD. He stepped down as SP1 Leader in March 2010, and is currently the Director of a multi-institutional research unit Genetic improvement and adaptation of Mediterranean and tropical plants (AGAP, by its French acronym) at France’s Centre de ccoopération internationale en recherche agronomique pour le développement (CIRAD) in Montpellier.

Jean Christophe continues, “The reference studies had been conducted with RFLP* markers, a very useful tool but far too cumbersome for undertaking large surveys. We mobilised Bioversity International, CIRAD and the International Institute of Tropical Agriculture for the project. The process took time, but delivered critical products.[*RFLP stands for restriction fragmented length polymorphism]

Fastforward to 2012, and gets just a little geeky…

Eight years down the road in 2012, the list of achievements is impressive, as evidenced by a suite of published papers which provide the details of the analysis of SSR diversity and describe how the data enabled the researchers to unravel the origin and genealogy of the most important dessert bananas. The origin of the predominant variety – Cavendish – suggested by the markers, involves two rounds of spontaneous hybridisation between three markedly differentiated subspecies. This scheme has been marvellously corroborated by linguistic patterns found in banana variety names as revealed in a paper published in 2011 in the proceedings of USA’s National Academy of Sciences.

But what else happened in between the start- and end-point? We now get to the really ‘sweet’ part of this bonanza for banana breeding!

It is now possible to conduct research to identify and incorporate genes for disease resistance within fertile populations that are close to the early progenitors, and then inter-cross them to re-establish sterility and obtain vigorous, disease-resistant and seedless progenies.

 2) Of bits, bananas, breeding and breadcrumbs

Threading all these bits together for breeding better bananas is akin to following a trail of breadcrumbs, in which GCP played an important facilitating role: where in the germplasm to undertake genetic recombination is one key; and then, how to expedite incorporation of disease resistance and how to control sterility – so as to first suppress it, then re-establish it – is another set of keys that are necessary for proficient breeding.

Hei Leung in the lab at IRRI.

In 2005, Hei Leung (pictured), then Leader of GCP’s Subprogramme 2 on Comparative Genomics (until June 2007) on a dual appointment with the International Rice Research Institute (IRRI), recognised that with GCP’s main focus being drought tolerance in crops, Musa (the banana and plantain botanical genus) was somewhat on the fringe. However, it was still important that GCP support the emergence of banana genomics.

Hei is currently Programme Leader of Genetic Diversity and Gene Discovery at IRRI. He remembers, “We had a highly motivated group of researchers willing to devote their efforts to Musa. Nicolas Roux at Bioversity was a passionate advocate for the partnership. The GCP community could offer a framework for novel interactions among banana-related actors and players working on other crops, such as rice. The team led by Takuji Sasaki of Japan’s National Institute of Agrobiological Science, which had vast experience in rice genome sequencing, added the scientific power. So, living up to its name as a Challenge Programme, GCP decided to take the gamble on banana genomics and help it fly.”

Angélique D’Hont, CIRAD researcher and lead author of the article published in ‘Nature’.

Through several projects, GCP helped consolidate Musa genomic resources, contributed to the establishment of medium-throughput DArT markers as well as the construction of the first saturated genetic map. Additional contributions included the first round of sequencing of large chromosome segments (BAC clones) and its comparison with the rice sequence and a detailed analysis of resistance gene analogues. All these findings have now been published in peer-reviewed journals. And while publication takes time, it still remains a high-premium benchmark for quality and validation of results, and for efficient sharing of information. It reinforces the value of collaboration, builds capacity and gives visibility to all partners, thereby providing potential new avenues for funding.

Such was the case with bananas: using a collaborative partnership framework established with the Global Musa Genomics Consortium, animated by Nicolas Roux and now chaired by Chris Town, the community developed a case for sequencing the genome. With the mentorship of Francis Quétier, contacts were made with various major players in genomics, which in the end formalised a project between France’s CIRAD and CEA–Genoscope, funded by the Agence Nationale de la Recherche and led by Angélique D’Hont (pictured) and Patrick Wincker.

GCP contributed DArT analysis for anchoring the sequence to the genetic map. But, as stressed by Angélique, CIRAD researcher and lead author of the Nature paper: “Above all, GCP has enabled us to lay a credible foundation, which gave us a leg-up in the intense competition that typifies the genome sequencing arena. We were delighted that France rolled the dice in our favour by funding this work.”

3) Musa musings on the road to and from Malaysia checkpoint

Three years down the road, the team published a description of the genome of a wild banana from Malaysia.

Jean Christophe communes with a Musa plant, perhaps musing “What’s your family history and when will you be fully grown?”

Let’s drill down to some technical facts and figures here: the Musa genome has some 520 million nucleotides distributed across 11 chromosomes, revealing traces of past duplications and bearing some 36,000 genes. While most genes derived from duplication tend to lose their function, some develop novel functions that are essential for evolution; bananas seem to have an outstanding range of transcription factors that could be involved in fruit maturity.

And while the road ahead remains long, we now have a good understanding of banana’s genetic diversity, we have genomic templates for functional studies (a whole-gene repertoire) as well as for structural studies (the chromosome arrangement in one subspecies) aimed at unraveling the genomic translocations that could control sterility in the species complex.

It is now possible to conduct research to identify and incorporate genes for disease resistance within fertile populations that are close to the early progenitors, and then inter-cross them to re-establish sterility and obtain vigorous, disease-resistant and seedless progenies.

This is undoubtedly an inspiring challenge towards unlocking the genetic diversity in this crop, which is central to food security for more than 400 million people in the tropics.

Links

 

Sep 072012
 

“It is very rare that scientists can take their projects wherever they go. I’ve been very lucky to be able to do this, and much of this has to do with the support I’ve received from GCP.” – Matthias Wissuwa

In the world of phosphorus, Matthias (pictured) is somewhat of a ‘rock star, not that he would admit to it. We don’t understand why not, since to borrow his words, the project he’s involved has becoming something of a ‘celebrity project’ in the scientific community.

For  a decade-and-a-half, he has searched tirelessly for a rice gene that could improve the crop’s yield in phosphorus-deficient soils –which make up half of the world’s soils. Last month, his transnational team published in Nature that their 15-year quest had ended, having finally found the elusive gene – Pup1.

We celebrate this happy ending, especially as we had the added pleasure of talking to Matthias recently: it was delightful in listening to the modest German recount the long journey which has taken him from his home town of Hamburg, to USA, Japan, The Philippines and back to Japan, all this while,  faithfully ‘carrying’ Pup1 with him as he switched employers. As you’ve seen, Japan scores a double strike, so our ‘rock star’ is also ‘big on Japan’! 

Talking to Matthias, we could sense the achievement was only just sinking in – that he and his team’s years of laboratory work was becoming a practical reality that will aid rice-growing farmers from Africa to Asia,  and hopefully other grain growers in years to come. Here’s what Matthias had to say…

You started this project back in 1997. Tell us how you became interested in phosphorus deficiency and rice.

After completing my PhD in the United States, I accepted a postdoc position in Tsukuba, Japan, with the National Institute of Agro-Environmental Sciences (NIAES). It was an easy decision because my wife is Japanese.

My postdoc host, Dr Ae was interested in phosphorus, particularly in legumes. I originally started work on tolerance to phosphorus deficiency in groundnuts, but soon changed to rice to take advantage of the molecular tools available for rice.

Tsukuba is a very new city. It’s called The Science City in Japan because the Japanese government built it to house all the national research institutes. This was great for me as I became interested in QTL mapping, which was pioneered by scientists in Tsukuba. I got talking to people in the rice research community in Tsukuba and was introduced to Dr Yano, who was developing mapping populations for rice at the National Institute of Agrobiological Sciences. He kindly gave me his populations and that’s how I started to map QTL for phosphorus-deficiency tolerance in rice.

Dr Ae was perplexed by my decision, believing that studying legumes was far more challenging than rice. He always told me: “Rice is boring. They just make long, fine roots to capture phosphorus.” That was 15 years ago and he turned out to be right. Long roots are the secret for phosphorus uptake in rice, particular in Kasalath and varieties like that.

Field trials for phosporus-efficient rice in The Philippines.

Did you share Dr Ae’s hypothesis that longer roots were the secret to some rice varieties being able to tolerate phosphorus-deficient soils?

For a long time, I was not sure if it was just long roots. It was a real chicken-and-egg scenario – does strong phosphorus uptake spur root growth, or the other way around?

As it turns out, it is the latter – plants growing longer roots help with the uptake of more phosphorus – and Pup1 is responsible for this.

We have now shifted our aim and are looking for varieties of rice tolerant to phosphorus-deficient soils that either:

  • release organic acids, phosphatases or some other compound that makes phosphorus more readily available for the plant to absorb, or
  • manipulate soil microorganisms to favour those that can aid in making phosphorus more soluble, or
  • very efficiently utilise phosphorus once it is taken up.

All three mechanisms are found in legumes, so there is reason to believe that they exist in rice and we are now working on finding them.

GCP has been interested in the project since 2004 as its outcome aligns with GCP’s goals to improve crop yields and security in developing countries… It has become something of a ‘celebrity project’ in the scientific community, attracting researchers to work on the project or collaborate with us.

In 2002 you left NIAES and accepted a position with the International Rice Research Institute (IRRI), and were encouraged to continue your work on Pup1. When you moved back to Tsukuba in 2005 to accept the position you currently hold with the Japan International Research Center for Agricultural Sciences (JIRCAS), you were again encouraged to continue your Pup1 project, collaborating with your successor at IRRI, Dr Sigrid Heuer. How important has it been to you and the project to have the support of your institutes?

It is very rare that scientists can take their projects wherever they go. I’ve been very lucky to be able to do this, and much of this has to do with the support I’ve received from GCP. They’ve been interested in the project since 2004 as its outcome aligns with GCP’s goals to improve crop yields and security in developing countries.

When I left IRRI, Sigrid was just starting and was more or less free to take on the project, so I asked her if she’d be interested in continuing my work with Pup1 at IRRI and collaborate with me in Japan. She was actually the perfect person for the project because her background in molecular biology complemented my background as a plant breeder.

Over the past seven years, we have worked together very well, and with the addition of Rico Gamuyao, a PhD student supervised by Sigrid, things have recently progressed quite quickly to the point that we were able to pinpoint Pup1.

So GCP has played a major role along your journey?

Yes, definitely. The support from GCP on the Pup1 project, now in its 8th year, was instrumental at getting this project to where it is.

Quite simply, the funding from GCP allowed us to hire Rico as well as Juan Pariasca-Tanaka, a project scientist with me at JIRCAS. Neither Sigrid nor myself had the time to do all the hands-on work so having both Rico and Juan has been hugely helpful.

How important has the collaboration between IRRI and JIRCAS been for the project?

Are they playing with mud? Not at all! Working. Matthias (L) and Rico (R) have zipped up their boots and gone back to their bee…er…. we mean, roots, mucking mud here as they do some fieldwork related to the search for PSTOL1.

Tremendously important. Sigrid’s group at IRRI is relatively small as is mine in Japan, so we rely on each other’s complementary expertise when working on complicated projects.

We have also been fortunate to have constant interest in the project from the scientific community. It has become something of a ‘celebrity project’, and as such, attracted researchers to work on the project or collaborate with us.

For example, we are working with two US groups at Cornell University and Penn State, that are also funded by GCP, trying to track down Pup1 in other crops and identifying genes that control root architecture, and how different architectures may affect P uptake.

These collaborations are really exciting, and make it possible to answer questions that we could not answer ourselves, or that we would have overlooked, were it not for the partnerships.

It really has been a team effort and we wouldn’t have got to where we are now without all the help of everyone involved

You’ve been described as the Godfather and Guru of Pup1. How do compliments like this make you feel?

It makes me laugh but of course it’s a very well-meant comment, and to some extent, considering I’ve worked on it for 15 years, you could say that there is some truth to it.

I’ve done all the original work, but Sigrid has been just as instrumental. She did the part where my expertise was no longer adequate – the molecular side, looking at genes and thinking about the function of a gene and testing for its function.

It really has been a team effort and we wouldn’t have got to where we are now without all the help of everyone involved, which also includes the support of Dr Yano over the years.

…phosphorus deficiency is a worldwide problem that has recently gained public attention because of how expensive phosphate fertilisers have become…Farmers are always interested in saving money and improving yields and we believe this discovery will help with both.

Have you been surprised by the attention this project has received?

As I said, the project has always been in the scientific spotlight because it was the first to map a major QTL for phosphorus uptake.

We knew from the Sub1 story – the submergence tolerance gene, which was published in Nature 4–5 years ago – that the media would probably be interested in this similar discovery. I’m still very surprised that this unsexy story has caused such interest.

You have to remember though, phosphorus deficiency is a worldwide problem that has recently gained public attention because of how expensive phosphate fertilisers have become. About four years ago, the price almost tripled and continues to stay high.

Farmers are always interested in saving money and improving yields and we believe this discovery will help with both.

Phosphorus deficiency is probably even more critical in Africa than it is in Asia… This means Pup1 may have its biggest impact in Africa.

How will the research continue?

Having focused so much on the basic research, we now want to turn our attention to the application. IRRI and JIRCAS will train national breeding programmes to use marker-assisted selection and help them breed their own rice varieties with Pup1.

Sigrid and IRRI are mainly working with Asian national breeding programmes and we at JIRCAS focus more on African programmes such as the Africa Rice Center. Phosphorus deficiency is probably even more critical in Africa than it is in Asia, as phosphate fertilisers aren’t used nearly as much as they are in Asia. This means Pup1 may have its biggest impact in Africa.

We are also looking for new sources of tolerance to phosphorus-deficiency. One very exciting project involves West African rice (Oryza glaberrima) the father of the Nerica ™ (New Rice for Africa) varieties.

So far, we have found that this rice is very tolerant to phosphorus-deficient soils. It does have Pup1, but in addition harbours novel genes that also enhance performance on phosphorus-deficient soils.

We hope to discover a Pup2 in the years to come.

Links

 

Jun 202012
 

Breathing life into support services

By addressing the needs at the heart of quality agricultural research, right there on the station, GCP was the first to cotton on to a crucial missing link between researcher, research station, and support services.” – Hannibal Muhtar (pictured)

“One thing that really energises me,“ enthuses GCP Consultant Hannibal Muhtar, “is seeing people understand why they need to do the work, and being given the chance to do the how.”

And so was born another wonderfully fruitful GCP collaboration. Hannibal, who describes the assignment as “a breath of fresh air,” was asked to identify, together with GCP project Principal Investigators, African research sites of ongoing or potential GCP Research Initiative projects where effective scientific research might be hampered by significant gaps in one fundamental area: infrastructure, equipment and support services. As at June 2012, 19 sites had been selected.

Meet Hannibal Muhtar (audio clip)

Embarking on the voyage to change, storms ‘n’ all
In 2010 and 2011, Hannibal visited these stations, meeting staff at all levels and functions, for an in-depth analyses and appropriate recommendations to assure high-quality field evaluations for GCP-funded projects. With funding from GCP’s Integrated Breeding Platform (IBP), and with the openness, commitment and energy of station staff to implement these recommendations, the efforts are, starting to bear fruit.

Photos: AgCommons

Flashback to 2010. Photo 1: Hannibal (centre) at a planning session at Sega, Western Kenya, with Samuel Gudu of Moi University  (right) and Onkware Augustino (left). Photo 2: Similarly, at Tanzania’s Agricultural Research Institute, Naliendele, with Omari Mponda (right).

But it has not all been smooth sailing, and the storms encountered along en route should not be underestimated.

Weeds, wear and tear, and a walk on the wild side
“The real challenge,” says GCP’s Director of Research, Xavier Delannay (pictured), “is not in the science, but rather in the real nuts-and-bolts of getting the work done in local field conditions.” The obstacles, are often mundane – missing or faulty, weather stations or irrigation systems; weed-infested fields ravaged, or poor drainage, for example. Yet such factors compromise brilliant research. Take unfenced plots for example – equipment gets stolen, and animals roam freely.

Getting down to the brass tacks of local empowerment, and aiming higher
The overarching objective is, in Xavier’s words, “The effective running of local stations, for facilitating local research, improving local crops, and ultimately leading to empowerment and self-reliance of local farming communities.”

In tackling the matter, Hannibal employed a multi-faceted customised approach, based on the needs of each site, for both equipment and training for technicians, tractor operators and station managers. The dedication of the managers to both learn and continue these efforts after the training was particularly gratifying, since it assures sustainability.

“At the end of the day, it’s about achieving food security and improving livelihoods… which pave the way for healthy families and profitable agriculture,” concludes Hannibal.

Lights, curtain… action!
Much like in theatre, with all the ‘props’ in place, field trials are now performing well, thanks to streamlined ‘backstage’ support. Hannibal likens the positive feedback from the partners he has worked with to “A glass of cold water, after a long day in the sun!”

“With proper infrastructure in place, and with research station staff duly equipped with the hands-on expertise and practical know-how to utilise and apply this infrastructure and training, we’re now seeing field experiments being conducted as they should be, and getting good-quality phenotyping data as a result,” says Xavier. “Moreover,” he continues, “by providing glass-houses or the capacity to irrigate in the dry season, we are enabling breeders to accelerate their breeding cycles, so that they can work all year round, rather than having to wait until the rain comes.”
Examples include sites in Kenya, Mali and Nigeria.

The missing link
As the nuts-and-bolts begin to fall in place for, Hannibal reveals: “By addressing the needs at the heart of quality agricultural research, right there on the station, GCP was the first to cotton on to a crucial missing link between researcher, research station, and support services.”

…and yet another missing link…
But the job is not quite done. One crucial gap is the sensitisation of upper management – those at the helm of national research institutes and research station Directors – to support and sustain infrastructure, training and related services. In some cases, costs could be easily met by utilising a priceless asset that most institutes already have, and which they could put to greater us – land and a controlled environment.

Upper management needs to be actively on board. “A research institute should work like a good sewing machine,” says Hannibal. “All well-oiled, all parts working well, and everybody knowing what they need to do.”

In the meantime, however, results from the field suggest that researchers in GCP projects are already reaping the benefits from improved infrastructure and support services, and are already off to a good start.

The ‘stage’ is therefore set: ‘backstage’ and ‘props’ are well primed, performance trials are acting like they should, and the ‘theatre directors’ have an eye on sustainability after GCP’s final curtain call in 2014.

So, long may the show go on, with a cautionary word, however, to continually seek ways to not only maintain but also enhance performance!

Want more details? Read the extended version of this story

Relevant links

  • PODCASTS: You can also listen to Hannibal, by tuning into Episode 2 for the entire interview, or zooming in on your particular area of interest in the mini-podcasts labelled Episodes 2.1 to 2.7 c here.
  • Capacity building
  • Research Initiatives
  • Integrated Breeding Platform website
Jun 202012
 

Breathing life into support services

By addressing the needs at the heart of quality agricultural research, right there on the station, GCP was the first to cotton on to a crucial missing link between researcher, research station, and support services.” – Hannibal Muhtar

Want to cut to the chase and only need the bare bones of this story? Skip over to the short version

“One thing that really energises me,” enthuses GCP Consultant Hannibal Muhtar, “is seeing people understand why they need to do the work, and being given the chance to do the how.” And so was born another wonderfully fruitful GCP collaboration. Hannibal, who describes the assignment as “a breath of fresh air,” was asked to identify, together with GCP project Principal Investigators, African research sites of ongoing or potential GCP Research Initiative projects where effective scientific research might be hampered by significant gaps in one fundamental area: infrastructure, equipment and support services.

Meet Hannibal Muhtar (Audio clip)

As at June 2012, the 19 sites selected were:

Burkina Faso – L’Institut de l’environnement et de recherches agricoles sites at :
1.  Banfora
2.  Farako-Bâ Regional Centre
Ethiopia
3.  Hawassa Agricultural Research Station
4.  The Southern Agricultural Research Institute
Ghana – Council for Scientific and Industrial Research, Crops Research Institute sites at:
5.  Kumasi
6.  Tamale
Kenya
7.    Moi University (site 1)
8.    Moi University (site 2)
9.    Egerton University (Njoro site)
10.    Egerton University (Koibatek Farmers Training Centre)
Mali – L’Institut d’Économie Rurale sites at:
11.    Sotuba
12.    Cinzana
13.    Longrola
Niger – ICRISAT site
14.    Sadore
Nigeria
15.    National Cereals Research Institute
National Root Crops Research Institute sites at:
16.    Umudike
17.    Kano
Tanzania – Agricultural Research Institute at:
18.    Naliendele
19.    Mtwara

Flashback to 2010. Picture on the left: Hannibal at a planning session at Sega, Western Kenya, with Samuel Gudu and  Onkware Augustino. Picture on the right: Similarly, at Naliendele, in Tanzania with Omari Mponda.

Flashback to 2010. Picture on the left: Hannibal at a planning session at Sega, Western Kenya, with Samuel Gudu and  Onkware Augustino. Picture on the right: Similarly, at Naliendele, in Tanzania with Omari Mponda.

Embarking on the voyage to change, storms ‘n’ all
Hannibal, armed with years of practical experience in the application of engineering sciences in agriculture and developing countries, as well as an attentive ear to the real needs of researchers, embarked on a series of visits to these research stations in 2010 and 2011, meeting with staff of all levels, departments and functions, carrying out in-depth analyses and draw up concrete recommendations for infrastructure and support service investments for each of the sites so that good-quality field evaluations (‘phenotyping’ in ‘breeder-speak) of GCP-funded projects could be conducted. Thanks to funding from GCP’s Integrated Breeding Platform (IBP), and to the openness, commitment and energy of research staff on the ground to implement these recommendations, the efforts of multiple cross-cutting partnerships across Sub-Saharan Africa are, in 2012, starting to bear fruit. But it has not all been smooth sailing, and the storms encountered along the way to reach this end goal should not be underestimated.

Weeds, wear and tear, and a walk on the wild side
The obstacles, says GCP’s Director of Research, Xavier Delannay (pictured, can often be mundane in nature – a  lack of or faulty weather stations or irrigation systems, or fields ravaged by weeds or drainage problems and in dire need of rehabilitation, for example. Yet such factors compromise brilliant research. A simple lack of fencing, Xavier and Hannibal expound, commonly results not only in equipment being stolen, but also in roaming cattle and wild animals – boars, monkeys, hippopotamus and hyena, to name but a few – stomping over precious experiment sites and posing serious threats to field staff safety. “The real challenge lies not in the science, but rather in the real nuts-and-bolts of getting the work done in local field conditions,” he explains.’’

Hannibal concurs: “If GCP had not invested in these research support infrastructure and services, then their investment in research would have been in vain. Tools and services must be in place as and when needed, and in good working order. Tractors must be able to plough when they should plough.’’

But a critical change is also needed in mindset and budgeting. ‘’The word ‘maintenance,’’’ a Senegalese partner commented to Hannibal, describing his institute, “does not exist in our vocabulary and is not a line-item on our budget.”

The problem then is not always about limited funds but rather much more on how the funds available are budgeted, excluding the all-essential support services.

Getting down to the brass tacks of local empowerment, and aiming higher
Multi-lingual and fluent in English, Arabic and French, Hannibal employed a multi-faceted customised approach, based on the needs of each site, be it sharing his tricks-of-the-trade and improvising local solutions, or guiding researchers in identifying their specific needs, as well as on where and how to request equipment, just to mention a few examples. In other cases he would teach local station managers to build and apply simple yet revolutionary tools such as land-levellers (referred to as ‘floats’ in industrial-speak), as well as row-markers for more uniform spacing between rows and plants in the field.

In addition, he would organise a training workshops in either English or French, with different content for technicians, machine operators and station managers. The dedication demonstrated by this latter group to both learn and continue these efforts after the training was particularly pertinent for ensuring the long-term sustainability of the investments.

A colourful menu of options, then, for achieving one common overarching objective, which, as summarised neatly by Xavier, is: “The effective running of local experiment stations, for facilitating local research, improving local crops, and ultimately leading to empowerment and self-reliance of local farming communities.”

“At the end of the day, it’s about achieving food security and improving livelihoods,” Hannibal emphasises. Looking back at some of the research stations that are now well-equipped and are being managed well, and the improved crop varieties being produced and projected, Hannibal highlights the “harmonious chain” triggered as a result: “Food security and better livelihoods pave way for healthy, well-fed families, and agriculture growing beyond subsistence into an economic activity,” Hannibal concludes.

Lights, curtain… ACTION!
Much like in theatre, with all the ‘props’ in place, Hannibal reports that field trials are now performing well, thanks to the all-important ‘backstage’ support service elements being in good shape. Hannibal likens the positive feedback from the partners he has worked with to “A glass of cold water, after a long day in the sun!”

And there’s a beautiful simplicity to the impacts described: “With proper infrastructure in place, and with research station staff duly equipped with the hands-on expertise and practical know-how to utilise and apply this infrastructure and training, we’re now seeing field experiments being conducted as they should be, and getting good-quality phenotyping data as a result,” says Xavier. “Moreover,” he continues, “by providing glass-houses or the capacity to irrigate in the dry season, we are enabling breeders to accelerate their breeding cycles, so that they can work all year round, rather than having to wait until the rain comes.” Sites hosting GCP projects on rice in Nigeria, as well as on sorghum and rice in Mali, are just a few examples of those enjoying off-season work thanks to new irrigation systems.

Similar good news is expected soon for cassava in Ghana and in northern Nigeria. And yet more good news: in some cases, the impacts have not been limited to the trials, or even to the research trials and stations alone, as Xavier highlights with an example from Kenya: “The establishment of an irrigation system on a plot at Koibatek Farmer Training Centre – a partner of Egerton University – yielded excellent results for chickpea experiments. We emphasised that we did not want the equipment to be ‘bracketed’ exclusively for science and experiments. So, it was also used to train staff and farmers from the local community as well. This was greatly appreciated.”

Seeing the nuts-and-bolts now firmly in place for the majority of the sites visited, Hannibal believes GCP has facilitated a pioneering approach to local capacity building: “By addressing the needs at the heart of quality agricultural research, right there on the station, GCP was the first to cotton on to a crucial missing link between researcher, research station, and support services,” he reveals.

…Another missing link…
But the job is not quite done. One crucial gap is the sensitisation of upper management – those at the helm of national research institutes and research station Directors – to support and sustain infrastructure, training and related services. In some cases, costs could be easily met by utilising a priceless asset that most institutes already have, and which they could put to greater us – land and a controlled environment.

Upper management needs to be actively on board. “A research institute should work like a good sewing machine,” says Hannibal. “All well-oiled, all parts working well, and everybody knowing what they need to do.”

In the meantime, however, results from the field suggest that researchers in GCP projects are already reaping the benefits from improved infrastructure and support services, and are already off to a good start.

The stage is therefore set: backstage and props are well primed, performance trials are acting like they should, and the ‘theatre directors’ have an eye on sustainability after GCP’s final curtain call in 2014.

So, long may the show go on, with a cautionary word, however, to continually seek ways to not only maintain but also enhance performance!

Relevant links

  • PODCASTS: You can also listen to Hannibal, by tuning into Episode 2 for the entire interview, or zooming in on your particular area of interest in the mini-podcasts labelled Episodes 2.1 to 2.7 c here.
  • Capacity building
  • Research Initiatives
  • Integrated Breeding Platform website

 

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