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

 Asia, Crop breeding, Genetics, Genomics, Researchers, Rice  No Responses »
Jan 232013
 

Abdelbagi Ismail

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

GCP helped IRRI attract support from other funders…”

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

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

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

Links

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

 Asia, Capacity building, Genetics, Genomics, Researchers, Rice, Women in science  1 Response »
Dec 212012
 

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

Zeba Seraj

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Links

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

 

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

 Africa, Asia, Crop breeding, Genetics, Genomics, Researchers, Rice, Women in science  2 Responses »
Nov 302012
 
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

 

 

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

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

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

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

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

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

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

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

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

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.”

Photo: N Palmer/CIAT

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. Photo: N Palmer/CIAT

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

Breeding beans to better battle drought and disease in Ethiopia

 Africa, Beans, Crop breeding, Genetics, Genomics, Legumes  No Responses »
Nov 132012
 

Bean breeding in his bones: Asrat A Amele

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

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

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

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

At that time, Asrat remarked:

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

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

The ravages wrought by bean stem maggot.

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

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

Two…and two

Fitsum Alemayehu

Daniel Ambachew

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

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

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

Of humans and machines

A training session on maintaining farm machinery.

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

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

Water drilling to install irrigation equipment at SARI.

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

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

 

 

 

Asrat on video

Links

SLIDES: Phenotyping common beans for tolerance of drought and bean stem maggots in Ethiopia

 

Beans: Sidestepping variety… to create varieties to combat drought, disease and pests

 Africa, Beans, Crop breeding, Genetics, Genomics, Legumes  No Responses »
Oct 302012
 

BREAK-TIME AND BRAKE-TIME from beans for a bit: Steve Beebe takes a pause to strike a pose in a bean field.

“These [molecular breeding] techniques, combined with conventional methods, shorten the time it takes to breed improved varieties  that simultaneoulsy combine several traits.

And this means that we also get them out to farmers more quickly compared to phenotypic selection alone.”
– Steve Beebe

THE NEAR-PERFECT FOOD: Common beans (Phaseolus vulgaris L) comprise the world’s most important food legume, feeding about 200 million people in sub-Saharan Africa alone. Their nutritional value is so high, they have been termed ‘a near-perfect food’. They are also easy to grow, adapting readily to different cropping systems and maturing quickly.

That said, this otherwise versatile, adaptable and dapper dicotyledon does have some inherent drawbacks and ailments that crop science seeks to cure….

Rains are rapidly retreating, and drought doggedly advancing
Despite the crop’s widespread cultivation in Africa, “yields are low, stagnating at between 20 and 30 percent of their potential,” remarks Steve Beebe, GCP’s Product Delivery Coordinator for beans, and a researcher at the International Center for Tropical Agriculture (CIAT, by its Spanish acronym).

“The main problem is drought, brought about by climate change,” he says. “And it’s spreading – it already affects 70 percent of Africa’s major bean-producing regions.”  Drought decimates bean harvests in most of Eastern Africa, but is particularly severe in the mid-altitudes of Ethiopia, Kenya, Tanzania, Malawi and Zimbabwe, as well as in southern Africa as a whole.

A myriad of forms and hues: bean diversity eloquently speaks for itself in this riot of colours.

Drought, doubt and duality − Diversity a double-edged sword
“Common beans can tolerate drought to some extent, using various mechanisms that differ from variety to variety,” explains Steve. But breeding for drought resistance is complicated by the thousands of bean varieties that are available. They differ considerably according to growth habit, seed colour, shape, size and cooking qualities, and cultivation characteristics.

“A variety might be fantastic in resisting drought,” says Steve, ‘but if its plant type demands extra work, the farmers won’t grow it,” he explains. “Likewise, if consumers don’t like the seed colour, or the beans take too long to cook, then they won’t buy.”

Molecular breeding deals a hand, waves a wand, and weaves a band
This is where molecular breeding techniques come in handy, deftly dealing with the complexities of breeding drought-resistant beans that also meet farmer and consumer preferences. No guesswork about it: molecular breeding rapidly and precisely gets to the heart of the matter, and helps weave all these different ‘strands’ together.

The bean research team has developed ‘genetic stocks’, or strains of beans that are crossed with the varieties favoured by farmers and consumers. The ‘crosses’ are made so that the gene or genes with the desired trait are incorporated into the preferred varieties.

The resulting new varieties are then evaluated for their performance in different environments throughout eastern and southern Africa, with particular focus on Ethiopia, Kenya, Malawi and Zimbabwe which are the target countries of the Tropical Legumes I (TLI) project.

Propping up the plant protein: a veritable tapestry of terraces of climbing beans.

GCP supported this foundation work to develop these molecular markers. This type of breeding – known in breeder parlance as marker-assisted selection (MAS) – was also successfully used to combine and aggregate resistance to drought; to pests such as bean stem maggot (BSM); and to diseases such as bean common mosaic necrosis potyvirus (BCNMV) and to bruchid or common bacterial blight (CBB). The resulting ‘combinations’ laden with all this good stuff were then bred into commercial-type bean lines.

“These techniques, combined with conventional methods, shorten the time it takes to breed improved varieties that simultaneoulsy combine several traits,” comments Steve. “This means that we also get them out to farmers more quickly compared to phenotypic selection alone.”

Informed by history and reality
Breeding new useful varieties is greatly aided by first understanding the crop’s genetic diversity, and by always staying connected with the reality on the ground: earlier foundation work facilitated by GCP surfaced the diversity in the bean varieties that farmers grow, and how that diversity could then be broadened with genes to resist drought, pests and disease.

What next?
Over the remaining two years of Phase II of the Tropical Legumes I (TLI) project, the bean team will use the genetic tools and breeding populations to incorporate drought tolerance into farmer- and market-preferred varieties. “Hence, productivity levels on smallholder farms are expected to increase significantly,” says Steve.

Partnerships
The work on beans is led by CIAT, working in partnership with Ethiopia’s South Agricultural Research Institute (SARI),  the Kenya Agricultural Research Institute (KARI),  Malawi’s Department of Agricultural Research and Technical Services (DARTS) and  Zimbabwe’s Crop Breeding Institute (CBI) of the Department of Research and Specialist Services (DR&SS).

Other close collaborators include the eastern, central and southern Africa regional bean research networks (ECABREN and SABRN, their acronyms) which are components of the Pan-African Bean Research Alliance (PABRA). Cornell University (USA) is also involved.

VIDEO: Steve talks about what has been achieved so far in bean research, and what remains to be done

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Breeding ‘sukses’ in Indonesia’s rice

 Asia, Crop breeding, Genetics, Genomics, Researchers, Rice  No Responses »
Sep 072012
 

Joko infront of his office at ICABIOGRAD’s Molecular Biology Division.

Indonesian upland rice growers can expect to receive improved varieties that thrive in phosphorus-poor soils within a few years, thanks to the hard work of their national breeding programmes.

Joko Prasetiyono is a proud Indonesian researcher who loves rice.

“I don’t know why. I just love researching ways to improve it so it grows and yields better. I also I love to eat it,” says Joko with a laugh.

Having worked as a molecular breeder, concentrating solely on rice for 17 years at the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD), one would expect a different reaction. But Joko says he’s as interested in the little white grain as much as when he started as an undergraduate with ICABIOGRAD.

And why wouldn’t he be when he and his team are contributing to research that has just been published in Nature and is set to reduce fertiliser application and improve rice yields in Indonesia and the world over by 20 percent!

Improving Indonesian varieties, no genetic modification

Farmers often use phosphate fertilisers to aid in growing rice in these areas, but this option is often too expensive for Indonesian upland growers.

The project has found plants that have a Pup1 locus (a collection of genes), with the specific gene PSTOL1, are able to tolerate phosphorus-deficient conditions and produce better yields than those not suited for the conditions. An Indian rice variety, Kasalath, was one such.

“We are breeding rice varieties that we know have a Pup1 locus and subsequent PSTOL1 gene in them with Indonesian varieties that are suited to Indonesia’s growing systems,” explains Joko.   

Partnering with the International Rice Research Institute (IRRI), ICABIOGRAD and their partner the Indonesian Center for Rice Research (ICRR) have improved the phosphorus tolerance of Indonesian rice varieties Dodokan, Situ Bagendit and Batur.

“The new plants we are creating are not genetically modified; just bred using smarter breeding techniques,” says Joko. “The aim is to breed varieties identical to those that farmers already know and trust, except that they will have the PSTOL1 gene and an improved ability to take up soil phosphorus.”

Joko says that these varieties are currently being tested in field trials and it will take another 2–3 years before Indonesian farmers will have a variety that will yield as well if not better, needing 30–50 percent less fertiliser.

Evolving Indonesian plant research 

ICABIOGRAD team selecting breeding material in 2010. L-R: Masdiar Bustamam, Tintin Suhartini and Ida Hanarida.

GCP is as much about its people and partnerships as its research and products. ICABIOGRAD benefited from a GCP capacity-building grant in mid-2007 to enhance the institute’s capacity in phenotyping and molecular analysis. The grant covered, among other areas, intensive residential staff training at IRRI; PhD student support; infrastructure such as a moist room, temperature-controlled centrifuge apparatus, computers and appropriate specialised software; and  a blast innoculation room. These capacity-building activities were coordinated by Masdiar Bustamam who has since retired, but was then a Senior Scientist at ICABIOGARD.

But coming back to Joko and the PSTOL1 work, Joko started on this project in 2005 as a GCP-funded PhD student at Bogor Agriculture University, Indonesia. He is grateful to be part of a transnational project, which has offered him technical support that he would not otherwise have been able to receive through ICABIOGRAD alone.

IRRI visits ICABIOGRAD in 2009. L-R: Matthias Wissuwa, Sigrid Heuer (both IRRI), Masdiar Bustaman (ICABIOGRAD) and Joong Hyoun Chin

Joko believes the experience of working with IRRI, as a joint partner on this project, will leave an important, and lasting, legacy for researchers at ICABIOGRAD and ICRR. The partnership has also challenged the two local institutes to broaden their horizons past their borders.

“IRRI is teaching us how to use marker-assisted selection and we [ICABIOGRAD and ICRR] are just as busy identifying phosphorus-deficient hotspots in upland areas, choosing the best Indonesian recipient rice varieties for the gene, conducting the breeding and phenotyping testing,” he clarifies.

Breeding for sustainability

The ultimate goal of this project is to help Indonesian growers use marginal land.

Over half the world rice lands are deficient of ‘plant-available’ phosphorus, and Indonesia is no different. Joko explains that while there is plenty of phosphorus in the soil, plants are not able to access it.

“Other minerals in the soil like aluminum, calcium and iron are bound to phosphorus, shielding it from plants roots so they can only absorb a fraction of it.”

Field test of Pup1 lines at Taman Bogo , Indonesia.

In most countries, farmers apply phosphate fertilisers to their crops to combat this deficiency. For Joko this is not a sustainable approach for a lot of Indonesia’s farmers because the fertilisers are expensive and costs will continue to rise as phosphate supplies dwindle.

“Our approach is a lot more sustainable and cost-effective than applying fertiliser. We’ll breed these new plants for phosphorus-poor soils to produce more roots so they can find more phosphorus. The more phosphorus they find, the more of it they can absorb.”

Joko hopes these new plants will help farmers on marginal lands to obtain decent yields without having to spend money on expensive phosphate fertilisers.

“It’s great that our work has been recognised by Nature for publication, but what we really want is to help rice growers here in Indonesia and around the world.”

Links

♫We’ll rock your world!♫

 Comparative genomics in cereals, Crop breeding, Genomics, Researchers, Rice  No Responses »
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

 

Rooting for the key to more phosphorus for rice

 Comparative genomics in cereals, Crop breeding, Genetics, Genomics, Rice  3 Responses »
Sep 072012
 

Preparing rice root samples (Photo: IRRI)ALL IN THE ROOTS: A plant’s roots are a marvellously multitalented organ. They act as fingers and mouths helping plants forage and absorb water and nutrients. They act like arms and legs offering a sturdy base of support so a plant doesn’t keel over. They help store food and water, like our stomach and fat cells. And in some plants, can spawn new life – we leave that to your imagination!

That is why it is of little surprise that this multitalented organ was the key to discovering why some rice lines yield better in phosphorus-poor soils, a puzzle whose answer has eluded farmers and researchers… until now.  And even better, the findings hold promise for sorghum, maize and wheat too. Please read on!

 In search of the key – The Gene Trackers
In 1999, Dr Matthias Wissuwa, now with the Japan International Research Centre for Agricultural Sciences (JIRCAS), deduced that Kasalath, a northern Indian rice variety, contained one or more genes that allowed it to grow successfully in low-phosphorus conditions.

For years, Matthias made it his mission to find these genes, only to find it was as easy as finding a needle in a genetic haystack. He teamed up with the International Rice Research Institute (IRRI), and with GCP’s support, the gene trackers were able to narrow the search down to five genes of interest.

“We had started with 68 genes and within three years, we had narrowed in on these five candidate genes. And then, one-by-one, we checked whether they were related to phosphorous uptake,” recollects Dr Sigrid Heuer, senior scientist at IRRI and leader of the team that published the discovery in Nature in August 2012.

Sigrid Heuer at a rice phosphorus uptake demonstration field in The Philippines.

“In the end we found that if a certain protein kinase gene was turned on in tolerant plants like Kasalath, then those plants would perform better in phosphorus-deficient soils.”

They named this protein kinase gene PSTOL1, which stands for Phosphorus Starvation Tolerance. “When we put this gene into intolerant rice varieties that did not have this gene, they performed better in phosphorus-deficient soils.”

The importance of phosphorus
Rice, like all plants, needs phosphorus to survive and thrive. It’s a key element in plant metabolism, root growth, maturity and yield. Plants deficient in phosphorus are often stunted.

Sigrid explains that whereas phosphorus is abundant in most soils, it is however not always easily accessible by plants. “Many soil types bond tightly to phosphorus, surrendering only a tiny amount to plant roots. This is why more than half of the world’s rice lands are phosphorus-deficient.”

Farmers can get around this by applying phosphate fertilisers. However this is a very expensive exercise and is not an option for the majority of the world’s rice growers, especially the poorer ones –the price of rock phosphate has more than doubled since 2007. The practice is also not sustainable since it is a finite resource.

By selecting for rice varieties with PSTOL1, growers will be less reliant on phosphate fertilisers.

How it works: unravelling PSTOL1 mechanics
In phosphorus-poor soils, PSTOL1 switches on during the early stage of root development. The gene tells the plant to grow larger longer roots, which are able to forage through more soil to absorb and store more nutrients.

“By having a larger root surface area, plants can explore a greater area in the soil and find more phosphorus than usual,” says Sigrid. “It’s like having a larger sponge to absorb more water.”

A rice variety — IR-74 — with Pup1 (left) and without Pup1 (right).

Although the researchers focussed on this one key nutrient, they found the extra root growth helped with other vital elements like nitrogen and potassium.

Another by-chance discovery was that phosphorus uptake 1 (Pup1), the collection of genes (locus) where PSTOL1 is found, is present within a large group of rice varieties.

“We found that in upland rice varieties – those bred for drought-prone environments – most have Pup1,” says Sigrid. “So the breeders in these regions have, without knowing it, been selecting for phosphorus tolerance.”

“When thinking about it, it makes sense as phosphorus is very immobile in dry soils, therefore these plants would have had to adapt to grow longer roots to reach water deeper in the soil and this, at the same time, helps to access more reservoirs of phosphorous .”

Breeding for phosphorus tolerance, and going beyond rice
Using conventional breeding methods, Sigrid says that her team introduced PSTOL1 into two irrigated rice varieties and three Indonesian upland varieties, and found that this increased yields by up to 20 percent.

“In our pot experiments,” she added, “when we use soil that is really low in phosphorus, we see yield increases of 60 percent and more. This will mean growers of upland rice varieties will probably benefit the most from these new lines, which is pleasing given they are among the poorest rice growers in the world.”

Read how Indonesian researchers are developing their own breeds of upland rice with the PSTOL1 gene

Sigrid also sheds light on broadening the research to other crop varieties: “The project team is currently looking at Pup1 in sorghum and maize and we are just about to start on wheat.”

Building capacity and ensuring impact
Like all GCP projects, this one invests as much time in building capacity for country breeding programmes as on research.

Sigrid and her team are currently conducting the first Pup1 workshop to train researchers from Bangladesh, India, Indonesia, Nepal, Philippines, Thailand and Vietnam. They will share molecular markers that indicate the presence of PSTOL1, techniques to select for the gene, as well as for new phosphorus-efficient varieties.

Breeding for phosphorus-efficient rice in the Philippines.

“The aim of these workshops is to take these important tools to where they are most needed and allow them to evolve according to the needs and requirements of each country,” says Dr Rajeev Varshney, GCP’s Comparative and Applied Genomics Leader. “Breeders will be able to breed new rice varieties faster and more easily, and with 100 percent certainty that their rice plants will have the gene. Within three to five years, each country will be able to breed varieties identical to those that growers know and trust except that they will now have the Pup1 gene and an improved ability to unlock and take up soil phosphorus.”

Joining hands in collaboration
This IRRI-led project was conducted in collaboration with JIRCAS and the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD) working with the Indonesian Centre for Rice Research. Other partners included: Italy’s University of Milano, Germany’s Max Planck Institute in Golm, the University of The Philippines at Los Baños, USA’s Cornell University and University of California (Davis and Riverside), Brazil’s EMBRAPA, Africa Rice Center, Iran’s Agricultural Biotechnology Research Institute, Australia’s Commonwealth Scientific and Industrial Research Organisation (CSIRO) and University of Dhaka in Bangladesh.

Links

Sigrid’s presentation at the GCP General Research Meeting 2011

Extract from a ‘genomicist’s’ diary: Excited in Seattle!

 Genomics, Integrated Breeding Platform  No Responses »
Aug 222012
 

Which we promise you is a much greater thriller than ‘Sleepless in Seattle’. We’d like to share with you an exciting day in the life of our Comparative Genomics Leader, Rajeev Varshney (pictured). And yes, we just made up the word ‘genomicist’ featuring in this blogpost’s title: if those who study economics are ‘economists’, then it’s logical that those who study genomics are…’genomicists’ of course!

Rewind to early July, and here’s the extract from Rajeev’s jottings in his diary on that day…

10 July 2012 – I had a wonderful day in Seattle today: I delivered a presentation on Genomics and informatics for digitalisation of crop breeding in the brainstorming session on A digital revolution in agriculture at the Bill & Melinda Gates Foundation.

The meeting was chaired by Bill Gates and attended by his former and present associates (high-level business executives, entrepreneurs, philanthropists) and selected officials from the Gates Foundation. Discussions centred on four main topics – architecture, genomics, ecological intensification and ICT for a digital revolution in agriculture.

I was privileged to be invited to the meeting as one of three specialists in genomics (the other two being Jun Wang, Executive Director of BGI [Beijing Genomics Institute in Shenzhen China]; and Bob Reiter, VP at Monsanto). In total, there were 10 external experts from all four core areas in the meeting. I never thought that I would have the opportunity to spend a day with such a group of eminent personalities!”

GCP’s work on the Integrated Breeding Platform and on crop ontology were of relevance at the meeting.

A couple of snapshots from that meeting follow, and do look at the links below the photos…

 

Rajeev (standing left) gives his presentation during the meeting

Rajeev on the left, and guess who’s on the right?….That’s right! Bill Gates!

 

 

 

 

 

 

 

 

Links: Rajeev’s profile | Comparative and Applied Genomics Theme | Comparative Genomics Research Initiative | Integrated Breeding Platform | Crop ontology (click on crop of interest from the menu along the top, then follow the ‘crop ontology’ link from the links in the box on the left)

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