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A new breed of Workbench – Introducing the Breeding Management System

 Crop breeding, Crop information and data management, Integrated Breeding Platform  2 Responses »
Feb 182014
 

Mark Sawkins

Mark Sawkins

Mark the man in the middle, and of the markers…

Today, we talk to Mark Sawkins (pictured), the ‘middleware’ man in our Integrated Breeding Platform (IBP) so to speak, seeing as he is the human ‘interface’ between crop breeders on the one hand, and the developers of our Integrated Breeding Platform (IBP) on the other hand. Mark is the ‘bridge’ that connects IBP users and IBP developers – a special position which gives him a privileged and fascinating perspective on both sides of the coin, with a dash of public–private sector pragmatic partnership thrown in too. Here’s more on Mark, in this dispatch from and on his special perch on the bench…

Bridge to bench, abuzz on BMS: A ‘tinker’ at Toulouse…
Mark Sawkins is always busy tinkering away on his Workbench at his base in Toulouse in southern France. It’s not your traditional wooden workbench, covered in sawdust, soil or splattering of paint. Nor is it one carpeted in documents lit by the warm glow of a computer monitor. In fact, the workbench Mark is working on is virtual, having no physical form and residing solely online, or on a user’s computer, once downloaded.

Known as the Breeding Management System (BMS) the Workbench, comprising software tools linked to a database for access to pedigree, phenotypic and genotypic data, has been developed by GCP’s Integrated Breeding Platform. The BMS has what a crop breeder would require to conduct an analysis of phenotypic and genotypic data generated as part of a crop-breeding or evaluation experiment, covering a broad spectrum of needs from conventional breeding to advanced molecular breeding applications. Version 2 of the Breeding Management System was released just last month.

… it [BMS] will be of most help to breeders both in the public and private sector in Africa and Asia who, up to now, have had little or no access to tools and data to allow them to shift gears in their breeding programme…The BMS has a lot of tools and all the foundational data necessary for a breeder’s routine day-to-day activities…The BMS is also anticipated to have enormous positive impact on food security in developing countries in the years ahead, enabling crop breeders to evaluate their progenies using the most sophisticated statistical methods available”

A hands-on BMS orientation workshop underway for breeders in Africa, held in Ethiopia in July 2013 under the auspices of the GCP-funded cassava breeding community of practice. Standing, Yemi Olojode, of Nigeria’s National Root Crops Research Institute (NRCRI), Umidike, who was one of the trainers.

Previously known as the Integrated Breeding Workflow System (IBWS), the BMS incorporates both statistical analysis tools and decision-support tools. The tools are assembled in a way that data can flow seamlessly from one application to the next in tandem with the various stages of the crop-breeding process. It allows the breeder to accurately collect, securely store and efficiently analyse and synthesise their data on a local private database, and also share, or compare, their data with other breeders via a central public crop database.

“The BMS has a lot of tools and all the foundational data necessary for a breeder’s routine day-to-day activities,” explains Mark, a plant geneticist who joined IBP in 2011. “Any breeder can use it, but it will be of most help to breeders both in the public and private sector in Africa and Asia who, up to now, have had little or no access to tools and data to allow them to shift gears in their breeding programme, particularly in adopting modern breeding practices, including the use of molecular markers.”

The BMS is also anticipated to have enormous positive impact on food security in developing countries in the years ahead, enabling crop breeders to evaluate their progenies using the most sophisticated statistical methods available, and make selections on which lines to advance to the next phase of development in the progression towards more productive and resilient crop varieties.

Phenotyping and field trials are becoming the most expensive part of the breeding process… The biggest hurdle in the public sector in the past was the massive investment required to set up genotyping laboratory facilities… outsourcing, we believe, will help convince breeders to consider integrating molecular techniques into their breeding programmes”

Why integrated breeding?
For almost 30 years, the private sector has been implementing molecular-breeding approaches in developing more productive and resilient crops. These approaches allow breeders to select for plant characteristics (traits) early in the breeding process and then test whether a plant has the targeted trait, which they cannot visually identify.

“Phenotyping and field trials are becoming the most expensive part of the breeding process,” says Mark. “Using molecular markers is a way to reduce the investment in that process. By using markers, early in the development of a given crop line, you can reduce the number of plants you need to grow and test, reducing the time and cost associated with field trials.”

Mark hopes that the Workbench will in time enable breeders, in under-resourced public breeding institutes to access some of the leading molecular-marker databases, and make use of the markers therein for the desired traits they are breeding for, along with technical support from molecular breeders to guide them in making their breeding decisions.

“The biggest hurdle in the public sector in the past was the massive investment required to set up genotyping laboratory facilities,” explains Mark “but now there are plenty of professional service providers that people can send their samples to and get back good results at a very reasonable cost. This time- and cost-saving reality of outsourcing, we believe, will help convince breeders to consider integrating molecular techniques into their breeding programmes.”

We are currently conducting a three-year course to train scientists from national programmes in West and Central Africa, East and Southern Africa and South and Southeast Asia, who we hope will promote and support the adoption of modern breeding in their institutes and countries.”

An IB-MYC training course in session in April 2013 for the West and Central Africa group. Clarissa Pimentel, IBP's Data Manager/Training Specialist, at the front, traching trainees tricks on using Fieldlab in the tablet for data collection.

An Integrated Breeding Multiyear Course (IB-MYC) training course in session in April 2013 for the West and Central Africa group. Clarissa Pimentel, IBP’s Data Manager/Training Specialist, at the front, giving trainees tricks and tips on using FieldLab on the electronic tablet for field data collection.

Running with champions
Mark knows that giving breeders the tools and means to integrate molecular breeding into their programmes is one thing. To actually have them adopt them is another. But he has a plan.

In keeping with the core mission of GCP, which is to build sustainable capacity in developing-country breeding programmes, Mark proposes to recruit and train selected breeders in molecular-breeding techniques and set them up as champions and advocates for their particular crop or region.

Marker implementation methods can be varied but the tools required need to help the breeder make a quick informed decision on what to take forward to the next generation: What plants need to be crossed? Which plants should be kept and which ones discarded? The decision-support tools provided by the IB Workbench will help the breeder make these decisions.

“We are currently conducting a three-year course to train scientists from national programmes in West and Central Africa, East and Southern Africa and South and Southeast Asia, who we hope will promote and support the adoption of modern breeding in their institutes and countries,” Mark enthusiastically explains. The three-year training programme is known as the Integrated Breeding Multiyear Course (IB–MYC). Mark continues, “We believe that people will be more willing to listen to someone who is right there on the ground, whom they know and trust and can easily get in contact with if they need help.”

While the champions concept is still in its infancy, Mark believes it has real merit but must overcome two major barriers – time and confidence. “Identifying the champions won’t be hard,” he observes, “What will be hard is getting them to add this extra task to their already busy agenda. It will require buy-in from management at the institutional level to enable the champions to carry out their mission. It will also be individually hard for each champion, who will only be successful when they have the confidence in their own integrated breeding and extension skills. This confidence would be the thing that would really help sell the message.”

Engaging the private sector
Mark oversees the design, testing and deployment of the system that underpins the BMS, ensuring that both the system and the tools embedded in it are easy to use and meet the needs and expectations of the breeders. However, he and his team have had some trouble getting feedback on the system from the breeders it is intended for, due to their inexperience with such tools and systems. That is why he has called on his private-sector contacts, developed when he was at Syngenta where he worked for five years prior to his current assignment.

“We hope to show them what we’ve been doing in IBP with the Workbench, and hopefully get some private-sector buy-in and see how they can help us – not in developing tools, but with feedback on functionality and usability of the tools we are developing,” he explains. “We don’t have a core set of breeders who are routinely using markers in their breeding programme amongst the partners we are working with on the IBP project. So we are tapping into the private sector which has teams of molecular breeders who are more familiar with the types of breeding workflows and tools we are developing. We’re hoping that we can take advantage of their knowledge and experience to get some really useful feedback, which we will use to improve the usability and effectiveness of our tools.”

To maximise adoption and use, GCP has been actively engaged in extensive capacity building, and this will be reinforced with a comprehensive awareness-creation and communication effort immediately before and after a projected mid-year release of a newer BMS version incorporating the all-essential user feedback. The impact of the analytical pipeline in developing countries will be particularly enhanced with the availability of efficient user support services, which Mark will be overseeing.

Access the Breeding Management System (no-cost registration required)

More information

VIDEO: IBP’s comparative advantage for developed countries, while also relevant for developed countries.

SLIDES: IBP’s Breeding Management System

 

Cultivating a culture of change – Tools and tips for ‘SHARP’ data management, in and for the Information Age

 Crop breeding, Crop information and data management, Integrated Breeding Platform, Researchers, Women in science  No Responses »
Jan 312014
 
Arllet Portugal

Arllet Portugal

Today, we chit-chat with Arllet Portugal (pictured) on crop research data management. Arllet’s greatest daily challenge is convincing crop breeders and other crop researchers that their research data are just as important as their core research work. She also educates us on what she means by ‘SHARP’ data management. But first, a little background on Arllet…

Transitions, travels and tools
Plant breeding is in Arllet Portugal’s blood. Her father (now retired), one of the original field staff of the International Rice Research Institute (IRRI) at Los Baños in The Philippines, nurtured it in her from a tender age. It’s easy to picture him sharing fascinating tales daily with his family upon coming home, after a day of hard work in sun-splashed paddies where he nurtured mysterious and exotic new lines of rice which he was told may hold the solution to world hunger.

“He loved what IRRI stood for and admired the research they did,” reminisces Arllet. “I think he hoped one day he would have a son or daughter working alongside the researchers, so I guess I fulfilled that wish!” She adds “His IRRI stories still continue to this day, and I have learnt much from him which continues to give me deeper insights in my work and interactions with crop scientists.”

Having lived most of her life under the canopy of IRRI, including 12 years working as a database administrator at the Institute, she decided it was time for a change, and she spread her wings – an adventure that would take her across the oceans, pose new challenges, and plunge her deeper into agricultural research beyond IRRI’s mandate crop, rice. So, in 2009, she packed her bags and headed to Mexico, having accepted a position as a crop informatician for wheat at the International Maize and Wheat Improvement Center (CIMMYT), and then moving over to GCP the following year as Informatics Coordinator, and later on Data Management Leader of GCP’s Integrated Breeding Platform (IBP).

The Platform is a one-stop shop for crop information, informatics tools and services designed to propagate and support the application of modern approaches to crop breeding, particularly targeting developing countries.

We are trying to show breeders that their ‘system’ can be enhanced and streamlined if they enter data straight into a computer when they’re in the field and then upload them into an online database.” 

Gunning for a digital data revolution: The challenge of changing mindsets
Arllet’s greatest daily challenge is convincing crop breeders and other crop researchers that their research data are just as important as their core research work, and they should therefore dedicate as much time, energy and resources to managing data.

“Like everyone else, most plant breeders tend to be generally comfortable with the ‘systems’ that they and their predecessors have always used,” says Arllet. “For plant scientists, this often consists of recording results using pen and paper when they are out in the field, then coming back to their office and either filing those paper records as is, or re-entering the data into a basic Excel spreadsheet that is for their eyes only. They will then pull these data out when they want to compare them with their previous data.”

Arllet explains that this age-old system is not necessarily wrong, but it wastes valuable time, is insecure and limits the capacity of breeders to efficaciously reuse and also share their data with colleagues – a practice by which they would help each others’ work. “We are trying to show breeders that their ‘system’ can be enhanced and streamlined if they enter data straight into a computer when they’re in the field and then upload them into an online database,” she says.

Walking with giants…” 

Dealing with data: maximising efficiency, security, value and sharing
“These data can then be better secured and managed for their benefit and that of other researchers doing similar or related work, in essence increasing their working capacity. They would also have access to the most current analytical tools to verify their results and do their research more efficiently.”

Arllet explains that such improved systems have been in place for decades in the developed world, particularly within the private sector but not as prevalent in the developing world or public sector. This is largely attributable to the high cost of the equipment and informatics tools, and a lack of personnel with the appropriate skills to make use of the tools.

Through a collaborative effort bringing together a wide array of partners, with funding primarily from the Bill & Melinda Gates Foundation, supplemented by the European Commission and the United Kingdom’s Department for International Development, IBP is working to overcome some of these barriers. With the release of the Integrated Breeding (IB) FieldBook, the foundational informatics tool for the proposed system, Arllet believes a giant step has been made towards achieving this objective.

Breeders will be able to use it to plan their trials from start to finish”

What is the IB FieldBook?
The IB FieldBook is a user-friendly computer program that facilitates the design of field trials and produces electronic field-books, field plans and labels. It collects together – in a single application – all the basic tools that a plant breeder requires for these diverse but intertwined functions.

“Breeders will be able to use it to plan their trials from start to finish,” says Arllet. “This is important as it will, for example, keep track of all the identities of plant crosses, minimising the chance that the breeder, or assisting technician, will record the data incorrectly, while emphasising the importance of accurate data for correct crop-breeding decisions.”

Live demonstration: Taking the tablet through the paces at a training workshop for research technicians in January 2012. The regional workshop for West Africa (in French and English) was hosted by L’Institut d’économie rurale (IER) at Sotuba, Mali. A similar workshop was held in Ethiopia in English for the Eastern and Southern Africa region.

She and her team have been conducting training workshops on data management for breeders at which they demonstrate the IB FieldBook and the use of handheld electronic devices (such as tablets) for data collection, which breeders can conveniently take to the field with them and directly enter the phenotyping data they would normally capture in paper field-books.

Tablets and feedback
“The training has been challenging but fun,” says Arllet. “When we present the breeders with a tablet at the start of the exercise, they get really excited. It takes a while for them to learn how to use it, but once they do, they see how this technology could save them time and reduce the risk of mistakes. It’s a little sad for them and for us though when we have to take the tablets back at the end of the exercise, as demand always outstrips supply. We have however distributed around 200 tablets to breeders, university academic staff, researchers and postgraduate students of plant breeding. Majority of the recipients are from Africa and Asia. And the good news is that,  as a result, some of the institutes and programmes the recipients come from have gone ahead to purchase more units for themselves.”

Arllet observes that the workshops have not only allowed her team to educate breeders and build awareness, but also to receive valuable feedback on how the IB FieldBook could be improved to make it even better, and learn what other tools breeders need. “Based on this feedback, we worked on the IB FieldBook version 4, which was released in June 2013, as well as on a number phenotypic and genotypic data management tools to incorporate into both the FieldBook and the primary crop databases.”

‘SHARP’ data – shareable, available, reusable and preservable. 

Left to right: Diarah Guindo (IER), Ardaly Abdou Ousseini (L’Institut national de la recherche agronomique du Niger, INRAN) and Aoua Maiga (IER) at the January 2012 training at IER Sotuba, Mali.

SHARP and secure data management
Plant breeders are collaborating more often than they used to, and also drawing much more on specialised experts for each stage of the crop variety development chain. These experts are able to verify the data to make sure they are correct, do their job quickly and pass the data onto the next expert, an economical resource- and time-efficient process. However, as Arllet explains, consistent and secure data management is key to the success of these collaborations.

For Arllet, data that are properly managed are ‘SHARP’ – shareable, available, reusable and preservable. “By collecting data in a consistent format, uploading them to a secure database with easily identifiable tags, and making them available to other researchers, the data will be more accessible to partners, enable reliable analysis and conclusions, be more likely to be reused, and most importantly, save time and money. For example, breeders who share their data on the IBP database will receive support from researchers outside of their own breeding programme and enlist the help of experts and specialists  they require for particular tasks,” says Arllet. “This includes access to, say, a molecular biologist in Europe or Asia for the breeder in Africa or America who may need that kind of specialist help, for example.”

Arllet and her team of four consultants are currently helping breeders from all around the world upload their historical research data into the central crop databases of the Integrated Breeding Platform, a massive task given the issues of trust, language barriers, slow internet connections, inadequate computer skills and the sheer volumes of the data. However, these are challenges that are becoming easier to handle with greater awareness and the enthusiasm that comes with that.

What next, and what difference will it make?
Adoption and broad use of the FieldBook will of course also make the process easier in the future, enabling a single step uploading of phenotypic data – hence setting breeders free to get on with their work without the wastefulness of having to enter and re-check the data multiple times.

“What it all means is that we will facilitate the more rapid and efficient development of higher-yielding  more stress-tolerant crops that can benefit the farmers and the people they feed,” says Arllet, “and that is the ultimate goal of a plant breeder’s work.”

Links

See videos below: ‘ Masses of crop breeding information: How can it be handled?’ and “Why use IBP’s breeding and data management tools?“, which, in the view of one of our Australian partners, explains why IBP is particularly important for developing countries, and why they have a comparative advantage compared to the developed world.

Next video below:

PRIZE AND FUN! If you’ve survived this far, you deserve a prize, in the form of seeing Ms Portugal in party mode. To see what Arllet gets up to when she’s not crunching data, flip through this fun album

Making an indelible mark – Indonesia’s marathon Mother Nature, in science as in spirit

 Asia, Capacity building, Crop breeding, Researchers, Rice, Women in science  No Responses »
Dec 122013
 

Down memory lane with Masdiar Bustamam, from generation to generation

Masdiar Bustamam

In some circles, Masdiar Bustamam (pictured right) is a mother figure of molecular breeding in Indonesia. In a marathon career spanning 37 years as a horticulturist and agricultural researcher, she helped develop and nurture the practice at the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD).  Staying with the marathon metaphor, this quote from a celebrated middle- and long-distance Kenyan champion runner, Kipchoge Keino, is very apt: “This life we have is short, so let us leave a mark for people to remember.”

Back to Masdiar: having retired in early 2012, we were recently lucky enough to gain a rare insight into Masdiar’s life, and to witness the mark she has already made, by simply tagging along when she checked in on two of her ICABIOGRAD charges and mentees whose PhD studies were supported by GCP – Wening Enggarin and Joko Prasetiyono. At ICABIOGRAD, Wening and Joko have both taken the torch from Masdiar for GCP projects, as well as for other projects.

She was the best teacher for me … instilled in me a spirit to never lose hope in the research I’m doing – Joko

She was a great role model… Her persistence and positive can-do nature was exactly what I needed as a young researcher … to not just offer me assistance in my work but also in life and religion. For me, she has become a second mother  – Wening

… That project really helped us out a lot and we are grateful to GCP  for recognising the potential in us and supporting it – Masdiar

Here’s more of what Masdiar (and her charges) had to say as we tagged along, and chatted her up…

Tell us about your early life
I grew up and lived in West Java for most of my life. My father was a farmer and my mother a housewife. I was their first of five children.

I went to Andalas University in Padang and graduated with a Bachelor in Biology in 1974. After graduating, I worked as a staff researcher at a local horticulture research institute focusing on pests and diseases, particularly fungi in tomato soils. I was lucky early in my career to have opportunities to visit research institutes in The Netherlands, Japan and USA, all of which enhanced my skills. While in USA, I completed my Masters in rice blast disease – a fungus-related disease, which severely hampers rice yields in Indonesia, and all around the world.

After my time in USA, I accepted a position at the International Rice Research Institute (IRRI) in The Philippines. This was the start of the second phase of my career, in which I began to focus on molecular biology. When I returned from The Philippines, I realised that we needed to improve our capacity to use molecular markers for breeding, which led me to take a job at ICABIOGRAD.

Setting up a lab – GCP lends a hand
When I first started at ICABIOGRAD we had empty benches. It took a lot of time and money to fill them with the equipment we have today. Rebecca Nelson from Cornell University in USA provided us with a lot of support in getting us started. We were involved in one of her GCP projects for two years working on blast resistance in rice.

We were also working on another GCP project led by Abdelbagi Ismail studying phosphorus-deficiency tolerance in rice too, dubbed the Pup1 project. Joko was actually my PhD student for that project and did a lot of the work.

Selecting Pup1 lines in farmers' fields in Sukabumi, West Java, in 2010. L–R: Masdiar Bustamam, Tintin Suhartini and Ida Hanarida Sumantri.

Selecting Pup1 lines in farmers’ fields in Sukabumi, West Java, in 2010. L–R: Masdiar Bustamam, Tintin Suhartini and Ida Hanarida Sumantri.

Both Rebecca and Adbdelbagi helped me draft a proposal to GCP in 2007 for a project to enhance our capacity in phenotyping and molecular analysis to develop elite rice lines suitable for Indonesia’s upland regions. We had the understanding to do the science, but needed to enhance our facilities to carry it out.

That project really helped us out a lot and we are grateful to GCP  for recognising the potential in us and supporting it.”

GCP recognised the need for such a project as many of Indonesia’s brightest researchers were leaving the country because of the lack of suitable facilities, and so funded the two-year ICABIOGRAD-defined capacity-building project. The grant covered – among other areas – intensive residential staff training at IRRI; PhD student support, which allowed Wening to complete her PhD; infrastructure such as a moist room, temperature-controlled centrifuge apparatus, computers and appropriate specialised software; and blast and inoculation rooms.

Writer’s note: The tailor-made grantee-driven capacity-building project above was a cornerstone of  GCP Phase I’s capacity-building strategy, and was dubbed ‘Capacity building à la carte’. With this historical note, we take an interlude here, to tour the facilities Masdiar has mentioned above.

Our first stop is the Rice Blast Nursery…

....Front view...

….Front view…

...side view...

…side view…

 

 

 

 

 

 

 

 

... and a close-up on the sign in the side view.

… and a close-up on the sign in the side view.

 

Next, we visit the Inoculation and Moist Rooms…

 

Inoculation and Moist Rooms

Inoculation and Moist Rooms…

 

Close-up

…and a close-up on the sign at the front.

 

 

 

 

 

 

 

After our tour of the facilities, Masdiar resumes her story: “That project really helped us out a lot and we are grateful to GCP  for recognising the potential in us and supporting it so that researchers like Wening bloom and blossom, now and into the future,” says Masdiar glowingly of one of her mentees and successors.

I’m proud of how they have matured and I’m really looking forward to when they and their teams produce new rice varieties, from the facilities I helped establish, that will help the farmers…I sacrificed what I enjoyed doing for a challenge whose benefits I recognised for my country.”

Mission-driven researcher, nurturer and mentor, all rolled into one
For Masdiar, it wasn’t work, but rather a passion and a hobby. “Throughout my career, I always enjoyed research, especially in plant pathogens,” she remembers. “Working with biotechnology was difficult because I didn’t have a background in the area. I sacrificed what I enjoyed doing for a challenge whose benefits I recognised for my country.”

Photo: ICABIOGRAD

From generation to generation: Masdiar (2L) drops in on her charges and torch-bearers at ICABIOGRAD’s Molecular Biotechnology Lab. L–R: Wening Enggarini, Masdiar Bustamam, Tasliah Zulkarnaeni, Ahmad Dadang and Reflinur Basyirin.

In the later half of her career, Masdiar recollects how she enjoyed training and mentoring younger researchers like Joko and Wening. “I’m proud of how they have matured and I’m really looking forward to when they and their teams produce new rice varieties, from the facilities I helped establish, that will help the farmers.”

Both Joko and Wening attest that Masdiar’s support and supervision were vital for their professional development and consequent career advancement. “She was the best teacher for me. She taught me how to manage a project, how to forge international collaborations, and how to write a good publication,” remembers Joko. “She also instilled in me a spirit to never lose hope in the research I’m doing.”

“She was a great role model for me!” exclaims Wening proudly. “Her persistence and positive can-do nature was exactly what I needed as a young researcher who was just starting a career. Even more so was her ability to take time out of her busy day to not just offer me assistance in my work but also in life and religion. For me, she has become a second mother  in this life. I’m blessed to be so lucky!”

Clearly, Masdiar has made her mark, leaving a cross-generational living legacy in molecular breeding embodied in these young researchers.

Links

  • Masdiar’s project report, with a picture of the blast nursery under construction (p 156 in this PDF)
  • Photo-story on Facebook
  • Rebecca Nelson’s project, Targeted discovery of superior disease QTL alleles in the maize and rice genomes (p 16 in this PDF)
  • GCP’s capacity building

 

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

 

 

Banana genetics: (not-so-)Easy as ♫ABC, 123♫

 Bananas, Genetics, Genomics  No Responses »
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

 

On common ground – A longstanding association

 Funders, GCP, History  No Responses »
Jul 082012
 

SDC and GCP

Today, we catch up with SDC’s Carmen Thönnissen (pictured). She walks us through the whys of Switzerland’s continued funding to GCP that has spanned nearly the Programme’s entire lifetime.

We were …drawn to GCP’s upstream–downstream connections, and its pre-conceived product delivery path. GCP produces global public goods, with a clear focus on strategic research for development, while also addressing important upstream research elements in crop science such as gene discovery and marker validation. In addition, GCP already had a Product Delivery Strategy to guarantee downstream application.

The way GCP uses and ‘bundles’ resources within and beyond CGIAR, then as now, is attractive to us as a meaningful approach, promising good value for money.”

GCP’s work is very results-oriented and pragmatic, forging partnerships followed by concrete actions to address bottlenecks in research for development in molecular crop breeding, without ruling out conventional breeding.

Carmen Thönnissen is Senior Advisor, Federal Department of Foreign Affairs, Swiss Agency for Development and Cooperation (SDC), Corporate Domain Global Cooperation of the Global Programme for Food Security. Through the years, SDC has been a consistent GCP funder. Today, Carmen gives us some insights into this longstanding relationship.

Tell us briefly about SDC and its funding to GCP
SDC is the Swiss Agency for Development and Cooperation, affiliated to the Ministry of Foreign Affairs of the Swiss Government.

We’ve funded GCP since 2006 with an annual contribution of 450,000 Swiss francs – a total of 1.9 million so far.

SDC provides GCP core unrestricted funds at Programme level, meaning that SDC does not tie its funding to specific GCP projects, giving GCP discretion over these funds.

Why does SDC support GCP?
We share a long history with GCP, going as far back as the Programme’s ‘pre-birth’.

Starting in 2001, CGIAR adopted a more programmatic systemwide approach and endorsed the concept of Challenge Programmes. Between 2002 and 2005, SDC actively supported this process and the emerging Challenge Programmes.

In 2005, SDC reviewed its support to CGIAR and identified SDC priority regions, research priorities, and guiding principles for its unrestricted funding to the CGIAR system.

From this review, SDC decided to invest 30 percent of its core unrestricted funds to several CGIAR Systemwide and Challenge Programmes, one being GCP.

The Challenge Programmes were perceived as results-oriented, poverty-relevant and responsive to the CGIAR reform process of that time. They were also partnership-oriented, with transparent communication strategies.

Several points convinced SDC to invest in GCP, and I’ll mention just some of these. One was GCP’s focus on crops in marginal areas and on drought tolerance in sub-Saharan Africa, and South and Southeast Asia. These overlap with SDC’s own thematic and geographical priorities.

We were also drawn to GCP’s upstream–downstream connections, and its pre-conceived product delivery path. GCP produces global public goods, with a clear focus on strategic research for development, while also addressing important upstream research elements in crop science such as gene discovery and marker validation. In addition, GCP already had a Product Delivery Strategy to guarantee downstream application.

The way GCP uses and ‘bundles’ resources within and beyond CGIAR, then as now, is attractive to us as a meaningful approach, promising good value for money. Back then, SDC was interested in the exploration of plant diversity and the application of advanced genomics and comparative biology to advance breeding of the main staple crops grown by resource-poor farmers, which was the very objective of GCP.

Our funds were intended to be used to increase the exploratory implementation of new research tools in applied breeding programmes to produce improved drought-tolerant crop varieties.

We liked GCP’s structured approach of a Global Access Policy backed by guidelines on public–private sector partnerships and addressing intellectual property.

We also found the ‘suite approach’ proposed by GCP attractive, since at that time, very little was being done in these fields by CGIAR. We were drawn to the mix of a research component – on the impact of modern and integrated breeding approaches on productivity in developing countries, plus a service component aiming to disseminate knowledge, resources and technology, alongside lab services and capacity building.

GCP’s work is very results-oriented and pragmatic, forging partnerships followed by concrete actions to address bottlenecks in research for development in molecular crop breeding, without ruling out conventional breeding.

You mentioned common SDC–GCP thematic and geographic scope. Are there other areas where the missions of SDC and GCP overlap?
SDC has a focus on genetic resource improvement, and also supported the CGIAR Systemwide Programme on Genetic Resources, as well as the Global Crop Diversity Trust.

Supporting GCP is in line with SDC’s internal guidelines on Green Biotechnology. Among other things, we avoid single-donor initiatives, instead working within larger programmes that not only have a clear focus but also aim to strengthen developing-country capacity.

GCP’s work is very results-oriented and pragmatic. GCP plays a strong facilitating role in forging partnerships, which is followed by concrete actions, services, tools, methods, and so on, to address the bottlenecks identified by the research-for-development network with the aim of supporting molecular crop breeding for various crops, regions and partners, without ruling out conventional breeding.

SDC shares the view that Green Biotechnology, including genetic modification, can never fully replace conventional breeding, but it can be an important tool in improving plant-breeding programmes.

What outcomes are you expecting from this support?
To mention just a few, improved accessibility to modern breeding tools, methods and approaches for the developing world, plus enhanced capacity for developing-world partners on using these tools, as well as them knowing their rights and obligations regarding access to, and use of, plant genetic resources and related tools.

We also hope to see improved services for breeders, including learning materials and information on new resources for crop breeding. The long-term outcome we’d like to see is improved crop varieties, more resistant to abiotic and biotic stresses.

What are some of the lessons learnt from investing in GCP?
The importance of a strong programmatic orientation and the role of an honest broker in effective partnerships: GCP plays the role of enabler and facilitator, while its research partners are the actors.

Investing in GCP enables us to project a clear flow from upstream to applied research – with capacity building included – in the critical areas of food security and climate change.

Relevant links

Policies 

Blogposts

Chickpea research in India – Getting to the root of the matter to enhance drought tolerance

 Asia, Chickpeas, Crop breeding, Legumes  No Responses »
Jun 272012
 

India is the world’s largest producer and consumer of chickpea, accounting for more than a third (66 percent) of world production.

The Indian Agricultural Research Institute (IARI) and the Indian Institute of Pulses Research (IIPR) are collaborating with the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) on marker-assisted backcrossing (MABC), to improve chickpeas for drought tolerance.

This complementary activity in the Tropical Legumes I project (TLI) Phase II is being funded by the Department of Biotechnology, Government of India.

Dr N Nadrajan (pictured left), IIPR Director, adds “We have been trained on the breeding tools offered by the Integrated Breeding Platform, including data management, and on electronic data collection using a handheld device.”

Shailesh Tripathi (pictured right) is a Senior Scientist working on chickpea breeding at IARI. “During Phase I of TLI, ICRISAT and its partners identified a root-trait QTL region which confers drought tolerance in chickpeas, and the markers by which to transfer this QTL region. By evaluating the chickpea reference set, ICRISAT and its partners in Africa identified about 40 lines for drought tolerance, and these lines are being used in Phase II of the project,” says Shailesh. [Editor’s note: A ‘reference set’ is a sub-sample of existing germplasm collections that facilitates and enables access to existing crop diversity for desired traits, such as drought tolerance or resistance to disease or pests]

“Through GCP, we have benefitted from training in molecular breeding. The benefits of this go beyond this project,” he adds.

The Indian scientists are using MABC as well as marker-assisted recurrent selection (MARS) in Phase II, applying genomic resources that came from Phase I of the project.

“Our goal is to obtain lines with good root traits for drought tolerance,” says Shailesh, realistically adding that “Variety release will take time, but the good news is that we already have the pre-release materials to identify donors for specific traits, like root biomass.”

Progress in chickpea research in Africa and Asia

Related links

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

 Africa, Chickpeas, Crop breeding, Legumes  No Responses »
Jun 262012
 

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

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

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

Who’s now calling the shots in chickpea research?

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

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

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

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

VIDEO CLIP: Recipe for chickpea success

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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