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Travelling from Timbuktu to learn from the world: Niaba Témé’s travels and travails

 Africa, Researchers, Sorghum  No Responses »
Aug 302014
 

In ancient Europe, Timbuktu, in Northern Mali, gained fame as a fabled city of knowledge and learning at a far end of the world – snuggled in the Sahara Desert, and almost impossible to get to. And so, then as in our times, the phrase ‘As far as Timbuktu’ came to mean a place that is unimaginably far away, is completely foreign, or is unreachable – at the other end of the earth. Sitting on the left bank of the River Niger on the southern edge of the Sahara, it was not only a seat of learning in the ancient world, but also an important trade and travel stop for merchants as they sought refuge from the desert.

Niaba Teme

Niaba Témé

Timbuktu ticks on today. And if you strike out south and travel 450km from Timbuktu, you would come to the village of Yendouma-Sogol. This is where Niaba Témé, a plant breeder at Mali’s L’Institut d’économie rurale (IER), was born and grew up on the family farm, and where his saga with sorghum began.

“We grew dryland crops like millet, sorghum, cowpeas, groundnuts, Bambara nuts, sesame and dah,” says Niaba. “I used to love harvesting the millet and helping my mother with her groundnut crops.”

Niaba describes the geography and climate of the region as being very harsh. Sandstone cliffs soar from the dusty sun-scorched lower plains where temperatures are only slightly lower than the plateaus, which bake in the intense heat – the daily temperature rarely falls below 30oC. As there is no major river, every single drop of the 500 millimetres of rainfall received each wet season is used for drinking, cropping and livestock husbandry.

“The rains during July and August make farming possible for our people,” says Niaba.“If we did not receive those rains, our crops would suffer and in some years, we were not able to harvest anything.”

Niaba says these crop failures contributed in part to his choosing a career where he could help farmers, like his parents and siblings, protect themselves from the risks of drought and extreme temperatures.

With molecular markers, you can easily see if the plant you’ve bred has the gene related to drought tolerance without having to grow the plant and or risk missing the trait through visual inspection.”

Breeding more sorghum with less water
For the past four years, Niaba and his team at IER have been collaborating with Jean-François Rami and his team at France’s Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), with support from Syngenta complemented by other GCP funding on a project to improve sorghum grain yield and quality for West African farmers.

A sorghum farmer in Mali.

A sorghum farmer in Mali.

Sorghum is an important staple crop for Mali. It is used to make to (a thick porridge), couscous, as well as malted and local beer beverages. “Anytime I talk with farmers, they are always asking for higher-yielding lines and lines that can produce sustainable yields during drought, or do so with less water,” says Niaba. “Since 2008, with the help of CIRAD and Syngenta, we have been learning how to use molecular markers to identify parental lines which are more tolerant and better adapted to the arable and volatile environment of Mali and surrounding areas which receive between 600 and 800 millimetres of rainfall per year. Using molecular markers is new and exciting for us as it will speed up the breeding process. With molecular markers, you can easily see if the plant you’ve bred has the gene related to drought tolerance without having to grow the plant and or risk missing the trait through visual inspection.”

In 2010, Niaba obtained GCP funding to carry out similar research with CIRAD and collaborators at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in Africa. “In this project, we are trying to enhance sorghum grain yield and quality for the Sudano-Sahelian zone of West Africa using the backcross nested association mapping [BCNAM] approach. This involves using an elite recurrent parent that is already adapted to local drought conditions, then crossing it with several different specific or donor parents to build up larger breeding populations. The benefit of this approach is it can lead to detecting elite varieties much faster.”

AB_Mali 2009 (3) 243_w

Niaba (foreground) examining a sorghum panicle at trials in Mali in 2009.

I spent eight months in Hyderabad. It was the first time I had to speak English every day… I spent almost 11 years at the University of Texas Tech, and enjoyed every moment… We have been collaborating with researchers…  in Australia “

Traversing the world seeking knowledge
But to backtrack a bit and find out how Niaba got to where he is today, let’s return to the family farm where he grew up, and where his career inspiration was forged and fired.

With a family background in farming now coupled with a keen interest in science, young Niaba enrolled at L’Institut Polytechnique Rural de Formation et de Recherche Appliquée (IPR/IFRA) at Katiboutou, in Eastern Bamako, Mali to study agronomy. He then went to IER, where, after two years there, he was offered a scholarship to study plant breeding in India.

“I spent eight months in Hyderabad. It was the first time I had to speak English every day so I was enrolled for an intensive English course at the University of Ousmania, Hyderabad, India, for the first two months. I then went on to do six months intensive training in the ICRISAT labs, learning how to set up experiments and collect and analyse data.”

His zest for plant breeding research and knowledge still unquenched, Niaba sought yet another intensive training course, this time in USA. During his time there, he made an impression on local researchers and it wasn’t long before he returned to complete his Bachelor’s, Master’s and PhD in Agronomy at the University of Texas Tech, Texas. “I spent almost 11 years at the University of Texas Tech, and enjoyed every moment. I love the opportunities and freedom that USA offers.”

Despite this attraction, Niaba remained true to Timbuktu and Mali. He left Texas and returned to Mali in January 2007 , where he was rapidly recruited by IER to take charge of their new biotechnology lab at Le Centre Regional de Recherche Agromique (CRRA). Shortly after, he became involved with GCP, working on three projects, one of which would take this native from near (or as far away as?) Timbuktu to yet another far-away place at the opposite end of the world known as Down Under – Australia.

“We have been collaborating with researchers at the Department of Agriculture, Fisheries and Forestry in Queensland, and the University of Queensland, Australia, since 2009, to introduce the stay-green drought-resistant gene into our local sorghum varieties.” says Niaba.

 

Left to right: Niaba Teme (Mali), David Jordan (Australia), Sidi Coulibaly (Mali) and Andrew Borrell (Australia) visiting an experiment at Hermitage Research Facility in Queensland, Australia.

Left to right: Niaba Témé (Mali), David Jordan (Australia), Sidi Coulibaly (Mali) and Andrew Borrell (Australia) visiting an experiment at Hermitage Research Facility in Queensland, Australia.

Sorghum staying-greener with less water
Stay-green is a post-flowering drought adaptation trait that has contributed significantly to sorghum yield stability in northeastern Australia and southern USA for the last two decades. The project has three objectives:

  • To evaluate the stay-green drought resistance mechanism in plant architectures and genetic backgrounds appropriate to Mali
  • To develop sorghum germplasm populations enriched for stay-green genes that also carry genes for adaptation to cropping environments in Mali.
  • To improve capacity of Mali researchers by carrying out training activities for African sorghum researchers in drought physiology and selection for drought adaptation in sorghum.

“In 2012 a colleague and myself were invited to Australia to take this training by Andrew Borrell and David Jordan,” says Niaba. “We learnt about association mapping, population genetics and diversity, molecular breeding, crop modelling using climate forecasts and sorghum physiology, plus a lot more! It was intense but rewarding, more so the fact that we have developed these new drought-tolerant crops which will enhance food security for my country.”

Thus ends today’s chapter in Niaba’s saga with sorghum. We expect to hear more on the latest from Niaba at the GCP General Research Meeting  (GRM) in October, so watch this space!

Meantime, see his slides from GRM 2013 below.

Links

 

 

2 – 1 = 3: Seeking sorghum solutions, breeding for more yield with less water

 Africa, Crop breeding, Genetics, Genomics, Sorghum  No Responses »
Aug 292014
 
One of the greatest challenges of our time is growing more crops to feed more people, but using less water

Sorghum is one of the most ‘efficient’ crops in terms of needing less water and nutrients to grow. And although it is naturally well-adapted to sun-scorched drylands, there is still a need to improve its yield and broad adaptability in these harsh environments. In West Africa, for example, while sorghum production has doubled in the last 20 years, its yield has remained stagnant – and low.

The GCP Sorghum Research Initiative comprises several projects, which are exploring ways to use molecular-breeding techniques to improve sorghum yields, particularly in drylands. All projects are interdisciplinary international collaborations with an original focus on Mali, where sorghum-growing areas are large and rainfall is getting more erratic and variable. Through the stay-green project, the research has since broadened to also cover Burkina Faso, Ethiopia, Kenya, Niger and Sudan.

Using molecular markers is new and exciting for us as it will speed up the breeding process. With molecular markers, you can easily see if the plant you’ve bred has the desired characteristics without having to grow the plant and or risk missing the trait through visual inspection.”

What’s MARS got to do with it?

Niaba Témé is a local plant breeder and researcher at Mali’s L’Institut d’économie rurale (IER). He grew up in a farming community on the southern edge of the Sahara Desert, where crops would constantly fail during drier-than-normal seasons.

Niaba Teme

Niaba Témé

Niaba says these crop failures were in part his inspiration for a career where he could help farmers like his parents and siblings protect themselves from the risks of drought and extreme temperatures.

For the past four years, Niaba and his team at IER have been collaborating with Jean-François Rami and his team at France’s Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), to improve sorghum grain yield and quality for West African farmers. The work is funded by the Syngenta Foundation for Sustainable Agriculture.

“With the help of CIRAD and Syngenta, we have been learning how to use molecular markers to improve breeding efficiency of sorghum varieties more adapted to the variable environment of Mali and surrounding areas which receive less than 600 millimetres of rainfall per year,” he says.

Jean-François Rami

Jean-François Rami

“Using molecular markers is new and exciting for us as it will speed up the breeding process. With molecular markers, you can easily see if the plant you’ve bred has the desired characteristics without having to grow the plant and or risk missing the trait through visual inspection.”

Jean-François Rami, who is the project’s Principal Investigator, has been impressed by the progress made so far. Jean-François is also GCP’s Product Delivery Coordinator for sorghum.

“Since its inception, the project has progressed very well,” says Jean-François. “With the help of the IER team, we’ve been able to develop two bi-parental populations from elite local varieties, targeting two different environments of sorghum cropping areas in Mali. We’ve then been able to use molecular markers through a process called marker-assisted recurrent selection [MARS] to identify and monitor key regions of the genome in consecutive breeding generations.”

The collaboration with Syngenta came from a common perspective and understanding of what approach could be effectively deployed to rapidly deliver varieties with the desired characteristics.

“Syngenta came with their long experience in implementing MARS in maize. They advised on how to execute the programme and avoid critical pitfalls. They offered to us the software they have developed for the analysis of data which allowed the project team to start the programme immediately,” says Jean-François.

Like all GCP projects, capacity building is a large part of the MARS project. Jean-François says GCP has invested a lot to strengthen IER’s infrastructure and train field technicians, researchers and young scientists. But GCP is not the only player in this: “CIRAD has had a long collaboration in sorghum research in Mali and training young scientists has always been part of our mission. We’ve hosted several IER students here in France and we are interacting with our colleagues in Mali either over the phone or travelling to Mali to give technical workshops in molecular breeding. The Integrated Breeding Platform [IBP] has also been a breakthrough for the project, providing to the project team breeding services, data management tools, and a training programme – the Integrated Breeding Multiyear Course [IB–MYC].”

We don’t have these types of molecular-breeding resources available in Mali, so it’s really exciting to be a part of this project… the approach has the potential to halve the time it takes to develop local sorghum varieties with improved yield and adaptability to drought… one of the great successes of the project has been to bring together sorghum research groups in Mali in a common effort to develop new genetic resources for sorghum breeding.”

Back-to-back: more for Mali’s national breeding programme

On the back of the MARS project, Niaba successfully obtained GCP funding in 2010 to carry out similar research with CIRAD and collaborators in Africa at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT).

“In this project, we are trying to enhance sorghum grain yield and quality for the Sudano-Sahelian zone of West Africa using the backcross nested association mapping (BCNAM) approach,” explains Niaba, who is the Principal Investigator of the BCNAM project. “This involves using an elite recurrent parent that is already adapted to local drought conditions. The benefit of this approach is that it can lead to detecting elite varieties much faster.”

Kirsten Vom Brocke (CIRAD) Michel Vaksmann (CIRAD) Mamoutou Kouressy (IER) Eva Weltzien (ICRISAT) Jean-Francois Rami (CIRAD) Denis Lespinasse (Syngenta) Niaba Teme (IER) Ndeye Ndack Diop (GCP) Ibrahima Sissoko (Icrisat) Fred Rattunde (Icrisat)

A ‘sample’ of the rich mix of international partners in sorghum research: Left to right – Kirsten Vom Brocke (CIRAD), Michel Vaksmann (CIRAD), Mamoutou Kouressy (IER), Eva Weltzien (ICRISAT), Jean-François Rami (CIRAD), Denis Lespinasse (Syngenta), Niaba Teme (IER), Ndeye Ndack Diop (GCP Capacity Building Leader), Ibrahima Sissoko and Fred Rattunde (both from ICRISAT).

Eva Weltzien has been the Principal Scientist for ICRISAT’s sorghum breeding programme in Mali since 1998. She says the project aligned with much of the work her team had been doing, so it made sense to collaborate considering the new range of sorghum genetic diversity that this approach aims to use.

“We’ve been working with Niaba’s team to develop 100 lines for 50 populations from backcrosses carried out with 30 recurrent parents,” explains Eva. “These lines are being genotyped by CIRAD. We will then be able to use molecular markers to determine if any of these lines have the traits we want. We don’t have these types of molecular-breeding resources available in Mali, so it’s really exciting to be a part of this project.”

Eva Weltzien (holding sheet of paper) presenting to Mali's Minister of Agriculture (in white cap) a graph on the superiority of new guinea race hybrids. Also on display are panicles and seed of the huybrids and released varieties of sorghum in Mali. The occasion was an annual field day at ICRISAT's research station at Samanko, Mali.

An annual field day at ICRISAT’s research station at Samanko, Mali. Eva Weltzien (holding sheet of paper) showing Mali’s Minister of Agriculture, Tiemoko Sangare, (in white cap) a graph on the superiority of new guinea race hybrids. Also on display are panicles and seed of the hybrids and released varieties of sorghum in Mali.

Eva says that the approach has the potential to halve the time it takes to develop local sorghum varieties with improved yield and adaptability to drought.

For Jean-François, one of the great successes of the project has been to bring together sorghum research groups in Mali in a common effort to develop new genetic resources for sorghum breeding.

“This project has strengthened the IER and ICRISAT partnerships around a common resource. The large multiparent population that has been developed is analysed collectively to decipher the genetic control of important traits for sorghum breeding in Mali,” says Jean-François.

 Plants with this ‘stay-green’ trait keep their leaves and stems green during the grain-filling period. Typically, these plants have stronger stems, higher grain yield and larger grain.”

Sorghum staying green and strong, with less water

In February 2012, Niaba and his colleague, Sidi B Coulibaly, were invited to Australia as part of another Sorghum Research Initiative project they had been collaborating on with CIRAD, Australia’s University of Queensland and the Queensland Department of Agriculture, Fisheries and Forestry (QDAFF).

“We were invited to Australia for training by Andrew Borrell and David Jordan, who are co-Principal Investigators of the GCP stay-green sorghum project,” says Niaba.

Left to right: Niaba Teme (Mali), David Jordan (Australia), Sidi Coulibaly (Mali) and Andrew Borrell (Australia) visiting an experiment at Hermitage Research Facility in Queensland, Australia.

Left to right: Niaba Témé (Mali), David Jordan (Australia), Sidi Coulibaly (Mali) and Andrew Borrell (Australia) visiting an experiment at Hermitage Research Facility in Queensland, Australia.

“We learnt about association mapping, population genetics and diversity, molecular breeding, crop modelling using climate forecasts, and sorghum physiology, plus a lot more. It was intense but rewarding – more so the fact that we understood the mechanics of these new stay-green crops we were evaluating back in Mali.”

It wasn't all work and there was clearly also time to play, as we can see her., Sidi Coulibaly and Niaba Teme visiting with the Borrell family in Queensland, Australia.

It wasn’t all work and there was clearly also time to play, as we can see here., where Sidi Coulibaly and Niaba Témé are visiting the Borrell family in Queensland, Australia.

Stay-green is a post-flowering drought adaptation trait that has contributed significantly to sorghum yield stability in northeastern Australia and southern USA over the last two decades.

Andrew has been researching how the drought-resistant trait functions for almost 20 years, including gene discovery. In 2010, he and his colleague, David Jordan, successfully obtained funding from GCP to collaborate with IER and CIRAD to develop and evaluate drought-adapted stay-green sorghum germplasm for Africa and Australia.

“Stay-green sorghum grows a canopy that is about 10 per cent smaller than other lines. So it uses less water before flowering,” explains Andrew. “More water is then available during the grain-filling period. Plants with this ‘stay-green’ trait keep their leaves and stems green during the grain-filling period. Typically, these plants have stronger stems, higher grain yield and larger grain.”

Andrew says the project is not about introducing stay-green into African germplasm, but rather, enriching the pre-breeding material in Mali for this drought-adaptive trait.

The project has three objectives:

  1. To evaluate the stay-green drought-resistance mechanism in plant architecture and genetic backgrounds appropriate to Mali.
  2. To develop sorghum germplasm populations enriched for stay-green genes that also carry genes for adaptation to cropping environments in Mali.
  3. To improve the capacity of Malian researchers by carrying out training activities for African sorghum researchers in drought physiology and selection for drought adaptation in sorghum.

…we have found that the stay-green trait can improve yields by up to 30 percent in drought conditions with very little downside during a good year, so we are hoping that these new lines will display similar characteristics”

Expansion and extension:  beyond Mali to the world

Andrew explains that there are two phases to the stay-green project. The project team first focused on Mali. During this phase, the Australian team enriched Malian germplasm with stay-green, developing introgression lines, recombinant inbred lines and hybrids. Some of this material was field-tested by Sidi and his team in Mali.

“In the past, we have found that the stay-green trait can improve yields by up to 30 percent in drought conditions with very little downside during a good year, so we are hoping that these new lines will display similar characteristics,” says Andrew. “During the second phase we are also collaborating with ICRISAT in India and now expanding to five other African countries – Niger and Burkina Faso in West Africa; and Kenya, Sudan and Ethiopia in East Africa. During 2013, we grew our stay-green enriched germplasm at two sites in all these countries. We also hosted scientists from Burkina Faso, Sudan and Kenya to undertake training in Queensland in February 2014.”

 

A sampling of some of stay-green sorghum partnerships in Africa. (1) Asfaw Adugna assessing the genetic diversity of sorghum panicles produced from the GCP collaboration at Melkassa, Ethiopia. (2) Clarisse Barro-Kondombo (Burkina Faso) and Andrew Borrell (Australia) visiting a lysimeter facility in Hyderabad, India, as part of GCP training. (3) Clement Kamau (Kenya, left) and Andrew Borrell (Australia, right) visiting the seed store at the Kenya Agricultural Research Institute (KARI) in Katumani, Kenya.

A sampling of some of stay-green sorghum partnerships in Africa. (1) Asfaw Adugna of the Ethiopian Institute of Agricultural Research (EIAR)  assessing the genetic diversity of sorghum panicles produced from the GCP collaboration at Melkassa, Ethiopia. (2) Clarisse Barro-Kondombo (left, INERA – Institut de l’environnement et de recherches agricoles , Burkina Faso) and Andrew Borrell (right) visiting a lysimetre facility at ICRISAT’s headquarters in Hyderabad, India, as part of GCP training, in February 2013. (3) Clement Kamau (left, Kenya Agricultural Research Institute [KARI] ) and Andrew Borrell (right) visiting the seed store at KARI, Katumani, Kenya.

Andrew says that the collaboration with international researchers has given them a better understanding of how stay-green works in different genetic backgrounds and in different environments, and the applicability is broad. Using these trial data will help provide farmers with better information on growing sorghum, not just in Africa and Australia, but also all over the world.

“Both David and I consider it a privilege to work in this area with these international institutes. We love our science and we are really passionate to make a difference in the world with the science we are doing. GCP gives us the opportunity to expand on what we do in Australia and to have much more of a global impact.”

We’ll likely be hearing more from Andrew on the future of this work at GCP’s General Research Meeting (GRM) in October this year, so watch this space! Meantime, see slides below from GRM 2013 by the Sorghum Research Initiative team. We also invite you to visit the links below the slides for more information.

Links

Eva’s endeavours: a professional path in plant science inspired by Norman Borlaug

 Africa, Comparative genomics in cereals, Crop breeding, Researchers, Sorghum, Women in science  No Responses »
Aug 292014
 

“…I wanted to contribute in a similar way” – Eva Weltzien

 

Eva Weltzien

Eva Weltzien

Learning about the work of Nobel laureate, Norman Borlaug, in high school inspired Eva Weltzien to become a plant breeder so she too could contribute to improving the living conditions in the developing world. Today, Eva is a Principal Scientist in sorghum breeding and genetic resources at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in Mali.

“Not only did Norman Borlaug revolutionise agriculture by breeding high-yielding wheat varieties, he then selflessly distributed these to the countries in the world that most needed them, saving hundreds of millions from starvation,” Eva recollects passionately, as she speaks about her scientific hero. “I remember being inspired when he won his Nobel Prize in 1970, mainly for the fact that agricultural research was actually being seen as contributing to world peace,” says Eva. “I knew then that I wanted to contribute in a similar way.”

I…wanted to take a break from… theory and instead gain an appreciation for plant breeding by working in the field”

The path to plant breeding, and pearls along the way
Eva was raised in her native Germany, as well as in Beirut, Lebanon, where she spent six years when her parents were stationed at the local university there. She credits her parents; both plant pathologists, for instilling in her a scientific mind-set from a tender age.

“They taught me to think outside the box and apply my knowledge and understanding to how I made sense of the world,” Eva recalls. “Being plant pathologists, they also encouraged me to observe the environment carefully and treat the earth with respect.”

Upon graduating from high school, Eva deferred going to university and instead worked as a seed technician for a private company in Germany. “I just wanted to take a break from studying theory and instead gain an appreciation for plant breeding by working in the field,” says Eva.

After one year with the company, Eva was ready to start university. During the decade that followed, she completed a Diploma in Agricultural Biology (University of Hohenheim, 1981) and a PhD in Agriculture (Munich University, 1986).

A year after completing her PhD, Eva accepted a postdoc position at Iowa State University, USA, where she met her future husband Fred Rattunde. After a few years, both Eva and Fred moved to India to work with ICRISAT. “I’ve been working for ICRISAT for almost 27 years now,” says Eva. “When I first started, I was working in pearl millet breeding.”

The key challenges have been improving the infrastructure of the national research facilities… as well as increasing the technical training for local researchers…this has slowly improved, particularly in the last four years with the funding and help through the GCP Sorghum Research Initiative.…we can see our work making an impact on people’s lives…”

Off to Africa, and bearing fruit
In 1998, ICRISAT offered Eva and Fred positions in Mali where they would take responsibility for the Institute’s sorghum-breeding programme in West Africa.

OLYMPUS DIGITAL CAMERA

Evaluating Eva: In Dioila district, Mali, evaluating the panicles of a new sorghum line after harvest.

“It was a great challenge that we both wanted to explore,” says Eva. “The key challenges have been improving the infrastructure of the national research facilities to do the research as well as increasing the technical training for local agronomists and researchers. Over the past 15 years, this has slowly improved, particularly in the last four years, with the funding and facilitation through the GCP Sorghum Research Initiative. Now we can see our work making an impact on people’s lives in West Africa.” (see GCP’s work on infrastructure improvement)

…we are closer to delivering more robust sorghum varieties which will help farmers and feed the ever-growing population in West Africa.”

Improving drought tolerance in sorghum for Africa
The second phase of GCP’s Sorghum Research Initiative focuses on Mali, where sorghum-growing areas are large, and distributed over a wide range of rainfall regimes.

Eva and her team are currently collaborating with local researchers at L’Institut d’économie rurale (IER), Mali and France’s Centre de coopération internationale en recherche agronomique pour le développement (CIRAD) on a project to test a novel molecular-breeding approach – backcross nested association mapping (BCNAM). Eva says the approach has the potential to halve the time it takes to develop local sorghum varieties with improved yield and adaptability to poor soil fertility conditions.

“We don’t have these type of molecular-breeding resources available in Mali, so it’s really exciting to be a part of this project.”  Still, Eva and her colleagues continue to press forwards in this new frontier in plant science, making good advances in another parallel but closely related project that Eva leads in the GCP Comparative Genomics Research Initiative.

Eva continues, “We’ve had good results in terms of field trials, despite the political situation. Overall, we feel the experience is enhancing our capacity here in Mali, and that we are closer to delivering more robust sorghum varieties which will help farmers and feed the ever-growing population in West Africa.”

Slides (with more links after the slides)

Links

Food for thought on video: a ‘rice-bowl of research’ spiced with flavours from Africa and Asia

 Africa, Asia, Capacity building, Crop breeding, Rice, Women in science  2 Responses »
Feb 212014
 

 

Steaming rice bowl

Steaming rice bowl

What’s the latest from ‘GCP TV’? Plenty! With a world-favourite – rice – featuring high and hot on the menu.

Now serving our latest news, to tease your taste-buds with a tantalising and tingling potpourri of memorable cross-continental rice flavours, all captured on camera for our viewers…

Our brand-new series on YouTube serves up a healthy seven-course video feast inviting our viewers to sink their teeth into rice research at GCP.

First, we settle down for a tête-a-tête in the rice research kitchen with chef extraordinaire, Marie-Noëlle Ndjiondjop, Principal Investigator (PI) of GCP’s Rice Research Initiative in Africa, and Senior Molecular Scientist at Africa Rice Center. Target countries are Burkina Faso, Mali and Nigeria.

Photo: A Okono/GCP

Marie-Noëlle Ndjiondjop

Starters, palate and pocket
Marie-Noëlle opens the feast with a short but succulent starter, as she explains succinctly in 30 seconds just how rice is becoming a staple in Africa. In the second course, Marie-Noëlle chews over the questions concerning combatting constraints and boosting capacity in rice research in Africa.

The third course is pleasing to the eye, the palate and the pocket! Marie-Noëlle truly sells us the benefits of molecular breeding, as she extolls the virtues of the “beauty of the marker”. Why should you use molecular tools? They’ll save you time and money!

Rice as beautiful as the markers Marie-Noëlle uses in molecular breeding

Wherefore art thou, capacity building in rice research in Africa?
The Shakespearean language alludes to the why of capacity building in Africa, as does video episode number four, which also tackles the what of this fourth dish in our banquet. Course number five offers the viewer a light look at how capacity building in Africa is carried out.

In the 6th course, Marie-Noëlle takes us out of this world and into MARS: she teaches us that ‘two are better than three’, as she explains how the novel bi-parental marker-assisted recurrent selection (MARS) method is proving effective when it comes to duelling with drought, the tricky three-headed monster comprising physiological, genetic and environmental components.

Blooming rice in the field

Of stars and scoundrels
The 7th and final course offers us a riveting tale of heroes and villains, that is, many heroes and a single villain! Our rice raconteuse, Marie-Noëlle, praises the power of the team, as a crew from cross-continental countries come together, carefully characterise their combatant (drought), before striking with environment-specific drought-tolerant varieties! AfricaRice’s project partners are Burkina Faso’s Institut de l’environnement et de recherches agricoles (INERA); Mali’s Institut d’économie rurale (IER); and Nigeria’s National Cereals Research Institute (NCRI). Collaborators are France’s Centre de coopération internationale en recherche agronomique (CIRAD); the International Center for Tropical Agriculture (CIAT); and the International Rice Research Institute (IRRI).

We hope these tasty teasers are enough to whet your appetite – you can savour each of the courses individually à la carte, or, for those with a daring desire to try the ‘all you can eat’ buffet for true rice gourmets, all seven courses are presented as a single serving on our YouTube channel.

Jonaliza Lanceras-Siangliw

Jonaliza Lanceras-Siangliw

Tastes from Asia
To further please your palate with our rice bowl of delights, our next stop is Asia. We are  pleased to offer you the Asian flavour through a peek into the world of molecular rice breeding in the Mekong region. Our connection to this project is through a GCP-funded capacity-building project entitled A Community of Practice for strengthening rice breeding programmes by using genotyping building strategy and improving phenotyping capacity for biotic and abiotic stresses in the Mekong region led by PI Jonaliza Lanceras-Siangliw, of the National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand (see project poster, and slides on a related drought-tolerance project led by Boonrat Jongdee). BIOTEC’s partners in the Mekong rice breeding CoP are the Cambodian Agricultural Research and Development Institute (CARDI); LAO PDR’s National Agricultural and Forestry Research Institute (NAFRI);  Myanmar’s Department of Agricultural Research (DAR); and Thailand’s Kasetsart University and Ubon Ratchathani University). The video also features former GCP PI, Theerayut Toojinda (BIOTEC) whose project was similarly entitled The ‘Community of Practices’ concept applied to rice production in the Mekong region: Quick conversion of popular rice varieties with emphasis on drought, salinity and grain quality improvement.

BIOTEC

Boonrat Jongdee

Shifting gears: golden oldie
If all of this talk of eating has been a little overwhelming, we also offer you the perfect digestif: a ‘golden oldie’ in terms of GCP video history showing a 2012 BBC interview with former GCP PI, Sigrid Heuer, then at the International Rice Research Institute (IRRI), who explains how her project isolated the rice root-enhancing gene PSTOL1. Bon appétit!

 

Might you still have a corner of your mind yearning for more material on rice research? If so, check out the following:

  • Our lip-smacking selection of rice-related blogposts
  • A gorgeous gallery of PowerPoint presentations on rice research (SlideShare)
  • Check out our one-stop Rice InfoCentre for all things rice and nice, that we have online!

 

A grand gathering: General Research Meeting (GRM) 2013

 Closing GCP, Crop breeding, Events  No Responses »
Nov 122013
 

 

 

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Hari Upadhyaya

Hari Upadhyaya

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

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

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

 

 

 

 

 

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.

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