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Systems Biology in agriculture – growing more with less
11 January 2011
Stuart John Dunbar from Syngenta discusses how partnering with BBSRC-funded programmes in systems biology can help address the fundamental issues facing agriculture today.
The world's population will rise to around 9 billion by 2050 from 6.5 billion today but, with increasing prosperity, calorific intake will increase by 50% over the same time period. In addition, the real effects of climate change mean we will have to grow crops in increasing temperatures with less water. We have to increase yields on the current land to address these issues.
At Syngenta we are working to increase yields by a wide variety of approaches, breeding high performing seed varieties using conventional and genetic modification (GM), as well as protecting the food grown with novel herbicides, fungicides and insecticides. 40% of the world's food would be lost to pests without crop protection chemistry but inventing a new chemical or breeding a new crop variety is a difficult and expensive process.
Doing things differently
Stuart John Dunbar. © Syngenta.
Over the past ten years, the convergence of technologies such as next generation sequencing, comparative genomics, metabolomics and transcriptomics coupled with bioinformatics, has meant that we have increasingly large data sets on the organisms and processes we are interested in. Taking a piecemeal approach to invention, where we studied single genes or the effects of chemistry on an isolated protein, was no longer an option as we did not understand the complexity of the interactions involved. We had to take a different approach.
We needed to be more predictive since we often did not have complete data sets, despite their size. We felt that taking a more predictive systems approach was the way forward. We began a journey to understand the value of systems biology in 2006. At around this time the BBSRC also launched their strategy 'Towards Predictive Biology' which resonated with our way of thinking. One of the outputs of this new BBSRC strategy was the creation of the six centres for systems biology. We visited these organisations in the early days of their formation, as well as other groups around the world, to see if there was any common ground and also to try to understand the potential of systems biology for us.
BBSRC's creation of the systems biology centres was fundamental to our decisions. Seeing the investment that BBSRC was making in the science and the focus the centres provided was very influential in our thinking. We identified Imperial College London as our partner as CISBIC (the Centre for Integrative Systems Biology at Imperial College) had a focus on biological interactions that shared some common ground with our concepts. We entered into a discussion phase where we co-created the projects. As a direct result we invested $3 million to establish a Syngenta University Innovation Centre (UIC) at Imperial College on Predictive Systems Biology. The technical focus builds on Imperial's strengths in Inductive Machine Learning and Informatics, with research led by Professor Stephen Muggleton and Professor Mike Sternberg.
The UIC was set up with two pioneer projects: predictive toxicology and tomato flavour. Both projects are focused on identifying molecular markers of complex end points.
In the predictive toxicology project we are looking to identify a marker we can use to design a simple laboratory test that is indicative of a cancerous endpoint. Testing a new agrochemical for safety is a long and expensive process. We wish to rule out compounds that might have a toxicological issue before they reach the animal models. This systems approach is designed to identify the molecular markers of liver cancer.
Tomatoes on vine. © iStockphoto/Thinkstock 2010
The tomato project's aim is to enable us to conventionally breed for tastier tomatoes. Over the years, tomatoes have been bred for commercial traits including transport and shelf life. We all recognise that a consequence of this is that some flavour has been lost. The tomato project is designed to identify molecular markers for flavour and ripening which we wish to use to bring the flavour components earlier in the ripening process so that the tomatoes we buy in the supermarket taste better! Both the tomato and toxicology projects are integrating large transcriptomic and metabolomic data sets.
Since the initial programmes were established, in late 2008, we have added a third project focused on using inductive logic programming to model ecological systems on a large scale.
The UIC at Imperial College is only one part of the jigsaw. We need data to model. We have partnered with BBSRC-funded researchers across the UK to do this. In the tomato project we are working with the University of Nottingham to provide transcriptomic data on a range of tomato genotypes coupled with in-house metabolomic data. The toxicology project integrates data from projects at the University of Cambridge, Imperial College and in-house, whilst the ecosystems project partners with data from the large scale field trials and some initial models created at Rothamsted Research, an institute of BBSRC.
These partnerships, bringing our own data together with experts in the academic arena, are an important way of working for us. This is especially so as our data sets and the systems we are trying to address become ever more complex. Having a vibrant well-funded academic community looking at complex systems is central to our efforts in agriculture, bringing plant potential to life.
Stuart John Dunbar has worked at Syngenta for 25 years. He leads the Biochemistry Group based at the Jealott's Hill International Research Centre in Berkshire, and is the overall project manager for the Systems Biology University Innovation Centre at Imperial College London.
He is a Senior Syngenta Fellow; the Syngenta Fellowship is a community of senior scientists in the company who have a science leadership role in technology foresight and communication. Stuart is also editor of 'Science Matters' the in-house science magazine published twice a year.
Syngenta is one of the world's largest Agriscience companies with 2009 sales of over $11 billion. It is number one in crop protection chemistry and number three in high value seeds. Jealott's Hill, near Bracknell in Berkshire, is Syngenta's largest research site with about 1000 employees.
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