Advanced plant phenomics centre represents new National Capability.
Blink and the future has arrived. Many modern inventions, from huge and mighty stealth bombers to electric-hybrid vehicles and handheld touchscreen smartphones, seem to arrive in an instant. But their presence defines where we are now and where we may be going.
The same could be said of the new multi-million pound National Plant Phenomics Centre (NPPC), the technological scale and capability of which provokes a similar "wow!" factor. The NPPC is unique within the UK and is the future of agricultural and horticultural science, where thousands of plants' physical characteristics are automatically measured on a cyber-industrial scale and recorded digitally: a true monument to the information age.
Scientists will use the centre to ask questions about plant characteristics – everything from growth rate to water use to formation useful metabolites – and how these physical parameters are affected by genes, the environment and the interplay between the two. The answers will feedback into twenty-first century food security challenges and the need for better, more efficient biofuels among other projects.
"The National Plant Phenomics Centre provides a step change in the way plant biology is implemented," says Professor John Doonan, Director of the NPPC. "The high throughput part allows whole populations of plants, such as breeding populations, mapping experiments, natural diversity collections, and mutant collections, to be analysed in parallel and under multiple defined environments."
The NPPC will be fully operational in 2013 and is part of the Institute of Biological, Environmental and Rural Sciences (IBERS), which receives strategic funding from BBSRC, and is based at Aberystwyth University. It's an important part of the campus' future, because the NPPC is a National Capability, meaning it has special status as a research hub for collaboration between scientists across many disciplines for years to come.
Plants are used for more than just food. They provide clothing, lubricant oils, medicinal ingredients, ropes and twine, paper, logs for heating, and biofuels too. Improving plants, however, still comes down to measuring physical aspects of the organism: height, growth rate, number of flowers, leaf shape. But until now, collecting this vast array of information has mostly been done by hand or automated only on a small scale. "Instead of plant characteristics being analysed piece-meal – one student, one trait – an increasingly wide range of traits can be measured automatically, objectively, and simultaneously," says Doonan.
To collect such a wealth of data, the NPPC has an extensive floor space the size of three tennis courts (750m2, see box: In numbers). It's been designed for 'medium'-sized plants such as the small grain cereals (wheat, barley, oats) and oilseed rape but can also handle smaller forage grasses and larger plants like maize and Miscanthus. What's special are the automated imaging chambers that can record in everything from infra-red to ultra-violet light to obtain information on the physiology of plants, such as organ temperature, water content and photosynthetic activity, as well as their shape and size. "One can imagine extending this approach to almost any trait for which variation exists within the breeding population of almost any crop," says Doonan.
This large scale multiplicity of 880 carriages (for up to 3400 plants) and five imaging chambers working simultaneously allows a wide range of questions to be asked, and answered, more quickly and objectively. For example, where are controlling genes and alleles for drought tolerance, resistance to biotic and abiotic stress, enhanced "yield" and improved nutrient use efficiency?
These are not new questions, but the NPPC will provide data faster and without the bias of the human hand. People have an eye for beauty and can dismiss inconspicuous traits as irrelevant. "Researchers have had to be very focused on the traits they thought most interesting – other potentially more useful ones would be ignored if they were inconspicuous or difficult to measure" Doonan explains.
By facilitating breeding and gene identification, the production of improved varieties of plants will be accelerated. New varieties take between 7 and 15 years, or more, of conventional breeding before they are commercially available. "If we can remove one or two years from the process, then we will make a significant difference," says Doonan.
A key part of the NPPC's work will be the identification of useful alleles [gene variants] or more likely combinations of alleles, that produce desirable physical traits, or phenotypes as they are known. Tracking these are other genetic markers of known DNA will allow molecular breeding techniques to be applied to a wider range of traits, and for this reason the NPPC is next door to the IBERS/Aberystwyth University Translational Genomics Lab where plants will be genotyped using the latest technology.
This new activity in 'phenomics' has been driven by the incredible advances seen in genomics over the past decade. Defining the genetic characteristics of an organism by DNA sequencing at the molecular level has gone from years and millions of dollars to just a few hours and hundreds. But plant and animal features cannot be characterised at the organismal level in the same way. "The NPPC presents a means to remedy this discrepancy by integrating automated plant handling and environmental control with computer vision and machine-learning approaches," says Doonan.
Doonan adds that one of the aims of the NPPC is to establish standards for objective phenotyping in plant biology, which has often been subjective, while associated environmental metadata can be inaccurate, incomplete or lacking. The controlled environment of the NPPC can counter this. "Since phenotype can be strongly influenced by the environment, it is really important that the environment is documented really thoroughly," he says. "The NPPC is actively involved in international efforts to establish commonly accepted standards that will enhance the value of phenotypic data, whether it is collected by automated large scale centres or individual investigators."
Agreeing phenotyping standards with scientists across the world could further increase the analytical power of similar centres, which are rare but growing in number. The NPPC is unique to the UK, but several facilities exist overseas and in the private plant biotech sector. "The horticultural industry, particularly in Holland, has realised the potential of automation combined with objective phenotyping for streamlining commercial production," says Doonan. "Academics are waking up to its potential in plant science research and there are now a handful of such facilities, mainly in research institutes in Germany and France, with one at the University of Adelaide in Australia."
Data can also be combined with programmes closer to home at IBERS and Aberystwyth University. One example is the Beacon project that aims to develop new ways of converting crops such as rye grass, oats and Miscanthus into products including pharmaceuticals, fuels and cosmetics; Beacon uses fundamental bioscience advances previously funded by BBSRC.
BBSRC have provided £1.2M to run the facility as a National Capability for five years with the expectation that this will be supplemented by external funding from bodies such as the EU, as well as Responsive Mode grants from BBSRC and other research councils.
- 750m2: total floor space area
- 880: carriages that can take one medium/large plant or 4 smaller plants
- 5: imaging cabins
- 2: chambers with individual environmental controls.
- 9: personnel planned, including two image specialists and a maths/informatics specialist);
- 300m+: of conveyor to ferry plants to and fro
- 16TB (16,000 gigabytes): initial data storage on dedicated server with remote back-up server. Directly connected motion control computer with linked specialised calculation PC