Wednesday, 13 March 2013

Sci-fi Facilities for Plant Sciences - National Plant Phenomics Centre

Arran Frood
Science Writer & Film Maker
 Biotechnology and Biological Sciences Research Council, Swindon, UK 
    Blink and the future has arrived. Many modern inventions, from huge and mighty stealth bombers to electric-hybrid vehicles and 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. ‘Phenomics’ is the large-scale study of physical characteristics and the NPPC is unique within the UK. It is the future of agricultural and horticultural science, where thousands of plant traits are automatically measured on a cyber-industrial scale and recorded digitally: a true monument to the information age.

''Phenomics is an area of biology concerned with the measurement of phenomes - the physical and biochemical traits of organisms — as they change in response to genetic mutation and environmental influences.''
    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.”

Video: Sci-fi plant science centre animation HD

     The NPPC is a part of the Institute of Biological,Environmental and Rural Sciences (IBERS), which receives strategic funding from the Biotechnology and Biological Sciences Research Council (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

Data relay
    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 750m2 floor space the size of three tennis courts. 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. 
    This large scale multiplicity of 880 carriages (for up to 3400 plants on over 300m of conveyor) 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?

Identification of useful alleles
    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. 

Measuring up
    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.”

Impact across the world
     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 towards the potentialof phenomics 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.

 Arran Frood, Science Writer and Film Maker is associated with Biotechnology and Biological Sciences Research Council (BBSRC), Polaris House North Star Avenue Swindon, SN2 1UH, UK.
@arranfrood on twitter

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