AUSTRALIAN PLANT PHENOMICS FACILITY

Transcription

1 AUSTRALIAN PLANT PHENOMICS FACILITY RESPONSE TO 2011 STRATEGIC ROADMAP FOR AUSTRALIAN RESEARCH INFRASTRUCTURE DISCUSSION PAPER MAY 2011 Summary We request that the importance of agriculture to the Australian economy be recognized in the 2011 Strategic Roadmap for Australian Research Infrastructure, and ask that the relevant EWGs note the existing, world class infrastructure that the APPF provides to the plant science community; that priority be given to consolidation and support of the existing APPF nodes so that this infrastructure, which is currently supporting word class researchers can continue to grow; that support be noted for expansion of the APPF to incorporate new functionality at additional nodes; and that a national germplasm characterization initiative be recognized as a critical need to support bioscience research for agriculture, environment, biosecurity and health. This response is relevant to five Expert Working Groups: Environmentally Sustainable Australia; Frontier Technologies; Safeguarding Australia; Promoting and Maintaining Good Health; and eresearch Infrastructure. The importance of agriculture to the Australian economy In the next 40 years, the world must increase food production at rates much higher than ever in history (Tester & Langridge, 2010, calculated using data from the UN s Food & Agriculture Organization). Furthermore this needs to be done: Sustainably, with reduced CO 2 emissions and reduced inputs, notably of nitrogenous fertilizers; In the face of global climate change, which is already challenging even current levels of food production; Knowing that one third of current food production occurs under irrigation, much of which is clearly unsustainable; In the face of an increasing diversion of crop production for the generation of biofuels; With a need to increase not only food quantity but also food quality, particularly to increase nutrient content. Food security is now of major political importance, listed as the highest priority for G20 leaders (Australian Financial Review, Feb 2011) and the economics of feeding 9 billion people by 2050 is receiving considerable attention (e.g. The Economist special report, 26 th Feb 2011). The current sharp spike in food prices is causing global concern and is attributed to be one of the main causes underlying the political unrest in North Africa, the Middle East and elsewhere. Sustainable intensification of agriculture is the buzz word (The Royal Society, 2009: Reaping the benefits: science and the sustainable intensification of global agriculture) using frontier Page 1 of 6

2 technologies to enhance food security, and thus national security, in the face of global climate change, and to do so in an environmentally sustainable way whilst also improving human health. This area crosses all national research priorities. More broadly, understanding and responding to the impact of climate change on plants in natural ecosystems is also of central importance for informing management of natural systems. Whilst this document focuses on food security and agriculture as a major tangible applied output of plant science research, the infrastructure developed for this purpose can also be used to address issues in natural systems and facilitate management of these systems. The role of plant and soil research infrastructure in underpinning the future of agriculture in Australia What are the scientific opportunities to address these clear imperatives? What innovation can Australia bring to bear on this global challenge? Crucially, it is important to appreciate that the biological sciences are now maturing to a level where they are becoming Big Science, like the physical sciences were years ago. As such, biology is well placed to benefit from investment in large centralized research programs that generate the critical mass necessary for significant breakthroughs to occur. We are now entering a post genomic era, where germplasm and its genetic diversity need to be revealed by combining genomics with other technologies, in particular phenomics and bioinformatics. Bringing together fields of research are now required to make the big breakthroughs. For example, in plant sciences, we are bringing together: Genomics and phenomics to improve breeding and genetics; Mathematical and biological sciences to address a wide range of issues in agriculture and food by generating, analyzing and interpreting the large volumes of data that can now be generated from high throughput assays; Mechatronics and agriculture to revolutionize both agronomy and genetics by exploiting opportunities opened up by robotics and computing; Genetics and health care to improve food quality. These are areas that need to be enhanced in the coming decade and will provide step changes in the understanding of plant function and crop production. Furthermore, the work is becoming increasingly international in scope and scale, so leadership at an international level is important for the ongoing development, and then application, of Australian science. Plant science in Australia provides such leadership, and the ongoing strength of Australia s primary production sector is testament to Australia s ability to apply such scientific advances. The next stage in biological research presents both a challenge and an opportunity. The challenge is that the research increasingly needs to be undertaken in large institutes where a critical mass of workers can benefit from each other and develop and operate the cutting edge technologies required to move the field forward. The opportunity is that the new biology provides a chance to develop the innovations essential for addressing global challenges such as food security. In the biological sciences, plant and agricultural science is clearly an area of widespread strength and one in which Australia is world leading. Skills and resources in the plant sciences have been developed in Australia that do not exist elsewhere in the world. Furthermore, agriculture remains a major export sector, and is a key contributor to Australia s economy that will continue to do so in perpetuity. As such, research in plant science is likely to attract both government and industry Page 2 of 6

3 support, and will spin out a range of commercial activities that will feed back to attract even further research activity. The role of the APPF Within Australia, the Waite Campus of the University of Adelaide and the Black Mountain laboratories of CSIRO Plant Industry and ANU in Canberra represent significant aggregations of researchers focused on excellence in plant and soil science. The APPF, currently located in these two centres, benefits from and serves one of the largest groupings of plant and soil science researchers in the world, as well as providing services to researchers from across Australia and overseas. It therefore underpins national and international research leadership in the area of pure and applied plant sciences at a time when scientific opportunities demand a critical mass of researchers collaborating across disciplines and geographical boundaries. "The creation of the Australian Plant Phenomics Facility was a world landmark in plant biology infrastructure" (Science, ). The APPF has provided Australian plant biologists with access to a world first facility for analyzing plant growth and performance in environments ranging from highly controlled growth cabinets to the field. The APPF has built and developed new tools for plant biologists utilizing the latest sensor technology, machine vision, robotics and computing. Countries around the world are emulating this investment and scrambling to build equivalent facilities (UK, Germany, France, China and India, for example). The APPF is only in its second year of operation but occupancy rates are approaching capacity in one node and predicted to do so at both nodes within a year. Research outcomes in crop plant yield potential from APPF research are now appearing in the published literature and major publicly funded international research alliances have been formed with the APPF in the area of crop based biofuels and in food security. Major multinational companies and Australian corporations have invested in projects at the APPF, catalyzed by this major infrastructure investment. The APPF has attracted, and will continue to attract, multiple participants from across the globe, contributing to: The pursuit of excellence in plant science and food and human nutrition research The engagement of industry to harness the transformational power of modern science to increase amount and quality of food production in Australia and internationally The development of the foundations to transform the future of Australia and make a better society Communication of the operation and outputs from the APPF to stakeholders and the general public The potential for the APPF to facilitate plant science research across Australia is significant, and for this work to underpin increases in crop production in Australia and globally is clear. The potential to increase crop production in Australia is still large, with average yields in Australia still falling well below the yield potential for cereals, even given Australia s low rainfall and poor soils. As such, the APPF has much potential to make significant contributions to the Australian economy by contributing to growth of a major export sector. To retain world leadership for Australian plant phenomics, we need to achieve the following: 1. Make sustainable and upgrade existing infrastructure over the longer term; 2. Expand existing infrastructure to meet research client needs; 3. Improve geographical access to facilities by developing regional nodes; 1 Finkel, E. (2009) With phenomics, plant scientists hope to shift breeding into overdrive. Science 325: Page 3 of 6

4 4. Subsidize and thus encourage student access to facilities; 5. Develop new cutting edge tools for plant phenomics; 6. Integrate high performance computing tools for high throughput analysis of complex plant models in silico; 7. Improve IT infrastructure for accessing, interrogating and sharing large phenomics datasets; and 8. Integrate plant phenomics data with high throughput gene sequencing data (a Phenomics / Genomics Pipeline ). While sustainability of the existing investment is recognized as a priority in the roadmap, this recognition needs to be realized in the form of funding of continued subsidized access and providing improved geographical access though bursaries and scholarships. Modest funding from local government has been very successful in engaging students with the Canberra node. Distributed nodes in regional areas is also a model favored by APPF to increase access to field phenotyping and specialized services not currently offered by APPF nodes. World leadership in phenomics at the APPF has been a result of both scale and scientific innovation. We need to continue to improve throughput and development of cutting edge tools. We have developed five world first instruments to analyze plant performance at APPF Canberra (PlantScan, TrayScan, Cabscan, Phenomobile and Phenonet), but new developments in sensor technologies promise cheap dust sized nanosensors, which could send crop data back from the field remotely though the growing season, and high throughput x ray CT, which could image cereal ears before they emerge into the air. Without development of these leading edge technologies, APPF will rapidly fall behind. APPF is already pushing the boundaries of IT infrastructure to support analysis of prodigious datasets. The 3D models from PlantScan are produced at a rate of 2 terabytes per day, approaching the data traffic dealt with in radio astronomy. While we are engaging well with the IT community to deal with these large 3D and 4D data sets, better integration with cloud computing technologies, GPU clusters and supercomputing infrastructure is required. Similarly, sustained investment in ontology driven databases to harness phenomics data and integrate it with genomic and environmental data is pivotal for research on gene function, eco genomics and agricultural and environmental research. PODD, the NeAT funded ontology driven database for phenomics, has generated intense international interest and must be expanded to provide a pipeline into diverse data sets such as those described above. The next phase of the APPF is planned to include consolidation of infrastructure at the existing nodes and the establishment of additional new nodes in several locations around Australia to service the strong research activity in the plant sciences that is distributed across the nation. Each of these nodes will be focused on a different aspect of plant phenomics to provide services where there are currently critical gaps while at the same time avoiding duplication. The new nodes will complement the existing centralized investments for national benefit. Potential new nodes include a model plant imaging capability at the Plant Energy Biology Centre of Excellence at the University of Western Australia, an x ray CT facility at the University of New England, a radioisotope scanning facility at Charles Sturt University and expansion and deployment of field phenotyping capacity at several field sites across Australia, such as the three GRDC sponsored Managed Environment Facilities in WA and NSW, the Department of Agriculture and Food, Western Australia s multi user New Genes for New Environment field GM phenotyping facilities, the Roseworthy Campus of the University of Adelaide and the University of Queensland/CSIRO field station in the summer grain cropping regions in Queensland. The APPF umbrella will continue to provide national coordination in the provision of research infrastructure for the plant science community Page 4 of 6

5 The APPF has already developed and deployed world leading plant imaging and image analysis technologies in controlled environments and in the field. However, in the rapidly changing landscape of machine vision and computing, continued investment in developing novel imaging technologies (particularly for roots, given the current interest in plant/soil interactions), image analysis software, 3D modelling capacity and database management is required. The APPF is currently working to expand its interactions with other capabilities in the biological sciences, both within the existing Integrated Biological Systems structure, but also with other biologically oriented capabilities such as BioPlatforms Australia and the Terrestrial Ecosystem Research Network. It plans to build on these interactions, particularly in the coordination and the generation underpinning framework datasets for organisms of agricultural significance including soil micro organisms. The plant science research community has identified a critical need for consistent and streamlined generation and curation of strategically selected genetic and phenotypic information for plants of agricultural and environmental significance. As part of the next investment phase, investment in the genomic and phenomic characterisation of national germplasm collections, both existing collections and those currently under development, would unlock genetic resources that are currently underutilised. It would provide much needed framework datasets that characterize important seed lines of significant Australian crops, Australian natives that are close relatives of major crops and Australian native plants of environmental significance. This will provide crucial data for the development of new crops specifically adapted to Australian conditions and underpin bioremediation and other environmental work. To conclude: The need for the application of plant science is greater than ever, with food security globally and even in Australia a major economic, social and political priority. Fortunately, there are exciting scientific opportunities to address these global imperatives. Internationally, the field is poised to make great breakthroughs due to the application of big science approaches by exploiting high throughput analyses. Plant science in Australia is notably strong and well placed to lead these scientific opportunities. Critical mass exists in Australian plant science research infrastructure, and this requires consolidation and expansion through further major infrastructure investments to allow Australia to lead the move of plant sciences in to the era of big science. The following named people endorse this document and support the general and specific issues raised in it. We consider that further support for the Australian Plant Phenomics Facility would be a valuable investment by the Australian government and other stakeholders, and would allow this capability to underpin a wide range of important activities in the Australian plant science community. We agree that this document can be made public. Professor Mark Tester Dr Bob Furbank Professor Murray Badger Mr Terry Enright Professor Graeme Hammer Professor Barry Osmond Director, Australian Plant Phenomics Facility Director, High Resolution Plant Phenomics Centre Chief Investigator, High Resolution Plant Phenomics Centre Farmer, Western Australia (Chair, APPF Advisory Board) School of Land, Crop & Food Sciences, University of Queensland, Brisbane IBS Review Committee Representative, Canberra Page 5 of 6

6 Professor Ian Small Professor Geoff Fincher Professor John Manners A/Professor Ros Gleadow Professor Hans Lambers Dr Robert Loughman Professor Harvey Millar Professor Ulrich Schurr Professor Roger Leigh Director, ARC Centre for Plant Energy Biology, UWA, Perth Director, ARC Centre of Excellence in Plant Cell Walls, University of Adelaide Deputy Chief, CSIRO Plant industry, Brisbane Cyanogenesis Group, Monash University, Melbourne Head, School of Plant Biology, UWA, Perth Director, Genetic & Product Innovation, Dept of Agric. & Food WA ARC Centre for Plant Energy Biology, UWA, Perth Head, Institute Phytosphere, Research Centre Jülich, Germany Director, Waite Research Institute, University of Adelaide References The aims of the APPF align well with two national priority documents: Grains Industry National Research, Development and Extension Strategy (GRDC, November 2010) Australia and Food Security in a Changing World (PMSEIC Expert Working Group, October 2010) The global context is summarized in the recent review: Tester, M. & Langridge, P. (2010) Breeding technologies to increase crop production in a changing world. Science 327: Page 6 of 6