AUSTRALIAN PLANT PHENOMICS FACILITY

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AUSTRALIAN

PLANT

PHENOMICS

FACILITY

R

ESPONSE TO 2011 STRATEGIC ROADMAP FOR AUSTRALIAN RESEARCH

I

NFRASTRUCTURE

D

ISCUSSION

P

APER

M

AY

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 CO2 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, 26‐27 Feb 2011) and the economics of feeding 9 billion people by 2050

is receiving considerable attention (e.g. The Economist special report, 26th 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

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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 20‐30 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

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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, 20091). 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;

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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

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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 under‐

utilised. 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

Director, Australian Plant Phenomics Facility

Dr Bob Furbank

Director, High Resolution Plant Phenomics Centre

Professor Murray Badger

Chief Investigator, High Resolution Plant Phenomics Centre

Mr Terry Enright

Farmer, Western Australia (Chair, APPF Advisory Board)

Professor Graeme Hammer

School of Land, Crop & Food Sciences, University of Queensland,

Brisbane

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Professor Ian Small

Director, ARC Centre for Plant Energy Biology, UWA, Perth

Professor Geoff Fincher

Director, ARC Centre of Excellence in Plant Cell Walls, University of

Adelaide

Professor John Manners

Deputy Chief, CSIRO Plant industry, Brisbane

A/Professor Ros Gleadow

Cyanogenesis Group, Monash University, Melbourne

Professor Hans Lambers

Head, School of Plant Biology, UWA, Perth

Dr Robert Loughman

Director, Genetic & Product Innovation, Dept of Agric. & Food WA

Professor Harvey Millar

ARC Centre for Plant Energy Biology, UWA, Perth

Professor Ulrich Schurr

Head, Institute Phytosphere, Research Centre Jülich, Germany

Professor Roger Leigh

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