About the APPF
The Australian Plant Phenomics Facility (APPF) is a world-leading infrastructure facility that underpins innovative plant phenomics research to accelerate the development of new and improved crops, healthier food and more sustainable agricultural practice.
The APPF is a national facility, available to Australian and international plant scientists, offering access to infrastructure that is not available at this scale or breadth in the public sector anywhere else in the world. Our facilities are based around automated image analysis of the phenotypic characteristics of extensive germplasm collections and large breeding, mapping and mutant populations. We utilise robotics, imaging and computing to enable sensitive, high throughput analyses to be made of plant growth and function. New technologies are continually being developed and implemented to ensure we remain at the forefront.
- Sophisticated controlled environments for growing plants across a range of climatic conditions
- Glasshouse automation technologies to study large populations of plants rapidly and efficiently
- Leading-edge digital imaging technologies and sophisticated software to measure plant characteristics and their performance in real-time
- The capacity to scale-up plant performance measurements from the greenhouse to the field
- A unique and integrated system for the rapid capture of genetic resource information and its shared use for plant science and agriculture, both within Australia and internationally
- Support with project management for customers located remotely or overseas
- High-level consultation and expertise in plant phenomics including project design, statistics, automated imaging and image analysis
- Expertise in data architecture, visualisation and management
- A national focus for scientists to collaborate on key biological and agricultural research problems.
- Development of advanced plant phenomics technology and methods, internationally competitive infrastructure and highly skilled, multi-disciplinary workforce.
- Consultation on plant phenomics, best practice protocols, project design and statistical layout.
- Facilitation of novel research approaches through access to, and training in, the use of plant phenomics infrastructure involving (i) Research hotel model – researchers working alongside our experts, or (ii) Full service delivery model – where APPF technicians undertake projects on behalf of researchers.
- Analysis of images, preparation of growth curves, and access to datasets and visualisation tools.
- Bioinformatics and biometry by performing quality control processes on datasets, providing standard data analysis, provision of open source algorithms and access to analytical pipelines, and assisting researchers in processing and interpreting complex data.
- Data management including data storage and access to data sharing tools.
- Education and training in plant phenomics, image analysis, bioinformatics, biometry and statistical design.
- Functional genomics of model and crop species
- Screening of mutant or mapping populations, screening for natural variation in diverse populations
- Unravelling signal transduction and environmental interactions
- Climate change research
- Development of novel products for healthy foods
- Development of sustainable practices in agriculture
- Maintenance of biodiversity and the development of new strategies for the remediation of degraded landscapes
- Using plants and biofactories to produce new pharmaceuticals and other products for industry
Our facility has well-established working relationships with Australian and international scientists and agricultural businesses. This includes our long-standing involvement in the International Plant Phenomics Network (IPPN), international initiatives aimed at crop improvement such as the Wheat Initiative, and interacting with the research community by delivering phenotyping services, providing consultation, participating in collaborations and promoting knowledge transfer through discussions at scientific meetings and conferences. Our facility attracts international organisations and policy makers, who seek to access our phenomics platforms or to visit our nodes to learn about Australia’s advances in plant phenomics.
The Australian Plant Phenomics Facility (APPF) supports excellence in research and offers access to state-of-the-art plant phenotyping technology and plant growth environments to national and international publicly-funded researchers and industry users.
Our multi-disciplinary team provides expert consultation in plant phenomics and is dedicated to assisting you in the design and management of your experiment. We encourage users to discuss requirements and project design prior to submitting an application to optimise your proposal and research outcome. Our streamlined application process involves the submission of a booking sheet/request for service form, assessment of the project proposal, preparation of a quote and the completion of a facility access agreement.
To discuss your project with our Scientific Team, head to our Contact page to find their contact details.
To make a booking head to the Capabilities page. All technology and services include a link to specific booking sheets.
What we do
The APPF invests in developing, maintaining and enhancing advanced technologies, expertise and data resources to facilitate innovative research projects in plant phenomics. Our services and resources involve three major focus areas:
Plant Phenomics | Bioinformatics & Biometry | Research Innovation & Collaboration
Plant phenomics
Consultation
The APPF consults with a range of stakeholders to understand the changing trends in plant phenomics in an effort to provide infrastructure and expertise that is aligned with the needs of the research community and agricultural industry. In addition, the facility takes into consideration the recommendations outlined in the National Innovation and Science Agenda, the 2016 Research Infrastructure Roadmap and the Decadal Plan for Agriculture. We provide facility user consultation on best practice project design in controlled environment and field phenotyping and deliver various ways to equip the next generation of scientists with the know-how to conduct novel research experiments in plant phenomics.
- Consultation with research community
- Interaction with farmers, breeders, research development corporations
- Industry support
- Alignment with National Innovation & Science Agenda
- Alignment with 2016 Roadmap
- Alignment with Decadal Plan for Agriculture
- Controlled environment and field phenotyping
- Tailored project design (traits-crops-treatments)
- Research community
- Farmers, breeders, research development corporations
- Industry
- Policy makers
- Funding agencies
- International plant phenomics networks
- Other NCRIS facilities
- Provision of user training
- Workshops and training courses delivered
- University and school student tours
- Organisation of conferences
- Delivery of seminars
- Delivery of talks at conferences and workshops
Phenotyping
We deliver project design solutions tailored to the specific needs of facility users by providing access to a range of advanced technologies that accurately measure the performance of plants in different environments non-destructively and over time. In addition, the Facility ensures quality controls are in place and research standards are maintained throughout each project facilitated at the APPF. Capability enhancements through R&D and method development, as well as continuous improvement in the way services are delivered to the research community, are another key focus of the APPF.
- Consultation on project design
- Statistical expertise to support project design
- Streamlined project management (end-to-end support)
- Flexible access option: ‘research hotel’ or full service delivery
- Providing a range of plant phenotyping platforms (see Technology)
- Capturing plant performance non-destructively and over time in controlled environments and in the field (in response to abiotic stress or to treatments, e.g. nutrients or chemicals)
- Programs to promote facility usage by postgraduate students
- Programs to assist with travel and facility access for interstate users
- Undertaking quality checks and data cleaning
- Packaging data for distribution (standardisation, formatting, ensuring data interoperability)
- Meeting requirements of legislative authorities (compliance with Biosecurity Australia and Office of the Gene Technology Regulator)
- Near real-time online monitoring of phenomics projects
- Providing mechatronics and biotechnology expertise to support technology development
- Development of new phenotyping tools, methods and processes
- Enhancing plant phenomics expertise (staff development programs, facility user training, student supervision and mentoring, hosting local and international students, membership of expert working groups
- Improvement of service delivery (user feedback, new services)
Bioinformatics & biometry
Data analysis
We provide access to a range of analytical and visualisation tools to facilitate the analysis of large and complex research datasets. APPF biometricians and bioinformaticians assist facility users in planning their projects and analysing the data acquired through the use of their technologies, whilst offering tailored support and user training.
- Provision of analytical software tools for multiple plant phenomics platforms
- Training in the use of analytical software
- Access to expertise in biometry and bioinformatics
- Development of improved analytical tools
- Open access to algorithms and analytical scripts
- Access to visualisation tools
- Provision of on- and off-site user training
- Hosting of facility users
- Delivery of post-project support to complete data analysis
Data management & sharing
The APPF has worked closely with the National eResearch Collaboration Tools and Resources project (NeCTAR), National Computational Infrastructure (NCI), Research Data Services (RDS) and Australian National Data Service (ANDS) to establish capabilities for reliable, long-term data storage. In the spirit of the National Collaborative Research Infrastructure Strategy (NCRIS), data sharing is strongly promoted and we have developed a number of online platforms that enable data discoverability and sharing of open datasets. We actively engage with RDS/NeCTAR/ANDS to explore options for closer collaboration within the domains, in particular biosciences and agriculture.
- Provision of long-term and reliable data storage
- Dedicated personnel to support data management
- Development and maintenance of online databases
- Provision of access to online datasets via APPF website links
- Promoting data sharing as part of facility access policy
- Development and maintenance of search engines
- APPF website as plant phenomics portal
- Publications in international journals
- Publication of phenomics data via ARDC services and Pawsey
- Dedicated data management group focussed on data standardisation and discoverability
- Meta data format policy
- Ontology based architecture
- Collaboration with related NCRIS facilities promoting data standards and procedures
Research innovation & collaboration
The APPF delivers world class plant phenotyping technologies and expertise to facilitate research projects aimed at solving complex problems in plant and agricultural science both here in Australia and around the globe. State-of-the-art imaging technologies, robotics, sensor networks and data analysis tools are combined at the APPF to help measure plant performance accurately and non-destructively, and thereby accelerating research outcomes and knowledge transfer. To promote research innovation and collaboration we offer a number of plant phenomics access programs and an interdisciplinary collaborations program.
Interdisciplinary collaboration
Linking with other NCRIS facilities, international plant phenomics centres and networks to improve end user benefit is a key objective of the APPF. We have strong linkages with international plant phenomics networks and research centres, and actively explore opportunities for collaboration with other NCRIS facilities.
Plant phenomics support programs
We have introduced a range of activities to promote the use of our NCRIS infrastructure and to facilitate ground-breaking research project.
- Phenotyping of publicly available crop populations funded by research development corporations (RDCs) or international consortia
- Phenotyping of crop collections of national importance to complement genotypic information made available by BPA
- Development of phenoSMART® as a marketplace for academic and industry partners
- Collaboration with various NCRIS facilities (ARDC, Terrestrial Ecosystem Research Network – TERN, NCI and NeCTAR) for visualisation and analysis of point cloud and hyperspectral data
- Linking with NCRIS facilities, international phenomics centres and networks to improve end user benefit
- Providing customers with access to multidisciplinary expertise to optimise research projects (plant science, horticulture, mechatronic engineering, biotechnology, biometry, biostatistics, software engineering, web development)
- Providing access to a critical mass of experts through co-location at key agricultural research precincts (University of Adelaide Waite Research Precinct, Australian National University School of Biological Sciences) and a range of Centres of Excellence in plant and computational sciences
- Postgraduate Internship Awards (PIA), a program to enable access to advanced technology for highly motivated and research focussed postgraduate students
- Travel Grants, a program to provide financial assistance to interstate researchers wishing to access APPF infrastructure in Adelaide or Canberra
The world needs to produce at least 50% more food to feed an estimated 9 billion people by 2050. But climate change could cut crop yields by more than 25%.
Our land, biodiversity, oceans, forests and other forms of natural capital are being depleted at unprecedented rates.
Unless we change how we grow our food and manage our natural capital, food security – especially for the world’s poorest – will be a risk. World Bank, 2016
Why we do what we do
We facilitate, advocate, collaborate, innovate and knowledge share to advance plant science for the global good.
Plant phenomics enables science that has the power to transform our lives. By exploring how the genetic makeup of an organism determines its appearance, function and performance, phenomics can help us tackle the most pressing challenges of our time – including global food shortages, the demand for alternative fuels, fewer resources and climate change.
With the global population expected to exceed 9 billion by 2050, a transformational advance in grain production must occur to increase yield by 50-60% to meet projected global food demand. Many global production issues are particularly pertinent to Australia which faces long periods of drought and increasing salinity, undermining farm productivity. Increasing the yield in crops, particularly in these marginal environmental conditions, using novel approaches that exploit robotics, machine learning, computer vision and genetics technologies will significantly increase global food quality and production, and reduce environmental degradation.
Phenomics data captured at the APPF enables the more rapid discovery of molecular markers and faster germplasm development, aimed at improving crop yields including the tolerance of major crops and other agriculturally important plants to biotic and abiotic stresses such as drought, salinity and a broad spectrum of plant diseases; putting the APPF at the forefront of the race to meet global food demands in the future.
The Australian Plant Phenomics Facility (APPF) is a distributed network of national research infrastructure platforms that offer open access to plant phenomics technologies and expertise. The capabilities and capacity provided by the APPF enable researchers to address complex problems in plant and agricultural science both here in Australia and around the globe.
The APPF was established in 2007 and commenced operations in 2009 with the aim of driving research excellence and collaboration between researchers, government and industry to deliver practical outcomes. Since then, the facility has embraced advances in robotics and automation, and developed infrastructure, expertise and methodologies to innovate the investigation of plant performance in different environments, e.g. drought, salinity, heat. Relating that performance to the genetic makeup of plants (plant phenomics) will lead to the development of new and improved crops, healthier food and more sustainable agricultural practices.
We facilitate new research programs in plant and agricultural science through:
- Providing access to high quality growth facilities and state-of-the-art automated phenotyping capabilities in controlled environments and in the field
- Providing high level consultation and expertise in plant phenomics including project design, statistics, automated imaging, image analysis and data management
- Promoting and engaging in multidisciplinary and cross-institutional research collaborations to facilitate and accelerate transfer of knowledge at the national and international level
- Continuously improving existing capabilities and developing and disseminating new technologies to meet the changing needs of the plant and agricultural research community
- Providing training opportunities to develop a critical mass of experts in plant phenomics
- Collaborating with the national and international plant phenomics community
- Collaboration and technology transfer with industry to increase yield in food crops
The APPF will advance Australia’s phenomics capacity and capability in plant science to deliver sustainable and profitable agricultural practices.
The APPF will facilitate world class research and innovation in plant phenomics by:
- Providing efficient access to state-of-the-art, science-ready platforms for plant science and agriculture
- Developing new technologies and capabilities to facilitate innovation in plant phenomics
- Contributing to multidisciplinary and cross-institutional collaborations that address critical challenges in agriculture
- Promoting scientific partnerships and collaborations between researchers and industry
- Upskilling technicians and next-generation scientists in the use of advanced technologies
- Expanding national and international research networks
- Sustaining Australia’s intellectual capability and capacity in plant phenomics
Our Goals
- Delivering outstanding infrastructure and customer service to underpin research excellence and innovation
- Developing new technologies and research methods
- Improving Australia’s plant phenotyping expertise to accelerate research outputs and impact
- Engaging with the research community, industry, RDCs and governments to advance Australia’s efforts in addressing the challenges faced by agriculture at a time of extreme climate variability
The APPF is supported by the Australian Government through its National Collaborative Research Infrastructure Strategy (NCRIS). NCRIS is a national network of world-class research infrastructure projects that support high-quality research to drive greater innovation in the Australian research sector and the economy more broadly. Projects support strategically important research through which Australian researchers and their international partners can address key national and global challenges.
The APPF substantially leveraged its NCRIS funding during the first decade of operation by attracting several million dollars in state government and host institution support, as well as RDC grants, to enhance existing, and add new, infrastructure to support the research community.
Today, NCRIS funding and substantial in-kind support from our host institutions, the University of Adelaide, CSIRO and Australian National University, cover much of the facility’s operating costs, providing facility users with highly subsidised access to advanced technologies and expertise. The remaining funds required to maintain the infrastructure is generated by user fees, RDC grants to support capability improvements and a recent $2.6 million research infrastructure investment made by the Federal Government. The grant was announced under the Federal Government’s new $1.9 billion Research Infrastructure Investment Plan, developed in response to the recommendations from the National Research Infrastructure Roadmap produced by a group of experts led by Australia’s Chief Scientist, Dr Alan Finkel AO.
Read how NCRIS recognises and supports Australian First Nations’ knowledge and research, on the APPF blog.
Our Board
The APPF Advisory Board is comprised of four independent members, representation from the APPF Lead Agent, and the APPF CEO (ex-officio).
We have helped researchers worldwide
“I had the honour to facilitate an essential part of my research at The Australian Plant Phemonics Facility.
Firstly, the team is a group of highly professional knowledgeable researchers with a great passion and love of science. From the application process, through the experiment at the facility and the data analysis, every person I had a chance to work with was an absolute expert.
Secondly, the data that was generated throughout the experiment enabled me to meet my research milestones and to get answers for my fundamental study’s questions.
Last but not least, the environment and the team spirit together with the best morning teas, made my time at the APPF’s Adelaide node an unforgettable experience”.
“The experience the APPF team offer while conducting these experiments will add a great deal to the impact of to the papers we are preparing and reveal a new layer of complexity that would not be possible without their expertise.”
“The staff at the APPF Adelaide is an exceptional group of individuals.
Our group at the University of Nebraska has been collaborating with the researchers at this APPF node in an effort to examine the genetic basis of dynamic salinity responses in rice. Throughout this collaboration, the APPF staff has provided an extremely welcoming and engaging environment for a visiting graduate student from our lab.
As with any new “omics” technology, the breadth and complexity of the data can be daunting. However, the APPF staff provided substantial support regarding image analysis and the interpretation of image-derived metrics. These efforts have come to fruition with the publication of a manuscript in 2015.
The staff APPF Adelaide is a collection of individuals from diverse backgrounds who are extremely professional and motivated. We look forward to working with them again in the future.”
“The APPF Adelaide team has delivered a world-class service to our research projects over the past five years, providing an integrated service from quarantine importation of plants, high-throughput phenomics, data analysis and reporting. Through their expertise in plant phenomics we have been able to access state-of-the-art technology to advance our research resulting in new funding, international partnerships, and publications.”
“Thanks to Dr Bettina Berger and her great team at APPF Adelaide, we recently obtained the independent-testing data required by our funders to progress our project on yield improvement in crops to the next level.
Although our plant species was new for TPA’s Lemnatec high-throughput phenotyping system and we had special requirements, we were quickly able to establish a strong working relationship with the APPF to troubleshoot the system and transfer our protocols prior to the large-scale trial.
An added touch was the interest shown in our project by the APPF staff, the true indicator of a facility dedicated to providing a service to researchers.”
“The phenotyping facility at the APPF Adelaide provided us with valuable data for our wheat growth study. We were able to capture the genetic and treatment effects through the images captured on a daily basis. The post experimental analysis was also flawless thanks to the good technical support.”
“Researchers at the ARC Centre of Excellence in Plant Cell Walls undertake several scientific projects in collaboration with international partners. In order to meet our research objectives we require easy access to high quality infrastructure. This is delivered by the APPF. The facility’s state-of-the-art plant growth environments in Adelaide are second to none and the team’s professional support services are fantastic. We currently grow in excess of 2,000 plants of different varieties at the facility. The capabilities available at the APPF are essential to our research programs.”