Adelaide’s World-class Plant Phenomics Research

Adelaide’s World-class Plant Phenomics Research
September 25, 2018 Joel Lomman

 Dr Bettina Berger and the team at The Plant Accelerator® here in Adelaide are conducting world-class plant phenomics research, supporting research from around the globe. The Plant Accelerator® is home to a wealth of infrastructure and expertise that helps support international research and create outcomes, from producing further research methodology, to helping farmers understand how to maximise yield and manage drought.

The Plant Accelerator® is a part of the Australian Plant Phenomics Facility (APPF) which is a distributed network of national research infrastructure platforms. Funded by the federal government, The Plant Accelerator® provides state-of-the-art plant phenomics technology, tools and expertise. Dr Bettina Berger is the Scientific Director. She works with a team of scientists, engineers, data scientist and statisticians to interpret and advance research in plant phenomics.

The size and infrastructure available at The Plant Accelerator®, located in Urrbrae just south of the Adelaide CBD, makes it one of the largest in the public sector globally. The facility is set up as an open access service facility which means researchers from around the world can come to have their experiments conducted.

We sat down with Bettina to find out more about the great things happening at The Plant Accelerator® and the collaboration with eRSA.

First of all…

What is phenotyping and phenomics research you ask?

Lucky, we asked that too. Phenotyping, or phenomics is essentially the study of a particular physical attribute of an object (that’s my layman’s understanding at least). Here is the scientific version – it is an area of biology concerned with the measurement of phenomes (a phenome is the set of physical and biochemical traits belonging to a given organism) as they change in response to genetic mutation and environmental influences.

In the area of plants, this means that depending on the research question, the study may be interested in the growth and size of a plant based on the environment it is subjected to, or, the effect that salt in the water has on growth and yield for example. Ultimately these studies create outcomes which lead to innovations in the agriculture and farming industries. Some of these phenotypes can be measured with photographic data produced by The Plant Accelerator’s® automated imaging system, whilst others are measured using destructive practices. [‘Destructive practices’ (in the case of plant research) is a scientific term for ‘cutting it off, and checking it out in the lab’.]

A world-class facility

The facilities available at The Plant Accelerator® make it one of the largest across the globe in the public sector. The facility houses some of the latest technology including DroughtSpotter platforms: a tool that waters plants automatically and measures the water use of individual plants; and a hyperspectral imaging system which allows researchers to non-destructively measure the constituents of a plant including the nutrients, water or other aspects which have a spectral signature.

The latest addition to the infrastructure toolkit is a first-of-its-kind, combined drought/heat phenotyping platform. This is a set of two identical rooms (pictured below) which each have 96 scales, for measuring the water use of individual plants, and individual irrigation taps for controlled watering. Each of these are completely controlled environments and are specifically fitted with light, temperature and humidity control. This simulation of environments gives researchers the opportunity to conduct studies based on severe drought and heat climates comparatively.

The Plant Accelerator® has recently sought pilot projects for this platform and hopes it will produce outcomes that develop our understanding of sustainable farming and heat/drought protection.

All this equipment is then supported by the expertise that Bettina and the team at The Plant Accelerator® provide. As a facility, the research is primarily in methodology, which is shared through publication and offered as a service to other researchers around the world. This service provides research projects with the expertise in plant phenomics to not just plan and conduct experiments, but to gather all the required data, and then through statistical analysis, provide outcomes.

eRSA’s role in all of this…

All this research produces extreme volumes of data. The aforementioned conveyor belt photography system which is housed in The Plant Accelerator’s® greenhouses produce colour imaging of up to 2,400 plants and hundreds of and hyperspectral images on a daily basis. This means – a lot of data.

When The Plant Accelerator® first started in 2010, they had their own server room to house and manage all their data. This infrastructure cost over $500K. When this came to end of life, the cost to host their own data and manage it all themselves wasn’t worth it, so they came to eRSA.

“Today, all our photos and data are stored on eRSA infrastructure. All in all, this means our software engineer can sleep at night and not worry about the security and reliability of all our data,” Bettina said when we sat down to speak with her.

“We also use Virtual Machines (VMs) on the eRSA TANGO Cloud which allows us to process the images and analyse them within 24 hours. One of our users, [located in Germany] can monitor the data of her plant experiment on a daily basis from the other side of the world.”

“The collaboration with eRSA means that our software engineer can focus on supporting our researchers and improving our software tools.”

“We love working with eRSA – we are extremely happy with the level of service provided and VMs can be spun up in no time. The local support and infrastructure are very beneficial to us.”

“With the ongoing NCRIS funding, we are working with eRSA to take a strategic approach over the next 5 years to research and collaboration nationally. ARDC funding is encouraging us to innovate and take a long-term approach to our development.”

“As a provider of eResearch services, eRSA has supported our strategic and collaborative approach to planning.”

 

eRSA exists to support the advancement of research and innovation by providing market leading IT platforms and whole solutions to university research, government and business sectors in South Australia. By providing access to a suite of advanced technology solutions and services that are reliable, easy to use and secure, we enable all researchers to explore new and innovative research opportunities that would not otherwise be accessible.

 

More About eRSA

Our Partners

University of South Australia logo
Adelaide uni logo
Flinders university logo