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Australian Plant Phenomics Facility

The University of Adelaide Australia

Frequently Asked Questions

FAQ about high-throughput phenotyping (The Plant Accelerator)

Research Value
  • Benefits of high throughput phenotyping
  • Revelance to field results
  • Why 'Accelerator'?
Project Planning
  • How much does it cost?
  • When can I start?
  • Do you provide training?
  • Data analysis?
Technical Specifics
  • Pot size?
  • Maximum plant size?
  • Pest and disease control?
  • Soil mixes?
  • Resolution of the system?
About the Plants
  • What plants have you tested?
  • Can I phenotype Arabidopsis?
  • Can I phenotype roots?
  • Can I grow quarantine / transgenic plants?
Treatments and Traits
  • Can I measure biomass?
  • What traits can I measure?
  • What treatments / experimental conditions can be tested?
  • What environmental conditions are available?
  • Can I use the spray booth to apply treatments?

 

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Research value

What are the benefits of high throughput phenotyping at The Plant Accelerator?

The major benefits of high throughput phenotyping at The Plant Accelerator are that you can accurately measure a large number of phenotypes, you can do so on a large number of plants, and those measurements can be taken repeatedly over time. This gives the potential for many applications that would not otherwise be possible, for example mapping and association studies for dynamic responses, screening of populations for specific or novel phenotypes, and dissection of physiologically complex trait into simpler individual components. View info sheet 'Advantages of the Accelerator'

We have published a number of case studies on our website giving specific examples of projects that have been made possible by the technology at The Plant Accelerator - see http://www.plantaccelerator.org.au/technology/publications/#case.

Are plant responses in The Plant Accelerator relevant to field results?

The Accelerator has been designed specifically for crop plant research, and we believe that it will provide results that are very relevant to field performance. We currently have a major project underway to confirm this, by directly compare phenotyping results in the Accelerator with measured field traits.

Why ‘Accelerator’ – will it make my plants grow faster?

The name “The Plant Accelerator” was chosen because its high throughput and leading-edge technologies can be used to accelerate your research. If needed, we can try to provide conditions that will speed up growth and development, but generally growth rates are comparable to those in the field.

 

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Project planning

How much does it cost to use the phenotyping facility at The Plant Accelerator?

All our projects are individually priced depending on the specific requirements of the project. Examples of costs for a typical project are available on our website at http://plantaccelerator.org.au/facilityaccess/pricing/.

Costing for collaborative projects will be established on a case by case basis.

Customers are encouraged to consult the Accelerator team to discuss project design and pricing as well as opportunities for collaboration.

 

When can I start my project?

Availability of space at the Accelerator varies, and we encourage you to talk to us as soon as possible if you need to run your project at a specific time.

Before each project we have a detailed project design consultation process, and it can take some weeks to finalise the ideal experiment for your research goals and budget. Transgenic and especially quarantine projects may need approval and pre-project treatments, so allow at least three months extra for these before your project can start.

 

Can I carry out my own project at The Plant Accelerator, and do you provide training?

We welcome customers to be involved as much or as little as they like in their projects, after a simple and quick induction course. The Accelerator team are happy to provide advice and help with setup, maintenance and analysis of projects, but they are not able to supervise students or other inexperienced individuals.

 

What data and analysis will you provide me with?

We will carry out routine image processing and provide you with a spreadsheet of raw phenotype data, and can help with basic analysis of characteristics such as growth rates, water usage and stress response. You can also access your data, including images, through our secure online web portal. If required, we can provide images on DVD, hard drive, or a download site.

We can try to assist with more detailed analyses, but would highly recommend that you collaborate with specialist statisticians to obtain the full value from your data.

 

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Technical specifics

What size pots do you use for phenotyping experiments?

Our standard pots are 15cm diameter by 20cm high, and hold about 2.5L of soil. If you need larger pots, we can also offer ones that are 20cm in diameter by 20cm high, and hold about 4.5L of soil. There is a small additional charge for using these larger pots.

How big plants can you phenotype?

The tallest plant that can physically fit in the phenotyping chambers is about 1.7m, measured from the soil surface. Most plants are likely to be constrained by pot size before reaching this height, and larger plants may also extend beyond the field of view of the imaging cameras.

Do you have disease outbreaks, and how do you treat them?

Despite our high standards of operation, occasional disease outbreaks are inevitable in a greenhouse environment. Our staff are trained and experienced in identifying these, and can advise on and carry out the best treatment program. We do not generally offer routine spraying, since we find this can affect growth and phenotype responses.

What soil mix do you use?

We have a range of standard soil mixes available, and can normally order specific custom mixes as required

What is the resolution of the system?

The different imaging stations have different resolution cameras, ranging from five megapixels for the visible light (RGB) cameras to 0.3 megapixels for the infrared cameras. One pixel in the RGB station corresponds to approximately 0.5mm at the plant.

 

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About the plants

What plants have you tested?

We have carried out phenotyping projects using: wheat, barley, maize (corn), canola, rice, soybean, sorghum, potato, tomato, sugarcane, chickpea, sunflower, safflower and Pongamia. We have successfully grown many other species in our greenhouses and growth chambers.

Can I use The Plant Accelerator for Arabidopsis research?

Technically it is possible to do so, but the Scanalyzer 3D system that we use is optimised for larger plants. For Arabidopsis projects, you may want to talk to our colleagues at the High Resolution Plant Phenomics Centre.

Can you phenotype roots?

We are trialling options, including transparent pots, to measure root growth non-destructively, but these are limited compared to what can be measured on above-ground parts of the plant. In some cases we can offer end-point imaging and biomass measurement by washing out the roots.

Techniques are being developed to image water content down a column of soil using near-infrared imaging – this will provide information about from where down a soil profile roots are removing water, thus giving information not only about where the roots are, but where the roots are active.

Can I grow quarantine/transgenic plants at The Plant Accelerator?

The Accelerator has extensive PC2 containment facilities for transgenic work, and QAP 6.1 quarantine-approved greenhouses. We are able to help with paperwork and regulatory approval for quarantine and transgenic projects.

 

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Treatments and traits

Can I measure biomass at The Plant Accelerator?

Because we use image-based methods for phenotyping, it is not possible to measure biomass directly. We have calibration curves for many species that give an accurate estimation of above-ground biomass (both fresh and dry weight) from the imaged plant area.

What traits can I measure using The Plant Accelerator?

The image processing software that we use at the Accelerator extracts a very large number of phenotype parameters, all of which could be regarded as traits. Of these, the more commonly used include plant height, projected leaf area, ‘greenness’ and steady-state fluorescence. Water usage is also recorded through weighing of the pot at each phenotyping cycle.

Popular ‘secondary’ traits (which are calculated or inferred from the direct measurements) include growth rate, stress tolerance, biomass, and water use efficiency.

What treatments or experimental conditions can I test at the Accelerator?

Generally, any treatment that can be applied and confined to an individual pot can be tested as an experimental condition; for example, salinity, nutrient application, water stress, different soil types, mineral and metal contamination, and inoculation with certain pathogens or symbionts. With the right experimental design, it can also be possible to study the effects of broader environmental conditions such as day length, temperature or humidity.

What modified environmental conditions are you able to provide?

All greenhouses and Smarthouses at The Plant Accelerator are temperature controlled with either reverse-cycle air conditioning or evaporative cooling and hot water convection heating. Please contact us if you would like detailed information about available temperature ranges and temperature regulation.

Elevated CO2 is available in some growth cabinets, but not in the Smarthouses or greenhouses.

Humidity control is available in all growth cabinets and selected greenhouses have elevated humidity capabilities.

The Plant Accelerator relies on natural sunlight for illumination. All greenhouses and Smarthouses have lighting for photoperiod extension, but these lights are not sufficient for enhancing photosynthesis.

Frost tolerance projects may be carried out with the use of the Australian Genome Research Facility’s frost chamber, just a couple of buildings away. 

Can I use the spray booth to compare the effect of different spraying treatments on my plants?

The spray booth is designed for pest management rather than application of experimental treatments. In certain cases, it may be possible to compare the effects of spraying in a simple treated/untreated comparison, but this is not the intended use of the booth.

 

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