Next gen chase research break-throughs with unrivalled access to plant phenotyping technology

Our latest round of Postgraduate Internship Award (PIA) students have kicked off their research projects at the Australian Plant Phenomics Facility (APPF)!

All our student interns have the unique opportunity to access the APPF’s cutting-edge phenotyping capabilities at no cost, learning about experimental design, and image and data anaylsis in plant phenomics while undertaking collaborative projects with the highly skilled APPF team. This experience allows our next generation of aspiring plant scientists to explore key research questions, reveal new data and make a real contribution to the global challenge of feeding future generations.

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Yue Qu (Julian) with his soybean plants in an automated, high-throughput plant phenotyping Smarthouse at the Australian Plant Phenomics Facility’s Adelaide node

Yue Qu (Julian)

In his project ‘Investigating novel mechanisms of abiotic stress tolerance in soybean’ Julian seeks to answer two questions, (1) Does GmSALT3, a protein linked to improved salt tolerance, also confer tolerance to drought and oxidative stress in soybean, and (2) Does GmSALT3 improve growth under standard conditions. He will use a non-destructive, high-throughput plant phenotyping Smarthouse, hyperspectral leaf phenotyping, leaf ion content, ROS activity/detoxification of roots, and gas exchange to investigate 8 lines of soybean in combination with 4 treatments (control, drought, 100mM NaCl, 150mM NaCl).

“For my PhD I have been functionally characterising GmSALT3. I have used heterologous expression systems to examine transport activity, as well as phenotyping salt tolerance in the NILs,” said Julian.

However, more recent phenotyping data and RNA-seq analysis has led us to the hypothesis that the salt tolerance phenotype of GmSALT3 plants is a consequence of their improved ability to detoxify reactive oxygen species, and therefore they may be more stress tolerant in general. This is contrary to the prevailing hypothesis that the protein is directly involved in salt transport and directly, rather than indirectly confers salt exclusion. To test this hypothesis we need to properly phenotype the Near Isogenic Lines (NILs). We believe that the phenotyping capabilities of the APPF will give unparalleled insights into the stress tolerance of soybean that would not otherwise be possible. Such a finding will be a significant breakthrough and likely result in a high impact publication when added to our existing data.”

Supervisor, Professor Matthew Gilliham, from the ARC Centre of Excellence in Plant Energy Biology agreed. “The experience the APPF team offer while conducting these experiments will add a great deal to the impact of the papers Julian is preparing and reveal a new layer of complexity that would not be possible without their expertise.”

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Daniel Menadue watches over his wheat plants in a Smarthouse at the Australian Plant Phenomics Facility’s Adelaide node

Daniel Menadue

Daniel is investigating a proton pumping pyrophosphatase (PPase) gene family in wheat and the role these genes play in the wheat plant’s response to environmental stress in and enhancing yield.

Vacuolar pyrophosphatase have been known for a while to be involved in a plant’s adaptation to the environment, however, the majority of the work on these genes has been using the gene from Arabidopsis, AVP1. Daniel’s research has identified the 12 wheat orthologs of AVP1 and from the sequence and expression data he has to date, he hypothesises that different PPases have different roles depending on their protein sequence and tissue localisation. To this end Daniel has generated transgenic bread wheat, cv Fielder, expressing two of the wheat genes (TaVP1-B and TaVP2-B) to further characterise the role of the PPase protein. Excitingly, Daniel has observed a growth phenotype, in the second generation of transgenic plants, with the transgenic plants appearing to grow faster and have larger biomass than wild type or null segregant plants. This is a phenotype previously seen in transgenic barley expressing the Arabidopsis AVP1 gene, plants which went on to show enhanced yield under salinity in the field (Schilling et al. 2014, Plant Biotech J.).

Given the very promising phenotype of these lines, Daniel will dissect this mechanism further using the non-destructive imaging capabilities at the APPF as an ideal platform for such experiments. He will investigate when the transgenic lines exhibit their enhanced growth, dissect whether they grow faster throughout the vegetative period or just for a short while at the start of their growth. He will also investigate the possibilities of following the growth of leaves through time and determine if the plants have enhanced resistance to salinity tolerance.

“In many ways we would like to replicate the study that we did in one of the APPF’s Adelaide Smarthouses which produced the barley data for the Schilling et al. 2014 paper, but in much more detail and using wheat plants with wheat genes,” said supervisor, Dr Stuart Roy from the University of Adelaide’s School of Agriculture, Food and Wine.

“We envision that the data obtained from Daniel’s study will form the basis of at least one research publication and, if the results are promising, open up new areas of research and delivery for bread wheat with altered PPases expression levels through my International Wheat Yield Partnership project, AVP1, PSTOL1 and NAS – Three high-value genes for higher wheat yield.” – shared in our recent blog story ‘International consortia tackle the global challenge to increase wheat yields at the APPF’.

It’s a pleasure to welcome Julian and Daniel to the team!

The next round of Postgraduate Internship Awards at this APPF will close 30 November, 2017 – Apply now!

Internships are offered at the APPF in Adelaide and Canberra for enthusiastic, highly motivated postgraduate students with a real interest in our research and technology. Current postgraduate students in the following areas are encouraged to apply:

  • Agriculture
  • Bioinformatics
  • Biology
  • Biotechnology
  • Computer Science
  • Genetics
  • Mathematics
  • Plant physiology
  • Science
  • Software engineering
  • Statistics

Interstate students are strongly encouraged to apply!

We offer postgraduate internship grants which, in general, comprise:

  • $1,500 maximum towards accommodation in Adelaide or Canberra, if required
  • $500 maximum towards travel / airfare, if required
  • $10,000 maximum toward infrastructure use

The APPF has identified a number of priority research areas, each reflecting a global challenge and the role that advances in plant biology can play in providing a solution:

  • Tolerance to abiotic stress
  • Improving resource use efficiency in plants
  • Statistics and biometry
  • Application of mechatronic engineering to plant phenotyping
  • Application of image analysis techniques to understanding plant form and function

Students proposing other topics will also be considered.

APPF postgraduate internship grants involve access to the facility’s phenotyping capabilities to undertake collaborative projects and to work as an intern with the APPF team to learn about experimental design, image and data analysis in plant phenomics.

Selection is based on merit. Applications are assessed on the basis of academic record, research experience and appropriateness of the proposed research topic. Interviews may be conducted.

Postgraduate students are encouraged to contact APPF staff prior to submitting their application to discuss possible projects.

For more information and to apply click here.

A step closer to salt tolerant chickpea crops

A recent study has collected phenotypic data of chickpea (Cicer arietinum L.) which can now be linked with the genotypic data of these lines. This will enable genome-wide association mapping with the aim of identifying loci that underlie salinity tolerance – an important step in developing salt tolerant chickpeas.

In this study, Judith Atieno and co-authors utilised image-based phenotyping at the Australian Plant Phenomics Facility to study genetic variation in chickpea for salinity tolerance in 245 diverse accessions (a diversity collection, known as the Chickpea Reference Set).

Chickpea is an important legume crop, used as a highly nutritious food source and grown in rotation with cereal crops to fix nitrogen in the soil or to act as a disease break. However, despite its sensitivity to salt, chickpea is generally grown in semi-arid regions which can be prone to soil salinity. This results in an estimated global annual chickpea yield loss of between 8–10%.

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Salinity tolerance phenotyping in a Smarthouse at the Australian Plant Phenomics Facility’s Adelaide node at the Waite Research Precinct – Plants were imaged at 28 DAS for 3 consecutive days prior to 40 mM NaCl application in two increments over 2 days. Plants were daily imaged until 56 DAS. Right pane shows 6-week-old chickpeas on conveyor belts leaving the imaging hall proceeding to an automatic weighing and watering station.


The study found, on average, salinity reduced plant growth rate (obtained from tracking leaf expansion through time) by 20%, plant height by 15% and shoot biomass by 28%. Additionally, salinity induced pod abortion and inhibited pod filling, which consequently reduced seed number and seed yield by 16% and 32%, respectively. Importantly, moderate to strong correlation was observed for different traits measured between glasshouse and two field sites indicating that the glasshouse assays are relevant to field performance. Using image-based phenotyping, we measured plant growth rate under salinity and subsequently elucidated the role of shoot ion independent stress (resulting from hydraulic resistance and osmotic stress) in chickpea. Broad genetic variation for salinity tolerance was observed in the diversity panel with seed number being the major determinant for salinity tolerance measured as yield. The study proposes seed number as a selection trait in breeding salt tolerant chickpea cultivars.

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Genotypic variation for salinity tolerance in the Chickpea Reference Set. Varying levels of salinity tolerance exhibited by different chickpea genotypes. Exposure of sensitive genotypes to 40 mM NaCl caused severe stunted growth, leaf damage, and led to less number of reproductive sites (flowers and pods) compared to moderately tolerant and tolerant genotypes.


The rapid development of new, high-resolution and high-throughput phenotyping technologies in plant science has provided the opportunity to more deeply explore genetic variation for salinity tolerance in crop species and identify traits that are potentially novel and relevant to yield improvement. The Australian Plant Phenomics Facility provides state-of-the-art phenotyping and analytical tools and expertise in controlled environments and in the field to help academic and commercial plant scientists understand and relate the performance of plants to their genetic make-up. A dedicated cross-disciplinary team of experts provides consultation on project design and high quality support.

To read the full paper in Scientific Reports, “Exploring genetic variation for salinity tolerance in chickpea using image-based phenotyping” (doi:10.1038/s41598-017-01211-7), click here.

To find out more about the Australian Plant Phenomics Facility and how we can support your research click here.




A better way to tackle environmental variation in your greenhouse research

Statistics prove the smart way to deal with variation in your controlled environment greenhouse.

Plant phenomics allows the measurement of plant growth with unprecedented precision. As a result, the question of how to account for the influence of environmental variation across the greenhouse has gained attention.

Controlled environment greenhouses offer plant scientists the ability to better understand the genetic elements of specific plant traits by reducing the environmental variances in the interaction between genetics and environment.

But controlled environments aren’t as controlled as they seem – variation does exist. For example, some days are cloudy, some are not. The sun, as it crosses the sky, casts shadows differently on plants, depending on their position within the greenhouse. In fact, a recent study by colleagues at INRA in Montpellier showed significant light gradients within a greenhouse and provided sophisticated tools for understanding how much light each plant receives.

One practice for dealing with variation has been to rearrange the position of the plants around the greenhouse during the experiment, however, there is a better way.


Rice plants growing in The Plant Accelerator® at the Australian Plant Phenomics Facility’s Adelaide node

The automated high-throughput phenotyping greenhouses at The Plant Accelerator® are controlled environment facilities which use sensor networks to identify and quantify environmental gradients (light, temperature, humidity) in the greenhouses. To further tackle environmental variation, Chris Brien, Senior Statistician at The Plant Accelerator®, led a study that showed good statistical design and analysis was key to accounting for the impact of environmental gradients on plant growth. It was argued that rearranging the plants during the experiment makes it impossible to adjust for the effect of gradients and should be avoided.

The study involved a two-phase wheat experiment involving four tactics in a conventional greenhouse and a controlled environment greenhouse at The Plant Accelerator® to investigate these issues by measuring the effect of the variation on plant growth.

To learn more about Chris’s study read the full paper here.

To discuss the benefits of good statistical design contact Chris Brien.

To access The Plant Accelerator® for your research:  The Plant Accelerator® at the Australian Plant Phenomics Facility (APPF) is available to all publicly or commercially funded researchers. We have a full team of specialists including statisticians, horticulturalists and plant scientists who can provide expert advice to you when preparing your research plans.