Education

Exciting internship opportunity closing soon – apply now!

internships

The Australian Plant Phenomics Facility (APPF) is looking for enthusiastic, highly motivated postgraduate students with a real interest in our research and technology to join our team as interns. 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

In order to attract the very best students, we offer postgraduate internship grants. In general, a grant is comprised of:

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

Interstate students are strongly encouraged to apply!

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.

APPLICATIONS CLOSE:  31 March 2017. For further information click here.

About us

The Australian Plant Phenomics Facility (APPF) underpins innovative plant phenomics studies to accelerate the development of new and improved crops, healthier food and more sustainable agricultural practice by providing researchers with access to high quality plant growth facilities and state-of-the-art automated phenotyping capabilities in controlled environments and in the field.

To help accelerate research outputs, our phenomics technologies are supported by experts from a number of fields, i.e. agriculture, plant physiology, biotechnology, genetics, horticulture, image and data analysis, mechatronic engineering, computer science, software engineering, mathematics and statistics.

 

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.

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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.

 

 

Professor Mark Tester to talk plant science in Adelaide

Professor Mark Tester from King Abdullah University of Science & Technology (KAUST), Saudi Arabia, will present a talk in Adelaide this March:

“Into the field and into the genome – increasing salinity tolerance of crops”

Time:  Wednesday 8 March, 3.30pm – 4:30pm
Venue:  Hosted by The University of Adelaide, Plant Science Department, the talk will be held in the Plant Genomics Centre seminar room (Waite Campus, The University of Adelaide, South Australia) with drinks and nibbles afterwards. All are welcome.

About the speaker

Mark Tester is Professor of Bioscience at KAUST. After a PhD in Cambridge and lectureship there, he went to Adelaide, as a Research Professor in the Australian Centre for Plant Functional Genomics and Director of the Australian Plant Phenomics Facility. Mark was part of the team that led the establishment of this Facility, a $55m organisation that develops and delivers state-of-the-art phenotyping facilities, including The Plant Accelerator, an innovative plant growth and analysis facility. In his research group, forward and reverse genetic approaches are used to understand salinity tolerance and improve this in crops such as barley and tomatoes. His aspiration is to develop a new agricultural system where brackish water and seawater can be unlocked for food production.

Abstract

One-third of the world’s food is produced under irrigation, and this is directly threatened by over-exploitation of water resources and global environmental change. In this talk, the focus will be on the use of forward genetics to discover genes affecting salinity tolerance in barley, rice and tomatoes, along with some recent genomics in quinoa, a partially domesticated crop with high salinity tolerance. Rather than studying salinity tolerance as a trait in itself, we dissect salinity tolerance into a series of components that are hypothesised to contribute to overall salinity tolerance.

For barley, two consecutive years of field trials were conducted at the International Center for Biosaline Agriculture, a site with sandy soil and very low precipitation. Drip irrigation systems allowed the control of salinity by supplying plots with low (1 dS/m) and high salinity water (17 dS/m). A barley Nested Association Mapping (NAM) population developed by Klaus Pillen has been used to dissect physiologically and genetically complex traits in response to salt stress. Ten traits related to yield and yield components (e.g. days to flowering, harvest index, 100 seed mass) were recorded and five stress-indices were derived from each of these measurements. We have identified two significant loci located on the long arms of chromosomes 1H and 5H, which are both associated with several traits contributing to salinity tolerance, namely days to flowering, days to maturity, harvest index and yield.

For tomatoes, the focus is on genetics of tolerance in wild tomatoes, specifically Solanum galapagense, Solanum cheesmaniae and Solanum pimpinellifolium. An association genetic approach is being taken. High quality genome sequences have been made, and genotyping-by-sequencing undertaken. Tomatoes have been phenotyped in The Plant Accelerator and in the field, and analyses are currently in progress.

The application of this approach provides opportunities to significantly increase abiotic stress tolerance of crops, and thus contribute to increasing agricultural production in many regions.

Mark is in Adelaide between Mon 6th and Sun 12th March. If you would like to meet with Mark, please contact him directly: mark.tester@kaust.edu.sa

The Plant Accelerator

Plant phenotyping research projects facilitated by The Plant Accelerator vary from large scale screening of early growth, to salinity tolerance and water and nutrient use efficiency. Possible applications are diverse with respect to the measured traits and plant species studied. Please contact our experts to discuss how your research might benefit from the capabilities and services provided by The Plant Accelerator.

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The Plant Accelerator®,  Australian Plant Phenomics Facility, Adelaide, South Australia

Sun protection and diversity could be key to more productive rice crops

With a rapidly growing population, improving the yield of global food staples such as rice has become an urgent focus for plant scientists.

In a recent study published on Plant Physiology, scientists have discovered they can improve rice productivity by selecting rice varieties that are better at capturing sunlight to produce grains instead of reflecting it as heat.

The team, which included Dr Xavier Sirault from the Australian Plant Phenomics Facility’s High Resolution Plant Phenomics Centre (APPF – HRPPC), focused on rice’s natural diversity by using traditional breeding techniques to select cultivated varieties – or cultivars – that are better at converting sunlight into food.

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“We studied hundreds of plants from five rice cultivars and found that there is variation between these varieties in relation to the quantity of light they use for growth or dissipate as heat. Some of them are capable of converting more sunlight into chemical energy, producing greater leaf area over time,” said lead researcher, Dr Katherine Meacham.

When leaves intercept sunlight, this sunlight is either; 1) absorbed by the leaf and converted via the process of photosynthesis into the plants own components; leaves, grains, roots, etc. 2) dissipated as heat as an strategy to protect the proteins of the plant from sun damage (photo-protection) or, 3) re-emitted as fluorescent light. In this study, the researchers measured fluorescence to infer the quantity of energy that is either converted into food or dissipated as heat.

“Recently scientists in the US found that they can produce transgenic plants that are better at catching sunlight without getting sun damage. Our work shows that this is also achievable by taking advantage of the natural variation of rice plants,” says Professor Robert Furbank, Director of the ARC Centre of Excellence for Translational Photosynthesis and one of the authors of this study.

“What is new about our research is that scientists had previously thought there was not much variation in how efficiently leaves could absorb and use light, and the reason for this is that they were not considering the full picture and measuring the plants throughout the entire day under natural illumination. We revealed that there are considerable differences between the five rice cultivars under moderate light and that means that there is room for selecting the most efficient plants,” said Professor Furbank.

“We found that there is room for improvement in some cultivars that can result in more photosynthesis without risking the plant’s protection strategies against sunlight damage.

The scientists measured fluorescence by clipping light receptors on leaves throughout a whole day to get a full picture of how the plant uses sunlight.

Traditional breeding for photosynthetic traits has not been a common strategy in any major cereal crop, in part due to the difficulty in measuring photosynthesis in thousands of plants. However, rapid screening tools are now available to study the interaction between the genes and the way they interact with the environment.

“Using unique facilities at the Australian Plant Phenomics Facility’s High Resolution Plant Phenomics Centre we were able to follow chlorophyll fluorescence in rice canopies throughout the entire day under natural illumination. This gave us completely different results when compared to the usual 30 min measurement of leaf level light use efficiency. By combining this with digital biomass analysis using PlantScan, we could link light use efficiency with growth, revealing genetic variation in rice varieties not previously detected,” said Professor Furbank.

“Our next step is to find varieties with superior photo-protection. We can directly use these for breeding and find the genes responsible. We have the capacity to screen many thousands of rice varieties for which we have gene sequence through the International Rice Research Institute,” said Dr Meacham.

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Measuring photosynthesis.  Photo credit:  International Rice Research Institute (IRRI)

 

 

It’s a date! 5th International Plant Phenotyping Symposium, 2-5 October 2018

The Australian Plant Phenomics Facility is thrilled to announce the dates for the 5th International Plant Phenotyping Symposium (IPPS) will be 2-5 October 2018!

We look forward to welcoming the international plant phenotyping community to the host city, Adelaide, South Australia, where you will get the full Australian experience all in one state. From cage diving to fine dining, there’s a wine barrel full of reasons why South Australia was named as one of Lonely Planet’s best regions to visit in 2017! Find out more about this vibrant city before you arrive here.

We will post more details about the symposium as they come to hand – make sure you have elected to follow our blog! – and on the Australian Plant Phenomics Facility‘s website.

Adelaide

2018 Host City, Adelaide, South Australia   (Image source: South Australian Tourism Commission)

 

Delicious potential: The genome of quinoa decoded

Scientists have successfully decoded the genome of quinoa, one of the world’s most nutritious and resilient crops.

The study, published online this week in Nature, was an international collaboration led by Professor Mark Tester at the King Abdullah University of Science and Technology (KAUST), Saudi Arabia.

The enormously popular “super-food” is gluten-free, has a low glycaemic index and contains an excellent balance of essential amino acids, fibre, lipids, carbohydrates, vitamins, and minerals, causing international demand for the grain to soar and prices to skyrocket as demand exceeds supply.

“Apart from its nutritional benefits, the ability of quinoa to grow on marginal land is possibly most exciting”, said Prof Mark Tester. “It can grow in poor soils, salty soils and at high altitudes. It really is a very tough plant. Quinoa could provide a healthy, nutritious food source for the world using land and water that currently cannot be used, and our new genome takes us one step closer to that goal.”

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Quinoa pilot trials in the Australian Plant Phenomics Facility’s high-throughput phenotyping Smarthouse at The Plant Accelerator®

Future research projects will focus on identifying the genes that make quinoa so tolerant to poor soils. In pilot experiments carried out at the Australian Plant Phenomics Facility‘s Adelaide node, The Plant Accelerator®, different growth conditions and salt applications were tested in preparation for larger-scale studies. The first studies showed that quinoa still grows well when watered with half-strength sea water, when many other crops would die. Since performing these initial experiments, Professor Tester and his team have secured further research funding to work towards establishing quinoa as a broadacre crop.

“We are extremely excited to support this important research”, said Dr Bettina Berger, Scientific Director at The Plant Accelerator®. “As part of this collaborative project, The Plant Accelerator® will perform two screening runs of a diversity panel in the second half of 2017 to identify the genetic basis of salt tolerance in quinoa”.

Further reading:

The full published study in Nature. doi:10.1038/nature21370

KAUST An Integrated Repository for Population Genomics in genus Chenopodium

BBC News online article

Nature Middle East online article

 

2017 Calendar of Global Plant Science Events

A Calendar of Global Plant Science Events for 2017 and beyond has now been established on the Australian Plant Phenomics Facility’s website.

Quickly find out what is happening each month around the world in plant science and where, then be sure to check back in regularly for updates (why not bookmark the page as a ‘favourite’).

If you don’t already follow our blog, be sure to subscribe to receive the latest APPF updates and research news.