The Australian Plant Phenomics Facility has joined the Twittersphere! Join us @AustPlantPhenom.
The Australian Plant Phenomics Facility has joined the Twittersphere! Join us @AustPlantPhenom.
Resource Recovery Australia together with CSIRO, Cape York Partnership, Balkanu and Kalan Enterprises are developing new income streams for Cape York’s Aboriginal communities by producing organic soil-conditioners from an unlikely source, feral pigs, which cause vast environmental damage to native ecosystems.
A pilot project at the Australian Plant Phenomics Facility’s (APPF) Adelaide node, tested the effect of the ‘Feraliser’ at different concentrations on tomato growth.
“The data collected using the high-throughput phenotyping Smarthouse at the APPF provided valuable insights into the effectiveness of our product. We now know Feraliser performs just as well as the leading organic soil-conditioners currently on the market,” said Emmaline Froggatt from Resource Recovery Australia.
“Feraliser is very much at the start-up phase of development so costs are a big issue for us. The Australian Plant Phenomics Facility provided the information we needed without the expense of a full field trial.”
Find out more about Resource Recovery Australia.
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%.
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.
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.
Five students from Australian National University‘s (ANU) TechLauncher program are receiving valuable hands-on industry experience at the Australian Plant Phenomics Facility‘s (APPF) Canberra node at the CSIRO for the next two semesters.
Co-tutored by Warren Creemers (Software Team Leader), Vidya Bala (Software Engineer – data) and Robert Fulton (Software Engineer – web development), the team will work to develop a front-end and data annotation tool for the Phenomics Ontology Driven Data and metadata repository, PODD.
The aim of PODD is to provide a search engine and statistical analysis for phenomics experiments, enabling scientists to quickly filter experiments and measurements against large, historical collections from the APPF as well as datasets from the phenomics community. Users will be able to quickly find the specific metadata they are looking for across several experiments and trials, the links to data locations and documentation, and retrieve the datasets they require for validation or testing new analysis techniques from one place without having to repeat experiments or search for missing metadata. PODD also allows users to share their experiments with the phenomics community, organise metadata and experiments in a standardised manner (matching international phenomics standards), and retrieve all the required metadata for publications in a standardised format.
This tool is part of a national initiative to increase the discoverability of data generated within research institutions across Australia to facilitate data re-use.
We wish a warm welcome to ANU TechLauncher students Xiongpan Zhang and Liwei He (preparing a Bachelor of Information Technology, ANU), Haitian Zhang and Yanlin Liu (preparing a Master of Computing, ANU) and Zihao Wang (preparing a Bachelor of Advanced Computing, ANU).
For more information contact Warren Creemers.
The Australian Plant Phenomics Facility (APPF) knows no bounds, developing new technologies to ensure that the facility remains at the international forefront of plant science.
We can capture an image of a plant with ease, but how many megapixels does it take to image a forest? Dr Tim Brown would tell you it is 780 megapixels.
Tim and Prof Justin Borevitz from the APPF’s node at ANU have developed a “Gigavision” camera that takes hourly panoramic images made up of 200 x 18MP DSLR photos to create a 780 megapixel image of the forest.
What can a researcher do with this massive image you might ask? The resolution of the image allows researchers to track daily, seasonal and diurnal variation (plant behaviours) in the forest, tree and even leaf levels for thousands of trees in each forest.
Sensing and monitoring tools the APPF is developing at the research forest can be applied to other field ecosystems, such as commercial forests and national parks. Other tools include a pipeline to convert drone flight information into 3D models. APPF staff are available to help individual researchers or research groups set up these field tools at their own field sites.
The ANU research forest at the arboretum is available to national and international researchers for their own field experiments in a unique environment. All data is available for research use upon request.
For more information contact Tim Brown.
We love visits from our global plant science community, so it was a treat to host Ruth Bastow, Executive Director of the Global Plant Council (GPC), this week.
While she was here, we took the opportunity to ask a few quick questions:
Ruth, could you tell us a little bit about the GPC?
The GPC is a not-for-profit coalition of national, regional, and international societies and affiliates representing thousands of plant, crop, agricultural, and environmental scientists. We bring together all those involved in plant and crop research, education and training, to provide a body that can speak with a single, strong voice in the policy and decision-making arena, and to promote plant science research and teaching around the world.
What do you do there?
As Executive Director of the GPC I am responsible for the day to day management of the organisation.
What is the reason for your visit here?
To meet up and discuss GPC initiatives with colleagues here at the University of Adelaide, to further develop current collaborations and hopefully initiate new ones.
For example the Australian Plant Phenomics Facility (APPF) is partner of the Diversity Seek Initiative (DivSeek). DivSeek is a global community driven effort consisting of a diverse set of partner organisations have voluntarily come together to enable breeders and researchers to mobilise a vast range of plant genetic variation to accelerate the rate of crop improvement and furnish food and agricultural products to the growing human population. DivSeek brings together large-scale genotyping and phenotyping projects, computational and data standards projects with the genebanks and germplasm curators. The aim is to establish DivSeek as a hub to connect and promote interactions between these players and activities and to establish common state-of-the-art techniques for data collection, integration and sharing. This will improve the efficiency of each project by eliminating redundancy and increasing the availability of data to researchers around the world to address challenges in food and nutritional security, and to generate societal and economic benefit.
So, whilst I am here, I will be learning about how the APPF team collate and analyse their data and try and understand how the approaches here could be translated into solutions for the wider community. For example, the Zegami platform used in the high-throughput phenotyping Smarthouses™ at the Adelaide node is a useful visualisation tool that could benefit others.
Where else have you visited?
Whilst I am here in Australia I have been working with colleagues in Canberra including Prof Barry Pogson who is currently the chair of the Global Plant Council, Dr Xavier Sirault (APPF node based at CSIRO), Prof Justin Borevitz (APPF node based at ANU), and Dr Norman Warthmann. I will also be taking time to visit friends in Sydney and on the Central Coast.
Where do you see plant phenomics research in 5-10 years time?
High throughput and field based phenotyping has seen huge transformational change in the last decade and in the next 5-10 years I hope that it will start to become part of the everyday toolkit of plant science researchers in the way that genomics has.
If you could solve one plant science question what would it be?
I would actually like to try and solve a social/conceptual problem that effects science rather than an actual biological question and that is the sharing of data, information, knowledge and best practice. The sharing of scientific theories, including experimental data and observations has been a core concept of the scientific endeavour since the enlightenment. Sharing allows others to evaluate research (peer review), to identify errors, and allow ideas to be corroborated, invalidated and built upon. It also facilitates the transmission of concepts and theories to a wider audience and that will hopefully inspire others to get involved in science, contribute ideas and further our understanding of the world around us.
However, the current systems of reward and evaluation in science; lack of appropriate mechanisms, standard and infrastructures to easily share and access information; and in some cases the debilitating effects of ‘IP thickets’ can act as a barrier to ‘open science’. It is not all bad news. In the last decade a number of changes at the government, funder, publisher and institutional level have promoted and facilitated the concept of open science. However, if science is to be a truly open endeavour it will require a change in mind-set at many levels to migrate towards a culture where open data is the norm. Without this we will not be able to fully realise the investment in research, in terms of both finance provided and the time and intellectual contribution of the individual involved, and contribute to developing solutions that will help ameliorate current global problems.
When I am not working I am?
Walking the dog or gardening and generally enjoying the beauty of my home in South Wales in the UK.
If you could have one super power what would it be?
For my work it would probably be telepathy or omnilinguism, as most problems seems to arise from lack of understanding or miscommunication at some level, so these would be very helpful superpowers. From a personal perspective perhaps the ability to predict the future would be good.
Do you have an exceptional plant science research project destined to deliver high impact outcomes for Australian agriculture? Do you need access to plant phenotyping capabilities?
The Phenomics Infrastructure for Excellence in Plant Science (PIEPS) scheme is open to all publicly funded researchers. Emphasis is placed on novel collaborations that bring together scientists preferably from different disciplines (e.g. plant physiology, computer science, engineering, biometry, quantitative genetics, molecular biology, chemistry, physics) and from different organisations, within Australia or internationally, to focus on problems in plant science.
The PIEPS scheme involves access to phenotyping capabilities at the Australian Plant Phenomics Facility (APPF) at a reduced cost to facilitate exceptional research projects. Researchers will work in partnership with the APPF to determine experimental design and optimal use of the equipment. Our team includes experts in agriculture, plant physiology, biotechnology, genetics, horticulture, image and data analysis, mechatronic engineering, computer science, software engineering, mathematics and statistics.
Applications are assessed in consultation with the APPF’s independent Scientific Advisory Board. Selection is based on merit.
This is an outstanding opportunity to gain access to invaluable expertise and cutting edge technology to accelerate your research project and make a real impact in plant science discovery.
Applications close: 30 September 2017
For more information and to apply: APPF Phenomics Infrastructure for Excellence in Plant Science (PIEPS)