australian plant phenomics facility

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.

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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.

 

Drought knows no borders

The Australian Plant Phenomics Facility (APPF) was delighted to welcome His Excellency Mr Mohamed Khairat, Ambassador of The Arab Republic of Egypt, to its Adelaide node recently.

Egyptians share our love of wheat, however, they are heavily reliant on wheat imports which are struggling to keep up with demand. As a remedy, 1.5 million hectares of Egyptian land has been set aside for local wheat production, but there are challenges ahead. Egyptian wheat growers suffer from the same yield limiting issues of heat and drought as we do here in southern Australia.

While touring the facility, His Excellency shared his enthusiasm for future collaboration with the APPF’s Dr Trevor Garnett.

“There is a wealth of knowledge and experience at the APPF and the Waite Campus of the University of Adelaide in plant phenotyping and wheat production. His Excellency sees exciting opportunities for Egyptian scientists and PhD students to collaborate on research and share ideas on how to improve this essential crop”, said Dr Garnett.

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His Excellency Mr Mohamed Khairat, Ambassador of The Arab Republic of Egypt (pictured right) talks with Dr Trevor Garnett in the DroughtSpotter greenhouse at The Plant Accelerator®, Australian Plant Phenomics Facility (Adelaide node)

 

Major investment in plant root phenotyping to answer key questions

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3-D image of root architecture – Lynch Laboratory, The Pennsylvania State University, USA

It all starts in the roots

Australian agriculture operates in a largely harsh, resource limited (nutrients, water) environment so the role of plant roots is even more vital to crop performance.

While advances in technology have resulted in a tenfold increase in crop productivity over the past century, soil quality has declined. Advanced root systems that increase soil organic matter can improve soil structure, fertiliser efficiency, water productivity, crop yield and climate resilience, while mitigating topsoil erosion — all of which provide near-term and sustained economic value.

It is acknowledged within the international plant science and phenotyping community that root phenotyping is a critical component for crop improvement, but no ideal hardware solution has been developed yet. There is always a compromise between destructive and non-destructive measurement, throughput and resolution, and ultimately, cost.

Recognition of these challenges and increased research investment to find the answers is now coming to the fore in international plant science.

USD $7 million for plant root research granted

Researchers in Penn State’s College of Agricultural Sciences have just received a USD $7 million grant from the U.S. Department of Energy’s Advanced Research Projects Agency-Energy, or ARPA-E, to design a low-cost, integrated system that can identify and screen for high-yielding, deeper-rooted crops.

The interdisciplinary team, led by Jonathan Lynch, distinguished Professor of Plant Nutrition, will combine a suite of technologies designed to identify phenotypes and genes related to desirable root traits, with the goal of enhancing the breeding of crop varieties better adapted for nitrogen and water acquisition and carbon sequestration.

“With ARPA-E’s support, we plan to create DEEPER, a revolutionary phenotyping platform for deeper-rooted crops, which will integrate breakthroughs in non-destructive field phenotyping of rooting depth, root modeling, robotics, high-throughput 3D imaging of root architecture and anatomy, gene discovery, and genomic selection modeling,” Lynch said.

“ARPA-E invests in programs that draw on a broad set of disciplines and require the bold thinking we need to build a better energy future,” said ARPA-E Director, Ellen D. Williams.

The project is part of ARPA-E’s Rhizosphere Observations Optimizing Terrestrial Sequestration, or ROOTS, program, which is aimed at developing crops that enable a 50 percent increase in carbon deposition depth and accumulation, while also reducing nitrous oxide emissions (a contributor to greenhouse gas) by 50 percent and increasing water productivity by 25 percent.

Read the full article, by Charles Gill from The Pennsylvania State University, here.

UDC Plant Science Centre

Through a € 1.3m investment from Science Foundation Ireland, the Integrated Plant Phenomics and Future Experimental Climate Platform has been established at University College Dublin (UCD) in Ireland. The combination of infrastructure and facilities available to researchers will represent the first of its kind globally.

The platform will be housed in the same building at UCD allowing seamless transition from experiment to scanner. It will consist of a large capacity 3D X-ray CT scanner which uses X-rays taken from multiple angles to non-destructively build-up a 3D image of whole plants and their internal structures, both above and below ground with fast (minutes) scan times and six reach-in, high-spec plant climate chambers with full (de)humidification capabilities. Novel custom additions will include full-spectrum variable LEDs, enabling more accurate representation of sunlight conditions experienced by crops under field conditions. The chambers will integrate thermal imaging to continuously capture leaf temperature and inferred ecophysiological processes (gas exchange).

Breakthroughs in crop/plant/soil/food science will be possible, particularly below ground and at night, because the consequences of climate change or new crop breeds on below-ground /night-time processes have not been readily accessible before the advance of X-ray CT, thermal imaging and integration of these components into an infrastructure platform.

The Centre unites a large number of UCD plant scientists that investigate fundamental and applied aspects of plant science and work alongside industry in exploiting research breakthroughs.

Read more here.

Danforth Plant Science Center

A new industrial-scale X-ray Computed Tomography (X-ray CT) system at the Danforth Plant Science Center in Missouri, USA, is the first of its kind in the U.S. academic research sector dedicated to plant science and can provide accelerated insight into how root systems affect plant growth. The technology was established in late July 2016 under a collaborative multi-year Master Cooperation Agreement with Valent BioSciences Corporation (VBC) and is also supported with funds from a recent National Science Foundation grant.

“X-ray imaging has been a mainstay in medical and industrial research and diagnostics for many decades, yet it is rarely used in plant science,” said Chris Topp, Ph.D., assistant member of the Danforth Center and principal investigator for the project. “The X-ray CT system will allow us to ‘see’ roots in soil and study plants as a connected system of roots and shoots growing in diverse environments.”

“This system is unlike any other in the United States,” said said Keith Duncan, research scientist in the Topp Lab and manager of the new system. “It gives us a great deal of control over the X-ray conditions and will allow us to gather structural data on any object we put into the machine. It provides us with an internal look at not only the root systems, but what’s going on inside the stem and other parts of the plant without taking invasive measures such as removing the plant from the ground or cutting into it.”

In addition to grain crops, this project will also advance research in root and tuber crops such as cassava, potato, groundnut and others that are important for food security in many regions around the globe, but are especially hard to study.

The project combines state-of-the-art technology with computational analysis, quantitative genetics and molecular biology to understand root growth and physiology to assist researchers in understanding roots as they grow in real time in real soil. Both Topp and Duncan agree, this collaboration is just the tip of the iceberg.

“I expect that in a short time, the X-ray imager will catalyze numerous research projects among Danforth Center, St. Louis, national and international researchers that were previously not possible,” said Chris Topp, Ph.D., assistant member of the Danforth Center and principal investigator for the project.

Read more here. Learn more about the partnership and X-ray system here.

Hounsfield Facility for Rhizosphere Research

The Hounsfield Facility for Rhizosphere Research is a unique platform established with €3.5 million in funding from the European Research Council, the Wolfson Foundation, BBSRC, and the University of Nottingham. It accommodates ERC funded postdoctoral researchers and PhD students, X-ray imaging research equipment and automated growth facilities in one state-of-the-art building and fully automated greenhouse complex.

A key impediment to genetic analysis of root architecture in crops has been the ability to image live roots in soil non-invasively. Recent advances in microscale X-ray Computed Tomography (μCT) now permit root phenotyping. However, major technical and scientific challenges remain before μCT can become a high throughput phenotyping approach.

This unique high throughput root phenotyping facility exploits recent advances in μCT imaging, biological image analysis, wheat genetics and mathematical modelling to pinpoint the key genes that control root architecture and develop molecular markers and new crop varieties with improved nutrient and water uptake efficiency.

The facility’s ambitious multi-disciplinary research program will be achieved through six integrated work packages. The first 3 work packages were designed create high-throughput μCT (WP1) and image analysis (WP2) tools that will be used to probe variation in root systems architecture within wheat germplasm collections (WP3). Work packages 4-6 will identify root architectures that improve water (WP4) and nitrate uptake efficiencies (WP5) and pinpoint the genes that regulate these traits. In parallel, innovative mathematical models simulating the impact of root architecture and soil properties will be developed as tools to assess the impact of architectural changes on uptake of other nutrients in order to optimise crop performance (WP6).

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The Hounsfield Facility for Rhizosphere Research, University of Nottingham, UK