non-destructive plant phenotyping

The hunt for high salt tolerant barley crops gets closer

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Soil salinity severely impacts crop growth and yield. Within minutes of exposure to salt, cell expansion, leaf expansion, photosynthesis, transpiration and tillering are reduced. When salts accumulate to toxic concentrations in the shoot, especially in older leaves, a secondary inhibition of growth occurs through damage to the plant’s metabolism and ion imbalances. These effects occur weeks to months following salt application.

Plants have evolved numerous mechanisms to detect and respond to the effects of salt stress including a range of signal transduction mechanisms. However, investigating the maintenance of growth under salt stress has been limited by the lack of techniques that allow nondestructive measurements of plant growth through time. The resources and technologies now exist to phenotype many genotypes and identify those with high shoot ion-independent and shoot ion-dependent tolerance under greenhouse conditions.

Barley is one of the more salt-tolerant crops, able to grow in higher concentrations of salt than wheat, rice or maize. However, the growth of barley is still significantly affected by salinity. A better understanding of the genetic variation for salinity tolerance mechanisms within barley cultivars is required for future breeding improvement.

In a study by Stuart Roy and his international collaborators, nondestructive and destructive measurements are used to evaluate the responses of 24 predominately Australian barley (Hordeum vulgare L.) lines at 0, 150 and 250 mM NaCl. Considerable variation for shoot tolerance mechanisms not related to ion toxicity (shoot ion-independent tolerance) was found, with some lines being able to maintain substantial growth rates under salt stress, whereas others stopped growing. Hordeum vulgare spp. spontaneum accessions and barley landraces predominantly had the best shoot ion independent tolerance, although two commercial cultivars, Fathom and Skiff, also had high tolerance. The tolerance of cv. Fathom may be caused by a recent introgression from H. vulgare L. spp. spontaneum.

This study shows that the most salt-tolerant barley lines are those that contain both shoot ion-independent tolerance and the ability to exclude Na+ from the shoot (and thus maintain high K+:Na+ ratios).

Read the full paper, ‘Variation in shoot tolerance mechanisms not related to ion toxicity in barley’, here (Functional Plant Biologyhttps://doi.org/10.1071/FP17049).

To find out how the Australian Plant Phenomics Facility can help facilitate your plant science research visit our website.

Growing rice faster – uncovering the triggers behind early canopy closure

By combining high-resolution image-based phenotyping with functional mapping and genome prediction, a new study has provided insights into the complex genetic architecture and molecular mechanisms underlying early shoot growth dynamics in rice.

The more rapidly leaves of a plant emerge and create canopy closure, the more successful the plant, in establishment, resource acquisition and ultimately yield. An early vigor trait is particularly important in aerobic rice environments, which are highly susceptible to water deficits. The timing of developmental ‘triggers’ or switches that initiate tiller formation and rapid exponential growth are a critical component of this trait, however, searching for the switch that initiates this growth has proven challenging due to the complex genetic basis and large genotype-by-environment effect, and the difficulty in accurately measuring shoot growth for large populations.

“The availability of large, automated phenotyping platforms, such as those at Australian Plant Phenomics Facility (APPF), allow plants to be non-destructively phenotyped throughout the lifecycle in a controlled environment, and provide high resolution temporal data that can be used to examine these important developmental switches,” said PhD student, Malachy Campbell.

Malachy and team, including Bettina Berger and Chris Brien from the APPF, phenotyped a panel of ~360 diverse rice accessions throughout the vegetative stage (11-44 day old plants) at The Plant Accelerator® at APPF. A mathematical equation was used to describe temporal growth trajectories of each accession. Regions of the genome that may regulate early vigor were inferred using genome-wide association (GWA) mapping. However, many loci with small effects on shoot growth trajectories were identified, indicating that many genes contribute to this trait. GWA, together with RNA sequencing identified a gibberellic acid (GA) catabolic gene, OsGA2ox7, which could be influencing GA levels to regulate vigor in the early tillering stage.

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Dr Malachy Campell in The Plant Accelerator® at the Australian Plant Phenomics Facility’s Adelaide node

For some traits where genetic variation is controlled by a small number of loci, breeders can use MAS to identify individuals carrying the favourable locus/loci for the given trait, and select them for the next generation. For complex traits that are regulated by many loci, it becomes very difficult to detect loci that are associated with the trait. However, an alternative approach, genomic selection (GS), considers the total genetic contribution of all loci to the given trait. With this approach, loci across the genome can be used to predict the performance of individuals that have not yet been phenotyped (i.e. those in future generations). Since many loci were found to be contributing to early vigor, the team explored the possibility of using GS for improving this trait. Shoot growth trajectories could be predicted with reasonable accuracy, with greater accuracies being achieved when a higher number of markers were used. These results suggest that GS may be an effective strategy for improving shoot growth dynamics during the vegetative growth stage in rice. The approach of combining high-resolution image-based phenotyping, functional mapping and genome prediction could be widely applicable for complex traits across numerous crop species.

Read the full paper, published in The Plant Genome, here. (doi:10.3835/plantgenome2016.07.0064).

Taking five with Prof. Justin Borevitz

The three national nodes of the Australian Plant Phenomics Facility (APPF) are home to a highly talented team of plant science researchers and specialists. This passionate, cross-disciplinary team is skilled in areas such as agriculture, plant physiology, biotechnology, genetics, horticulture, image and data analysis, mechatronic engineering, computer science, software engineering, mathematics and statistics. But who are they?

Today we take five minutes to get to know…

Prof. Justin Borevitz

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Tell us about where you work within the APPF.

I lead the Canberra ANU node of the APPF. Our node is part of the Australian National University (ANU) Plant Science Division which is a world leader in plant research. In addition to the APPF, ANU Plant Sciences contains the Centre of Excellence (CoE) in Plant Energy Biology (PEB), CoE Translational Photosynthesis (CoETP) and the ANU-CSIRO Centre for Genomics, Metabolomics and Bioinformatics.

The Canberra ANU node of the APPF offers:

  • On-site phenomics and plant growth services – NextGen growth and phenotyping facilities for Australian and international researchers including greenhouses and growth chambers with timelapse imaging.
  • Genomics and bioinformatics, study design and data analysis support – analysis of phenotypic and genomics data and the opportunity to collaborate with world-class researchers in genomics, photosynthesis and bioinformatics.
  • Development and streamlining of cross-scale approaches in monitoring for scaling from lab to field, chamber to crop and forest.
  • Research and development of open source hardware and software pipelines and visualisation tools for enabling lower cost high-throughput phenotyping (HTP) and environmental monitoring.
  • A collaborative, cross-disciplinary approach to tackling the grand challenges associated with HTP and environmental monitoring.

We provide the only quarantine approved growth cabinets in Canberra for research purposes. A range of growth cabinets are available, capable of high resolution phenotyping of up to 2,000 small plants continuously in custom and climate-simulated growth environments (LED-based). Quantitative phenotypic screening for Arabidopsis and similar sized small plants can be conducted.

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Virtual reality is the new frontier in scientific visualisation. We also offer the ability to visualise a forest in virtual reality with sensor data overlays for a visually integrated understanding of the landscape. The APPF is a leader in the development of systems for visualising phenomics and environmental sensing data and point clouds in virtual and augmented reality (VR an AR). EcoVR is a virtual reality tool for recreating any forest or field site as a virtual space, where timelapse sensor and phenomics data can be overlaid on a 3-dimensional model of the landscape. VR and AR represent immense opportunities for revolutionising phenomics and education and for industry collaborations to develop new visualisation platforms for precision agriculture. These tools can help farmers understand their farming landscape and can be used by the forestry industry to understand how the landscape, environment and genetics interact to impact forest growth.

What do you do there?

I’m Scientific Director, overseeing all research projects.

What is the best part of your job?

I get the most enjoyment out of planning new experiments.

Where do you see plant phenomics research in 5-10 years time?

Digital, machine learning, interconnected sensors and farm equipment, and providing food and environmental services (carbon, water, nutrient management).

“The moment I realised I loved plant science was…”

On my dad’s farm, growing new release strawberries when I was 15 years old.

If you could solve one plant science question, what would it be?

Climate ready, high yielding crops that increase soil fertility.

“When I’m not working I am…”

You’ll find me kayaking or gardening (integrative problem solving).

If you could have one super power, what would it be?

I’d like to be able to communicate knowledge into understanding for rational decision making.

“If I wasn’t a plant scientist I would be a…”

Definitely a ski bumb!

What is your idea of absolute happiness?

My family.

What is your most treasured possession?

Again, my family.

What scares you?

Cancer, but also reaching global limits.

If you could go backwards or forwards in time, where would you go?

I’d like to see my grandfather as a child in Poland on his family farm, and my daughter as a grandmother on her urban farm.

Contact Professor Justin Borevitz

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Supporting the agricultural industry through R&D to deliver successful new products to market

Developing and bringing new agricultural products to market can be costly and time consuming for industry. Nufarm Limited recently sought the technology and expertise of the Australian Plant Phenomics Facility (APPF) to provide independent testing on potential new foliar sprays under development.

“The full service approach at the APPF, from the technology to the specialist staff, really appealed to us”, said Chad Sayer from Nufarm’s Product Strategy Group.

“The non-destructive, high-throughput phenotyping technology at the APPF gave us the ability to gain insights into our products under development that we could not achieve anywhere else. Their highly skilled, specialist team helped us design our experiments and provided invaluable advice throughout the project, right through to the data analysis.

“This has been exciting for us. Our pilot project delivered such promising results, we already have a large project underway”.

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(L) Plants undergoing spray treatment.  (R) Daily observation and analysis by the horticultural team

“We have a bespoke approach, working closely with our customers to design their experiments to deliver the best results”, said Dr Bettina Berger, Scientific Director at the Adelaide node of the APPF.

Dr Berger and her colleagues provide consultation on all projects carried out at the Adelaide node, supporting the development of the initial design and execution of the research. The specialist horticultural team set up the experiments and manage them through to completion. Customers can make use of online monitoring and access of projects throughout the experiment stage via Zegami (‘live processing’ which allows result checking on a day-to-day basis). On completion of experiments image analysis and data analysis are handled by our skilled engineering, software and statistics team. The research team then provide consultation on results and further follow-up as required.

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Plants in a Smarthouse at the Adelaide node of the APPF undergo daily image analysis throughout the experiment

The APPF is available to all publicly or commercially funded researchers. For further information or to discuss how we can support your research, please visit the APPF website for contact details. For more information about this project, contact Dr Berger.

Nufarm Limited is an Australian company. It is one of the world’s leading crop protection and specialist seeds companies, producing products to help farmers protect their crops against damage caused by weeds, pests and disease. With operations based in Australia, New Zealand, Asia, Europe and the Americas, Nufarm sells products in more than 100 countries around the world. Find out more about Nufarm here.

Zegami is a web application which allows users to filter, sort and chart data from experiments undertaken in the Smarthouses at the APPF Adelaide node, with the unique feature of being able to group that data with the corresponding images. To get a real feel for the application, we highly recommend you watch the video. Further reading here.

Solving the challenges of computer vision for plant phenotyping

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Plants in Spectral Pheno Climatron at the Australian Plant Phenomics Facility’s Canberra ANU node

A ‘Computer Vision Problems in Plant Phenotyping‘ (CVPPP) workshop will be held in conjunction with ICCV 2017 this October in Venice, Italy.

Recommended by Dr Tim Brown from the Australian Plant Phenomics Facility‘s Canberra ANU node, the goal of this third CVPPP workshop is to continue to showcase the challenges raised by and extend state-of-the-art computer vision for plant phenotyping.

Workshop date:

  • 28 October

Target audience:

  • computer vision experts interested in novel application fields, well accessible to computer vision, but different in requirements, and
  • plant phenotyping scientists with rich expertise in image processing and computer vision interested in standardisation, as exact problem formulations in fact allow defining standards.

Find out more CVPPP 2017.

ICCV 2017 (International Conference on Computer Vision) is the premier international computer vision event comprising the main conference and several co-located workshops and tutorials. The conference will be held in Venice, Italy from 22-29 October, 2017. Find out more ICCV 2017.

To discover a full calendar of unmissable plant science events for 2017 and beyond, go to ‘Events‘ on the Australian Plant Phenomics Facility’s website, or our blog.

Be sure to subscribe to our blog for more plant science news and stay connected on Twitter @AusPlantPhenom.

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