non-destructive plant research

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.

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.

More salad please!

With indoor-vertical farming on the rise, lettuce production can be customised more than ever, by choosing the right varieties, temperature, lighting and nutrient supply to produce the leaves consumers want. Achieving this goal requires optimisation of numerous components and a recent collaborative study between the USA and Australia, published in Frontiers in Plant Science, has proven optical sensors can be used to evaluate lettuce growth, color and health non-destructively.

The research team, Ivan Simko and Ryan Hayes from the US Department of Agriculture and Robert Furbank from the ARC Centre of Excellence for Translational Photosynthesis and formerly Australian Plant Phenomics Facility – High Resolution Plant Phenomics Centre, designed the study to test the feasibility of using optical sensors for physiological evaluation of lettuce plants in early stages of their development. The method developed can help in breeding programs and optimising farming practices to meet the requirements of an increasingly demanding market.

Read the full study, Non-destructive phenotyping of lettuce plants in early stages of development with optical sensors, published in Frontiers in Plant Science, here.

Or read the abstract here:

Abstract

Rapid development of plants is important for the production of ‘baby-leaf’ lettuce that is harvested when plants reach the four- to eight-leaf stage of growth. However, environmental factors, such as high or low temperature, or elevated concentrations of salt, inhibit lettuce growth. Therefore, non-destructive evaluations of plants can provide valuable information to breeders and growers. The objective of the present study was to test the feasibility of using non-destructive phenotyping with optical sensors for the evaluations of lettuce plants in early stages of development. We performed the series of experiments to determine if hyperspectral imaging and chlorophyll fluorescence imaging can determine phenotypic changes manifested on lettuce plants subjected to the extreme temperature and salinity stress treatments. Our results indicate that top view optical sensors alone can accurately determine plant size to approximately 7 g fresh weight.

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Comparison of the size and the colour of plants cultivated at optimal (OPT), low (COLD) and high (HOT) temperatures (experiment 3). Plants were initially grown at OPT for 10 days and the either continuously kept in OPT or transferred to COLD or HOT for 8 days. Sides of the square pots are 68mm long.

Hyperspectral imaging analysis was able to detect changes in the total chlorophyll (RCC) and anthocyanin (RAC) content, while chlorophyll fluorescence imaging revealed photoinhibition and reduction of plant growth caused by the extreme growing temperatures (3 and 39°C) and salinity (100 mM NaCl). Though no significant correlation was found between Fv/Fm and decrease in plant growth due to stress when comparisons were made across multiple accessions, our results indicate that lettuce plants have a high adaptability to both low (3°C) and high (39°C) temperatures, with no permanent damage to photosynthetic apparatus and fast recovery of plants after moving them to the optimal (21°C) temperature. We have also detected a strong relationship between visual rating of the green- and red-leaf color intensity and RCC and RAC, respectively. Differences in RAC among accessions suggest that the selection for intense red color may be easier to perform at somewhat lower than the optimal temperature.

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Genomic position of the quantitative trail locus (QTL) for light green colour (qLG4) on linkage group 4. Visual rating of the green colour intensity was performed on adult plants in field, while the relative chlorophyll content (RCC) was determined from hyperspectral reflectance measured on cotyledons of seedlings cultivated in plastic boxes (experiment 7). The orange line parallel with the linkage map shows the significance threshold (a = 0.05). The allele for light green colour and low RCC originates from cv. La Brilliante. Detailed description of the linkage map for this population and its construction was published previously (Hayes et al., 2014; Simko et al., 2015b). Distance in cM is shown on the right site of the linkage map. LOD, logarithm of odds.

This study serves as a proof of concept that optical sensors can be successfully used as tools for breeders when evaluating young lettuce plants. Moreover, we were able to identify the locus for light green leaf color (qLG4), and position this locus on the molecular linkage map of lettuce, which shows that these techniques have sufficient resolution to be used in a genetic context in lettuce.

Citation

Simko I, Hayes RJ and Furbank RT (2016) Non-destructive Phenotyping of Lettuce Plants in Early Stages of Development with Optical Sensors. Front. Plant Sci. 7:1985. doi: 10.3389/fpls.2016.01985

 

 

Getting to the root of the problem wins

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Congratulations to Olivia Cousins, one of the Adelaide-Nottingham PhD students, who won the student poster prize at a joint conference between Soil Science Australia and New Zealand Soil Science Society, held in Queenstown, NZ recently.

Olivia’s poster, which included co-authors from The University of Adelaide, The University of Nottingham and The Plant Accelerator® at the Australian Plant Phenomics Facility, was one of approximately 100 posters presented at the conference. The award also includes a cash prize for Olivia.

We announced Olivia’s study here in our blog in May. The aim of her study was to quantify the impact of different soil moisture regimes and increasing levels of soil nitrogen supply on shoot and root response in wheat plants. Olivia’s experiment utilised the DroughtSpotter, a precision irrigation platform allowing accurate and reproducible water application for drought stress or related experiments. She also used the facility’s PlantEye laser scanner to non-destructively measure plant growth.

Olivia plans an exciting move to Nottingham in 2018 to continue her research including root traits and responses across different wheat species.

To view Olivia’s poster… soilecology.org/conference-posters.

The Australian Plant Phenomics Facility is available to all researchers and/or industry. For bookings please contact Dr Trevor Garnett.