CSIRO

New discovery to accelerate development of salt-tolerant grapevines

Grapes-on-vine-for-blog

A recent discovery by Australian scientists is likely to improve the sustainability of the Australian wine sector and significantly accelerate the breeding of more robust salt-tolerant grapevines.

With funding from Wine Australia, a team of scientists from the ARC Centre of Excellence in Plant Energy Biology at the University of Adelaide and CSIRO Agriculture and Food identified genes expressed in grapevine roots that limit the amount of sodium – a key component of salt – that reaches berries and leaves.

The research has been published this week in the journal New Phytologist.

‘Berries that contain too much sodium may be unsuitable for wine production and this can lead to vineyards remaining unpicked, resulting in financial losses for vineyard owners,’ says Dr Sam Henderson, co-first author of the study, from the University of Adelaide.

‘We set out to determine why some grapevines accumulate salt and others don’t, and found a specific mutation in a sodium transport protein found in grapevine roots, which prevents it from working effectively. This leads to more salt leaking into the shoots of vines from the soil,’ Dr Henderson says.

While low levels of salt can improve the flavour of wine, in excess it can lead to unpalatable tastes, reduce fruit yield and damage the long-term health of grapevines – it is a problem experienced in premium wine regions around the world. In Australia’s broader agriculture, food and wine sectors, issues caused by salinity have been estimated to cost in excess of $1 billion each year.

‘By comparing the DNA of different grapevines we identified a specific gene that is associated with sodium exclusion from shoots,’ says co-first author Dr Jake Dunlevy from CSIRO.

‘This discovery has allowed us to develop genetic markers that are being used to breed more salt-tolerant grapevine rootstocks, allowing new genotypes to be screened at the seedling stage rather than through lengthy and expensive field-based vineyard trials.’

‘Traditionally, winegrape rootstocks have been developed in wine producing regions in the United States and Europe. This new research supports a breeding program to combine multiple beneficial traits in grapevines using conventional breeding, to develop robust rootstocks specifically for Australian conditions and support the local wine sector’s sustainability well into the future,’ says Dr Liz Waters, Wine Australia’s General Manager Research, Development and Extension.

A family of 40 hybrid rootstocks, together with both parents, were screened for leaf sodium (Na+) exclusion ability at the Australian Plant Phenomics Facility‘s Adelaide node as part of the research.

The research was led by Dr Mandy Walker, CSIRO, and Professor Matthew Gilliham, University of Adelaide, who are continuing to collaborate on additional factors that will further improve grapevine salt tolerance, such as the exclusion of chloride.

Story shared by ARC Centre of Excellence Plant Energy Biology.

A presidential visit from Sri Lanka

The Australian Plant Phenomics Facility’s (APPF) node based at the CSIRO in Canberra was thrilled to host His Excellency Maithripala Sirisena, President of Sri Lanka, and his delegation during their visit to Australia, 24 – 26 May.

This was the first time a Sri Lankan Head of State has made a state visit to Australia and marks the 70th anniversary of diplomatic relations between the two countries.

“President Sirisena’s visit will be an opportunity to advance key areas of bilateral cooperation, including education, defense, science and technology, economic development, medical research and the fight against people smuggling,” Australian Prime Minister, Malcolm Turnbull said in a statement before their meeting.

5D3_3803_JamieScarrow

Dr Xavier Sirault (right) demonstrates the PlantScan 3D imaging platform to President Sirisena (left) and his delegation at the Australian Plant Phenomics Facility’s node based at the CSIRO in Canberra.

As part of the Canberra visit, the President, who also holds the Cabinet portfolio of Environment, visited the APPF to learn more about plant phenomics which is being used to help tackle the major global challenges of future food production, sustainable agriculture, biodiversity conservation and climate change. The world class facility focuses on deep phenotyping (delving into metabolism and physiological processes within the plant) and reverse phenomics (dissection traits to discover their mechanistic basis).

5D3_3731_JamieScarrow

Dr Sirault discusses the benefits of the Phenomobile Lite with President Sirisena

Dr Xavier Sirault, Director of the node, shared a number of the facility’s highlights including PlantScan (a 3D imaging platform), ArduCrop (a wireless infrared canopy temperature sensor network), HeliPod (airborne imaging), Phenomobile Lite (an advanced mobile research platform used in non-destructive, high throughput plant phenotyping in the field) and growth chambers.

The President also visited the National Arboretum in Canberra, where he planted a sapling of Mahogany (Toona ciliata) and the ANU-CSIRO Centre for Genomics, Metabolomics and Bioinformatics.

“Sri Lanka can learn a lot from these centres about preserving environment, increasing forest density, and agriculture and food crop research,” said His Excellency Somasundaram Skandakumar, High Commissioner of Sri Lanka.

To find out more about Phenomobile Lite or any other services offered by the APPF node at CSIRO Canberra, please contact Dr Xavier Sirault.

Find out more about the Australian Plan Phenomics Facility.

Taking five with… Michael Schaefer

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…

Michael Schaefer, PhD

Tell us a little about where you work within the APPF.

I am based at the CSIRO node of the APPF in Canberra. This centre focuses on “deep phenotyping” (delving into metabolism and physiological processes within the plant) and “reverse phenomics” (dissecting traits to discover their mechanistic basis). Here, next generation research tools are being developed and applied to probe plant function and performance, under controlled conditions and in the field.

What do you do there?

I’m a Research Scientist and Team Leader of the Translational Phenomics and Services team. My team looks after all of the new projects that come into our node of the APPF, from dealing with clients directly, to designing experiments based on the client’s needs, right through to providing the final data products and support with analysis.

What is the best part of your job?

As one of the newest team members, the best part of my job has been meeting and working with new people and dealing with new projects in different plants and crops. Every case is different, so designing and running each project is unique which provides a lot of variety.

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

I think in 5-10 years’ time plant phenomics research will be very different. We can already see that sensors and technology are getting smaller, faster and cheaper. I think much of what we do with large sensors (lidar for example) will be replaced by much smaller handheld devices or drones that will process data on the fly and give you a result straight away. This will affect all areas of science, not just plant science, so I think it will just be something that we have to adjust to.

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

Somewhere during my undergraduate degree. I was doing straight science, biology, chemistry and physics – very broad – and then I started making links with how physics could be related to the environment (i.e. plants etc.). This seemed to make more sense to me, as I could see the application and how it could directly affect people now, rather than working on something theoretical that may or may not ever be used.

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

For me, I’m really interested in pastures, so it would be the holy grail to be able to accurately, remotely measure above-ground biomass and split it into the green and senesced fractions.

Pic of Michael Schaefer for blog

Michael Schaefer at the western entry of Angkor Wat, Cambodia

“When I am not working I am…”

At home spending time with my wife Ali and daughter Emilia, or outdoors playing cricket, golf or fishing.

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

Good question…. being able to bend time and space like Dr. Strange. That would be pretty cool!

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

Fishing guide!

What is your most treasured possession?

They’re not a possession but my family are the most important to me.

If you could have dinner with two famous people who would they be?

Barack Obama and Tiger Woods.

What’s the one thing about you that would surprise people?

I have my private aeroplane pilot licence. I did my pilot training while I was doing my PhD – not that I get to fly much these days.

The APPF provides academic and commercial researchers with expert advice and access to high quality plant growth facilities and state-of-the-art automated phenotyping capabilities in controlled environments and in the field. We provide a suite of analytical tools to support high-throughput phenotyping and deep phenotyping in either controlled environments or in the field. Our dedicated team of experts provide consultation on project design and high quality customer support. If you would like to know more about our services and how we can support your plant science research, please contact us!

Accurate field canopy temperature measured in seconds

A method for cost-effective, reliable and scalable airborne thermography has been developed, resolving a number of challenges surrounding accurate high-throughput phenotyping of canopy temperature (CT) in the field, such as weather changes and their influence on more time consuming measurement methods. Utilising a manned helicopter carrying a radiometrically-calibrated thermal camera, thermal image data is captured in seconds and processed within minutes using custom-developed software; an invaluable advantage for large forward genetic studies or plant breeding programs.

The method and research results, by a collaboration between CSIRO Agriculture and Food, the Australian Plant Phenomics Facility – High Resolution Plant Phenomics Centre, CSIRO Information Management and Technology, and the ARC Centre of Excellence for Translational Photosynthesis were published recently in Frontiers in Plant Science.

Read the full study“Methodology for high-throughput field phenotyping of canopy temperature using airborne thermography”, here or the abstract below.

field-canopy-temp-blog-image-2

Airborne thermography image acquisition and processing pipeline. Total time to acquire and process images for an experiment comprising 1,000 plots of size 2 x 6 m is ca. 25 min. (A) Image acquisition with helicopter. The images are recorded on a laptop and the passenger, left, provides real time assessment of the images and feedback to the pilot. This step takes < 10 s for an experiment comprising 1,000 plots of size 2 x 6 m. (B) Screenshot of custom-developed software called ChopIt. ChopIt is used for plot segmentation and extraction of CT from each individual plot for statistical analysis. This step takes ca. 20 min for an experiment comprising 1,000 plots of size 2 x 6 m.

field-canopy-temp-blog-image-1

Airborne thermography image acquisition system comprising a helicopter cargo pod with thermal camera and acquisition kit mounted on the skid of a Robinson R44 Ravel helicopter. Photo insert shows the inside of the helicopter cargo pod with arrow denoting FLR® SC645 thermal camera: ±2°C or ±2% of reading; < 0.05°C pixel sensitivity; 640×480 pixels; 0.7 kg without lens.

Abstract

Lower canopy temperature (CT), resulting from increased stomatal conductance, has been associated with increased yield in wheat. Historically, CT has been measured with hand-held infrared thermometers. Using the hand-held CT method on large field trials is problematic, mostly because measurements are confounded by temporal weather changes during the time required to measure all plots. The hand-held CT method is laborious and yet the resulting heritability low, thereby reducing confidence in selection in large scale breeding endeavors. We have developed a reliable and scalable crop phenotyping method for assessing CT in large field experiments. The method involves airborne thermography from a manned helicopter using a radiometrically-calibrated thermal camera. Thermal image data is acquired from large experiments in the order of seconds, thereby enabling simultaneous measurement of CT on potentially 1000s of plots. Effects of temporal weather variation when phenotyping large experiments using hand-held infrared thermometers are therefore reduced. The method is designed for cost-effective and large-scale use by the non-technical user and includes custom-developed software for data processing to obtain CT data on a single-plot basis for analysis. Broad-sense heritability was routinely >0.50, and as high as 0.79, for airborne thermography CT measured near anthesis on a wheat experiment comprising 768 plots of size 2 × 6 m. Image analysis based on the frequency distribution of temperature pixels to remove the possible influence of background soil did not improve broad-sense heritability. Total image acquisition and processing time was ca. 25 min and required only one person (excluding the helicopter pilot). The results indicate the potential to phenotype CT on large populations in genetics studies or for selection within a plant breeding program.

Citation:  Deery DM, Rebetzke GJ, Jimenez-Berni JA, James RA, Condon AG, Bovill WD, Hutchinson P, Scarrow J, Davy R and Furbank RT (2016) Methodology for High-Throughput Field Phenotyping of Canopy Temperature Using Airborne Thermography. Front. Plant Sci. 7:1808. doi: 10.3389/fpls.2016.01808

 

 

Hello, ni hau, hola, guten tag, marhaba, bonjour… knowledge sharing the key to plant science success

The Australian Plant Phenomics Facility (APPF) is a national facility, available to all plant scientists, offering access to infrastructure that is not available at this scale or breadth in the public sectors anywhere else in the world.

Our three nodes in Adelaide and Canberra frequently welcome international research, industry and government guests to tour facilities and share knowledge in plant phenomics. Encouraging and supporting a global community focused on providing better nutrition and food security is key to the APPF vision we uphold.

Recently the CSIRO based HRPPC node of the APPF hosted a VIP visit by the Secretary of the Department of Industry, Innovation and Science, Glenys Beauchamp, CSIRO CEO, Larry Marshall, and the Canadian High Commissioner, His Excellency Paul Maddison.

jamie_scarrow_canadahighcomm-at-appf-act

Larry Marshall (CEO, CSIRO), Glenys Beauchamp (Secretary, Department of Industry, Innovation and Science) and His Excellency Paul Maddison (Canadian High Commissioner) in front of a Phenomobile Lite at the APPF HRPPC           (Image courtesy of the CSIRO)

Hosted by Drs Xavier Sirault and Jose Jimenez-Berni, the visitors observed aspects of the work done by the APPF’s HRPPC in the controlled environment and had the opportunity to see first-hand one of the centre’s purpose built and designed Phenomobile Lite buggies which are used in the field for capturing plant traits.

The group discussed an overview of the range of research and development activities and issues facing Australia in science and technology and the Canadian High Commissioner shared his interested in areas of existing and potential collaboration between Australia and Canada.

We welcome and encourage engagement with the international plant science community. If you would like to visit one of our sites, discuss your plant phenomics research or book one of our facilities, please contact us – we love plant science!