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Last chance to secure an internship – apps close tomorrow!

This is your chance to investigate your plant science questions with the support of the highly skilled Australian Plant Phenomics Facility (APPF) team and the incredible technology and infrastructure we have available.

Internships are offered at the APPF in Adelaide and Canberra for enthusiastic, highly motivated postgraduate students with a real interest in our research and technology. Current postgraduate students in the following areas are encouraged to apply:

  • Agriculture
  • Bioinformatics
  • Biology
  • Biotechnology
  • Computer Science
  • Genetics
  • Mathematics
  • Plant physiology
  • Science
  • Software engineering
  • Statistics

Interstate students are strongly encouraged to apply!

We offer postgraduate internship grants which, in general, comprise:

  • $1,500 maximum towards accommodation in Adelaide or Canberra, if required
  • $500 maximum towards travel / airfare, if required
  • $10,000 maximum toward infrastructure use

The APPF has identified a number of priority research areas, each reflecting a global challenge and the role that advances in plant biology can play in providing a solution:

  • Tolerance to abiotic stress
  • Improving resource use efficiency in plants
  • Statistics and biometry
  • Application of mechatronic engineering to plant phenotyping
  • Application of image analysis techniques to understanding plant form and function

Students proposing other topics will also be considered.

APPF postgraduate internship grants involve access to the facility’s phenotyping capabilities to undertake collaborative projects and to work as an intern with the APPF team to learn about experimental design, image and data analysis in plant phenomics.

Selection is based on merit. Applications are assessed on the basis of academic record, research experience and appropriateness of the proposed research topic. Interviews may be conducted.

Postgraduate students are encouraged to contact APPF staff prior to submitting their application to discuss possible projects.

APPLICATIONS CLOSE:  31 March 2017. For further information click here.

 

Why apply for an internship with the APPF?

Well, aside from the fact we are a pretty nice bunch…

PhD student Rohan Riley, from Western Sydney University, undertook his research at APPF’s Adelaide node (The Plant Accelerator®) after being awarded a Postgraduate Student Internship Grant with us in 2015.

His research attempted to explain the unpredictability of plant growth responses in terms of resource limitation by introducing fungal communities to plants which are isolated from soils containing high or low levels of salinity and analysing the effects on plant stress at the phenotypic level.

This is what he had to say about his experience:

”Using daily phenotyping following the application of salt stress and controlled watering-to-weight in The Plant Accelerator® allowed for an unprecedented resolution and range of plant genetic changes in response to combinations of nutrient level, salinity and two different fungal communities that would not otherwise be achievable in a regular greenhouse,” said Rohan.

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”As a PhD student with limited experience in greenhouse experiments, the highly controlled growth conditions, large-scale automation, digital imaging and software technology (high-throughput phenotyping) at The Plant Accelerator® provided me with the work-space, expertise and technical support to make a complicated experiment possible.”

“It has been an amazing experience to conduct this experiment at The Plant Accelerator®. I am walking away from the facility with a big smile on my face, an incredible dataset for my PhD research and invaluable experience in greenhouse based plant research.”

To find out more about Rohan’s research:  https://www.researchgate.net/profile/Rohan_Riley

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.

non-destruct-pheno-on-lettuce-pic-3

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

 

 

Adelaide to host 5th International Plant Phenotyping Symposium

The Australian Plant Phenomics Facility is thrilled to announce the city of Adelaide, South Australia will host the 5th International Plant Phenotyping Symposium in October 2018!

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2018 Host City, Adelaide, South Australia   (Image source: South Australian Tourism Commission)

The International Plant Phenotyping Network (IPPN) voted during its general assembly, held alongside the 4th International Plant Phenotyping Symposium in Mexico recently.

We look forward to welcoming the international plant phenotyping community to Adelaide in 2018!

 

 

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.

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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!

 

 

What the experts are saying about plant phenotyping and food security

‘It takes a village to raise a child’ states the age-old saying, but now it will take a village to feed the child as well – if we’re smart.

“Agriculture’s critical challenges of providing food security and better nutrition in the face of climate change can only be met through global communities that share knowledge and outputs; looking inward will not lead to results,” said Ulrich Schurr, Director of the Institute of Bio- and Geosciences of the Forschungszentrum Jülich and Chair of the International Plant Phenotyping Network (IPPN), speaking at the 4th International Plant Phenotyping Symposium in Mexico recently.

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Dr Jose Jimenez-Berni (keynote speaker), Dr Xavier Sirault (Co-Chair IPPN), Dr Trevor Garnett and Dr Bettina Berger from the Australian Plant Phenomics Facility at the symposium

200 world-class scientists from over 20 countries gathered from 13 to 15 December 2016 to share knowledge and technology at the symposium, co-hosted by IPPN and the Mexico-based International Maize and Wheat Improvement Center, known by its Spanish acronym, CIMMYT.

The symposium was attended by Dr Bettina Berger, Dr Trevor Garnett, Dr Xavier Sirault and Dr Jose Jimenez-Berni from the Australian Plant Phenomics Facility (APPF). Dr Sirault is also Co-Chair of the IPPN and Dr Jimenez-Berni gave a keynote lecture on field phenotyping techniques developed at the High Resolution Plant Phenomics Facility (HRPPC) node of the APPF and how they can be applied to screen for plant development including biomass and canopy architecture in the field.

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Dr Jimenez-Berni (APPF) delivering his keynote lecture at the symposium

The symposium focused on three themes:

  • Advances in Plant Phenotyping Technologies to explore the frontiers of what can be sensed remotely and other technological breakthroughs.
  • Phenotyping for Crop Improvement to consider the application of phenotyping technologies for crop improvement (breeding, crop husbandry, and estimating the productivity of agro-ecosystems).
  • Adding Value to Phenotypic Data to review how phenomics and genomics can combine to improve crop simulation models and breeding methodologies (e.g., genomic selection).

Read the full article ‘Harnessing medical technology and global partnerships to drive gains in food crop productivity’ written by Mike Listman on CIMMYT’s website.

Read more excellent plant science articles by Mike Listman here.

 

 

Drip-fed success

The Australian Plant Phenomics Facility (APPF) is pleased to announce the new DroughtSpotter precision irrigation platform has been fully tested and commissioned, and is now ready to support your plant phenomics research.

The DroughtSpotter is a gravimetric platform with precision irrigation allowing accurate and reproducible water application for drought stress or related experiments.

droughtspotter-and-cecilia-and-viviana

Left:  Wheat plants on the DroughtSpotter  –  Right:  Cecilia and Viviana from Monash University harvest sorghum plants during their research

A number of pilot projects were carried out to test the platform with excellent results.

Monash University researchers, led by Associate Professor Ros Gleadow, investigated the impacts of dhurrin (a chemical that is toxic to grazing animals) on drought tolerance in sorghum plants. Plants were grown under a range of drought stresses and then harvested throughout growth for biomass characterisation, metabolomics and transcriptomic responses.

“We found the DroughtSpotter to be an excellent platform to apply accurate, reproducible amounts of water to large numbers of individual plants for growth and compositional analysis under different levels of water limitation,”said Associate Professor Gleadow.

Led by Professor Steve Tyerman, researchers from the ARC Centre of Excellence in Plant Energy Biology at the University of Adelaide and TA EEA-CONICET Mendoza, Argentina investigated the relationship between hydraulic and stomatal conductance and its regulation by root and leaf aquaporins under water stress.

“A better understanding of these mechanisms is highly relevant to irrigation scheduling and to ensure sustainable vineyard management in a context of water scarcity” said Professor Tyerman.

“The DroughtSpotter platform allowed us to achieve precise control over soil moisture and vine water stress, which was the most critical aspect to the success of this project.”

The DroughtSpotter greenhouse is available to all publicly or commercially funded researchers. For further information, please visit the APPF website or contact Dr Trevor Garnett.

To read the DroughtSpotter pilot project reports:  “Drought Response in Low-Cyanogenic Sorghum bicolor Mutants”  and  “Investigating the relationship between hydraulic and stomatal conductance and its regulation by root and leaf aquaporins under progressive water stress and recovery, and exogenous application of ABA in grapevine”

Phenotyping takes to the skies

This year the Australian Plant Phenomics Facility (APPF) partnered with the Unmanned Research Aircraft Facility (URAF) at the University of Adelaide to provide improved phenotyping capabilities to support Australia plant and agricultural scientists.

The researchers use sensors on board remotely piloted aircraft to monitor plant growth and vigour for agricultural and ecological research. Platforms range from multi-copters to fixed wing aircraft, carrying cameras and multispectral and thermal sensors. Imagery captured produce GIS (geographic information system) layers used to integrate with field data to further develop relationships between plant growth, environmental conditions and plant treatment. The potential to measure parameters on field trials such as establishment, height, biomass, stress and nutritional status can be explored using this technology.

A recent episode on the youth science television show ‘Scope’ features the APPF field phenotyping capacity with Dr Ramesh Raja Searan from the research team demonstrating the use of drones to investigate wheat tolerant of sodic soils. You can watch the episode here (the story commences at 16 min 19 sec)… https://tenplay.com.au/channel-eleven/scope/season-3/episode-131

ramesh-with-uav

Dr Ramesh Raja Searan demonstrating field phenotyping