crop stress

Next gen chase research break-throughs with unrivalled access to plant phenotyping technology

Our latest round of Postgraduate Internship Award (PIA) students have kicked off their research projects at the Australian Plant Phenomics Facility (APPF)!

All our student interns have the unique opportunity to access the APPF’s cutting-edge phenotyping capabilities at no cost, learning about experimental design, and image and data anaylsis in plant phenomics while undertaking collaborative projects with the highly skilled APPF team. This experience allows our next generation of aspiring plant scientists to explore key research questions, reveal new data and make a real contribution to the global challenge of feeding future generations.

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Yue Qu (Julian) with his soybean plants in an automated, high-throughput plant phenotyping Smarthouse at the Australian Plant Phenomics Facility’s Adelaide node

Yue Qu (Julian)

In his project ‘Investigating novel mechanisms of abiotic stress tolerance in soybean’ Julian seeks to answer two questions, (1) Does GmSALT3, a protein linked to improved salt tolerance, also confer tolerance to drought and oxidative stress in soybean, and (2) Does GmSALT3 improve growth under standard conditions. He will use a non-destructive, high-throughput plant phenotyping Smarthouse, hyperspectral leaf phenotyping, leaf ion content, ROS activity/detoxification of roots, and gas exchange to investigate 8 lines of soybean in combination with 4 treatments (control, drought, 100mM NaCl, 150mM NaCl).

“For my PhD I have been functionally characterising GmSALT3. I have used heterologous expression systems to examine transport activity, as well as phenotyping salt tolerance in the NILs,” said Julian.

However, more recent phenotyping data and RNA-seq analysis has led us to the hypothesis that the salt tolerance phenotype of GmSALT3 plants is a consequence of their improved ability to detoxify reactive oxygen species, and therefore they may be more stress tolerant in general. This is contrary to the prevailing hypothesis that the protein is directly involved in salt transport and directly, rather than indirectly confers salt exclusion. To test this hypothesis we need to properly phenotype the Near Isogenic Lines (NILs). We believe that the phenotyping capabilities of the APPF will give unparalleled insights into the stress tolerance of soybean that would not otherwise be possible. Such a finding will be a significant breakthrough and likely result in a high impact publication when added to our existing data.”

Supervisor, Professor Matthew Gilliham, from the ARC Centre of Excellence in Plant Energy Biology agreed. “The experience the APPF team offer while conducting these experiments will add a great deal to the impact of the papers Julian is preparing and reveal a new layer of complexity that would not be possible without their expertise.”

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Daniel Menadue watches over his wheat plants in a Smarthouse at the Australian Plant Phenomics Facility’s Adelaide node

Daniel Menadue

Daniel is investigating a proton pumping pyrophosphatase (PPase) gene family in wheat and the role these genes play in the wheat plant’s response to environmental stress in and enhancing yield.

Vacuolar pyrophosphatase have been known for a while to be involved in a plant’s adaptation to the environment, however, the majority of the work on these genes has been using the gene from Arabidopsis, AVP1. Daniel’s research has identified the 12 wheat orthologs of AVP1 and from the sequence and expression data he has to date, he hypothesises that different PPases have different roles depending on their protein sequence and tissue localisation. To this end Daniel has generated transgenic bread wheat, cv Fielder, expressing two of the wheat genes (TaVP1-B and TaVP2-B) to further characterise the role of the PPase protein. Excitingly, Daniel has observed a growth phenotype, in the second generation of transgenic plants, with the transgenic plants appearing to grow faster and have larger biomass than wild type or null segregant plants. This is a phenotype previously seen in transgenic barley expressing the Arabidopsis AVP1 gene, plants which went on to show enhanced yield under salinity in the field (Schilling et al. 2014, Plant Biotech J.).

Given the very promising phenotype of these lines, Daniel will dissect this mechanism further using the non-destructive imaging capabilities at the APPF as an ideal platform for such experiments. He will investigate when the transgenic lines exhibit their enhanced growth, dissect whether they grow faster throughout the vegetative period or just for a short while at the start of their growth. He will also investigate the possibilities of following the growth of leaves through time and determine if the plants have enhanced resistance to salinity tolerance.

“In many ways we would like to replicate the study that we did in one of the APPF’s Adelaide Smarthouses which produced the barley data for the Schilling et al. 2014 paper, but in much more detail and using wheat plants with wheat genes,” said supervisor, Dr Stuart Roy from the University of Adelaide’s School of Agriculture, Food and Wine.

“We envision that the data obtained from Daniel’s study will form the basis of at least one research publication and, if the results are promising, open up new areas of research and delivery for bread wheat with altered PPases expression levels through my International Wheat Yield Partnership project, AVP1, PSTOL1 and NAS – Three high-value genes for higher wheat yield.” – shared in our recent blog story ‘International consortia tackle the global challenge to increase wheat yields at the APPF’.

It’s a pleasure to welcome Julian and Daniel to the team!

The next round of Postgraduate Internship Awards at this APPF will close 30 November, 2017 – Apply now!

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.

For more information and to apply click here.

Collaborating for the common good: CIMMYT and CSIRO meet to capitalise on strengths

Plant scientists around the world share a common goal:  understanding plants to improve their tolerance of environmental stresses, resist disease and ultimately, increase yield. Global collaborations that share knowledge and technology are rich in experience and are essential to help accelerate our understanding to meet future challenges.

A recent meeting in El Batán, Mexico, is an excellent example of great minds coming together. Three team members from the Australian Plant Phenomics Facility joined host institution, CSIRO, and CIMMYT in a two-day workshop aimed at achieving critical steps towards a common framework for field phenotyping techniques, data interoperability and sharing experience.

CSIRO at CIMMYT

Front row:  Warren Creemers (4th from left), Xavier Sirault (5th) and Michael Schaefer (7th)

“Capitalising on our respective strengths, we developed basic concepts for several collaborations in physiology and breeding, and will follow up within ongoing projects and through pursuit of new funding,” said Matthew Reynolds, CIMMYT wheat physiologist, signaling the following:

  • Comparison of technologies to estimate key crop traits, including GreenSeeker and hyperspectral images, IR thermometry, digital imagery and LiDAR approaches, while testing and validating prediction of phenotypic traits using UAV (drone) imagery.
  • Study of major differences between spike and leaf photosynthesis, and attempts to standardise gas exchange between field and controlled environments.
  • Work with breeders to screen advanced lines for photosynthetic traits in breeding nurseries, including proof of concept to link higher photosynthetic efficiency/performance to biomass accumulation.
  • Validation/testing of wheat simulation model for efficient use of radiation.
  • Evaluation of opportunities to provide environment characterisation of phenotyping platforms, including systematic field/soil mapping to help design plot and treatment layouts, considering bioassays from aerial images as well as soil characteristics such as pH, salinity, and others.
  • Testing the heritability of phenotypic expression from parents to their higher-yielding progeny in both Mexico and Australia.
  • Extraction of new remote sensed traits (e.g., number of heads per plot) from aerial images by machine learning (ML) of scored traits by breeders and use of ML to teach those to the algorithm.
  • Demonstrating a semantic data framework’s use in identifying specific genotypes for strategic crossing, based on phenotypes.
  • Exchanging suitable data sets to test the interoperability of available data management tools, focusing on the suitability of the Phenomics Ontology Driven Data (PODD) platform for phenotypic data exchanges, integration, and retrieval.

CSIRO and CIMMYT share a long history in crop modelling and physiology, spanning more than 40 years. CIMMYT works throughout the developing world to improve livelihoods and foster more productive, sustainable maize and wheat farming. The centre’s portfolio squarely targets critical challenges, including food insecurity and malnutrition, climate change and environmental degradation. Through collaborative research, partnerships, and training, the centre helps to build and strengthen a new generation of national agricultural research and extension services in maize- and wheat-growing nations. As a member of the CGIAR System composed of 15 agricultural research centres, CIMMYT leads the CGIAR Research Programs on Maize and Wheat, which align and add value to the efforts of more than 500 partners.

 

Decadal Plan for Australian Agricultural Sciences 2017-2026 released

Grow. Make. Prosper. The Decadal Plan for Australian Agricultural Sciences was published in June 2017 and presents the strategic vision for Australian Agricultural Sciences in the next decade.

The plan outlines strategies to improve the strength and efficiency of agricultural research in Australia in ways that will increase the ability of governments and producers to maintain productivity and efficiency in the face of evolving natural challenges. Successfully identifying, developing and deploying the next generation of game-changing scientific advances remains an active and ongoing challenge. The plan also outlines strategies to capitalise on emerging technologies that will affect the agricultural sciences.

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Agriculture is vitally important to Australia’s economy and social fabric, and contributes to global health and wellbeing. It faces a range of challenges across biophysical, economic and social arenas. Opportunities for technological and production improvements are continuously being identified from scientific research. However, to attain step change improvements in profitability, productivity and sustainability into the future will require integrated multidisciplinary research underpinned by a well-resourced science research pipeline.

The Australian Plant Phenomics Facility plays a key role in supporting the next generation of agricultural research designed to answer some of these challenges. This month we will meet with colleagues from fellow NCRIS facilities TERN, BPA, ALA, NeCTAR and NCI to explore opportunities for collaboration, determine where overlaps or synergies occur and discuss bigger picture ideas to ensure NCRIS funding is used most effectively.

Read the full Decadal Plan for Australian Agricultural Sciences (2017-2026) here.

Find out more about the APPF here.

National National Collaborative Research Infrastructure Strategy (NCRIS)

Terrestrial Ecosystem Research Network (TERN)

Bioplatforms Australia (BPA)

Australian Atlas of Living (ALA)

National eResearch Collaboration Tools and Resources (NeCTAR)

National Computational Infrastructure (NCI)

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This is your chance! An invaluable opportunity to access phenotyping capabilities to further your plant science research

Do you have an exceptional plant science research project destined to deliver high impact outcomes for Australian agriculture? Do you need access to plant phenotyping capabilities?

The Phenomics Infrastructure for Excellence in Plant Science (PIEPS) scheme was announced in May and is open to all publicly funded researchers. Emphasis is placed on novel collaborations that bring together scientists preferably from different disciplines (e.g. plant physiology, computer science, engineering, biometry, quantitative genetics, molecular biology, chemistry, physics) and from different organisations, within Australia or internationally, to focus on problems in plant science.

The PIEPS scheme involves access to phenotyping capabilities at the Australian Plant Phenomics Facility (APPF) at a reduced cost to facilitate exceptional research projects. Researchers will work in partnership with the APPF to determine experimental design and optimal use of the equipment. Our team includes experts in agriculture, plant physiology, biotechnology, genetics, horticulture, image and data analysis, mechatronic engineering, computer science, software engineering, mathematics and statistics.

Applications are assessed in consultation with the APPF’s independent Scientific Advisory Board. Selection is based on merit.

Don’t miss this an outstanding opportunity to gain access to invaluable expertise and cutting edge technology to accelerate your research project and make a real impact in plant science discovery.

Applications close:  30 September 2017

For more information and to apply:  APPF Phenomics Infrastructure for Excellence in Plant Science (PIEPS)

To find out how we can support your research, contact us.

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.

A step closer to salt tolerant chickpea crops

A recent study has collected phenotypic data of chickpea (Cicer arietinum L.) which can now be linked with the genotypic data of these lines. This will enable genome-wide association mapping with the aim of identifying loci that underlie salinity tolerance – an important step in developing salt tolerant chickpeas.

In this study, Judith Atieno and co-authors utilised image-based phenotyping at the Australian Plant Phenomics Facility to study genetic variation in chickpea for salinity tolerance in 245 diverse accessions (a diversity collection, known as the Chickpea Reference Set).

Chickpea is an important legume crop, used as a highly nutritious food source and grown in rotation with cereal crops to fix nitrogen in the soil or to act as a disease break. However, despite its sensitivity to salt, chickpea is generally grown in semi-arid regions which can be prone to soil salinity. This results in an estimated global annual chickpea yield loss of between 8–10%.

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Salinity tolerance phenotyping in a Smarthouse at the Australian Plant Phenomics Facility’s Adelaide node at the Waite Research Precinct – Plants were imaged at 28 DAS for 3 consecutive days prior to 40 mM NaCl application in two increments over 2 days. Plants were daily imaged until 56 DAS. Right pane shows 6-week-old chickpeas on conveyor belts leaving the imaging hall proceeding to an automatic weighing and watering station.

 

The study found, on average, salinity reduced plant growth rate (obtained from tracking leaf expansion through time) by 20%, plant height by 15% and shoot biomass by 28%. Additionally, salinity induced pod abortion and inhibited pod filling, which consequently reduced seed number and seed yield by 16% and 32%, respectively. Importantly, moderate to strong correlation was observed for different traits measured between glasshouse and two field sites indicating that the glasshouse assays are relevant to field performance. Using image-based phenotyping, we measured plant growth rate under salinity and subsequently elucidated the role of shoot ion independent stress (resulting from hydraulic resistance and osmotic stress) in chickpea. Broad genetic variation for salinity tolerance was observed in the diversity panel with seed number being the major determinant for salinity tolerance measured as yield. The study proposes seed number as a selection trait in breeding salt tolerant chickpea cultivars.

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Genotypic variation for salinity tolerance in the Chickpea Reference Set. Varying levels of salinity tolerance exhibited by different chickpea genotypes. Exposure of sensitive genotypes to 40 mM NaCl caused severe stunted growth, leaf damage, and led to less number of reproductive sites (flowers and pods) compared to moderately tolerant and tolerant genotypes.

 

The rapid development of new, high-resolution and high-throughput phenotyping technologies in plant science has provided the opportunity to more deeply explore genetic variation for salinity tolerance in crop species and identify traits that are potentially novel and relevant to yield improvement. The Australian Plant Phenomics Facility provides state-of-the-art phenotyping and analytical tools and expertise in controlled environments and in the field to help academic and commercial plant scientists understand and relate the performance of plants to their genetic make-up. A dedicated cross-disciplinary team of experts provides consultation on project design and high quality support.

To read the full paper in Scientific Reports, “Exploring genetic variation for salinity tolerance in chickpea using image-based phenotyping” (doi:10.1038/s41598-017-01211-7), click here.

To find out more about the Australian Plant Phenomics Facility and how we can support your research click here.

 

 

 

An exciting offer of help for significant plant science research projects

Do you have an exceptional plant science research project destined to deliver high impact outcomes for Australian agriculture? Do you need access to plant phenotyping capabilities?

The Phenomics Infrastructure for Excellence in Plant Science (PIEPS) scheme is open to all publicly funded researchers. Emphasis is placed on novel collaborations that bring together scientists preferably from different disciplines (e.g. plant physiology, computer science, engineering, biometry, quantitative genetics, molecular biology, chemistry, physics) and from different organisations, within Australia or internationally, to focus on problems in plant science.

The PIEPS scheme involves access to phenotyping capabilities at the Australian Plant Phenomics Facility (APPF) at a reduced cost to facilitate exceptional research projects. Researchers will work in partnership with the APPF to determine experimental design and optimal use of the equipment. Our team includes experts in agriculture, plant physiology, biotechnology, genetics, horticulture, image and data analysis, mechatronic engineering, computer science, software engineering, mathematics and statistics.

Applications are assessed in consultation with the APPF’s independent Scientific Advisory Board. Selection is based on merit.

This is an outstanding opportunity to gain access to invaluable expertise and cutting edge technology to accelerate your research project and make a real impact in plant science discovery.

Applications close:  30 September 2017

For more information and to apply:  APPF Phenomics Infrastructure for Excellence in Plant Science (PIEPS)