crop research

China taps into Australian plant phenomics expertise

Trevor-and-Egypt-Ambass

The Australian Plant Phenomics Facility’s (APPF) Dr Trevor Garnett and Dr Xavier Sirault are delighted to have been invited as a feasibility evaluation experts to review the Nanjing Agricultural University’s (NAU) plans for a new high-tech Phenotyping Research Centre later this month.

While in Nanjing, China, they will also give a talks at a phenotyping workshop at NAU and are invited guests of the Modern Agricultural Science and Technology Conference. Dr Garnett and Dr Sirault will return again to Nanjing in March 2018 as a keynote speakers at the 2nd Asia-Pacific Plant Phenotyping Conference.

Earlier this year Prof. Yanfeng Ding, Professor of Agronomy, Vice President NAU and colleagues traveled to Australia and met with Dr Garnett and Dr Sirault to tour the APPF’s facilities, and learn more about the latest plant phenotyping technology and expertise. The APPF is visited regularly by international agricultural research groups; most recently from Egypt, Sri Lanka, China, France, Morocco, Taiwan, Iran, Chile and New Zealand.

The APPF is a distributed network of national research infrastructure platforms that offer open access to plant phenomics technologies and expertise not available at this scale or breadth in the public sector anywhere else in the world. We provide state-of-the-art plant phenotyping tools and expertise to enable academic and commercial plant scientists, from Australia and around the world, address complex problems in plant and agricultural science.

About Dr Trevor Garnett

Dr Garnett is Technology Development Director at the APPF’s Adelaide node, based at the Waite Campus of the University of Adelaide. There, he is implementing new phenotyping technologies for the Australian phenomics community, such as hyperspectral imaging in controlled environments and the field, field phenotyping using UAVs and ground based platforms, and root phenotyping. Dr Garnett is also the Phenomics Program Leader of the Australian Research Council Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate. His research interests include nitrogen use efficiency in cereals. (Dr Garnett is pictured above, talking with His Excellency Mr Mohamed Khairat, Ambassador of The Arab Republic of Egypt, in the APPF’s DroughtSpotter).

About Dr Xavier Sirault

Dr Sirault is Director of the APPF’s Canberra (CSIRO) node where he is responsible for its operational management, international engagement and transfer of its technology to industries. In parallel to this role, Dr Sirault works as a Senior Research Scientist for CSIRO Agriculture and Food. His research aims at understanding the factors that regulate and limit photosynthesis in crop plants, and in particular, how these factors influence plant growth and performance. Dr Sirault is also Vice Chair of the International Plant Phenotyping Network where he hopes to spearhead the development of solutions for maximising data inter-operability and data re-use globally. (Dr Sirault is pictured below, welcoming His Excellency Maithripala Sirisena, President of Sri Lanka, and his delegation).

Xavier-welcoming-Sri-Lankan-guests

About Nanjing Agricultural University

NAU is one of the earliest institutions of higher agricultural education in China and a national key university under the Chinese Ministry of Education. A 2012 analysis of research citations by Thomson Reuters Essential Science Indicators found NAU among the top 1% of institutions in the fields of Agricultural Science, Plant & Animal Science and Environment/Ecology. Building on its century-long history, NAU is today pursuing a strategy of developing into one of the best agricultural universities in the world. The main campus of the university is situated in Weigang, in the picturesque eastern part of Nanjing near the UNESCO World Heritage Ming Imperial Tombs and the Sun Yat-sen Mausoleum. (NAU is pictured below).

Nanjing-Agri-Uni

Small group scoops international effort to sequence huge wheat genome

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The wheat genome is finally complete. A giant international consortium of academics and companies has been trying to finish the challenging DNA sequence for more than a decade, but in the end, it was a small US-led team that scooped the prize. Researchers hope that the genome of bread wheat (Triticum aestivum) will aid efforts to study and improve a staple crop on which around 2 billion people rely.

The wheat genome is crop geneticists’ Mount Everest. It is huge — more than five times the size of a single copy of the human genome — and harbours six copies of each chromosome, adding up to between 16 billion and 17 billion letters of DNA. And more than 80% of it is made of repetitive sequences. These stretches are especially vexing for scientists trying to assemble the short DNA segments generated by sequencing machines into much longer chromosome sequences.

It’s like putting together a jigsaw puzzle filled with pieces of blue sky, says Steven Salzberg, a genomicist at Johns Hopkins University in Baltimore, Maryland, who led the latest sequencing effort. “The wheat genome is full of blue sky. All these pieces look like a lot of other pieces, but they’re not exactly alike.”

Read the full story, written by Ewen Callaway and published in Nature, here.

The hunt for high salt tolerant barley crops gets closer

Barley-(optimised-for-web)

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.

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.

 

Want to fly drones? New Remote Pilot Licence training course available

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Dr Ramesh Raja Segaran from APPF partner, URAF

The Unmanned Research Aircraft Facility (URAF) at the University of Adelaide, is offering a commercial drone course leading to the award of a Remote Pilot Licence (RePL) by the Civil Aviation Safety Authority of Australia (CASA).

This five-day intensive RePL course is conducted on University of Adelaide campuses by a team of CASA-certified drone operators and trainers from the University.

Course inclusions

  • All required theory and practical syllabus and requirements of CASA for a RePL.
  • Aeronautical Radio Operator Certificate (AROC).
  • English Language Proficiency certification (ELP).
  • Textbook: Remote Pilot Licence RePL Study Guide by Bob Tait and Ben Harris.
  • In-house examinations for ELP, AROC and RePL.

Assured quality teaching

Courses available

The URAF run regular RePL courses 4-6 times a year. Ad hoc RePL courses for government and industry groups are also available.

  • Remote Pilot Licence Course, Multi-rotor up to 7kg
    • $3500 + GST (includes textbook and application fees for RePL, AROC, ELP)
  • Practical type training for Multi-rotor/ Fixed wing up to 25kg
  • Others
    • If you have passed an aeronautical knowledge exam for a flight crew licence (e.g. PPL/ CPL), you can complete practical type training with the URAF to get type rated for a RePL.

Who needs a RePL?

Please contact the URAF for more information on the courses and how to enrol.

Invitation: ‘Drones in research’ webinar series

Ramesh Booleroo field Drone flight 2 (edited)

Dr Ramesh Raja Segaran from APPF partner, URAF, demonstrating field phenotyping with a drone

Australian National Data Service (ANDS) is running two webinars on ‘Drones in Research’ this July. The webinars are free of charge and open to anybody who uses drones for research, or has an interest in doing so. They will be of particular interest to:

  • Researchers (academia, industry and government)
  • Data managers and data librarians
  • Data scientists, analysts, developers and technologists
  • Environmental and geo-scientific research data community
  • Research Office, Ethics Committee members and Legal Counsel for institutions

 

  • Webinar #1:  An eye on legal, ethics, safety & privacy
    When:  Thursday, 20 July 2017 at 12.30pm AEST (one hour duration)
    Description:  When deploying drones for research, it is important to be aware of legal and privacy issues under current Australian law, and have an understanding of public safety and community attitude.

    Speakers:  Melanie Olsen, AIMSA requirement of special licensing from CASA for drone useDes Butler, QUTThe privacy implication of using drones under current Australian lawLeanne Wiseman, Griffith UniversityDrones and geospatial data: A look at the legal and ethical issues [IP and copyright].

  • Webinar #2:  Rise of drones in the Australian research space
    When:  Thursday, Thursday 27 July 2017 at 12.30 AEST (one hour duration)Description:  This second webinar brings together researchers and data specialists from various disciplines to showcase their drone applications and data expertise, and to share knowledge to enhance research capabilities.

    Speakers:  Siddeswara Guru, TERN – Making drone data open for scientific research – Kim Bryceson, QUT – Automation of drone data capture in agriculture and development of GIS data library – Third speaker TBC.

The webinars are free, however, registration is required.

Both webinars will be recorded. If you can’t attend, please do register and ANDS will send you the recording and additional links.

Click here for more information and to register.

The Australian Plant Phenomics Facility (APPF) and ANDS are part of a community of facilities supported by the National Collaborative Research Infrastructure Strategy (NCRIS). The NCRIS network currently supports national research capability through 27 active projects and is comprised of 222 institutions employing well over 1,700 highly skilled technical experts, researchers and facility managers. NCRIS facilities are used by over 35,000 researchers, both domestically and internationally.