australian plant phenomics facility

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.

Julian montage test

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.”

Daniel montage

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

Ramesh and drone cropped

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.

International consortia tackle the global challenge to increase wheat yields at the APPF

Field of ripe wheat

Two international consortia of scientists from the United States, Great Britain, Mexico and Australia are currently carrying out research projects of global importance at the Australian Plant Phenomics Facility’s (APPF) Adelaide node for the International Wheat Yield Partnership (IWYP).

The first research project, Improving Yield by Optimising Energy Use Efficiency, is phenotyping an Excalibur x Kukri RIL population to determine genetics controlling energy use efficiency (EUE) in wheat. The aim is to identify genetic loci and markers to enable breeding of high-yielding germplasm with:

  • low rates of leaf respiratory CO2 released per unit growth,
  • optimised levels of sugars, organic and amino acids for growth, and
  • increased biomass at anthesis.

More than 85-90% of the energy captured by plants is used in high-cost cellular processes, such as transport of nutrients and respiration, meaning about only 10-15% is allocated to yield. Thus, any small gain in energy redistribution and use for a costly process can have a marked positive impact on biomass accumulation and yield.

Improvements in EUE can be achieved at the cell, tissue and whole-plant level, with respiration being a prime target.

“Our initial screening of 138 Australian commercial cultivars revealed a two-fold variation in rates of leaf respiration, three-fold variation in the ratio of respiration to growth rate during early development, and significant heritability of 35%. This demonstrates there is untapped genetic variation in EUE amenable to fine-tuning and optimisation of biomass accumulation in the lead-up to anthesis, with concomitant positive knock-on effects on yield”, said Australian National University’s Barry Pogson, Project Lead and Director of the ARC Centre of Excellence in Plant Energy Biology (AUS).

The project has partners at University of Western Australia (AUS), CIMMYT (MEX) and  the University of Adelaide (AUS).

The second research project, AVP1, PSTOL1 and NAS – Three High-Value Genes for Higher Wheat Yield, aims to enhance wheat yield by exploiting and building synergy of three high value genes (AVP1, PSTOL1 and NAS) and enabling molecular breeding by:

  • developing two-gene and three-gene pyramiding combinations of AVP1, PSTOL1 and NAS using available transgenic wheat lines and quantifying the additive effects on yield in multi-location field and greenhouse trials (as a proof of concept),
  • identifying wheat orthologs and allelic variants of TaAVP1, TaPSTOL1 and TaNAS, and designing molecular markers to the best alleles for marker-assisted breeding,
  • providing basic understanding of the physiological and molecular mechanisms behind improved yield and selecting wheat lines with the best allelic combination and field performance, and
  • assessing the necessity for using genome editing technologies to optimise gene function and enhance positive effect on wheat yield by modifying expression of the wheat alleles.

The genes Vacuolar Proton Pyrophosphatase 1 (AVP1), Phosphorus Starvation Tolerance 1 (PSTOL1) and Nicotianamine Synthase (NAS) have been shown to improve plant biomass production and grain yield. Over-expression of these genes results in improved biomass production and grain yield in a range of plant species, including cereals (rice, barley, wheat), in optimal growing conditions. The enhanced yield of the plants is believed to be due to improved sugar transport from source to sinks (AVP1), enhanced root growth and nutrient uptake (AVP1, PSTOL1) and increase in shoot biomass and tiller number (AVP1, PSTOL1, NAS2).

“Identifying and pyramiding the wheat orthologues of these high-value genes provides a real opportunity to produce wheat with significantly improved field performance and higher grain yield,” said Project Lead, Stuart Roy, from the University of Adelaide (AUS).

The project has partners at University of Melbourne (AUS), Arizona State University (USA), Cornell University (USA), University of California, Riverside (USA) and Rothamsted Research (GBR).

These extensive projects will continue throughout 2017 and into 2018.

 

Why is this research so important?

Wheat is the most widely grown of any crop globally, providing 20% of daily calories and protein. By 2050 wheat demand is expected to increase by 60%. To meet this demand, annual potential wheat yield increases must effectively double – an exceptional challenge.

In November 2012, funding agencies and organisations from the G20 countries agreed to work together and formed the global Wheat Initiative to develop a strategic approach to supporting research that would lead to dramatically increasing the genetic yield potential of wheat.

An essential pillar of this strategy is the International Wheat Yield Partnership (IWYP), a novel collaborative approach, enabling the best scientific teams from across the globe to work together in an integrated program to address the challenge of raising the genetic yield potential of wheat by up to 50% in the next two decades all over the world. IWYP builds on the initial research concepts of the Wheat Yield Consortium established by CIMMYT.

To deliver increased wheat yield, a combination of fundamental bioscience and applied research will be needed. IWYP will deliver this through a focused program of research to develop new knowledge, models and wheat lines suited to multiple environments ensuring global gains in wheat yields are achieved.

IWYP will target six key research scope areas:

  • uncovering genetic variation that creates the differences in carbon fixation and partitioning between wheat lines,
  • harnessing genes from wheat and other species through genetic modification to boost carbon capture and fixation to increase biomass production,
  • optimising wheat development and growth to improve grain yields and harvest index,
  • developing elite wheat lines for use in other breeding programs,
  • building on discoveries in wheat relatives and other species, and
  • fostering breakthrough technology development that can transform wheat breeding.

The “IWYP Science Program” provides a unique plan to generate new discoveries and provides for their rapid incorporation into wheat crops grown throughout the world. IWYP’s overarching aims are to stimulate new research, amplify the output from existing programs and make scientific discoveries available to farmers in developing and developed nations.

 

The Australian Plant Phenomics Facility

The APPF provides state-of-the-art phenotyping tools and expertise to help academic and commercial plant scientists from Australia and around the world understand and relate the performance of plants to their genetic make-up. Research facilitated at the APPF is leading to the development of new and improved crops, more sustainable agricultural practices, improved maintenance and regeneration of biodiversity in the face of declining arable land area and the challenges of climate change. Our services.

Do you need access to plant phenotyping capabilities? The PIEPS scheme can help!

Do you have an exceptional plant science research project destined to deliver high impact outcomes for agriculture? 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 applyAPPF Phenomics Infrastructure for Excellence in Plant Science (PIEPS).

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

Learn more about projects at the Australian Plant Phenomics Facility and keep in touch.

 

 

Growing rice faster – uncovering the triggers behind early canopy closure

By combining high-resolution image-based phenotyping with functional mapping and genome prediction, a new study has provided insights into the complex genetic architecture and molecular mechanisms underlying early shoot growth dynamics in rice.

The more rapidly leaves of a plant emerge and create canopy closure, the more successful the plant, in establishment, resource acquisition and ultimately yield. An early vigor trait is particularly important in aerobic rice environments, which are highly susceptible to water deficits. The timing of developmental ‘triggers’ or switches that initiate tiller formation and rapid exponential growth are a critical component of this trait, however, searching for the switch that initiates this growth has proven challenging due to the complex genetic basis and large genotype-by-environment effect, and the difficulty in accurately measuring shoot growth for large populations.

“The availability of large, automated phenotyping platforms, such as those at Australian Plant Phenomics Facility (APPF), allow plants to be non-destructively phenotyped throughout the lifecycle in a controlled environment, and provide high resolution temporal data that can be used to examine these important developmental switches,” said PhD student, Malachy Campbell.

Malachy and team, including Bettina Berger and Chris Brien from the APPF, phenotyped a panel of ~360 diverse rice accessions throughout the vegetative stage (11-44 day old plants) at The Plant Accelerator® at APPF. A mathematical equation was used to describe temporal growth trajectories of each accession. Regions of the genome that may regulate early vigor were inferred using genome-wide association (GWA) mapping. However, many loci with small effects on shoot growth trajectories were identified, indicating that many genes contribute to this trait. GWA, together with RNA sequencing identified a gibberellic acid (GA) catabolic gene, OsGA2ox7, which could be influencing GA levels to regulate vigor in the early tillering stage.

IMG_1014

Dr Malachy Campell in The Plant Accelerator® at the Australian Plant Phenomics Facility’s Adelaide node

For some traits where genetic variation is controlled by a small number of loci, breeders can use MAS to identify individuals carrying the favourable locus/loci for the given trait, and select them for the next generation. For complex traits that are regulated by many loci, it becomes very difficult to detect loci that are associated with the trait. However, an alternative approach, genomic selection (GS), considers the total genetic contribution of all loci to the given trait. With this approach, loci across the genome can be used to predict the performance of individuals that have not yet been phenotyped (i.e. those in future generations). Since many loci were found to be contributing to early vigor, the team explored the possibility of using GS for improving this trait. Shoot growth trajectories could be predicted with reasonable accuracy, with greater accuracies being achieved when a higher number of markers were used. These results suggest that GS may be an effective strategy for improving shoot growth dynamics during the vegetative growth stage in rice. The approach of combining high-resolution image-based phenotyping, functional mapping and genome prediction could be widely applicable for complex traits across numerous crop species.

Read the full paper, published in The Plant Genome, here. (doi:10.3835/plantgenome2016.07.0064).

Highest honour awarded to Dr Graham Farquhar

Graham Farquhar ANU

Dr Graham Farquhar          (photo: Stuart Hay, ANU)

Congratulations to Australian National University (ANU) scientist, Dr Graham Farquhar, who has become the first Australian to receive the prestigious Nobel-equivalent Kyoto Prize.

The prize is the highest accolade available to scientists in his field and recognises his outstanding body of work improving water-efficient crops and analysing climate change.

ANU vice-chancellor Brian Schmidt, himself a Nobel laureate, said Dr Farquhar’s work was of benefit to the entire world.

A regular user of the Australian Plant Phenomics Facility’s ANU node, Graham’s work has improved world food security by developing strains of wheat that can grow with less water, and has helped to solve mysteries about why clouds and wind patterns were not changing as climate change models suggested they should.

The Kyoto Prize was established in 1985 and recognises achievements in three fields: basic sciences, arts and philosophy, and advanced technology.

The prize is the latest in a string of accolades for Graham, including the Prime Minister’s Prize for Science in 2015 and Britain’s prestigious Rank Prize, which he shared in 2014 with CSIRO colleague Dr Richard Richards.

More: ABC News