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The 5th International Plant Phenotyping Symposium, IPPS2018


 brought together an exciting, multidisciplinary community including plant scientists, agronomists, ecologists, engineers, biostatisticians and computer scientists in a rich networking environment to foster knowledge sharing, collaboration, innovation, and the beginning of new partnerships, ideas and research projects.

The Symposium addressed three areas of interest:

From plant ...

Trying to understanding the interaction of a plant’s genotype with the environment is a key driver of plant phenomics. How can we measure large numbers of plants in varying environmental conditions to identify the traits that will make them more tolerant to our changing climate? How can we use latest camera and sensor technology to get a better understanding of plant physiological processes and the environment in which they grow?

 To data ..

As data acquisition improves rapidly in volume and complexity, the phenotyping bottleneck is shifting to data. How do we ensure the data we capture is high-quality and relevant? How do we combine different data sources to enrich the phenotyping measurement information? How do we annotate and manage data so it can be shared, re-used and queried?

 To impact

Plant phenomics brings together a whole suite of expertise, from plant biologists to engineers and statisticians. Working collaboratively, these disciplines can advance our understanding of plant performance and resilience, and we can make progress towards identifying the genetics of stress tolerance and breeding higher yielding crops.

IPPS 2018 Program


Tuesday 2 October

Day 1 - Satellite Meetings

12:00 – 17:00 Registration open

Affordable Phenotyping WG Workshop

  • Coast to coast low-cost plant imaging
    David Rousseau (University of Angers, France)
  • Raspberry Pi-powered imaging and open source software for plant phenotyping
    Noah Fahlgren (Donald Danforth Plant Science Center, United States)
  • Low-cost disposable sensors: Potential applications to plant phenotyping
    Paulo Sergio de Paula Herrmann Jr.
  • Plant Screen Mobile: a smartphone app for plant growth monitoring
    Mark-MüllerLinow (Forschungszentrum Jülich)

 

 

 David Rousseau:

Noah Fahlgren:

Paulo Herrmann:

Mark-Müller Linow:

 

15:00 – 17:00 Controlled Environment WG Workshop

  • Introduction of the ICEPPG Workshop: aims and goals of the working group
    Thomas Altman (IPK, Germany)
  • Exracting valuable traits from a plant phenotyping platform requires model-assisted dissection of the phenotype
    Llorenc Cabrera-Bosquet (INRA, France)
  • Enviratron: An accelerator for climate change research
    Carolyn J Lawrence-Dill (Iowa State University, United States)
  • Connecting Lab-to-Field: the role of controlled environment phenotyping from physiological background
    Uli Schurr (Forschungszentrum Jülich)      

17:00 – 19:00 Welcome reception – proudly sponsored by the Grains Research & Development Corporation (GRDC)

 

Thomas Altmann:

Llorenç Cabrera-Bosquet:

Carolyn J. Lawrence Dill:

Ulrich Schurr:

 

IPPS 2018 Main Program


Wednesday 3 October

Day 2 – “From Plant …”

08:00 - 08:30 Registration open

Keynote speaker

    • Plant phenotyping for plant genetics
      Mark Tester (Centre for Desert Agriculture, King Abdullah University of Science & Technology, Saudi Arabia)

 Mark Tester:  

 SESSION 1 - What's going on underground?

  • CIAT phenomics platform: Aiming at improving eco-efficiency of cassava crops in the changing global climate
    Michael Gomez Selvaraj (International Centre for Tropical Agriculture, Colombia)
  • Phenotyping underground: Anatomical traits of roots under compaction
    Dorien J Vanhees (University of Nottingham, United Kingdom)
  • The Soybean Nodule Acquisition Program: Solving a phenomics challenge in a SANP using machine learning solutions
    Clayton Carley (Iowa State University, United States)
  • Root phenotyping in wheat – from cabinets to Cootamundra
    Anton P Wasson (CSIRO, Australia)
  • Phenotyping spatial and temporal dynamics of roots by Magnetic Resonance Imaging and Positron Emission Tomography
    Robert Koller (Forschungszentrum Jülich, IBG-2, Germany)

10:55 – 11:20 Networking refreshments (25 mins)

 

Dorien J Vanhees:

Clayton N. Carley:

Anton Wasson:

Robert Koller:

SESSION 2 - Phenotyping small things

  • Phenotyping seeds: Traits of interest to enhance use and management of genetic resource collections
    Christina Walters (USDA-ARS National Laboratory for Genetic Resources Preservation, United States)
  • Advancing the phenomics of intact grains and spikes to facilitate selection for grain filling attributes
    M. Fernanda Dreccer (CSIRO, Australia)
  • Automated phenotyping of individual seeds of very different size and species
    Ulrich Schurr (Forschungszentrums Jülich, Germany)
  • Non-invasive determination of internal traits of wheat ears using computed tomography
    Joelle Claussen (Fraunhofer IIS, Germany)
  • Variability of fructan accumulation in mature grains of a European two row spring barley population
    Andrea Matros (University of Adelaide, Australia)

13:10 – 14:00 Lunch (50 mins)

 

Christina Walters:

Ulrich Schurr:

Joelle Claussen:

Andrea Matros:

SESSION 3 - Under control

  • Use of high-throughput plant phenotyping for the detection of developmental phase-specifically acting growth QTL in maize and growth dynamics-related transcriptome analysis
    Thomas Altmann (Leibniz-Insitute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Germany)
  • Non-destructive fast vibration phenotyping for plants
    Emmanuel de Langre (Ecole Polytechnique, France)
  • High-throughput greenhouse and field-plot phenotyping tools to reveal the genetic architecture of drought resistance in rice
    Wanneng Yang (Huazhong Agricultural University, China)
  • Not a load of rubbish: Simulated field trials in large-scale containers
    Andreas Stahl (Justus Liebig University, Germany)

15:20 – 15:45 Networking refreshments (25 mins)

  • Presentation by the Grains Research & Development Corporation (GRDC)

 

SESSION 4 - Out of control

  • High-throughput phenotyping to improve early stage selection in the Australian sugarcane breeding program
    Sijesh Natarajan (Sugar Research Australia, Australia)
  • Field phenotyping photosynthesis
    Onno Muller (Forschungszentrums Jülich, Germany)
  • Hyperspectral reflectance to measure photosynthetic traits in wheat
    Viridiana Silva Perez (CSIRO, Australia)
  • Clustering analysis of maize plant height and canopy spectral dynamics based on field-based UAV phenotyping platform
    Guijun Yang (National Engineering Research Center for Information Technology in Agriculture (NERCITA), China)

 

 

Sijesh Natarajan

Onno Muller

Viridiana Silva Perez

 

Day 3 – “To Data…”

08:00 - 08:30 Registration open

SESSION 5 - Scrutinising the data - information management and pipelines

  • Computational classification of phenologs across biological diversity
    Ian R Braun (Iowa State University, United States)
  • Dealing with multi-source and multi-scale information in plant phenomics: The PHIS ontology-driven information system
    Llorenç Cabrera-Bosquet (INRA, France)
  • MaizeGDB: How phenotype curation has co-evolved with genomic representations
    Carson Andorf (United States Department of Agriculture, Agricultural Research Service (USDA-ARS), United States)
  • From FAIRer data do faster discovery - A comprehensive infrastructure to serve plant phenotypic research data
    Daniel Arend (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Germany)
  • Challenges and opportunities for statistical applications in high-throughput phenomics
    Scott Chapman (CSIRO, Australia)
  • From seeds to field and lab to forest - Scalable architectures for collaborative phenomics
    Tim Brown (Australian Plant Phenomics Facility, ANU node, Australia)

10:30 – 11:00 Networking refreshments (30 mins)

 

 

 

PANEL DISCUSSION - Data management

Chair:

- Uli Schurr (Forschungszentrum Jülich, IBG-2, Germany)

Panel:

- Carolyn Lawrence-Dill (Genetics, Development & Cell Biology, Iowa State University, United States)

- Mark Cooper (Centre for Crop Science, QAAFI, The University of Queensland, Australia)

- Bjoern Usadel (RWTH Aachen & Forschungszentrum Jülich, Germany)

- Nicole Jensen (Grains Research & Development Corporation, Australia)

- Ross Wilkinson (ANDS, Australia)

12:30 – 13:30 Lunch (60 mins)

SESSION 6 - A picture's worth a thousand words

  • Current challenges for high throughput field plant phenotyping based on images
    Seishi Ninomiya (Institute for Sustainable Agro-ecosystem Services, University of Tokyo, Japan)
  • Land-based crop phenotyping by image analysis
    Josh Chopin (Phenomics & Bioinformatics Research Centre, University of South Australia, Australia)
  • Seeing behind leaves: Multi-view reconstruction of three-dimensional branch structure
    Fumio Okura (Osaka University, Japan)
  • High-throughput 3D imaging to dissect the genetic control of leaf elongation in barley
    Bettina Berger (Australian Plant Phenomics Facility, University of Adelaide node, Australia)
  • 3D phenotyping of root crown and inflorescence architecture across diverse genetics in maize and sorghum with X-Ray CT
    Mon-Ray Shao (Donald Danforth Plant Science Center, United States)

15:45 – 16:15 Networking refreshments (30 mins)

:00 - 23:00 Symposium dinner – Adelaide Town Hall – proudly sponsored by the Australian Plant Phenomics Facility (APPF)

Friday 5 October

Day 4 – “To Impact…”

08:00 - 08:30 Registration open

08:30 - 08:40

Welcome and introduction to the day: “To Impact…”

Plant phenomics brings together a whole suite of expertise, from plant biologists to engineers and statisticians.

Working collaboratively, these disciplines can advance our understanding of plant performance

and resilience, so we can make progress towards identifying the genetics of stress tolerance

and breeding higher yielding crops.

08:40 - 09:25

Keynote speaker

Translating genome and phenotyping information to develop superior varieties in legume crops

Rajeev Varshney (International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), India)

SESSION 7 - Perfecting plants - selection and phenotyping

Chair: Greg Rebetzke (CSIRO, Australia)

09:25 – 09:45 Greenhouse phenotyping technologies used for trait characterization and ranking of transgenic soybean events

Kurt Boudonck (BASF, United States)

09:45 – 10:05 Field-based high throughput phenotyping for physiological and morphological traits in bread wheat

Muhammad Adeel Hassan (Chinese Academy of Agricultural Sciences, China)

10:05 – 10:15 Genetic components of unmanned aerial systems phenotyping variability in maize breeding

Nathália Penna-Cruzato (Texas A&M University, United States) EC

10:15 – 10:35

An integrated sensing pipeline to map the genetic loci associated with

canopy radiation use efficiency in sorghum

Barbara George-Jaeggli (University of Queensland, Australia)

10:35 – 10:55 Is high-throughput phenotyping achievable in commercial wheat breeding?

James Walter (Australian Grain Technologies, Australia)

10:55 - 11:20 Networking refreshments (25 mins)

SESSION 8 - From fungi, to cockatoos, to kangaroos (biotic stress)

Chair: Asheesh K Singh (Department of Agronomy, Iowa State University, United States)

11:20 – 11:40 Machine learning approaches for automated plant stress phenotyping

Arti AS Singh (Iowa State University, United States)

11:40 – 12:00

Comparison of UAV and UGV measurements for the assessment of genotypic resistances to

Cercospora on sugar beet

Alexis AC Comar (Hi-phen, France)

12:00 – 12:20 Optimal wavebands for plant disease remote sensing

Dmitrii G Shadrin (Skolkovo Institute of Science and Technology, Russia)

12:20 – 12:40

Combination of high-throughput multispectral and deep physiological phenotyping of barley resistances

against powdery mildew in a controlled environment

Thomas Roitsch (University of Copenhagen, Denmark)

12:40 – 13:30 Lunch (50 mins)

SESSION 9 - When soils and weather don't cooperate (abiotic stress)

Chair: M. Fernanda Dreccer (CSIRO, Australia)

13:30 – 13:50 Non-destructive phenomic tools for drought and heat tolerance at anthesis in Brassica species

Sheng Chen (University of Western Australia, Australia)

13:50 – 14:10

Toward the integrative modelling of drought tolerance in soybean: Collaborative phenotyping and

multi-omics measurements

Hiroyoshi Iwata (University of Tokyo, Japan)

14:10 – 14:30

Defining signatures of enhanced water and nitrogen use efficiency in bioenergy sorghum using controlled

environment phenotyping and integrative genomics

Andrea L Eveland (Donald Danforth Plant Science Center, United States)

14:30 – 14:50 Phenotyping for water-N interactions

Cesar Mariano Cossani (South Australian Research & Development Institute (SARDI), Australia)

14:50 – 15:15 Networking refreshments (25 mins)

15:15 – 15:25 Presentation by the Australian Plant Phenomics Facility (APPF)

SESSION 10 - From idea to reality - developing novel tech for future challenges

Chair: Xavier Sirault (Australian Plant Phenomics Facility, CSIRO node, Australia)

15:25 – 15:55

Keynote speaker

Title TBA

Nicole Jensen (Grains Research & Development Corporation, Australia)

15:55 – 16:15 Agronomic applications using field high throughput phenotyping data

Katia KB Beauchene (Arvalis - Institut du végétal, France)

16:15 – 16:35 Affordable and open source technology development in plant phenotyping for DIY phenology

Takanari Tanabata (Kazusa DNA Research Institute, Japan)

16:35 – 16:55 Coping with drought: Anin-vivo sensor allows for the early detection of drought stress in tomato

Francesco Cellini (Lucana Agency for Development and Innovation in Agriculture, Italy)

16:55 – 17:15 Application of "E-nose" as a gas multi-sensor array to investigate soybean under water stress

Paulo Herrmann (Embrapa, Brazilian Agricultural Research Corporation, Brazil)