Presentation by Michaël Chelle delivered at e-ROSA's 2nd Stakeholder Workshop in Wageningen, 27/11/2017

1. Février 2017
Michaël Chelle
michael.chelle@inra.fr
Think
of
color-blind
vision
!
Genomics?

2. Février 2017
(plant) phenomics
Michaël Chelle
michael.chelle@inra.fr
Think
of
color-blind
vision
!

3. .03
Phenotyping
Genotype
Environment
Phenotype
Development
of
individuals
From the neo-Darwinian model
x
≈
Evolution
of
populations
spatio-temporal scale(individual, intra-life) (population, generations)

4. .04
Phenotyping
Swedish University of Agricultural Sciences
Characterization of traits of individuals under given environments
Phenomics is the systematic measurement and analysis of qualitative and quantitative traits,
including clinical, biochemical, and imaging methodologies, for the refinement and characterization of a phenotype.
Phenomics requires both
“deep phenotyping,” referring to a thorough collection of a wide breadth of accurate and precise phenotypes,
“phenomic analysis,” referring to evaluation of patterns and relationships between genotype–phenotype associations
and between individuals with related phenotypes.
Phenomics
Change of scale
speed, volume

5. Typical
mechanism
Hydraulics,
Metabolism,
signalling
Light interception,
Water transfer,
Whole-plant signaling
Over-ruling
emergent properties
Trades off
Relevance for yield
prediction
Ratio Biology/
other processes
Multi-scale phenotyping
A tension between genetic variability of
- “mechanisms” (organ, minutes)
- yield (canopy, months)
Level of
organization
High precision
platforms
Field multi-
environment
network
High throughput
platforms (controlled
or field)
Canopies in a range
of environments
Weeks to months
Cell- Organ
Minute/days
Plant or Canopy
Minute to weeks
Physiology
Genetics, genomic prediction
Genomic selection
Tardieu et al 2017 Current Biol
From lab to plot to fieldS: connecting such diverse infrastructures !

6. From Schurr et al.

7. From Schurr et al.

8. From Schurr et al.

9. From Schurr et al.
SmartCow2018-2022FNH-RI

10. .010
Phenomics & e-infrastructure?
From Yang et al., 2013.
Phytotron
Field
e-infra?
improving
platform
improving
measurement
improving
simulation
e-infrastructure will « connect » phenotyping infrastructures to provide knowledge
bottom-up
but also should play a role in phenomics developpement it-self
top-down

11. From Schurr et al.
+
High-tech engineering
Sensors (imagery, l), automatisation, robots/UAV
(Big) Data management and analysis (visualization, deep learning)
Modeling / simulation
Diseases control
Food quality
Breeders
Seed companies
Farmers
Suppliers
….

12. .012What societal challenges can benefit from open science in phenotyping?
How do these benefit?
What scientific challenge have to be overcome to achieve these benefits?
August 2017
Estimated Total Program Funding:
$6,000,000
2016 NSF Call

13. To contact me?
michael.chelle@inra.fr
Michaël Chelle
Special thanks
to François Tardieu
Think
of
color-blind
vision
!