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An infrastructure for multi-scale phenomics

¹ Time definition: min, minutes, h hours; d, day; w, week. ² Method for photosynthesis proxy, Fluo, Fluorescence imaging, RUE indirect calculation via the ratio biomass/intercepted light

a. Controlled conditions

Installations can host 600-2200 (Montpellier) and 1800 (Dijon) plants of various species. Montpellier essentially focuses on plant responses to drought and high temperatures at resolutions from minutes to 24h. Installations allow either measuring growth and transpiration or reconstructing time series of plant 3D representations for calculations of growth rates, architectural features and proxies of photosynthesis. The Dijon installation is dedicated to root growth in interaction with biotic partners, via the development of patented rhizotrons built with a French SME. Both installations share robotic tools and imaging workflows, built in collaboration with a French SME. They follow a common environmental characterization and have a common information system. In 2018, three installations, located in Toulouse and Angers, joined Phenome-Emphasis for phenotyping the effect of biotic interactions (parasitic and mutualistic interactions). Two have S2 and quarantine capabilities. Chlorophyll fluorescence, and multispectral imaging of diseased leaf tissues enables quantifying symptoms and functional responses.

Characterization of root systems and aerial parts of 100s of genotypes: Dijon (a), and Montpellier platforms (b), images of roots and nodules (c), false-colour image of photosynthesis (d), virtual canopies built from 3D plants for simulation of genotypic effects on light interception (false colours) in diverse environmental scenarios (e).

Field

- Two field installations involve close environmental control in Ouzouer-le-Marché (centre France) and Clermont-Ferrand. Drought scenarios can be imposed over 5 000 m² by automatic rainout shelters. A free-air carbon enrichment installation (FACE) allows growing plants in natural conditions but high atmospheric CO₂. This allows studying the response of small canopies of each genotype to elevated CO₂ and/or drought, via functional traits involved in canopy photosynthesis and transpiration. Sensor networks precisely characterize micrometeorological conditions and soil water status at different positions and depth in the fields. Both installations are equipped with a common system for multi spectral multi directional canopy imaging, for calculation of leaf area, canopy architecture and light interception, together with growth rate and indirect estimations of plant nitrogen status, and water status via infra-red imaging.

- Three high throughput installations in natural conditions analyse 1000s of microplots in Dijon, Montpellier and Toulouse, with a particular attention to drought and biotic interactions. Environment is closely monitored (climate, maps of soil heterogeneity and soil moisture) as above. Canopies are imaged with a Phenomobile developed within the project and with drones for rapid phenotyping. All installations benefit from common workflows for image analysis and an information system that is common to field and controlled-conditions installations.

Field equipped with rainout shelters (Ouzouer) (a), distribution of CO₂ in a wheat field (Clermont Ferrand) (b), field imaging with a Phenomobile (c) and a drone (d). 

c. Omic platforms

Platforms for high throughput metabolomics (Bordeaux), chemotyping and seed structure (Nantes) allow characterizing the thousands of samples generated in phenomic installations, at throughputs higher than those in other infrastructures (e.g. Metabohub). This needed specific development for a throughput capacity of up to 1M samples per year, but for a limited number of metabolites, chemical or structural features.