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Plant Observatory : a set of resources dedicated to multi-level phenotyping of plants

The Plant Observatory is a set of resources dedicated to multi-level phenotyping of plants. The Plant Observatory is hosted by the Jean-Pierre Bourgin Institute (UMR 1318, INRA-AgroParisTech) at Versailles, which is one of the main European Institute in Plant Biology with around 300 co-workers, and the Institute of Plant Sciences Paris-Saclay (UMR 1403-9213, INRA-CNRS-UPSud-UEVE-UP7) at Gif-sur-Yvette.

Aerial photo Versailles

Aerial Photo - Versailles - IGN Map

Purpose

Our goal is to achieve an integrated and high-throughput plant phenotyping combining macroscopic, biochemical, cytological and metabolic approaches. Our platform integrates several existing platforms that already have a long operating experience, i.e. plant imaging and microscopy, plant chemistry and metabolomics, plant protein biochemistry, Phenoscope phenotyping robots, Arabidopsis biological resource center, plant growth facility and transcriptomic.

This platform is mainly based on the model plants Arabidopsis thaliana and Brachypodium dystachion but also hosts projects on crops (pea, corn, canola, cotton, barley, linseed, camelina, wheat…)

Our project has allowed the emergence of a homogeneous, coherent and large facility allowing an integrated plant culture, phenotyping, imaging, biochemical, metabolic and chemical analysis. In addition we integrate and host the Biological Resource Centers for Arabidopsis and Brachypodium which provide users with a very high number of ecotypes, mutant or recombinant lines.

The Plant Observatory cooperates with both academic and industrial partners and provides access to state-of-the-art phenotyping and analysis systems as well as experimental facilities. The Plant Observatory capacities for plant phenotyping are instrumental for both national and international research programs such as ERC starting grants, EU ITNs and numerous ANR (The French National Research Agency) projects. Our expertise in plant culture and phenotyping are integrated with -omics approaches.

Available facilities

5500 m2 of greenhouses (all in biosecurity S2 level), 320 m2 of fully programmable growth chambers (S2 and S3), 1200 m2 for plant imaging, biochemical and metabolic analyses.

Services offered

Growing plants

In controlled conditions in greenhouses, growth chambers, quarantine or bio-security S3 level.

Automated phenotyping

2 high-throughput phenotyping robots for Arabidopsis allowing macroscopic imaging (Phenoscope platform). In 2014 we will make available two new improved phenotyping robots, which will allow to apply multiple abiotic stress (nitrogen deficiency, water deficit, high CO2 etc) as well as IR and fluorescence imaging.

Propagation, storage and distribution of genetic material

The Arabidopsis Biological Resource Center makes available to the scientific community : a set of 55,000 T-DNA insertion lines built in the Ws (Wassilewskija) background via Agrobacterium tumefaciens in planta transformation with the binary vector pGKB5. Flanking sequences tags (FST) have been identified for each mutant in the collection: 46,236 FSTs are available in the database Flagdb++, as well as SIGnAL and TAIR. More than 600 natural variants from different geographical origins were collected in order to exploit the natural diversity of the species. Every seed batch was genotyped in order to check the conformity of all reference and distribution batches (Simon et al. 2012). The genotyping data, as well as tools that we have developed to verify or determine the identity of accessions, are available on the dedicated web interface ANATool. More than 100 F2 mapping populations are available. They result from crosses between natural accessions, in particular between the 8 accessions of the most reduced core-collection. A panel of epigenetic recombinant inbred lines (epiRILs) was generated with the aim of studying the impact of epigenetic changes such as DNA methylation on phenotypic variation. These epiRILs derive from two parents with little DNA sequence differences, but contrasting DNA methylation profiles.

Plant proteomics

2D gels, purification, crystallization robot.

Plant imaging

Confocal and visible microscopy, in situ hybridization, laser dissection microscopy, electron microscopy, flow cytometry, subcellular localization and dynamics (spinning-disk microscopy) immunolocalization and FISH.

Metabolic profiling

Analysis of primary (amino acids and sugars) and secondary metabolites (cell walls, flavonoids, etc.) by GC-MS, GC-TOF, MALDI-TOF and LC-MS/MS, HPLC determination of lipids and hormones by nanoLC-MS/MS, isotope labeling and isotopic analysis (elemental analysis and IR-MS), in situ analysis (infrared spectroscopy FT-IR and NIRS).

Labels

Label CNOC

Strategic platform CNOC (National committee of the Collective Tools) since 2013.

Label IBISA

Ibisa recognized platform (Infrastructures in biology health and agronomy) since 2012.