GEM experiment: script and datasets

This submission contains the datasets and the R script used in the study Blouin et al., 2026: 'Quantifying microbiota impact on plant traits for the guidance of breeding programs'. This study aimed to quantify the relative contribution of the soil microbiota in plant trait variance. Specifically, we estimated how much the soil microbiota (M) could explain plant shoot biomass and resistance to a pathogen infection (Botrytis cinerea), relatively to plant genotype (G) and the soil environment (E). For this purpose, we used three Arabidopsis thaliana accessions (G: Can, Col, Cvi), three soils from three locations in Bourgogne (France) with contrasted physico-chemical properties (E: Auxonne, Breteniere, Champdotre), and the three soil microbiota that were extrated from the same three soils (M: microbiota Auxonne, microbiota Breteniere, microbiota Champdotre). This submission contains three R scripts and the associated data that were used to generate the figures of the study. The script 'Rscript_gem_microbiota_2025_R1" is for the rhizosphere microbiota analysis. The script 'Rscript_gem_plant_2025_R1' is for the analysis of the dry biomass and leaf necrosis size of plants. The script "Rscript_gem_power_2025_R1" is for the power simulation requested by reviewers. The raw sequencing fastq files were submitted to the Sequence Read Archive (SRA, https://www.ncbi.nlm.nih.gov/sra). This new version was implemented after the scientific review of our work.