GEM experiment: script and datasets

This submission contains the datasets and the R script used in the study Blouin et al., 2025: 'Soil microbiota matters: Quantifying its impact on plant traits for breeding program guidance' (pending doi). 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: i) the plant trait dataset, ii) the inoculation control dataset, iii) the pH control dataset, iv) the 16S rRNA OTU table with v) its associated taxonomy file and vi) design file, vii) the ITS1 OTU table with viii) its associated taxonomy file and ix) design file, and finally x) the R script that was used to generate the figures of the study with the data previously mentionned. The raw sequencing fastq files were submitted toe teh Sequence Read Archive (SRA, https://www.ncbi.nlm.nih.gov/sra)