GWAS results used for the analysis of 4 multi-environment trials experiments data through metaGE meta-analysis:

• The Arabidopsis dataset of Frachon et al. 2017, where GWAS analyses were performed on the local mapping population TOU-A, with a panel of 195 whole-genome sequenced accessions evaluated in six controlled micro-habitats (combinations of three soils × presence/absence of inter-specific competition, noted A to F). Each accession was genotyped at 981,278 SNPs (after quality control and a MAF threshold of 0.07) and phenotyped for bolting time.

• The maize Amaizing-DROPS dataset of Millet et al. 2016, where GWAS analyses were performed on a panel of 244 maize dent lines evaluated as hybrids with a common parental line in 22 environments (combinations of location × year x treatment). Each line was genotyped at 602,356 SNPs (after quality control) and phenotyped for grain yield in the 22 environments. In addition, environmental variables were measured in each environment.

• The multi-parental population maize EU-NAM Flint dataset of Bauer et al. 2013 and Lehermeier et al. 2014, which includes 11 biparental populations obtained from crosses between UH007 and 11 peripheral parents representative of the Northern Europe maize diversity. In each population, double haploid (DH) lines were produced and genotyped at 5,263 SNPs (after quality control). All populations were evaluated for biomass dry matter yield (DMY) in 4 locations. Three populations with less than 30 progenies were removed from the present analysis. GWAS analyses were performed on each combination of cross and location, resulting in 32 individual analysis.

• The Wheat dataset of Robert et al. 2020, where GWAS analyses were performed on a panel of 210 wheat lines phenotyped for grain yield in 16 environments (combinations of location x year x treatment). Lines were genotyped at 108,410 SNPs (after quality control) and phenotyped for grain yield.