EcoCore; An ecologically diverse panel of Arabidopsis thaliana accessions for studying plant-environment interactions

Arabidopsis thaliana naturally occurs across a wide geographic range and displays extensive natural variation in several traits including adaptive responses to the abiotic environment (e.g. temperature, drought, salt). Quantitative techniques like Genome Wide Association Studies (GWAS) enable mapping the genetic basis of such environmental responses and benefits from extensive genetic variation, but the size of the chosen diversity panel is often limited by phenotyping capacity. Most studies therefore use subpanels, often based on maximization of genetic diversity. However, this type of selection may overrepresent cosmopolitan alleles and underrepresent rare environment-specific alleles. Here, we demonstrate that the genetic variation in a GWAS subpanel of Arabidopsis thaliana accessions depends almost entirely on the number of accessions in the panel and very little on the composition of the panel. We present the EcoCore panel designed by grouping accessions of the 1001 genomes (1001G; 1135 accessions) collection, based on their native collection environment and selecting an equal number of accessions from each environment. We assessed hypocotyl lengths of plants grown at control and ambient high temperatures (20{degrees}C and 28{degrees}C) for 913 accessions of the 1001G and mapped these traits with the full 1001G panel versus the EcoCore panel. The EcoCore panel revealed novel genetic associations with hypocotyl length which is attributed to enrichment of alleles from rare environments. We present the EcoCore panel as a manageable resource for studying phenotypic plasticity and the genetic basis of plant-environment interactions.