The genetic architecture of freezing tolerance varies across the range of Arabidopsis thaliana

The capacity to tolerate freezing temperatures limits the geographical distribution of many plants, including several species of agricultural importance. However, the genes involved in freezing tolerance remain largely unknown. Here, we describe the variation in constitutive freezing tolerance that occurs among worldwide accessions of Arabidopsis thaliana. We found that although plants from high latitudes tend to be more freezing tolerant than plants from low latitudes, the environmental factors that shape cold adaptation differ across the species range. Consistent with this, we found that the genetic architecture of freezing tolerance also differs across its range. Conventional genome‐wide association studies helped identify a priori and other promising candidate genes. However, simultaneously modelling climate variables and freezing tolerance together pinpointed other excellent a priori candidate genes. This suggests that if the selective factor underlying phenotypic variation is known, multi‐trait mixed models may aid in identifying the genes that underlie adaptation. The ability to withstand freezing temperatures limits the geographical distribution of many plants, but the genes involved remain largely unknown. Here, we investigate the genetic bases of freezing tolerance in the model system, Arabidopsis thaliana. By using quantitative trait locus and genome‐wide association studies and data from the 1001 Genomes Project, we identified several promising candidate genes. Our results suggest that the genetic architecture of freezing tolerance varies across the species range. Moreover, we found evidence that the climate variables that shape freezing tolerance also vary across the range, and that modelling climate variables with freezing tolerance may improve power in genome‐wide association studies.