Analysis of individual plants reveals the genetic control for local adaptation in European maize landraces

European maize landraces encompass a large amount of genetic diversity, allowing them to be well-adapted to their local environments. This diversity can be exploited to improve the fitness of elite material in the face of a changing climate. We characterized the genetic diversity of 333 individual plants from 40 European maize landrace populations (EMLPs). We identified five genetic groups that mirrored the proximities of their geographical origins. Fixation indices (Fst) showed moderate differentiation among genetic groups (0.034 to 0.093). More than half of the genetic variance was observed to be partitioned among individuals. Nucleotide diversity of EMLPs decreased significantly as latitude increased (from 0.16 to 0.04), suggesting serial founder events during maize expansion in Europe. GWAS with latitude, longitude, and elevation as response variables identified 28, 347, and 68 significant SNP positions, respectively. We pinpointed significant SNPs near dwarf8, tb1, ZCN7, ZCN8, and ZmMADS69, and identified 137 candidate genes with ontology terms indicative of local adaptation in maize, regulating the adaptation to diverse abiotic and biotic environmental stresses. This study suggests a quick and cost-efficient approach to identifying genes involved in local adaptation without requiring field data. The EMLPs used in this study have been assembled to serve as a continuing resource of genetic diversity for further research aimed at improving agronomically relevant adaptation traits.