Seedling establishment is one of the most important, yet stress-sensitive, stages in the plant life-cycle. Seedling quality is largely established during seed development and maturation as a result of often complex interactions between the genome and the environment. The molecular genetic dissection of these interactions will allow the identification of genes that control seed and seedling quality. These genes will be the starting point to unravel the signalling pathways in which they are involved and will reveal the regulatory processes that ultimately influence seed and seedling quality. In the here proposed project we will use a quantitative trait loci (QTL) approach to unlock the genetic variation for seedling quality that is present in tomato and Arabidopsis recombinant inbred line (RIL) populations grown under different environmental conditions. The ‘classical’ QTL analysis will be combined with transcriptome, metabolome and hormone analysis of all lines in the population in a so called genetical genomics approach to facilitate the identification of the genes, metabolites and hormone changes that are responsible for the changes in the measured phenotypes. In Arabidopsis, candidate gene selection will be made even easier by combining this approach with a comprehensive genome wide association analysis (GWA). Candidate genes affecting seedling quality and the molecular pathways in which they function, will be further analysed by reverse genetics, using knock-out mutants, and subsequent analysis of these mutants by extensive phenotyping (germination under sub optimal conditions), transcriptome, metabolome and hormone analysis. This will not only unambiguously confirm the function of the genes in seedling quality, but also the underlying regulatory pathways. A global study of the function of these pathways in additional species will proof their suitability as ‘universal’ markers for seed and seedling quality.