Currently, we are applying GWAS in a set of 240 Arabidopsis accessions to find the gene(s) underlying the chrom1 and chrom4 QTL for seed size, identified previously by classical linkage mapping in a Ler´Cvi RIL mapping population (Alonso-Blanco et al. 1999). Whereas GWAS scan large numbers of anonymous markers across the entire genome, candidate gene studies specifically target genes with known or potential functions in the trait of interest. Candidate gene association studies are a potentially powerful approach in A. thaliana, because many of the genetic pathways have been dissected through forward and reversed genetic approaches, providing strong candidate for genes and pathways that might underlie natural trait variation (Ehrenreich et al. 2007; 2009). Over the last years, we applied QTL mapping to endoreduplication parameters and nominated cell cycle genes underlying identified QTL as candidate genes. A candidate gene association mapping supported the nomination of a number of cell cycle genes as candidate genes underlying the QTL for endoreduplication. Transgenic studies involving overexpression and downregulation of the candidate genes will eventually confirm their involved in endoreduplication in plants.