Sunflower, maize and potato are among the world’s principal crops. In order to improve various traits, these crops have been genetically engineered to a great extent. Even though molecular markers for simple traits such as, fertility, herbicide tolerance or specific pathogen resistance have been successfully used in marker-assisted breeding programs for years, agronomical important complex quantitative traits like yield, biotic and abiotic stress resistance and seed quality content are challenging and require whole genome approaches. Collections of genetic resources for these crops are conserved worldwide and represent valuable resources to study complex traits. Nowadays technological advances and the availability of genome sequence have made novel approaches on the whole genome level possible. Molecular breeding, including both transgenic approach and marker-assisted breeding have facilitated the production of large amounts of markers for high density maps and allowed genome-wide association studies and genomic selection in sunflower, maize and potato. Marker-assisted selection related to hybrid performance has shown that genomic selection is a successful approach to address complex quantitative traits and to facilitate speeding up breeding programs in these crops in the future.