With the development of the earliest sequencing technologies (Maxam and Gilbert 1977; Sanger et al. 1977a) and the release of the fi rst DNA sequence, that of the bacteriophage ȹ X174 in 1977 (Sanger et al. 1977b, 1978), foundations were laid for transition from the genetic to the genomic era of life science research. The ability of reading a nucleotide sequence has opened the way to study the secrets that lie within an organism’s genome from many different perspectives at unprecedented levels of resolution. Whole genome sequencing has been regarded as a priority for the human species and for those representatives of animal and plant organisms of main importance. The possibility to obtain the DNA sequence of an organism on a whole genome scale provides a powerful tool to look into the complete catalog of genes, and their regulative elements and variation at the highest resolution possible. Similarly, sequencing of target DNA regions, or of the transcribed fraction of the genome, is a priority to identify genes involved in many different biological processes and mechanisms. Access to genetic variation lying within a given genomic region at a resolution as high as a single nucleotide and on a scale as wide as an entire germplasm collection, is crucial to explain and correlate phenotypic variation among individuals or populations of related species.