Barley breeders cross complementary parents for desirable characters and use suitable screening systems to select superior recombinant lines. The advent of molecular markers, especially high throughput genome-wide systems, means that selection for characters, e.g. quality can be conducted indirectly earlier in the breeding cycle. Genome wide association studies (GWAS) have been applied to elite germplasm collections to identify the genomic regions that control key characters and hence markers for use in selection. This chapter shows how GWAS has highlighted contrasts between different breeding germplasm groups, revealing where crossing between groups can produce greater advance than continuing to cross within. GWAS can also be used as training populations for genomic selection but will remain a key R&D technology as it provides a route to candidate gene identification and hence to suitable sources of genetic diversity to maintain breeding progress. Integration of multi-environment GWAS with climatic variables is essential to breed for adaptation to climate change.