SSRs in barley breeding and genomics

Abstract

The use of molecular markers to track loci and genome regions in barley is routinely applied in many breeding programs. The location of major loci is now known for many disease resistance genes, tolerances to abiotic stresses and quality traits. There are three aspects that are particularly significant. First, we now have markers closely linked to many traits of importance in the breeding programs. Indeed we have markers for more loci than we can screen in a conventional breeding program. Second, we have tools that allow marker scanning of the whole genome. SSR markers form the base for this analysis and highly multiplexed SSR screens have been developed for barley. This has improved our capacity for whole genome screens. Third, through association mapping projects we have or are in the process of developing, whole genome fingerprints for many key lines and varieties of importance in breeding. Existing strategies for marker-assisted selection (MAS) were initiated with a view of markers as providing a rapid and cheap alternative to bioassays and they have largely been used in this role. While highly successful, this strategy does not fully utilize the technology. The key challenge of new work is to investigate strategies for whole genome breeding: that is, to see how we can use genome information to design optimal breeding strategies that integrate as much of the available information as possible.