Genome mapping and sequencing is the core of structural genomics. While no whole genome draft sequences are yet available with aquaculture species, genomes of many aquaculture species have been subjected to mapping. Genome mapping can be classified into several categories based on resource needs, technology requirement, and principles used in mapping, i.e., genetic linkage mapping, QTL mapping, physical mapping, cytogenetic mapping, radiation hybrid mapping, and comparative mapping. Understanding how inherited characteristics relate to specific genomes will eventually allow researchers to develop tools that can be used to guide animal breeding, selection, and management decisions.

Traits that are usually controlled by more than just one or two genes - polygenic traits. The study of these polygenic, or quantitative, traits is the basis of quantitative genetics. Unlike qualitative trait loci, genes that are assumed to be influencing or controlling a quantitative trait are very rarely identified. They are given the overarching title of quantitative trait loci (QTL). QTLs can be mapped genetically by correlation of segregating markers with the traits, and such a process is referred to as QTL mapping. Aquaculture species are very diverse in terms of systematic groups (fish, crustaceans, mollusks) and, more importantly, in terms of their level of domestication related to breeding and biological constraints. Salmonids are the most important fish group for aquaculture. Domestication and large- scale selective breeding, mostly based on family designs, have been initiated for several decades

Several QTLs have been mapped to different linkage maps on the salmon genome QTL mapping is the core of aquaculture genomics as the ultimate practical goal of aquaculture genomic research is to provide tools for genetic improvements.

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