Genome-based technologies useful for aquaculture research and genetic improvement of aquaculture species

In spite of the relatively late start of aquaculture genome research, significant progress has been made in aquaculture genomics. Many of the genomic resources, tools, and technology developed from genomics have wide applications for aquaculture research and genetic improvements of aquaculture species. The major genome technologies include DNA marker technologies, novel sequencing technologies, gene discovery technologies, genome mapping technologies, and technologies for analysis of genome expression. This chapter was written to provide basic information such as theories behind the technologies, principles of the technologies, and potential applications of each of these genome technologies relevant to aquaculture. In some cases, research and technology development trends are discussed such that the readers are aware of the direction of future research. For instance, single nucleotide polymorphisms (SNP) are clearly the markers of choice in the future even though microsatellites are currently the predominant type of markers in aquaculture research and applications; the next generation of sequencing technologies will not only play a dominant role in sequencing, but also may replace the traditional genome expression analysis technologies such as microarrays.