The Application of Genomic Selection in Aquaculture

Genomic selection (GS) is currently increasingly applied in livestock breeding programs, and most commonly used in dairy cattle. GS is a form of marker assisted selection applied on a genome wide scale, without detecting the precise location of genes. It overtook earlier approaches of marker assisted selection, which relied on the discovery of genes of large effects. Although, the latter approach had some success with traits that are controlled by single genes, most traits of economic importance are quantitative and complex and controlled by many genes and the environment. Some genes that affect complex traits have been detected, but the majority of the genetic variation in the breeding goal remains unexplained. GS can address all genetic variance of the breeding goal and thus has the potential to reach a selection accuracy of 100%, especially in aquacultural species where family sizes are large. The successful application of GS requires: (i) the discovery of large numbers of single nucleotide polymorphisms (SNPs); (ii) a cost effective method to genotype the polymorphisms on many individuals; (iii) the availability of a large genotyped and phenotyped training population where the marker effects are estimated; and (iv) genotyping of the selection candidates. The benefits of GS are greatest when the selection candidates cannot themselves be trait recorded, as often occurs in disease challenge tests in fish breeding. Due to the large family sizes in fish breeding, GS may be applied within families, where relatively sparse marker densities are sufficient.