Abstract
Over the past 20 years, the introduction of new molecular techniques has given a new impetus to genetic and genomic studies of fishes. The main traits selected in the aquaculture sector conform to the polygenic model, and, thus far, effective breeding programmes based on genome-wide association studies (GWAS) and marker-assisted selection (MAS) have been applied to simple traits (e.g. disease resistance and sexual maturation of salmonids) and known Quantitative Trait Loci (QTLs). Genomic selection uses the genomic relationships between candidate loci and SNPs distributed over the entire genome and in tight linkage disequilibrium (LD) with genes that encode the traits. SNP (low and high density) arrays are used for genotyping thousands of genetic markers (single nucleotide polymorphisms, SNPs). The genomic expected breeding value (GEBV) of selection candidates is usually calculated by means of the GBLUP or ssGBLUP (single step) methods. In recent years, in several aquaculture breeding programmes, the genomic selection method has been applied to different fish and crustacean species. While routine implementation of genomic selection is now largely carried out in Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), it is expected that, in the near future, this method will progressively spread to other fish species. However, genomic selection is an expensive method, so it will be relevant mostly for traits of high economic value. In several studies (using different salmonid species), the accuracy of the GEBVs varied from 0.10 to 0.80 for different traits (e.g. growth rate and disease resistance) compared to traditional breeding methods based on geneology. Genomic selection applied to aquaculture species has the potential to improve selection programmes substantially and to change ongoing fish breeding systems. In the long term, the ability to use low-pass genome sequencing methods, low-cost genotyping and novel phenotyping techniques will allow genomic selection to be applied to thousands of animals directly at the farm level.
Highlights
Aquaculture is currently one of the fastest-growing agricultural production sectors worldwide
Recent studies have shown that the genomic selection method can be effectively used to improve some salmonid production and disease resistance traits (Yáñez et al 2016; Yoshida et al 2018), and the first example of a genomic selection programme was established for the genetic improvement of Atlantic salmon (Houston et al 2014; Ødegård et al 2014; Tsai et al 2015)
Whole-genome sequencing of selected individuals and the imputation method can improve the accuracy of the estimate (Badke et al 2013; Browning and Browning 2016; Bilton et al 2018)
Summary
Aquaculture is currently one of the fastest-growing agricultural production sectors worldwide. Recent studies have shown that the genomic selection method can be effectively used to improve some salmonid production and disease resistance traits (Yáñez et al 2016; Yoshida et al 2018), and the first example of a genomic selection programme was established for the genetic improvement of Atlantic salmon (Houston et al 2014; Ødegård et al 2014; Tsai et al 2015). Improved genome annotation techniques and RNA sequencing (RNA-seq) allow the identification and characterization of new SNPs. The high fecundity and the family sizes used in fish breeding plans allow us to obtain a high selection accuracy (because of the close relationship between the reference population and selected candidates). The commercial applicability in the genetic improvement of fish species will, depend on how these animals are considered by the regulatory authority (Abdelrahman et al 2017)
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