Abstract
Selective breeding is increasingly recognized as a key component of sustainable production of aquaculture species. The uptake of genomic technology in aquaculture breeding has traditionally lagged behind terrestrial farmed animals. However, the rapid development and application of sequencing technologies has allowed aquaculture to narrow the gap, leading to substantial genomic resources for all major aquaculture species. While high‐density single‐nucleotide polymorphism (SNP) arrays for some species have been developed recently, direct genotyping by sequencing (GBS) techniques have underpinned many of the advances in aquaculture genetics and breeding to date. In particular, restriction‐site associated DNA sequencing (RAD‐Seq) and subsequent variations have been extensively applied to generate population‐level SNP genotype data. These GBS techniques are not dependent on prior genomic information such as a reference genome assembly for the species of interest. As such, they have been widely utilized by researchers and companies focussing on nonmodel aquaculture species with relatively small research communities. Applications of RAD‐Seq techniques have included generation of genetic linkage maps, performing genome‐wide association studies, improvements of reference genome assemblies and, more recently, genomic selection for traits of interest to aquaculture like growth, sex determination or disease resistance. In this review, we briefly discuss the history of GBS, the nuances of the various GBS techniques, bioinformatics approaches and application of these techniques to various aquaculture species.
Highlights
Despite the critical role for aquaculture in global food security, the vast majority of world fish and shellfish production is based on stocks without advanced selective breeding programmes (Gjedrem et al 2012; Janssen et al 2016)
Aquaculture breeding schemes tend to lag behind their terrestrial livestock counterparts in terms of the uptake of genomic technologies, and for many aquaculture species, molecular genetic tools are only applied for pedigree reconstruction (Chavanne et al 2016)
Most modern breeding programmes in livestock are underpinned by genomic selection (GS, Meuwissen et al 2001), the benefits of which are well-illustrated in dairy cattle (Hayes et al 2009)
Summary
Despite the critical role for aquaculture in global food security, the vast majority of world fish and shellfish production is based on stocks without advanced selective breeding programmes (Gjedrem et al 2012; Janssen et al 2016). This random shearing step can be a benefit, as the variable size of the genomic fragments anchored at the RE cut site facilitates the assembly of a contig based on the paired-end reads This augments annotation of the RAD loci when there is no reference genome available, and the design of specific primers for re-genotyping of targeted SNPs. In addition, the paired-end data from RAD-Seq allow identification and removal of putative PCR duplicates (reads originated from the same original DNA fragment, presenting identical sequences), which can hinder analysis and interpretation of Illumina sequencing data (Schweyen et al 2014). SNPs generated by RAD techniques have been applied to produce SNP arrays for several aquaculture species, including Atlantic salmon (Houston et al 2014), rainbow trout
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