Genome-wide approaches to understanding and improving complex traits in aquaculture species

The rapid drop in cost and increase in throughput of nucleic acid sequencing has provided many opportunities for aquaculture genetics and breeding. Genome-wide genetic marker data can now be readily generated in a cost-effective manner, even for species without extensive prior genomic tools. The result is that genome-wide association studies (GWAS) and genomic selection (GS) in aquaculture species are becoming increasingly routine. With only a small percentage of global aquaculture production obtained through selective breeding, it holds tremendous potential for the industry. GWAS and GS can help realize this potential, and the last 5 years has seen numerous studies in aquaculture species focusing mainly on growth-related and disease resistance traits. The current review discusses background information relating to methods of using genome-wide marker data for GWAS and GS, and discusses lessons learned through their practical implementations in commercial aquaculture breeding for genetic improvement. Future directions for these techniques and technologies are discussed.