Research advances in the genomics and applications for molecular breeding of aquaculture animals

High-throughput sequencing technologies have been extensively applied to genetics and breeding in the aquaculture industry. To date, many aquaculture animal genomes have been sequenced, and single nucleotide polymorphisms (SNPs) have become the most popular genetic markers. SNP applications include high-density genetic linkage map construction, quantitative trait loci (QTL) mapping, genome-wide association study (GWAS), and genomic selection (GS). In this review, we assess the availability of complete genomes of aquaculture animals and then briefly discuss the sequencing technologies and SNP array for SNPs genotyping. Finally, we summarize the current status of genetic linkage map construction, QTL mapping, GWAS, and GS in aquatic animals. As the overall research programs and aims are similar across aquaculture animals, successful practices in some species might act as reference frameworks for in-depth investigations in other species.