Genomics Era on Breeding Aquaculture Stocks

Abstract

Over 80% of the aquaculture production in Europe originates from selective breeding programs aiming to improve several traits simultaneously. Selecting for increased feed efficiency combines economic benefits and a reduced environmental impact. Additionally, disease outbreaks pose serious challenges for organic aquaculture with limited therapeutic agents. Therefore, selective breeding comprises a valuable tool combined with strict biosecurity and effective management practices. Phenotypic sex is labile in fish exhibiting sexual dimorphism in a range of traits of interest. Identified genomic regions concerning sex determination demonstrates the importance of selective breeding. The existence of GxE interactions imply that fish derived from the single nucleus might show lower-than-expected genetic gains in different environments. Understanding their key contribution among different environments is critical for the optimization of a selective breeding program. Next-generation sequencing (NGS) techniques have resulted in the annotation of many teleost genomes, and omics are becoming a powerful multidisciplinary strategy (genomics, transcriptomics, proteomics, and metabolomics). Given the importance of selective breeding programs, particular attention should be paid to the continuous enhancement and development of scientific knowledge, so that the EU legislative framework on organic aquaculture is always up to new challenges toward sustainability increasing the organic logo credibility for the consumers.