Integrating Multi-Omics in Aquaculture: From Genetic Gains to Sustainable Aquaculture

In recent years, aquaculture, a critical pillar of global food security, has faced challenges including germplasm resource degradation, frequent disease outbreaks, and insufficient environmental adaptability. To address these issues, omics technologies—centered on genomics, transcriptomics, and related fields—are driving the transformation of aquaculture toward precision and intelligence by establishing a three-dimensional “genotype–phenotype–environment” knowledge network. In this review, we outline foundational applications of omics in aquaculture and highlight the characteristics and current applications of distinct omics approaches. Furthermore, we summarize three core application domains of omics in aquaculture: (1) genetic breeding via genomic selection (GS), gene editing, and multi-omics molecular dissection of economic traits; (2) disease prevention through host–pathogen interaction studies and microbial engineering; and (3) environmental assessment through multi-omics characterization of biological and ecological responses. Additionally, we identify challenges in applying omics technologies to aquatic breeding and database development. Overall, this review aims to provide aquaculture practitioners with actionable insights by enhancing understanding of omics-driven innovations in sustainable aquaculture advancement.