Genomic resources and their applications in aquaculture of Asian seabass (Lates calcarifer)

Abstract

Genomic resources, including nuclear DNA markers, mitochondrial DNA markers, highresolution linkage maps, transcriptomes, reference genome sequences and their annotations, are critically important in aquaculture. Their potential applications are plenty, such as enabling the analysis of genetic diversity in population structures, mating and spawning behaviour; genetic traceability; reconstructing pedigrees; mapping quantitative trait loci (QTL) for important phenotypic traits; marker-assisted selection and genomic selection; and to understand genetic and epigenetic regulation of traits. Asian seabass (Lates calcarifer) is becoming a popular aquaculture species. In the past 30 years, many genomic resources have been developed and used to understand the genetic diversity of wild and cultured populations, setting up mating schemes, genetic traceability, mapping QTL and genome-wide association studies for growth, omega-3 fatty acid content, resistance to diseases and genetic improvement of important traits in breeding programmes. In this review, we systematically synthesize the status of available genomic resources and their applications in enhancing the genetic improvement and aquaculture production of Asian seabass. We also critically discuss the challenges and future research directions of developing, optimizing and applying genomic resources in Asian seabass aquaculture.