Toward Genome-Based Selection in Asian Seabass: What Can We Learn From Other Food Fishes and Farm Animals?

Abstract

Due to the steadily increasing need for seafood and the plateauing output of fisheries, more fish need to be produced by aquaculture production. In parallel with the improvement of farming methods, elite food fish lines with superior traits for production must be generated by selection programs that utilize cutting-edge tools of genomics. The purpose of this review is to provide a historical overview and status report of a selection program performed on a catadromous predator, the Asian seabass (Lates calcarifer, Bloch 1790) that can change its sex during its lifetime. We describe the practices of wet lab, farm and lab in detail by focusing onto the foundations and achievements of the program. In addition to the approaches used for selection, our review also provides an inventory of genetic/genomic platforms and technologies developed to (i) provide current and future support for the selection process; and (ii) improve our understanding of the biology of the species. Approaches used for the improvement of terrestrial farm animals are used as examples and references, as those processes are far ahead of the ones used in aquaculture and thus they might help those working on fish to select the best possible options and avoid potential pitfalls.

Assessing Genetic Variation in Wild and Domesticated Pikeperch Populations: Implications for Conservation and Fish Farming

“…Current results already provide valuable insight for fish farmers. First, knowing genetic divergences between domesticated fish stocks paves the way (i) to develop accurate pedigree assignment (e.g., [55]) and (ii) to compare genetic specificities and aquaculture potential (sensu [56]; e.g., growth rate, filet yielding), which can ultimately lead to genomebased selection (e.g., [57]).…”

Mapping of a major QTL for increased robustness and detection of genome assembly errors in Asian seabass (Lates calcarifer)

“…Regional production of this species in major producing countries increased from ~ 20,000 tons in 1998 to 90,000 tons in 2017 [ 3 ]. In Singapore, marine net-cages from small family-owned and mid-sized fish farms (using brooders collected either from the sea or unknown sources) are the most popular method for culturing the species [ 4 ].…”

“…Our former research team – together with our collaborators – has been working on seabass selective breeding for nearly two decades, mainly focusing on the improvement of growth-related traits (for review see: [ 4 ]). In addition, several studies on traits potentially associated with increased disease tolerance of seabass have also been conducted using lab-based setups in which fish were challenged with a single pathogen in every experiment.…”