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

László Orbán,Norman Phua,László Varga,Xueyan Shen

doi:10.3389/fgene.2021.506754

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.

Highlights

The combined effects of rapidly increasing human population, growing need for seafood products, constraints on freshwater use and depleted marine fish populations (Lotze et al, 2018) exert an enormous pressure onto our aquaculture production
By following the footsteps of those working with terrestrial farm animals, researchers have been developing genomic toolboxes of an increasing number of food fish species used in aquaculture production
This review describes the history of the selection program performed on Asian seabass in Singapore over the last 15 years

Summary

INTRODUCTION

The combined effects of rapidly increasing human population, growing need for seafood products, constraints on freshwater use and depleted marine fish populations (Lotze et al, 2018) exert an enormous pressure onto our aquaculture production (for review see Ahmed and Thompson, 2018). Additional, highly polymorphic microsatellite markers were isolated from the genome of Asian seabass by the Yue team (Zhu et al, 2006, 2010) Following their characterization, a selected set was combined into multiplexes based on their average allelic size and the width of their allelic range. In those rare cases, when the efficiency has dropped substantially below this value, several other 5- and 4plexes could be utilized for obtaining additional genotypes The development of these multiplex genotyping sets was a crucial step, as it allowed the upgrade from a slow and laborious familybased selection strategy to a more effective process based on testing the origin of best performing offspring from mass crosses using molecular parent-offspring matching as described above (Figure 1). BAC, bacterial artificial chromosome; DEG, differentially expressed gene; qPCR, quantitative PCR; QTL, quantitative trait locus

A FEW CONSIDERATIONS FOR FOOD FISH SELECTION PROGRAMS

Findings

CONCLUSION