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.

Keywords: teleost; aquaculture; genome sequencing and assembly; genome-wide association study; marine predator; marker-assisted selection; selected lines; transcriptome.

FIGURE 1

Schematic representation of the differences between a family-based traditional selection vs. a modern selection program supported by parentage analysis. The left panel depicts a family-based selection, where selected pairs of brooders are crossed, their offsprings are raised together and their performance analysis is performed by comparing siblings within the family. In this approach, many families must be analyzed individually and often repeatedly as environmental effects can have a substantial effects on the results of these comparisons. On the right panel, the essence of a modern selection program supported by parentage analysis based on genotyping with polymorphic DNA markers is shown. In this protocol, mass crosses involving up to 25 males × 25 females are performed. Following the validation of multi-family contribution by microsatellite-based genotyping, offspring are raised together to the age, when their performance can be assessed. The best-performing offspring individuals are then fin-clipped and genotyped with multiplexed microsatellite sets to reveal their parents. The brooders are then crossed again to (i) validate the results of the first cross; and (ii) possibly generate new families with even better results.

FIGURE 2

Principal component analysis of SNPs collected from 61 re-sequenced genomes supports the existence of a Asian seabass species complex and its separation into two species and a third variety [adapted from Figure 5A of Vij et al. (2016) with the authors’ permission]. Fin clip samples were collected from twelve geographical locations representing the native range of the species extending from North-Western India, through South-East Asia to North-Eastern Australia and sequenced to an average 6.7-fold coverage by Illumina short read technology. Three groups (Indian region – red ellipse, SE Asia/Philippines – green, and Australia/Papua New Guinea – blue) bearing clear allopatric signatures of separation could be observed through Principal Component Analysis. With the exception of Philippines, Vietnam and Singapore, all individuals from the remaining locations were wild-caught.

FIGURE 3

Molecular events during gonad transformation in teleosts using the zebrafish and the protandrous Asian seabass as models. All immature zebrafish develop a “juvenile ovary” before the future males undergo gonadal transformation to form the testis. Several pathways and genes have been shown to be involved in this process. We propose that many of these are also involved in the testis-to-ovary transformation of Asian seabass, despite the direction being the opposite. The arrows show the observed (zebrafish; top – blue) and/or predicted and later partially confirmed (Asian seabass; bottom – pink) differentially regulated genes or pathways during the gonadal transformation process. Apopotosis (black) is the first pathway activated at the beginning of the transformation in both systems to eliminate cells that cannot be trans-differentiated, independently from the direction. The trigger is unknown in both cases [improved Figure 6 of Ravi et al. (2014) with the authors’ permission].

FIGURE 4

Protandrous sequential hermaphroditism opens up the possibility for producing “intermediate generations” during breeding programs. Left panel: schematic representation of the first three (P, F1, and F2) generations in a typical breeding program performed on a gonochoristic species, when the two sexes mature during the same period. Right panel: breeding scheme for a protandrous sequential hermaphrodite, like Asian seabass. All individuals first mature as males, making the production of so-called “intermediate generations” (labeled with gray circle on the right side) possible by crossing these young males with females from the previous generation. For an F1 × P cross the resulting generation is called F1.5 as they are F2s from the paternal side and F1s from the maternal one. Labels: P – parental (F0) generation; F1 and F2 – the first two generations of selected individuals. F1.5 – an “intermedate generation” produced by back-crossing protandrous hermaphroditic F1 males to founder (P) females.