Potential of Genome Editing to Improve Aquaculture Breeding and Production

Abstract

Aquaculture is the fastest growing food production sector and is rapidly becoming the primary source of seafood for human diets. Selective breeding programs are enabling genetic improvement of production traits, such as disease resistance, but progress is limited by the heritability of the trait and generation interval of the species. New breeding technologies, such as genome editing using CRISPR/Cas9 have the potential to expedite sustainable genetic improvement in aquaculture. Genome editing can rapidly introduce favorable changes to the genome, such as fixing alleles at existing trait loci, creating de novo alleles, or introducing alleles from other strains or species. The high fecundity and external fertilization of most aquaculture species can facilitate genome editing for research and application at a scale that is not possible in farmed terrestrial animals. The Role of Aquaculture in Food SecurityFood security is a major and increasing global challenge, associated with a rapidly growing demand for high-quality animal protein. Competition for land use will present a serious limitation to the scope for increases in terrestrial crop and animal production [1,2]. Therefore, it is likely that aquaculture will have a growing role in meeting this rising food and nutrition demand. Fish production via aquaculture is now approximately equal to capture fishery production for the first time in history, will be the dominant source of seafood within a few decades [3], and is the fastest growing food production sector, predicted to grow by 31% over the next 10 years [4]. Fortunately, development potential is huge, with only~1% of suitable marine sites currently being used for aquaculture [5]. Furthermore, aquaculture production is considered efficient in terms of feed conversation and protein retention compared with most terrestrial livestock [6], and seafood is the major source of long-chain polyunsaturated fatty acids, which are considered essential for human health [7]. However, relative to many crop and livestock production systems, most aquaculture is at a formative stage and is typically a high-risk activity. Sustainability can be hindered by an initial lack of control of the reproduction cycles of species, and periodic collapses due to infectious diseases. Upscaling and improving the reliability of production will require disruptive innovation in engineering, health, nutrition, and genetic improvement technologies, the latter being the focus of this review. Genetic Improvement for Sustainable Aquaculture ProductionDomestication and genetic improvement of terrestrial livestock has occurred for several millennia, with organized breeding programs for most species in place for N50 years. The results have been striking; for example, selective breeding has led to a threefold increase in efficiency of milk production in cows, with similar gains for other target traits [8]. By contrast, relatively little aquaculture production is underpinned by modern selective breeding programs [9,10]. Most farmed aquatic species are eith...

Efficient CRISPR/Cas9 genome editing in a salmonid fish cell line using a lentivirus delivery system

“…The prospect of developing and applying a genome wide CRISPR KO screen in fish cell lines is very attractive for many reasons (Doench, 2018; Gratacap et al 2019) and the present system paves the way towards such a platform for salmonids. This has the potential to be transformative for the testing of candidate disease resistance genes generated by Genome-Wide Association Studies as well as de novo discovery of genes involved in host-pathogen interactions in fish.…”

“…This knowledge raises the possibility of enhancing genomic selection accuracy via increased weighting on functional variants. In addition, genome editing can potentially by applied to create de novo variation, or to introduce favourable alleles segregating in closely related strains or species (Gratacap et al, 2019).…”

“…The aforementioned genome editing approaches typically focus on a single target locus, and there are several examples of successful CRISPR editing of single loci in vivo in farmed fish species (e.g. Datsomor et al, 2019; Edvardsen et al, 2014), reviewed in (Gratacap et al, 2019)). CRISPR/Cas9 has also been successfully applied in salmonid cell culture models to investigate specific components of the interferon pathway (Dehler et al, 2019).…”

Livestock breeding for the 21st century: the promise of the editing revolution

“…The field of aquaculture was quick to adopt genome editor technology, with many groups reporting on its application in a diverse range of species (reviewed in Gratacap et al [39] ). Li and colleagues were among the first groups to highlight this potential [40] , demonstrating efficient editing of a number of genes in Nile tilapia, one of the most important aquaculture species globally. The establishment of effective culture conditions for pluripotent tilapia spermatogonial stem cells (SSCs) could prove to be a significant development [41] , as it offers the opportunity to sequentially introduce more complex changes into the germline than would be practical by the direct injection of the reagents into zygotes.…”

Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing

“…Finally, with the potential role for targeted genome editing (e.g. using CRISPR/Cas9) in future aquaculture breeding programmes, understanding the functional mechanisms underlying disease resistance traits is key to identifying target genes and variants for editing [15]. Previous studies into AGD-infected Atlantic salmon have suggested that the amoebae might elicit an immunosuppressive effect on the innate response of the host, with a concurrent up-regulation of the adaptive Th2-mediated response [16][17][18].…”