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Harnessing genomics to fast-track genetic improvement in aquaculture

Nature Reviews Genetics volume 21, pages 389–409 (2020)Cite this article

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Abstract

Aquaculture is the fastest-growing farmed food sector and will soon become the primary source of fish and shellfish for human diets. In contrast to crop and livestock production, aquaculture production is derived from numerous, exceptionally diverse species that are typically in the early stages of domestication. Genetic improvement of production traits via well-designed, managed breeding programmes has great potential to help meet the rising seafood demand driven by human population growth. Supported by continuous advances in sequencing and bioinformatics, genomics is increasingly being applied across the broad range of aquaculture species and at all stages of the domestication process to optimize selective breeding. In the future, combining genomic selection with biotechnological innovations, such as genome editing and surrogate broodstock technologies, may further expedite genetic improvement in aquaculture.

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Fig. 1: Summary of global aquaculture diversity and production.
Fig. 2: Genomic selection within an aquaculture breeding programme.
Fig. 3: Discovering functional variants using genomics and genome editing.
Fig. 4: Potential application of surrogate broodstock technology to accelerate genetic gain.

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Acknowledgements

The authors acknowledge funding from the UK Biotechnology and Biological Sciences Research Council (BBSRC), the UK Natural Environment Research Council (NERC) and the Scottish Aquaculture Innovation Centre via the AquaLeap project (reference numbers BB/S004343/1, BB/S004181/1, BB/S004416/1 and BB/S004300/1), and BBSRC Institute Strategic Programme grants (BBS/E/D/20241866, BBS/E/D/20002172 and BBS/E/D/20002174).

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Authors and Affiliations

  1. The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK

    Ross D. Houston, Tim P. Bean, Daniel J. Macqueen, Manu Kumar Gundappa, Ye Hwa Jin & Diego Robledo

  2. Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK

    Tom L. Jenkins, Jamie R. Stevens & Eduarda M. Santos

  3. Institute of Aquaculture, University of Stirling, Stirling, UK

    Sarah Louise C. Selly & Andrew Davie

  4. School of Biological Sciences, University of Aberdeen, Aberdeen, UK

    Samuel A. M. Martin

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  1. Ross D. Houston
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  2. Tim P. Bean
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  4. Manu Kumar Gundappa
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  12. Diego Robledo
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The authors contributed equally to all aspects of the article.

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Correspondence to Ross D. Houston.

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Nature Reviews Genetics thanks L. Bernatchez, D. Jerry, N. H. Nguyen and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Glossary

Aquaculture

The farming of fish, crustaceans, molluscs, aquatic plants and algae in freshwater or saltwater environments, typically for human food.

Genetic gains

Improvement in average genetic value, and therefore improved phenotypes, in a population due to selection over cycles of selective breeding.

Base populations

Populations of animals used to start a selective breeding programme.

Genomic selection

The selection of breeding individuals for genetic improvement of a trait of interest based on the use of genome-wide genetic markers to estimate genomic breeding values. Genetic marker genotypes and phenotypes are measured in a reference population to predict breeding values of selection candidates that have genotypes only.

Breeding nuclei

The elite broodstock animals that are maintained only for breeding, which is followed by multiplication and dissemination of the genetically improved animals for production.

Surrogate broodstock

Sterile animals used for the production of gametes of another individual, strain or species.

Broodstock

A group of sexually mature individuals used in aquaculture for breeding purposes.

Behavioural plasticity

The ability of an organism to change its behaviour following exposure to stimuli, such as changing environmental conditions.

Genetic bottlenecks

Sharp reductions in genetic diversity, typically due to large reductions in population size caused by environmental events or human activities.

Linked reads

Linking together of short sequence reads to provide long-range orientation, based on the addition of a unique DNA barcode to each read generated from an individual molecule.

Scaffolding

An approach during genome assembly where contigs (that is, continuous assembled sequences) are linked into larger contiguous sequences including gaps of known length.

Genotyping by sequencing

(GBS). A method using high-throughput sequencing to discover and genotype genome-wide single-nucleotide polymorphisms within a population.

Inbreeding depression

The reduced biological fitness in a given population as a result of inbreeding, typically due to deleterious recessive alleles.

Sequential hermaphroditism

Where an individual in a species is born as one sex but can later change to the opposite sex.

Mass spawning

Release of high numbers of eggs and sperm into the water, where fertilization occurs externally. Also known as broadcast spawning.

Soft sweeps

Increases in frequency and/or fixation of a favourable allele at an existing polymorphic locus due to strong positive selection pressure.

Marker-assisted selection

(MAS). The selection of breeding individuals for genetic improvement of a trait of interest based on genetic markers linked to a quantitative trait locus affecting that trait.

Quantitative trait locus

(QTL). A region of the genome that explains a significant component of variation in a trait of interest.

Mendelian sampling

The chance factor in the process of distributing half the genetic material from each parent to the offspring, which is the source of within-family genetic variation.

SNP arrays

A type of DNA microarrays that are used to genotype genome-wide polymorphisms within a population.

Reference population

In genomic selection, the population of animals that have both genotypes and phenotypes. These data are used to estimate genetic marker effects, which are then applied to predict breeding values for genotyped selection candidates.

Accuracy

In the context of genomic selection, accuracy is the correlation between the estimated genomic breeding values and the true breeding values.

Phenotyping

Collection of measurements relating to traits of interest in the goals of a breeding programme.

Genomic best linear unbiased prediction

(GBLUP). A modification of the pedigree-based best linear unbiased prediction method that incorporates SNP information in the form of a genomic relationship matrix and defines the additive genetic covariance among individuals to predict breeding values.

Bayesian models

In the context of genomic selection, the use of multiple-regression methods incorporating prior information on marker effects, which are used widely for genomic prediction of breeding values.

Genotype imputation

The statistical inference of unobserved genotypes based on knowledge of haplotypes in a population, typically used to predict high-density marker genotypes when most individuals are genotyped for low-density marker genotypes.

Causative variants

Polymorphisms within the genome of a population that have a direct effect on a trait of interest, as opposed to simply being a genetic marker associated with the trait.

Genotype–phenotype gap

The gap in knowledge of how variation at the level of the genome causes an effect on a phenotype of interest.

Internet of things

A network of physical objects that use sensors and application program interfaces to connect and exchange data over the Internet.

Genomic relationship matrix

A matrix containing the estimation of the proportion of total genomic DNA shared by any two individuals based on genome-wide genetic marker data.

Introgression

The deliberate movement of a target locus from one species or strain (donor) into another (recipient) by the creation and repeated backcrossing of a hybrid with one of the donor species or strains.

Effective population size

The size of an idealized population that would give rise to the rate of inbreeding and the rate of change in variance of allele frequencies actually observed in the population under consideration. It is approximate to the number of individuals that contribute gametes to the next generation.

Germplasm

In the context of animal breeding, the genetic material of a breeding programme.

Primordial germ cells

The stem cells specified during early development that will differentiate to form male and female gametes, therefore representing the precursors of the germline.

Pleiotropic effects

In the context of genome editing, the unintended impacts on traits other than the target trait due to a specific edit.

Selection intensity

The number of phenotypic standard deviation units that selected parents are superior to the mean of a population.

Ovoviviparous

Producing offspring by means of eggs that are hatched within the body of the parent.

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Houston, R.D., Bean, T.P., Macqueen, D.J. et al. Harnessing genomics to fast-track genetic improvement in aquaculture. Nat Rev Genet 21, 389–409 (2020). https://doi.org/10.1038/s41576-020-0227-y

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