Received: 30 March 2022 Revised: 14 July 2022 Accepted: 17 July 2022

DOI: 10.1111/raq.12716

REVIEW

Genomic selection and its research progress in aquaculture

breeding

Hailiang Song | Tian Dong | Xiaoyu Yan | Wei Wang | Zhaohui Tian |
Ai Sun | Ying Dong | Hua Zhu | Hongxia Hu

Fisheries Science Institute, Beijing Academy of

Agriculture and Forestry Sciences & Beijing Abstract
Key Laboratory of Fisheries Biotechnology,
Since its introduction in 2001, genomic selection (GS) has progressed rapidly. As a
Beijing, China
research and application hot topic, GS has led to a revolution in the field of animal
Correspondence
and plant breeding. Thanks to its ability to overcome the shortcomings of traditional
Hongxia Hu, Fisheries Science Institute, Beijing
Academy of Agriculture and Forestry breeding methods, GS has garnered increasing attention. Both theoretical and practi-
Sciences & Beijing Key Laboratory of Fisheries
cal breeding studies have revealed the higher accuracy of GS than that of traditional
Biotechnology, Beijing 100068, China.
Email: huhongxia@bjfishery.com breeding, which can accelerate genetic gain. In recent years, many GS studies have
been conducted on aquaculture species, which have shown that GS produces higher
Funding information
Beijing Natural Science Foundation, Grant/ prediction accuracy than traditional pedigree-based method. The present study
Award Number: 6222014; China Agriculture
reviews the principles and processes, preconditions, advantages, analytical methods
Research System of MOF and MARA, Grant/
Award Number: CARS-45-32; Beijing Joint and factors influencing GS as well as the progress of research in aquaculture into
Research Program for Germplasm Innovation
these aspects. Furthermore, future directions of GS in aquaculture are also discussed,
and New Variety Breeding, Grant/Award
Number: G20220628008; Youth Foundation which should expand its application to more aquaculture species.
of Beijing Academy of Agriculture and Forestry
Sciences, Grant/Award Number: QNJJ202105 KEYWORDS
aquaculture, breeding, future direction, genomic selection, method, research progress

1 | I N T RO DU CT I O N
In 2018, the estimated global fish production reached about 179 mil-
lion tons. Of this, 156 million tons were used for human consumption,
which is equivalent to an average person eating about 20.5 kg of fish
every year.1 However, at present less than 10% of aquaculture pro-
duction is based on genetically improved animals, despite the rapid
2
growth in annual genetic gain of aquaculture species. Furthermore,
with continuous population growth, pressure on global fisheries is
3
expected to rise. Although conventional breeding programmes have
played a critical role in the genetic improvement of
50 important
4,5
aquaculture species, the low efficiency of this approach can not
meet human needs. Therefore, modern breeding technologies must
be urgently applied to accelerate the genetic improvement of aquacul-
ture species.
In conventional breeding, highest genetically ranked individuals
are selected based primarily on their phenotypes. This approach is
more effective for the selection of quality traits controlled by a single
gene but less effective for the selection of quantitative traits that are
greatly affected by the environment. With advances in the theory of
quantitative genetics, breeders have successively proposed best linear
unbiased prediction (BLUP),6 which combines pedigree and pheno-
type records using all relevant information to estimate the breeding
value (EBV) of individuals. Furthermore, with the development of
computational technologies, BLUP (selective breeding) has been used
to improve various economic traits in many aquaculture species, such
as Vibrio alginolyticus resistance in Pacific oyster (Crassostrea gigas),7
carotenoid traits in Chinese mitten crab (Eriocheir sinensis),8 gill-
associated virus resistance in black tiger shrimp (Penaeus monodon),9
tilapia lake virus resistance in Nile tilapia (Oreochromis niloticus),10
growth and survival in rohu carp (Labeo rohita)11 and growth and egg-
related traits in Russian sturgeon (Acipenser gueldenstaedtii).12 How-
ever, conventional BLUP yields low genetic gain for certain traits, such
as traits with low heritability (e.g., disease resistance traits), traits that
are difficult to measure (e.g., disease resistance and behavioural traits),
sex-restricted traits (e.g., reproductive and oviposition traits) and traits

274 © 2022 John Wiley & Sons Australia, Ltd. wileyonlinelibrary.com/journal/raq Rev Aquac. 2023;15:274–291.

SONG ET AL.
that require slaughter for measurement (e.g., meat quality and carcass
composition traits), necessitating breakthroughs using novel breeding
methods.
With advances in genome sequencing and reduction in the cost
of related technologies, massive molecular marker (e.g., single-
nucleotide polymorphism [SNP] marker) data have been accumulated.
Breeders have started exploring the use of genomic information to
improve the accuracy of individual selection. Currently, there are two
major breeding methods that apply genomic information, namely,
marker-assisted selection (MAS)13 and genomic selection (GS).14
Marker-assisted selection has only proven to be useful when there
are genes with a relatively large effect on a trait, for example, for
infectious pancreatic necrosis resistance in Atlantic salmon (Salmo
salar), where a single gene explains 80%–100% of the genetic varia-
tion for the trait.15,16 However, the application of MAS to improve
complex traits controlled by many genes with a small effect is limited.
This is because (1) quantitative trait loci (QTL) detection is difficult,
and most effort is spent on finding major genes. Moreover, (2) few
large-effect QTLs are known, and even those found still only partly
explain the genetic variation in given traits. Therefore, despite sub-
stantial efforts devoted to detect QTLs in aquaculture species, pro-
moting MAS application in aquaculture breeding remains a
challenge.17 To overcome the deficiencies of MAS, Meuwissen et al.14
suggested a different approach, known as GS. Unlike MAS, GS
enables the estimation of breeding values by estimating the effects of
markers at a high density (HD) covering the whole genome, thus being
able to explain greater genetic variations in given traits. Furthermore,
GS gives a better estimate of true genetic relationships among individ-
uals than pedigree data and achieves higher prediction accuracy of
the EBV, for example, without considering inbreeding, the kinship
coefficient between full siblings estimated using pedigree information
is 0.5, whereas the true kinship coefficient obtained using genomic
information may be less or greater than 0.5.
To this end, the present review summarises the technology of GS,
outlines research progress related to the application of GS in aquacul-
ture breeding, and discusses future directions of GS in aquaculture.
The present review aims to provide aquaculture scientists and breed-
ing companies a general overview of the potential and gaps of GS in
aquaculture breeding.
2 | TEC HNOLOGY OF GS
2.1 | Principle and process of GS
Genomic selection is a molecular breeding method proposed by Meu-
14
wissen et al. The principle of this method is to use whole genome
marker and phenotypic data to estimate the effect value of each
molecular marker or chromosome segment and obtain the individual
EBV by adding the effect values of all markers.14 The EBV obtained
thus is called the genomic EBV (GEBV). Also, by fitting all markers
simultaneously, GS potentially uses all of the total genetic variance
available. A basic assumption of GS is that every QTL or gene that
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275
affects quantitative traits is in linkage disequilibrium (LD) with at least
one molecular marker (e.g., SNP marker) among genome-wide markers
(Figure 1). Therefore, GS can simultaneously fit all markers in the
model, regardless of whether they are statistically significant or not,
and can be traced back to all QTLs that affect traits, which explains
the “polygene hypothesis” of quantitative genetics from a molecular
perspective and achieves accurate prediction of GEBVs.
The basic process of GS is as follows. First, reference and candi-
date populations are established. Individuals in the reference popula-
tion possess the genotypic and phenotypic information, and the
reference population is representative of the whole population.
Meanwhile, individuals in the candidate population only require geno-
typic information. The statistical model used for GS is:
y ¼ 1μ þ W 1 X1 þ W 2 X 2 þ … þ W n X n þ e, where W 1 is the coded geno-
type of SNP j for j = 1,…, n, X 1 is the allele substitution effect of SNP j
for j = 1,…, n and n is the number of SNPs. X1 as random effects with
prior distribution N(0, σ 2j ). Different statistical models are used to esti-
mate the SNP effect (x1, x2, x3…) of the reference population. Next,
according to the SNP effect and SNP genotype (w1, w2, w3…, coded
as 0, 1 and 2 based on the number or copy of one allele) of the candi-
date population, GEBV (GEBV = w1x1 + w2x2 + w3x3…) of the can-
didate population is calculated. Alternatively, GEBV of the candidate
population can be calculated directly by solving the mixed model
equations. Finally, highest genetically ranked individuals are selected
based on GEBV (Figure 2).
2.2 | Precondition for GS
The precondition for GS is high-throughput genotyping technology of
genome-wide markers. In general, phenotypic records of traits are
available in conventional breeding systems; however, HD marker
genotypes require rapid detection of markers covering the whole
genome. Currently, SNPs, which are DNA sequence polymorphisms
caused by a single nucleotide variation in the genome, are considered
the ideal markers due to their high abundance, high reproducibility
and relatively easy high-throughput detection.18 In recent years,
genomic sequencing and reference genome assembly of many aqua-
culture species, including Atlantic salmon,19 grass carp (Ctenopharyn-
godon idella),20 Pacific white shrimp (Litopenaeus vannamei)21 and
Manila clam (Ruditapes philippinarum),22 have been completed. For
specific species, the large number of SNP markers generated through
genome sequencing have laid the foundation for the application of
GS. Low-coverage resequencing can reduce the cost of genotyping
and has broad application prospects. Studies have shown that when
sequencing depth is less than or equal to 1X, the use of genotype
imputation can produce genomic prediction accuracy similar to high-
coverage resequencing in pig (Sus scrofa)23 and dairy cattle (Bos tau-
rus).24 Zhang et al.25 compared the effect of different sequencing
depths on the accuracy of genome prediction in large yellow croaker
(Larimichthys crocea) populations and noted that the genomic predic-
tion accuracy obtained using 0.5X was similar to that obtained using
8X. In addition, genotyping by sequencing (GBS) has allowed for rapid
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276 SONG ET AL.

F I G U R E 1 Linkage disequilibrium between SNP markers and QTLs/genes in the whole genome. Quantitative traits (disease resistance and
growth) are usually affected by many genes with large or small effects (the peak of black bands), but these genes are as unknown as the black
box, and consequently the benefit from marker-assisted selection is limited by the proportion of the genetic variance explained by the
quantitative trait loci (QTL). However, a large number of single-nucleotide polymorphisms (SNPs) (genotype coded as 0, 1 and 2) in genome can
be obtained by SNP genotyping technology. Given the large number of SNPs, it is expected that every QTL or gene that affects quantitative traits
is in linkage disequilibrium (LD) with at least one SNP marker. Therefore, genomic selection can be traced back to all QTLs that affect traits

F I G U R E 2 Basic process of genomic selection in aquaculture. Reference population and candidate population are established from a number
of families. These individuals in reference population can be phenotyped for growth or disease resistance traits using phenotyping technology
(e.g., machine vision). Both candidate population and reference population are genotyped by genotyping technology (e.g., re-sequencing), and the
phenotype of candidate population is unknown. The genotypes can be represented by a variable (w), which takes the values 0 or 1 or
2 corresponding to one of the homozygotes, the heterozygote or the other homozygote. The statistical analysis of the reference population
estimates effects for each marker (x) using statistical method (e.g., GBLUP), and hence a prediction equation can be generated that combines all
the marker genotypes with their effects to predict the breeding value (GEBV) of each individual. This prediction equation can then be applied to
candidate population and excellent breeders are selected based on GEBV

advances in aquaculture genetics and breeding to date, as reviewed
26
by Robledo et al. In particular, restriction site-associated DNA
sequencing (RAD-Seq) has been widely used to generate population-
level SNP data. Genotyping by sequencing techniques are suitable for
species with high-quality reference genomes, even species without
reference genomes can be assembled by de novo, and the assembled
fragments can be used as reference sequences to develop markers.
Therefore, these methods have been widely used by researchers and
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SONG ET AL. 277

companies in relatively understudied non-model aquaculture species.
Vallejo et al.27 compared the prediction accuracy of RAD-Seq and
SNP chips for the bacterial cold water disease resistance of rainbow
trout (Oncorhynchus mykiss) and found that although the marker den-
sity of the SNP chip was higher (
40K for SNP chip vs. 10K for RAD-
Seq), the selection accuracy of the two technologies was comparable.
In addition, they found that compared with the resequencing technol-
ogy, the SNP chip technology required a lower cost and provided a
faster detection speed. SNP chips have been widely used in livestock
GS. Table 1 lists commercial SNP chips commonly used in aquaculture
species, such as low-density Pacific Oyster Illumina GoldenGate 1K
chip (marker number 1K, commonly called the 1K chip), medium-
density Atlantic salmon Affymetrix Axiom 50K chip and HD catfish
(Silurus spp.) Affymetrix Axiom 690 K chip.
2.3 | Advantages of GS
The advantages of GS are mainly reflected in the following four
aspects. First, it does not rely on phenotypic information for candidate
individuals and candidate individuals are selected based on the GEBV,
which can distinguish the differences between individuals. Genomic
selection can be performed as soon as DNA is available, which allows
accurate selection in early stage of life, shortens the generation
interval,47 offers greater advantages in the selection of sex-restricted
traits47 and low-heritability traits.48 Second, GS can explain all genetic
variations in the genome. A basic premise of GS is to exploit the LD
between SNPs and QTLs (major sources of genetic variation), which
can explain all genetic variants in the genome, thereby improving the
accuracy of selection. Third, GS can negate potential limiting effects
of genotype by environment (G  E) interactions. Mulder49 reported
that GS was much better able to increase resilience and reduce envi-
ronmental sensitivity than traditional breeding schemes. Finally, GS is
expected to reduce inbreeding50 and increase in rate of genetic gain
at a set level of inbreeding.51 This is mainly because GS gives a more
accurate prediction of the true genetic similarity between individuals
than pedigree data, which increases the difference between full-sib-
lings, thereby reducing the probability of their co-selection for seeding
and ultimately preventing inbreeding. Genetic progress (G) can be cal-
irσ g
culated using the following formula: G ¼ L , where i is the intensity
of selection, r is the accuracy of selection, σ g is the genetic standard
deviation and L is the generation interval. Based on the formula, GS
can accelerate genetic progress. Genomic selection offers diverse
advantages in different species. In dairy cattle, GS significantly
enhanced genetic progress mainly by reducing the generation interval
and improving the GEBV accuracy of candidate individuals.52 In pigs,
however, GS did not significantly shorten the generation interval due
to the short breeding cycle, which improved GEBV accuracy and
accelerated genetic progress. Genomic selection is particularly suitable
for selecting traits that are difficult to measure (disease resistance,
feed utilisation, reproductive traits, health traits and meat quality
traits),53 for example, Lillehammer et al.54 demonstrates large
potential for further genetic improvement of White spot syndrome
virus resistance in the evaluated L. vannamei population using

TABLE 1 SNP chips commonly used in aquaculture species

Species Number of SNPs Platform technology Reference

Salmo salar 286,021 Affymetrix Axiom 28
200,000 Affymetrix Axiom 29
55,000 Affymetrix Axiom 30
5919 Illumina Infinium 31
Silurus spp. 250,113 Affymetrix Axiom 32
693,567 Affymetrix Axiom 33
Oncorhynchus kisutch 220,001 Affymetrix Axiom 34
Cyprinus caprio 250,000 Affymetrix Axiom 35
Crassostrea gigas and Ostrea edulis 14,950 Affymetrix Axiom 36
Penaeus monodon 6000 Illumina Infinium 37
Larimichthys crocea 579,400 Affymetrix Axiom 38
Paralichthys olivaceus 48,697 Affymetrix Axiom 39
Oreochromis niloticus 58,466 Affymetrix Axiom 40
65,000 ThermoFisher Axiom 41
Crassostrea gigas 1536 Illumina GoldenGate 42
190,420 Affymetrix Axiom 43
40,625 Affymetrix Axiom 36
Litopenaeus vannamei 8967 Illumina Infinium 44
Oncorhynchus mykiss 57,501 Affymetrix Axiom 45
Pinctada maxima 2782 Illumina Infinium 46

278
GS. Compared with livestock, aquatic animals exhibit higher fecundity
and larger family size, which offers two major advantages. First, the
closer relationship between reference and candidate populations
leads to a higher prediction accuracy even at a lower SNP marker den-
sity, because related individuals share longer genome fragments. Sec-
ond, traditional pedigree records are strictly not needed, because the
relationships between individual fish are calculated based on the
genetic marker information only. In addition, some aquatic animals,
such as sturgeons, show a long breeding cycle and late sexual matu-
rity. Specifically, cultured Russian sturgeons require 5–6 years to
mature. The application of GS in sturgeons can improve the prediction
accuracy, especially for the traits that are difficult to measure, for
example, caviar yield, so as to improve the genetic gain.
2.4 | Methods of GEBV calculation
GEBV calculation methods can be classified into the following three
categories. The first category is based on the BLUP theory. As one of
the earliest proposed methods, ridge regression BLUP (RRBLUP)14
first estimates the SNP marker effect values and then calculates the
GEBV of the candidate population. VanRaden55 proposed genomic
BLUP (GBLUP) that can directly calculate the GEBV of the candidate
population and produces the same result as RRBLUP. Genomic BLUP
replaces the conventional pedigree-based relationship matrix (A)
matrix of BLUP by constructing a genomic relationship matrix (G).
56
Misztal et al. proposed a method that combines phenotype, pedi-
gree and genotype data into a single step evaluation. This method is
called single-step GBLUP (ssGBLUP) and involves replacing the A in
conventional BLUP with a realised relationship matrix (H), which com-
bines pedigree and genomic relationships. As a modification of
GBLUP, the superiority of ssGBLUP over GBLUP has been proven in
several studies.57–64 Furthermore, the algorithm for proven and young
animals,65 which was proposed to make getting the inverse for mil-
lions of animals simple and improve the computational efficiency of
GBLUP and ssGBLUP. In addition, many other improved methods
based on GBLUP have been proposed. For instance, TABLUP pro-
posed by Zhang et al.66 weights G for different traits and offers obvi-
ous advantages for traits with major genes. Moreover, the BLUPjGA
method proposed by Zhang et al.67 divides the genomic relationship
matrix into two parts, namely one marker with large effect and
another with small effect, and assigns different weights to each part.
68
The GFBLUP method proposed by Edwards et al. divides additive
variance in the mixed linear model into a genomic feature part and the
remaining part, providing high accuracy on simulation data,68 dairy
cattle69 and pigs.70,71
The second category is based on the Bayesian theory. According
to variance distribution of the SNP effect, BayesA, BayesB, BayesCπ
and BayesR models have been developed. In the BayesA model, the
SNP effect is assumed to present a t-distribution,14 under which some
SNPs produce a larger effect than under the assumption of normality,
because a t-distribution presents broader tails than a normal distribu-
tion. In the BayesB model, a fraction (π) of the SNPs is assumed to
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SONG ET AL.
produce no effect, while the other fraction (1  π) produces an effect
drawn from a t-distribution.14 BayesCπ is similar to BayesB, except
that SNPs with an effect are assumed to show a normal distribution
instead of a t-distribution.72 BayesCπ is computationally simpler to
solve than BayesB, although it still yields almost the same accuracy.72
BayesR is an extension of BayesCπ with multiple normal distributions,
which allows reliable prediction under a range of genetic architec-
tures, including traits whose genetic variants produce a moderate
effect.73 The advantage of the Bayesian method is that it assumes
that markers have different variances, which is more consistent with
the biological basis of complex traits; however, the disadvantage is
that the calculation time is rather long. Recent studies have proven
that the Bayesian method is better than the GBLUP method for simu-
lated data74; however, for real data, Bayesian methods perform simi-
larly or slightly better than GBLUP method.18,47 MacLeod et al.75
proposed the BayesRC method using omics information, in which the
markers are divided into several groups based on prior information
(≥2). For instance, markers within or close to the candidate gene are
assigned to the first group, and the other markers are assigned to the
second group. Analysis is performed using BayesR for each group. In
addition, Fernando et al.76 proposed a single-step Bayesian method,
which can simultaneously analyse both individuals with and without
genotype information. Compared with the conventional Bayesian
method, which uses only animals with genotype information, this
method shows a higher prediction accuracy.
The third category is based on machine-learning algorithms.
Thanks to rapid developments in this field, machine learning algo-
rithms have found applications in genomic prediction.77 Commonly
used algorithms include support vector machine (SVM),78 random for-
est (RF),79 reproducing kernel Hilbert space (RKHS)80 and deep learn-
ing (DL).81 These methods offer the flexibility to model multiple types
of genetic effects, including additive and dominant effects as well as
epistasis effects. Machine learning methods primarily differ from con-
ventional statistical methods (based on BLUP and Bayesian theory) in
that they are nonparametric models providing tremendous flexibility
to adapt to the complex associations between data and output.82
Overall, no current method offers absolute advantages in all situa-
tions, in practical breeding, it is necessary to evaluate the performance
of various statistical methods and then select the most suitable
method. Genomic BLUP and Bayesian methods are widely used in
aquaculture species (Table 2). Table 3 summarises common GS
methods.
2.5 | Factors affecting the accuracy of genomic
prediction
The accuracy of genomic prediction is measured using correlation
coefficient between the GEBV and true breeding values (TBV). How-
ever, in actual breeding, TBV cannot be obtained. Typically, individuals
with desired phenotypic performance and high reliability in terms of
conventional breeding values are selected as candidates to form a val-
idation population, and the accuracy of genomic prediction is
 TABLE 2 Studies of genomic selection in aquaculture species

Number of
genotyped Accuracy of genomic
SONG ET AL.

Species individuals SNPs Traits Method prediction Reference

Atlantic Salmon (Salmo 622 111,908 Growth GBLUP 0.700 83

salar)
531/588 33,000 Sea lice resistance GBLUP 0.340–0.610 84
624 78,362 Sea lice resistance, body weight GBLUP 0.580–0.690 85
2404 36,616 Sea lice resistance GBLUP, BayesC, BayesLASSO 0.490–0.500 86
2392 49,684 Salmon rickettsial syndrome resistance GBLUP, RRBLUP, BayesC, BayesLASSO 0.368–0.424 87
1430 7168 Amoebic gill disease (AGD) resistance GBLUP 0.620–0.700 88
1333 53,109 AGD resistance GBLUP 0.490–0.720 89
610 78,362 Sea lice resistance GBLUP 0.530 90
563 49,726 Omega-3 fatty acid content GBLUP 0.321–0.563 91
1385 745,998 Sea lice resistance GBLUP, BayesC 0.605–0.676 92
2258/2345 35,479/32,579 Sea lice resistance, body weight GBLUP 0.390–0.780 93
Rainbow trout 636 10,052 Bacterial cold water disease (BCWD) resistance BayesB, BayesC, WssGBLUP 0.410–0.500 27
(Oncorhynchus mykiss) 1473 35,636 BCWD resistance BayesB, ssGBLUP, WssGBLUP 0.630–0.710 94
930 35,636 BCWD resistance BayesB, ssGBLUP, WssGBLUP 0.500–0.720 95
1934 27,490 Salmon rickettsial syndrome resistance GBLUP, ssGBLUP, BayesC, BayesLASSO 0.470–0.798 96
768 38,292 Infectious pancreatic necrosis virus disease resistance ssGBLUP 0.530–0.560 97
1044 35,397 Infectious haematopoietic necrosis virus disease ssGBLUP, WssGBLUP 0.300–0.390 98
resistance
1185/1137 35,900/33980 Columnaris disease resistance WssGBLUP 0.770–0.810 99
1624 34,640 Infectious haematopoietic necrosis virus disease ssGBLUP, WssGBLUP, BayesB, BayesC 0.330–0.380 100
resistance
1343 57,000 Female reproduction traits GBLUP 0.500–0.600 101
1568 35,303 Fillet yield and firmness ssGBLUP 0.260–0.380 102
1382 29,652 Fatty acid composition GBLUP 0.360–0.700 103
Large yellow croaker 500 29,748 Eviscerated weight, whole body weight GBLUP, BayesB 0.050–0.450 104
(Larimichthys crocea) 222 5,391,554 Visceral white spot disease resistance GBLUP 0.380 25
811 16,515 Parasitic ciliate Cryptocaryon irritans resistance BayesLASSO 0.200–0.600 105
326/565 34,994 Adapting to high plant protein diet GBLUP, BayesB 0.064–0.214 106
Gilthead sea bream 825 12,085 Pasteurellosis resistance RRBLUP, BayesA, BayesB, BayesC 0.380–0.460 107
(Sparus aurata)
1296 28,330 Pasteurellosis resistance GBLUP, BayesB, BayesC, BayesLASSO 0.545–0.569 108
841 21,773 Sparicotyle chrysophrii resistance GBLUP 0.550 109
1026 43,618 Pasteurellosis resistance GBLUP 0.610–0.640 110

(Continues)
279

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 TABLE 2 (Continued)
280

Number of
genotyped Accuracy of genomic
Species individuals SNPs Traits Method prediction Reference

Nile Tilapia (Oreochromis 1238 32,306 Growth and fillet weight and fillet yield ssGBLUP 0.601–0.621 111
niloticus)
1444 18,960 Growth and fillet yield GBLUP 0.290–0.540 112
2684 35,745 Streptococcus agalactiae resistance GBLUP 0.730–0.840 113
755 48,431 Feed-efficiency traits GBLUP, ssGBLUP 0.400–0.500 114
1780 45,595 Francisellosis resistance GBLUP, BayesB, BayesC, BayesS 0.310–0.630 115
2472 50,690 Streptococcus agalactiae resistance BayesB, BayesC, BayesR, BayesS, GBLUP 0.560–0.780 116
Pacific white shrimp 205 6359 Growth RRBLUP, BayesA, BayesLASSO 0.284–0.413 117
(Litopenaeus vannamei)
200 23,049 Growth RRBLUP, BayesA, BayesLASSO 0.499–0.619 118
200 23,049 Acute hepatopancreatic necrosis disease resistance GBLUP 0.199–0.500 119
474 35,869 Feed efficiency traits GBLUP, ssGBLUP 0.566–0.706 120
Yellowtail kingfish 752 14,448 Growth GBLUP 0.440–0.830 121
(Seriola lalandi)
752 14,448 Skim fluke disease resistance GBLUP, KAML 0.165–0.432 122
Common carp (Cyprinus 1425 12,311 Growth GBLUP 0.660–0.710 123
carpio) 1425 15,615 Koi herpesvirus disease resistance RRBLUP, BayesA, BayesB, BayesC 0.510–0.550 124
Pacific oyster 820 23,388 Growth GBLUP 0.540–0.670 125
(Crassostrea gigas)
762 17,919 Ostreid herpesvirus resistance GBLUP 0.758 126
Japanese flounder 931 1,934,475 Edwardsiella tarda disease resistance GBLUP, BayesCπ 0.603–0.604 127
(Paralichthys olivaceus)
1099 4,978,724 Edwardsiella tarda disease resistance BayesB, ssGBLUP, WssGBLUP 0.600–0.660 128
European seabass 1538 9195 Viral nervous necrosis disease resistance RRBLUP, BayesA, BayesB, BayesC 0.660–0.710 129
(Dicentrarchus labrax)
972 50,136 Stress response, Vibrio anguillarum resistance, body GBLUP 0.310–0.600 130
weight
Yesso scallop 349 2364 Growth GBLUP, RRBLUP, BayesA, BayesB, LASSO 0.150–0.400 131
(Patinopecten
yessoensis)
Zhikong scallop (Chlamys 509 31,361 Growth GBLUP, BayesB, RKHS, SNN 0.370–0.580 132
farreri)
Channel catfish (Ictalurus 2911 54,837 Harvest and carcass weight ssGBLUP 0.240–0.380 133
punctatus)
Coho salmon 764 9389 Piscirickettsia salmonis disease resistance GBLUP, BayesC, ssGBLUP, WssGBLUP 0.299–0.807 134
(Oncorhynchus kisutch)
Yellow drum (Nibea 371 53,677 Body size-related traits BayesA, BayesB, BayesC, MMixp, GBLUP, CNN 0.145–0.412 135
albiflora)
Banana shrimp 562 9472 Hepatopancreatic parvovirus resistance and growth, GBLUP, BayesC, BayesCπ 0.420–0.760 136
(Fenneropenaeus carcass and quality traits
merguiensis)
SONG ET AL.

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SONG ET AL. 281

evaluated using the correlation coefficient between GEBV and response

Reference

Abbreviations: Bayes-Alphabet (e.g., BayesA, BayesB, BayesC, BayesS, BayesCπ, BayesR, BayesLASSO), Bayesian methods with different assumptions of SNP effect distribution; CNN, convolutional neural network; GBLUP,
variables. Common response variables include the original phenotype,88

genomic best linear unbiased prediction; KAML, machine learning-based method incorporating cross-validation, multiple regression, grid search and bisection algorithms; MMixp, Bayesian using markov chain Monte Carlo-
corrected phenotype value59 and de-regressed proof.140,141

137

138

139

based Pareto principle; RKHS, reproducing kernel Hilbert space; RRBLUP, ridge regression best linear unbiased prediction; SNN, sparse neural networks; ssGBLUP, single-step GBLUP; WssGBLUP, weighted ssGBLUP.
The accuracy of genomic prediction is affected by several factors,
which are divided into two major types: uncontrollable and controlla-
ble factors. Uncontrollable factors include the average length of chro-
Accuracy of genomic

mosomes, number of genes affecting traits and heritability of traits.

For instance, Daetwyler et al.142 found that the accuracy of GEBV
0.230–0.310

0.400–0.550
prediction

gradually decreased with increase in the number of QTLs but

0.460

increased with increase in the heritability of traits. These uncontrolla-

ble factors lead to significant differences in the implementation
effects of GS in different species, populations and traits. Controllable
factors include reference population size, marker density, GEBV esti-
mation method and the relationship between the reference and candi-
GBLUP, BayesLASSO, RRBLUP, BayesA,

date populations. These factors can be controlled via artificial means

to improve the accuracy of GEBV, which is another key consideration
and work direction in GS.
BayesB, BayesC
GBLUP, BayesB

2.5.1 | Reference population size

Method

GBLUP

Phenotypic information for the reference population is essential for

estimating the GEBV; therefore, the size of the reference population
plays a crucial role in the accuracy of GS. The larger the reference
population, the richer the phenotypic information, the more pheno-
typic records corresponding to each marker, and the higher the accu-
racy of GS.48,143 Conversely, if the reference population is small,
marker effect value or chromosome fragment effect value cannot be
accurately estimated. Regardless of the heritability of traits, the accu-
Note: Before and after the slash (/) represent two different populations that were analysed separately.

racy of GS increases with increase in the size of the reference popula-

tion. For small reference populations, combining populations of the
Scuticociliatosis resistance

same breed or populations of related breeds could increase the accu-

racy of genomic prediction, as observed for Holstein populations in
EuroGenomics144 as well as North American consortia145 and pig
Heat tolerance

populations in China.71,143 Similar study has also been reported for

disease resistance in European sea bass (Dicentrarchus labrax) and the
Growth
Traits

gilthead sea bream (Sparus aurata), in which with the increase of refer-
ence population size, the accuracy of genome prediction is
improved.110 Our previous study has also clarified that as the refer-
ence population size decreased, the accuracy of genomic prediction
18,125

16,162

64,788

decreased in four aquaculture species (Atlantic salmon, common carp

SNPs

[Cyprinus carpio], sea bream and rainbow trout).146

Number of
genotyped
individuals

1349

1122

2.5.2 | Marker density

455
(Continued)

GS uses a whole-genome panel of dense markers simultaneously so

(Oplegnathus fasciatus)
Pacific abalone (Haliotis
Turbot (Scophthalmus

that all QTLs are in LD with at least one marker. Increase in marker
density increases the LD between markers and QTLs, and the resul-
discus hannai)

tant increase in the estimation accuracy of marker effect value or

Rock Bream
maximus)
TABLE 2

chromosome segment effect value improves the accuracy of

Species

GS. Generally, the higher the marker density, the higher the accuracy
of GS.147,148 Occasionally, however, the increase in marker density
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282 SONG ET AL.

TABLE 3 Methods of genomic selection

Category Method Feature Reference

Based on the BLUP RRBLUP All SNPs have an effect, and effects follow a normal distribution 14
theory GBLUP Equivalent to RRBLUP, but constructs a genomic relationship matrix (G) 55
ssGBLUP Constructs a combined genotype–pedigree relationship matrix (H) 56
TABLUP Constructs a trait-specific relationship matrix (TA) based on marker 66
genotypes and their weights relative to the trait of interest
BLUPjGA Constructs a trait-specific relationship matrix (GA), which puts an optimal 67
weight on a subset of SNPs with the strongest effects
GFBLUP Divides additive variance in the mixed linear model into a genomic 68
feature part and the remaining part
Based on the BayesA All SNP effects follow Student's t-distribution 14
Bayesian theory BayesB A fraction (π) of the SNPs with zero effect and remainder (1  π) with a 14
t-distribution
BayesC/Cπ A fraction (π) of SNPs with zero effect and the remainder (1  π) with a 72
normal distribution, π was estimated from the data (BayesCπ)
BayesR SNP effects are assumed to follow a mixture of normal distributions 73
BayesRC Allocates a priori all genotyped variants into (≥2) classes according to 75
their genome sites; all variants within or close to the candidate genes
are allocated to Class I and all other variants to Class II
Single-step Uses individuals with and without genotype information at the same time 76
Bayesian method
Based on machine RF Uses multiple decision trees and bootstrap aggregation to perform 79
learning classification or regression tasks
algorithms SVM Relies on the construction of multidimensional hyperplanes that separate 78
similarly labelled objects into linearly separable sets
RKHS Uses a nonlinear kernel function to map the data to a higher dimensional 80
kernel space
DL Uses neural networks with a large number of simple computational units, 81
growing into more complex modelling systems

Abbreviations: Bayes-Alphabet (e.g., BayesA, BayesB and BayesCπ), Bayesian methods with different assumptions of SNP effect distribution; BLUPjGA,
BLUP-given genetic architecture; DL, deep learning; RF, random forest; GBLUP, genomic best linear unbiased prediction; GFBLUP, genomic feature BLUP;
RKHS, reproducing kernel Hilbert space; RRBLUP, ridge regression best linear unbiased prediction; ssGBLUP, single-step GBLUP; SVM, support vector
machine; TABLUP, BLUP including a trait-specific relationship matrix.

induces some noise markers, which interfere with the accuracy of the
GEBV estimation. For example, Pérez-Enciso et al.149 stated that using
whole-genome sequencing data did not increase prediction accuracy
150
compared to HD array data. van Binsbergen et al. reported that GP
with imputed whole-genome sequencing data did not lead to a higher
prediction accuracy, compared to the HD array data from more than
5000 Holstein–Friesian bulls. Similar results were also reported by
Gong et al.,138 in which models with
1000 SNPs will provide predic-
tive ability equivalent to that by using all the available SNPs for com-
plex growth-related traits in Rock Bream (Oplegnathus fasciatus). In
addition, the cost of chips with different densities and sequencing
must be considered to balance efficiency and cost.
2.5.3 | GEBV estimation methods
The GEBV estimation method is the core of GS. The commonly used
GEBV estimation methods are introduced above (Table 3). Owing to
the different assumptions of various calculation methods, their scope
of application varies. In addition, species type, population size and
traits lead to differences in evaluation methods. Therefore, the evalu-
ation method must be selected according to the desired scenario and
its effects should be verified to maximise the advantages of GS.
2.5.4 | Relationship between reference and
candidate populations
Generally, the closer the relationship between the reference and can-
didate populations, the higher the accuracy of GS.58,151,152 In aquatic
animals, the close relationship between the reference and candidate
populations yields a high GS accuracy. Saura et al.153 reported that
the current effective population size is small (equal to or less than
50 fish) for turbot (Scophthalmus maximus), gilthead sea bream,
European sea bass and common carp, which indicates the often close
genetic relationship between populations of most aquaculture species.

SONG ET AL.
Fraslin et al.93 confirmed the importance of close genetic relationships
between training and selection populations in salmon breeding pro-
grammes. The accuracy of GS decreased with increase in the number
of generations between the candidate and reference populations.152
This is mainly because the degree of LD between molecular markers
and QTLs affecting the traits decreases with increase in the number
of generations, which in turn affects the accuracy of GEBV estima-
tion.152 Therefore, the reference population should be updated regu-
larly rather than statically.
3 | P R O G R E S S O F R E S EA RC H O N G S I N
A Q U A C U L T U RE B RE E D I N G
GS proposed almost 20 years ago has revolutionised design and
implementation of plant and animal breeding programmes, and has
become a promising tool for plant and animal breeding programmes
to accelerate the rate of genetic gain.154,155 Since the implementation
of GS in the United States, the rates of genetic gain per year have
increased from 50% to 100% for medium heritability traits (milk yield,
milk fat and milk protein) and 300% to 400% for low heritability traits
(somatic cell score, productive life and daughter pregnancy rate) in
154
dairy cattle. To date, GS has been conducted in about 20 aquacul-
ture species, among these aquaculture species, GS was first studied in
Atlantic salmon, and its application was realised thanks to the devel-
opment of the first HD SNP array and demonstration of its utility and
accuracy in predicting breeding values in a typical salmon breeding
programme.28,156 With the development of whole-genome sequenc-
ing technology and reduction in the cost of re-sequencing, research
on GS in aquaculture species has gradually advanced. Genomic selec-
tion has been applied to the complex traits of several important aqua-
culture species (Table 2), including Atlantic salmon,83,84,90 rainbow
trout,27,95,101 large yellow croaker,105 Nile tilapia,41,112 Pacific white
shrimp,54 Japanese flounder (Paralichthys olivaceus)128 and rock
138
bream, and so forth. Studies in aquaculture species have shown
that the accuracy of genomic predictions varies from 0.165 to 0.840
for traits associated with disease resistance, from 0.145 to 0.830 for
traits associated with growth and from 0.064 to 0.780 for traits asso-
ciated with feed efficiency, production yield and female reproduction,
the number of genotyped individuals and SNPs used in GS ranged
from 200 to 2911 and 2364 to 5,391,554, respectively (Table 2). In
addition, Houston et al.17 reviewed several cases in which the accu-
racy of genomic prediction was higher than that of conventional pre-
diction based on pedigree information in aquaculture species. On
average, the prediction accuracy increased by 22% for disease resis-
tance traits and by 24% for growth-related traits. Moreover, Boudry
157
et al. reviewed the current status of and developments in GS in
several major aquaculture species, including Atlantic salmon, rainbow
trout, Atlantic cod (Gadus morhua), American catfish, Pacific oyster,
European sea bass and gilthead sea bream, in member countries of
the International Council for the Exploration of the Sea, which pointed
out that the potential of GS is clear. For the practical application value
of GS, Verbyla et al.158 reported significant increases in the rate of
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283
genetic gain for amoebic gill disease resistance and harvest weight
attributed to the implementation of GS in Tasmanian Atlantic salmon,
whose value was estimated at AU$1 and AU$5 million per year,
respectively. Jerry et al.159 also indicated that higher levels of genetic
gain for barramundi (Lates calcarifer) growth-related traits would result
from the application of GS (GBLUP) than pedigree-based selection
(BLUP). These studies suggest that GS has great potential to improve
the rate of genetic gain in aquaculture species.
Most GS studies in aquaculture species used the GBLUP and
Bayesian methods to estimate the GEBV (Table 2), for example, Joshi
et al.115 reported that GBLUP and Bayesian methods (BayesB and
BayesC) could increase the predictive ability for resistance to Franci-
sellosis in commercial Nile tilapia population, compared to pedigree-
based models. Furthermore, incorporating preselected potential causal
markers into the GS model is an effective strategy to improve predic-
tion accuracy. For instance, Dong et al.160 reported that the accuracy
of genomic prediction for body weight-related traits in large yellow
croaker could be improved by preselecting SNPs based on SNP
effects. Yoshida and Yáñez161 reported that in rainbow trout, the
accuracy of genomic prediction for growth under chronic thermal
stress could be improved using preselected variants from GWAS.
Mapping and understanding the causative variants that have an
impact on complex traits has potential additional benefits for increas-
ing rates of genetic gain in breeding through improved selection accu-
racy, for example, Ni et al.162 reported that using only SNPs in or
around a gene from whole-genome sequencing data increased the
accuracy of GS in laying chickens. However, identifying causative vari-
ants of target traits is a knowledge gap to help bridge relationships
between phenotypes and genotypes in most aquaculture species. In
addition, several studies have reported the use of machine learning
methods (e.g., SVM, RF and DL) for genomic prediction of disease
resistance and growth traits of aquaculture species, and these
methods have been shown to improve the accuracy of genomic
prediction.163–165 In general, as assumptions and information used
vary with models, no model performs best in all situations and GBLUP
and Bayesian models are more commonly used in aquaculture species.
4 | FU T U R E D I R E C T I O N S
4.1 | Developing accurate phenotyping techniques
It is crucial to obtain accurate phenotypes in breeding programme
because the accuracy of trait measurements directly affects the accu-
racy of GS and thus the genetic gain per generation. Traditional man-
ual measurement methods are easily affected by subjective factors
such as experience, habits, preferences, and external environmental
interference, which make the measurement process time-consuming
and labour-intensive. In addition, aquatic animals are often highly sen-
sitive and easily coerced animals, and manual measurement can easily
cause harm to them, even lead to disease and death, affecting the nor-
mal growth of aquatic animals. Therefore, collecting such data directly
on selected candidates in the breeding nucleus and their relatives in

284
the test or production environments can limit genetic progress in
breeding programmes. Yang et al.166 and Zenger et al.18 reviewed the
application of machine learning and artificial intelligence in phenotyp-
ing of aquaculture species. Machine vision systems have been exten-
sively explored, and high concordance (>97%) between aquaculture
animal and image analysis and phenotypic measurements has been
167–169
demonstrated. Other emerging aquaculture phenotyping tech-
niques include hyperspectral imaging and near-infrared spectroscopy,
which can quantify the physical (e.g., size, weight and colour) and
chemical (e.g., protein, fat and unsaturated fatty acids) attributes of
169,170
aquatic animals with high prediction accuracy (>80%). Combina-
tion of high-throughput and high-resolution phenotyping in breeding
programme with GS is expected to allow for effective genetic
improvement of aquaculture species.
4.2 | Developing strategies to reduce GS cost
The main challenge for further implementation of GS is associated
with the costs and benefits of genotyping. In aquaculture breeding
programmes, genotyping of thousands of animals in each generation
is essential, which is expensive. Therefore, cost-effective strategies
must be developed to translate the benefits of GS into most aquacul-
ture species. Different strategies of selecting SNPs for low-density
panels have been reported to reduce the cost of GS. For instance,
Robledo et al.88 evaluated the effect of reduced SNP density based
on their minor allele frequency and their even position in the genome
on prediction accuracy in Atlantic salmon, and a reduction in marker
density to
2000 SNPs was sufficient to obtain high accuracy. Kriari-
dou et al.171 investigated the accuracy of genomic prediction by ran-
domly selecting markers from SNP chips in four aquaculture species and
found that SNP densities between 1000 and 2000 provided selection
accuracies close to those obtained with HD genotyping. Our previous
study on four species (Atlantic salmon, sea bream, common carp and
rainbow trout) showed that reducing the density of SNP panels to 3 K
was sufficient to obtain accuracies similar to those obtained using the
whole dataset, and the cost of GS with reduced SNP density was esti-
mated to be 50% lower than that of genotyping of all animals with HD
panels. In addition, when the reference population size was reduced by
10% uniformly from a full-sib family, the accuracy of genomic prediction
remained nearly unchanged, and the cost was reduced by 8%.146
In addition, genotype imputation, GBS and low-coverage
sequencing have also been used to reduce GS costs. First, genotype
imputation, which utilises LD information from haplotypes of a known
reference panel to predict missing genotypes and is achieved by
imputing low- to high-density SNP markers, and many studies have
reported that the use of imputation-based HD SNP markers could
improve the accuracy of GS without increasing the cost.90,94,172 Sec-
ond, as mentioned above, GBS and low-coverage sequencing are also
likely to help reduce GS costs by reducing genotyping costs. There-
fore, methods of low-cost genotyping and low-density panels com-
bined with genotype imputation hold potential and will help transfer
the benefits to aquaculture industries.
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SONG ET AL.
4.3 | Considering genotype by environment
(G  E) interactions in GS
Typically, economically important traits are complex and influenced by
genes, the environment and G  E interaction. Different production
systems and climates can induce G  E interactions on populations,
and consideration of these interactions in breeding decisions is imper-
ative. A G  E interaction is defined as different genotypes reacting
unequally to environment changes.173 Ignoring possible G  E inter-
actions may reduce genetic gains. In aquaculture production systems,
breeding companies typically supply fish to various farms worldwide,
either directly or via hatcheries. The environment of breeding farms
may be rather different from that of commercial production farms
(e.g., altitude, temperature, daylight, water quality, salinity and
farm management systems). Many studies have shown moderate or
strong G  E interactions in fish.174–181 In addition, Mulder49
expounded that GS offers great opportunities to exploit G  E to
increase resilience of animals. Jerry et al.159 reported that GBLUP pro-
vided greater accuracy for EBV prediction, higher expected genetic
gains and more effectively accounted for G  E interactions for the
cohort of fish reared in the two different commercial environments.
Therefore, G  E interactions must be considered in GS models for
aquaculture species. Multi-trait and reaction norm models are the two
common methods for handling G  E interactions in genetic evalua-
tions. Falconer et al.173 detected G  E interactions using a multi-trait
model, in which the same trait in different environments was regarded
as different traits and genetic correlation between traits in different
environments was a measure of G  E. The multi-trait model could
capture all the G  E interactions between these environments, while
its computational requirements will increase with the number of envi-
ronments. The application scenario of multi-trait model is when the
environment can be split into several discrete classes.182,183 For reac-
tion norm model, trait expression is on a continuous environmental
scale and breeding value and genetic parameters change gradually
along the environmental scale. At different locations on the environ-
mental scale, traits may have different means and (co)variances, and
there is a genetic correlation between trait expression at different
points of the environment scale.184 However, reaction norm model
captures only part of the G  E interactions in contrast to the multi-
trait model because it needs to accommodate a continuous range of
environmental values and cannot select excellent individuals using the
unique estimated breeding value in actual breeding.185,186 The main
application of reaction norm model is when the environmental vari-
ables explaining the G  E interactions are continuous.187 Therefore,
in aquatic animal breeding, the corresponding model should be
selected for G  E analysis according to the environment.
4.4 | Considering allele dosage in genomic
prediction for polyploid fish
Among vertebrates, fish have abundant polyploidization. The most dis-
tinctive and recognised autopolyploid fish include Salmonidae188,189 and

SONG ET AL.
Acipenseridae.190–192 In particular, within Acipenseridae, different stur-
geon species show diverse ploidy levels. While sterlets (Acipenser ruthe-
nus) are tetraploid, and most sturgeons are octoploid (e.g., Russian
sturgeon and Siberian sturgeon [Acipenser baerii]).190–192 A previous
study showed that polyploidy affected phenotypes through allelic dosage
(additive effect of multiple copies of the same alleles).193 Therefore, sim-
plifying a polyploid genotype as a diploid genotype may induce bias in
genomic predictions due to higher-order interactions and allele substitu-
tion effects. In this context, GS methods must be modified for the
improvement of tetraploid or octoploid performance, since available
studies and theories are largely based on diploids. There are few studies
on genomic prediction for autopolyploid species using allele dosage,
although majority of these are related to plant breeding.194–196 In a
previous study, we compared the impact of ploidy parametrization on
prediction accuracy in a simulated polyploid sturgeon population using
the GBLUP and RKHS methods. Our results showed that a higher
accuracy of genomic prediction could be obtained by considering allele
dosage in autopolyploidy.197 Currently, with the development of
sequencing technologies, genotyping of polyploid aquaculture species is
possible. Thus, allele dosage should be considered in genomic prediction
for polyploid, particularly hyperploid species (e.g., Russian sturgeon and
Siberian sturgeon).197
4.5 | Integrating multi-omics data and genome
editing into GS
Currently, GS strategies mainly rely on direct association analysis
between phenotypes and SNPs in the genome or prior biological
information in public databases.66,68,71,198,199 However, the genetic
links between phenotype and genome variants are too complex to
determine directly at the genome sequencing level. At present, multi-
omics data (e.g., genomics, transcriptomics, proteomics and metabolo-
mics) can be obtained for genomic predictions, allowing to uncover
genotype–phenotype relationships and provide a ridge between
organismal phenotype and genome variation that cannot be readily
captured at the genome sequence level. Previous studies have used
omics data for genomic prediction of complex traits in humans,200,201
202–205 206,207
plants and model animals. Therefore, with the accumula-
tion of data, application of multi-omics data in GS is anticipated to
more comprehensively and reliably understand the physiological
mechanisms and genetic bases of character formation.
Moreover, gene and genome editing technologies, including
ZFNs, TALLENS and CRISPR/Cas9, are promising tools for accelerat-
ing genetic improvement.208,209 Genome editing is widely used to
analyse the functions of candidate genes in aquaculture species.210,211
By the knocking out and knocking in of different alleles of candidate
genes, the favourite alleles for important traits can be identified.212 In
addition, gene editing can be integrated with GS in breeding. Genomic
selection of gene-edited animals can further increase selection accu-
racy and accelerate genetic progress.213 A previous simulation study
on Holstein cattle showed that in comparison to GS only, editing all
sires for 20 edited quantitative trait nucleotides per sire doubled the
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285
rate of genetic gain after a few and many generations of selection.214
However, the application of genome editing for improving complex traits
requires the discovery of quantitative trait nucleotides associated with
traits, which in turn requires larger datasets than currently available. Many
SNPs associated with traits obtained from GWASs, family-based QTL
mapping and gene function annotation can be rapidly fixed in breeding
populations through genome editing. Based on this, the implementation
of GS can further accelerate genetic improvement in aquaculture species.
5 | CONC LU SION
Genomic selection, a technology that uses markers covering the
whole genome to predict genomic estimated breeding values of indi-
viduals, has revolutionised livestock breeding. In recent years, many
GS studies have been conducted on aquaculture species, which have
shown that GS produces higher prediction accuracy than traditional
pedigree-based method. However, as assumptions and information
used vary with models, no model performs best in all situations and
GBLUP and Bayesian models are more commonly used in aquaculture
species. In the future, novel phenotyping (e.g., machine vision) and
genomics (e.g., low-coverage re-sequencing) technologies, coupled
with related advances in statistical methods and computational effi-
ciency, will further facilitate the use of GS in aquaculture. In addition,
GS will become more widespread as phenotyping and genomics tech-
nologies become more affordable, coupled with tailor-made
approaches to apply low-cost methods to aquaculture species. Due to
the large differences in the production environments, it is possible
that G  E interaction is important for the breeding of aquaculture
species, thus G  E should be considered in GS model, which can
effectively improve fish performance across multiple environments
will aid farmers in diverse environmental conditions to produce food
for the growing human population. Moreover, with the development
of sequencing technologies, allele dosage should be considered in GS
model to further improve the accuracy of GS for polyploid species. In
addition, integrating multi-omics data (e.g., genomics, transcriptomics,
proteomics and metabolomics) and genome editing into GS can fur-
ther accelerate genetic improvement in aquaculture species in the
future. With continuous progress of related technologies, GS is
expected to become widespread in aquaculture breeding and produce
a far-reaching impact in this field.
AUTHOR CONTRIBU TIONS
Hailiang Song: Writing – original draft. Tian Dong: Writing – review
and editing. Xiaoyu Yan: Writing – review and editing. Wei Wang:
Writing – review and editing. Zhaohui Tian: Writing – review and
editing. Ai Sun: Writing – review and editing. Ying Dong: Writing –
review and editing. Hua Zhu: Writing – review and editing. Hongxia
Hu: Writing – review and editing.
AC KNOW LEDG EME NT S
This work was supported by Beijing Natural Science Foundation
(6222014), Beijing Joint Research Program for Germplasm

286
Innovation and New Variety Breeding; (G20220628008), the
Youth Foundation of Beijing Academy of Agriculture and Forestry
Sciences (QNJJ202105) and China Agriculture Research System of
MOF and MARA (CARS-45-32).
CONF LICT OF IN TE RE ST
The authors declare no conflict of interest.
DATA AVAI LAB ILITY S TATEMENT
Since this is a review paper, there is no data available. All information
can be found in the cited references.
ORCID
Hailiang Song https://orcid.org/0000-0003-4915-0002
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How to cite this article: Song H, Dong T, Yan X, et al.
Genomic selection and its research progress in aquaculture
breeding. Rev Aquac. 2023;15(1):274‐291. doi:10.1111/raq.
12716