Hula Ta 2009

2
Genetic improvement of finfish

G. Hulata, Agricultural Research Organization, Israel, and B. Ron, Israel
Oceanographic & Limnological Research Ltd, Israel
Abstract: This chapter focuses on the major genetic approaches, technologies and
methodologies that have shaped the aquaculture industry in recent years. Classic
selective breeding programs (cross-breeding and hybridization) are the
mainstream of finfish genetic improvement, and will continue to be the main
engine driving the global finfish aquaculture industry forward. Breeding programs
have been expanded, their design optimized and many new ones initiated since
the late 1990s. Advances in application of biotechnology to fishes have provided
tools that can be used to genetically change (improve) cultured populations using
non-selective breeding methods through manipulations of genes and
chromosomes (mainly triploidy). Cytological methodologies are useful tools
helping with chromosomal gene mapping and with validation of aquacultured
finfish species and hybrids. Modern technology has brought new types of
molecular markers into play, and their application has allowed rapid progress into
many aquaculture investigations. These include quantification of genetic
variability and inbreeding, parentage assignments, species and strain
identification, construction of high-resolution genetic linkage maps for
aquaculture species and the detection of quantitative trait loci. They also offer
the opportunity to include genomic information in breeding programmes (marker
assisted selection; MAS). Advances have been made in developing genomic and
bioinformatic tools. Although gene transfer technology has yielded promising
products, their future is questionable due to severe controversies over public
health and environmental issues. Use of embryonic stem (ES) cell lines is being
investigated and may prove to be an alternative approach for gene transfer.
Key words: Breeding programs, biotechnology, manipulations of genes and

chromosomes, cytogenetics, quantitative trait loci (QTL), marker assisted
selection (MAS), genomic and bioinformatic tools, gene transfer, embryonic stem
cells.
2.1 Introduction: current status of aquaculture genetics

The status and prospects of aquaculture genetics have been repeatedly
reviewed during the last decade for specific groups of fish or for the industry
in general (e.g., Gjedrem, 2000, 2002; Knibb, 2000; Lymbery et al., 2000;
56 New technologies in aquaculture
Dunham et al., 2001; Hulata, 2001; Myers et al., 2001; Fjalestad et al., 2003;
Okamoto, 2005; Hershberger, 2006; Mair, 2007). A few relevant books,
each covering a specific aspect of the field, have also been published
(Hallerman, 2003; Dunham, 2004; Gjedrem, 2005; Liu, 2007a).
Although classic selective breeding methods as well as emerging tech-
nologies are available and contribute to the progress of the industry, their
application is not yet evenly spread over globally cultured species and
culture areas (Hulata, 2001). How much of the nearly 48 million tonnes
cultured globally (2005 estimate; FAO, 2007) stems from genetically
improved stocks is hard to tell. Some five years ago, Gjedrem (2002) esti-
mated that genetically improved stocks accounted for no more than 10 %
of aquaculture production. ‘This figure is undoubtedly rising in developed
countries, as the benefits of genetic improvement become apparent, but
it is almost certainly much lower in most developing countries’ (Mair,
2007). With major producers such as China and other south-eastern Asian
countries (FAO, 2007) lagging behind in application of genetic technologies
in their aquaculture industries, it is unlikely to be more than 20 % at
present.
It is not our intention to duplicate the above-mentioned reviews, but
rather to focus on the new approaches, technologies and methodologies
that have shaped the field in recent years.
2.2 Key drivers for genetic improvement of finfish

2.2.1 Improving growth rate, disease resistance and other quality traits
by selective breeding and other methods
Classical breeding programs (selective breeding, cross-breeding and hybrid-
ization) are the mainstream of finfish genetic improvement (Bartley et al.,
2001; Gjedrem, 2005). The impact of selective breeding programs on the
aquaculture industry can be exemplified by the wide global distribution of
the Donaldson strain of rainbow trout (Parsons, 1998), the success of the
Norwegian Atlantic salmon breeding program (Gjedrem, 2000) and the
progressing dissemination of the selectively bred Nile tilapia, known as
genetically improved farmed tilapia – GIFT (Pullin, 2007). Breeding pro-
grams have been expanded, and many new ones initiated during the last
decade – see examples in Table 2.1. The breeding goal in most of these
programs was improving growth rate. Whereas in the past improving growth
rate was the most common breeding goal, new traits have been incorpo-
rated more recently in breeding programs (Table 2.2).
As fish welfare is becoming a crucial issue for the aquaculture industry
(Ashley, 2007), attention has also been given recently to selection for sus-
tainability and animal welfare-related traits (Olesen et al., 2000, 2003;
Bentsen and Olesen, 2002). Attention is also given to the possible effects
of selection on the social behaviour and growth pattern of the fish (Brännäs
Genetic improvement of finfish 57
Table 2.1 Examples of recent breeding programmes
Species Reference
Atlantic cod (Gadus morhua) Gjerde et al., 2004

Atlantic salmon (Salmo salar) Quinton et al., 2005; Kolstad et al., 2006
Common carp (Cyprinus carpio) Vandeputte, 2003; Kocour et al., 2007
Gilthead seabream (Sparus aurata) Gorshkov et al., 2004
Hybrid striped bass (Morone chrysops Garber and Sullivan, 2006
× M. saxatilis)
Lake Malawi tilapia (Oreochromis Maluwa and Gjerde, 2006a,b, 2007;
shiranus) Maluwa et al., 2006
Mediterranean sea bass (Dicentrarchus Saillant et al., 2006
labrax L.)
Nile tilapia (O. niloticus) Ponzoni et al., 2005; Li et al., 2006
Red sea bream (Pagrus major) Murata et al., 1996
Rohu carp (Labeo rohita) Gjerde et al., 2002; Reddy et al., 2002
Table 2.2 Examples of production- and consumer-related breeding-goal traits in

recent breeding programmes
Trait Species Reference
Production-related
Age at maturity Rainbow trout Kause et al., 2003a
(On. mykiss)
Eliminating vertebral Atlantic salmon Gjerde et al., 2005
deformity (S. salar)
Atlantic cod Kolstad et al., 2006
(Gadus morhua)
Feed efficiency Atlantic salmon Kolstad et al., 2004, 2005b; Kause
(S. salar) et al., 2006b; Quinton et al., 2007
Reproductive traits Coho salmon Gall and Neira, 2004; Gallardo
(On. kisutch) et al., 2004a
Stress, disease and Rainbow trout Pottinger and Carrick, 1999;
parasite resistance (On. mykiss) Henryon et al., 2005
Atlantic salmon Kolstad et al., 2005a; Ødegård
(S. salar) et al., 2006, 2007a,b
Consumer-related
Appearance Rainbow trout Kause et al., 2003b, 2004
(On. mykiss)
Body composition Rainbow trout Tobin et al., 2006; Kause et al.,
(On. mykiss) 2007; Quillet et al., 2007
Carcass quality Coho salmon Neira et al., 2004
(On. kisutch)
et al., 2005). Improvements have also been made in breeding programs

through the introduction of new methodology for measuring complex traits,
such as flesh color or feed efficiency [in rainbow trout (On. mykiss) – Helge
Stien et al., 2006; Kause et al., 2006a].
Advances in designing breeding programs in aquaculture

Because broodstocks are limited in size, inbreeding is an inherent problem
in many breeding programs (Gjedrem, 2005). Efforts have been made
recently to optimize mating designs for reducing effects of inbreeding in
breeding programs (Gjerde et al., 1996; Villanueva et al., 1996; Sonesson
and Meuwissen, 2000, 2002; Sonesson et al., 2003; Gallardo et al., 2004b;
Dupont-Nivet et al., 2006; Holtsmark et al., 2006, 2008; D’Agaro et al.,
2007), and in improving the experimental designs and statistical models to
enhance genetic gains (Sonesson et al., 2005; Hinrichs et al., 2006; Martinez
et al., 2006a,b). In addition, emerging technologies based on molecular
markers and genomic approaches are progressively rising in importance,
and efforts are being made to involve molecular approaches in breeding
programs (Fjalestad et al., 2003; Silverstein et al., 2006). A step further
towards improving the design of breeding program was taken by Hayes et
al. (2006) in their comparison of different strategies for using molecular
marker information in order to maximize genetic diversity in the base
population. Combining available phenotypic information for the traits of
interest with marker data, they propose, would ‘ensure that as much genetic
variance as possible, for as many traits as possible, is captured in the base
population’.
2.2.2 Improving performance and other traits by non-selective

breeding methods
Advances in application of biotechnology to fishes (reviewed by Melamed
et al., 2002) have provided tools that can be used to genetically change
(improve) cultured populations using non-selective breeding methods
through manipulations of genes and chromosomes (Rasmussen and
Morrissey, 2007). The different approaches will be discussed in more detail
below.
Chromosome set manipulations (gynogenesis, androgenesis

and polyploidy)
Although chromosome-set manipulations, which have been heavily inves-
tigated since the 1970s, have not resulted in many commercial applications
to advance the aquaculture industry (Khan et al., 2000; Hulata, 2001), these
manipulations still attract interest (Arai, 2001; Felip et al., 2001a; Gomelsky,
2003; Komen and Thorgaard, 2007), and research has expanded to more
species with emphasis on newly-cultured species (Table 2.3).
The physiological effects of polyploidy are also being investigated (e.g.,
Peruzzi et al., 2005; Taylor et al., 2007; Maxime, 2008). The most common
applications of these procedures are production of triploids to prevent
reproduction and improve growth rate (reviewed by Tiwary et al., 2004),
and cloning through gynogenesis and androgenesis (reviewed by Pandian
and Kirankumar, 2003; Komen and Thorgaard, 2007). Triploidy is also used
Table 2.3 Examples of chromosome manipulations in newly culture species
Species Reference
European sea bass (Dicentrarchus Felip et al., 2001a,b, 2002; Peruzzi et al.,
labrax) 2004; Bertotto et al., 2005
Sunshine bass (M. chrysops × M. Kerby et al., 2002
saxatilis)
Largemouth bass (Micropterus Gomelsky et al., 2004; Neal et al., 2004
salmoides)
Turbot (Scophthalmus maximus) Piferrer et al., 2000, 2003, 2004; Cal et al.,
2006
Barfin flounder (Verasper moseri) Mori et al., 2006
Sturgeon (Acipenser sp.) Flynn et al., 2006; Grunina et al., 2005, 2006
Atlantic halibut (Hippoglossus Tvedt et al., 2006
hippoglossus)
for genetic mapping (Nomura et al., 2006). Although resulting in high

degree of sterility, triploidy does not always confer significant improvement
of growth (e.g., Mori et al., 2006). Production of triploids would be more
efficient by mating induced tetraploids with normal diploids; this has so far
been restricted to rainbow trout, since in no other commercial finfish species
have viable and fertile tetraploids been obtained (Arai, 2001; Babiak et al.,
2002a,b). For other species, triploids are produced as all-female populations
by using spermatozoa of artificially sex-reversed (often gynogenetic) males,
so as to assure their complete sterility (e.g., Arai, 2000; Rothbard et al.,
2000; Rothbard, 2006 and Fig. 2.1). This is because triploid males some-
times show gonadal development and often are not completely sterile (e.g.,
Pandian and Koteeswaran, 1998; Arai, 2000, 2001; Felip et al., 2001a;
Oshima et al., 2005; Sousa-Santos et al., 2007). Commercial production and
culture of (all-female) triploid fish is so far limited to brown trout, rainbow
trout, Atlantic and Chinook salmon and European sea bass. Additionally,
commercial production of triploid grass carp is carried out for stocking
native bodies of water to control vegetation.
Cytogenetics
During the 1990s, the number of cytogenetic studies of marine fishes has
increased. Its main application, however, has been in solving systematic and
taxonomy issues rather than genetic improvement. Cytogenetic studies can
help in predicting the success of inter-specific hybridization between species;
successful hybridization occurs predominantly between closely-related
species having identical chromosome structure and numbers, or at least
identical number of chromosome arms (e.g., Kim et al., 1995). Resulting F1
are often reproductively viable, although in some cases they are sterile (in
most cases due to being triploids).
♂ Albino ♀ Wild-type ♀ Albino ♂ Common

grass carp grass carp grass carp carp
(XY) (XX) (XX) (XY)
Sperm (X & Y) UV-irradiated eggs Eggs (X) UV-irradiated sperm
Fertilization Fertilization
Shock
Late-
shock ♀♀ XX
Female monosex MT sex-
(2nd Task) inversion
♂♂ ♀♀
♂♂ XX
(YY) (XX)
Gynogenetic
Homozygous males
progeny
Sperm Fertilization
bank Sperm
Early-shock bank
Late-
♀♀ XXX shock
♂♂ XY Female triploids
Male monosex (3rd Task)
(1st Task)
♀♀ XXXX
4N-females
(4th Task)
2N gametes
Fertilization
♀♀ XXX
Female triploids
(5th Task)
Fig. 2.1 Schematic presentation of ploidy manipulations on grass carp

to produce XXX female triploids (reproduced with permission from
Rothbard, 2006).
Another area where cytogenetics has played an important role is studies

of sex determination (reviewed by Ezaz et al., 2006). Knowledge on sex
determination may contribute to efficient production of monosex popula-
tions, which in turn may contribute to improved production efficiency in
various cultured species (e.g., tilapias). Cytogenetics is also playing an
important role in the verification of chromosome-set manipulations as well
as for gene mapping (Gorshkova, 2006).
Study of sex chromosomes: Ten sex-determination systems are known

among fishes. The unusual cytology and exceptional evolution of sex chro-
mosomes lead to numerous basic questions related to why and how sex
chromosomes evolved. This was the source of a century-long debate from
the time when H.J. Muller suggested that sex chromosome pairs evolved
eventually from a pair of autosomes (Muller, 1914). With regard to cyto-
logical examination of sex chromosome evolution, fishes are the most fas-
cinating of vertebrate groups. Fishes represent the largest vertebrate group
which displays the widest diversity of sex determination and sex chromo-
somal systems, including gonochorism (separate sexes), hermaphroditism
(individuals displaying both sexes) and unisexuality (all female-species).
Using cytogenetic methodologies, among others, it was revealed that in
gonochoristic fishes, the gender may be determined genetically – ranging
from a single-allele determination to chromosomal sex determination. In
addition, it was shown that polygenic sex determination and sex determina-
tion by genotype–environment interaction take place in fishes (see reviews
by Devlin and Nagahama, 2002 and Ezaz et al., 2006).
Cytogenetic studies play an important role in the identification of the
various sturgeon species and hybrids. Inter-specific hybridization is well
known in Acipenseriformes and can be advantageous in aquaculture
(Steffens et al., 1990; Gorshkova et al., 1996; Fontana, 2002; Gorshkova,
2006). Lately, Fopp-Bayat et al. (2007) performed cytogenetic analysis by
preparing chromosomes from the gill epithelium of Acipenser baeri × (Huso
huso × Acipenser ruthenus) hybrids in both diploid and triploid states.
Karyological inspection of Russian imported sturgeons, reared at the
Kibbutz Dan fish farm, Israel, were conducted on hybrids of Russian stur-
geon (Acipenser guldenstadti) and great (beluga) sturgeon (Huso huso).
Results showed that the consistent mode of 2N was 181–190 and the karyo-
type consisted of 78 metacentric and submetacentric, 16 acrocentric, and
about 88 micro-chromosomes. The intermediate origin of the imported
sturgeon hybrid confirmation, based on different number of chromosomes,
points at the polyploidy origin of the Acipenseridae, and allowed the genet-
icists to formulate recommendations concerning conservation and genetic
management of cultured sturgeon stocks in Israel (Gorshkova et al., 1996;
Gorshkova, 2006).
During 1992–1995, Groshkova and co-workers conducted chromosome
set manipulation research using the economically important marine finfish,
gilthead seabream (Gorshkova et al., 1995; Knibb et al., 1998a, b). These
studies led to the establishment of a protocol that provided gilthead sea

bream gynogenetic and triploid progenies. In addition, these researchers
achieved the production of meiotic gynogenetic sea bass progeny using heat
shocks to eggs fertilized with UV-irradiated sperm (Gorshkova et al., 1995;
Knibb et al., 1998a, b). As a result, a direct karyological confirmation con-
cerning the hybrid nature and triploid origin of the offspring were described
using karyotypes of chromosomally-manipulated forms with ‘marker’ chro-
mosomes (Gorshkov et al., 1998).
Another study was done during 1999, when Gorshkova and co-workers
commenced cytogenetic inspection of white grouper (E. aeneus) early
embryonic development (Gorshkova et al., 2002b). Although one of the
most valuable fishes in the Mediterranean basin, white grouper has a severe
limitation in commercial culture as a result of the unpredictable and often
low quality of spawned eggs, embryos with low survival rates and escalating
larvae mortality. The percentage of cytogenetically abnormal embryos car-
rying diverse types of chromosomal aberrations varied significantly amongst
spawnings and ranged from 35.5–79 %. Continuous examination of subse-
quent spawning of different parental fishes using cytogenetic monitoring of
the early embryonic stages would be of immediate interest for future genetic
broodstock management of the white grouper (Gorshkova et al., 2002a).
Aid in gene mapping: Cytological methodologies have been employed in

chromosomal gene mapping of some aquacultured finfish species. This
technique has been used mainly as a complementary approach to identify
particular chromosomes (Phillips and Reed, 1996; Cnaani et al., 2007a, b;
Phillips et al., 2006). Using fluorescence in situ hybridization (FISH) and
linkage mapping, Cnaani and co-workers showed that in tilapia the sox2
and sox14 genes are on separate chromosomes. The rainbow trout (On.
mykiss) genetic linkage groups have been assigned to specific chromosomes
in the OSU (2N = 60) strain using FISH with bacterial artificial chromo-
somes (BAC) probes containing genes mapped to each linkage group. The
set of BACs compiled for this research will be especially useful in construc-
tion of genome maps and identification of quantitative trait locus/loci
(QTL) for important traits in other salmonid fishes (Phillips et al., 2006; see
further discussion below).
Molecular markers
Since the 1960s, electrophoretic studies of proteins (allozymes, or allelic
forms of isozymes) have provided the primary tool for studying genetic
diversity in fisheries and aquacultured stocks (Liu and Cordes, 2004;
Verspoor et al., 2005; Kucuktas and Liu, 2007). The main uses of allozyme
electrophoresis have been for stock identification and management (in the
wild as well as aquaculture), analysis of population genetics processes such
as inbreeding and genetic drift, molecular tagging and parentage analysis
and, to a much lesser extent, for genetic mapping (Liu and Cordes, 2004).
The major drawbacks of allozymes, apart from the need for fresh or frozen
samples of relatively large quantities, are the limited variability and poor
coverage of the genome. Nevertheless, allozyme analysis has made a sig-
nificant contribution to our understanding of the genetic diversity and the
structure of wild genetic resources in many species, and especially the
Atlantic salmon (Verspoor et al., 2005). Since the mid-1980s, DNA-based
analyses (e.g., Artamonova, 2007) that are characterized by higher genetic
variation and polymorphism, as well as higher genome coverage, have
gradually substituted for allozymes.
Modern biotechnology has introduced into play new types of molecular
markers, as well as other techniques that will be discussed below (see
Chapter 1 in this volume for a detailed account). The new platform tech-
nologies have opened up vast possibilities to the aquacultural biotechnolo-
gist (Melamed et al., 2002).The various types of DNA markers – mitochondrial
DNA, restriction fragment length polymorphism (RFLP), random ampli-
fied polymorphic DNA (RAPD), amplified fragment length polymorphism
(AFLP), microsatellite, single nucleotide polymorphisms (SNP) and
expressed sequence tag (EST) markers – have been described in detail by
Liu and Cordes (2004) and in Chapters 2–8 in Liu (2007a). The application
of DNA markers has allowed rapid progress in aquaculture investigations
of genetic variability and inbreeding, parentage assignments, species and
strain identification and construction of high-resolution genetic linkage
maps for aquaculture species (Liu and Cordes, 2004), as well as detection
of QTL and enabling the use of genomic information in breeding programs
(viz MAS). Chistiakov et al. (2006) state that in aquaculture research, mic-
rosatellites are the ‘workhorse markers’ and review the genomic distribu-
tion, function, evolution and practical applications of microsatellites to fish
genetics and aquaculture. Gradually, SNPs are becoming the future markers
of choice (Liu, 2007b), mainly because of the need for very high densities
of genetic markers (SNPs by far exceed microsatellites in this respect), and
the recent progress in genotyping techniques and detection of polymor-
phism. Genomic resources continue to be developed (e.g., Hayes et al.,
2007; Somridhivej et al., 2008). These and the other new marker types paved
the way for various applications that are re-shaping aquaculture breeding
programs.
Parental assignment and molecular pedigrees: DNA markers, notably mic-

rosatellites, have solved one of the major obstacles in breeding programs,
namely the ability to individually mark small fish. In order to utilize
maximum information available on relatives, and increase the accuracy of
selection, fish should be marked individually so that pedigrees can be
tracked across generations (Villanueva et al., 2002). Since newborn fish are
too small to be physically tagged, families must be reared separately until
the fish reach the size at which they can be safely tagged individually (Doyle
and Herbinger, 1994; Herbinger et al., 1995). Apart from limiting the
number of families that can be used, and the extra expenses incurred by
rearing each family separately, this also introduces common-environment
correlations that reduce the accuracy of selection. Furthermore, it allows
applying family selection to fish species that are not easily reproduced by
single-pair matings (e.g., gilthead sea bream; Knibb, 2000). The develop-
ment of DNA markers has enabled solution of this problem, when it was
shown that by using a series of polymorphic markers, each individual in a
mix of several or many families can be uniquely assigned to its parents with
nearly complete accuracy (e.g., Herbinger et al., 1995, 1999; Estoup et al.,
1998; O’Reilly et al., 1998; Perez-Enriquez et al., 1999; Norris et al., 2000).
The pioneering study by Herbinger et al. (1995) was designed to ‘assess the
feasibility of establishing pedigrees in mixed aquaculture populations and
of selection programs for commercial aquaculture operations based on
genetic profiling data from microsatellite markers’, and in fact paved the
way for the application of DNA markers in breeding programs. The
Herbinger et al. (1995) study ‘showed that the pedigree of a mixed rainbow
trout population could be satisfactorily determined using as few as four
microsatellite markers even though the fish could have originated from 100
possible pairs (ten sires × ten dams). The ability to establish the pedigree
of completely mixed fish from their single locus DNA profile means that
this pilot study was able to take place in a production farm with practically
no interference with the normal routine’. Using this approach, families
produced separately can be mixed and reared communally from hatching,
or pools of males and females can be bred in the same pond or tank and
their progeny reared together, until a posteriori parentage assignment at a
later stage, even just before selection of breeding candidates.
Villanueva et al. (2002) attempted to answer the key questions related
to this application – the number of loci and the level of information (i.e.,
the numbers of alleles per loci and their relative frequency) required for
accurate assignment. Application to breeding programs is already under
way, e.g., in the estimation of heritability with a microsatellite parentage
assignment-based pedigree in common carp cultured under traditional
pond conditions as demonstrated by Kocour et al. (2007). Another applica-
tion of DNA markers that is becoming of major importance is for tracing
live fish or fish products at any stage along the production chain. Hayes
et al. (2005) compare and discuss three alternate traceability schemes using
DNA markers.
Linkage maps: Since the late 1990s, linkage maps have been developed for
most commercially important finfish species (Table 2.4; see also Table 10.2
in Danzmann and Gharbi, 2007).
Work is also underway to develop the necessary genomic resources to
develop maps of barramundi (Lates calcarifer – Zhu et al., 2006) and striped
bass (Morone saxatilis – Rexroad et al., 2006). Some maps are quite pre-
liminary, although for a few species more advanced maps have already been
Table 2.4 Examples of linkage maps for commercially important species. Those
already listed in Danzmann and Gharbi (2007) are marked in bold face
Species Reference
American catfish (Ictalurus punctatus ¥ Liu et al., 2003

I. furcatus)
Arctic char (S. alpinus) Woram et al., 2004
Atlantic salmon (S. salar) Moen et al., 2004
Ayu (Plecoglosus altivelis) Watanabe et al., 2004
Baramundi (Lates calcarifer) Wang et al., 2007
Bighead carp (Aristichthys nobilis) Liao et al., 2007
Brown trout (S. trutta) Gharbi et al., 2006
Common carp (C. carpio) Sun and Liang, 2004
European sea bass (Dicentrarchus Chistiakov et al., 2005
labrax)
Gilthead sea bream (Sparus aurata) Franch et al., 2006; Senger et al., 2006;
Sarropoulou et al., 2007a,b; 2008
Japanese flounder (Paralichthys Coimbra et al., 2003
olivaceus)
Rainbow trout (On. mykiss) Nichols et al., 2003; Danzmann et al.,
2005
Silver carp (Hypophthalmichthys Liao et al., 2007
molitrix)
Thai catfish (Clarias macrocephalus) Poompuang and Na-Nakorn, 2004
Tilapia (O. niloticus ¥ O. aureus; F2) Lee et al., 2005
Yellowtail (Seriola spp.) Ohara et al., 2005
obtained. The number of markers mapped range from 146 (C. Macrocepha-
lus – Poompuang and Na-Nakorn, 2004) to over 1400 (On. mykiss –
Danzmann et al., 2005) in the more advanced maps, and some contain genes
as well (those of rainbow trout, brown trout, Atlantic salmon, Arctic charr,
channel catfish, European sea bass, common carp and tilapia – for details
see Table 10.2 in Danzmann and Gharbi, 2007). Apart from the Danzmann
et al. (2005) map of rainbow trout and the preliminary map of common carp
(Sun and Liang, 2004), all other maps have either more or less linkage
groups (LG) than the haploid number of chromosomes (N) in the species.
As long as no commercially important species has its genome fully
sequenced, linkage maps constitute the basic prerequisite for detection of
QTL (Korol et al., 2007) and fine mapping of genes through comparative
mapping to sequenced genomes of model species, and for positional cloning
(Lee and Kocher, 2007; Sarropoulou et al., 2008).
QTL detection: A QTL is a segment of a chromosome with a significant

effect on the expression (phenotype) of a trait of interest; this issue was
recently reviewed by Korol et al. (2007). The chapter presents an overview
of QTL detection, lists the four steps in the detection of QTL, and outlines
their application in MAS; see below) – marker development; development
of a linkage map of at least moderate density; mapping of QTL using

genetic markers placed on the map, with development of a model for
inheritance and expression of the trait; and finally, use of the identified
association between marker(s) and QTL in practical breeding program (i.e.,
MAS). It then discusses recent advances in detection of QTL, and presents
a list of traits for which QTL have been detected in various aquacultured
species. Among the traits are growth rate and body shape traits, resistance
to stress, pathogens and diseases, coloration, sex determination. These have
been detected in Atlantic salmon, rainbow trout, coho salmon, Arctic char,
tilapias and common carp (see references in Korol et al., 2007 and Sonesson,
2007a). Most recently, a QTL for early maturation was identified in rainbow
trout (Haidle et al., 2008). Moen et al. (2004) present a testing strategy for
detection of QTL affecting disease resistance in Atlantic salmon. Sonesson
(2007a) reviewed the efforts to detect QTL in aquaculture species. Such
studies yield knowledge of marker–QTL linkages and estimates of the
effects of QTL alleles on the trait in the population. Komen and Thorgaard
(2007) discuss the advantage of using double haploids for QTL mapping
and present case studies for rainbow trout, but also mention the obstacles
to implementation of this approach (related to yield, survival, fertility,
quality control and sustained commitment of resources). They conclude
that the biggest challenge is the extremely low yields of doubled haploids
in experiments with a variety of fish species.
MAS: The development of large numbers of genetic markers and genetic

maps for many aquacultured species (as mentioned above), which enables
detection of QTL, has further led to search for genes associated with com-
mercial traits. Opportunities that were proposed about 25 years ago (Soller
and Beckmann, 1982; Beckmann and Soller, 1983), namely the use of
genetic markers for selection, are finally becoming a reality. And yet, ‘only
a handful of cases demonstrating practical usefulness of MAS’ have been
reported in livestock (Rothschild and Ruvinsky, 2007) and even fewer in
aquacultured species. The most remarkable application so far is the breed-
ing of a lymphocystis disease-resistant Japanese flounder (Paralichthys oli-
vaceus) (Fuji et al., 2006, 2007; Sakamoto et al., 2006), although this is not
a real selective breeding program. They identified a major locus that is
mapped to LG15 of the Japanese flounder linkage map, which is highly
associated with resistance to the lymphocyctis disease (LD). Specifically,
one allele of this marker is tightly linked to LD resistance. LD resistance
and the marker are inherited in a Mendelian fashion, with LD resistance
behaving as a dominant trait. This inference enabled selection of resistant
parents for establishing an LD-resistant stock. With the many projects of
marker development, QTL and linkage mapping in progress (see for exam-
ples Liu, 2007a; Martinez, 2007), it is anticipated that the industry will adopt
the MAS strategy in the near future (Rothschild and Ruvinsky, 2007).
Sonesson (2007a) and Martinez (2007) reviewed the current status of aqua-
culture breeding schemes and evaluated the possibilities for applying MAS.
So far, MAS schemes have been mostly developed for livestock. Sonesson
(2007b) is developing and optimizing models for combining MAS with the
classical aquaculture breeding schemes using the best linear unbiased pre-
diction (BLUP) model.
Genomics
Wenne et al. (2007) reviewed the current development of genomic technolo-
gies and their potential applications and implications for fisheries manage-
ment and aquaculture. Full genome sequences are so far available only for a
few model fish species such as zebrafish Danio rerio (http://www.sanger.ac.uk/
Projects/D_rerio/), fugu Takifigu rubripes (http://www.fugu-sg.org/), puffer
fish Tetraodon nigroviridis (http://www.genome.gov/11008305), medaka
Oryzias latipes (http://dolphin.lab.nig.ac.jp/medaka/index.php) and stickle-
back Gasterosteus aculeatus (http://www.genome.gov/12512292). A Tilapia
Genome Sequencing Project is currently underway at the Broad Institute [a
research collaboration involving the Massachusetts Institute of Technology
(MIT) and Harvard University], and the release of a first high-coverage
genome is expected before the end of 2009 (TD Kocher, University of Mary-
land, USA, pers comm). Sequenced genomes of the model species have been
well exploited so far with bioinformatics analyses and molecular biology
techniques. It is anticipated that integration of more traditional disciplines
such as biochemistry and physiology and expanding the study to additional
species such as carp, catfish, salmon, trout or tilapia will further exploit the
potential of fish genomics. This will be accompanied by applications to envi-
ronmental biology and aquaculture (Crollius and Weissenbach, 2007).
Various aspects of fish genomics have recently been reviewed in great
detail in a book edited by Liu (2007a). Therein, Davidson (2007) and Xu
et al. (2007) discuss the importance and utility of BAC libraries as the key
genomic resource required for building genetic maps and integrating them
with the respective physical maps. Guo et al. (2007) reviewed the utility of
FISH as a tool in genome mapping. Many FISH studies have been pub-
lished, but the full potential of this tool for gene and genomic mapping as
well as for comparative genomic analysis in aquacultured species has not
yet been realized. Rexroad (2007) reviewed the construction of radiation
hybrids (RH) and discuss the perspective of RH mapping for aquaculture
species. Apart from zebrafish, the only RH map reported so far for an
aquacultured species is for the gilthead sea bream (Senger et al., 2006;
Sarropoulou et al., 2008). Lee and Kocher (2007) presented an example of
how comparative mapping and positional cloning were employed in an
attempt to identify the gene(s) underlying a QTL for sex determination
identified on LG1 of Nile tilapia. Their conclusion is that ‘conservation of
gene order among fish at scales of several Mbs allows the use of the rela-
tively complete sequences of model fish species to accelerate gene discovery
and positional cloning of these genes’.
Bioinformatic tools already available and those that will be further

developed enable prediction of genes in important aquaculture species
using the genome sequences of the model fishes. The sequencing of the
genome of Nile tilapia, expected to be completed during 2009 (TD Kocher,
University of Maryland, USA, pers comm), will further boost the use of
comparative mapping of aquacultured species. Chapters 20–24 in Liu
(2007a) review and discuss the status and perspective of analyzing genome
expression and gene function in fish using expressed sequence tags
(EST) and microarrays. More details on the status of genome mapping
and genomics in salmonids, cyprinids, catfish, tilapias, European sea
bass and Japanese flounder can be found in the recently published book
Genome Mapping and Genomics in Fishes and Aquatic Animals (Kocher
and Kole, 2008).
Transgenesis
Gene transfer technology leading to the production of genetically modified
organisms (GMOs) is probably the most controversial issue dealt with in
this chapter. On one hand, its successful application in several aquaculture
species has produced stocks with improved traits, such as enhanced growth
rate. The most notable of these are in salmonids, e.g., Devlin et al. (2004)
and Fletcher et al. (2004), mud loach, e.g., Nam et al. (2001, 2002, 2004),
and tilapia, e.g., Martínez et al. (2000), Maclean et al. (2002) and Caelers
et al. (2005). Another case is increased cold tolerance through expression
of an antifreeze polypeptide that might potentially expand culture range of
salmon (Devlin et al., 2004). Gene transfer also has the potential to con-
tribute to disease resistance [e.g., enhanced bacterial disease resistance of
cecropin-transgenic channel catfish (Ictalurus punctatus) – Dunham et al.
(2002) – and resistance to Aeromonas hydrophila infection in human
lactoferrin-transgenic grass carp (Ctenopharyngodon idellus) – Mao et al.
(2004)] and other traits. On the other hand, GMOs pose environmental
threats and have raised public concerns that, so far, prevent their commer-
cial use by the aquaculture industry (e.g., Kapuscinski and Hallerman, 1990;
Levy et al., 2000; NRC, 2002; Pew, 2003; Myhr and Dalmo, 2005; Rasmussen
and Morrissey, 2007).
Galli (2002) presented a quite comprehensive overview of the current
status of modern biotechnology research in aquaculture. Directed to policy
and decision makers, it highlights issues relevant to research and the
potential for commercialization of genetically modified (GM) aquacul-
tured organisms. Teufel et al. (2002) reviewed the research on transgenic
trout and salmon, their potential and the constraints for implementation.
The issues of public concerns and implications to the aquaculture industry
have been further discussed by several scientists, e.g., Aerni (2004),
Maclean (2003) and Millar and Tomkins (2007). A special volume
(Kapuscinski et al., 2007) published recently has focused on the potential
environmental risks (threats to biodiversity and natural ecosystems) and
benefits of uses of aquacultured GMOs. It covers all aspects from the

development of transgenic fish, through assessment of environmental risks
from their use, to suggestions for risk management of transgenic fish. The
main conclusion and message of the book is that the risks ‘must be honestly
and accurately analysed and understood by society’ in order to allow the
potential benefits of transgenic aquaculture research to be realized. It
further suggests that ‘using this book’s chapters for guidance, countries can
begin to approach the task of creating effective, scientifically sound and
socially responsible biosafety policies for transgenic fish and other aquatic
organisms’.
Commercialization of transgenic fish, however, poses not only ecologi-
cal, food safety and regulatory issues, but also animal welfare concerns.
Hallerman et al. (2007) reviewed the effects of growth hormone transgenes
on the welfare and behavior of four species: Atlantic salmon, coho salmon,
tilapia and common carp. Various morphological, physiological and behav-
ioral alternations occur in GH-transgenics that seem to negatively
affect, among other traits, swimming ability and reproductive behavior.
Possible means for reducing the welfare issues that arise are discussed,
such as the use of weaker promoters in expression vectors and selection
of transgenic lines with physiologically appropriate levels of GH expres-
sion. Furthermore, since GH-transgenic animals have higher energy
demands than non-transgenic fish, optimizing their formulated diets may
improve production potential of transgenic animals and help maintain
their welfare.
The production of transgenics in itself has met with various difficulties,
one of which is lack of control over integration of a single copy of a trans-
gene and its proper expression. In recent years, use of embryonic stem
(ES) cell lines has been investigated as an alternative approach for gene
transfer. Hong et al. (2000) have reviewed the status and perspectives of
using ES for transgenesis in fish. Since then, more studies have focused on
the model fishes medaka (Bubenshchikova et al., 2005) and zebrafish (e.g.,
Ma et al., 2001; Fan et al., 2004; Hong and Schartl, 2006; Alvarez et al.,
2007; Chen et al., 2007), and in recent years, a few attempts have also been
made in aquacultured species (Holen and Hamre, 2003; Parameswaran
et al., 2007).
2.3 Case studies – risks associated with selective

breeding programs
Species or strains of many fish species have been translocated from their
place of origin, or from places to which they have been introduced, and
deliberately released for stocking or escaped from culture facilities, thereby
affecting wild stocks (Cross, 2000). A few outstanding examples will be
discussed.
The farming of Atlantic salmon (Salmo salar), which has greatly

expanded in the last 50–60 years, resulted in large numbers of escaped farm
salmon invading native salmon populations throughout the North Atlantic
(e.g., Fleming et al., 2000; Gilbey et al., 2005; Carr and Whoriskey, 2006;
Hindar et al., 2006; O’Reilly et al., 2006). The nature of this interaction has
been investigated by McGinnity et al. (2003, 2004), Weir et al. (2004, 2005)
and others. Naylor et al. (2005) presented a thorough analysis of the problem
in their assessment of the risks of escaped salmon from net-pen aquacul-
ture, and listed various potential biological consequences of farm salmon
escapes: risk of feral stock establishment; risks of competition with wild fish
for mates, space and prey; risk of pathogen transmission; and, most relevant
to this review, risks associated with genetic interactions with wild stocks.
These were further discussed in the framework of the EU GENIMPACT
project: Evaluation of genetic impact of aquaculture activities on native
populations (Verspoor et al., 2006). Moreover, the culture of Atlantic
salmon has been shown to genetically affect wild populations of other sal-
monids as well, e.g., sea trout (Salmo trutta) (Coughlan et al., 2006).
Of even greater concern are the risks associated with the Atlantic salmon
selective breeding programs. Since the 1980s, a series of corporate merger
and spin-off through purchase and sale of Atlantic salmon breeding and/or
growing companies has resulted in translocations of stocks among countries
in Europe as well as North America and Chile. For example, the origin of
Donegal Silver Irish salmon lies in the MOWI Norwegian broodstock,
eggs from which were introduced at Fanad Fisheries in 1982. Marine
Harvest, one of the largest salmon companies in the world resulting from
these mergers, with branches in Ireland, Norway, Scotland, Canada and
Chile, has moved stocks within Europe as well as from Europe to North
and South America (A. Norris, Marine Harvest, pers comm; http://www.
marineharvest.com/).
The effects of cultured species on their respective wild populations is
visible in the last two or three decades also with the Mediterranean gilthead
sea bream (Sparus aurata) and sea bass (Dicentrarchus labrax). These
effects include interaction and competition for resources by accidentally
escaping fish (whose numbers are increasing according to the records) and
contribution of escaped fish to reproduction in the wild. Data suggest that
the contribution of escaped spawners ‘is not negligible’ and that a decrease
in mean size of fish caught in the longline fishery in Greek coastal lagoons
has already been detected (Dimitriou et al., 2007). Naylor et al. (2005)
predict that the rising production of two new marine species – cod and
halibut – may lead to similar processes.
Escaped hybrid catfish (female Thai walking catfish, Clarias macroceph-
alus × male African catfish, C. gariepinus) from farms in central Thailand
may interbreed with C. macrocephalus individuals in the wild. Senanan
et al. (2004) assessed genetic introgression of C. gariepinus genes into four
wild and two broodstock populations of C. macrocephalus.
Tilapias are a group of fish that have been widely spread around the
world since the 1950s (Pullin et al., 1997). More recently, stocks of Nile
tilapia (O. niloticus) were introduced from various regions in Africa into
the Philippines and mixed with cultured (earlier – introduced) strains to
form the base population for the GIFT breeding program carried out by
the WorldFish Center (formerly ICLARM) and collaborators (Eknath
et al., 1993, 2007; Eknath, 1995). Improved descendants from this program
were disseminated to several countries in Southeast Asia for evaluation
against local stocks, eventually leading to commercial culture of this intro-
duced strain, which showed superior growth rate and survival relative to
that of other strains used by farmers (De Silva, 2003). Since no native wild
populations of tilapia existed in those countries, escapement did not result
in any damage to wild populations. Upon termination of the GIFT research
program, sub-samples were transferred to several countries in the region
and served as founders for separate, parallel, further breeding programs
(Gupta and Acosta, 2004). According to Ponzoni (2007, WorldFish Center,
pers comm), the WorldFish policy has been not to transfer GIFT to Africa
because of biodiversity considerations, namely, due to concerns that the
fish could escape and cross with wild populations in Africa, thus contami-
nating their gene pool. Consequently, countries from which wild fish were
sampled to initiate the breeding program (Egypt, Ghana, Kenya and
Senegal) did not benefit from the genetic gain made, and have received
nothing in return for their collaboration. The issue has been raised by some
African representatives and it has re-kindled the debate on the matter. This
has resulted in a recommendation to allow controlled introduction followed
by a properly designed comparison of GIFT with relevant local strains to
ascertain that there is a productivity advantage exhibited by GIFT. At
present, WorldFish is finalizing the policy document that will define the
circumstances under which the introduction of GIFT to an African country
will be authorized. ‘Given a favorable outcome for GIFT from the above
comparison, multiplication and dissemination of GIFT will be authorized.
The multiplication and dissemination programs will be accompanied by a
package of measures attempting to minimize the risk of escapes and to
mitigate the impact in case these should occur’ (Ponzoni, 2007, WorldFish
Center, pers comm).
2.4 Future trends

Conventional breeding programs will continue to be the main engine
driving the global finfish aquaculture industry forward. Efforts will persist
to increase efficiency and optimize the design of breeding programs by
maximising the use of pedigree information while using both established
and cutting-edge technologies mentioned above. However, since these
methods are less suitable for economically important traits that are
difficult to measure on candidates for selection (such as carcass and disease

traits), alternative approaches will have to be further developed and opti-
mized. Here is where incorporation of recent biotechnological tools may
come into play. The potential for accelerating breeding programs expected
from applying these tools has yet to be realized in the aquaculture industry.
Nevertheless, MAS and gene-assisted selection (GAS) methodologies,
when mature, may eventually become practical in efforts towards identify-
ing genes that underlie economically-important traits and towards combin-
ing quantitative and molecular data in breeding programs. A potential
alternative breakthrough may arise from solving containment problems
currently limiting the use of GM aquacultured organisms; once the public
prefers education to regulation, antagonism to the use of GM may fade
out.
2.5 Sources of further information and advice

Several books devoted to various aspects and methodologies discussed in
this chapter were published in recent years. These will obviously serve as
the main sources for further information for the near future. Among them
are Fingerman and Nagabhushanam’s (2000) Recent Advances in Marine
Biotechnology: Aquaculture – Fishes, Beaumont and Hoare’s (2003) Bio-
technology and Genetics in Fisheries and Aquaculture; Hallerman’s (2003)
Population Genetics: Principles and Applications for Fisheries Scientists;
Dunham’s (2004) Aquaculture and Fisheries Biotechnology: Genetic
Approaches; Gjedrem’s (2005) Selection and Breeding Programs in Aqua-
culture; Liu’s (2007a) Aquaculture Genome Technologies; and Kocher and
Kole’s (2008) Genome Mapping and Genomics in Fishes and Aquatic
Animals.
2.6 Acknowledgement
The authors would like to thank Eric Hallerman for his valuable comments
and suggestions that helped shape the view-point expressed in the paper
and improved its prose. This paper is contribution No. 526/08 from the
ARO, The Volcani Center, Bet Dagan, Israel.
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2

Genetic improvement of finfish

Key words: Breeding programs, biotechnology, manipulations of genes and

2.1 Introduction: current status of aquaculture genetics

2.2 Key drivers for genetic improvement of finfish

Table 2.1 Examples of recent breeding programmes

Atlantic cod (Gadus morhua) Gjerde et al., 2004

Table 2.2 Examples of production- and consumer-related breeding-goal traits in

Trait Species Reference

et al., 2005). Improvements have also been made in breeding programs

Advances in designing breeding programs in aquaculture

2.2.2 Improving performance and other traits by non-selective

Chromosome set manipulations (gynogenesis, androgenesis

Table 2.3 Examples of chromosome manipulations in newly culture species

for genetic mapping (Nomura et al., 2006). Although resulting in high

♂ Albino ♀ Wild-type ♀ Albino ♂ Common

Sperm (X & Y) UV-irradiated eggs Eggs (X) UV-irradiated sperm

Fig. 2.1 Schematic presentation of ploidy manipulations on grass carp

Another area where cytogenetics has played an important role is studies

Study of sex chromosomes: Ten sex-determination systems are known

studies led to the establishment of a protocol that provided gilthead sea

Aid in gene mapping: Cytological methodologies have been employed in

Parental assignment and molecular pedigrees: DNA markers, notably mic-

American catfish (Ictalurus punctatus ¥ Liu et al., 2003

QTL detection: A QTL is a segment of a chromosome with a significant

of a linkage map of at least moderate density; mapping of QTL using

MAS: The development of large numbers of genetic markers and genetic

Bioinformatic tools already available and those that will be further

benefits of uses of aquacultured GMOs. It covers all aspects from the

2.3 Case studies – risks associated with selective

The farming of Atlantic salmon (Salmo salar), which has greatly

2.4 Future trends

difficult to measure on candidates for selection (such as carcass and disease

2.5 Sources of further information and advice

arai k (2000) Chromosome manipulation in aquaculture: recent progress and per-

Aquaculture in the Third Millenium, 20–25 February 2000, Bangkok, Bangkok

fontana f (2002) A cytogenetic approach to the study of taxonomy and evolution

gjerde b, pante m j r and baeverfjord g (2005) Genetic variation for a vertebral

polymorphism markers associated with Atlantic salmon (Salmo salar) expressed

kause a, ritola o, paananen t, eskelinen u and mäntysaari e (2003b) Big and

martínez r, juncal j, zaldívar c, arenal a, guillén i, morera v, carrillo o,

nrc (2002) Animal Biotechnology: Science-Based Concerns, Washington, DC,

NRAES-106, Ithaca, NY, Northeast Regional Aquacultural Engineering Ser-

senanan w, kapuscinski a r, na-nakorn u, miller l m (2004) Genetic impacts of

tvedt h b, benfey t j, martin-robichaud d j, mcgowan c and reith m (2006) Gyno-

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