7 Genomic Approaches in Aquaculture and Fisheries
223
from related individuals to increase the accuracy of predicting breeding values, is
often lacking. Molecular markers can be used for this purpose as well as to detect
regions of interest in the genomes linked to a trait of interest, i.e. QTL. This section is dedicated to the possibilities and first realizations of incorporating molecular
marker information into fish and shellfish breeding programmes by considering
their use for (1) genealogical traceability and genetic variability maintenance, and
(2) QTL search and marker-assisted selection (MAS).
Practically, two of the main constraints facing effective breeding programmes for
fish and shellfish are the fact that (1) in most species early stages are too small to
be tagged individually and, at the same time, (2) spatial and technical constraints
strongly limit the number of rearing vessels that can be managed at one time. To
address this issue, mixtures of equal-aged progenies from different families can be
reared together to avoid family-specific environmental effects. Molecular markers
can be used subsequently to assign animals to families after the evaluation of their
performance, which is of particular interest for individual traits such as growth rate.
SSRs are currently the type of marker most commonly used for paternity analysis
and traceability in aquaculture species (Herbinger et al. 1995, Fishback et al. 2002,
Vandeputte et al. 2004), mainly due to their high levels of variability and power to
discriminate at the individual level. Although it depends on the size of the breeding
population, typically, 10–20 variable genetic markers are needed to assign >95% of
individuals to single pairs of parents (e.g. Vandeputte et al. 2006). However, high
frequencies of null alleles are commonly observed in bivalves (Hedgecock et al.
2004), and fish (Castro et al. 2004, 2006) which can lead to difficulties and bias in
such analyses. Parentage assignment and relatedness studies have been made using
microsatellite markers in several species, on an experimental level involving a limited number of genitors in molluscs (Boudry et al. 2002, Taris et al. 2006, Li and
Kijima 2006, McAvoy et al. 2008), seabream (Castro et al. 2007), Atlantic salmon
(Norris et al. 2000), Atlantic cod (Herlin et al. 2007, 2008), rainbow trout (Mcdonald
et al. 2004), turbot (Borrell et al. 2004) and sole (Porta et al. 2006). However, the
suitability of such approaches for mixed-family breeding programs has not been
yet demonstrated, despite the large number of markers already available (Li et al.
2003a). AFLPs (Gerber et al. 2000) as well as SNPs have also been considered
(Anderson and Garza 2006), with the need for these latter to develop cost-efficient
high-throughput genotyping methods (Hayes et al. 2005). As mean SNP density is
very high in oysters (Curole and Hedgecock 2005, Sauvage et al. 2007), and likely
to be of a similar level in many other marine bivalves, the number of potential SNP
markers is extremely high.
Traceability has also become an area of interest for aquaculture species in order
to follow individuals back to their origin for estimates of escapees from farms or
to identify sources of diseases and/or toxins in market fish (see Section 7.5 of this
chapter and Chapter 1 of this book).
Other potential applications for molecular markers are walk-back selection (Li
et al. 2003b, Sonesson 2005) and pedigree-assisted selection methods such as animal model-based methods (Lynch and Walch 1998). Bias in estimating genetic
parameters is expected to arise due to the low level of self-fertilisation that can
223
from related individuals to increase the accuracy of predicting breeding values, is
often lacking. Molecular markers can be used for this purpose as well as to detect
regions of interest in the genomes linked to a trait of interest, i.e. QTL. This section is dedicated to the possibilities and first realizations of incorporating molecular
marker information into fish and shellfish breeding programmes by considering
their use for (1) genealogical traceability and genetic variability maintenance, and
(2) QTL search and marker-assisted selection (MAS).
Practically, two of the main constraints facing effective breeding programmes for
fish and shellfish are the fact that (1) in most species early stages are too small to
be tagged individually and, at the same time, (2) spatial and technical constraints
strongly limit the number of rearing vessels that can be managed at one time. To
address this issue, mixtures of equal-aged progenies from different families can be
reared together to avoid family-specific environmental effects. Molecular markers
can be used subsequently to assign animals to families after the evaluation of their
performance, which is of particular interest for individual traits such as growth rate.
SSRs are currently the type of marker most commonly used for paternity analysis
and traceability in aquaculture species (Herbinger et al. 1995, Fishback et al. 2002,
Vandeputte et al. 2004), mainly due to their high levels of variability and power to
discriminate at the individual level. Although it depends on the size of the breeding
population, typically, 10–20 variable genetic markers are needed to assign >95% of
individuals to single pairs of parents (e.g. Vandeputte et al. 2006). However, high
frequencies of null alleles are commonly observed in bivalves (Hedgecock et al.
2004), and fish (Castro et al. 2004, 2006) which can lead to difficulties and bias in
such analyses. Parentage assignment and relatedness studies have been made using
microsatellite markers in several species, on an experimental level involving a limited number of genitors in molluscs (Boudry et al. 2002, Taris et al. 2006, Li and
Kijima 2006, McAvoy et al. 2008), seabream (Castro et al. 2007), Atlantic salmon
(Norris et al. 2000), Atlantic cod (Herlin et al. 2007, 2008), rainbow trout (Mcdonald
et al. 2004), turbot (Borrell et al. 2004) and sole (Porta et al. 2006). However, the
suitability of such approaches for mixed-family breeding programs has not been
yet demonstrated, despite the large number of markers already available (Li et al.
2003a). AFLPs (Gerber et al. 2000) as well as SNPs have also been considered
(Anderson and Garza 2006), with the need for these latter to develop cost-efficient
high-throughput genotyping methods (Hayes et al. 2005). As mean SNP density is
very high in oysters (Curole and Hedgecock 2005, Sauvage et al. 2007), and likely
to be of a similar level in many other marine bivalves, the number of potential SNP
markers is extremely high.
Traceability has also become an area of interest for aquaculture species in order
to follow individuals back to their origin for estimates of escapees from farms or
to identify sources of diseases and/or toxins in market fish (see Section 7.5 of this
chapter and Chapter 1 of this book).
Other potential applications for molecular markers are walk-back selection (Li
et al. 2003b, Sonesson 2005) and pedigree-assisted selection methods such as animal model-based methods (Lynch and Walch 1998). Bias in estimating genetic
parameters is expected to arise due to the low level of self-fertilisation that can