7 Genomic Approaches in Aquaculture and Fisheries
225
et al. (2007) described QTLs for shell, muscle, gonad, digestive gland and gill
weight in Pacific abalone Haliotis discus hannai. In addition, positive results have
recently been obtained in European flat oyster Ostrea edulis for Bonamia ostreaea
resistance (Lallias et al. 2008), and in the Pacific oyster C. gigas for summer mortality resistance (C. Sauvage, personal communication) and heterosis for growth
(D. Hedgecock, personal communication).
The candidate gene approach is another alternative, which consists in looking
for variation at genes with a known role in the physiology underlying complex
traits to explain phenotypic variability for those traits. Hence, direct association
between gene polymorphism and phenotypic variation in growth has recently been
reported in oysters (Prudence et al. 2006). Physiological causes of such differences
have also been investigated in relationship with feeding-related traits and specific
amylase activity revealed an association between specific alleles of amylase genes
(Huvet et al. 2008). Similarly, relationship of both glutamine synthetase (amino acid
metabolism) and delta-9 desaturase (lipid metabolism) genes with resistance to summer mortality was reported by David et al. (2007). In the Arctic charr, candidate
genes have been studied for growth related traits using ten conserved gene sequences
known to be related to the growth hormone axis (Tao and Boulding 2003) and one
SNP was found to be associated with growth rate. In the Atlantic salmon, specific
alleles or heterozygotes at genes of the major histocompatibility complex (MHC)
were associated with resistance and susceptibility to the infectious haematopoietic
necrosis virus (Langefors et al. 2001, Lohm et al. 2002, Arkush et al. 2002, Grimholt
et al. 2003, Bernatchez and Landry 2003).
In addition to these a priori approaches, differential gene expression studies can
provide new candidate genes. Differential gene expression between oysters selected
to be resistant or sensitive to summer mortality (Huvet et al. 2004), or exposure to
pollutants (Boutet et al. 2004, Tanguy et al. 2005), have led to the identification of
large numbers of candidate ESTs. Until now, Suppression Subtractive Hybridization
(SSH) has been the method the most frequently used to identify genes differentially expressed between contrasting individuals. However, novel high-throughput
transcriptome analysis methods such as microarrays (Jenny et al. 2007), MPSS
(Hedgecock et al. 2007), or SAGE are likely to increasingly contribute to the identification of genes of interest in the near future. In salmonids, a microarray has been
used to study gene expression in fish exposed or not to Pisciricketsia salmonis (Rise
et al. 2004). Finally, through the co-localization of QTLs and candidate genes, there
should be a mutual reinforcement of both approaches that would benefit the ultimate
progression of improvement programs based on such knowledge.
Although molecular markers can already be used in fish and shellfish breeding programmes to trace individuals for easier rearing, escapes estimation, or
optimizing population size in bloodstocks, on a case by case study basis, QTL
mapping and MAS are not as well advanced in aquaculture species as in farmed
terrestrial plants and animals. However, the merging efforts between genetics and
genomics are expected to allow the detection of variation affecting complex traits
in fish and shellfish species and their use for increasing the usefulness of MAS
schemes.
225
et al. (2007) described QTLs for shell, muscle, gonad, digestive gland and gill
weight in Pacific abalone Haliotis discus hannai. In addition, positive results have
recently been obtained in European flat oyster Ostrea edulis for Bonamia ostreaea
resistance (Lallias et al. 2008), and in the Pacific oyster C. gigas for summer mortality resistance (C. Sauvage, personal communication) and heterosis for growth
(D. Hedgecock, personal communication).
The candidate gene approach is another alternative, which consists in looking
for variation at genes with a known role in the physiology underlying complex
traits to explain phenotypic variability for those traits. Hence, direct association
between gene polymorphism and phenotypic variation in growth has recently been
reported in oysters (Prudence et al. 2006). Physiological causes of such differences
have also been investigated in relationship with feeding-related traits and specific
amylase activity revealed an association between specific alleles of amylase genes
(Huvet et al. 2008). Similarly, relationship of both glutamine synthetase (amino acid
metabolism) and delta-9 desaturase (lipid metabolism) genes with resistance to summer mortality was reported by David et al. (2007). In the Arctic charr, candidate
genes have been studied for growth related traits using ten conserved gene sequences
known to be related to the growth hormone axis (Tao and Boulding 2003) and one
SNP was found to be associated with growth rate. In the Atlantic salmon, specific
alleles or heterozygotes at genes of the major histocompatibility complex (MHC)
were associated with resistance and susceptibility to the infectious haematopoietic
necrosis virus (Langefors et al. 2001, Lohm et al. 2002, Arkush et al. 2002, Grimholt
et al. 2003, Bernatchez and Landry 2003).
In addition to these a priori approaches, differential gene expression studies can
provide new candidate genes. Differential gene expression between oysters selected
to be resistant or sensitive to summer mortality (Huvet et al. 2004), or exposure to
pollutants (Boutet et al. 2004, Tanguy et al. 2005), have led to the identification of
large numbers of candidate ESTs. Until now, Suppression Subtractive Hybridization
(SSH) has been the method the most frequently used to identify genes differentially expressed between contrasting individuals. However, novel high-throughput
transcriptome analysis methods such as microarrays (Jenny et al. 2007), MPSS
(Hedgecock et al. 2007), or SAGE are likely to increasingly contribute to the identification of genes of interest in the near future. In salmonids, a microarray has been
used to study gene expression in fish exposed or not to Pisciricketsia salmonis (Rise
et al. 2004). Finally, through the co-localization of QTLs and candidate genes, there
should be a mutual reinforcement of both approaches that would benefit the ultimate
progression of improvement programs based on such knowledge.
Although molecular markers can already be used in fish and shellfish breeding programmes to trace individuals for easier rearing, escapes estimation, or
optimizing population size in bloodstocks, on a case by case study basis, QTL
mapping and MAS are not as well advanced in aquaculture species as in farmed
terrestrial plants and animals. However, the merging efforts between genetics and
genomics are expected to allow the detection of variation affecting complex traits
in fish and shellfish species and their use for increasing the usefulness of MAS
schemes.