3 Populations and Pathways
87
such markers, however, is essential for the production of fine-scale linkage maps,
which ultimately can lead to identification of adaptive traits and/or genes.
Linkage analysis is the traditional method of identifying chromosomal regions
containing QTLs (Quantitative Trait Loci) in model organisms. The methodology
relies on following the inheritance of segregating traits in pedigrees and seeking to
find (co)inheritance of traits and numerous genetic markers. Hence, statistical analyses of genome-wide molecular markers such as microsatellites and AFLPs, and
phenotypes measured in the progeny of controlled crosses can be used to identify
chromosomal regions contributing to phenotypic differentiation for a trait or a suite
of traits of interest (reviewed in Mackay 2001, Erickson et al. 2004). If this can be
established, trait loci are inferred to map in the vicinity of marker loci and markers
such as microsatellites, AFLPs and even SNPs can lose their purely anonymous status. The determinism of the trait under study can then theoretically be investigated
by looking at the polymorphism of a few markers. The use of inbred lines in genetic
crosses is the most powerful method for QTL analysis, because it maximizes linkage
disequilibrium between markers and trait loci (Lynch and Walsh 1998). Analysis is
then mostly pedigree-based.
The power of linkage analysis increases with number of meioses that can be studied. Linkage maps have so far mainly been constructed for species that can be bred in
captivity, including fishes, insects and mammals. In marine organisms, studies have
concentrated on aquaculture species including the European sea bass (Chistiakhov
et al. 2005), the sea bream (Sparus aurata; Franch et al. 2006), the European flat
oyster (Ostrea edulis; Lallias et al. 2007a), the Pacific oyster (Crassostrea gigas;
Hubert and Hedgecock 2004, Li and Guo 2004), the Eastern oyster (Crassostrea virginica; Yu and Guo 2003); the bay scallop (Argopecten irradians; Qin et al. 2007),
the blacklip abalone (Haliotis rubra; Baranski et al. 2006), and the blue mussel
(Mytilus edulis; Lallias et al. 2007b). However, the number of linkage maps available for aquatic organisms is rapidly increasing (Wenne et al. 2007). Most of the
QTL studies to date have concerned growth related traits, and to a lesser extent disease resistance traits. Even though growth is one important proxy of fitness, other
ecologically relevant traits (e.g. reproductive performance, larval duration, gene
expression response to various stresses) should certainly be investigated as these
could explain performances of individuals.
At present, the genetic maps available for aquatic organisms are not sufficiently
fine to map adaptations as they rarely comprise more than >1,000 markers disseminated throughout the genome. An average marker distance of 20 cM is required
for the location of a QTL to the correct chromosome arm (e.g. Rogers et al. 2001,
Chistiakhov et al. 2005), but, for finer mapping, a marker distance of 1 cM or less
is needed. Mapping chromosomal regions that co-segregate with traits of interest
represents just the first step towards the identification of the causative genetic variants that shape the phenotype. Numerous genes usually reside within a targeted
chromosomal region and the eventual identification of such variants requires refined
mapping and nomination of candidate genes. There are only a few examples of such
studies so far in natural populations, notably the mapping and subsequent identification of ectodysplasin (Eda gene) the armour plate patterning gene in different
87
such markers, however, is essential for the production of fine-scale linkage maps,
which ultimately can lead to identification of adaptive traits and/or genes.
Linkage analysis is the traditional method of identifying chromosomal regions
containing QTLs (Quantitative Trait Loci) in model organisms. The methodology
relies on following the inheritance of segregating traits in pedigrees and seeking to
find (co)inheritance of traits and numerous genetic markers. Hence, statistical analyses of genome-wide molecular markers such as microsatellites and AFLPs, and
phenotypes measured in the progeny of controlled crosses can be used to identify
chromosomal regions contributing to phenotypic differentiation for a trait or a suite
of traits of interest (reviewed in Mackay 2001, Erickson et al. 2004). If this can be
established, trait loci are inferred to map in the vicinity of marker loci and markers
such as microsatellites, AFLPs and even SNPs can lose their purely anonymous status. The determinism of the trait under study can then theoretically be investigated
by looking at the polymorphism of a few markers. The use of inbred lines in genetic
crosses is the most powerful method for QTL analysis, because it maximizes linkage
disequilibrium between markers and trait loci (Lynch and Walsh 1998). Analysis is
then mostly pedigree-based.
The power of linkage analysis increases with number of meioses that can be studied. Linkage maps have so far mainly been constructed for species that can be bred in
captivity, including fishes, insects and mammals. In marine organisms, studies have
concentrated on aquaculture species including the European sea bass (Chistiakhov
et al. 2005), the sea bream (Sparus aurata; Franch et al. 2006), the European flat
oyster (Ostrea edulis; Lallias et al. 2007a), the Pacific oyster (Crassostrea gigas;
Hubert and Hedgecock 2004, Li and Guo 2004), the Eastern oyster (Crassostrea virginica; Yu and Guo 2003); the bay scallop (Argopecten irradians; Qin et al. 2007),
the blacklip abalone (Haliotis rubra; Baranski et al. 2006), and the blue mussel
(Mytilus edulis; Lallias et al. 2007b). However, the number of linkage maps available for aquatic organisms is rapidly increasing (Wenne et al. 2007). Most of the
QTL studies to date have concerned growth related traits, and to a lesser extent disease resistance traits. Even though growth is one important proxy of fitness, other
ecologically relevant traits (e.g. reproductive performance, larval duration, gene
expression response to various stresses) should certainly be investigated as these
could explain performances of individuals.
At present, the genetic maps available for aquatic organisms are not sufficiently
fine to map adaptations as they rarely comprise more than >1,000 markers disseminated throughout the genome. An average marker distance of 20 cM is required
for the location of a QTL to the correct chromosome arm (e.g. Rogers et al. 2001,
Chistiakhov et al. 2005), but, for finer mapping, a marker distance of 1 cM or less
is needed. Mapping chromosomal regions that co-segregate with traits of interest
represents just the first step towards the identification of the causative genetic variants that shape the phenotype. Numerous genes usually reside within a targeted
chromosomal region and the eventual identification of such variants requires refined
mapping and nomination of candidate genes. There are only a few examples of such
studies so far in natural populations, notably the mapping and subsequent identification of ectodysplasin (Eda gene) the armour plate patterning gene in different