218
M.L. Cancela et al.
presented as “preliminary” and are complemented in a second step by co-dominant
markers (e.g. Pacific abalone: Liu et al. 2006). Microsatellite-based maps (e.g.
Pacific oyster: 88 markers mapped; Hubert and Hedegock 2004; Pacific abalone:
167 markers mapped; Sekino and Hara 2007) are more demanding to develop and
often still present fewer markers than those based on AFLP markers. SNP-based
linkage maps are currently been developed in several species.
Comparative genomics has its foundation in the presence of conserved regions
across species, which are putatively homologous and can be used to align and compare genomes. A small proportion of SSR loci are conserved, allowing anchoring
across genomes (Stemshorn et al. 2005, Franch et al. 2006), but typically microsatellite markers are species-specific and homologous genomic regions are often not
recognizable in other genomes. This is especially the case in shellfish species
showing high levels of nucleotide polymorphism leading to poor cross-species
amplification (e.g. Hedgecock et al. 2004).
7.2.2 Radiation Hybrid (RH) Maps
RH maps were originally developed precisely to overcome the limitations of genetic
linkage maps (Walter et al. 1994). A detailed description of RH map construction
is beyond the scope of the present book and the reader should refer to specific publications (e.g. Kwok et al. 1998). Briefly, hybrid cell lines are established, which
contain random fragments of the donor genome (the species of interest) mixed with
the whole genome of host cells (generally hamster cells). A set of independent cell
lines recapitulates the genome of the target organism several-fold. Markers or genes
of interest are analyzed by PCR using DNA isolated from each cell line. Statistical
tools are applied to determine both the linear order of markers on each chromosome,
and the confidence of each placement. Any genomic region that is PCR-amplified
(i.e. coding genes, SSR, ESTs) selectively from the donor genome can be located
on the RH map (Fig. 7.2). This allows mapping of loci that are not polymorphic.
Moreover, protein-coding loci are often well-conserved even between distantlyrelated species; therefore most markers located on a RH map find their homologue
in the genomic map of other species, allowing comparison between genomes.
So far, technical problems (compatibility between host and donor cells, sensitivity of donor cells to irradiation) have limited the development of RH mapping
panels in non-mammalian vertebrates, and especially in fish. RH maps are available for only two teleost species, the zebrafish (Geisler et al. 1999, Hukriede et al.
1999) and the gilthead seabream (Senger et al. 2006, Sarropoulou et al. 2007).
For a third species, the European sea bass, a RH panel has been produced with
an improved methodology that is virtually cell-culture free (F. Galibert, personal
communication), and a RH map is being constructed. Such technical improvements
are expected to make RH panel development faster and easier for any vertebrate
species. At the same time, application of high-throughput methods for RH panel
scoring (e.g. McKay et al. 2007, Park et al. 2008) hold the promise to drastically
M.L. Cancela et al.
presented as “preliminary” and are complemented in a second step by co-dominant
markers (e.g. Pacific abalone: Liu et al. 2006). Microsatellite-based maps (e.g.
Pacific oyster: 88 markers mapped; Hubert and Hedegock 2004; Pacific abalone:
167 markers mapped; Sekino and Hara 2007) are more demanding to develop and
often still present fewer markers than those based on AFLP markers. SNP-based
linkage maps are currently been developed in several species.
Comparative genomics has its foundation in the presence of conserved regions
across species, which are putatively homologous and can be used to align and compare genomes. A small proportion of SSR loci are conserved, allowing anchoring
across genomes (Stemshorn et al. 2005, Franch et al. 2006), but typically microsatellite markers are species-specific and homologous genomic regions are often not
recognizable in other genomes. This is especially the case in shellfish species
showing high levels of nucleotide polymorphism leading to poor cross-species
amplification (e.g. Hedgecock et al. 2004).
7.2.2 Radiation Hybrid (RH) Maps
RH maps were originally developed precisely to overcome the limitations of genetic
linkage maps (Walter et al. 1994). A detailed description of RH map construction
is beyond the scope of the present book and the reader should refer to specific publications (e.g. Kwok et al. 1998). Briefly, hybrid cell lines are established, which
contain random fragments of the donor genome (the species of interest) mixed with
the whole genome of host cells (generally hamster cells). A set of independent cell
lines recapitulates the genome of the target organism several-fold. Markers or genes
of interest are analyzed by PCR using DNA isolated from each cell line. Statistical
tools are applied to determine both the linear order of markers on each chromosome,
and the confidence of each placement. Any genomic region that is PCR-amplified
(i.e. coding genes, SSR, ESTs) selectively from the donor genome can be located
on the RH map (Fig. 7.2). This allows mapping of loci that are not polymorphic.
Moreover, protein-coding loci are often well-conserved even between distantlyrelated species; therefore most markers located on a RH map find their homologue
in the genomic map of other species, allowing comparison between genomes.
So far, technical problems (compatibility between host and donor cells, sensitivity of donor cells to irradiation) have limited the development of RH mapping
panels in non-mammalian vertebrates, and especially in fish. RH maps are available for only two teleost species, the zebrafish (Geisler et al. 1999, Hukriede et al.
1999) and the gilthead seabream (Senger et al. 2006, Sarropoulou et al. 2007).
For a third species, the European sea bass, a RH panel has been produced with
an improved methodology that is virtually cell-culture free (F. Galibert, personal
communication), and a RH map is being constructed. Such technical improvements
are expected to make RH panel development faster and easier for any vertebrate
species. At the same time, application of high-throughput methods for RH panel
scoring (e.g. McKay et al. 2007, Park et al. 2008) hold the promise to drastically