7 Genomic Approaches in Aquaculture and Fisheries
219
reduce the most expensive and time-consuming step of RH map construction, i.e.
marker genotyping on hybrid cell lines. Rapid and relatively inexpensive RH maps
will in turn allow much broader genome comparisons and the transfer of information from complete or high-quality draft genome sequences to less characterized
ones (Sarropoulou et al. 2008), speeding up the identification of loci involved in
biologically important phenotypes. At the same time, medium-high resolution RH
maps coupled with low-coverage (1–2X) whole-genome sequencing will provide
essentially the same comparative data with respect to gene order that is derived
from high-coverage (greater than 7X) genome sequencing (Hitte et al. 2008). The
possibility of developing a RH map for the Pacific oyster is also currently being
examined (F. Galibert, personal communication).
7.2.3 BAC-Based Physical Maps
While genetic maps provide an indirect estimate of the distance between two loci, a
genome-wide physical map gives an estimate of the true distance, in measurements
called base pairs, between items of interest (note that RH maps may be considered either to be a type of physical map or to be similar to genetic maps, with
the frequency of association between markers being determined by the irradiation
dose rather than by genetic recombination). A physical map usually comprises a
set of ordered large-insert clones such as bacterial artificial chromosomes (BACs).
Physical maps can be independent of genetic information but are more valuable
if linked to genetically mapped markers, and are even more powerful if integrated
with genomic sequence data. Current physical maps are based on technologies to
detect overlaps among BACs. The most commonly used is BAC fingerprinting,
where restriction profiles of individual BACs are used to order clones on the map
(Meyers et al. 2004). While BAC libraries have been constructed for several marine
fish species, high-resolution BAC-based physical maps are not available yet for
marine fish species. A low resolution BAC-based map, linking 84 BAC clones to the
existing linkage map (Wang et al. 2007b), has been recently reported (Wang et al.
2008) for the barramundi or Asian sea bass (Lates calcarifer). Technical improvements in BAC DNA preparation (Kuhl et al. 2010) coupled with high-throughput
DNA sequencing led recently to sequencing of both ends of over 50,000 clones
of a Dicentrarchus labrax BAC library (Whitaker et al. 2006) and of a Sparus
aurata BAC library. In this case, BAC-end sequences have been ordered by comparison with a high quality genome sequence draft from the three-spined stickleback
(Fig. 7.2). Comparison with a closely-related species genome for ordering clones
has been already used to provide a complementary framework to other methods
(Gregory et al. 2002) and appears to be a good tool for preliminary assembly of
BAC clones (R. Reinhardt, personal communication).
Few BAC libraries are yet available in molluscan shellfish. Cunningham et al.
(2006) first reported a BAC library for Pacific and American oysters. More recently,
Zhang et al. (2008b) have reported the construction of two BAC libraries for the
219
reduce the most expensive and time-consuming step of RH map construction, i.e.
marker genotyping on hybrid cell lines. Rapid and relatively inexpensive RH maps
will in turn allow much broader genome comparisons and the transfer of information from complete or high-quality draft genome sequences to less characterized
ones (Sarropoulou et al. 2008), speeding up the identification of loci involved in
biologically important phenotypes. At the same time, medium-high resolution RH
maps coupled with low-coverage (1–2X) whole-genome sequencing will provide
essentially the same comparative data with respect to gene order that is derived
from high-coverage (greater than 7X) genome sequencing (Hitte et al. 2008). The
possibility of developing a RH map for the Pacific oyster is also currently being
examined (F. Galibert, personal communication).
7.2.3 BAC-Based Physical Maps
While genetic maps provide an indirect estimate of the distance between two loci, a
genome-wide physical map gives an estimate of the true distance, in measurements
called base pairs, between items of interest (note that RH maps may be considered either to be a type of physical map or to be similar to genetic maps, with
the frequency of association between markers being determined by the irradiation
dose rather than by genetic recombination). A physical map usually comprises a
set of ordered large-insert clones such as bacterial artificial chromosomes (BACs).
Physical maps can be independent of genetic information but are more valuable
if linked to genetically mapped markers, and are even more powerful if integrated
with genomic sequence data. Current physical maps are based on technologies to
detect overlaps among BACs. The most commonly used is BAC fingerprinting,
where restriction profiles of individual BACs are used to order clones on the map
(Meyers et al. 2004). While BAC libraries have been constructed for several marine
fish species, high-resolution BAC-based physical maps are not available yet for
marine fish species. A low resolution BAC-based map, linking 84 BAC clones to the
existing linkage map (Wang et al. 2007b), has been recently reported (Wang et al.
2008) for the barramundi or Asian sea bass (Lates calcarifer). Technical improvements in BAC DNA preparation (Kuhl et al. 2010) coupled with high-throughput
DNA sequencing led recently to sequencing of both ends of over 50,000 clones
of a Dicentrarchus labrax BAC library (Whitaker et al. 2006) and of a Sparus
aurata BAC library. In this case, BAC-end sequences have been ordered by comparison with a high quality genome sequence draft from the three-spined stickleback
(Fig. 7.2). Comparison with a closely-related species genome for ordering clones
has been already used to provide a complementary framework to other methods
(Gregory et al. 2002) and appears to be a good tool for preliminary assembly of
BAC clones (R. Reinhardt, personal communication).
Few BAC libraries are yet available in molluscan shellfish. Cunningham et al.
(2006) first reported a BAC library for Pacific and American oysters. More recently,
Zhang et al. (2008b) have reported the construction of two BAC libraries for the