222
M.L. Cancela et al.
situ synthesis method based on ink-jet technology, two non-overlapping oligos
were designed for each unique transcript. For S. aurata 19,715 gene transcripts
are represented on an array platform that is coupled with a dedicated database
(http://enne.cribi.unipd.it:5555/biomart/martview). This array is now fully validated
and publicly accessible (Ferraresso et al. 2008). Likewise, 19,048 unique transcripts
have been used to develop a D. labrax oligo microarray (L. Bargelloni, personal
communication). A similar platform albeit with a reduced transcriptome representation is available for two marine flatfish, Scophthalmus maximus (P. Martinez,
personal communication) and Solea senegalensis (Cerda et al. 2008). The drastically reduced cost of large-scale DNA sequencing will greatly increase available
ESTs for a large number of marine fish species, making functional genomic tools
easily accessible to the majority of research groups. Ultimately, the trend toward
cheaper massive sequencing technologies will lead to direct sequencing becoming
the method of choice for transcriptome analysis (Sultan et al. 2008).
The very powerful method of MPSS (Brenner et al. 2000) was used to study
heterosis (hybrid vigor), a widely observed phenomena in bivalve molluscs. MPSS
technology generates short sequence tags from complex RNA samples to analyse
gene expression pattern. MPSS offers advantages for organisms with poorly characterized genomes: (1) it requires no previous sequence information and relies on
open-based sampling of transcripts, allowing for the identification of novel transcribed sequences, even if a large EST collection is a great advantage to assign
MPSS signatures, (2) MPSS is an unbiased, comprehensive and quantitative method
as tag counting provides a digital measurement of the abundancies of transcripts,
and (3) MPSS is able to detect rare messages (down to about 3 transcripts per million). Up to now, 4.5 M sequence tags have been identified in C. gigas genotypes
containing 23,274 distinct signatures that allowed the characterisation of some 350
candidate genes for growth heterosis (Hedgecock et al. 2007). SAGE is another
method producing signatures to generate transcriptome profiling (Velculescu et al.
1995). This method makes the same assumptions and has the same advantages as
MPSS. To date, there are no published articles describing SAGE analysis of marine
molluscs but SAGE will be soon applied to the oyster for genome-wide expression profiling of the hemocytes, the immuno competent cells (E. Bachère, personal
communication). Finally, a recent interesting comparison of these three methods
(Nygaard et al. 2008) has concluded that the oligoarrays can provide quantitative
transcript concentrations that are correlated with MPSS and SAGE data but the
absolute scale of the measurements differs across the technologies.
7.3 Genomic Approaches in Breeding and Reproduction
The ultimate goal of fish and shellfish selective breeding programmes is to increase
the sustainability and profitability of aquaculture, while maintaining the genetic
variability in the cultured stocks and limiting its impact on wild population and
the environment. Pedigree information, which is required for efficient breeding programmes in order to maximise effective population sizes and to use information
M.L. Cancela et al.
situ synthesis method based on ink-jet technology, two non-overlapping oligos
were designed for each unique transcript. For S. aurata 19,715 gene transcripts
are represented on an array platform that is coupled with a dedicated database
(http://enne.cribi.unipd.it:5555/biomart/martview). This array is now fully validated
and publicly accessible (Ferraresso et al. 2008). Likewise, 19,048 unique transcripts
have been used to develop a D. labrax oligo microarray (L. Bargelloni, personal
communication). A similar platform albeit with a reduced transcriptome representation is available for two marine flatfish, Scophthalmus maximus (P. Martinez,
personal communication) and Solea senegalensis (Cerda et al. 2008). The drastically reduced cost of large-scale DNA sequencing will greatly increase available
ESTs for a large number of marine fish species, making functional genomic tools
easily accessible to the majority of research groups. Ultimately, the trend toward
cheaper massive sequencing technologies will lead to direct sequencing becoming
the method of choice for transcriptome analysis (Sultan et al. 2008).
The very powerful method of MPSS (Brenner et al. 2000) was used to study
heterosis (hybrid vigor), a widely observed phenomena in bivalve molluscs. MPSS
technology generates short sequence tags from complex RNA samples to analyse
gene expression pattern. MPSS offers advantages for organisms with poorly characterized genomes: (1) it requires no previous sequence information and relies on
open-based sampling of transcripts, allowing for the identification of novel transcribed sequences, even if a large EST collection is a great advantage to assign
MPSS signatures, (2) MPSS is an unbiased, comprehensive and quantitative method
as tag counting provides a digital measurement of the abundancies of transcripts,
and (3) MPSS is able to detect rare messages (down to about 3 transcripts per million). Up to now, 4.5 M sequence tags have been identified in C. gigas genotypes
containing 23,274 distinct signatures that allowed the characterisation of some 350
candidate genes for growth heterosis (Hedgecock et al. 2007). SAGE is another
method producing signatures to generate transcriptome profiling (Velculescu et al.
1995). This method makes the same assumptions and has the same advantages as
MPSS. To date, there are no published articles describing SAGE analysis of marine
molluscs but SAGE will be soon applied to the oyster for genome-wide expression profiling of the hemocytes, the immuno competent cells (E. Bachère, personal
communication). Finally, a recent interesting comparison of these three methods
(Nygaard et al. 2008) has concluded that the oligoarrays can provide quantitative
transcript concentrations that are correlated with MPSS and SAGE data but the
absolute scale of the measurements differs across the technologies.
7.3 Genomic Approaches in Breeding and Reproduction
The ultimate goal of fish and shellfish selective breeding programmes is to increase
the sustainability and profitability of aquaculture, while maintaining the genetic
variability in the cultured stocks and limiting its impact on wild population and
the environment. Pedigree information, which is required for efficient breeding programmes in order to maximise effective population sizes and to use information