7 Genomic Approaches in Aquaculture and Fisheries
243
livestock (Stear et al. 2001, Andersson and Georges 2004). However, the lack of
appropriate tools for aquaculture species has limited the application of advanced
techniques like mapping of QTL and MAS. The few QTL studies performed so far
in aquaculture species aimed at improved growth (Moghadam et al. 2007, Wang
et al. 2008) and disease resistance (Moen et al. 2007). For QTL detection, molecular tools such as genetic maps, genome maps, and sufficient genomic information
(e.g. large collections of ESTs or BAC-end sequences) are required but nowadays, recent developments in bony fishes and aquatic animals are providing the
required molecular tools. At present, genome maps of Salmonidae, Cyprinidae,
Cichlidae, Moronidae, Paralichthyidae and Ictaluridae are available (Kocher and
Kole 2008) as well as molecular markers (Bouza et al. 2007, Sanetra and Meyer
2008), BAC libraries (Matsuda et al. 2001, Whitaker et al. 2006, Wang et al. 2008),
expression data (Ewart et al. 2005, Sarropoulou et al. 2005b, Tilton et al. 2005,
Gunnarsson et al. 2007, Darawiroj et al. 2008, Darias et al. 2008, Peatman et al.
2008) and mapping panels (Gilbey et al. 2006, Houston et al. 2008). Maps and
polymorphic molecular markers are essential molecular tools to better understand
host–pathogen interactions and host immune responses at the genome level, and to
unravel genes underlying QTL determining host resistance, tolerance and susceptibility to infection. Mapping of candidate genes can significantly narrow down the
regions for QTL scanning. Analysis of channel catfish ESTs revealed that approximately 10% of them contained shorts-tandem repeats (Serapion et al. 2004a, b).
However none of these STR-containing ESTs represent immune related transcripts
or appear to be indirectly in the immune response. Therefore, mapping of immunerelated transcripts will enhance the finding of markers linked to QTL related to
immune response. Candidate markers can be identified by expression analysis studies, either by microarray technology, qPCR screen or sequencing of cDNA libraries
of infected tissues.
7.6.4 Host–Parasite Interactions in Shellfish
7.6.4.1 Improvement of Diagnostic Tools Using Molecular Approaches
Nowadays molecular biology can offer a vast number of tools that allow simple
and reliable diagnostics, replacing the more traditional time-consuming techniques
requiring greater amounts of sample. PCR has brought to shellfish diagnostic many
new advantages and improvements but mostly specificity, swiftness and reliability. PCR has been used to detect Vibrio (Hill et al. 1991, Brauns et al. 1991),
viruses (Desenclos et al. 1991, Batista et al. 2007), Listeria spp. (Jeyasekaran and
Karunasagar 1996), Bonamia ostreae (Cochennec et al. 2000), Salmonella spp.
(Dupray et al. 1997), Perkinsus spp. (Reece et al. 1997), Giardia spp. (Graczyk
et al. 1999), Marteilia spp. (Le Roux et al. 1999) and Criptosporidium spp. (GomezBautista et al. 2000). More complex methods, which use PCR as part of an integrated
approach, have been also used to detect shellfish pathogens, e.g. RFLP (Buchrieser
et al. 1995, Gomez-Bautista et al. 2000, Hine et al. 2001, Le Chevalier et al. 2003,
243
livestock (Stear et al. 2001, Andersson and Georges 2004). However, the lack of
appropriate tools for aquaculture species has limited the application of advanced
techniques like mapping of QTL and MAS. The few QTL studies performed so far
in aquaculture species aimed at improved growth (Moghadam et al. 2007, Wang
et al. 2008) and disease resistance (Moen et al. 2007). For QTL detection, molecular tools such as genetic maps, genome maps, and sufficient genomic information
(e.g. large collections of ESTs or BAC-end sequences) are required but nowadays, recent developments in bony fishes and aquatic animals are providing the
required molecular tools. At present, genome maps of Salmonidae, Cyprinidae,
Cichlidae, Moronidae, Paralichthyidae and Ictaluridae are available (Kocher and
Kole 2008) as well as molecular markers (Bouza et al. 2007, Sanetra and Meyer
2008), BAC libraries (Matsuda et al. 2001, Whitaker et al. 2006, Wang et al. 2008),
expression data (Ewart et al. 2005, Sarropoulou et al. 2005b, Tilton et al. 2005,
Gunnarsson et al. 2007, Darawiroj et al. 2008, Darias et al. 2008, Peatman et al.
2008) and mapping panels (Gilbey et al. 2006, Houston et al. 2008). Maps and
polymorphic molecular markers are essential molecular tools to better understand
host–pathogen interactions and host immune responses at the genome level, and to
unravel genes underlying QTL determining host resistance, tolerance and susceptibility to infection. Mapping of candidate genes can significantly narrow down the
regions for QTL scanning. Analysis of channel catfish ESTs revealed that approximately 10% of them contained shorts-tandem repeats (Serapion et al. 2004a, b).
However none of these STR-containing ESTs represent immune related transcripts
or appear to be indirectly in the immune response. Therefore, mapping of immunerelated transcripts will enhance the finding of markers linked to QTL related to
immune response. Candidate markers can be identified by expression analysis studies, either by microarray technology, qPCR screen or sequencing of cDNA libraries
of infected tissues.
7.6.4 Host–Parasite Interactions in Shellfish
7.6.4.1 Improvement of Diagnostic Tools Using Molecular Approaches
Nowadays molecular biology can offer a vast number of tools that allow simple
and reliable diagnostics, replacing the more traditional time-consuming techniques
requiring greater amounts of sample. PCR has brought to shellfish diagnostic many
new advantages and improvements but mostly specificity, swiftness and reliability. PCR has been used to detect Vibrio (Hill et al. 1991, Brauns et al. 1991),
viruses (Desenclos et al. 1991, Batista et al. 2007), Listeria spp. (Jeyasekaran and
Karunasagar 1996), Bonamia ostreae (Cochennec et al. 2000), Salmonella spp.
(Dupray et al. 1997), Perkinsus spp. (Reece et al. 1997), Giardia spp. (Graczyk
et al. 1999), Marteilia spp. (Le Roux et al. 1999) and Criptosporidium spp. (GomezBautista et al. 2000). More complex methods, which use PCR as part of an integrated
approach, have been also used to detect shellfish pathogens, e.g. RFLP (Buchrieser
et al. 1995, Gomez-Bautista et al. 2000, Hine et al. 2001, Le Chevalier et al. 2003,