title: An integrated approach to gene discovery and marker development in Atlantic cod (Gadus morhua).
abstract: Atlantic cod is a species that has been overexploited by the capture fishery. Programs to domesticate this species are underway in several countries, including Canada, to provide an alternative route for production. Selective breeding programs have been successfully applied in the domestication of other species, with genomics-based approaches used to augment conventional methods of animal production in recent years. Genomics tools, such as gene sequences and sets of variable markers, also have the potential to enhance and accelerate selective breeding programs in aquaculture, and to provide better monitoring tools to ensure that wild cod populations are well managed. We describe the generation of significant genomics resources for Atlantic cod through an integrated genomics/selective breeding approach. These include 158,877 expressed sequence tags (ESTs), a set of annotated putative transcripts and several thousand single nucleotide polymorphism markers that were developed from, and have been shown to be highly variable in, fish enrolled in two selective breeding programs. Our EST collection was generated from various tissues and life cycle stages. In some cases, tissues from which libraries were generated were isolated from fish exposed to stressors, including elevated temperature, or antigen stimulation (bacterial and viral) to enrich for transcripts that are involved in these response pathways. The genomics resources described here support the developing aquaculture industry, enabling the application of molecular markers within selective breeding programs. Marker sets should also find widespread application in fisheries management.
authors.affiliation: The Atlantic Genome Centre, NRC Institute for Marine Biosciences, 1411 Oxford Street, Halifax, NS, B3H 3Z1, Canada. sbowman@genomeatlantic.ca
authors.forename: Sharen
authors.initials: S
authors.lastname: Bowman
authors.forename: Sophie
authors.initials: S
authors.lastname: Hubert
authors.forename: Brent
authors.initials: B
authors.lastname: Higgins
authors.forename: Cynthia
authors.initials: C
authors.lastname: Stone
authors.forename: Jennifer
authors.initials: J
authors.lastname: Kimball
authors.forename: Tudor
authors.initials: T
authors.lastname: Borza
authors.forename: Jillian Tarrant
authors.initials: JT
authors.lastname: Bussey
authors.forename: Gary
authors.initials: G
authors.lastname: Simpson
authors.forename: Catherine
authors.initials: C
authors.lastname: Kozera
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Curtis
authors.forename: Jennifer R
authors.initials: JR
authors.lastname: Hall
authors.forename: Tiago S
authors.initials: TS
authors.lastname: Hori
authors.forename: Charles Y
authors.initials: CY
authors.lastname: Feng
authors.forename: Marlies
authors.initials: M
authors.lastname: Rise
authors.forename: Marije
authors.initials: M
authors.lastname: Booman
authors.forename: A Kurt
authors.initials: AK
authors.lastname: Gamperl
authors.forename: Edward
authors.initials: E
authors.lastname: Trippel
authors.forename: Jane
authors.initials: J
authors.lastname: Symonds
authors.forename: Stewart C
authors.initials: SC
authors.lastname: Johnson
authors.forename: Matthew L
authors.initials: ML
authors.lastname: Rise
mesh_terms: D000818:Animals; D017756:Aquaculture; D001947:Breeding; D020224:Expressed Sequence Tags / Q000378:metabolism; D029941:Fish Proteins / Q000235:genetics / Q000378:metabolism; D048389:Gadus morhua / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D005819:Genetic Markers; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D029941:Fish Proteins; D005819:Genetic Markers
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