Selection of reference genes for qRT-PCR examination of wild populations of Atlantic cod Gadus morhua
Identifieur interne : 000E28 ( Main/Exploration ); précédent : 000E27; suivant : 000E29Selection of reference genes for qRT-PCR examination of wild populations of Atlantic cod Gadus morhua
Auteurs : P L A. Olsvik [Norvège] ; Liv S Fteland [Norvège] ; Kai K. Lie [Norvège]Source :
- BMC Research Notes [ 1756-0500 ] ; 2008.
Abstract
Extensive sequencing efforts have been taking place for the Atlantic cod (
The stability of 10 potential reference genes was examined in six tissues of Atlantic cod obtained from four populations, to determine the most suitable genes to be used in qRT-PCR analyses. Relative transcription levels of genes encoding β-actin (ACTB), elongation factor 1A (EF1A), actin-related protein-2 (ARP-2), glyceraldehyde-3P-dehydrogenase (GAPDH), ubiquitin (Ubi), acidic ribosomal protein (ARP), ribosomal protein S9 (S9), ribosomal protein L4 (RPL4), RPL22 and RPL37 were quantified in gills, brain, liver, head kidney, muscle and middle intestine in six juvenile fish from three wild populations and from farmed Atlantic cod. Reference gene stability was investigated using the
Overall, this work suggests that the Ubi and ARP can be useful as reference genes in qRT-PCR examination of gene expression studying wild populations of Atlantic cod.
Url:
DOI: 10.1186/1756-0500-1-47
PubMed: 18710500
PubMed Central: 2527504
Affiliations:
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Olsvik</name><affiliation wicri:level="1"><nlm:aff id="I1">National Institute of Nutrition and Seafood Research, Nordnesboder 2, N-5005 Bergen, Norway</nlm:aff><country xml:lang="fr">Norvège</country><wicri:regionArea>National Institute of Nutrition and Seafood Research, Nordnesboder 2, N-5005 Bergen</wicri:regionArea><wicri:noRegion>N-5005 Bergen</wicri:noRegion></affiliation></author><author><name sortKey="S Fteland, Liv" sort="S Fteland, Liv" uniqKey="S Fteland L" first="Liv" last="S Fteland">Liv S Fteland</name><affiliation wicri:level="1"><nlm:aff id="I1">National Institute of Nutrition and Seafood Research, Nordnesboder 2, N-5005 Bergen, Norway</nlm:aff><country xml:lang="fr">Norvège</country><wicri:regionArea>National Institute of Nutrition and Seafood Research, Nordnesboder 2, N-5005 Bergen</wicri:regionArea><wicri:noRegion>N-5005 Bergen</wicri:noRegion></affiliation></author><author><name sortKey="Lie, Kai K" sort="Lie, Kai K" uniqKey="Lie K" first="Kai K" last="Lie">Kai K. Lie</name><affiliation wicri:level="1"><nlm:aff id="I1">National Institute of Nutrition and Seafood Research, Nordnesboder 2, N-5005 Bergen, Norway</nlm:aff><country xml:lang="fr">Norvège</country><wicri:regionArea>National Institute of Nutrition and Seafood Research, Nordnesboder 2, N-5005 Bergen</wicri:regionArea><wicri:noRegion>N-5005 Bergen</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">18710500</idno><idno type="pmc">2527504</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527504</idno><idno type="RBID">PMC:2527504</idno><idno type="doi">10.1186/1756-0500-1-47</idno><date when="2008">2008</date><idno type="wicri:Area/Pmc/Corpus">000266</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000266</idno><idno type="wicri:Area/Pmc/Curation">000266</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000266</idno><idno type="wicri:Area/Pmc/Checkpoint">000643</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000643</idno><idno type="wicri:Area/Ncbi/Merge">000123</idno><idno type="wicri:Area/Ncbi/Curation">000123</idno><idno type="wicri:Area/Ncbi/Checkpoint">000123</idno><idno type="wicri:Area/Main/Merge">000E32</idno><idno type="wicri:Area/Main/Curation">000E28</idno><idno type="wicri:Area/Main/Exploration">000E28</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Selection of reference genes for qRT-PCR examination of wild populations of Atlantic cod <italic>Gadus morhua</italic></title><author><name sortKey="Olsvik, P L A" sort="Olsvik, P L A" uniqKey="Olsvik P" first="P L A" last="Olsvik">P L A. Olsvik</name><affiliation wicri:level="1"><nlm:aff id="I1">National Institute of Nutrition and Seafood Research, Nordnesboder 2, N-5005 Bergen, Norway</nlm:aff><country xml:lang="fr">Norvège</country><wicri:regionArea>National Institute of Nutrition and Seafood Research, Nordnesboder 2, N-5005 Bergen</wicri:regionArea><wicri:noRegion>N-5005 Bergen</wicri:noRegion></affiliation></author><author><name sortKey="S Fteland, Liv" sort="S Fteland, Liv" uniqKey="S Fteland L" first="Liv" last="S Fteland">Liv S Fteland</name><affiliation wicri:level="1"><nlm:aff id="I1">National Institute of Nutrition and Seafood Research, Nordnesboder 2, N-5005 Bergen, Norway</nlm:aff><country xml:lang="fr">Norvège</country><wicri:regionArea>National Institute of Nutrition and Seafood Research, Nordnesboder 2, N-5005 Bergen</wicri:regionArea><wicri:noRegion>N-5005 Bergen</wicri:noRegion></affiliation></author><author><name sortKey="Lie, Kai K" sort="Lie, Kai K" uniqKey="Lie K" first="Kai K" last="Lie">Kai K. Lie</name><affiliation wicri:level="1"><nlm:aff id="I1">National Institute of Nutrition and Seafood Research, Nordnesboder 2, N-5005 Bergen, Norway</nlm:aff><country xml:lang="fr">Norvège</country><wicri:regionArea>National Institute of Nutrition and Seafood Research, Nordnesboder 2, N-5005 Bergen</wicri:regionArea><wicri:noRegion>N-5005 Bergen</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Research Notes</title><idno type="eISSN">1756-0500</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Extensive sequencing efforts have been taking place for the Atlantic cod (<italic>Gadus morhua</italic>) in recent years, the number of ESTs in the Genbank has reached more than 140.000. Despite its importance in North Atlantic fisheries and potential use in aquaculture, relatively few gene expression examination exists for this species, and systematic evaluations of reference gene stability in quantitative real-time RT-PCR (qRT-PCR) studies are lacking.</p></sec><sec><title>Results</title><p>The stability of 10 potential reference genes was examined in six tissues of Atlantic cod obtained from four populations, to determine the most suitable genes to be used in qRT-PCR analyses. Relative transcription levels of genes encoding β-actin (ACTB), elongation factor 1A (EF1A), actin-related protein-2 (ARP-2), glyceraldehyde-3P-dehydrogenase (GAPDH), ubiquitin (Ubi), acidic ribosomal protein (ARP), ribosomal protein S9 (S9), ribosomal protein L4 (RPL4), RPL22 and RPL37 were quantified in gills, brain, liver, head kidney, muscle and middle intestine in six juvenile fish from three wild populations and from farmed Atlantic cod. Reference gene stability was investigated using the <italic>geNorm </italic>and <italic>NormFinder </italic>tools. Based on calculations performed with the <italic>geNorm</italic>, which determines the most stable genes from a set of tested genes in a given cDNA sample, ARP, Ubi, S9 and RPL37 were among the most stable genes in all tissues. When the same calculations were done with <italic>NormFinder</italic>, the same genes plus RPL4 and EF1A were ranked as the preferable genes.</p></sec><sec><title>Conclusion</title><p>Overall, this work suggests that the Ubi and ARP can be useful as reference genes in qRT-PCR examination of gene expression studying wild populations of Atlantic cod.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Norvège</li></country></list><tree><country name="Norvège"><noRegion><name sortKey="Olsvik, P L A" sort="Olsvik, P L A" uniqKey="Olsvik P" first="P L A" last="Olsvik">P L A. Olsvik</name></noRegion><name sortKey="Lie, Kai K" sort="Lie, Kai K" uniqKey="Lie K" first="Kai K" last="Lie">Kai K. Lie</name><name sortKey="S Fteland, Liv" sort="S Fteland, Liv" uniqKey="S Fteland L" first="Liv" last="S Fteland">Liv S Fteland</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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