dc.contributor.author	Ferraresso, Serena
dc.contributor.author	Milan, Massimo
dc.contributor.author	Pellizzari, Caterina
dc.contributor.author	Vitulo, Nicola
dc.contributor.author	Reinhardt, Richard
dc.contributor.author	Canario, Adelino V. M.
dc.contributor.author	Patarnello, T.
dc.contributor.author	Bargelloni, Luca
dc.date.accessioned	2011-06-03T10:03:37Z
dc.date.available	2011-06-03T10:03:37Z
dc.date.issued	2010-06-03
dc.date.updated	2011-06-03T10:03:38Z
dc.description.abstract	Abstract Background The European sea bass (Dicentrarchus labrax) is a marine fish of great importance for fisheries and aquaculture. Functional genomics offers the possibility to discover the molecular mechanisms underlying productive traits in farmed fish, and a step towards the application of marker assisted selection methods in this species. To this end, we report here on the development of an oligo DNA microarray for D. labrax. Results A database consisting of 19,048 unique transcripts was constructed, of which 12,008 (63%) could be annotated by similarity and 4,692 received a GO functional annotation. Two non-overlapping 60mer probes were designed for each unique transcript and in-situ synthesized on glass slides using Agilent SurePrint™ technology. Probe design was positively completed for 19,035 target clusters; the oligo microarray was then applied to profile gene expression in mandibles and whole-heads of fish affected by prognathism, a skeletal malformation that strongly affects sea bass production. Statistical analysis identified 242 transcripts that are significantly down-regulated in deformed individuals compared to normal fish, with a significant enrichment in genes related to nervous system development and functioning. A set of genes spanning a wide dynamic range in gene expression level were selected for quantitative RT-PCR validation. Fold change correlation between microarray and qPCR data was always significant. Conclusions The microarray platform developed for the European sea bass has a high level of flexibility, reliability, and reproducibility. Despite the well known limitations in achieving a proper functional annotation in non-model species, sufficient information was obtained to identify biological processes that are significantly enriched among differentially expressed genes. New insights were obtained on putative mechanisms involved on mandibular prognathism, suggesting that bone/nervous system development might play a role in this phenomenon.
dc.description.version	Peer Reviewed
dc.identifier.citation	BMC Genomics. 2010 Jun 03;11(1):354
dc.identifier.doi	http://dx.doi.org/10.1186/1471-2164-11-354
dc.identifier.other	AUT: ACA00258;
dc.identifier.uri	http://hdl.handle.net/10400.1/206
dc.language.iso	eng
dc.title	Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformity
dc.type	journal article
dspace.entity.type	Publication
person.familyName	Canario
person.givenName	Adelino
person.identifier	143624
person.identifier.ciencia-id	1F1E-D3B3-F804
person.identifier.orcid	0000-0002-6244-6468
person.identifier.rid	C-7942-2009
person.identifier.scopus-author-id	56568523700
rcaap.rights	openAccess
rcaap.type	article
relation.isAuthorOfPublication	5f6e51ee-9113-469e-8b9e-f30f2d452521
relation.isAuthorOfPublication.latestForDiscovery	5f6e51ee-9113-469e-8b9e-f30f2d452521

Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformity

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