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Open Access Research article

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

Serena Ferraresso1, Massimo Milan12, Caterina Pellizzari1, Nicola Vitulo3, Richard Reinhardt4, Adelino VM Canario5, Tomaso Patarnello1 and Luca Bargelloni1*

Author Affiliations

1 Department of Public Health, Comparative Pathology, and Veterinary Hygiene, Faculty of Veterinary Medicine, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy

2 Department of Evolutionary Biology, University of Florence, 50125 Florence, Italy

3 CRIBI, University of Padova, Complesso Biologico Vallisneri, Via Ugo Bassi 58/B, Padova, Italy

4 Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany

5 Centro de Ciências do Mar, Universidade do Algarve, Gambelas, 8005-139 Faro, Portugal

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BMC Genomics 2010, 11:354  doi:10.1186/1471-2164-11-354

Published: 3 June 2010

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.