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Open Access Research article

Development and validation of a gene expression oligo microarray for the gilthead sea bream (Sparus aurata)

Serena Ferraresso1, Nicola Vitulo2, Alba N Mininni1, Chiara Romualdi2, Barbara Cardazzo1, Enrico Negrisolo1, Richard Reinhardt3, Adelino VM Canario4, 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 CRIBI, University of Padova, Complesso Biologico Vallisneri, Via Ugo Bassi 58/B, Padova, Italy

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

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

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BMC Genomics 2008, 9:580  doi:10.1186/1471-2164-9-580

Published: 3 December 2008

Abstract

Background

Aquaculture represents the most sustainable alternative of seafood supply to substitute for the declining marine fisheries, but severe production bottlenecks remain to be solved. The application of genomic technologies offers much promise to rapidly increase our knowledge on biological processes in farmed species and overcome such bottlenecks. Here we present an integrated platform for mRNA expression profiling in the gilthead sea bream (Sparus aurata), a marine teleost of great importance for aquaculture.

Results

A public data base was constructed, consisting of 19,734 unique clusters (3,563 contigs and 16,171 singletons). Functional annotation was obtained for 8,021 clusters. Over 4,000 sequences were also associated with a GO entry. Two 60mer probes were designed for each gene and in-situ synthesized on glass slides using Agilent SurePrint™ technology. Platform reproducibility and accuracy were assessed on two early stages of sea bream development (one-day and four days old larvae). Correlation between technical replicates was always > 0.99, with strong positive correlation between paired probes. A two class SAM test identified 1,050 differentially expressed genes between the two developmental stages. Functional analysis suggested that down-regulated transcripts (407) in older larvae are mostly essential/housekeeping genes, whereas tissue-specific genes are up-regulated in parallel with the formation of key organs (eye, digestive system). Cross-validation of microarray data was carried out using quantitative qRT-PCR on 11 target genes, selected to reflect the whole range of fold-change and both up-regulated and down-regulated genes. A statistically significant positive correlation was obtained comparing expression levels for each target gene across all biological replicates. Good concordance between qRT-PCR and microarray data was observed between 2- and 7-fold change, while fold-change compression in the microarray was present for differences greater than 10-fold in the qRT-PCR.

Conclusion

A highly reliable oligo-microarray platform was developed and validated for the gilthead sea bream despite the presently limited knowledge of the species transcriptome. Because of the flexible design this array will be able to accommodate additional probes as soon as novel unique transcripts are available.