Understanding the molecular basis for growth, stress and disease in marine organisms has the potential to significantly improve aquaculture production. A team of European researchers has recently reported the application of a custom-designed Agilent microarray platform for gene expression profiling of the gilthead sea bream Sparus aurata, an important farmed species with high commercial value. Currently little is known about this organism’s transcriptome. All available expressed sequence tags (ESTs) for the species were compiled and a high-density microarray was designed with two non-overlapping 60-mer oligonucleotide probes for each transcript cluster. The resulting custom array contained 39,379 target probes that were in situ synthesized using Agilent SurePrint™ Technology.

Using a one-color labeling assay, gene expression profiles of 19,715 unique transcripts were characterized for two early stages of sea bream development, larvae at one day (Stage 1) and at four days (Stage 4) post-hatching. A two class SAM test identified 1,050 differentially expressed genes between the two developmental stages. In the more differentiated Stage 4 larvae, tissue- and cell-specific transcripts were found to be upregulated, with concomitant down-regulation of essential/housekeeping genes. For selected target genes, strong correlation was observed between probe pairs, and the microarray data was validated using qRT-PCR (Figure 1). It was concluded that a flexible array design is ideal for studying non-model species with low genomic sequence coverage because it allows for the accommodation of additional probes as novel unique transcripts become available.
 

Figure 1. Comparison between microarray and qPCR results.

Expression values for the eleven target genes were compared between microarray probes and real time RT-PCR data. Triangles: ratio between Probe 1 and qPCR-estimated fold changes. Circles: ratio between Probe 2 and qPCR-estimated fold-changes.