Transcriptome profiling reveals that feeding live zooplankton to larval Atlantic cod (Gadus morhua) influences suites of genes involved in oxidation-reduction, mitosis, and selenium homeostasis.

In this study, microarrays were used to investigate the larval cod transcriptome response to zooplankton supplementation in the diet. The experiment consisted of three different feeding regimes/diets as follows: Treatment 1 (6 replicate tanks): rotifers/Artemia with Ori-Green (Skretting, USA) enrichment (RA) 3 feedings per day (9 am, 3 pm and 9 pm), with rotifers fed until the fish reached ~ 9 mm [~ 30 days post-hatch (dph)]. Treatment 2 (4 replicate tanks): rotifers with Ori-Green enrichment, supplemented with 5-10% wild caught zooplankton (RA-Zoo: zooplankton were > 90% copepods) from 2 dph until 30 dph. Treatment 3 (6 replicate tanks): Rotifers/Artemia with Ori-Green enrichment 4 days per week and Rotifers/Artemia with protein hydrolysate (RA-PH) enrichment 3 days per week (Monday, Wednesday and Friday),with rotifers fed until the fish reached ~ 9 mm. Whole larvae from each feeding regimes/diets were sampled when fish in particular treatment reached an average length of ~ 9 mm. Individual DNAse-treated, column-purified total RNA samples from 8 fish per group (9 mm RA, 9 mm RA-PH and 9 mm RA-Zoo larvae) were used for microarray analysis using the Atlantic cod 20K oligonucleotide microarray platform (Booman et al. 2011) and a common reference experimental design. On each array, RNA from an individual fish was hybridized together with a common reference RNA. All test samples were labeled with Cy5. The common reference was labeled with Cy3.