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

Abstract

BackgroundLarval nutrition and growth are key issues for wild and cultured cod. While it was shown previously that larval cod fed wild zooplankton grow faster than those fed only rotifers, the mechanisms involved in this enhanced growth are not completely understood. We used microarrays to identify larval cod transcripts that respond to feeding with small amounts of wild zooplankton (5–10 % of live prey items). The larval transcriptome was compared between 3 treatment groups [fed rotifers (RA), rotifers with protein hydrolysate (RA-PH), or rotifers with zooplankton (RA-Zoo)] at 9–10 mm length [26–30 days post-hatch (dph)] to identify a robust suite of zooplankton-responsive genes (i.e. differentially expressed between RA-Zoo and both other groups).ResultsThe microarray experiment identified 147 significantly up-regulated and 156 significantly down-regulated features in RA-Zoo compared with both RA and RA-PH. Gene ontology terms overrepresented in the RA-Zoo responsive gene set included “response to selenium ion” and several related to cell division and oxidation-reduction. Ten selenoprotein-encoding genes, and 2 genes involved in thyroid hormone generation, were up-regulated in RA-Zoo compared with both other groups. Hierarchical clustering of RA-Zoo responsive genes involved in oxidation-reduction and selenium homeostasis demonstrated that only the zooplankton treatment had a considerable and consistent impact on the expression of these genes. Fourteen microarray-identified genes were selected for QPCR involving 9–13 mm larvae, and 13 of these were validated as differentially expressed between RA-Zoo and both other groups at ~9 mm. In contrast, in age-matched (34–35 dph; ~11 mm RA and RA-PH, ~13 mm RA-Zoo) and size-matched (~13 mm) older larvae, only 2 and 3 genes, respectively, showed the same direction of RA-Zoo-responsive change as in ~9 mm larvae.ConclusionsThe modulation of genes involved in selenium binding, redox homeostasis, and thyroid hormone generation in ~9 mm RA-Zoo larvae in this study may be in response to the relatively high levels of selenium, iodine, and LC-PUFA (potentially causing oxidative stress) in zooplankton. Nonetheless, only a subset of zooplankton-responsive genes in ~9 mm larvae remained so in older larvae, suggesting that the observed transcriptome changes are largely involved in initiating the period of growth enhancement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2120-1) contains supplementary material, which is available to authorized users.

The circadian transcriptome of marine fish (Sparus aurata) larvae reveals highly synchronized biological processes at the whole organism level

“…For instance, voluntary energy intake in fish was suggested to be limited by oxidative metabolism capacity, likely due to the detrimental effects of ROS 76 . Up-regulation of genes involved in the maintenance of the oxidative status was observed in Senegalese sole 77 and cod 78 larvae under high growth rate conditions. We suggest the combined evaluation of upc1/2/3 at ZT0 and gst , hmox , and several hsp at ZT12 (Supplementary Table S3 ) as putative indicators of the scope of oxidative metabolism of larvae.…”

Influence of Dietary Long-Chain Polyunsaturated Fatty Acids and ω6 to ω3 Ratios on Head Kidney Lipid Composition and Expression of Fatty Acid and Eicosanoid Metabolism Genes in Atlantic Salmon (Salmo salar)

“…The relative quantity (RQ) of each GOI was calculated using a qBase relative quantification framework (Hellemans et al, 2007 ; Booman et al, 2014 ) with primer amplification efficiencies incorporated ( Table 1 ). The expression levels of each GOI were normalized to both normalizer genes, and the sample with the lowest normalized expression was used as the calibrator sample (i.e., RQ = 1.0) for each GOI (Rise et al, 2015 ). Transcript expression data are presented as RQ values relative to the calibrator.…”

Influence of Varying Dietary ω6 to ω3 Fatty Acid Ratios on the Hepatic Transcriptome, and Association with Phenotypic Traits (Growth, Somatic Indices, and Tissue Lipid Composition), in Atlantic Salmon (Salmo salar)

“…The relative quantity (RQ) of each transcript was calculated using ViiA 7 Software v1.2 (Applied Biosystems) for Comparative CT (∆∆C T ) analysis [45], with primer amplification efficiencies incorporated (Table 1). The expression levels of each GOI were normalized to both normalizer genes, and the sample with the lowest normalized expression was used as the calibrator sample (i.e., RQ = 1.0) for each GOI, as in [46]. Transcript expression data are presented as RQ values (mean ± SE) relative to the calibrator.…”