Liver transcriptome profiling reveals that dietary DHA and EPA levels influence suites of genes involved in metabolism, redox homeostasis, and immune function in Atlantic salmon (Salmo salar). Liver transcriptome profiling reveals that dietary DHA and EPA levels influence suites of genes involved in metabolism, redox homeostasis, and immune function in Atlantic salmon (Salmo salar)

The optimal dietary requirement of omega-3 long-chain polyunsaturated fatty acids (ω3 LC-PUFA), namely docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), for Atlantic salmon that promotes optimal growth and health warrants careful investigation. We used 44K microarrays to study the influence of increasing levels of dietary DHA + EPA (0, 1.0 and 1.4% of the diet, as formulated) in the presence of high linoleic acid (LA) on Atlantic salmon growth and liver transcriptome. After a 14-week feeding trial, Atlantic salmon fed diet ω3LC0 (i.e. 0% of DHA + EPA) showed significantly lower final weight and weight gain, and higher feed conversion ratio compared with ω3LC1.0 and ω3LC1.4 diet groups. The microarray experiment identified 55 and 77 differentially expressed probes (Rank Products analyses; PFP < 10%) in salmon fed diets ω3LC1.4 and ω3LC1.0 compared with those fed diet ω3LC0, respectively. The comparison between ω3LC1.4 and ω3LC1.0 revealed 134 differentially expressed probes. Overall design: Atlantic salmon were fed the three experimental diets (ω3LC0, ω3LC1, and ω3LC1.4; four tanks per diet) for 14 weeks. Liver samples were taken from 5 fish from each tank at week 16. A universal reference design was used for the microarray experiment. For the test samples, RNA was used from individual livers of fish from the 3 treatment groups. For each treatment group we used 8 biological replicates (2 fish from each of 4 tanks). All test samples were labeled with Cy5. The common reference was a pool of 24 RNA samples from livers of fish from all individuals invovled in microarray experiment. The common reference was labeled with Cy3. Each individual test sample was hybridized together with the common reference sample on an array, so the experiment consisted of 24 arrays. Please note that sample titles represent 'diet_tank number_individual fish number' for each sample. variable: other: ω3LC0: ω3LC0_T8_2, ω3LC0_T8_3, ω3LC0_T23_1, ω3LC0_T23_3, ω3LC0_T31_2, ω3LC0_T31_4, ω3LC0_T35_1, ω3LC0_T35_3 variable: other: ω3LC1: ω3LC1_T7_1, ω3LC1_T7_3, ω3LC1_T20_1 ,ω3LC1_T20_2, ω3LC1_T34_1, ω3LC1_T34_3, ω3LC1_T38_2, ω3LC1_T38_3 variable: other: ω3LC1.4: ω3LC1.4_T3_3, ω3LC1.4_T3_4, ω3LC1.4_T19_2, ω3LC1.4_T19_3, ω3LC1.4_T26_1, ω3LC1.4_T26_2, ω3LC1.4_T33_1, ω3LC1.4_T33_2 repeat: biological replicate: ω3LC0_T8_2, ω3LC0_T8_3, ω3LC0_T23_1, ω3LC0_T23_3, ω3LC0_T31_2, ω3LC0_T31_4, ω3LC0_T35_1, ω3LC0_T35_3 repeat: biological replicate: ω3LC1_T7_1, ω3LC1_T7_3, ω3LC1_T20_1 ,ω3LC1_T20_2, ω3LC1_T34_1, ω3LC1_T34_3, ω3LC1_T38_2, ω3LC1_T38_3 repeat: biological replicate: ω3LC1.4_T3_3, ω3LC1.4_T3_4, ω3LC1.4_T19_2, ω3LC1.4_T19_3, ω3LC1.4_T26_1, ω3LC1.4_T26_2, ω3LC1.4_T33_1, ω3LC1.4_T33_2