MicroRNAs (miRNAs) are a class of endogenous small non-coding RNA molecules that regulate post-transcriptional expression of target genes and play important roles in animal development. The objectives of this study were to characterize the egg miRNA transcriptome and identify novel egg-predominant miRNAs in rainbow trout. Small RNAs isolated from mature unfertilized rainbow trout eggs were subjected to deep sequencing using an Illumina Genome Analyzer. The massive sequencing produced 24,621,741 quality reads, among which, 266 known miRNAs were identified and 230 putatively novel miRNAs were predicted. The most abundantly known miRNAs are let-7 and miR-21, accounting for 24.06% and 18.71% of the known miRNAs, respectively. Other known miRNAs which are abundantly present in eggs include miR-24, miR-202, miR-148, miR-30, miR-10, miR-146, miR-25, and miR-143. Real time PCR analysis using cDNAs derived from 10 tissues validated 87 out of 90 selected putative miRNAs and identified three novel miRNAs predominantly expressed in rainbow trout eggs. Each of these novel egg-predominant miRNAs is predicted to target a significant number of genes, most of which are significantly down-regulated in naturally ovulated rainbow trout eggs based on analysis of publicly available microarray data sets. Quantitative real time PCR analysis also demonstrated low expression of a selected number of target genes in eggs relative to liver and muscle tissues. This study represents the first complete survey of miRNAs in fish eggs and provides a starting point for future studies aimed at understanding the roles of miRNAs in controlling egg quality and early embryogenesis in rainbow trout.

The efficient use of feed for growth and meat production is important for all animal production industries including aquaculture. Residual feed intake (RFI) is an alternative measure of feed efficiency that has been widely used in livestock production. Residual feed intake was calculated as the difference between intake observed and intake predicted on the basis of a bioenergetics model; a low RFI indicates greater efficiency. Residual feed intake offers some advantages as a selection criterion for improving production efficiency over traditional feed efficiency statistics because it is not a ratio and it typically has a larger coefficient of variation. The RFI of individually reared rainbow trout progeny from six different genetic cross‐types was examined for genetic variation. Proximate analysis and nitrogen retention were also evaluated to determine if differences in RFI correlate to differences in body composition and nutrient retention and varied by cross‐type. Differences between cross‐types indicated a genetic component for RFI, with the most efficient fish of approximately 160 g consuming 0.99 g less and inefficient fish consuming 0.05 g more feed per day than expected. Lower RFI was associated with higher growth rates (r=−0.38, P<0.05) and greater nitrogen retention (r=−0.82 P<0.001).

BackgroundEgg quality is an important aspect in rainbow trout farming. Post-ovulatory aging is one of the most important factors affecting egg quality. MicroRNAs (miRNAs) are the major regulators in various biological processes and their expression profiles could serve as reliable biomarkers for various pathological and physiological conditions. The objective of this study was to identify miRNAs that are associated with egg qualities in rainbow trout using post-ovulatory aged eggs.ResultsEgg samples from females on day 1, day 7, and day 14 post-ovulation (D1PO, D7PO and D14PO), which had the fertilization rates of 91.8%, 73.4% and less than 50%, respectively, were collected and small RNAs isolated from these samples were subjected to deep sequencing using the Illumina platform. The massive sequencing produced 27,342,477, 26,910,438 and 29,185,371 reads from the libraries of D1PO, D7PO and D14PO eggs, respectively. A three-way comparison of the miRNAs indicated that the egg samples shared 392 known and 236 novel miRNAs, and a total of 414, 481, and 470 known and 243, 298, and 296 novel miRNAs were identified from D1PO, D7PO and D14PO eggs, respectively. Four known miRNAs (omy-miR-193b-3p, omy-miR-203c-3p, omy-miR-499-5p and omy-miR-7550-3p) and two novel miRNAs (omy-miR-nov-95-5p and omy-miR-nov-112-5p) showed significantly higher expression in D1PO eggs relative to D14PO eggs as revealed by both deep sequencing and real time quantitative PCR analysis. GO analysis of the predicted target genes of these differentially expressed miRNAs revealed significantly enriched GO terms that are related to stress response, cell death, DNA damage, ATP generation, signal transduction and transcription regulation.ConclusionsResults indicate that post-ovulatory ageing affects miRNA expression profiles in rainbow trout eggs, which can in turn impact egg quality. Further characterization of the differentially expressed miRNAs and their target genes may provide valuable information on the role of these miRNAs in controlling egg quality, and ultimately lead to the development of biomarkers for prediction of egg quality in rainbow trout.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1400-0) contains supplementary material, which is available to authorized users.

This study was undertaken to analyze the sources of variation in timing of lirst cleavage in rainbow trout Oncorhynchus mykiss embryos in order to adjust treatment protocols to maximize tetraploid induction. The first cleavage interval (FCI), or the time from fertilization to the mid-point of the appearance of first cleavage, was determined at several temperatures for eggs from individual females from each of four different strains. Statistical analyses of the data did not reveal any significant differences among samples taken on different dates or among females within populations, but there was a significant difference shown among the populations. Further analyses revealed this difference was due to a significantly shorter FCI in one population. Data on two of the populations incubated at elevated temperatures showed a decreased FCI within the populations, but the differences between the populations remained. The results suggested that modification of the treatment protocols for induction of tetraploidy (and, perhaps, gynogenesis and androgenesis) are needed to compensate for variation noted among populations if maximum induction and minimum mortality are to be achieved.

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