Abstract
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.
Highlights
Egg quality is an important aspect in rainbow trout farming
The massive sequencing produced 27,342,477, 26,910,438 and 29,185,371 reads from the libraries constructed from One day post ovulation (D1PO), D7PO and D14PO eggs, respectively (Table 1)
Predication of novel miRNAs was carried out according to the criteria that the extended sequences of the miRNAs at the aligned rainbow trout genomic locations have the propensity of forming hairpin structures, and the sequences do not meet the criteria of known miRNAs
Summary
Egg quality is an important aspect in rainbow trout farming. Post-ovulatory aging is one of the most important factors affecting egg quality. It has been reported that the quality of rainbow trout eggs is dependent on the genetic characteristics of parents [5], and the age of female [7], and are susceptible to environmental influences, such as the diet of brood fish [8,9,10,11,12], stress [13,14,15], photoperiod [16], and the physiochemical conditions of the water [17] All of these factors make egg quality highly variable and difficult to control [18,19]. As the ovulated eggs in reared rainbow trout do not usually oviposit naturally, post-ovulatory aging of the eggs is widely accepted as a common determinant for egg quality [20,21,22]
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