MicroRNA expression profiles from eggs of different qualities associated with post-ovulatory ageing in rainbow trout (Oncorhynchus mykiss)

Ma et al. BMC Genomics MicroRNA expression profiles from eggs of different qualities associated with post-ovulatory ageing in rainbow trout (Oncorhynchus mykiss) Hao Ma 0 Gregory M Weber 2 Mark A Hostuttler 2 Hairong Wei 1 Lei Wang 0 Jianbo Yao 0 0 Division of Animal and Nutritional Sciences, West Virginia University , Morgantown, WV 26506 , USA 1 School of Forest Resources and Environmental Science, Michigan Technological University , Houghton, MI 49931 , USA 2 National Center for Cool and Cold Water Aquaculture, USDA/ARS , Kearneysville, WV 25430 , USA Background: Egg 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. Results: Egg 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. Conclusions: Results 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. microRNA; Egg quality; Post ovulation; Rainbow trout - Background Fish egg quality is defined as the capability of an egg to become fertilized and subsequently develop into a normal embryo or the probability of eggs to exhibit low mortalities at fertilization, eyeing, hatching, and first feeding [1]. The production of high quality eggs is a major objective of the aquaculture industry, as egg quality not only affects fertilization rate, but also is an important attribute of robust embryonic development [2,3]. However, visible differences between good and bad eggs at oviposition is not usually conspicuous in rainbow trout, and therefore, the inclusion of eggs from individual females with poor egg quality into mass incubation units not only results in unexpected losses in egg production, but also problems associated with the removal of dead eggs and embryos after fertilization and fungi infection in the hatchery [4]. Therefore, enabling evaluation of the egg quality before fertilization is highly desirable in aquaculture production. In teleost fish, a mature egg is developed through multiple phases, including primary oocyte growth, secondary growth including the cortical alveolus stage and vitellogenesis, follicle maturation and ovulation [5,6]. The coordinated multiple developmental stages can be affected by many genetic, biological, and environmental factors [3]. It has been reported that the quality of rainbow trout eggs is dependent not only on the genetic characteristics of parents [5], but also the age of female [7], and are susceptible to environmental influences, such as the diet of brood fish [8-12], stress [13-15], 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 [20-22]. The importance to distinguish good and bad quality eggs before fertilization has driven studies on the identification of markers associated with egg quality in rainbow trout. Wojtczak and coworkers found that very poor quality eggs turn water turbid [23]. Egg survival rate has (...truncated)