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

item MA, HAO - West Virginia University
item Weber, Gregory - Greg
item Hostuttler, Mark
item WEI, HAIRONG - Michigan Technological University
item WANG, LEI - West Virginia University
item YAO, JIANBO - West Virginia University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/24/2015
Publication Date: 3/17/2015
Citation: Ma, H., Weber, G.M., Hostuttler, M.A., Wei, H., Wang, L., Yao, J. 2015. MicroRNA expression profiles from eggs of different qualities associated with post-ovulatory ageing in rainbow trout (Oncorhynchus mykiss). Biomed Central (BMC) Genomics. 16(201).1-9. DOI: 10.1186/s12864-015-1400-0.

Interpretive Summary: Post-ovulatory aging is known to impact fertilization rates in rainbow trout. We sequenced small RNA molecules from eggs aged 1, 7 and 14 days post-ovulation to identify biomarkers associated with egg quality. MicroRNAs are biomarkers known to play important roles in embryonic development, observing their presence in new vs. aged eggs provided insight into factors impacting fertilization rates. Further investigation of these biomarkers and the genes they control will improve our understanding of factors that contribute to egg quality and offer insights on how to improve management practices.

Technical Abstract: 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, espectively. A three-way comparison of the miRNAs indicated that the egg samples shared 430 known and 532 novel miRNAs, and a total of 187, 81, and 97 known and 92, 271, and 336 novel miRNAs were identified specifically from D1PO, D7PO and D14PO eggs, respectively. Fifteen miRNAs were found to be differentially expressed between D1PO and D14PO eggs. GO analysis of the target genes of 14 miRNAs that were up-regulated in D14PO eggs revealed significantly enriched GO terms that are related to signal ransduction, ATP generation, DNA damage, cell death 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.