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

Ma H, Weber GM, Hostuttler MA, Wei H, Wang L, Yao J - BMC Genomics (2015)

Bottom Line: The objective of this study was to identify miRNAs that are associated with egg qualities in rainbow trout using post-ovulatory aged eggs.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.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.

View Article: PubMed Central - PubMed

Affiliation: Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, 26506, USA. hao.ma@mail.wvu.edu.

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, 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.

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Percentage of known and novel miRNAs showing higher expression in high quality eggs (D1PO) or low quality eggs (D14PO).
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Fig3: Percentage of known and novel miRNAs showing higher expression in high quality eggs (D1PO) or low quality eggs (D14PO).

Mentions: A three-way comparison of the miRNAs among the samples indicated that D1PO, D7PO and D14PO eggs shared 392 known and 236 novel miRNAs (Figure 1). A total of 414, 481, and 470 known miRNAs and 243, 298, and 296 novel miRNAs were identified from D1PO, D7PO, and D14PO samples, respectively (Table 2). To identify miRNAs that are related to egg quality, the miRNA reads in D1PO and D14PO samples were quantile normalized and compared. A total of 189 miRNAs showed differential expression between the 2 samples (fold change greater than 3). Eighty-eight miRNAs showed higher expression in high quality eggs, while 101 miRNAs displayed higher expression in low quality eggs (Additional file 1: Table S3). Differentially expressed miRNAs with a fold change greater than 10 are shown in Figure 2. Interestingly, the majority of the miRNAs highly expressed in D1PO eggs are known miRNAs (70.45%), while majority of the miRNAs with higher expression in D14PO eggs are novel miRNAs (64.36%) (Figure 3).Figure 1


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

Ma H, Weber GM, Hostuttler MA, Wei H, Wang L, Yao J - BMC Genomics (2015)

Percentage of known and novel miRNAs showing higher expression in high quality eggs (D1PO) or low quality eggs (D14PO).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4374207&req=5

Fig3: Percentage of known and novel miRNAs showing higher expression in high quality eggs (D1PO) or low quality eggs (D14PO).
Mentions: A three-way comparison of the miRNAs among the samples indicated that D1PO, D7PO and D14PO eggs shared 392 known and 236 novel miRNAs (Figure 1). A total of 414, 481, and 470 known miRNAs and 243, 298, and 296 novel miRNAs were identified from D1PO, D7PO, and D14PO samples, respectively (Table 2). To identify miRNAs that are related to egg quality, the miRNA reads in D1PO and D14PO samples were quantile normalized and compared. A total of 189 miRNAs showed differential expression between the 2 samples (fold change greater than 3). Eighty-eight miRNAs showed higher expression in high quality eggs, while 101 miRNAs displayed higher expression in low quality eggs (Additional file 1: Table S3). Differentially expressed miRNAs with a fold change greater than 10 are shown in Figure 2. Interestingly, the majority of the miRNAs highly expressed in D1PO eggs are known miRNAs (70.45%), while majority of the miRNAs with higher expression in D14PO eggs are novel miRNAs (64.36%) (Figure 3).Figure 1

Bottom Line: The objective of this study was to identify miRNAs that are associated with egg qualities in rainbow trout using post-ovulatory aged eggs.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.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.

View Article: PubMed Central - PubMed

Affiliation: Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, 26506, USA. hao.ma@mail.wvu.edu.

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, 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.

Show MeSH
Related in: MedlinePlus