The fat fraction appeared to be enriched with RNA mostly from mammary epithelial cells. The lowest similarity was observed between milk cells and mammary gland tissue which agrees with the heterogeneity of somatic cells. Highest similarity with that of mammary gland tissue followed by whey. _ indicate medium expressed miRNAs (Top30-50) in those studies.
The miRNome correlation between milk fat and mammary gland tissue (rmean = 0.866) was significantly higher than the other two pairs (p 2, FDR 2, FDR Top50) The three milk fractions demonstrated a clear separation from each other using a hierarchical cluster analysis with milk fat and whey being most closely related. Among 20 most highly expressed miRNAs in each fraction, 14 were expressed in common and 11 were further shared with mammary gland tissue. In addition, 33, 31 and 36 novel miRNAs from milk fat, whey and cells were identified, with 28 common in the three fractions. We identified 210, 200 and 249 known miRNAs from milk fat, whey and cells, respectively, with 188 universally expressed in the three fractions. In addition, miRNA transcripts of mammary gland tissues from twelve Holstein cows in our previous study were used to compare our data. Total RNA extracted from each fraction was used for library preparation followed by small RNA sequencing. Milk from four healthy Canadian Holstein cows in mid lactation was collected and fractionated. The objectives of this study were to (1) characterize the miRNA expression spectra from three milk fractions- fat, whey and cells (2) compare miRNome profiles of milk fractions (fat, whey and cells) with mammary gland tissue miRNome, and (3) determine which milk fraction miRNome profile could be a better representative of the miRNome profile of mammary gland tissue. However, it has not been adequately validated if the miRNA transcriptome of any milk fraction could be representative of that of mammary gland tissue. Typically, RNA in milk can be extracted from different fractions including fat, whey and cells and the mRNA transcriptome of milk could serve as an indicator of the transcriptome of mammary gland tissue. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ībundant miRNAs have been identified in milk and mammary gland tissues of different species. Ran Li was supported by a doctoral fellowship from the China Scholarship Council (201206300128). Funding: This work was supported by funding from Agriculture and Agri-Food Canada (grant number J000733) to EIA and from National Science Foundation of China (grant number 31372282) to XZ. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. pone.0154129 Editor: Tiffany Seagroves, University of Tennessee Health Science Center, UNITED STATES Received: JanuAccepted: ApPublished: ApCopyright: © 2016 Li et al. OPEN ACCESS Citation: Li R, Dudemaine P-L, Zhao X, Lei C, Ibeagha-Awemu EM (2016) Comparative Analysis of the miRNome of Bovine Milk Fat, Whey and Cells. Comparative Analysis of the miRNome of Bovine Milk Fat, Whey and Cells Ran Li1,2, Pier-Luc Dudemaine2, Xin Zhao1,3, Chuzhao Lei1*, Eveline Mengwi IbeaghaAwemu2* 1 College of Animal Science and Technology, Northwest A & F University, Xi’an, Shaanxi, 712100, China, 2 Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, Quebec, J1M 0C8, Canada, 3 Department of Animal Science, McGill University, 21111, Lakeshore Road, Ste-Annede Bellevue, Quebec, J1M 0C8, Canada * (EMIA) (CL)
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