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Integrated Small RNA Sequencing, Transcriptome, and GWAS Data Reveal miRNA Regulation in Response to Milk Protein Traits in Chinese Holstein Cattle
Shengli Zhang
China Agricultural University
Corresponding Author
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This work is licensed under a CC BY 4.0 License. Read Full License
Background: Milk protein is one of the most important economic traits in the milk industry. Our previous study has revealed some functional genes responsible for milk protein synthesis in mammals. Yet, the miRNA-mediated gene regulatory network for the synthesis of milk protein in mammary is poorly understood.
Results: 12 samples from Chinese Holstein Cows with three too high and three low phenotypic values for milk protein percentage in lactation and non-lactating were examined through deep small RNA sequencing. By bioinformatics analysis, we characterized 387 known and 212 novel miRNAs in the mammary gland. Differentially expressed analysis detected 28 miRNAs in lactation and 52 miRNAs in the non-lactating period with a highly significant correlation with milk protein concentration. Target prediction and correlation analysis identified some key miRNAs and their targets potentially involved in the synthesis of milk protein. Using genome-wide association signal (GWAS) enrichment analysis among five milk production traits, we found the differentially expressed targets were significantly related to milk protein traits.
Conclusions: This integrated study on the transcriptional and post-transcriptional regulatory profiles between significantly differential phenotype of milk protein concentration provides new insights into the mechanism of milk protein synthesis, which should reveal the regulatory mechanisms of milk secretion.
Keywords
MicroRNA, Transcriptome, GWAS, Milk protein, Holstein, Milk production traits
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Due to technical limitations, full-text HTML conversion of this manuscript could not be completed. However, the manuscript can be downloaded and accessed as a PDF.
This is a list of supplementary files associated with this preprint. Click to download.
- FigureS1.tif
Figure S1: The expression of the top 20 associate miRNAs in lactation and non-lactation period.
- TableS1.xlsx
Table S1: The information of small RNA sequencing for 12 Chinese Holstein cattle.
- TableS2.xlsx
Table S2: Summary of sequence reads alignment.
- TableS3.xlsx
Table S3: The locations and expressions of the identified novel miRNAs.
- TableS4.xlsx
Table S4: The information of differentially expressed miRNAs in HP vs. LP and HD vs. LD.
- TableS5.xlsx
Table S5: The functional annotation of targets of DE miRNAs
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This preprint is under consideration at Journal of Animal Science and Biotechnology. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research
Integrated Small RNA Sequencing, Transcriptome, and GWAS Data Reveal miRNA Regulation in Response to Milk Protein Traits in Chinese Holstein Cattle
Shengli Zhang
China Agricultural University
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
Version 1
Posted 13 Jan, 2021
No community comments so far
Reviewers invited
Invitations sent on 09 Jan, 2021
Editor assigned
On 07 Jan, 2021
Submission checks complete
On 07 Jan, 2021
Editor invited
On 07 Jan, 2021
First submitted
On 06 Jan, 2021
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Milk protein is one of the most important economic traits in the milk industry. Our previous study has revealed some functional genes responsible for milk protein synthesis in mammals. Yet, the miRNA-mediated gene regulatory network for the synthesis of milk protein in mammary is poorly understood.
Results: 12 samples from Chinese Holstein Cows with three too high and three low phenotypic values for milk protein percentage in lactation and non-lactating were examined through deep small RNA sequencing. By bioinformatics analysis, we characterized 387 known and 212 novel miRNAs in the mammary gland. Differentially expressed analysis detected 28 miRNAs in lactation and 52 miRNAs in the non-lactating period with a highly significant correlation with milk protein concentration. Target prediction and correlation analysis identified some key miRNAs and their targets potentially involved in the synthesis of milk protein. Using genome-wide association signal (GWAS) enrichment analysis among five milk production traits, we found the differentially expressed targets were significantly related to milk protein traits.
Conclusions: This integrated study on the transcriptional and post-transcriptional regulatory profiles between significantly differential phenotype of milk protein concentration provides new insights into the mechanism of milk protein synthesis, which should reveal the regulatory mechanisms of milk secretion.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Due to technical limitations, full-text HTML conversion of this manuscript could not be completed. However, the manuscript can be downloaded and accessed as a PDF.