Integrated Small RNA Sequencing, Transcriptome, and GWAS Data Reveal miRNA Regulation in Response to Milk Protein Traits in Chinese Holstein Cattle
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.
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Figure S1: The expression of the top 20 associate miRNAs in lactation and non-lactation period.
Table S1: The information of small RNA sequencing for 12 Chinese Holstein cattle.
Table S2: Summary of sequence reads alignment.
Table S3: The locations and expressions of the identified novel miRNAs.
Table S4: The information of differentially expressed miRNAs in HP vs. LP and HD vs. LD.
Table S5: The functional annotation of targets of DE miRNAs
Posted 13 Jan, 2021
Invitations sent on 09 Jan, 2021
On 07 Jan, 2021
On 07 Jan, 2021
On 07 Jan, 2021
On 06 Jan, 2021
Integrated Small RNA Sequencing, Transcriptome, and GWAS Data Reveal miRNA Regulation in Response to Milk Protein Traits in Chinese Holstein Cattle
Posted 13 Jan, 2021
Invitations sent on 09 Jan, 2021
On 07 Jan, 2021
On 07 Jan, 2021
On 07 Jan, 2021
On 06 Jan, 2021
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.