Co-expression network and pathway analyses reveal important modules of miRNAs regulating milk yield and component traits

In this study, groups or modules of microRNAs with similar expression patterns during an entire lactation cycle were detected. The relationship between the microRNA groups or modules and milk yield and component traits (fat, protein, somatic cell count (SCC), lactose, and milk urea nitrogen (MUN)) were detected by statistical means. MicroRNAs are small genes (about 22 base pairs long) on the genome. The main function of microRNAs is to disrupt the expression of messenger RNA. Messenger RNA are larger genes that when expressed becomes proteins. Examples of proteins are enzymes, hormones, etc. The expression data of 713 microRNAs, and milk yield and components (Fat%, Protein%, lactose, SCC, MUN) data of nine cows at each of six different time points (day 30 (D30), D70, D130, D170, D230 and D290) of an entire lactation curve were used. Four microRNA modules or clusters (GREEN, BLUE, RED and TURQUOISE) were identified as having important relationship with milk yield and component traits. The GREEN and BLUE modules were significantly correlated (|r| > 0.5) with milk yield and lactose, respectively. The RED and TURQUOISE modules were significantly correlated (|r| > 0.5) with both SCC and lactose. Three abundantly expressed miRNAs (miR-148a, miR-186 and miR-200a) in the green module were most related to milk yield, and may be most important miRNAs for milk yield. DDR1 and DDHX1 are hub genes for miRNA regulatory networks controlling milk yield, while HHEX is an important transcription regulator for these networks. miR-18a, miR-221/222 cluster, and transcription factors HOXA7, and NOTCH 3 and 4, are important for the regulation of lactose. miR-142, miR-146a, and miR-EIA17-14144 (a novel miRNA), and transcription factors in the SMAD family and MYB, are important for the regulation of SCC. Important signaling pathways enriched for target genes of miRNAs of significant modules, included protein kinase A and PTEN signaling for milk yield, eNOS and Noth signaling for lactose, and TGF β, HIPPO, Wnt/β-catenin and cell cycle signaling for SCC. Other gene networks related to milk and mammary gland traits included cell differentiation, G-protein coupled receptor activity, and intracellular signaling transduction. Overall, this study uncovered regulatory networks in which miRNAs interacted with each other to regulate lactation traits.