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Background Dairy cattle are economically important animal resources contributing to human health and well-being by providing nutritious milk and other products. Non-coding RNAs are involved in biological processes, regulating gene expressions at the levels of messenger. However, the effects on miRNA expression and their function in dairy cattle are still unclear.

Objective We aimed to understand better miRNA expressions associated with milk and reproduction quantitative trait loci (QTLs) and their locations in dairy cattle.

Methods In this study, miRNA profiling was performed in blood samples collected from three non-pregnant cows using the Illumina HiSeq 2500 platform. The expression levels of miRNAs were estimated by miRDeep2 and QTLs associated with milk and reproduction were identified using cattleQTLdb. Functional enrichment analysis was performed to determine biological functions or pathways using DAVID.

Results In total, 406 known and 562 novel expressed miRNAs were identified in three dairy cattle using miRDeep2. A total of 27,652 and 31,064 QTLs associated with milk and reproduction traits were identified by QTL mapping for known and novel miRNAs, respectively. Of these, 1835 and 1020 miRNAs were related to milk and reproduction traits, respectively.

Conclusion Our study provides a basis for further research to understand the miRNA expressions in dairy cattle and their role in milk and reproduction traits. We suggest that miRNAs may be helpful as biomarkers for improving milk and reproduction traits in dairy cattle through genetic selection.

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