The aim of this study was to analyze the expression profiles of long-stranded non-coding RNA in the hypothalamus tissue of Qinchuan cattle at high and low residual feed intake (RFI), to explore the regulatory relationship between lncRNA and feed efficiency in Qinchuan cattle, and to provide a theoretical basis for explaining the molecular mechanisms of lncRNA in feed efficiency in Qinchuan cattle. Theoretical basis was provided to explain the molecular mechanism of lncRNA in feed efficiency of Qinchuan cattle. In this study, five cattle with extreme high and low RFI each were selected and divided into high RFI and low RFI groups, and hypothalamic tissue samples were collected from which total RNA was extracted to construct a sequencing library for transcriptome sequencing, and the differential lncRNAs were screened, and the cis-target genes and trans-target genes were predicted by the significantly different lncRNAs, and their functions were enriched for analysis. Finally, six differential lncRNAs were randomly selected for real-time fluorescence quantitative validation. The results showed that a total of 1406 differentially expressed lncRNAs were identified in this study, of which 626 lncRNAs showed up-regulation and 780 lncRNAs were down-regulated in the high RFI group. The screened differentially expressed lncRNAs may be candidate lncRNAs for the regulation of RFI in Qinchuan cattle, including ENSBTAT00000079159, TCONS_00230640 and TCONS_00209991. The target genes of these candidate lncRNAs (ADCY4, CHRM3, AQP8, etc.) were mainly enriched in signaling pathways such as insulin secretion pathway, cholinergic synaptic pathway, bile secretion pathway, etc. The quantitative results were verified by qRT-PCR and were consistent with sequencing results. The results inferred that the differentially expressed lncRNAs such as ENSBTAT00000079159, TCONS_00230640 and TCONS_00209991 have important regulatory roles in RFI of Qinchuan cattle. 

RFI;Qinchuan cattle;hypothalamus;transcriptome