Analysis of liver miRNA in Hu sheep with different residual feed intake

Changchun Lin; Weimin Wang; Deyin Zhang; Kai Huang; Yukun Zhang; Xiaolong Li; Yuan Zhao; Liming Zhao; Jianghui Wang; Bubo Zhou; Jiangbo Cheng; Dan Xu; Wenxin Li; Xiaoxue Zhang; Wenxin Zheng

doi:10.3389/fgene.2023.1113411

Analysis of liver miRNA in Hu sheep with different residual feed intake

Front Genet. 2023 Oct 19:14:1113411. doi: 10.3389/fgene.2023.1113411. eCollection 2023.

Authors

Changchun Lin^{1

2}, Weimin Wang³, Deyin Zhang³, Kai Huang³, Yukun Zhang³, Xiaolong Li³, Yuan Zhao³, Liming Zhao³, Jianghui Wang¹, Bubo Zhou¹, Jiangbo Cheng³, Dan Xu¹, Wenxin Li¹, Xiaoxue Zhang¹, Wenxin Zheng²

Affiliations

¹ College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China.
² Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China.
³ The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China.

Abstract

Feed efficiency (FE), an important economic trait in sheep production, is indirectly assessed by residual feed intake (RFI). However, RFI in sheep is varied, and the molecular processes that regulate RFI are unclear. It is thus vital to investigate the molecular mechanism of RFI to developing a feed-efficient sheep. The miRNA-sequencing (RNA-Seq) was utilized to investigate miRNAs in liver tissue of 6 out of 137 sheep with extreme RFI phenotypic values. In these animals, as a typical metric of FE, RFI was used to distinguish differentially expressed miRNAs (DE_miRNAs) between animals with high (n = 3) and low (n = 3) phenotypic values. A total of 247 miRNAs were discovered in sheep, with four differentially expressed miRNAs (DE_miRNAs) detected. Among these DE_miRNAs, three were found to be upregulated and one was downregulated in animals with low residual feed intake (Low_RFI) compared to those with high residual feed intake (High_RFI). The target genes of DE_miRNAs were primarily associated with metabolic processes and biosynthetic process regulation. Furthermore, they were also considerably enriched in the FE related to glycolysis, protein synthesis and degradation, and amino acid biosynthesis pathways. Six genes were identified by co-expression analysis of DE_miRNAs target with DE_mRNAs. These results provide a theoretical basis for us to understand the sheep liver miRNAs in RFI molecular regulation.

Keywords: gene interactions; liver; miRNA; residual feed intake; sheep.

Grants and funding

This work was supported by the National Key R&D Program of China (2022YFD1302000), the National for joint research on improved breeds of livestock and poultry (19210365), the West Light Foundation of the Chinese Academy of Sciences (CN), and the China Agriculture Research System (CARS-39).