Identification and Functional Prediction of Long Non-Coding RNA in Longissimus Dorsi Muscle of Queshan Black and Large White Pigs

Yaqing Dou; Kunlong Qi; Yingke Liu; Chenlei Li; Chenglei Song; Yilin Wei; Zhe Zhang; Xinjian Li; Kejun Wang; Xiuling Li; Ruimin Qiao; Feng Yang; Xuelei Han

doi:10.3390/genes14010197

Identification and Functional Prediction of Long Non-Coding RNA in Longissimus Dorsi Muscle of Queshan Black and Large White Pigs

Genes (Basel). 2023 Jan 12;14(1):197. doi: 10.3390/genes14010197.

Authors

Yaqing Dou¹, Kunlong Qi¹, Yingke Liu¹, Chenlei Li¹, Chenglei Song¹, Yilin Wei¹, Zhe Zhang¹, Xinjian Li¹, Kejun Wang¹, Xiuling Li¹, Ruimin Qiao¹, Feng Yang¹, Xuelei Han¹

Affiliation

¹ College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China.

Abstract

Long non-coding RNA (lncRNA) participates in the regulation of various biological processes, but its function and characteristics in intramuscular fat (IMF) deposition in different breeds of pigs have not been fully understood. IMF content is one of the important factors affecting pork quality. In the present study, the differentially expressed lncRNAs (DE lncRNAs) and their target genes were screened by comparing Queshan Black (QS) and Large White (LW) pigs based on RNA-seq. The results displayed 55 DE lncRNAs between QS and LW, 29 upregulated and 26 downregulated, with 172 co-located target genes, and 6203 co-expressed target genes. The results of GO and KEGG analysis showed that the target genes of DE lncRNAs were involved in multiple pathways related to lipogenesis and lipid metabolism, such as the lipid biosynthetic process, protein phosphorylation, activation of MAPK activity, and the Jak-STAT signaling pathway. By constructing regulatory networks, lincRNA-ZFP42-ACTC1, lincRNA-AMY2-STAT1, and/or lincRNA-AMY2/miR-204/STAT1 were sieved, and the results indicate that lncRNA could participate in IMF deposition through direct regulation or ceRNA. These findings provide a basis for analyzing the molecular mechanism of IMF deposition in pigs and lay a foundation for developing and utilizing high-quality resources of local pig breeds.

Keywords: LncRNAs; intramuscular fat; large white pigs; pork quality; queshan black pigs.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Lipid Metabolism / genetics
Muscle, Skeletal / metabolism
RNA, Long Noncoding* / genetics
RNA, Long Noncoding* / metabolism
RNA, Messenger / genetics
RNA-Seq
Swine / genetics

Substances

RNA, Long Noncoding
RNA, Messenger

Grants and funding

This research was funded by the 14th Five-Year National Key R&D Program, grant number 2021YFD1301202; Agricultural Breeds Research Project of Henan Province, grant number 2022020101.