Identification of key lncRNAs and mRNAs related intramuscular fat in pigs by WGCNA

Abstract Background: Intramuscular fat (IMF) is an important indicator of pork quality, whose content directly affects the tenderness, juiciness and other flavour traits of pork, and it also influences consumers' choice of pork. Long non-coding RNA (lncRNA) plays an important role as key regulators in IMF deposition, but its function and characteristics in IMF deposition are not fully understood. Weighted gene co-expression network analysis (WGCNA) is an accurate and powerful method for studying gene interactions of quantitative traits, but so far, there is no report on weighted gene co-expression network analysis on the regulation of fat deposition in porcine muscle based on both mRNA and lncRNA datasets. Therefore, this study aimed to construct an mRNA-lncRNA co-expression network using WGCNA to mine and identify potential candidate genes affecting IMF deposition in pigs. Results: We used whole-transcriptome sequencing data generated from 31 longest dorsal muscle tissues of Yimeng Black pigs to construct a gene expression matrix containing 8093 mRNAs and 198 lncRNAs. A total of nine co-expression modules were identified using the WGCNA method, of which the magenta and turquoise modules were significantly associated with IMF deposition. We identified 15 mRNAs and 4 lncRNAs as key genes that might play an important role in the regulation of IMF deposition. Conclusions: This study used WGCNA to construct a lncRNA-mRNA co-expression network and reveal key genes that regulate intramuscular fat deposition and to construct lncRNA-mRNA-pathway network. We provided new insights into the complex biology of IMF deposition in pigs and may help to improve pork quality.