Co-expression analysis of long non-coding RNAs and mRNAs involved in intramuscular fat deposition in Muchuan black-bone chicken

Abstract

ABSTRACT 1. The intramuscular fat (IMF) content in meat products is positively correlated with meat quality, making it an important consumer trait. Long non-coding RNAs (lncRNAs) play central roles in regulating various biological processes, but little is currently known about the mechanisms by which they regulate IMF deposition in chickens. 2. This study sampled the breast muscles of chickens with high (H) and low (L) IMF content and constructed six small RNA libraries. High-throughput sequencing technology was used to profile the breast muscle transcriptome (lncRNA and mRNA) and to identify the differentially expressed lncRNAs (DELs) and mRNAs (DEGs) between the H and L groups. In total, 263 DELs (118 up-regulated and 145 down-regulated lncRNAs) and 443 DEGs (203 up-regulated and 240 down-regulated genes) were identified between the two groups. 3. To analyse the DELs-DEGs interaction network, co-expression analysis was conducted to identify lncRNA-mRNA pairs. In total, 19270 lncRNA/mRNA pairs were identified, including 16 398 significant correlation pairs that presented as positive and 2872 pairs that presented as negative. The lncRNA – mRNA network comprised 263 lncRNA nodes and 440 mRNA nodes. 4. Pathway analysis, using the Kyoto Encyclopedia of Genes and Genomes, indicated pathways associated with fat deposition and lipid metabolism such as the MAPK, PPAR, GnRH, ErbB and calcium signalling pathways, fatty acid elongation and fatty acid metabolism. Overall, the study identified potential candidate lncRNAs, genes and regulatory networks associated with chicken IMF deposition. These findings provide new insights to help clarify the regulatory mechanisms of IMF deposition in chickens which can be used to improve the IMF content in poultry.