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

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.

1. 肉制品中的肌内脂肪（intramuscular fat, IMF）含量与肉品质呈正相关，是消费者关注的重要性状。长链非编码RNA（long non-coding RNAs, lncRNAs）在调控各类生物过程中发挥核心作用，但目前关于其调控鸡肌内脂肪沉积的分子机制尚不清楚。
2. 本研究采集了肌内脂肪含量高（H组）与低（L组）的鸡胸肌样本，构建了6个小RNA文库。采用高通量测序技术对胸肌转录组（长链非编码RNA与mRNA）进行测序分析，筛选得到两组间差异表达的长链非编码RNA（differentially expressed lncRNAs, DELs）与差异表达mRNA（differentially expressed mRNAs, DEGs）。最终在两组间共鉴定出263个差异表达长链非编码RNA（其中118个上调、145个下调）以及443个差异表达基因（其中203个上调、240个下调）。
3. 为分析差异表达长链非编码RNA-差异表达基因的互作网络，本研究开展共表达分析以筛选lncRNA-mRNA调控对。最终共鉴定得到19270个lncRNA/mRNA调控对，其中包含16398个呈正相关的显著关联对，以及2872个呈负相关的关联对。构建的lncRNA-mRNA调控网络包含263个lncRNA节点与440个mRNA节点。
4. 基于京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）的通路富集分析显示，多条与脂肪沉积及脂质代谢相关的通路被显著富集，包括MAPK、PPAR、GnRH、ErbB及钙信号通路，脂肪酸延长与脂肪酸代谢通路等。综上，本研究鉴定得到与鸡肌内脂肪沉积相关的潜在候选lncRNAs、基因及调控网络。本研究结果为阐明鸡肌内脂肪沉积的调控机制提供了新视角，可用于提升家禽的肌内脂肪含量。