Identification of genes and lncRNAs for intramuscular and subcutaneous fat deposition in ducks by transcriptome analysis.

The purpose of this study was to identify key lncRNAs and mRNAs involved in fat deposition of meat ducks based on whole transcriptome sequencing for intramuscular preadipocyte (IMP-0), intramuscular adipocyte after 4 days of induction (IMP-4), subcutaneous preadipocyte (SCP-0), and subcutaneous adipocyte after 4 days of induction (SCP-4). We found 1419 and 697 differentially expressed genes and lncRNAs in the IMP-0-vs-IMP-4 group, respectively. There were 2307 and 1180 differentially expressed genes and differential lncRNAs, respectively, in the SCP-0-vs-SCP-4 group. The IMP-0-vs-IMP-4 and SCP-0-vs-SCP-4 groups were plotted using a venn diagram to obtain unique differential genes in each group, such as CHKA, PNPLA2, PLPP1, FABP4, ACSL5, UGT8, FAT1 and FADS2. In IMP-0-vs-IMP-4, significant enriched GO terms and KEGG pathways were regulation of MAPK cascade, lipid binding, Arachidonic acid metabolism, etc. In SCP-0-vs-SCP-4, beta-alanine metabolism, Wnt signaling pathway, lipid metabolic process and so on were most significant . Based on correlation analysis, the IMP-0-vs-IMP-4 group constructes a co-expression network of 193 nodes and 275 edges, while the SCP-0-vs-SCP-4 group constitutes a lncRNA-mRNA co-expression network with 564 nodes and 3,471 edges. Key lncRNAs, including MSTRG.8652.4, MSTRG.15586.1, MSTRG.6393.1, XR_217450.4, MSTRG.10341.22, XR_003492841.1, MSTRG.13937.5, and XR_003493886.1 were screened according to connectivity degree. Taken together, the current findings indicated that there are differentially regulated differential genes, lncRNAs, and enrichment pathways in IMP-0-vs-IMP-4 and SCP-0-vs-SCP-4. Because of being differentially regulated, some differential factors were significantly increased in expression in intramuscular adipocyte induction while significantly downregulated in subcutaneous adipocyte induction, such as FABP3, MSTRG.13937.5, and MSTRG.6393.1. Meanwhile, there were also some factors that were specifically regulated, CHKA, PLA2G4A, FADS2, MSTRG.13842.1, MSTRG.16051.2 and MSTRG.13842.1 were significantly downregulated only in subcutaneous adipocytes. This suggests that these lncRNAs and their target genes may play important roles in intramuscular fat and subcutaneous fat deposition.