Identification of genes and long non-coding RNAs for intramuscular and subcutaneous fat deposition in ducks by transcriptome analysis.

Objective: Fat deposition is an important factor that affects meat production and quality in livestock and poultry. Long non-coding RNAs (lncRNAs) play an important role in duck fat deposition. 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).

Methods: Differentially expressed mRNAs and lncRNAs were identified across groups through differential expression analysis, specific gene screening, and functional enrichment analysis. Subsequently, a lncRNA-mRNA co-expression network was constructed and key nodes were identified. Finally, preliminary expression validation was performed at the mRNA level.

Results: Differential expression analysis revealed 1,419 mRNAs and 697 lncRNAs in the IMP-0-vs-IMP-4 comparison, and 2,307 mRNAs and 1,180 lncRNAs in the SCP-0-vs-SCP-4 comparison. Venn analysis identified unique differentially expressed genes for each group, including CHKA, PNPLA2, PLPP1, FABP4, ACSL5, UGT8, FAT1, and FADS2. Functional enrichment showed that the IMP-0-vs-IMP-4 group was significantly associated with regulation of the MAPK cascade, lipid binding, and arachidonic acid metabolism. The SCP-0-vs-SCP-4 group was notably enriched in beta-alanine metabolism, the Wnt signaling pathway, and lipid metabolic processes. Co-expression network analysis further constructed a network of 193 nodes and 275 edges for the IMP-0-vs-IMP-4 group, and a larger network of 564 nodes and 3,471 edges for the SCP-0-vs-SCP-4 group. Key lncRNAs, such as MSTRG.8652.4, MSTRG.15586.1, and MSTRG.6393.1, were identified based on their high connectivity degree.

Conclusion: 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.