Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China.
State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China.
Poult Sci. 2024 Nov;103(11):104173. doi: 10.1016/j.psj.2024.104173. Epub 2024 Aug 3.
The Shitou goose, the largest meat-type goose breed, is an ideal model for offering insights into enhancing meat production efficiency through understanding its genetic regulation of muscle development. Here, through whole-transcriptomic analysis of embryonic leg muscles, we identified 847 differentially expressed genes (DEG), 244 differentially expressed lncRNAs (DEL), 37 differentially expressed circRNAs (DEC), and 84 differentially expressed miRNAs (DEM). Gene ontology (GO) analysis highlighted the significant enrichment of differentially expressed RNAs in muscle structure development, actin filament-based processes, and the actin cytoskeleton pathway. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified pathways associated with the FoxO signaling pathway, AMPK signaling pathway, Wnt signaling pathway and calcium signaling pathway. Furthermore, we utilized Miranda, TargetScan, and miRDB to identify regulatory networks that involve interactions between lncRNA-mRNA, circRNA-mRNA, miRNA-mRNA, lncRNA-miRNA-mRNA, and circRNA-miRNA-mRNA, which regulated the growth and development of skeletal muscle. Notably, differentially expressed genes within the ceRNA network were most significantly enriched in the regulation of actin cytoskeletal organization. Additionally, a lncRNA/circRNA-miRNA-mRNA ceRNA network related to muscle growth and development was constructed based on protein-protein interaction (PPI) analysis and hub genes selection using Cytoscape. This further elucidated the regulatory roles of noncoding RNAs (ncRNA) in the formation of muscle fibers in Shitou goose. In summary, this study provides a valuable transcriptional regulatory network for goose muscle development laying the groundwork for further exploration of the molecular regulatory mechanisms underlying the excellent meat production performance of Shitou goose.
狮头鹅是最大的肉用鹅种，是研究通过了解其肌肉发育的遗传调控来提高肉用生产效率的理想模型。在这里，我们通过对胚胎腿部肌肉的全转录组分析，鉴定了 847 个差异表达基因（DEG）、244 个差异表达长非编码 RNA（DEL）、37 个差异表达环状 RNA（DEC）和 84 个差异表达 microRNA（DEM）。基因本体（GO）分析强调了差异表达 RNA 在肌肉结构发育、肌动蛋白丝为基础的过程和肌动蛋白细胞骨架途径中的显著富集。京都基因与基因组百科全书（KEGG）分析确定了与 FoxO 信号通路、AMPK 信号通路、Wnt 信号通路和钙信号通路相关的途径。此外，我们利用 Miranda、TargetScan 和 miRDB 鉴定了涉及 lncRNA-mRNA、circRNA-mRNA、miRNA-mRNA、lncRNA-miRNA-mRNA 和 circRNA-miRNA-mRNA 相互作用的调控网络，这些网络调节骨骼肌的生长和发育。值得注意的是，ceRNA 网络中的差异表达基因在肌动蛋白细胞骨架组织的调节中最为显著。此外，还基于蛋白质-蛋白质相互作用（PPI）分析和 Cytoscape 中的枢纽基因选择，构建了与肌肉生长和发育相关的 lncRNA/circRNA-miRNA-mRNA ceRNA 网络。这进一步阐明了非编码 RNA（ncRNA）在狮头鹅肌肉纤维形成中的调控作用。总之，本研究为鹅肌肉发育提供了有价值的转录调控网络，为进一步探索狮头鹅优异的肉用生产性能的分子调控机制奠定了基础。
