Transcriptional Profiling Identifies Location-Specific and Breed-Specific Differentially Expressed Genes in Embryonic Myogenesis in Anas Platyrhynchos

Skeletal muscle growth and development are highly orchestrated processes involving significant changes in gene expressions. Differences in the location-specific and breed-specific genes and pathways involved have important implications for meat productions and meat quality. Here, RNA-Seq was performed to identify differences in the muscle deposition between two muscle locations and two duck breeds for functional genomics studies. To achieve those goals, skeletal muscle samples were collected from the leg muscle (LM) and the pectoral muscle (PM) of two genetically different duck breeds, Heiwu duck (H) and Peking duck (P), at embryonic 15 days. Functional genomics studies were performed in two experiments: Experiment 1 directly compared the location-specific genes between PM and LM, and Experiment 2 compared the two breeds (H and P) at the same developmental stage (embryonic 15 days). Almost 13 million clean reads were generated using Illumina technology (Novogene, Beijing, China) on each library, and more than 70% of the reads mapped to the Peking duck (Anas platyrhynchos) genome. A total of 168 genes were differentially expressed between the two locations analyzed in Experiment 1, whereas only 8 genes were differentially expressed when comparing the same location between two breeds in Experiment 2. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes pathways (KEGG) were used to functionally annotate DEGs (differentially expression genes). The DEGs identified in Experiment 1 were mainly involved in focal adhesion, the PI3K-Akt signaling pathway and ECM-receptor interaction pathways (corrected P-value

骨骼肌的生长与发育是高度调控的复杂过程，伴随基因表达谱的显著改变。其所涉及的部位特异性与品种特异性基因及通路差异，对肉品生产与肉品质具有重要影响。本研究通过RNA测序（RNA-Seq）技术，针对两个鸭品种的不同肌肉部位开展肌肉沉积差异分析，以服务于功能基因组学研究。为达成上述目标，本研究于胚胎第15天，采集两个遗传背景不同的鸭品种——黑武鸭（Heiwu duck, H）与北京鸭（Peking duck, P）的腿肌（leg muscle, LM）与胸肌（pectoral muscle, PM）样本。本研究通过两项实验开展功能基因组学研究：实验1直接比较胸肌与腿肌的部位特异性基因表达差异，实验2则在同一发育阶段（胚胎第15天）下，比较两个鸭品种（H与P）的基因表达差异。每个测序文库均通过Illumina测序技术（诺禾致源，中国北京）生成近1300万条清洁读段，其中超过70%的读段可比对至北京鸭（Anas platyrhynchos）参考基因组。实验1中，两个肌肉部位间共鉴定出168个差异表达基因；而实验2中，同一部位在两个鸭品种间仅鉴定出8个差异表达基因。本研究采用基因本体（Gene Ontology, GO）与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）通路富集分析，对差异表达基因（differentially expressed genes, DEGs）进行功能注释。实验1中鉴定出的差异表达基因主要富集于黏着斑、PI3K-Akt信号通路及细胞外基质-受体相互作用通路（校正后P值