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

Abstract

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<0.05). In Experiment 2, the DEGs were associated with only the ribosome signaling pathway (corrected P-value<0.05). In addition, quantitative real-time PCR was used to confirm 15 of the differentially expressed genes originally detected by RNA-Seq. A comparative transcript analysis of the leg and pectoral muscles of two duck breeds not only improves our understanding of the location-specific and breed-specific genes and pathways but also provides some candidate molecular targets for increasing muscle products and meat quality by genetic control.

Gene expression differences in Longissimus muscle of Nelore steers genetically divergent for residual feed intake

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Bioinformatics method identifies potential biomarkers of dilated cardiomyopathy in a human induced pluripotent stem cell-derived cardiomyocyte model

“…PENK encodes for the proenkephalin protein, and has been reported as one of the DEGs identified in skeletal muscle, while the muscle development-associated DEGs are implicated in the DCM pathway (36). APLNR encodes a family member of the G protein-coupled receptors.…”

Transcriptome profiling reveals the immune response of goose T cells under selenium stimuli

“…Additionally, two SBP2 proteins (the SECIS‐binding protein 2), a vital component in selenoprotein synthesis, were detected in all samples (Zhang et al . ,b) and were slightly up‐regulated in the S group compared to the C group. DNA replication related DEGs were primarily down‐regulated in this study.…”

“…; Zhang et al . ,b). Differential expression analysis between two groups was performed using DESeq2 (v1.4.5).…”

“…To identify the transcription factor (TF) in goose, the TF‐related hidden Markov models (HMM) were collected from AnimalTFDB2 (Zhang et al . ,b) and Pfam (version 29) database. HMM search in HMMER 3.0 package was employed to search the TF‐related domains in the proteins, with e‐value of 0.01 as the threshold for domain identification (Hu et al .…”