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.
Highlights
Myogenesis is a highly complex physiology process that involves myogenic progenitor proliferation, myoblast proliferation and differentiation, and the formation of none-nuclei and multi-nuclei myotubes and eventually mature muscle
To take into account the carcass weight of each duck, we calculated the ratio of leg muscle (LM) and pectoral muscle (PM) weight to carcass weight and found that every ratio was significantly different between locations, and this was true of both breeds (Fig 1B)
These data indicate that Peking duck and Heiwu duck are two phenotypically extreme duck breeds, and these differences are more obvious in PM than in LM
Summary
Myogenesis is a highly complex physiology process that involves myogenic progenitor proliferation, myoblast proliferation and differentiation, and the formation of none-nuclei and multi-nuclei myotubes and eventually mature muscle. Embryo myogenesis is pivotal for muscle production in adult livestock because the myofiber number is determined during the embryonic stage for most animals and does not increase in the postnatal period. The number of myofibers established in the embryo stage is the critical determinant of muscle production in livestock. A previous study using microarray hybridization reported that, in turkeys, a higher number of differentially expressed genes occurred early in development (day 18 of the embryonic stage) than at 1 day and 16 weeks after birth, suggesting that the phenotypic differences in adults between the two turkey lines may largely be determined during embryonic myogenesis [8]. Evidence indicates that the embryonic stage is an important period in the research of muscle development, and a better understanding of the genes and pathways involved is necessary.
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