Animal Molecular Breeding 2024, Vol.14, No.5, 318-325 http://animalscipublisher.com/index.php/amb 320 Microarray analysis has also been pivotal in broiler research. A study on a male broiler line phenotyped for high or low feed efficiency used a chicken 44K oligo microarray to identify differentially expressed genes associated with muscle growth and feed efficiency (Bottje et al., 2012). This approach has provided insights into the molecular mechanisms that differentiate high-efficiency broilers from their low-efficiency counterparts, highlighting the importance of anabolic processes and stress response genes in muscle development. 3.3 Bioinformatics tools for gene identification and analysis Bioinformatics tools play a crucial role in the analysis and interpretation of gene expression data. Ingenuity Pathway Analysis (IPA) is one such tool that has been used to overlay canonical pathways onto gene sets, helping to identify key regulatory networks and focus genes involved in muscle development (Bottje et al., 2011). Other tools, such as miRDB, are used for miRNA target prediction, enabling the integration of miRNA and mRNA data to elucidate the regulatory mechanisms underlying muscle growth (Li et al., 2011; Khatri et al., 2018). Additionally, weighted gene co-expression network analysis (WGCNA) has been employed to identify gene modules associated with traits of interest, such as breast muscle weight and intramuscular fat content. This approach helps to uncover the complex interactions between genes and their contributions to muscle development and metabolism (Kang et al., 2021). These bioinformatics tools, combined with high-throughput gene expression analysis techniques, provide a comprehensive framework for identifying key genes and regulatory networks involved in muscle development in broilers. 4 Key Genes Involved in Muscle Development 4.1 Identification of essential muscle development genes Several studies have identified key genes involved in muscle development in broilers. For instance, a study using microarray and qPCR techniques identified differentially expressed genes (DEGs) related to muscle growth, myostatin signaling, and fatty acid metabolism in broiler embryos (Kanakachari et al., 2022). Another study highlighted the up-regulation of muscle growth factor genes such as IGF-1 and GH, and muscle marker genes including MyoD, Myogenin, Pax7, and PCNA during embryonic development and post-hatch days. Additionally, genes like MSTN, IGF-I, MyoD, and MyoGwere found to be differentially expressed in various broiler strains, indicating their crucial roles in muscle development (Jawasreh et al., 2019). 4.2 Functional analysis of identified genes The functional roles of these identified genes have been extensively studied. For example, the myostatin (MSTN) gene is known to inhibit muscle growth, while IGF-1 promotes muscle cell proliferation and differentiation. The MyoD and Myogenin genes are critical for myogenic differentiation, playing essential roles in muscle fiber formation (Al-Zghoul and El-Bahr, 2019). Furthermore, the study on DNA methylation and transcriptomic networks revealed that genes like MyH1-AS and other long non-coding RNAs (lncRNAs) are involved in the regulation of muscle development through epigenetic mechanisms (Liu et al., 2019). Another study identified circRNAs such as circPPP1R13B, which promotes muscle satellite cell proliferation and differentiation by targeting miR-9-5p and activating the IGF/PI3K/AKT signaling pathway (Shen et al., 2021). 4.3 Regulation of gene expression during different growth stages Gene expression regulation during different growth stages is a complex process involving various signaling pathways and regulatory networks. For instance, the Jak-STAT, mTOR, and TGF-β signaling pathways were found to be significantly involved in muscle development during different embryonic stages. Thermal manipulation during embryogenesis was shown to up-regulate muscle growth factor genes and muscle marker genes, leading to increased body weight and muscle mass in post-hatch broilers. Additionally, the differential expression of miRNAs such as miR-2131-5p, miR-221-5p, and miR-206 was associated with muscle growth, indicating their regulatory roles in gene expression during muscle development (Khatri et al., 2018). The study on transcriptomic profiles also identified several pathways, including the insulin signaling pathway and regulation of the actin cytoskeleton, which are crucial for early growth and muscle development in chickens (Xue et al., 2017).
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