Animal Molecular Breeding 2024, Vol.14, No.5, 318-325 http://animalscipublisher.com/index.php/amb 322 6 Applications in Broiler Breeding 6.1 Use of gene expression data in selective breeding Gene expression data has become a pivotal tool in selective breeding programs for broilers. By identifying and selecting for specific genes associated with desirable traits, breeders can enhance growth performance and muscle development. For instance, the expression levels of IGF-I and MyoG genes have been shown to correlate with improved body weight and carcass cuts, making them valuable markers in artificial selection programs (Jawasreh et al., 2019). Additionally, the identification of single nucleotide polymorphisms (SNPs) in genes such as TGFβ3 has been linked to growth performance traits, suggesting that these genetic markers can be used to accelerate genetic improvement in broiler lines (Hosnedlova et al., 2020). The use of RNA-seq and transcriptome analysis has further enabled the identification of differentially expressed genes that regulate myogenic growth, providing a deeper understanding of the genetic architecture underlying muscle development (Davis et al., 2015). 6.2 Enhancing muscle yield through genetic manipulation Genetic manipulation offers a promising avenue for enhancing muscle yield in broilers. By targeting specific genes involved in muscle growth and development, it is possible to achieve significant improvements in muscle mass. For example, the down-regulation of myostatin signaling pathway genes combined with the up-regulation of genes that enhance muscle formation has been associated with higher feed efficiency and muscle development in broilers (Lassiter et al., 2019). Moreover, thermal manipulation during embryogenesis has been shown to up-regulate muscle growth factor genes such as IGF-1 and GH, leading to increased body weight and carcass yield in post-hatch broilers (Al-Zghoul and El-Bahr, 2019). These findings highlight the potential of genetic and environmental interventions to optimize muscle yield in broiler chickens. 6.3 Future prospects for improving broiler muscle traits The future of broiler breeding lies in the integration of advanced genetic tools and technologies to further enhance muscle traits. The use of large-scale transcriptome sequencing and weighted gene co-expression network analysis (WGCNA) has already identified key candidate genes and pathways involved in muscle development and lipid metabolism (Kang et al., 2021). As our understanding of the molecular mechanisms underlying muscle growth continues to expand, it is likely that new genetic markers and targets for manipulation will be discovered. Additionally, the application of gene editing technologies such as CRISPR/Cas9 holds great promise for precise genetic modifications to improve muscle traits. Continued research and innovation in this field will undoubtedly lead to more efficient and productive broiler breeding programs, ultimately benefiting the poultry industry as a whole. By leveraging gene expression data, genetic manipulation, and future technological advancements, the potential for improving muscle development in broilers is vast. These strategies not only enhance growth performance but also contribute to the overall efficiency and sustainability of broiler production. 7 Challenges and Limitations 7.1 Technical challenges in gene expression analysis Gene expression analysis in broilers presents several technical challenges. One significant issue is the complexity of the regulatory networks involved in muscle development. For instance, the identification of key genes such as Atp2a1, Tmod4, Lmod3, Ryr1, and Mybpc2 in bovine muscle development through co-expression analysis highlights the intricate pathways that need to be deciphered (Zhang et al., 2023). Additionally, the use of advanced techniques like RNA-seq and microarray analysis requires substantial computational resources and expertise in bioinformatics to accurately interpret the data (Bottje et al., 2011; Davis et al., 2015). The variability in gene expression due to environmental factors and genetic background further complicates the analysis, necessitating large sample sizes to achieve statistically significant results. 7.2 Limitations in translating gene data to breeding programs Translating gene expression data into practical breeding programs is fraught with limitations. One major challenge is the gap between identifying candidate genes and understanding their functional roles in muscle development. For example, while studies have identified differentially expressed genes associated with feed efficiency and muscle growth, such as IGF1, IGF1R, and MSTN, the direct application of this knowledge to breeding strategies
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