Bioscience Methods 2025, Vol.16, No.2, 83-99 http://bioscipublisher.com/index.php/bm 94 molecular level, the role of the transcription factor TCF7L2 is a brilliant example. As a downstream factor of the Wnt signaling pathway, it was found to be a switch that favors adipogenic differentiation. When TCF7L2 activity is high, FAPs are more likely to turn to adipocytes, thereby increasing intramuscular fat; when its activity is inhibited, adipose differentiation is weakened, and more cells may retain myogenic potential. Epigenetic reprogramming accompanies muscle development and responds to external conditions plastically. Muscle cells of different types or stages have significantly different transcriptional states, and there must be epigenetic changes behind these state changes. For example, in lean pig muscle cells, the chromatin of myogenesis-related genes may be more open, while in obese pigs, fat-related genes are more open (Qiu et al., 2020). If further ATAC or ChIP analysis is performed, this is expected to be verified. Similarly, when goat satellite cells are activated into myoblasts, some key gene promoters are demethylated and H3K27ac increases, which are expected epigenetic changes. Therefore, these transcriptional changes essentially reflect epigenetic reprogramming. And importantly, this reprogramming is plastic. Interactions across cell types are an important level of muscle development regulation. Traditionally, muscle biology has focused on the differentiation regulation of muscle cells themselves (myoblasts, myofibers). However, the case emphasizes the impact of fibroblast/adipocyte progenitor cells (FAPs) on the muscle environment (Zhu et al., 2024). FAPs have long been regarded as the culprits of scar formation and fat infiltration in regenerative medicine, but single-cell studies have found that they also provide necessary matrix support in normal development. Muscle tissue is not an isolated island of muscle cells. It forms a unified niche together with surrounding connective tissue, nerves, and immune cells. Single-cell multi-omics allows us to observe these different cells at the same time, so as to understand, for example, how cytokines secreted by immune cells affect satellite cells and how ECM production by fibroblasts regulates the mechanical environment of muscle fibers. This is indistinguishable in traditional bulk sequencing. Taking goat muscle as an example, if we also introduce spatial transcriptomics or multi-omics in the future, we can directly see the relationship between the location of immune cell aggregation and muscle fiber growth on tissue sections, thereby taking cell interaction research a step further. 6.3 Implications for future research and animal husbandry improvement On the one hand, in scientific research, the case demonstrates the power and necessity of single-cell multi-omics. In the past, many genetic studies on muscle growth were unable to clarify cellular heterogeneity and multi-layer regulation due to the lack of single-cell resolution, so that some conclusions remained at the correlation level. Now that we have these technologies, we should vigorously apply them to livestock research. For example, we can conduct systematic single-cell transcriptome and epigenomics analysis on goat skeletal muscle of different breeds, different growth stages, and different nutritional conditions to establish a multi-omics reference map of goat skeletal muscle development. On this basis, further functional experiments can be more targeted around key genes and pathways, thereby accelerating the output of results. On the other hand, for animal husbandry practice, these studies provide new ideas for genetic improvement and feeding management (Zhou et al., 2024). In terms of genetic improvement, the core regulatory factors and pathways found by single-cell multi-omics can be converted into molecular markers for breeding. For example, traditional breeding indicators (weight gain, backfat thickness, intramuscular fat content, etc.) can be combined with molecular markers to improve selection accuracy. The rise of gene editing technology also gives us the opportunity to directly modify these factors. If the role of a certain factor is critical and has no obvious adverse effects (such as knocking out the inhibitory factor in muscle), in theory, gene editing can be used to create a new strain with more ideal muscle growth. Of course, the application of gene editing in production still faces ethical and regulatory challenges, but it is technically feasible, such as the creation of sheep without muscle growth inhibitor MSTN has been reported (Figure 2) (Wang et al., 2017). Single-cell multi-omics will tell us that a more delicate regulatory network than MSTN allows us to combine multiple means to achieve breeding goals. In terms of feeding management, after understanding the regulatory mechanism of muscle development, we can design refined nutritional strategies or environmental interventions to optimize the phenotype. For example, if it is
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