Insights into tissue- and cell type-specific effects of Grb10 on pig skeletal muscle growth by multi-omics analysis

Domestic pigs are shaped by artificial and natural selection into obese and lean types that are closely related to muscle tissue. However, the key genes and regulatory mechanisms behind these developments remain largely unknown. Here, we pinpoint GRB10 specificity in muscle tissue and cells between obese and lean pigs by combining genomics, transcriptomics, epigenomics, and single-cell transcriptomics. GRB10 shows notable differences in divergent selection on haplotype blocks and expression levels between obese and lean pig breeds, with its expression profiles varying significantly by tissue and development stage. Notably, we identify a muscle-specific promoter of GRB10 and its transcription factor KLF15. This TF-promoter binding is verified by dual luciferase and chromatin immunoprecipitation (ChIP) assays, and is suggested to be conserved in humans. Single-nucleus RNA sequencing further highlights differential expression patterns of GRB10 between obese and lean pig breeds across various cell types. Type IIa myonuclei and TTN⁺ FAPs, which are more predominant in lean pigs, play a crucial role in myofibril assembly and muscle tissue development. These findings offer insights into the regulatory mechanisms controlling muscle growth. They highlight the tissue- and cell type-specific effects of GRB10 on muscle heterogeneity, which has potential applications in livestock breeding and human obesity research.