Single-nucleus profiling of neonatal broilers identifies early molecular signatures associated with the divergence in the potential of meat quality.

Meat quality is a critical determinant of the economic value in the broiler industry, with its foundational characteristics established during early post-hatch development. Skeletal muscles comprise a complex mixture of myofiber types, whose initial distribution and molecular signatures set the stage for post-mortem meat quality. However, the early regulatory landscapes governing these myofiber compositions remain to be fully elucidated. In this study, we employed high-resolution single-nucleus RNA sequencing (snRNA-seq) to characterize the transcriptomic divergence between broiler breast muscle (BM) and leg muscle (LM) at the neonatal stage (Day 1). Our panoramic atlas of muscle-resident cells revealed that neonatal LM already possesses a significantly higher proportion of oxidative fibers (Type I and Type IIA) and an enriched population of preadipocytes/adipocytes compared to BM. Functional enrichment analysis identified a prominent upregulation of the adipocytokine signaling pathway in D1 LM, suggesting an early molecular framework for the flavor and juiciness characteristics typically associated with leg meat. Furthermore, GSEA and KEGG analyses revealed a correlation between elevated FOS expression and apoptosis signatures in Type IIA and IIB myonuclei within LM, suggesting its potential involvement in shaping early myofiber type proportions. Additionally, PRKAG2 was identified as a candidate regulator linked to intramuscular lipid and fatty acid biosynthetic pathways. Our analysis indicated a regulatory link between the transcription factor EGR1 and its putative target PRKAG2, which coincides with initial lipid droplet accumulation in intramuscular adipocytes. Collectively, these findings provide a high-resolution genetic blueprint of early-postnatal muscle fiber characteristics and lipid deposition, offering novel developmental insights that may inform molecular breeding strategies aimed at predetermining the nutritional and sensory potential of broiler meat.