Single-cell RNA transcriptome uncovers distinct developmental trajectories in the embryonic skeletal muscle of Daheng broiler and Tibetan chicken

Different chicken breeds exhibit distinct muscle phenotypes resulting from selective breeding, but little is known about the molecular mechanisms responsible for this phenotypic difference. Skeletal muscle is composed of a large number of heterogeneous cell populations. Differences in differentiation and interaction of cell populations play a key role in the difference of skeletal muscle phenotype. In the current study, we performed a single-cell RNA sequencing (scRNA-seq) on the leg muscle of Daheng broiler (DH, cultivated breed) and Tibetan chicken (TC, native breed) at embryonic (E) 10, E14 and E18. A comprehensive cell atlas of embryonic chicken skeletal muscle, consisting of 29,579 high-quality cells representing 6 distinct cell types was built. The differentiation trajectory of Myoblasts and fibro-adipogenic progenitors (FAPs) was constructed through pseudotemporal trajectory analysis. Our results revealed the different developmental trajectories and dynamic gene expression profiles in 3 subtypes of myoblasts and 5 FAPs subtypes of the two chicken breeds. Tibetan chicken showed earlier embryonic myogenesis and less myoblasts compared with Daheng broiler. By comparing the switch status and switch time of genes in the two breeds, SNRPG,SNRPE,EIF4EBP1 and HSP90AB1 were considered as potentially critical genes for embryonic myogenesis, and the genes MYOG,MYBPH,APOA1, and MGP played dominant roles in the embryonic adipogenesis. Intercellular interaction networks showed that strong and complex intercellular communication was contained during embryonic skeletal muscle growth and development. These findings revealed the differences of molecular mechanisms in the skeletal muscle development between TC and DH chickens. Our data provide a better understanding of skeletal muscle developmental differences between cultivated and native breeds and valuable information for genetic breeding of chicken.