Identification of diverse cell populations in skeletal muscles and biomarkers for intramuscular fat of chicken by single-cell RNA sequencing

Abstract

Background The development of skeletal muscle is closely related to the efficiency of meat production and meat quality. Chicken skeletal muscle development depends on myogenesis and adipogenesis and occurs in two phases—hyperplasia and hypertrophy. However, cell profiles corresponding to the two-phase muscle development have yet to be determined. Single-cell RNA-sequencing (scRNA-seq) can elucidate the cell subpopulations in tissue and capture the gene expression of individual cells, which can provide new insights into the myogenesis and intramuscular adipogenesis. Results Ten cell clusters at the post-hatching developmental stage at Day 5 and seven cell clusters at the late developmental stage at Day 100 were identified in chicken breast muscles by scRNA-seq. Five myocyte-related clusters and two adipocyte clusters were identified at Day 5, and one myocyte cluster and one adipocyte cluster were identified at Day 100. The pattern of cell clustering varied between the two stages. The cell clusters showed clear boundaries at the terminal differentiation stage at Day 100; by contrast, cell differentiation was not complete at Day 5. APOA1 and COL1A1 were selected from up-regulated genes in the adipocyte cluster and found to be co-expressed with the ADIPOQ adipocyte marker gene in breast muscles by RNA in situ hybridization. Conclusions This study is the first to describe the heterogeneity of chicken skeletal muscle at two developmental stages. The genes APOA1 and COL1A1 were identified as biomarkers for chicken intramuscular fat cells.

Identification of molecular regulation on difference of lipid deposition in dedifferentiated preadipocytes from different chicken tissues

“…Furthermore, we identi ed the DEGs related to lipid metabolism according to the enriched GO terms and signaling pathways. Among the 72 DEGs related to lipid metabolism, 19 genes were enriched in the PPAR signaling pathway with the classic mediation on lipid metabolism [34,35], and the enriched genes included the representative ACSL1, APOA1, ADIPOQ, FABP3, FABP4, FABP5, FABP7, HMGCS2, LPL, PCK2, PDPK1, PPARG, RXRG, SCD, SCD5 and SLC27A6, etc., which had the important regulation on lipid metabolism [21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37]. Therfore, it was considered that these genes and PPAR signaling pathway had the important effects in vitro on regulating the difference of lipid deposition between DIMPs and DAFPs of chicken.…”

Towards Tabula Gallus

“…The Tabula Gallus is currently at an early stage (~20 scRNA-seq studies using chicks as of early 2022) [ 89 , 90 , 91 , 92 , 93 , 94 , 95 , 96 , 97 , 98 , 99 , 100 , 101 , 102 , 103 , 104 , 105 , 106 , 107 , 108 ]. Nonetheless, a couple of fledging studies support the feasibility of this project revealing diverse cell types and their states in the chick limb buds [ 96 , 102 ], the early primitive streak stage [ 95 , 103 ], neural crests [ 94 , 100 ], and the developing neural retina [ 98 , 107 ].…”

Recent Applications of RNA Sequencing in Food and Agriculture

“…The use of scRNA-Seq and single-cell gene regulatory networks (scGRN) frameworks in studying complex agronomic traits and resistance to various stresses in crops have been proposed [187]. Gene expression profiles among subcellular populations of the skeletal muscle and its development in chicken have been determined using scRNA-Seq, which are important in producing quantity and quality meat in poultry [188]. In sea urchins, using scRNA-Seq, different cell types commonly seen during the embryo development have been identified by the selective inhibition of Delta/ Notch and Wnt responsive pathways [189].…”