title: Transcriptome analysis of cattle muscle identifies potential markers for skeletal muscle growth rate and major cell types.
abstract: BACKGROUND
  This study aimed to identify markers for muscle growth rate and the different cellular contributors to cattle muscle and to link the muscle growth rate markers to specific cell types.
  
  
  RESULTS
  The expression of two groups of genes in the longissimus muscle (LM) of 48 Brahman steers of similar age, significantly enriched for "cell cycle" and "ECM (extracellular matrix) organization" Gene Ontology (GO) terms was correlated with average daily gain/kg liveweight (ADG/kg) of the animals. However, expression of the same genes was only partly related to growth rate across a time course of postnatal LM development in two cattle genotypes, Piedmontese x Hereford (high muscling) and Wagyu x Hereford (high marbling). The deposition of intramuscular fat (IMF) altered the relationship between the expression of these genes and growth rate. K-means clustering across the development time course with a large set of genes (5,596) with similar expression profiles to the ECM genes was undertaken. The locations in the clusters of published markers of different cell types in muscle were identified and used to link clusters of genes to the cell type most likely to be expressing them. Overall correspondence between published cell type expression of markers and predicted major cell types of expression in cattle LM was high. However, some exceptions were identified: expression of SOX8 previously attributed to muscle satellite cells was correlated with angiogenesis. Analysis of the clusters and cell types suggested that the "cell cycle" and "ECM" signals were from the fibro/adipogenic lineage. Significant contributions to these signals from the muscle satellite cells, angiogenic cells and adipocytes themselves were not as strongly supported. Based on the clusters and cell type markers, sets of five genes predicted to be representative of fibro/adipogenic precursors (FAPs) and endothelial cells, and/or ECM remodelling and angiogenesis were identified.
  
  
  CONCLUSIONS
  Gene sets and gene markers for the analysis of many of the major processes/cell populations contributing to muscle composition and growth have been proposed, enabling a consistent interpretation of gene expression datasets from cattle LM. The same gene sets are likely to be applicable in other cattle muscles and in other species.
authors.affiliation: Key Laboratory of Meat Processing and Quality Control, Synergetic Innovation Centre of Food Safety and Nutrition, College of Food Science and Technology, Nanjing Agriculture University, Nanjing, 210095, P. R. China. guobingflying@gmail.com.|CSIRO Agriculture Flagship, St. Lucia, QLD, 4067, Australia. guobingflying@gmail.com.
authors.forename: Bing
authors.initials: B
authors.lastname: Guo
authors.affiliation: CSIRO Agriculture Flagship, Armidale, NSW, 2350, Australia. Paul.Greenwood@csiro.au.|NSW Department of Primary Industries, University of New England, Armidale, NSW, 2351, Australia. Paul.Greenwood@csiro.au.
authors.forename: Paul L
authors.initials: PL
authors.lastname: Greenwood
authors.affiliation: NSW Department of Primary Industries, University of New England, Armidale, NSW, 2351, Australia. Linda.Cafe@dpi.nsw.gov.au.
authors.forename: Linda M
authors.initials: LM
authors.lastname: Cafe
authors.affiliation: Key Laboratory of Meat Processing and Quality Control, Synergetic Innovation Centre of Food Safety and Nutrition, College of Food Science and Technology, Nanjing Agriculture University, Nanjing, 210095, P. R. China. ghzhou@njau.edu.cn.
authors.forename: Guanghong
authors.initials: G
authors.lastname: Zhou
authors.affiliation: Key Laboratory of Meat Processing and Quality Control, Synergetic Innovation Centre of Food Safety and Nutrition, College of Food Science and Technology, Nanjing Agriculture University, Nanjing, 210095, P. R. China. wangang.zhang@yahoo.com.
authors.forename: Wangang
authors.initials: W
authors.lastname: Zhang
authors.affiliation: CSIRO Agriculture Flagship, St. Lucia, QLD, 4067, Australia. Brian.Dalrymple@csiro.au.
authors.forename: Brian P
authors.initials: BP
authors.lastname: Dalrymple
mesh_terms: D050156:Adipogenesis / Q000235:genetics; D000818:Animals; D015415:Biomarkers; D002417:Cattle; D002453:Cell Cycle / Q000235:genetics; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D005109:Extracellular Matrix; D015870:Gene Expression; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D008954:Models, Biological; D058977:Molecular Sequence Annotation; D018482:Muscle, Skeletal / Q000254:growth & development* / Q000378:metabolism*; D019655:Quantitative Trait, Heritable; D032496:Satellite Cells, Skeletal Muscle / Q000378:metabolism; D059467:Transcriptome
chemical_list: D015415:Biomarkers