Transcriptome profiling of muscle in Nelore cattle phenotypically divergent for the ribeye muscle area

Genomics. 2020 Mar;112(2):1257-1263. doi: 10.1016/j.ygeno.2019.07.012. Epub 2019 Jul 24.

Abstract

This study aimed to use RNA-Seq to identify differentially expressed genes (DEGs) in muscle of uncastrated Nelore males phenotypically divergent for ribeye muscle area (REA). A total of 80 animals were phenotyped for REA, and 15 animals each with the highest REA and the lowest REA were selected for analyses. DEGs found (N = 288) belonging to families related to muscle cell growth, development, motility and proteolysis, such as actin, myosin, collagen, integrin, solute carrier, ubiquitin and kelch-like. Functional analysis showed that many of the significantly enriched gene ontology terms were closely associated with muscle development, growth, and degradation. Through co-expression network analysis, we predicted three hub genes (PPP3R1, FAM129B and UBE2G1), these genes are involved in muscle growth, proteolysis and immune system. The genes expression levels and its biological process found this study may result in differences in muscle deposition, and therefore, Nelore animals with different REA proportions.

Keywords: Bovine; Carcass trait; Co-expression; Genes; Hub genes; RNA-Seq.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Calcineurin / genetics
  • Calcineurin / metabolism
  • Cattle / genetics*
  • Evolution, Molecular
  • Male
  • Muscle Development
  • Muscle Proteins / genetics
  • Muscle Proteins / metabolism
  • Muscle, Skeletal / growth & development
  • Muscle, Skeletal / metabolism*
  • Phosphoproteins / genetics
  • Phosphoproteins / metabolism
  • Transcriptome*
  • Ubiquitin-Conjugating Enzymes / genetics
  • Ubiquitin-Conjugating Enzymes / metabolism

Substances

  • Muscle Proteins
  • Phosphoproteins
  • Ubiquitin-Conjugating Enzymes
  • Calcineurin