Differences in global gene expression in muscle tissue of Nellore cattle with divergent meat tenderness

Abstract

BackgroundMeat tenderness is the consumer’s most preferred sensory attribute. This trait is affected by a number of factors, including genotype, age, animal sex, and pre- and post-slaughter management. In view of the high percentage of Zebu genes in the Brazilian cattle population, mainly Nellore cattle, the improvement of meat tenderness is important since the increasing proportion of Zebu genes in the population reduces meat tenderness. However, the measurement of this trait is difficult once it can only be made after animal slaughtering. New technologies such as RNA-Seq have been used to increase our understanding of the genetic processes regulating quantitative traits phenotypes. The objective of this study was to identify differentially expressed genes related to meat tenderness, in Nellore cattle in order to elucidate the genetic factors associated with meat quality. Samples were collected 24 h postmortem and the meat was not aged.ResultsWe found 40 differentially expressed genes related to meat tenderness, 17 with known functions. Fourteen genes were up-regulated and 3 were down-regulated in the tender meat group. Genes related to ubiquitin metabolism, transport of molecules such as calcium and oxygen, acid-base balance, collagen production, actin, myosin, and fat were identified. The PCP4L1 (Purkinje cell protein 4 like 1) and BoLA-DQB (major histocompatibility complex, class II, DQ beta) genes were validated by qRT-PCR. The results showed relative expression values similar to those obtained by RNA-Seq, with the same direction of expression (i.e., the two techniques revealed higher expression of PCP4L1 in tender meat samples and of BoLA-DQB in tough meat samples).ConclusionsThis study revealed the differential expression of genes and functions in Nellore cattle muscle tissue, which may contain potential biomarkers involved in meat tenderness.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4323-0) contains supplementary material, which is available to authorized users.

Gene Co-expression Analysis Indicates Potential Pathways and Regulators of Beef Tenderness in Nellore Cattle

“…Many of the genes identified in this study were involved in skeletal muscle contraction and lipid metabolism ( Zhao et al, 2012b ). Finally, an RNA-Seq study of tenderness in Nellore cattle identified 40 DE genes, however, just 17 had known functions ( Fonseca et al, 2017 ). This number of DE genes is consistent with our results, and some of the genes with known functions were also related to ubiquitin metabolism and transport of calcium ( Fonseca et al, 2017 ).…”

“…Finally, an RNA-Seq study of tenderness in Nellore cattle identified 40 DE genes, however, just 17 had known functions ( Fonseca et al, 2017 ). This number of DE genes is consistent with our results, and some of the genes with known functions were also related to ubiquitin metabolism and transport of calcium ( Fonseca et al, 2017 ). A GWAS analysis was previously performed in the same population of Nellore cattle, and many QTLs were identified for meat quality traits.…”

“…USP2 was previously associated with beef tenderness in a transcriptome study between male and female Qinchuan cattle ( Zhang et al, 2011 ). In addition, another gene from the same family, ubiquitin specific peptidase 32 ( USP32 ), was associated with tenderness in Nellore cattle ( Fonseca et al, 2017 ). TRIM45 , from the TRIM family ubiquitin ligases, is a component of the ubiquitin-proteasome and is involved in a variety of functions like growth regulation, apoptosis, and may suppress transcriptional activities of mitogen-activated protein kinase (MAPK) signaling pathway targets ( Shibata et al, 2012 ).…”

Aggregation of Omic Data and Secretome Prediction Enable the Discovery of Candidate Plasma Biomarkers for Beef Tenderness

“…From the corpus of the 44 remaining publications, 26 articles were identified as eligible for proteomic data [17,. Eleven articles including the series accession number GSE9256 (PMID: 18443416) were found as eligible for transcriptomic data [15,17,18,24,41,[48][49][50][51][52][53]. Twelve articles were found as eligible for genetic data [18,50,[54][55][56][57][58][59][60][61][62][63].…”

RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beef

“…Recently, RNA sequencing (RNA-seq) has allowed for transcriptional profiling of biological systems through identification of differentially expressed (DE) genes and pathways in order to identify biological mechanisms associated to the phenotypic condition being assessed [6]. Understanding the biological mechanisms associated with complex and economically important traits would help identify genes that could potentially be used as biomarkers in animal selection [7]. Differential expression is most often derived from comparing two or more conditions; however, converting a continuous phenotype such as meat quality into categories leads to loss of phenotypic variability.…”