Transcriptomic investigation of meat tenderness in two Italian cattle breeds

Abstract

Our objectives for this study were to understand the biological basis of meat tenderness and to provide an overview of the gene expression profiles related to meat quality as a tool for selection. Through deep mRNA sequencing, we analyzed gene expression in muscle tissues of two Italian cattle breeds: Maremmana and Chianina. We uncovered several differentially expressed genes that encode for proteins belonging to a family of tripartite motif proteins, which are involved in growth, cell differentiation and apoptosis, such as TRIM45, or play an essential role in regulating skeletal muscle differentiation and the regeneration of adult skeletal muscle, such as TRIM32. Other differentially expressed genes (SCN2B, SLC9A7 and KCNK3) emphasize the involvement of potassium-sodium pumps in tender meat. By mapping splice junctions in RNA-Seq reads, we found significant differences in gene isoform expression levels. The PRKAG3 gene, which is involved in the regulation of energy metabolism, showed four isoforms that were differentially expressed. This distinct pattern of PRKAG3 gene expression could indicate impaired glycogen storage in skeletal muscle, and consequently, this gene very likely has a role in the tenderization process. Furthermore, with this deep RNA-sequencing, we captured a high number of expressed SNPs, for example, we found 1462 homozygous SNPs showing the alternative allele with a 100% frequency when comparing tender and tough meat. SNPs were then classified into categories by their position and also by their effect on gene coding (174 non-synonymous polymorphisms) based on the available UMD_3.1 annotations.

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

“…In a study comparing methodologies for RNA-Seq analysis, QuasiSeq was the top ranked method ( Burden et al, 2014 ). Beef tenderness is a complex trait that can be influenced by many factors (i.e., breed, muscle, nutrition) ( Bongiorni et al, 2016 ). As such, it is not unexpected that the number of DE genes identified as a function of beef tenderness would be prone to large variability based on the influence of these many contributing factors.…”

Tissue Engineering for Clean Meat Production

“…Gene expression tools are often used to study metabolic pathways in farm animals, particularly of IMF. These works are highly valuable for clean meat research, as they are not aimed for regenerative medicine, but rather focus on meat traits, such as marbling (Lee et al, 2010;Sadkowski et al, 2014;Chen et al, 2015;Hudson et al, 2015;Meadus et al, 2018), myogenesis (Wang et al, 2005(Wang et al, , 2015Lee et al, 2014;Dai et al, 2016), and sensory qualities (Bernard et al, 2007;Hocquette et al, 2007;Bongiorni et al, 2016;Tizioto et al, 2016). Research on correlations between gene expression and meat quality has been recently summarized in several publications.…”

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

“…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]. The computational data aggregation from these 44 publications gave an overview of 1299 ID gene name (GN) related to meat tenderness whatever the muscle, breed, animal type, sex, age at slaughter, geographic area, and methodologies used for tenderness evaluation.…”