title: 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.
authors: Department for Innovation in Biological, Agro-food and Forest systems, DIBAF, University of Tuscia, via S. Camillo de Lelliss.n.c., Viterbo, 01100, Italy.
authors: S
authors: S
authors: Bongiorni
authors: Molecular Digital Diagnostics (MDD), s.r.l., via San Camillo de Lellis, Viterbo, 01100, Italy.
authors: C E M
authors: CE
authors: Gruber
authors: Cineca Supercomputing Center, via dei Tizii 6, Rome, 00185, Italy.
authors: S
authors: S
authors: Bueno
authors: Cineca Supercomputing Center, via dei Tizii 6, Rome, 00185, Italy.
authors: G
authors: G
authors: Chillemi
authors: Cineca Supercomputing Center, via dei Tizii 6, Rome, 00185, Italy.|Centre for Molecular Bioinformatics, Biology Department, University of Rome Tor Vergata, Rome, Italy.
authors: F
authors: F
authors: Ferrè
authors: Consiglio per la Ricerca e la sperimentazione in Agricoltura, Monterotondo, Italy.
authors: S
authors: S
authors: Failla
authors: Consiglio per la Ricerca e la sperimentazione in Agricoltura, Monterotondo, Italy.
authors: B
authors: B
authors: Moioli
authors: Department for Innovation in Biological, Agro-food and Forest systems, DIBAF, University of Tuscia, via S. Camillo de Lelliss.n.c., Viterbo, 01100, Italy.
authors: A
authors: A
authors: Valentini
mesh_terms: D055372:AMP-Activated Protein Kinases / Q000235:genetics; D000483:Alleles; D017398:Alternative Splicing; D000818:Animals; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D007558:Italy; D008460:Meat / Q000032:analysis*; D009124:Muscle Proteins / Q000235:genetics*; D018482:Muscle, Skeletal / Q000502:physiology; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D009124:Muscle Proteins; D055372:AMP-Activated Protein Kinases
keywords: Chianina; Maremmana; PRKAG3 gene; meat quality; skeletal muscle transcriptome