Expression patterns and genetic variation of the ovine skeletal muscle transcriptome of sheep from five Spanish meat breeds

Abstract

The goal of the current study is to analyse the gene expression profile of the ovine skeletal muscle as well as to characterize the genetic variation of transcripts expressed in such tissue. This aim has been achieved by sequencing the longissimus dorsi transcriptomes of 50 sheep distributed in five pools representing the Canaria de Pelo, Roja Mallorquina, Gallega, Xisqueta and Ripollesa Spanish autochthonous breeds. Approximately, 363 million reads per pool have been produced and 71.9–82.9% have been successfully mapped to the ovine genome in a paired-end mode (2 × 75 bp). The 200 most expressed muscle transcripts (≈1% of the total transcript count) account for 51% (Canaria de Pelo) to 67% (Gallega) of the total ovine skeletal muscle mRNA expression. These highly expressed genes play key roles in pathways related with striated muscle contraction, gluconeogenesis, glycolysis, citric acid cycle and respiratory electron transport. RNA-Sequencing of muscle transcripts has also revealed that ~72% of the SNPs detected with this approach are shared by at least two pools, and 10% of them segregate in the five pools under analysis. Most of the substitutions detected by RNA-Seq are synonymous or missense and only a minority are predicted to have consequences on protein function.

lncRNA–miRNA–mRNA ceRNA Network Involved in Sheep Prolificacy: An Integrated Approach

“…This gene has a role in the structural constituent of the cytoskeleton, myosin binding, RhoGDI pathway, and cytoskeleton remodeling regulation of actin cytoskeleton by Rho GTPases [ 88 ]. Kelch like family member 17 (KLHL17) is an actin-binding protein that has a role in actin filament binding and POZ domain binding and is predominantly expressed in neurons of most regions of the brain [ 89 ]. A process that is fulfilling at the cellular level results in the arrangement, assembly of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their related proteins [ 90 ].…”

Novel Genes Associated with Dairy Traits in Sarda Sheep

“…We also genotyped three SNPs of the PRKAG3 gene and evidenced that SNP rs159573167 AA was associated with an increase of dMY in the sampled population (+17% in comparison with genotype GG; data not shown in the tables) and a decrease of the protein and casein contents. The variability at the PRKAG3 gene was investigated in New Zealand Suffolk sheep [ 47 ], and the variability and expression profile in skeletal muscle were investigated in five local Spanish breeds, where PRKAG3 was found to be highly expressed [ 48 ]. Here, for the first time, we highlighted an association between PRKGA3 and dMY and the protein and casein contents.…”

Key Genes Regulating Skeletal Muscle Development and Growth in Farm Animals

“…Skeletal muscle transcriptome analysis revealed candidate genes affecting muscle development in Bandur sheep; genes of the Kelch superfamily ( KLHL6 , KLHL34 , and KLHL40 ) were upregulated more than two-fold, and ANKRD2 and KLH13 were found to be involved in muscle development [ 129 ]. Based on analysis of gene expression profiles in ovine skeletal muscle from five Spanish meat breeds, candidate genes related to muscle contraction, including actin α1 ( ACTA1 ), myosin light chain phosphorylatable fast skeletal muscle ( MYLPF ), myosin heavy chains 2 ( MYH2 ) and 7 ( MYH7 ), tropomyosin 2 ( TPM2 ), and titin ( TTN ), were identified [ 130 ]. Fan et al [ 131 ] employed whole-genome bisulfite sequencing to examine genome-wide DNA methylation profiles in Hu sheep and identified many important differentially methylated genes associated with muscle growth and metabolism ( Figure 3 ).…”