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

A Noce,A Pons,V Landi,L A Bermejo,A Martínez,M Amills,A Sànchez,A Manunza,A Cánovas,J Jordana,G M Vacca,S Adán,M Pazzola,O Vidal,J V Delgado,T F Cardoso,J Capote,J Casellas

doi:10.1038/s41598-018-28760-9

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.

Highlights

The development of generation sequencing techniques has made possible to characterize in depth the ovine transcriptome across multiple tissues
RNA-Seq has been used to generate large collections of single nucleotide polymorphisms (SNPs) mapping to transcripts expressed in certain tissues[2,3], though SNP calling from sequencing data can be challenging due to the intrinsic complexity of the transcriptome[5,6]
We considered as “previously reported variants” those described in the Single Nucleotide Polymorphism database[18]

Summary

Introduction

The development of generation sequencing techniques has made possible to characterize in depth the ovine transcriptome across multiple tissues. A high resolution atlas of gene expression in sheep was generated by combining data from 441 RNA-Seq libraries representing all major organ systems[1]. RNA-Seq has been used to generate large collections of single nucleotide polymorphisms (SNPs) mapping to transcripts expressed in certain tissues[2,3], though SNP calling from sequencing data can be challenging due to the intrinsic complexity of the transcriptome[5,6]. The current study aimed to analyse the gene expression profile of the ovine skeletal muscle by sequencing RNA extracted from longissimus dorsi samples of 50 individuals distributed in pools representing five meat sheep breeds from Spain i.e. Canaria de Pelo, Roja Mallorquina, Gallega, Xisqueta and Ripollesa (Supplementary Table S1). We were interested in characterizing the SNP variation of transcripts expressed in the ovine skeletal muscle and to investigate if such variation is shared across breeds with different origins and demographic histories

Objectives

Methods

Results

Conclusion