RNA-seq transcriptome analysis of extensor digitorum longus and soleus muscles in large white pigs

Abstract

Skeletal muscle fibers are mainly categorized into red and white fiber types, and the ratio of red/white fibers within muscle mass plays a crucial role in meat quality such as tenderness and flavor. To better understand the molecular difference between the two muscle fibers, this study takes advantage of RNA-seq to compare differences in the transcriptome between extensor digitorum longus (EDL; white fiber) and soleus (Sol; red fiber) muscles of large white pigs. In total, 89,658,562 and 46,723,568 raw reads from EDL and Sol were generated, respectively. Comparison between the two transcriptomes revealed 561 differentially expressed genes, with 408 displaying higher and 153 lower levels of expression in Sol. Quantitative real-time polymerase chain reaction validated the differential expression of nine genes. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis discovered several differentially enriched biological functions and processes of the two muscles. Moreover, transcriptome comparison between EDL and Sol identified many muscle-related genes (CSRP3, ACTN2, MYL1, and MYH6) and pathways related to myofiber formation, such as focal adhesion, tight junction formation, extracellular matrix (ECM)-receptor pathway, calcium signaling, and Wnt signaling. In addition, 58,362 and 58,359 single nucleotide polymorphisms were identified in EDL and Sol, respectively, and the sequence of 9069 genes was refined at the 5', 3' or both ends. Numerous novel transcripts and alternatively spliced RNAs were also identified. Our transcriptome analysis constitutes valuable sequence resource for uncovering important genes and pathways involved in muscle fiber type determination, and might help further our understanding of the molecular mechanisms in different types of muscle.

Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins

“…Some of the genes that overlap between statistical methods in Canadian populations (Bayescan and LFMM) included supervillin‐like gene, which is a protein involved in actin and myosin II assembly that promotes cell growth (Fang & Luna, ). This gene has been shown to be involved in muscle fiber type determination in large white pigs (Zhu et al., ). We suggest that this gene may be associated with muscle development in Atlantic salmon and be under selection for improving growth‐related traits.…”

Oxidative and glycolytic skeletal muscles show marked differences in gene expression profile in Chinese Qingyuan partridge chickens

“…Our results showed significant phenotypic differences between SOL and EDL muscles in Qingyuan partridge chickens, wherein EDL exhibited a significant higher cross-sectional area (CSA), diameter, and white myofiber ratio than SOL. Although some DEGs between different skeletal muscles have recently been identified in several species, such as mice [ 17 ], pigs [ 18 – 20 ], and duck [ 21 ], the molecular mechanism underlying muscle fiber characteristics in chicken remains unclear. Therefore, our objective was to clarify the biological events, which could explain phenotypic differences between the SOL and EDL in chicken.…”

“…The number of genes found differentially expressed between oxidative and glycolytic muscles is relatively high, when compared with those DEGs found in pigs and ducks. There were 159 DEGs between red (soleus) and white muscles (extensor digitorum longus) in Chinese Meishan pigs [ 19 ], 561 DEGs between red (soleus) and white muscles (extensor digitorum longus) in large white pigs [ 20 ], and 168 DEGs between leg muscle and pectoralmuscle in ducks [ 21 ]. However, different experimental conditions such as species, sample size, technology platform, FC threshold might account for this discrepancy.…”

“…Bai et al (2003) found many candidate genes, which determine muscle red/white phenotype in Berkshire pigs [ 18 ]. Li et al (2010) found 28 signalling pathways, including MAPK and Wnt pathways, which responded to metabolic differences between muscle types in Meishan pigs using Affymetrix Porcine Genechip [ 19 ].Zhu et al (2015) revealed 561 differentially expressed genes between extensor digitorum longus and soleus muscles of large white pigs by RNA-seq technology, and identified many muscle-related genes and pathways related to myofiber formation [ 20 ]. Zhang et al (2015) revealed 168 DEGs between leg muscle (LM) and pectoral muscle (PM) in ducks [ 21 ].…”

Identification of candidate genes of growth traits in pigs using RNA-sequencing

“…A total of 1919 genes that differentially expressed more than twice were screened in the subcutaneous adipose tissue of castrated boars, and the selective splicing and transcripts were identified. Zhu et al (2016) analysed the transcriptome of extensor digitorum longus and soleus muscles of Large White pig using RNA-seq technology, obtaining 561 DEGs and four genes associated with muscle CRSP3, ACTN2, MYL1 and MYH6. constructed two RNA libraries from pooled samples of longissimus dorsi muscles with the highest and lowest drip loss pig longissimus dorsi and obtained 150 different genes using RNA-seq technology, screening two candidate genes, TRDN and MSTN.…”