Comparative Transcriptome Analysis of Slow-Twitch and Fast-Twitch Muscles in Dezhou Donkeys

Abstract

The skeletal muscle fiber profile is closely related to livestock meat quality. However, the molecular mechanisms determining muscle fiber types in donkeys are not completely understood. In this study, we selected the psoas major muscle (PM; mainly composed of oxidative-type muscle fibers) and biceps femoris muscle (BF; mainly composed of glycolytic-type muscle fibers) and systematically compared their mRNA and microRNA transcriptomes via RNA-seq. We identified a total of 2881 differentially expressed genes (DEGs) and 21 known differentially expressed miRNAs (DEmiRs). Furthermore, functional enrichment analysis showed that the DEGs were mainly involved in energy metabolism and actin cytoskeleton regulation. The glycolysis/gluconeogenesis pathway (including up-regulated genes such as PKM, LDHA, PGK1 and ALDOA) was more highly enriched in BF, whereas the oxidative phosphorylation pathway and cardiac muscle contraction (including down-regulated genes such as LDHB, ATP2A2, myosin-7 (MYH7), TNNC1, TPM3 and TNNI1) was more enriched in PM. Additionally, we identified several candidate miRNA–mRNA pairs that might regulate muscle fiber types using the integrated miRNA–mRNA analysis. Combined with the results of protein–protein interaction (PPI) analysis, some interesting DEGs (including ACTN3, TNNT3, TPM2, TNNC2, PKM, TNNC1 and TNNI1) might be potential candidate target genes involved in the miRNA-mediated regulation of the myofibril composition. This study is the first to indicate that DEmiRs, especially eca-miR-193a-5p and eca-miR-370, and potential candidate target genes that are mainly involved in actin binding (e.g., ACTN3, TNNT3 and TNNC1) and the glycolysis/gluconeogenesis pathways (e.g., PKM) might coregulate the myofibril composition in donkeys. This study may provide useful information for improving meat quality traits in Dezhou donkeys.

Diversity and Differential Expression of MicroRNAs in the Human Skeletal Muscle with Distinct Fiber Type Composition

“…We found that the expression of miR-208b-3p and miR-499a-5p was upregulated in samples with a predominance of slow-twitch fibers. This is consistent with some previous studies performed on vertebrate species [ 33 , 34 , 35 , 36 , 37 , 38 ]. The upregulation of these muscle-specific miRNAs in slow-twitch fibers is most likely due to the increased expression of their host genes MYH7 and MYH7B , which was described earlier [ 33 ] and was confirmed by the correlation analysis in this study.…”

“…Analysis of miRNA expression in bovine skeletal muscle by massively parallel sequencing found increased expression of miR-1, miR-133a/b and miR-206, and decreased expression of miR-208a in fast-type muscles compared to slow-type ones [ 35 ]. In recent studies, RNA sequencing has been applied to analyze transcriptomic differences and miRNA–mRNA interactions between muscles with a prevalence of fast and slow fibers in chickens, horses and donkeys [ 36 , 37 , 38 ]. In horses, the expression of miR-499 and miR-206 was elevated in muscles with a predominance of slow fibers.…”

“…The authors suggest a co-regulatory model of regulating the proportion of fast and slow fiber types based on the interactions of Sox6 with Myh7b and myomiRs [ 37 ]. In donkeys, miR-208a and miR-499-3p were among the upregulated miRNAs in muscles with a predominance of slow fibers [ 38 ]. The common factor in all of the above vertebrate skeletal muscle miRNA studies is that the expression of either miR-499-3p/5p or miR-208a/b was elevated in muscles with a predominance of slow fibers.…”

Exploring Genetic Markers: Mitochondrial DNA and Genomic Screening for Biodiversity and Production Traits in Donkeys

“…Recently, several studies have employed transcriptomic analysis to identify genetic markers associated with production traits in donkeys [66][67][68][69]. Similarly, Chai et al [32] conducted transcriptomic analysis of different muscles in donkeys and discovered several genes (MYH1, MYH7, TNNC1, TNNI3, TPM3, ALDOA, ENO3, and PGK1) that were found to be associated with tenderness in donkey meat.…”

Muscle fiber characteristics and expression level of Troponin T3, Toll-like receptor 2, and Toll-like receptor 4 genes in chicken meat with white striping

“…The composition of muscle fiber types may affect meat quality by influencing the content of postmortem metabolites in livestock [ 13 ]. Troponin T3 has been identified as a potential candidate gene primarily involved in actin binding and myofibril composition [ 14 ]. A higher abundance of TNNT3 has been found in myopathy of the pectoralis major muscle in fast-growing broilers, which could be caused by a reduced supply of oxygen to the breast muscle [ 15 ].…”