Dynamic transcriptome profiles of skeletal muscle tissue across 11 developmental stages for both Tongcheng and Yorkshire pigs

Abstract

BackgroundThe growth and development of skeletal muscle directly impacts the quantity and quality of pork production. Chinese indigenous pig breeds and exotic species vary greatly in terms of muscle production and performance traits. We present transcriptome profiles of 110 skeletal muscle samples from Tongcheng (TC) and Yorkshire (YK) pigs at 11 developmental periods (30, 40, 55, 63, 70, 90, and 105 days of gestation, and 0, 1, 3, and 5 weeks of age) using digital gene expression on Solexa/Illumina’s Genome Analyzer platform to investigate the differences in prenatal and postnatal skeletal muscle between the two breeds.ResultsMuscle morphological changes indicate the importance of primary fiber formation from 30 to 40 dpc (days post coitus), and secondary fiber formation from 55 to 70 dpc. We screened 4,331 differentially expressed genes in TC and 2,259 in YK (log2 ratio >1 and probability >0.7). Cluster analysis showed different gene expression patterns between TC and YK pigs. The transcripts were annotated in terms of Gene Ontology related to muscle development. We found that the genes CXCL10, EIF2B5, PSMA6, FBXO32, and LOC100622249 played vital roles in the muscle regulatory networks in the TC breed, whereas the genes SGCD, ENG, THBD, AQP4, and BTG2 played dominant roles in the YK breed. These genes showed breed-specific and development-dependent differential expression patterns. Furthermore, 984 genes were identified in myogenesis. A heat map showed that significantly enriched pathways (FDR <0.05) had stage-specific functional regulatory mechanisms. Finally, the differentially expressed genes from our sequencing results were confirmed by real-time quantitative polymerase chain reaction.ConclusionsThis study detected many functional genes and showed differences in the molecular mechanisms of skeletal muscle development between TC and YK pigs. TC pigs showed slower muscle growth and more complicated genetic regulation than YK pigs. Many differentially expressed genes showed breed-specific expression patterns. Our data provide a better understanding of skeletal muscle developmental differences and valuable information for improving pork quality.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1580-7) contains supplementary material, which is available to authorized users.

Comparison of skeletal muscle miRNA and mRNA profiles among three pig breeds

“…It has been reported that larger quantities of muscle mass and cross-sectional area lead to greater muscular contraction force (Jones et al 2008). As the muscle fiber diameter of western pigs was larger than that of indigenous Chinese pigs, and western pigs were leaner and had larger muscle mass than indigenous Chinese pigs (Zhao et al 2011(Zhao et al , 2015Fan et al 2006), we speculated that the skeletal muscles of different pig breeds have varying capacities for contraction. A number of differentially expressed genes involved in muscle contraction were found in our results.…”

“…The results from twodimensional fluorescence difference gel electrophoresis suggest that longissimus muscles of western lean-type pigs might have a greater oxidative capacity than those of indigenous Chinese obese-type pigs . The transcriptome profiles of skeletal muscle from Tongcheng and Yorkshire pigs across 11 developmental stages have been determined by Solexa sequencing and revealed that muscle fiber formation in Tongcheng pigs is initiated earlier than in Yorkshire pigs (Zhao et al 2015). miRNAs from skeletal muscle and adipose tissues of Lantang and Landrace pigs have been identified by both Solexa sequencing and microarray analysis and confirmed that miRNAs relevant to muscle development are differentially expressed between these two pig breeds .…”

“…GO term analysis showed that the differentially expressed genes were mainly associated with fatty acid metabolism, oxidative stress, muscle contraction, and muscle organ development. Several studies have reported transcriptome and miRNAome analyses in porcine skeletal muscle in recent years (Zhao et al 2015;Chen et al 2012;Liu et al 2013;Qin et al 2013;Siengdee et al 2013). Li et al performed expression miRNA profiling in Landrace (lean-type) and Lantang (obese-type) pigs by Solexa sequencing to investigate miRNA function in the regulation of porcine skeletal muscle development and fat storage ).…”

“…Primary myofibers are mainly formed at 38-64 days post coitus (dpc) and secondary myofibers at 54-90 dpc. In early embryonic periods, primary fibers in indigenous Chinese pigs are formed earlier than in western pigs and the muscle fiber diameter of western pigs is larger than that of indigenous Chinese pigs in later developmental periods (Zhao et al 2011(Zhao et al , 2015. Diversity in myofiber formation and characteristics, which might be caused by different proliferative abilities of satellite cells, might be a reason for the differences in muscle growth rates between indigenous Chinese pigs and western pigs .…”

Developmental Stage, Muscle and Genetic Type Modify Muscle Transcriptome in Pigs: Effects on Gene Expression and Regulatory Factors Involved in Growth and Metabolism

“…With this goal, some studies based on microarray technology investigated transcriptome differences between genotypes, such as Iberian vs. Large White or Duroc in endocrine tissues [22]. On the other hand, several studies have addressed the effect of the developmental stage (prenatally and postnatally) on muscle transcriptome [23–25] and the effect of muscle type on transcriptome and proteome, showing important functional differences [26, 27]. For example, 15–30% of proteome has been reported to differ between Longissimus dorsi (LD) and Biceps femoris (BF) muscles [27, 28].…”