Integrative analysis of transcriptomics and proteomics of skeletal muscles of the Chinese indigenous Shaziling pig compared with the Yorkshire breed

Abstract

Background: The Shaziling pig (Sus scrofa) is a well-known indigenous breed in China. One of its main advantages over European breeds is its high meat quality. However, little genetic information is available for the Shaziling pig. To screen for differentially expressed genes and proteins that might be responsible for the meat quality, the longissimus dorsi muscles from Shaziling and Yorkshire pig breeds were investigated using an integrative analysis of transcriptomics and proteomics, involving high-throughput sequencing, the two-dimensional gel electrophoresis, and mass spectrometry.

Results: Sequencing produced 79,320 unigenes by de novo assembly, and 488 differentially expressed genes in the longissimus dorsi muscle of Shaziling pig compared with the Yorkshire breed were identified. Gene Ontology term enrichment of biological functions and Kyoto Encyclopedia of Genes and Genomes analysis showed that the gene products were mainly involved in metabolism, protein binding, and regulation of skeletal muscle development. At the protein level, 23 differentially expressed proteins were identified, which were potentially associated with fatty acid metabolism, the glycolytic pathway, and skeletal muscle growth. Eight differentially expressed genes were confirmed by real-time PCR. These results give an insight into the mechanisms underlying the formation of skeletal muscle in the Shaziling pig.

Conclusions: Certain differentially expressed genes and proteins are involved in fatty acid metabolism, intramuscular fat deposition, and skeletal muscle growth in the Shaziling pig. These results provide candidate genes for improving meat quality and will promote further transcriptomic research in Shaziling pigs.

Keywords: Meat quality; Proteomics; RNA-seq; Shaziling Pig.

Fig. 1

2-DE map of longissimus dorsi musle from Yorkshire and Shaziling pig breeds. Scanned 2-DE image of separated using an IPG pH 3–10 strip in the first dimension (12 cm, BioRad, USA), and 12.5 % SDS gel in the second dimension. Tag show 38 spots that were significantly changed between the two breeds [a Yorkshire pigs (up-regulation), b Shaziling pigs (up-regulation)]

Fig. 2

GO annotation of different proteinic spots (a: molecular function distribution, b: Biological process distribution)

Fig. 3

Length distribution of the assembled final unigenes of Illumina sequences

Fig. 4

Column chart presentation of GO classification of unigenes

Fig. 5

KOG functional classification of transcriptome

Fig. 6

The fold change distribution of up- and down-regulated DEGs. Green bars refer to down-regulated DEGs and red bars refer to up-regulated DEGs in Shaziling pigs compared with Yorkshire pigs. The X axis shows fold change of DEGs and the Y axis number of DEGs

Fig. 7

qRT-PCR validation of the differentially expressed genes analyzed by RNA-seq and 2-DE. qRT-PCR was performed for eight genes that were identified as differential expressed genes between the Yorkshire and Shaziling pig breeds. The Y axis shows the relative expression levels