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

Abstract

BackgroundThe 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.ResultsSequencing 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.ConclusionsCertain 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0389-y) contains supplementary material, which is available to authorized users.

Genetic Marker Discovery in Complex Traits: A Field Example on Fat Content and Composition in Pigs

“…Most of these experiments compared lean, fast growing breeds such as Yorkshire or Landrace with indigenous Chinese or Korean breeds [69,70,71,72], or with European local breeds [73], which have an overall fattier phenotype. There is a common trend among these results, which is the overexpression in the leaner breeds of genes related to: (i) muscle differentiation and contraction along with changes in gene expression which promote; (ii) glucose production via gluconeogenesis and glycolysis; but also (iii) lipid catabolism; and (iv) mitochondria function.…”

Proteomics in Meat Science — Current Status and Future Perspective

“…Большинство исследований используют 2DGE высокого разрешения или жидкостную хроматогра-фию в комбинации с масс спектрометрией (MS) для идентификации белка с высокой пропускной способ-ностью [2,3,4,5,6].…”

“…Most studies use highresolution 2DGE or liquid chromatography, in combination with mass spectrometry (MS) for high-throughput protein identification [2,3,4,5,6].…”

Comparative Skeletal Muscle Proteomics Using Two-Dimensional Gel Electrophoresis

“…Gel-based meat proteomics has been used to establish reference maps of bovine muscle [113,119], rabbit muscle [122] and pig muscle [114], as well as for studying tissue growth [164,165,241,242] and p ost mortem changes in bovine, porcine and chicken muscles [243,244,245,246,247,248]. The findings from meat proteomics are important for maximizing muscle growth, meat production, slaughter methods, muscle-to-meat processing and meat storage [249,250,251].…”