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Identification of differentially expressed genes in longissimus dorsi muscle between Wei and Yorkshire pigs using RNA-sequencing

ABSTRACT: Intramuscular fat (IMF) content is an important trait closely correlated with meat quality, which is highly variable among swine breeds from diverse genetic backgrounds. In order to elucidate the molecular mechanism underlying porcine meat quality, we adopted RNA-sequencing to detect transcriptome in the longissimus dorsi muscle of Wei pigs (a Chinese indigenous breed) and Yorkshire pigs (a Western lean-type breed) with different IMF content. A total of 717 differentially expressed genes (DEGs) were identified in our study, with 323 up-regulated and 394 down-regulated genes in Wei pigs compared with Yorkshire pigs. GO analysis showed that DEGs significantly related to muscle proliferation and development, lipid storage and catabolic, extracellular matrix structural constituent, and neutral amino acid transmembrane transporter activity. Pathway analysis revealed that DEGs associated with fatty acid metabolism, steroid biosynthesis, glycerophospholipid metabolism, protein digestion and absorption, and amino acid metabolism. Quantitative real time PCR confirmed the differential expression of 11 selected DEGs from both pig breeds. The results provide useful information to investigate the transcriptional profiling in skeletal muscle of different pig breeds with divergent phenotypes, and several DEGs can be taken as functional candidate genes for affecting pork quality.

ORGANISM(S): Sus scrofa

PROVIDER: GSE99092 | GEO | 2017/05/20

SECONDARY ACCESSION(S): PRJNA387276

REPOSITORIES: GEO

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Project description:There are clear phenotypic differences between Korean native pig (KNP) and Yorkshire (YS) breeds because of different interests for selection. YS has been artificially selected by industrial interests such as a growth rate and a lean meat production, however, KNP has been maintained as a regional breed by local interests such as a fat content in or between muscle and a disease resistance. A comparison of gene expression profile from a major tissue liver can reflect the overall effects of the artificial selection between the two pig breeds through long history. KNP (n=4) and YS (n=4) pigs were raised under the identical conditions. Global gene expression levels were measured in liver samples from these pigs using Affymetrix porcine genome array containing 23,937 probe sets. The clustering analysis based on the individual transcriptome data showed a clear separation between two breeds in the liver tissue. We collected hepato-transcriptome data including 11,993 genes fully detected from four independent samples either in KNP or in YS. Based on both minimum positive false discovery rate (less than 15%) and fold change (|FC| > 1.5), 160 differentially expressed genes (DEGs) were collected from the liver between the two breeds. The functional analysis of these DEGs indicated clear distinctions in intra- and extra-cellular structure, cell proliferation, membrane trafficking, glycolytic pathway, mitochondrial function, protein metabolism, and immune response. The functional characteristics based on the DEGs were useful indicators to explain the differences between these two breeds developed for the specific purposes each other. The hepatic DGEs indicate that the YS has been lost expressivity of genes not required for the fast growth but maintained expressivity of genes for lean muscle production. The tissue-wise gene expression profiles indicate that the liver could be a major place to make the economic distinction between these two pig breeds. Comparing gene expression profiles to discover differentially expressed genes from liver tissue of two different pig breeds: KNP (n=4) vs. YS (n=4).

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Identification of differentially expressed genes in longissimus dorsi muscle between Wei and Yorkshire pigs using RNA-sequencing

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