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

ABSTRACT: Western commercial pig breeds have been intensively selected, resulting in a sizeable, rapid, and efficient accretion of muscle but a reduction in meat quality. When compared with Western commercial pig breeds, Chinese indigenous pig breeds exhibited slower growth rates and reduced lean meat content but superior perceived meat quality. To study the factors that determine meat quality, we examined piglets of one Western commercial breed (Yorkshire) and one Chinese indigenous breed (Wannanhua) and sequenced the longissimus dorsi muscle using RNA-sequencing (RNA-seq). We analyzed their transcriptomes, focusing on identifying candidate genes that may influence porcine muscle growth, meat quality and adipose deposition. Gene ontology functional enrichment and pathway enrichment analyses identified differentially expressed genes primarily associated with glycolytic metabolism, biological processes of muscle development and signaling pathways related to fatty acid metabolism, growth and carcass traits. This finding suggests that the differentially expressed genes may play important roles in determining meat quality traits. Quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) confirmed the differential expression of twelve selected differentially expressed genes. This study identified a number of novel candidate genes for porcine meat quality and carcass traits that merit further investigation to elucidate the molecular mechanisms responsible for muscle growth and fat deposition.

ORGANISM(S): Sus scrofa

PROVIDER: GSE75045 | GEO | 2015/11/30

SECONDARY ACCESSION(S): PRJNA302287

REPOSITORIES: GEO

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Project description:In the last 20 years, there has been significant research towards defining the genetic basis of lipid metabolism and meat quality related traits in pigs. Nowadays, the study of the transcriptome and its regulatory mechanisms allows going far beyond in the genetic dissection of these complex traits. In present study, a genome-wide eQTL scan aiming to detect pig genome regions regulating levels of skeletal muscle mRNA expression has been performed. This study has been conducted on a commercial Duroc population where a number of QTL for muscle fat deposition and fatty acid composition had been detected. GeneChip Porcine Genome® arrays (Affymetrix) were used to determine the gene expression levels of gluteus medius samples from 105 Duroc pigs belonging to two groups with divergent phenotypes for fatness traits. This experimental design aimed to favour detection of eQTL affecting genes related to lipid metabolism and meat quality traits. The whole genome scan with a panel of 110 microsatellites allowed us detecting 613 genome-wide significant eQTL unequally distributed across the pig genome, SSC5 and SSC3 harbouring the highest number of eQTL. Moreover, 11 genome regions with eQTL affecting the expression levels of a high number of genes (eQTL hot spots) have been described. After mapping target probes and discarding low quality probes, a total of 59 cis- and 396 trans-acting eQTL were retained for further analyses. The functional classification showed that lipid-related GO terms were not the most enriched by the list of eQTL-regulated genes. However, a number of regulated genes functionally related to lipid metabolism and fat deposition traits were identified, and their functional relationship with these phenotypes were further investigated. With this purpose, eQTL results were integrated with 1) QTL linkage maps and 2) correlation data between phenotypes and gene expression levels. As a result, a comprehensive list of 29 positional and functional candidate genes was elaborated. These results represent a valuable contribution to the comprehension of genetic regulation of skeletal muscle individual gene expression in swine species, and a first step towards disentangling gene networks and molecular mechanisms involved in lipid metabolism and meat quality traits. 105 gluteus medius samples from 105 animals belonging to two groups of 53 and 52 animals each: HIGH group had higher carcass, plasma and muscle fat content; LOW group had lower carcass, plasma and muscle fat content

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

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