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RNA-seq Analysis of the Longissimus Muscle of Laiwu and Yorkshire Pigs

ABSTRACT: RNA-seq Analysis of the Longissimus Muscle of Laiwu and Yorkshire Pigs

PROVIDER: PRJNA1114715 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29128300_1.fastq.gz	Fastqsanger.gz
	SRR29128300_2.fastq.gz	Fastqsanger.gz
	SRR29128301_1.fastq.gz	Fastqsanger.gz
	SRR29128301_2.fastq.gz	Fastqsanger.gz
	SRR29128302_1.fastq.gz	Fastqsanger.gz

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RNA-seq Analysis of the Longissimus Muscle of Laiwu and Yorkshire Pigs

Project description:Intramuscular fat (IMF) content is the determining factor for meat taste. To reveal the genetic basis of IMF content, genetic studies have made some progress in lean-type pig breeds, but fewer studies have been conducted in Chinese fat-type pigs. We selected Laiwu and Yorkshire pigs as models, and transcriptomic analysis was conducted on the longissimus dorsi muscle to investigate the gene expression patterns linked to high and low intramuscular fat (IMF) content. The purpose of the study was to determine the differences in intramuscular fat between the two breeds and identify the reasons for the differences. To further systematically investigate the potential biologic significance of phenotype divergence, the identified DEGs were annotated into multiple pathways based on KEGG bioinformatic databases (P < 0.05). According to the identified DEGs, the results revealed a number of enriched pathways in AMPK signaling pathway, cAMP signaling pathway, PPAR signaling pathway, and so on. Functional enrichment analysis showed that PPARγ, ADIPOQ, LEP, LIPE, SCD, FABP4 and PLIN1 were represented.

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Project description: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.

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