Screening Of Differentially Expressed Genes In The Longissimus Dorsi Muscles Of The Wannanhua Pig And The Yorkshire Pig Based On RNA-seq Technology

The Chinese pig and Western pig have significant differences in growth rate and meat quality traits. The Western pig breeds such as the Yorkshire(YY) pig have been intensively selected resulting in rapid, large, efficient accretion of muscle;however, this process has led to a reduction in meat quality. While indigenous Chinese pig breeds such as the Wannanhua(WH) pig have slower growth rates and lower lean meat contents than conventional western pig breeds, but they have superior perceived meat quality. This study focused on the molecular mechanism of different varieties of pork quality traits between the WH pig and YY pig. The high-throughput transcriptome sequencing(RNA-seq) technology was used to find the differentially expressed genes(DGEs) in longissimus dorsi muscle of WH pig and YY pig. Analysis of GO function annotation and pathway on different gene were analysed by DAVID database. The differential expression of all twelve selected DGEs were confirmed by quantitative real-time RT-PCR. The main results of this study were as follows:(1)The RNA-seq yielded a total of 60 994 560, 60 660 114 and 55 782 042 reads for WH03, WH05 and WH12, respectively and 54 388 532, 63 973 340 and 67 809428 reads for YY01, YY02 and YY06, respectively. Overall, ~93.7% of the raw reads were classified as high-quality reads, indicating sufficient sequencing depth and read quality and demonstrating that the data were suitable for analysis of DEGs in the longissimus dorsi muscle of adult WH pigs and YY pigs.(2)We identified 347 genes were differentially expressed in the longissimus dorsi muscle of adult WH pigs and YY pigs. Of these, 94 genes were upregulated and 253 genes were downregulated in YY pig compared to WH pig.(3)487 annotations were assigned to GO classes with functional terms. Of these,the majority of assignments were to biological processes(309, 63.4% of total),followed by cellular components(62, 12.7%) and molecular functions(116, 23.9%).GO analysis revealed that DGEs upregulated in WH and YY pigs were involved mainly in glucose metabolic process, glycolysis, muscle contraction and muscle organ development and DGEs downregulated in WH and YY pigs were muscle contraction,cytoskeletal protein binding, fatty acid metabolic process, lipid catabolic process,mitochondrial matrix,oxidation reduction, and ATP metabolic process.(4)The DGEs of KEGG database were notes 6620. Pathway significant enrichment analysis revealed that these genes involved in 145 biological metabolic pathway and there are 22 significant enrichment(P<0.01). The more differences genes number was in lipid metabolism(37). The important pathway of the lipid metabolism were fatty acid metabolism, PPAR signaling pathway, propanoate metabolism, fatty acid biosynthesis, fatty cytokine signal transduction pathway, fatty acid elongation and unsaturated fatty acid biosynthesis and so on.(5)The steady-state transcription levels of 12 selected DEGs were analyzed by qRT-PCR to validate the RNA-seq expression profiles. The 12 DEGs included three upregulated genes(SLC37A4, GPI, AK1) and eleven downregulated genes(CPT1B,CAST, PFKL, ACTN2, AMPD3, PDK4, CSRP3, PRKG1, FABP3). Verified by qRT-PCR test, the results showed the comsistent expression level of DGEs between qRT-PCR test the expression level and the RNA-seq sequencing. The results of study demonstrate that the results of the RNA-seq sequencing were accurate and reproducible.In summary, this study obtained the gene expression profile of porcine longissimus dorsi muscle tissue and identified a number of novel candidate genes for porcine meat quality and growth traits. And provided a theoretical basis for further research on the molecular mechanism of differences meat quality traits between Chinese and Western pig breeds and mining meat quality related candidate genes.