Transcriptome And Proteome Study On Longissimus Dorsi Muscle Between Shaziling And Yorkshire Pigs

China is abundant in breed resources of animal. Shaziling pig is an excellent native breed in the Xiangtan region of Hunan province. It has some positive features, such as obvious marbling,3.5-4.5% intramuscular fat, rich amino acids, no PSE and DFD meat, and is very applicable to the current requirement. In this study, the transcriptomics and proteomics techniques were used to investigate longissimus dorsi muscles in Shaziling and Yorkshire pig breeds, and the purpose of the research was to find the differentially expressed genes in longissimus dorsi muscle, and discover molecular mechanisms to regulat muscle growth and development.The main results as follows:(1) Longissimus dorsi muscle transcriptomes of 25-days-old Shaziling and Yorkshire pigs were analyzed using next-generation sequencing (NGS). A total of 29,522,984 and 34,937,710 clean reads were generated for Shaziling and Yorkshire pigs, and these were de novo assembled into 79,320 unigenes. Of all unigenes,29.07%(n=23,055) are aligned to NR database. In total,489 differential expression genes (DEGs) were discovered between two samples, among which the numbers of up-regulated genes were 297, while the numbers of down-regulated genes were 192 in Shaziling pigs compared to Yorkshire pigs.(2) We analyzed composition of Longissimus dorsi proteins from Shaziling and Yorkshire pigs by 2-DE gel.38 differentially expressed protein spots (p<0.05) were found. Of the protein spots,27 spots were up-regulated in Shaziling pigs and 11 in Yorkshire pigs. A total of 23 proteins were successfully identified by MALDI-TOF-TOF/MS system. GO term enrichment analysis of differentially expressed proteins were performed, the result revealed that the function of the proteins was focused on regulating muscle growth and development of cytoskeleton, energy metabolism.(3) To validate the differential expression of genes, eight genes selected from 2-DE and RNA-seq results were analyzed by using qRT-PCR. We have got the consistent results of mRNA abundance between qRT-PCR and RNA-seq, therefore, these results from RNA-seq about the research of longissimus dorsi of Shaziling and Yorkshire were credible.(4) According to the sequence from RNA-seq data, we cloned the full coding region of NR1H4 and JAZF1 genes from porcine Longissimus dorsi by rapid amplification of cDNA end (RACE), and have completed bioinformatic analysis. The study of NR1H4 and JAZF1 mRNA expression patterns from longissimus dorsi muscle, liver, lung, kidney, spleen, crureus, intestine, cecum, pancreas and cardiac muscle of Yorkshire pigs and Shaziling pigs had been performed by qRT-PCR; One single nucleotide polymorphism (SNP) was detected by PCR-RFLP in 3’untranslated region of NR1H4.