Identification Of Different Expressed Genes And Pathway Analysis Of Fast And Slow Skeletal Muscles Between Two Pig Breeds

Pork is one of the main kind of meat food in China and the pig industry occupies a pivotal position in China Agriculture.And meat quality is complicatedly influenced by muscle fibers characters, particularly the myofibre type. Chinese indigenous pigand foreign commercial pig breeds display different production traits according to the difference of genetic background and breeding method. For instance, Luchuan pig, a typical Chinese indigenous pig, shows better meat quality and poorer production performance when compared with the Yorkshire pig. To analyze the difference between breeds/muscle with special character, using next generation sequencing can be efficient and effective. Different expressed genes and pathways which resulted in those trait difference might be identified from comparison of the transcriptomes. In this study, we detected the difference of phenotype and transcriptome between myofibre types(slow-twitch and fast-twitch type) and breeds, analysed the reason of those difference.Those result laid the basis for the subsequent functional researches and the breeding practice.The results from the study were as follows:1. The muscle fiber characters of Luchuan pig and Yorkshire pig’s muscle soleus(SOL), extensor digitorum longus(EDL), biceps femoris(BF), longissimus(LM) was detected using paraffin sections technology, HE staining and immunohistochemical technique. The result indicates that the muscle fiber diameter is smaller in Luchuan pig than that in Yorkshire pig in the tested muscles. The percentage of slow-twitch fiber of SOL and LM in Luchuan pig is lower than that in Yorkshire pig, but the percentage of slow-twitch fiber of EDL and LM in Luchuan pig is higher than that in Yorkshire pig. The percentage of slow-twitch fiber of muscles detected in Luchuan pig: BF > SOL > EDL > LM. The percentage of slow-twitch fiber of muscles detected in Yorkshire pig: SOL > LM > BF > EDL.2. We built the c NDA libraries of SOL and EDL of both breeds successfully. RNA-seq was applied to sample transcripts of the muscles between the two pig breeds to gain insights into whole-genome transcription profiles in this study. After quality control, we analyzed the gene expression levels. The reslut indicates that the overall gene expression levels of all groups are similar. In all libraries, over 24,500 genes aredetectedexpressed and 16,404 genes expressed in all samples. There are 825 genes specifically expressed in Luchuan pig and 366 genes in Yorkshire pig while the number of genes expressed in both breeds is 17,248. Alternative splicing(AS) events at transcription start site and transcription terminal site aremost common among all AS events with an over 80% percentage occupation.3. We detected the different expressed genes(DEGs) in all comparison groups and finally identified 754 known DEGs. Among those DEGs, 229 ares identified in the breeds comparison groups, 14 are identified in the muscles comparison groups, 17 areidentified in three comparison groups.4. The result of GO enrichment analysis with the DEGs shows that the DEGs significantly enrich in the biological process GO terms about muscle development(muscle organ development,skeletal system development,skeletal muscle tissue development), energy metabolism(gluconeogenesis,lipid storage,monosaccharide metabolic process)and ion transport(metal ion transport,organic anion transport). The biological process GO terms, hexose metabolic process,glucose metabolic proces,monosaccharide metabolic process,rhythmic process,are enriched in comparison between two breeds.5. The result of KEGG pathway enrichment analysis with the DEGs shows that the Glycolysis/Gluconeogenesis, TCA cycle, and the pathway associated with fatty acid metabolism(Fatty acid degradation, Glycerolipid metabolism) were enriched significantly. There are 15 pathway, including the milti-fuction MAPK signaling pathway and PI3K-Akt signaling pathway, was enriched in all four comparison groups.