Transcriptomic Analysis Of Longissimus Dorsi Muscle On Duroc Pig And Huai Pig

With the improvement of people’s quality of life, people’s demand for pork quality is becoming more and more strict. It is essential to cultivate pig breeds with high quality meat. Huai pig is well-known domestic fat swine breed with good meat and good taste, but its growth is slow. Duroc pigs is foreign typical lean swine breed with fast growth, but i meat is not good as Huai pig. In this study, longissimus muscle transcriptomes of Duroc pig and Huai pig were sequenced, and bioinformatics analysis was used to screened differentially expressed genes between the two breeds, and the functional annotation and pathway enrichment of these genes also be analyzed. The purpose of this study is to reveal genetic differences between domestic and foreign breeds at the transcriptome level, and provide scientific basis for further study the molecular mechanisms of fat deposition of longissimus muscle, and provide a theoretical basis for breeding swine breeds with high quality meat. The results are as follows:(1) The cDNA sequencing libraries of the longissimus muscles of two swine breeds were constructed, and sequencing of which were completed.45775612 and 46337424 raw reads were obtained in the longissimus muscles of Duroc pig and Huai pig via sequencing, respectively, and 34496450 and 36177844 clean reads were obtained after quality control, respectively. The GC contents of two swine breeds were about 49%. The Q30 of two swine breeds were above 94%. The mapped ratio of clean reads and reference genome of two swine breeds were above 78%.(2) 44582 and 103583 SNPs were obtained in the longissimus muscles of Duroc pig and Huai pig, respectively, and ratio of transition above 74%.8216 and 8608 alternative splicing events were obtained in two swine breeds, and there were 4151 and 4305 exon skipping evens.(3) 16012 and 15839 expressed genes were obtained in Duroc pig and Huai pig with selected standard that was FPKM>0.1, of which 14943 genes were expressed in both swine breeds.937 differentially expressed genes were obtained when compared gene expression between two muscle tissues with selected standard that were FDR <0.01 and absolute log2FC>1. Compared to Duroc pig, there were 582 up-regulated genes and 355 down-regulated genes in Huai pig.(4) The differentially expressed genes were annotated via NR, Swiss-Prot, GO, COG and KEGG databases, the annotation ratio were 94.12%.82.58%.84.47%, 48.58% and 31.58%, respectively. The differentially expressed genes were classify into 48 GO terms, of which 13 terms were in cellular component,12 terms in molecular function and 23 terms in biological process via GO function analysis, of which 747, 705 and 743 differentially expressed genes were categorized, respectively.315 differentially expressed genes were enriched into 185 KEGG pathways, PPAR signaling pathway and Adipocytokine signaling pathway were found, which relate to the regulation of lipid metabolism.6 pathways were significantly enriched pathways.(5) 8 differentially expressed genes were selected to validate RNA-seq data by qPCR method, the qPCR results of gene expression were consistent with RNA-seq, which revealed a strong correlation between the qPCR and RNA-seq data.