Screening And Analysis Of Differentially Expressed Genes About Subcutaneous Fat Between Duroc Pig And Huai Pig

Huai pigs and Duroc pigs are lean-type and fat-type pigs respectively,two breeds in great contrast on fat deposition traits,what’s more,traits are regulated by polygenic minor interaction on the basis of molecular mechanism.To explore key genes affecting fat deposition and lipid metabolism mechanisms has a positive role in accelerating high-quality pigs for new lines,as well as accelerating the development of lines’ industrialization.Swines’ subcutaneous adipose tissue of 190 day old Duroc and Shanghang Huai were researched by the technology of high-throughput sequencing RNA-seq,for the purpose of screening of differentially expressed genes of which affecting fat deposition and exploring the mechanism of the corresponding metabolic pathways.In this experiment,the alternative splicing locust numbers of Duroc pigs and Huai pigs were 9,457 and 9,612 respectively,showing a rich diversity of biological characters.6 kinds of variable alternative splicing were found,from which the highest frequency is the spliced exon skipping.The total SNP numbers of Duroc pigs and Huai pigs were 67,246 and 150,864,What’s more,their main form of the variation was conversion,which accounted for 74.97%and 74.20%respectively,showed a higher proportion of heterozygosity.The total SNP numbers of Huai pig,the total numbers of SNP in gene region,as well as the total numbers SNP in intergenic region of Huai pigs were more than twice as Duroc’s.The total numbers of SNP in gene region were twice more than those in intergenic region for both pigs.The above results indicating that Shanghang Huai pig has more plentiful genetic variation of single nucleotide than Duroc pig.The numbers of quantitative estimates gene expression levels for this two breeds are 23,290,of which FPKM>0.1 genes of Duroc pig and Huai pig found 16369 and 16846 respectively.Two breeds back fat tissue found 2389 new genes,Duroc and Huai pig FPKM>0.1 respectively genes 2129 and 2180.There are two breeds screened 709 differentially expressed genes.Compared with Duroc,395 up-regulated genes were found in Huai,314 genes were down-regulated.The total number of differential expressed annotated genes were 693,including 642 in GO database and 402 in KEGG database.Through GO analysis,603 differential expressed genes were annotated in the cellular compount group,of which the cluster numbers were 15.Where the 15 clusters had more than 30 genes were enriched.What’s more,4 clusters whose value of p is less than 0.05,ther were"extracellular matrix"、"endoplasmic reticulum membrane"、"extracellular region" and"intercellular space";570 differential expressed genes were annotated in the molecular functional classes,of which the cluster numbers were 7.Where the 7 clusters had more than 30 genes were enriched.What’s more,2 clusters whose value of p is less than 0.05,"calcium-binding" and the other is the "receptor binding"609 differential expressed genes were annotated in the biological process group,of which the cluster numbers were 15.Where the 15 clusters had more than 30 genes were enriched.What’s more,only one cluster whose value of p is less than 0.05,that was "the mechanism of redox reaction".191 metabolitics pathways were found in the KEGG database,of which the total number of differentially expressed genes were 314.By hypergeometric test,48 pathwasy were accorded with not only the value of p is less than 0.05,but also more than 10 differentially expressed genes were annotated.There were 27 metabolic pathways from which differential annotated 48 pathways.These 27 pathways of which had relationship with fat deposition,what’s more the value of Q is less than 0.05 was insulin signaling pathway,alone.12 differentially expressed genes were annotated in insulin signaling pathway,these genes were 8 up-regulated genes were:phosphoenolpyruvate carboxykinase(PEPCK or PCK1),muscle glycogen phosphorylase gene(PYGM)hexokinase,glucokinase gene 3(HK3)gene(GCK),phosphatidyl inositol-3-kinase 5(PIK3R5)gene receptor,insulin receptor 1(IRS])gene,stromal sarcoma viral oncogene homolog(KRas)gene and suppressor of cytokine signaling 3(SOCs3)gene;4 down regulated genes were:Pig_newGene 23681,hexokinase 1(HKDC1)gene,fructose-1,6-phosphate inositol phosphatase 2(FBP2)gene and camp protein kinase(PKA)gene.In summary,the research revealed the molecular basis of fat deposition in the two breeds.For accelerated high-quality pigs for new lines and supporting breeding and industrialization provided.