Analysid Of Allele Specific Expression Of Target Cells And Peripheral Immune Organs Before And After PRRSV Infection In Tongcheng And Large White Pigs

Porcine reproductive and respiratory syndrome(PRRS)is an immunosuppressive infectious disease caused by porcine reproductive and respiratory syndrome virus(PRRSV).In our group previous study found that Tong Cheng(TC)pigs had stronger resistance to PRRSV than Large White(LW)pigs in PRRSV infection,furthermore,genome and transcriptome sequencing of alveolar macrophages,spleen,inguinal lymph nodes and testis of infected and control the two breeds were carried out.It was found that a lot of different genes were found in both infection and control of the same breed and different tissues of the two breeds.Many studies have found that allele specific expression(ASE)is closely related to many diseases,but the role of ASE in PRRSV infection is still unknown.Based on the transcriptome and genomic data of three different tissues(testis,inguinal lymph nodes and spleen)of TC pigs and LW pigs in infection and control,allele specific expression(ASE)analysis was carried out to screen the allele specific expression genes in PRRSV infection and study their role in antiviral infection.The main contents and results are as follows:(1)ASE is analysed in both infection and control of the same breed and different tissues of the two breeds : in this study,transcriptome data of groin lymph nodes,spleen tissues and alveolar macrophages of 6 Tongcheng pigs and 6 large white pigs(3 pigs in each infection group and control group)and genomic data of corresponding individuals were used for allele specific expression appraisal.In inguinal lymph nodes,spleen and alveolar macrophages,there are 188 ASE genes per individual in each tissue.At present,the number of annotated genes in Sus scrofa 11.1 are 24651,and ASE in each individual accounts for about 4.6%.1443,1478 and 1242 genes arise ASE in inguinal lymph nodes,spleen and alveolar macrophages of TC pigs,and 999,914 and 689 genes arise ASE in inguinal lymph nodes,spleen and alveolar macrophages of TC pigs.The results showe that ASE increased in all three tissues and cells of TC pig,but ASE increases only in alveolar macrophages of LW pigs and decreases in inguinal lymph node and spleen of LW pigs.In the study of ASE level,it is found that ASE levels in different tissues and varieties showed different trends after PRRSV infection.(2)Analysis of ASE in alveolar macrophages: 443 and 383 specific ASE genes are found in infection and control of TC pigs,the specific ASE genes in infection of TC pigs are mainly enrichment in apoptosis and cell division related pathways.The specific ASE genes in control of TC pigs are mainly enrichment in the protein biosynthesis and basic cell metabolis.250 and 225 genes arise ASE in infection and control of LW pigs,the specific ASE genes in infection of LW pigs are mainly enrichment in protein targeting.The specific ASE genes in control of TC pigs are mainly enrichment in signal transduction.The analysis of ASE in TC pigs and LW pigs is found that ASE of TC pigs are mainly enrichment in immunity and hemoglobin metabolism,specific ASE genes of LW pigs are mainly enrichment in basic cell metabolis.These results explained that TC pigs had stronger disease resistance than LW pigs to some extent.(3)Analysis of ASE in inguinal lymph nodes: there are 698 and 390 specific ASE genes in infection and control of TC pigs,the specific ASE genes in infection of TC pigs are mainly enrichment in cell repair.The specific ASE genes in control of TC pigs are mainly enrichment in basic cell metabolis.There are 358 and 387 specific ASE genes in infection and control of LW pigs,the specific ASE genes in infection of LW pigs are mainly enrichment in fat and protein metabolism.The specific ASE genes in control of TC pigs are mainly enrichment in apoptosis and cell differentiation.The analysis of ASE in TC pigs and LW pigs is found that ASE of TC pigs are mainly enrichment in immunity and leukocyte migration,specific ASE genes of LW pigs are mainly enrichment in cell differentiation.(4)Analysis of ASE in testis: there are 645 and 469 specific ASE genes in infection and control of TC pigs,the specific ASE genes in infection of TC pigs are mainly enrichment in body regulation.The specific ASE genes in control of TC pigs are mainly enrichment in negative regulation of interleukin-12 production.There are 698 and 390 specific ASE genes in infection and control of LW pigs,the specific ASE genes in infection of LW pigs are mainly enrichment in growth and development.The specific ASE genes in control of TC pigs are mainly enrichment in signal transduction.The analysis of ASE in TC pigs and LW pigs is found that ASE genes of TC pigs are mainly enrichment in cell adhesion and immunity,specific ASE genes of LW pigs are mainly enrichment in development.(5)ASE is analysed in TC pigs and LW pigs: there are 13 ASE genes in alveolar macrophage,inguinal lymph node and spleen in control of TC pigs,there are 8 ASE genes in alveolar macrophage,inguinal lymph node and spleen in control of TC pigs.In the analysis of tissue specific ASE gene,ASE genes of inguinal lymph nodes are mainly enrichment in tissue biological function of extracellular matrix.In testis of extracellular matrix ASE genes are mainly related to immunity.ASE genes of alveolar macrophages are mainly related to antigen processing,presentation,secretion and immune regulation.This indicates that ASE has obvious tissue specificity.(6)Based on the above analysis,candidate genes related to immunity were screened,and there were multiple non-synonymous mutation sites on the domains of PDGFRB,VWF,CASP9 and BRCA1 genes.Allele specific expression of these genes may affect the function of genes.