Research On Genetic Variations And Its Associations With Porcine Reproductive And Respiratory Syndrome Resistance

Porcine Reproductive and Respiratory Syndrome(PRRS)caused by Porcine Reproductive and Respiratory Syndrome Virus(PRRSV)is responsible for reproductive failure in pregnant sows and respiratory problems in every age pigs(especially in piglets).And it has caused significant economic losses in pig industry.Vaccination has generally not been effective in prevention of PRRS because of the rapid mutation rate,antibody-dependent enhancement,immunity to delay,immunosuppression and other characteristics of the virus.It has been proved that it is one of the effective measures to improve porcine resistance to diseases using molecular marker assisted selection for genetic improvement in pigs.With RNA-seq technology,we can call Single Nucleotide Polymorphisms(SNPs)from genome and gain insight into the characteristics of genetic variations and its distributing regions in resistant breed(such as Tongcheng pigs),providing references for research on PRRS-resistance mechanisms in future.With associations of PRRS resistance and variations in differentially expressed genes detected in PRRSV infection experiments,we can detect candidate molecular markers to improve host resistance to PRRS,providing references for genetic improvement.RNA sequencing and analyzes on Tongcheng pigs and Landrace infected with PRRSV were performed by our experimental group collaborated with China Agricultural University.On the present study,the raw data obtained from the RNA-seq experiments was filtered and aligned to genome.The SNPs were called,and the distribution characteristics of the breed-specific SNPs on chromosomes,immune capacity quantitative Trait Loci(QTLs)and PRRS associated QTLs were analyzed.And the results are as follws:(1)The distribution of breed-specific SNPs counts on chromosomes differs significantly in the two breeds.Tongcheng-specific SNPs counts are about 15% of total number of SNPs on chromosomes while Landrace-specific SNPs counts are about 5% of total number of SNPs on chromosomes.(2)1438 chromosomal units with great difference in breed-specific SNPs distributed on chromosomes were detected between the two breeds.Dividing all chromosomes with 1 Mb as a unit,and summarizing the breed-specific SNPs counts within all 1 Mb units,we detected 1438 chromosomal units with great difference in breed-specific SNPs distribution.(3)The breed-specific SNPs were distributed on important QTL.Analyses on the distribution of 1438 chromosomal units in immune capacity QTLs and PRRS associated QTLs,we screened 151 chromosomal units distributed on 217 immune capacity QTLs and 23 PRRS associated QTLs.(4)There are important functions in the 151 chromosomal units.We detected 1287 genes within the 151 chromosomal units by gene enrichment.And GO analysis further performed on the 1287 genes revealed that the major biological processes enrichment of genes are Negative regulation of apoptotic process,Intracellular signal transduction,Positive regulation of transcription from RNA polymerase II promoter and Negative regulation of transcription from RNA polymerase II promoter,suggesting Tongcheng pigs anti PRRSV proliferation is likely to achieve by the process of apoptotic,virus entry,transcription by miRNAs,etc.In addition,BID?BTG2?MX1?IFIT1 were selected from significant differentially expressed genes detected in RNA-seq experiments.SNPs on the four genes were detected and then associations between gene polymorphisms and PRRS resistance or farrowing performance of PRRSV-infection sows were analyzed.The main results are as follows:(1)The 3'UTR variant rs344115266 on pig gene BTG2 is significantly associated with farrowing performance in sow population with PRRSV infection.Genotype AA is the superior genotype of farrowing performance to sows with PRRSV infection.(2)Synonymous variant rs339602414 on pig gene MX1 is significantly associated with PRRS resistance.Genotype AA is the resistant genotype to PRRS in sow population.(3)On pig gene IFIT1,there are 5 SNPs(rs338627247,rs320936507,rs340275986,rs330605358,rs341499787)are significantly associated with PRRS resistance and farrowing performance in sow population with PRRSV infection.Genotype CC of synonymous variant rs338627247,genotype CC of missense variant rs320936507 and genotype GG of missense variant rs340275986 are resistant genotypes to PRRS in commercial pig population.Genotype TT of missense variant rs330605358,genotype CC of missense variant rs341499787 and genotype AA of missense variant rs340275986 are resistant genotypes to PRRS in sow population;and these genotypes are the superior genotypes of farrowing performance to sows with PRRSV infection.(4)The haplotype combinations formed by SNPs on gene IFIT1 are significantly associated with PRRS resistance and farrowing performance in sow population with PRRSV infection.Haplotype combination H2H3 formed by missense variant rs320936507,missense variant rs340275986 and synonymous variant rs321919981 is resistant haplotype combination to PRRS in commercial pig population;and haplotype combination H1H2 is the superior haplotype combination to sows with PRRSV infection.Haplotype combination H1H1 formed by missense variant rs330605358 and missense variant rs341499787 is resistant haplotype combination PRRS in sow population;and haplotype combination H1H1 is the superior haplotype combination to sows with PRRSV infection.