Screening And Identification Of Genes Related With The Litter Size Of Xiang Pig Based On SNP Chip

Pigs are economically important livestock animals that supply animal protein for human food.The pig also constitutes a reliable animal model for clinical studies of certain human diseases.Reproductive trait is one of the most important economic traits in pigs,and litter size trait is a key factor in measuring its reproductive ability.In current pig breeding,improve litter size has been an important part of the breeding goal for pig breeding.Litter size trait is a quantitative trait which was controlled by several major genes and many minor genes.Two major genes,ESR and FSH-? affected pigs reproductive traits,had been found and located.However,many minor genes have not been found yet.Xiang pigs are raised in the moon mountainous area of Guizhou Province with lower litter size(6.7 on average).But the variation of litter size is larger,range from 3 to 21 piglets,and we do not know about its variation mechanism.With the rapid development of high density chip and bioinformatics,it provided ideal tools to study the reproductive traits and molecular breeding of pigs.For the sake of finding important candidate genes affecting reproductive traits of pigs,a Illumina Porcine SNP60 K chip was used for genome wide association studies and copy number variation detection to resolve the genetic mechanism of litter size variation.Part?Genome-wide association studies with litter size traits of Xiang pigsA Illumina Porcine SNP60 K chip was generated for GWAS to find SNPs and candidate genes significant associated with litter size traits of Xiang pigs.After the quality control procedure,The SNP effects were calculated using a linear mixed model implemented using Plink.The significant threshold was 1.77E-06 and the suggestive significant threshold was 3.55E-05.In total,32 SNPs(including 25 genome-wide and 7 suggestive SNPs)were identified associated with litter size traits.All significantly associated SNPs were validated via AS-PCR.Overall,70 Ensembl genes were retrieved around 100 kb of the associated SNPs,GO analysis showed these genes were enriched with 16 statistically significant GO terms.The relevant GO terms were mainly associated with response to virus,sensory perception of smell,defense response,cytokine activity,interferon-alpha/beta receptor binding and extracellular space.Candidate genes ZEB1,PDIA4,MARCKS,HDAC2,CDC42,FSH-? and PRSS21 may have effect on reproduction.Part ? Detection of copy number variations in Xiang pigsThe objectives of this study were to comprehensively interrogate and characterize CNVs in Xiang pig to identify the relationships between CNVRs and quantitative traits,to assess the genetic diversity between or within populations.PennCNV was conducted to detect CNVs on the genome.One hundred seventy-two CNVRs were identified on autosomes and the X chromosome;these elements covered 80.41 Mb of the pig genome and corresponded to 2.98% of the pig genome sequence,97 CNVRs were called as gain events,65 were called as loss events,and the remaining 10 CNVRs were called as gain-loss events.Ninety-seven CNVRs either overlapped with or were identical to previous studies,and the remaining 75 CNVRs were likely novel.GO,KEGG and QTL analysis demonstrated that the CNV-associated genes retrieved in the CNV-associated genes(ADAMTS-1,AR,KIT,MED 12,PN-1 and SOD1)might play an important role in reproductive traits.Besides,candidate gene ADAMTS-1 was cloned contained 8 introns and 9 exons.Pvu II can restrict the SNP(5996)within the 7th exon,the dominant genotype in Xiang pig is BB while AA and AB dominant in western pig breeds.Moreover,the copy number of ADAMTS-1 was variation between large and small litter size Xiang population.Most of the large litter size population harbored three of more than three copies while two copy in the small population.In summary,significant SNPs and candidate genes found in this study may offer valuable information for revealing the regulation mechanism of reproductive capacity of Xiang pig.The CNV map of Xiang pig is helpful for investigating the associated between phenotypes and CNV.The copy number of ADAMTS-1 and its polymorphism in position 5996 may be one of the important factor to affect reproductive capacity of Xiang pig.