Constuction Of Copy Number Varations Draft And Genome-wide Association Studies For Body Measurement Traits In Swine

Pig is not only an important economic animal, but also an expected study model of diseaseresearch. Some of the important qualitive and quantitive traits such as reproduction, meat quality,performance or anti-disease of pig have sepecial attraction to researchers. Follow the development ofbioinformatics, the detection method of molecular markers has run to the third generation. Thedevelopment of molecular techonology could provide ideal tools to study the traits of swine that ishelpful for molecular breeding. In our paper, in order to provide some useful bases for pig molecularassisted breeding though the research of pig genome wide structure variation and mutation, we havecarried out genome-wide copy number variation inferring and genome-wide associated study using anIllumina Porcine SNP60K DNA chip and a Large White×Minzhu pig recource family.Part1Detection of copy number variations (CNVs) in swineFour different programs (GADA, PennCNV, QuantiSNP and CnvPartition) were employed toanalyze Porcine SNP60genotyping data of585pigs from one Large White×Minzhu intercrosspopulation to detect copy number variants regions (CNVRs). Overlapped CNVRs recalled by at leasttwo programs were used to construct a powerful and comprehensive CNVR map which contains249CNVRs (Gain70, Loss43, Gain-loss136) and covers26.22%regions of swine genome. Ten CNVRsrepresenting different predicted status were selected for validation via quantitative real time PCR(QPCR), nine out of these ten CNVRs (90%) were validated. When being traced back to the F0generation,58events were identified only in Minzhu F0parents and2events were identified only inLarge White F0parents. Series of CNVRs function analysis were carried out, some of the CNVRsfunctions were predicted and four interesting CNVRs for meat quality traits and hematologicalparameters were obtained.Part2Genome-wide association studies for body measurement traits585pigs of F2generation from a Large White×Minzhu intercross resource population were usedas the experimental animals. The Illumina PorcineSNP60BeadChip, Genome-wide Rapid Associationusing the Mixed Model and Regression-Genomic Control(GRAMMAR-GC) method, DMU softwareand GenABEL software package under the R statistical environment were used to carry out the GWASanalysis on pigWaist width (WD),Chest depth(CD), Chest width (CW), Rump Cirumference(RC),Rump width(RW), Body height(BH), Scapula width(SW), Cannon bone circumference(CBC)andAbdominal circumference(AC)in order to search for the genetic variation related to pig bodymeasurement traits.The results indicatied that, A total of331SNPs on chromosome7and1were foundto be associated with4traits(CD、RC、BH and CBC) at a genome-wide significance level (corrected forthe number of SNPs on whole genome). The SNPs numbers were2、45、129and155respectively.However, no significant SNPs were found for5traits.Significant SNPs which probe sequence weredetermined the physical location according to the pig genome draft from the Ensembl database. Wescreened candidate genes based on SNP location and gene function within the section, and predictedtheir function by means of bioinformatics analysis.