Genome Wide Association Studies For Reproductive Traits And CNV Detection In Pigs

In the pig industry,reproductive traits are important economic traits,and the level of reproductive ability is an important factor influencing farm production capacity and economic efficiency.Combing the identified genetic variants or functional genes that affect target traits,and implementing molecular breeding can increase the efficiency and accuracy of selection.In this study,we performed the genetic parameter estimation,genome wide association study(GWAS)for reproductive traits in a Large White pig population,and conducted the detection of copy number variation(CNV).We also identified the candidate genes for pig reproductive traits.Section I:Genetic parameters estimation for pig reproductive traitsWe collected 19036 reproductive records of Large White pigs from 2 nucleus pig breeding farm of Beijing Shunxin Agriculture Co.,Ltd.Animal model and restricted maximum likelihood method was used to estimate the genetic parameters by ASReml software for 7 reproductive traits,including total number born(TNB),number born alive(NBA),litter birth weight(LBW),average birth weight(ABW),gestation length(GL),age at first service(AFS)and age at first farrowing(AFF).The results showed that the heritability of 7 traits were 0.104,0.091,0.095,0.12,0.26,0.25 and 0.26,respectively.Among them,between TNB,NBA and LBW,between AFS and AFF,and the same traits at different parities showed higher genetic correlation,and the correlation coefficient was between 0.32 and 0.99.Section 2:Genome-wide association study for pig reproductive traitsFirstly,using the Geneseek PorcineSNP80 BeadChip,1207 Large White pigs form Beijing Shunxin Agriculture Co.,Ltd and Beijing Liuma Co.,Ltd were genotyped.After quality control,1198 samples and 51443 SNPs were retained.GEMMA software was used to perform a GWAS for 7 reproductive traits,including TNB,NBA,LBW,ABW,GL,AFS and AFF.Except for LBW,we detected 12 genome-wide significant(P<4.42E-6)and 41 suggestive significant SNPs(P<8.84E-5)associated with 6 reproductive traits,and the proportion of phenotypic variance explained by all significant SNPs for each trait ranged from 4.46%(NBA)to 11.49%(GL).Compared with Pig QTL database,29 significant SNPs were located within known QTL regions for swine reproductive traits.Combing the gene annotation containing or near the 53 significant SNPs,14 genes—BHLHA15,OCM2,IL1B2,GCK,SMAD2,HABP2,PAQR5,GRBIO,PRELID2,DMKN,GPI,GPIHBP1,ADCY2 and ACVR2B were considered important candidates for swine reproductive traits based on their critical roles in embryonic development,energy metabolism and growth development.Secondly,using a repeatability model,we performed a GWAS in ASReml software underlying the phenotypic records at different parities for piglet uniformity(PU)and farrowing interval(FI)in a population of 884 Large White pigs from Beijing Shunxin Agriculture Co.,Ltd.After quality control of genotyping data,880 samples and 51727 SNPs were retained.For PU and FI,5 significant SNPs(P<1.01E-4)and 7 significant SNPs(P<1.05E-4)were detected,respectively,which collectively explained 1～1.79%of the phenotypic variance for PU,and 2.58～4.11%for FI at different stages.Of these,seven SNPs were located within 20 QTL regions related to swine reproductive traits,including birth body weight,teat number,corpus luteum number,etc.Finally,7 functional genes—SMAD7,LIPG,ACAA2,UBTFL1,GPAM,ADAR2A,EMP2—for PU and FI were identified near the significant SNPs because of their roles in prenatal skeletal muscle development,pre-implantation,and the expression of mammary gland epithelium.Section 3:Genome-wide detection and analysis of copy number variation of the pig genomeUsing PennCNV software,we performed a genome-wide CNV detection based on SNP genotyping data of 857 Large White pigs.A total of 312 CNV regions(CNVR)were detected,including 155(49.68%)novel CNVR,and 8 of selected CNVR were validated by qPCR.The length of these CNVR covered 57.76 Mb of the pig genome and correspond to 2.36%of the genome sequence.The length of the CNVR on autosomes ranged from 1.77 Kb to 1.76 Mb with an average of 185.11 Kb.Based on swine genome assembly,220 out of these CNVR completely or partially overlap with 1092 annotated genes,which enriched a great variety of biological processes,such as multicellular organism development,embryonic skeletal system morphogenesis,and signal transduction.Furthermore,our results demonstrated that CNVR61 and CNVR283 significantly associated with litter size at different status(P<0.05).Our findings provide valuable knowledge on further identification of functional genes for repeoductive traits,and increasing the accuracy of genomic selection breeding in pigs.