Molecular Markers And Candidate Genes Discovery For Reproductive Traits In Large White Pigs Based On Genome-wide SNP Data

Reproductive trait is one of the most important economic traits in pig production.However,the progress of genetic improvement of sow reproductive traits by traditional breeding methods was extremely limited,due to the low heritability of the traits and their susceptibility to environmental factors.It is helpful for accelerating the application of molecular breeding techniques and the genetic improvement of sow reproductive performance to reveal the molecular genetic basis of reproductive traits,and identify molecular markers and functional genes closely related to reproductive traits.The genetic parameters of 4 reproductive traits,total number born(TNB),number born alive(NBA),litter weight at birth(LWB),and litter weight at 21 d(LW21D)were estimated,using a multitrait repeatability model,based on the reproductive performance data of 1969 litters of 518 Large White sows.Selection signature analysis and genome-wide association analysis(GWAS)were conducted to identify molecular markers and candidate genes related to reproductive traits.The main results were as follows:(1)Genetic parameter estimation for reproductive traits.A multi-trait repeatability model in DMU software was utilized to estimate the genetic parameters of reproductive traits.The estimated heritabilities of TNB,NBA,LWB,and LW21 D in Large White sows were 0.034,0.042,0.049,and 0.016,respectively.The stronger positive genetic correlations among the four traits were shown,which ranged from 0.559 to 0.971.(2)Detection of selection signature for high-prolificacy traits in sows.Using the whole-genome SNP data,selection signature analysis was conducted on two groups of Large White sows,each group had 15 individuals with extremely high or low estimated breeding values(EBV)for TNB.Eight genes,NKAIN2,IGF1 R,KISS1R,TYRO3,SPINT1,PTBP1,ADGRF5,and APC2 were identified as selected genes,and it was inferred that they are the candidate genes associated with reproductive traits in sows.(3)Discovery of molecular markers and candidate genes for reproductive traits in sows based on GWAS.A total of 34 SNP markers and 15 candidate genes significantly associated with reproductive traits were identified by GWAS,based on the data of genomewide SNP and 1969 litters reproductive performance records.Among them,5 genes,NKAIN2,ZFYVE9,CLCN3,HPF1 and CLIC1 were associated with TNB;4 genes,SPATA33,GABRA2,GABRA4 and EPC2 were associated with NBA and LWB;and 6 genes,PERP,GABRG2,GABRA1,NCOA7,RSPO3 and HEY2 were associated with LW21 D.The results further enriched the study of the genetic basis of sow reproductive traits,which was important for further analysis of the genetic basis of sow reproductive traits,accelerating the application of molecular breeding technology and genetic improvement of reproductive traits.