Genome-wide Association Study For Two Reproductive Traits In Jinhua Pigs

The objective of this study was to identify candidate genes related to total number born(TNB)and number born alive(NBA)in Jinhua pigs by genome-wide association analysis(GWAS).205 Jinhua pigs were used as experimental materials,and the genotype data were obtained by Illumina 50K SNP BeadChip after genomic DNA extracted from blood samples.Quality control was carried out using PLINK v1.09.The mixed linear model(MLM)and FarmPCU model were used to analyze the association between each SNP and traits to locate significant or suggestive SNPs.Meanwhile,the performance of the two models was compared according to GWAS result.Bioinformatics analysis,including gene ontology analysis,pathway analysis and network analysis,was used to identify the candidate genes.The result showed that the more significant or suggestive SNPs were detected by FarmPCU model,which overlapped the most SNPs detected by MLM and performed a higher detection power than MLM.There were 35 and 18 SNPs associated with TNB and NBA,respectively and 16 SNPs associated with both traits.Finally,26 candidate genes were identified and the function of the genes mainly involved cell development,tissue homeostasis,cell proliferation,protein phosphorylation,mRNA metabolic process,brain development and phosphorylation,etc.some genes among them were confirmed association with reproduction.In summary,According to the gene functional annotation,NANOS1,AEBP2,CAPZA3,KRAS,NDP and HOOK1 genes were preliminary identified as the candidate genes for TNB and NBA.