Abstract：The Zygote arrest 1(ZAR1) gene （gi:83727928） was employed to investigate variation character and associate with reproductive traits in five pig purebreds (Small Meishan, Qingping, Duroc, Landrace and Large White). We identified six new SNPs in the second and third exons, addition with one 5 bp deletion/insertion mutation in the third intron in the ZAR1 gene by using PCR-SSCP and DNA sequencing technique. Exon3-BstU I (C54/T54) located in the 54th of exon3 and Intron3-TspR I (5 bp deletion/insertion mutation) in intron3 were genotyped and associated with reproductive traits in these five pig breeds. Association results showed that Exon3-BstU I polymorphism had a significant effective （P<0.05）with total number born in first litter TNB1)and total number born in second litter(TNB2). Total number born (NBA) with CC genotype had more piglets than that of other genotypes in the Exon3-BstU I in the Duroc. Intron3-TspR I polymorphism had a significant effective （P<0.05）with total number born in first litter (TNB1)and total number born in later litters(TNB2) in the Duroc.
