Abstract: This study aimed to discover the functional genes potentially associated with mare early abortion. Ten mares that had the presence of embryo at 45^th day after mating but miscarried two to four months after mating and ten mares that normally delivered were selected from the same confined rearing horse herd. Blood samples from the selected mares were collected, and the genomic DNA was extracted. The average sequencing depth of the whole genome was 10×, the genome coverage was over 97%, and about 4×10⁶ SNPs were obtained from each sample. The whole genome resequencing data between the mares in miscarriage group and normal delivery group were compared. The results showed that Fst analysis obtained 1 381 SNPs, π analysis obtained 1 614 SNPs, and the combinative analysis of Fst and π obtained 203 SNPs; by filtering out the intergenic regions of mutagenesis, non-coding regions, introns and synonymous SNVs, a total of 82 SNPs locating on 69 genes were found; through GO term, signal pathway enrichment analysis and literature review, 12 genes were considered as important candidate genes involved in early abortion and embryo implantation in mares; the screened candidate genes affected the embryo implantation by ways such as participating in hormone regulation, embryo invasion, vitamin anabolism. The results of this study provide reference data in bioinformatics for unraveling the molecular mechanism underlying the causes of early abortion in mares.

Key words: mares, early abortion, embryo implantation, whole genome resequencing, hormone regulation, vitamin anabolism