Abstract: The purpose of this study was to analyze the genomic SNP characteristics of sika deer, red deer and their hybrid progenies (F1, F2) based on GBS(genotyping by sequencing) technology. In this experiment, the genomic DNA from 226 blood samples was sequenced by GBS. All samples were consisted of 63 sika deer, 12 red deer, 112 F1 generation individuals, 38 F2 generation individuals and 1 unknown individual. Furthermore, the previous sequencing data contained 110 sika deer, 197 red deer and 1 F1 generation individual. All the sequencing data was mapped to the reference genome of the sika deer which assembled at the chromosomal level. The sequence results produced 322.683 Gb Clean data for 226 individuals, averaging of 1 427.802 Mb for per sample. All samples were used as a population to detect SNP variation, and a total of 23 943 582 SNP loci were identified, while 31 630 SNP loci were remained after screening and filtering. A phylogenetic tree was constructed with 31 630 SNP loci by the maximum likelihood(ML) method, sika deer, red deer, F1, and F2 individuals were significantly distinguished in the phylogenetic. The SNPs of sika deer and red deer were compared and analyzed, and 1 032 specific SNPs were screened out for identifying red deer, sika deer, F1 and F2 generation (474 specific SNP loci for red deer, 558 specific SNP loci for sika deer). The calculation results showed that the proportion of F1 generation individuals containing red deer specific SNPs was mainly between 40% to 60%, and the proportion of F2 generation individuals containing red deer specific SNPs was mainly between 10% to 30%. The red deer did not contain the specific SNPs for sika deer; 55.49% of the individuals in the sika deer did not contain the specific SNPs for red deer,17.34% of the individuals contained less than 1% specific SNPs for red deer, and 13.29% of the individuals contained the 1%-10% specific SNPs for red deer, the rest individuals contained the 10%-20% specific SNPs for red deer except one individual who contained 33.3% specific SNPs for red deer. This study had established reliable markers for identifying hybrid progenies of sika deer and red deer, and the proportion of red deer's specific SNPs in F1 and F2 generation individuals was estimated. The red deer doesn't contain any specific SNPs for sika deer. The result of this study is of great significance to the identification of sika deer, red deer and their hybrid progenies (F1, F2).

Key words: GBS, sika deer, red deer, hybrid deer, SNP, identification