A new method was found which integrated Motif specific-PCR, SSCP and direct sequencing to identify the exon 2 of alleles of DRB genes in sika deer. Using this method, the detected 15 sequences which included no artificial sequences from mutation or recombination in the process all met the criterion to distinguish a new allele. The criterion is that there have to be identical sequences identified from at least two different individuals by PCR and direct sequencing. Compared with PCR-SSCP-cloning sequencing previously, this method can efficiently remove artificial sequences. Combined with the above criterion, this method provided a new approach for investigating DRB gene polymorphism of sika deer and other deer species.
