Development of SNP markers to identify the sex of the giant panda from naturally degraded fecal samples

A non-invasive, fast, and reliable method for sex identification of the giant panda ( Ailuropoda melanoleuca ) was developed by genotyping five SNPs located at the sex chromosome amelogenin ( AMEL ) paralogs. The giant panda’s sex can be accurately distinguished by the homozygous or heterozygous SNP genotypes. Mass spectrometry assay and Sanger sequencing both successfully genotyped tissue and fresh fecal samples collected from known-sex giant pandas. Additionally, we simulated the conditions of wild fecal samples, which were naturally degraded for up to two weeks, and successfully genotyped these samples by mass spectrometry assay in parallel. These results suggest that this is a powerful method for sex determination in highly degraded and lower concentrated DNA samples.