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

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Abstract

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.

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Data Availability

The AMELX gene sequence, annotation, and Y-linked SNPs were deposited on NCBI nucleotide database with accession ON987233 and synchronously committed to our Github repository (https://github.com/xuweixw/annotation).

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Funding

This study is supported by the grants from the Sichuan Natural Science Foundation Project (2022NSFSC0009) and an independent project of the Chengdu Research Base of Giant Panda Breeding (No. 2020CPB-B01). We sincerely thank James Ayala for polishing the English grammar of the manuscript.

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Authors and Affiliations

  1. The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China

    Wei Xu, Jie Kou, Yan Li, Ye Wang, Liang Zhang, Hong Liu, Jiawen Liu, Juan Wang, Li Luo, Xiaolan Wang, Kongju Wu & Fujun Shen

  2. Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, China

    Daxing Xie & Xiuyue Zhang

Authors
  1. Wei Xu
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  2. Daxing Xie
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  3. Jie Kou
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  4. Xiuyue Zhang
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  5. Yan Li
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  6. Ye Wang
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  7. Liang Zhang
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  8. Hong Liu
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  9. Jiawen Liu
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  10. Juan Wang
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  11. Li Luo
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  12. Xiaolan Wang
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  13. Kongju Wu
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  14. Fujun Shen
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Contributions

FS and WX designed this study. WX analyzed the data and wrote this manuscript. WX, DX, JK, XZ, and other colleagues collected those samples and performed experiments.

Corresponding author

Correspondence to Fujun Shen.

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Xu, W., Xie, D., Kou, J. et al. Development of SNP markers to identify the sex of the giant panda from naturally degraded fecal samples. Conservation Genet Resour 16, 23–26 (2024). https://doi.org/10.1007/s12686-023-01326-2

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  • DOI: https://doi.org/10.1007/s12686-023-01326-2

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