Large-scale genome sequencing of giant pandas improves the understanding of population structure and future conservation initiatives

The extinction risk of the giant panda has been demoted from "endangered" to "vulnerable" on the International Union for Conservation of Nature Red List, but its habitat is more fragmented than ever before, resulting in 33 isolated giant panda populations according to the fourth national survey released by the Chinese government. Further comprehensive investigations of the genetic background and in-depth assessments of the conservation status of wild populations are still necessary and urgently needed. Here, we sequenced the genomes of 612 giant pandas with an average depth of ~26× and generated a high-resolution map of genomic variation with more than 20 million variants covering wild individuals from six mountain ranges and captive representatives in China. We identified distinct genetic clusters within the Minshan population by performing a fine-grained genetic structure. The estimation of inbreeding and genetic load associated with historical population dynamics suggested that future conservation efforts should pay special attention to the Qinling and Liangshan populations. Releasing captive individuals with a genetic background similar to the recipient population appears to be an advantageous genetic rescue strategy for recovering the wild giant panda populations, as this approach introduces fewer deleterious mutations into the wild population than mating with differentiated lineages. These findings emphasize the superiority of large-scale population genomics to provide precise guidelines for future conservation of the giant panda.

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Publication Details

Journal
Proceedings of the National Academy of Sciences
Published
2024-08-26
DOI
https://doi.org/10.1073/pnas.2406343121
Citations
17
Primary Topic
Genetic diversity and population structure
Type
article
Field-Weighted Citation Impact
9.36

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article

Large-scale genome sequencing of giant pandas improves the understanding of population structure and future conservation initiatives

Shanlin Liu, Qiu‐Hong Wan, Shangchen Yang, Tao Deng et al.
17 citations
Proceedings of the National Academy of Sciences
Genetic diversity and population structure
9.36
article

Large-scale genome sequencing of giant pandas improves the understanding of population structure and future conservation initiatives

Shanlin Liu, Qiu‐Hong Wan, Shangchen Yang, Tao Deng, Karsten Kristiansen, Ming‐Huei Chen, Haorong Lu, Minhui Shi, Tianming Lan, Boyang Liu, Qiye Li, Sheng‐Guo Fang, Lei Han, Rengui Li, Wenwen Deng, Xiaoyu Huang, Sunil Kumar Sahu, Huan Liu, Qing Wang, Yi Zhang, Shiqing Wang, Desheng Li, Yajie Zhou, Haimeng Li, Hanyu Du
article en
17 citations

Abstract

The extinction risk of the giant panda has been demoted from "endangered" to "vulnerable" on the International Union for Conservation of Nature Red List, but its habitat is more fragmented than ever before, resulting in 33 isolated giant panda populations according to the fourth national survey released by the Chinese government. Further comprehensive investigations of the genetic background and in-depth assessments of the conservation status of wild populations are still necessary and urgently needed. Here, we sequenced the genomes of 612 giant pandas with an average depth of ~26× and generated a high-resolution map of genomic variation with more than 20 million variants covering wild individuals from six mountain ranges and captive representatives in China. We identified distinct genetic clusters within the Minshan population by performing a fine-grained genetic structure. The estimation of inbreeding and genetic load associated with historical population dynamics suggested that future conservation efforts should pay special attention to the Qinling and Liangshan populations. Releasing captive individuals with a genetic background similar to the recipient population appears to be an advantageous genetic rescue strategy for recovering the wild giant panda populations, as this approach introduces fewer deleterious mutations into the wild population than mating with differentiated lineages. These findings emphasize the superiority of large-scale population genomics to provide precise guidelines for future conservation of the giant panda.

Proceedings of the National Academy of SciencesVol. 121(36)
BGI Group (China) (CN), University of Copenhagen (DK), Chinese Academy of Sciences (CN), Chengdu Research Base of Giant Panda Breeding (CN), State Forestry and Grassland Administration (CN), China National GeneBank (CN), Institute of Zoology (CN), Northeast Forestry University (CN), Zhejiang University (CN)
Northeast Forestry University, National Forestry and Grassland Administration, Fundamental Research Funds for the Central Universities
Life in Land
Openalex Percentile: Top 2%
Genetic diversity and population structure
9.36
DOIOpen Access PDFOpenAlex
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