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

Author:

Lan Tianming123,Yang Shangchen1ORCID,Li Haimeng245,Zhang Yi1,Li Rengui6,Sahu Sunil Kumar37ORCID,Deng Wenwen6,Liu Boyang2,Shi Minhui3,Wang Shiqing3,Du Hanyu1,Huang Xiaoyu6,Lu Haorong8,Liu Shanlin9,Deng Tao6,Chen Jin8,Wang Qing3,Han Lei2,Zhou Yajie3,Li Qiye37,Li Desheng6,Kristiansen Karsten1011ORCID,Wan Qiu-Hong1,Liu Huan3412,Fang Sheng-Guo1ORCID

Affiliation:

1. Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China

2. Wildlife Evolution and Conservation Omics Laboratory, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China

3. State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China

4. Heilongjiang Key Laboratory of Complex Traits and Protein Machines in Organisms, Harbin 150040, China

5. BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China

6. Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China

7. BGI Research, Beijing Genomics Institute, Wuhan 430074, China

8. China National GeneBank, BGI Research, Beijing Genomics Institute, Shenzhen 518120, China

9. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China

10. Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark

11. Qingdao-Europe Advanced Institute for Life Sciences, Qingdao 266555, China

12. Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China

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.

Funder

the Foundation of Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park

the Fundamental Research Funds for the Central Universities of the People's Republic of China

Start-up Scientific Foundation of Northeast Forestry University

Publisher

Proceedings of the National Academy of Sciences

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