Plant Diversity ›› 2024, Vol. 46 ›› Issue (01): 78-90.DOI: 10.1016/j.pld.2023.06.005

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Conservation genomic investigation of an endangered conifer, Thuja sutchuenensis, reveals low genetic diversity but also low genetic load

Tongzhou Taoa, Richard I. Milneb, Jialiang Lia, Heng Yanga, Shiyang Wanga, Sihan Chena, Kangshan Maoa,c   

  1. a. Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China;
    b. Institute of Molecular Plant Science, School of Biological Science, University of Edinburgh, Edinburgh EH9 3BF, UK;
    c. College of Science, Tibet University, Lhasa 850000, Xizang Autonomous Region, PR China
  • Received:2023-04-14 Revised:2023-06-06 Online:2024-01-25 Published:2024-03-02
  • Contact: Kangshan Mao,
  • Supported by:
    This study was financially supported by National Natural Science Foundation of China (grant No. U20A2080, 31622015), the Institutional Research Fund from Sichuan University (2021SCUNL102) and Fundamental Research Fund for the Central Universities of China (SCU 2021D006, SCU 2022D003).

Abstract: Endangered species generally have small populations with low genetic diversity and a high genetic load. Thuja sutchuenensis is an endangered conifer endemic to southwestern China. It was once considered extinct in the wild, but in 1999 was rediscovered. However, little is known about its genetic load. We collected 67 individuals from five wild, isolated T. sutchuenensis populations, and used 636,151 SNPs to analyze the level of genetic diversity and genetic load in T. sutchuenensis to delineate the conservation units of T. sutchuenensis, based on whole transcriptome sequencing data, as well as target capture sequencing data. We found that populations of T. sutchuenensis could be divided into three groups. These groups had low levels genetic diversity and were moderately genetically differentiated. Our findings also indicate that T. sutchuenensis suffered two severe bottlenecks around the Last Glaciation Period and Last Glacial Maximum. Among Thuja species, T. sutchuenensis presented the lowest genetic load and hence might have purged deleterious mutations efficiently through purifying selection. However, distribution of fitness effects analysis indicated a high extinction risk for T. sutchuenensis. Multiple lines of evidence identified three management units for T. sutchuenensis. Although T. sutchuenensis possesses a low genetic load, low genetic diversity, suboptimal fitness, and anthropogenic pressures all present an extinction risk for this rare conifer. This might also hold true for many endangered plant species in the mountains all over the world.

Key words: Sichuan Arborvitae, Genetic load, Deleterious mutations, Demographic history, Conservation genomics