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. 2022 Mar 8;12(1):4126.
doi: 10.1038/s41598-022-07870-5.

SSR individual identification system construction and population genetics analysis for Chamaecyparis formosensis

Chiun-Jr Huang  1   2   3 , Fang-Hua Chu  4 , Yi-Shiang Huang  5 , Yu-Ching Tu  6 , Yu-Mei Hung  6 , Yu-Hsin Tseng  7 , Chang-En Pu  6 , Cheng Te Hsu  8 , Chi-Hsiang Chao  6 , Yu-Shyang Chou  6 , Shau-Chian Liu  9 , Ya Ting You  10 , Shuo-Yu Hsu  4 , Hsiang-Chih Hsieh  4 , Chieh-Ting Wang  11 , Chi-Tsong Chen  12
Affiliations

SSR individual identification system construction and population genetics analysis for Chamaecyparis formosensis

Chiun-Jr Huang et al. Sci Rep. .

Abstract

Chamaecyparis formosensis is an endemic species of Taiwan, threatened from intensive use and illegal felling. An individual identification system for C. formosensis is required to provide scientific evidence for court use and deter illegal felling. In this study, 36 polymorphic simple sequence repeat markers were developed. By applying up to 28 non-linked of the developed markers, it is calculated that the cumulative random probability of identity (CPI) is as low as 1.652 × 10-12, and the identifiable population size is up to 60 million, which is greater than the known C. formosensis population size in Taiwan. Biogeographical analysis data show that C. formosensis from four geographic areas belong to the same genetic population, which can be further divided into three clusters: SY (Eastern Taiwan), HV and GW (Northwestern Taiwan), and MM (Southwestern Taiwan). The developed system was applied to assess the provenance of samples with 88.44% accuracy rate and therefore can serve as a prescreening tool to reduce the range required for comparison. The system developed in this study is a potential crime-fighting tool against illegal felling.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Flowchart of Chamaecyparis formosensis individual identification system development. N: the number of individuals; P: the number of populations; MISA: MicroSAtellite software; CPI : combined probability of identity.
Figure 2
Figure 2
The biogeographic information of Chamacyparis formosensis in this study. A total of 92 samples composed of 20 MM, 25 HV, 23 GW, and 24 SY individuals were analyzed (a) Biogeographic analysis data suggests that the samples fall into three genetical categories: SY (Eastern Taiwan), HV & GW (Northwestern Taiwan), and MM (Southwestern Taiwan) (b)–(e) The red spots represent the individuals that have been mis-assigned (denoted as M in figure legend) from provenance simulation result. N: the number of individuals, M: the number of mis-assigned.
Figure 3
Figure 3
Genetic composition of Chamaecyparis formosensis. (a) The scatter plots of Delta K. (b) The 2, 3 and 4 clusters obtained from STRUCTURE analyses.
See this image and copyright information in PMC

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