Population Genetic Diversity and Structure of Ancient Tree Populations of <i>Cryptomeria japonica</i> var. <i>sinensis</i> Based on RAD-seq Data
Research highlights: Our study is the first to explore the genetic composition of ancient <i>Cryptomeria</i> trees across a distribution range in China. Background and objectives: <i>Cryptomeria japonica</i> var. <i>sinensis</i> is a native forest species of China...
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MDPI AG
2020-11-01
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| Series: | Forests |
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| Online Access: | https://www.mdpi.com/1999-4907/11/11/1192 |
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| author | Mengying Cai Yafeng Wen Kentaro Uchiyama Yunosuke Onuma Yoshihiko Tsumura |
| author_facet | Mengying Cai Yafeng Wen Kentaro Uchiyama Yunosuke Onuma Yoshihiko Tsumura |
| author_sort | Mengying Cai |
| collection | DOAJ |
| description | Research highlights: Our study is the first to explore the genetic composition of ancient <i>Cryptomeria</i> trees across a distribution range in China. Background and objectives: <i>Cryptomeria japonica</i> var. <i>sinensis</i> is a native forest species of China; it is widely planted in the south of the country to create forests and for wood production. Unlike <i>Cryptomeria</i> in Japan, genetic Chinese <i>Cryptomeria</i> has seldom been studied, although there is ample evidence of its great ecological and economic value. Materials and methods: Because of overcutting, natural populations are rare in the wild. In this study, we investigated seven ancient tree populations to explore the genetic composition of Chinese <i>Cryptomeria</i> through ddRAD-seq technology. Results: The results reveal a lower genetic variation but higher genetic differentiation (<i>Ho</i> = 0.143, <i>F<sub>ST</sub></i> = 0.1204) than Japanese <i>Cryptomeria</i> (<i>Ho</i> = 0.245, <i>F<sub>ST</sub></i> = 0.0455). The 86% within-population variation is based on an analysis of molecular variance (AMOVA). Significant excess heterozygosity was detected in three populations and some outlier loci were found; these were considered to be the consequence of selection or chance. Structure analysis and dendrogram construction divided the seven ancient tree populations into four groups corresponding to the geographical provinces in which the populations are located, but there was no obvious correlation between genetic distance and geographic distance. A demographic history analysis conducted by a Stairway Plot showed that the effective population size of Chinese <i>Cryptomeria</i> had experienced a continuing decline from the mid-Pleistocene to the present. Our findings suggest that the strong genetic drift caused by climate fluctuation and intense anthropogenic disturbance together contributed to the current low diversity and structure. Considering the species’ unfavorable conservation status, strategies are urgently required to preserve the remaining genetic resources. |
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| institution | Directory Open Access Journal |
| issn | 1999-4907 |
| language | English |
| last_indexed | 2024-03-10T14:54:51Z |
| publishDate | 2020-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Forests |
| spelling | doaj.art-485b36f05f9c4d41b13b8b8e491929832023-11-20T20:40:18ZengMDPI AGForests1999-49072020-11-011111119210.3390/f11111192Population Genetic Diversity and Structure of Ancient Tree Populations of <i>Cryptomeria japonica</i> var. <i>sinensis</i> Based on RAD-seq DataMengying Cai0Yafeng Wen1Kentaro Uchiyama2Yunosuke Onuma3Yoshihiko Tsumura4Graduate School of Life and Environmental Science, University of Tsukuba, Tsukuba 305-8572, JapanCollege of Landscape and Architecture, Central South University of Forestry and Technology, Changsha 410004, ChinaDepartment of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Tsukuba 305-8687, JapanGraduate School of Life and Environmental Science, University of Tsukuba, Tsukuba 305-8572, JapanFaculty of Life and Environmental Science, University of Tsukuba, Tsukuba 305-8572, JapanResearch highlights: Our study is the first to explore the genetic composition of ancient <i>Cryptomeria</i> trees across a distribution range in China. Background and objectives: <i>Cryptomeria japonica</i> var. <i>sinensis</i> is a native forest species of China; it is widely planted in the south of the country to create forests and for wood production. Unlike <i>Cryptomeria</i> in Japan, genetic Chinese <i>Cryptomeria</i> has seldom been studied, although there is ample evidence of its great ecological and economic value. Materials and methods: Because of overcutting, natural populations are rare in the wild. In this study, we investigated seven ancient tree populations to explore the genetic composition of Chinese <i>Cryptomeria</i> through ddRAD-seq technology. Results: The results reveal a lower genetic variation but higher genetic differentiation (<i>Ho</i> = 0.143, <i>F<sub>ST</sub></i> = 0.1204) than Japanese <i>Cryptomeria</i> (<i>Ho</i> = 0.245, <i>F<sub>ST</sub></i> = 0.0455). The 86% within-population variation is based on an analysis of molecular variance (AMOVA). Significant excess heterozygosity was detected in three populations and some outlier loci were found; these were considered to be the consequence of selection or chance. Structure analysis and dendrogram construction divided the seven ancient tree populations into four groups corresponding to the geographical provinces in which the populations are located, but there was no obvious correlation between genetic distance and geographic distance. A demographic history analysis conducted by a Stairway Plot showed that the effective population size of Chinese <i>Cryptomeria</i> had experienced a continuing decline from the mid-Pleistocene to the present. Our findings suggest that the strong genetic drift caused by climate fluctuation and intense anthropogenic disturbance together contributed to the current low diversity and structure. Considering the species’ unfavorable conservation status, strategies are urgently required to preserve the remaining genetic resources.https://www.mdpi.com/1999-4907/11/11/1192<i>Cryptomeria japonica</i> var. <i>sinensis</i>genetic diversitypopulation structuredemographic historySNPRAD-seq |
| spellingShingle | Mengying Cai Yafeng Wen Kentaro Uchiyama Yunosuke Onuma Yoshihiko Tsumura Population Genetic Diversity and Structure of Ancient Tree Populations of <i>Cryptomeria japonica</i> var. <i>sinensis</i> Based on RAD-seq Data Forests <i>Cryptomeria japonica</i> var. <i>sinensis</i> genetic diversity population structure demographic history SNP RAD-seq |
| title | Population Genetic Diversity and Structure of Ancient Tree Populations of <i>Cryptomeria japonica</i> var. <i>sinensis</i> Based on RAD-seq Data |
| title_full | Population Genetic Diversity and Structure of Ancient Tree Populations of <i>Cryptomeria japonica</i> var. <i>sinensis</i> Based on RAD-seq Data |
| title_fullStr | Population Genetic Diversity and Structure of Ancient Tree Populations of <i>Cryptomeria japonica</i> var. <i>sinensis</i> Based on RAD-seq Data |
| title_full_unstemmed | Population Genetic Diversity and Structure of Ancient Tree Populations of <i>Cryptomeria japonica</i> var. <i>sinensis</i> Based on RAD-seq Data |
| title_short | Population Genetic Diversity and Structure of Ancient Tree Populations of <i>Cryptomeria japonica</i> var. <i>sinensis</i> Based on RAD-seq Data |
| title_sort | population genetic diversity and structure of ancient tree populations of i cryptomeria japonica i var i sinensis i based on rad seq data |
| topic | <i>Cryptomeria japonica</i> var. <i>sinensis</i> genetic diversity population structure demographic history SNP RAD-seq |
| url | https://www.mdpi.com/1999-4907/11/11/1192 |
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