Genetic Variation for Wild Populations of the Rare and Endangered Plant <i>Glyptostrobus pensilis</i> Based on Double-Digest Restriction Site-Associated DNA Sequencing
<i>Glyptostrobus pensilis</i> is an endangered tree species, and detecting its genetic diversity can reveal the mechanisms of endangerment, providing references for the conservation of genetic resources. Samples of 137 trees across seven populations within Fujian Province were collected...
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2024-12-01
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| author | Yongrong Huang Yu Li Xiaojie Hong Suzhen Luo Dedan Cai Xiangxi Xiao Yunpeng Huang Yushan Zheng |
| author_facet | Yongrong Huang Yu Li Xiaojie Hong Suzhen Luo Dedan Cai Xiangxi Xiao Yunpeng Huang Yushan Zheng |
| author_sort | Yongrong Huang |
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| description | <i>Glyptostrobus pensilis</i> is an endangered tree species, and detecting its genetic diversity can reveal the mechanisms of endangerment, providing references for the conservation of genetic resources. Samples of 137 trees across seven populations within Fujian Province were collected and sequenced using double-digest restriction site-associated DNA (ddRAD-seq). A total of 3,687,189 single-nucleotide polymorphisms (SNPs) were identified, and 15,158 high-quality SNPs were obtained after filtering. The genetic diversity in the populations was found to be low (<i>H<sub>o</sub></i> = 0.08630, <i>H<sub>e</sub></i> = 0.03475, <i>π</i> = 0.07239), with a high genetic differentiation coefficient (<i>F<sub>st</sub></i>). When <i>K</i> = 4, the coefficient of variation (CV) error value was minimized, suggesting that the 137 individuals could be divided into four groups, with frequent gene flow between them. Principal component analysis (PCA) divided the seven populations into two major categories based on their north–south geographic location. The clustering was consistent with those obtained from the PCA. The main reasons for the endangerment of <i>G. pensilis</i> are likely to be poor natural regeneration, human disturbances, and climatic factors. It is recommended that methods such as in situ conservation, ex situ conservation, and the establishment of germplasm banks be implemented to maintain the genetic diversity of <i>G. pensilis</i> populations. |
| format | Article |
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| institution | Kabale University |
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| spelling | doaj-art-6f5665188c9248599e8a7b29f03b26512025-01-24T13:27:23ZengMDPI AGCurrent Issues in Molecular Biology1467-30371467-30452024-12-014711210.3390/cimb47010012Genetic Variation for Wild Populations of the Rare and Endangered Plant <i>Glyptostrobus pensilis</i> Based on Double-Digest Restriction Site-Associated DNA SequencingYongrong Huang0Yu Li1Xiaojie Hong2Suzhen Luo3Dedan Cai4Xiangxi Xiao5Yunpeng Huang6Yushan Zheng7College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaCollege of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaCollege of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaYouxi State-Owned Forest Farm of Fujian Province, Youxi 365100, ChinaJianning State-Owned Forest Farm of Fujian Province, Jianning 354500, ChinaFujian Academy of Forestry, Fuzhou 350012, ChinaFujian Academy of Forestry, Fuzhou 350012, ChinaCollege of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China<i>Glyptostrobus pensilis</i> is an endangered tree species, and detecting its genetic diversity can reveal the mechanisms of endangerment, providing references for the conservation of genetic resources. Samples of 137 trees across seven populations within Fujian Province were collected and sequenced using double-digest restriction site-associated DNA (ddRAD-seq). A total of 3,687,189 single-nucleotide polymorphisms (SNPs) were identified, and 15,158 high-quality SNPs were obtained after filtering. The genetic diversity in the populations was found to be low (<i>H<sub>o</sub></i> = 0.08630, <i>H<sub>e</sub></i> = 0.03475, <i>π</i> = 0.07239), with a high genetic differentiation coefficient (<i>F<sub>st</sub></i>). When <i>K</i> = 4, the coefficient of variation (CV) error value was minimized, suggesting that the 137 individuals could be divided into four groups, with frequent gene flow between them. Principal component analysis (PCA) divided the seven populations into two major categories based on their north–south geographic location. The clustering was consistent with those obtained from the PCA. The main reasons for the endangerment of <i>G. pensilis</i> are likely to be poor natural regeneration, human disturbances, and climatic factors. It is recommended that methods such as in situ conservation, ex situ conservation, and the establishment of germplasm banks be implemented to maintain the genetic diversity of <i>G. pensilis</i> populations.https://www.mdpi.com/1467-3045/47/1/12<i>Glyptostrobus pensilis</i>ddRAD-seqgenetic diversitygenetic structureconservation |
| spellingShingle | Yongrong Huang Yu Li Xiaojie Hong Suzhen Luo Dedan Cai Xiangxi Xiao Yunpeng Huang Yushan Zheng Genetic Variation for Wild Populations of the Rare and Endangered Plant <i>Glyptostrobus pensilis</i> Based on Double-Digest Restriction Site-Associated DNA Sequencing Current Issues in Molecular Biology <i>Glyptostrobus pensilis</i> ddRAD-seq genetic diversity genetic structure conservation |
| title | Genetic Variation for Wild Populations of the Rare and Endangered Plant <i>Glyptostrobus pensilis</i> Based on Double-Digest Restriction Site-Associated DNA Sequencing |
| title_full | Genetic Variation for Wild Populations of the Rare and Endangered Plant <i>Glyptostrobus pensilis</i> Based on Double-Digest Restriction Site-Associated DNA Sequencing |
| title_fullStr | Genetic Variation for Wild Populations of the Rare and Endangered Plant <i>Glyptostrobus pensilis</i> Based on Double-Digest Restriction Site-Associated DNA Sequencing |
| title_full_unstemmed | Genetic Variation for Wild Populations of the Rare and Endangered Plant <i>Glyptostrobus pensilis</i> Based on Double-Digest Restriction Site-Associated DNA Sequencing |
| title_short | Genetic Variation for Wild Populations of the Rare and Endangered Plant <i>Glyptostrobus pensilis</i> Based on Double-Digest Restriction Site-Associated DNA Sequencing |
| title_sort | genetic variation for wild populations of the rare and endangered plant i glyptostrobus pensilis i based on double digest restriction site associated dna sequencing |
| topic | <i>Glyptostrobus pensilis</i> ddRAD-seq genetic diversity genetic structure conservation |
| url | https://www.mdpi.com/1467-3045/47/1/12 |
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