Exploring Genetic Diversity and Phylogenetic Relationships in <i>Camellia reticulata</i> Cultivars Using Novel Low-Copy Nuclear Gene Markers
This study delves into the exploration of genetic diversity and phylogenetic relationships within <i>Camellia reticulata</i> cultivars, providing a vital reference for horticultural research on this hetero-hexaploid species. Utilizing available transcriptome data from <i>C. reticul...
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| Format: | Article |
| Language: | English |
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MDPI AG
2024-03-01
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| Series: | Horticulturae |
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| Online Access: | https://www.mdpi.com/2311-7524/10/3/303 |
| _version_ | 1797240767956123648 |
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| author | Xiaodan Xu Ya Gao Wei Zheng |
| author_facet | Xiaodan Xu Ya Gao Wei Zheng |
| author_sort | Xiaodan Xu |
| collection | DOAJ |
| description | This study delves into the exploration of genetic diversity and phylogenetic relationships within <i>Camellia reticulata</i> cultivars, providing a vital reference for horticultural research on this hetero-hexaploid species. Utilizing available transcriptome data from <i>C. reticulata</i>, novel low-copy nuclear gene sequences were successfully identified. With tailored primer design, these genes were amplified and sequenced from 100 <i>C. reticulata</i> cultivars originating from Kunming, Chuxiong, Dali, and Tengchong in China. Five distinct low-copy nuclear gene sequences were found to collectively span 3481 bp, showcasing 71 polymorphic mutation sites (<i>P</i><sub>i</sub> = 0.0077) and 91 haplotypes (<i>H</i><sub>d</sub> = 0.9974). The genetic diversity among cultivars from the four provenances ranked Tengchong > Dali > Kunming > Chuxiong. AMOVA analysis revealed that 96.50% of the genetic variation exists within the provenances. Low genetic distance and differentiation (<i>F<sub>st</sub></i>= 0.0199) were observed among cultivars from the four provenances. Ninety-nine cultivars were clustered into four clades, corresponding to the three ancestors of <i>C. reticulata</i> (diploid <i>C. reticulata</i>, <i>C. pitardii</i>, and <i>C. saluenensis</i>). The novel low-copy nuclear gene sequence markers developed in this study provide an effective tool for analyzing genetic diversity, phylogenetic relationships, and origination of <i>C. reticulata</i> cultivars. |
| first_indexed | 2024-04-24T18:12:40Z |
| format | Article |
| id | doaj.art-acbd7767fef84e42abb6bba9a40425fe |
| institution | Directory Open Access Journal |
| issn | 2311-7524 |
| language | English |
| last_indexed | 2024-04-24T18:12:40Z |
| publishDate | 2024-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Horticulturae |
| spelling | doaj.art-acbd7767fef84e42abb6bba9a40425fe2024-03-27T13:44:33ZengMDPI AGHorticulturae2311-75242024-03-0110330310.3390/horticulturae10030303Exploring Genetic Diversity and Phylogenetic Relationships in <i>Camellia reticulata</i> Cultivars Using Novel Low-Copy Nuclear Gene MarkersXiaodan Xu0Ya Gao1Wei Zheng2Laboratory of Landscape Plants, Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming 650500, ChinaLaboratory of Landscape Plants, Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming 650500, ChinaLaboratory of Landscape Plants, Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming 650500, ChinaThis study delves into the exploration of genetic diversity and phylogenetic relationships within <i>Camellia reticulata</i> cultivars, providing a vital reference for horticultural research on this hetero-hexaploid species. Utilizing available transcriptome data from <i>C. reticulata</i>, novel low-copy nuclear gene sequences were successfully identified. With tailored primer design, these genes were amplified and sequenced from 100 <i>C. reticulata</i> cultivars originating from Kunming, Chuxiong, Dali, and Tengchong in China. Five distinct low-copy nuclear gene sequences were found to collectively span 3481 bp, showcasing 71 polymorphic mutation sites (<i>P</i><sub>i</sub> = 0.0077) and 91 haplotypes (<i>H</i><sub>d</sub> = 0.9974). The genetic diversity among cultivars from the four provenances ranked Tengchong > Dali > Kunming > Chuxiong. AMOVA analysis revealed that 96.50% of the genetic variation exists within the provenances. Low genetic distance and differentiation (<i>F<sub>st</sub></i>= 0.0199) were observed among cultivars from the four provenances. Ninety-nine cultivars were clustered into four clades, corresponding to the three ancestors of <i>C. reticulata</i> (diploid <i>C. reticulata</i>, <i>C. pitardii</i>, and <i>C. saluenensis</i>). The novel low-copy nuclear gene sequence markers developed in this study provide an effective tool for analyzing genetic diversity, phylogenetic relationships, and origination of <i>C. reticulata</i> cultivars.https://www.mdpi.com/2311-7524/10/3/303Yunnan camelliapolyploidmolecular markerprovenancehaplotype |
| spellingShingle | Xiaodan Xu Ya Gao Wei Zheng Exploring Genetic Diversity and Phylogenetic Relationships in <i>Camellia reticulata</i> Cultivars Using Novel Low-Copy Nuclear Gene Markers Horticulturae Yunnan camellia polyploid molecular marker provenance haplotype |
| title | Exploring Genetic Diversity and Phylogenetic Relationships in <i>Camellia reticulata</i> Cultivars Using Novel Low-Copy Nuclear Gene Markers |
| title_full | Exploring Genetic Diversity and Phylogenetic Relationships in <i>Camellia reticulata</i> Cultivars Using Novel Low-Copy Nuclear Gene Markers |
| title_fullStr | Exploring Genetic Diversity and Phylogenetic Relationships in <i>Camellia reticulata</i> Cultivars Using Novel Low-Copy Nuclear Gene Markers |
| title_full_unstemmed | Exploring Genetic Diversity and Phylogenetic Relationships in <i>Camellia reticulata</i> Cultivars Using Novel Low-Copy Nuclear Gene Markers |
| title_short | Exploring Genetic Diversity and Phylogenetic Relationships in <i>Camellia reticulata</i> Cultivars Using Novel Low-Copy Nuclear Gene Markers |
| title_sort | exploring genetic diversity and phylogenetic relationships in i camellia reticulata i cultivars using novel low copy nuclear gene markers |
| topic | Yunnan camellia polyploid molecular marker provenance haplotype |
| url | https://www.mdpi.com/2311-7524/10/3/303 |
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