Elucidating SNP-Based Population Structure and Genetic Diversity of Bruguiera gymnorhiza (L.) Savigny in Thailand
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and DNA Extraction
2.2. RAD-Seq Library Construction and RAD-Seq Sequencing
2.3. SNP Identification and LD Pruning
2.4. Phylogenetic Analysis
2.5. Population Genetic Structure Analysis
2.6. Genetic Diversity Analysis
3. Results
3.1. SNP Identification and Characterization
3.2. Phylogenetic Tree
3.3. Population Genetic Structure and PCA
3.4. Genetic Diversity and Differentiation
4. Discussion
4.1. Genetic Relationship and Genetic Structure
4.2. Genetic Diversity and Genetic Differentiation
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Population | N | Na | Ne | I | Ho | He | PPL (%) | F |
---|---|---|---|---|---|---|---|---|
Gulf of Thailand | 46 | 2.510 ± 0.013 | 1.517 ± 0.008 | 0.515 ± 0.005 | 0.383 ± 0.007 | 0.311 ± 0.004 | 100.00 | −0.135 ± 0.009 |
Andaman Sea | 27 | 2.417 ± 0.013 | 1.557 ± 0.009 | 0.529 ± 0.005 | 0.410 ± 0.008 | 0.323 ± 0.004 | 99.01 | −0.157 ± 0.010 |
Overall | 73 | 2.463 ± 0.009 | 1.537 ± 0.006 | 0.522 ± 0.004 | 0.397 ± 0.005 | 0.317 ± 0.003 | 99.51 | −0.146 ± 0.007 |
Source of Variation | df | Sum of Squares | Variance Components | Percentage of Variation | F-Statistics |
---|---|---|---|---|---|
Among populations | 1 | 2772.27 | 37.83 | 16.05 | FST = 0.16 *** |
Within populations | 144 | 28,495.58 | 197.89 | 83.95 | |
Total | 145 | 31,267.85 | 235.71 |
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Ruang-areerate, P.; Sonthirod, C.; Sangsrakru, D.; Waiyamitra, P.; Maknual, C.; Wanthongchai, P.; Chomriang, P.; Pootakham, W.; Tangphatsornruang, S. Elucidating SNP-Based Population Structure and Genetic Diversity of Bruguiera gymnorhiza (L.) Savigny in Thailand. Forests 2023, 14, 693. https://doi.org/10.3390/f14040693
Ruang-areerate P, Sonthirod C, Sangsrakru D, Waiyamitra P, Maknual C, Wanthongchai P, Chomriang P, Pootakham W, Tangphatsornruang S. Elucidating SNP-Based Population Structure and Genetic Diversity of Bruguiera gymnorhiza (L.) Savigny in Thailand. Forests. 2023; 14(4):693. https://doi.org/10.3390/f14040693
Chicago/Turabian StyleRuang-areerate, Panthita, Chutima Sonthirod, Duangjai Sangsrakru, Pitchaporn Waiyamitra, Chatree Maknual, Poonsri Wanthongchai, Pranom Chomriang, Wirulda Pootakham, and Sithichoke Tangphatsornruang. 2023. "Elucidating SNP-Based Population Structure and Genetic Diversity of Bruguiera gymnorhiza (L.) Savigny in Thailand" Forests 14, no. 4: 693. https://doi.org/10.3390/f14040693