Next Generation Sequencing-Based Molecular Marker Development: A Case Study in Betula Alnoides
Abstract
:1. Introduction
2. Results and Discussion
2.1. Information of Sequencing Data
2.2. Distribution of SSR in the Genome
2.3. Characteristics of SSR Sequences
2.4. Primer Screening and SSR Markers Polymorphism Detecting
2.5. Cross-Species Transferability
3. Materials and Methods
3.1. Plant Material and DNA Isolation
3.2. Genome Sequencing, SSR Finding and Survey
3.3. SSR Primer Design and Screening
3.4. SSR Markers Polymorphism Detection
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Sample Availability: Samples of the compounds are available from the authors. |
Repeat Type | Repeat Number | Total | Frequency (%) | |||||
---|---|---|---|---|---|---|---|---|
3–8 | 9–14 | 15–20 | 21–26 | 27–32 | ≥33 | |||
Mono-nucleotide | - | 106,526 | 16,966 | 2328 | 821 | 4 | 126,645 | 77.05 |
Di-nucleotide | 13,777 | 2601 | 296 | 37 | 15 | - | 16,726 | 10.18 |
Tri-nucleotide | 5675 | 163 | 15 | 3 | - | - | 5856 | 3.56 |
Tetra-nucleotide | 10,053 | 2 | - | - | - | - | 10,055 | 6.12 |
Penta-nucleotide | 3509 | 1 | 2 | - | - | - | 3512 | 2.14 |
Hexa-nucleotide | 1562 | 1 | - | - | - | - | 1563 | 0.95 |
Total | 34,576 | 109,294 | 17,279 | 2368 | 836 | 4 | 164,357 | 100 |
Frequency (%) | 21.04 | 66.50 | 10.51 | 1.44 | 0.51 | 0.24 × 10−4 |
Related Species | Collection Locality | Longitude (°E) | Latitude (°N) |
---|---|---|---|
B. platyphylla | Baihuashan Mountain, Beijing | 115.57 | 39.85 |
B. austro-sinensis | Yangdongshan Shierdushui Provincial Nature Reserve, Lechang, Guangdong | 113.39 | 25.28 |
B. cylindrostachya | Hill behind Cizhong Church, Weixi County, Yunnan | 98.92 | 28.48 |
B. fujianensis | Luoboyan Natural Reserve, Fujian | 117.57 | 27.43 |
B. hainanensis | Jianfengling Natural Reserve, Hainan | 109.17 | 18.73 |
B. luminifera | Qinwang Mountain, Tianlin County, Guangxi | 106.62 | 23.91 |
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Tan, J.; Guo, J.-J.; Yin, M.-Y.; Wang, H.; Dong, W.-P.; Zeng, J.; Zhou, S.-L. Next Generation Sequencing-Based Molecular Marker Development: A Case Study in Betula Alnoides. Molecules 2018, 23, 2963. https://doi.org/10.3390/molecules23112963
Tan J, Guo J-J, Yin M-Y, Wang H, Dong W-P, Zeng J, Zhou S-L. Next Generation Sequencing-Based Molecular Marker Development: A Case Study in Betula Alnoides. Molecules. 2018; 23(11):2963. https://doi.org/10.3390/molecules23112963
Chicago/Turabian StyleTan, Jing, Jun-Jie Guo, Ming-Yu Yin, Huan Wang, Wen-Pan Dong, Jie Zeng, and Shi-Liang Zhou. 2018. "Next Generation Sequencing-Based Molecular Marker Development: A Case Study in Betula Alnoides" Molecules 23, no. 11: 2963. https://doi.org/10.3390/molecules23112963