Genetic Diversity Analysis of Different Populations of Lutjanus kasmira Based on SNP Markers
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and DNA Extraction
2.2. RAD-Seq Library Construction and Sequencing
2.3. Sequence Alignment and SNP Genotyping
2.4. Genetic Diversity and Population Structure
3. Results
3.1. Genomic Data Statistics and SNP Discovery
3.2. Genetic Diversity and Population Structure
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Sample ID | Sample Location | Length (mm) | Sampling Date | Sample ID | Sample Location | Length (mm) | Sampling Date |
---|---|---|---|---|---|---|---|
ZB_SDDD_1 | Zhubi Dao | 136 | 2019 | MJ_SDDD_1 | Meiji Dao | 153 | 2019 |
ZB_SDDD_2 | Zhubi Dao | 146 | 2019 | MJ_SDDD_2 | Meiji Dao | 179 | 2019 |
ZB_SDDD_3 | Zhubi Dao | 150 | 2019 | MJ_SDDD_3 | Meiji Dao | 153 | 2019 |
ZB_SDDD_4 | Zhubi Dao | 128 | 2019 | MJ_SDDD_4 | Meiji Dao | 164 | 2019 |
ZB_SDDD_5 | Zhubi Dao | 133 | 2019 | MJ_SDDD_5 | Meiji Dao | 123 | 2019 |
ZB_SDDD_6 | Zhubi Dao | 137 | 2019 | MJ_SDDD_6 | Meiji Dao | 154 | 2019 |
ZB_SDDD_7 | Zhubi Dao | 146 | 2019 | MJ_SDDD_7 | Meiji Dao | 126 | 2019 |
ZB_SDDD_8 | Zhubi Dao | 148 | 2019 | MJ_SDDD_8 | Meiji Dao | 137 | 2019 |
ZB_SDDD_9 | Zhubi Dao | 152 | 2019 | MJ_SDDD_9 | Meiji Dao | 146 | 2019 |
ZB_SDDD_10 | Zhubi Dao | 139 | 2019 | MJ_SDDD_10 | Meiji Dao | 125 | 2019 |
ZB_SDDD_11 | Zhubi Dao | 120 | 2019 | MJ_SDDD_11 | Meiji Dao | 143 | 2019 |
ZB_SDDD_12 | Zhubi Dao | 149 | 2019 | MJ_SDDD_12 | Meiji Dao | 135 | 2019 |
ZB_SDDD_13 | Zhubi Dao | 132 | 2019 | MJ_SDDD_13 | Meiji Dao | 154 | 2019 |
ZB_SDDD_14 | Zhubi Dao | 125 | 2019 | MJ_SDDD_14 | Meiji Dao | 144 | 2019 |
ZB_SDDD_15 | Zhubi Dao | 165 | 2019 | ||||
ZB_SDDD_16 | Zhubi Dao | 143 | 2019 |
Sample ID | Number of Clean Reads | Bases (Q20%) | GC% | Sample ID | Number of Clean Reads | Bases (Q20%) | GC% |
---|---|---|---|---|---|---|---|
ZB_SDDD_1 | 7,974,070 | 99.32 | 39 | MJ_SDDD_1 | 9,265,891 | 95.32 | 39 |
ZB_SDDD_2 | 6,867,444 | 96.12 | 40 | MJ_SDDD_2 | 13,500,657 | 96.75 | 39 |
ZB_SDDD_3 | 11,342,742 | 93.64 | 39 | MJ_SDDD_3 | 9,120,598 | 99.30 | 39 |
ZB_SDDD_4 | 6,831,672 | 95.40 | 40 | MJ_SDDD_4 | 12,363,573 | 99.64 | 39 |
ZB_SDDD_5 | 10,947,352 | 96.32 | 40 | MJ_SDDD_5 | 8,022,139 | 98.20 | 39 |
ZB_SDDD_6 | 8,673,002 | 98.89 | 39 | MJ_SDDD_6 | 10,972,365 | 97.67 | 39 |
ZB_SDDD_7 | 8,040,810 | 96.63 | 39 | MJ_SDDD_7 | 14,935,273 | 94.03 | 39 |
ZB_SDDD_8 | 7,251,357 | 97.60 | 39 | MJ_SDDD_8 | 10,483,102 | 96.43 | 39 |
ZB_SDDD_9 | 8,440,580 | 96.30 | 40 | MJ_SDDD_9 | 9,245,798 | 94.60 | 39 |
ZB_SDDD_10 | 7,441,155 | 94.56 | 39 | MJ_SDDD_10 | 6,732,763 | 98.75 | 39 |
ZB_SDDD_11 | 8,497,499 | 93.21 | 39 | MJ_SDDD_11 | 9,673,994 | 95.30 | 39 |
ZB_SDDD_12 | 6,672,063 | 95.63 | 39 | MJ_SDDD_12 | 9,046,087 | 98.00 | 39 |
ZB_SDDD_13 | 9,912,874 | 99.11 | 39 | MJ_SDDD_13 | 6,814,092 | 95.19 | 39 |
ZB_SDDD_14 | 7,340,574 | 98.65 | 39 | MJ_SDDD_14 | 7,280,377 | 96.32 | 39 |
ZB_SDDD_15 | 21,514,652 | 99.30 | 39 | ||||
ZB_SDDD_16 | 11,059,675 | 97.21 | 39 |
Population ID | π | Ho | He | Average_Fis | Fst |
---|---|---|---|---|---|
ZB population | 0.02478 | 0.46834 | 0.33585 | −0.18729 | 0.00255102 |
MJ population | 0.02154 | 0.23103 | 0.22098 | 0.03256 |
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Zhao, F.; Guo, L.; Zhang, N.; Yang, J.; Zhu, K.; Guo, H.; Liu, B.; Liu, B.; Zhang, D.; Jiang, S. Genetic Diversity Analysis of Different Populations of Lutjanus kasmira Based on SNP Markers. J. Mar. Sci. Eng. 2022, 10, 1547. https://doi.org/10.3390/jmse10101547
Zhao F, Guo L, Zhang N, Yang J, Zhu K, Guo H, Liu B, Liu B, Zhang D, Jiang S. Genetic Diversity Analysis of Different Populations of Lutjanus kasmira Based on SNP Markers. Journal of Marine Science and Engineering. 2022; 10(10):1547. https://doi.org/10.3390/jmse10101547
Chicago/Turabian StyleZhao, Fangcao, Liang Guo, Nan Zhang, Jingwen Yang, Kecheng Zhu, Huayang Guo, Baosuo Liu, Bo Liu, Dianchang Zhang, and Shigui Jiang. 2022. "Genetic Diversity Analysis of Different Populations of Lutjanus kasmira Based on SNP Markers" Journal of Marine Science and Engineering 10, no. 10: 1547. https://doi.org/10.3390/jmse10101547