Genetic Diversity and Relationship of Shanlan Upland Rice Were Revealed Based on 214 Upland Rice SSR Markers
Abstract
:1. Introduction
2. Results
2.1. Development of Polymorphic SSR Primers
2.2. Gene Flow among Upland Rice Populations from Different Geographical Origin
2.3. Genetic Diversity of Upland Rice from Different Geographical Sources
2.4. Genetic Similarity Analysis of Upland Rice from Different Geographical Sources
2.5. Analysis of Molecular Variance
2.6. Cluster Analysis and Principal Coordinate Analysis of Upland Rice from Different Geographical Sources
3. Discussion
4. Materials and Methods
4.1. Experimental Materials and DNA Extraction
4.2. Primer Screening and Genetic Diversity Analysis
4.3. Molecular Variance Analysis (AMOVA) and Gene Flow Estimation
4.4. Data Processing
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Locus | Na | Ne | I | Ho | He | F | PIC | Fis | Fit | Fst | Nm |
---|---|---|---|---|---|---|---|---|---|---|---|
LRJ49 | 12.000 | 3.947 | 1.652 | 0.084 | 0.747 | 0.887 | 0.712 | 0.869 | 0.879 | 0.074 | 3.145 |
LRJ50 | 10.000 | 4.162 | 1.624 | 0.093 | 0.760 | 0.877 | 0.721 | 0.885 | 0.892 | 0.058 | 4.039 |
LRJ51 | 16.000 | 7.579 | 2.241 | 0.151 | 0.868 | 0.826 | 0.854 | 0.811 | 0.815 | 0.025 | 9.834 |
LRJ53 | 20.000 | 2.499 | 1.578 | 0.061 | 0.600 | 0.898 | 0.585 | 0.897 | 0.898 | 0.012 | 21.093 |
LRJ54 | 16.000 | 3.814 | 1.719 | 0.094 | 0.738 | 0.873 | 0.704 | 0.869 | 0.873 | 0.031 | 7.748 |
LRJ62 | 23.000 | 5.830 | 2.194 | 0.099 | 0.828 | 0.881 | 0.809 | 0.874 | 0.877 | 0.030 | 8.002 |
LRJ65 | 17.000 | 6.989 | 2.309 | 0.113 | 0.857 | 0.868 | 0.845 | 0.877 | 0.881 | 0.031 | 7.938 |
LRJ71 | 11.000 | 4.396 | 1.790 | 0.123 | 0.772 | 0.841 | 0.747 | 0.838 | 0.840 | 0.009 | 26.146 |
LRJ73 | 11.000 | 3.353 | 1.552 | 0.098 | 0.702 | 0.860 | 0.663 | 0.860 | 0.861 | 0.008 | 32.639 |
LRJ81 | 9.000 | 3.451 | 1.499 | 0.065 | 0.710 | 0.908 | 0.666 | 0.904 | 0.907 | 0.030 | 7.971 |
LRJ88 | 11.000 | 3.030 | 1.447 | 0.066 | 0.670 | 0.902 | 0.625 | 0.915 | 0.915 | 0.009 | 26.846 |
LRJ89 | 8.000 | 2.194 | 1.136 | 0.079 | 0.544 | 0.854 | 0.513 | 0.867 | 0.870 | 0.024 | 10.149 |
Mean | 13.667 | 4.270 | 1.728 | 0.094 | 0.733 | 0.873 | 0.704 | 0.872 | 0.876 | 0.028 | 13.796 |
Philippines | Guangdong (China) | Guangxi (China) | Guizhou (China) | Hainan (China) | Hunan (China) | Cambodia | Laos | Myanmar | Malaysia | Thailand | India | Indonesia | Vietnam | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Philippines | - | 6.302 | 6.932 | 5.698 | 4.766 | 4.518 | 3.394 | 12.174 | 6.668 | 7.35 | 6.356 | 3.678 | 10.337 | 2.103 |
Guangdong (China) | 0.038 | - | 7.58 | 5.064 | 5.958 | 4.349 | 2.656 | 5.489 | 5.201 | 3.887 | 4.883 | 3.006 | 7.396 | 2.327 |
Guangxi (China) | 0.035 | 0.032 | - | 3.477 | 5.353 | 3.66 | 3.881 | 6.969 | 5.2 | 4.664 | 6.306 | 4.402 | 7.241 | 3.278 |
Guizhou (China) | 0.042 | 0.047 | 0.067 | - | 5.086 | 5.004 | 1.952 | 5.327 | 3.784 | 3.497 | 3.973 | 2.153 | 5.919 | 1.298 |
Hainan (China) | 0.05 | 0.04 | 0.045 | 0.047 | - | 6.343 | 2.412 | 4.657 | 3.375 | 4.059 | 4.465 | 3.586 | 5.133 | 1.79 |
Hunan (China) | 0.052 | 0.054 | 0.064 | 0.048 | 0.038 | - | 2.177 | 4.167 | 3.191 | 3.889 | 4.225 | 2.873 | 4.122 | 1.64 |
Cambodia | 0.069 | 0.086 | 0.061 | 0.114 | 0.094 | 0.103 | - | 4.905 | 4.312 | 2.924 | 4.008 | 5.595 | 4.069 | 2.131 |
Laos | 0.02 | 0.044 | 0.035 | 0.045 | 0.051 | 0.057 | 0.048 | - | 7.699 | 6.81 | 9.764 | 4.796 | 12.376 | 2.368 |
Myanmar | 0.036 | 0.046 | 0.046 | 0.062 | 0.069 | 0.073 | 0.055 | 0.031 | - | 3.555 | 5.75 | 3.904 | 10.075 | 1.954 |
Malaysia | 0.033 | 0.06 | 0.051 | 0.067 | 0.058 | 0.06 | 0.079 | 0.035 | 0.066 | - | 5.14 | 3.169 | 4.499 | 1.843 |
Thailand | 0.038 | 0.049 | 0.038 | 0.059 | 0.053 | 0.056 | 0.059 | 0.025 | 0.042 | 0.046 | - | 4.643 | 7.31 | 2.538 |
India | 0.064 | 0.077 | 0.054 | 0.104 | 0.065 | 0.08 | 0.043 | 0.05 | 0.06 | 0.073 | 0.051 | - | 3.894 | 2.183 |
Indonesia | 0.024 | 0.033 | 0.033 | 0.041 | 0.046 | 0.057 | 0.058 | 0.02 | 0.024 | 0.053 | 0.033 | 0.06 | - | 2.577 |
Vietnam | 0.106 | 0.097 | 0.071 | 0.161 | 0.123 | 0.132 | 0.105 | 0.096 | 0.113 | 0.119 | 0.09 | 0.103 | 0.088 | - |
Sample Plot | Na | Ne | I | Ho | He | F | |
---|---|---|---|---|---|---|---|
Philippines | Mean | 6.583 | 4.512 | 1.621 | 0.032 | 0.754 | 0.957 |
SE | 0.543 | 0.449 | 0.092 | 0.011 | 0.024 | 0.014 | |
Guangdong | Mean | 4.500 | 3.248 | 1.276 | 0.039 | 0.669 | 0.942 |
(China) | SE | 0.337 | 0.265 | 0.080 | 0.012 | 0.027 | 0.018 |
Guangxi | Mean | 5.833 | 3.501 | 1.400 | 0.089 | 0.674 | 0.876 |
(China) | SE | 0.575 | 0.359 | 0.107 | 0.015 | 0.038 | 0.019 |
Guizhou | Mean | 7.333 | 3.729 | 1.482 | 0.162 | 0.684 | 0.768 |
(China) | SE | 0.829 | 0.492 | 0.125 | 0.021 | 0.034 | 0.025 |
Hainan | Mean | 6.583 | 3.008 | 1.268 | 0.076 | 0.630 | 0.882 |
(China) | SE | 0.657 | 0.296 | 0.095 | 0.011 | 0.036 | 0.012 |
Hunan | Mean | 4.167 | 3.055 | 1.145 | 0.131 | 0.613 | 0.789 |
(China) | SE | 0.588 | 0.420 | 0.122 | 0.027 | 0.046 | 0.041 |
Cambodia | Mean | 4.167 | 3.092 | 1.158 | 0.031 | 0.592 | 0.945 |
SE | 0.423 | 0.374 | 0.148 | 0.016 | 0.071 | 0.028 | |
Laos | Mean | 7.917 | 4.223 | 1.556 | 0.081 | 0.704 | 0.887 |
SE | 0.933 | 0.688 | 0.137 | 0.014 | 0.041 | 0.016 | |
Myanmar | Mean | 4.833 | 3.978 | 1.427 | 0.012 | 0.713 | 0.983 |
SE | 0.322 | 0.424 | 0.091 | 0.012 | 0.033 | 0.017 | |
Malaysia | Mean | 4.417 | 3.398 | 1.282 | 0.205 | 0.668 | 0.702 |
SE | 0.379 | 0.344 | 0.097 | 0.032 | 0.036 | 0.045 | |
Thailand | Mean | 4.750 | 3.546 | 1.307 | 0.075 | 0.656 | 0.878 |
SE | 0.494 | 0.399 | 0.135 | 0.028 | 0.055 | 0.049 | |
India | Mean | 4.917 | 3.076 | 1.193 | 0.072 | 0.588 | 0.876 |
SE | 0.596 | 0.372 | 0.156 | 0.015 | 0.069 | 0.031 | |
Indonesia | Mean | 7.250 | 4.466 | 1.625 | 0.067 | 0.740 | 0.907 |
SE | 0.592 | 0.537 | 0.103 | 0.014 | 0.029 | 0.022 | |
Vietnam | Mean | 2.333 | 1.952 | 0.714 | 0.042 | 0.453 | 0.860 |
SE | 0.142 | 0.157 | 0.072 | 0.028 | 0.040 | 0.101 | |
Total | Mean | 5.399 | 3.485 | 1.318 | 0.080 | 0.653 | 0.875 |
SE | 0.186 | 0.118 | 0.034 | 0.006 | 0.013 | 0.011 |
Source | df | SS | MS | Est. Var. | PV% | Fst | Fis | Fit |
---|---|---|---|---|---|---|---|---|
Among Pops | 1 | 40.418 | 40.418 | 0.197 | 4.340% | |||
Among Indiv | 212 | 1726.285 | 8.143 | 3.791 | 83.333% | |||
Within Indiv | 214 | 120.000 | 0.561 | 0.561 | 12.326% | |||
Total | 427 | 1886.703 | 4.549 | 100% | 0.043 *** | 0.871 *** | 0.877 *** |
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Share and Cite
Li, R.; Huang, Y.; Yang, X.; Su, M.; **ong, H.; Dai, Y.; Wu, W.; Pei, X.; Yuan, Q. Genetic Diversity and Relationship of Shanlan Upland Rice Were Revealed Based on 214 Upland Rice SSR Markers. Plants 2023, 12, 2876. https://doi.org/10.3390/plants12152876
Li R, Huang Y, Yang X, Su M, **ong H, Dai Y, Wu W, Pei X, Yuan Q. Genetic Diversity and Relationship of Shanlan Upland Rice Were Revealed Based on 214 Upland Rice SSR Markers. Plants. 2023; 12(15):2876. https://doi.org/10.3390/plants12152876
Chicago/Turabian StyleLi, Rongju, Yinling Huang, **nsen Yang, Meng Su, Huaiyang **ong, Yang Dai, Wei Wu, **nwu Pei, and Qianhua Yuan. 2023. "Genetic Diversity and Relationship of Shanlan Upland Rice Were Revealed Based on 214 Upland Rice SSR Markers" Plants 12, no. 15: 2876. https://doi.org/10.3390/plants12152876