Phylogeography and Antioxidant Activity of Proso Millet (Panicum miliaceum L.)
Abstract
:1. Introduction
2. Results
2.1. Genetic Diversity Analysis
2.2. Population Structure and Phylogenetic Analysis
2.3. Geographical Distributions and Agronomic Characteristics of Subclusters
2.4. Gene Migration Analysis
2.5. Evaluation of Antioxidant Potentials
2.6. Association Analysis
3. Discussion
3.1. Gene Flow and Geographic Distributions
3.2. Association Analysis
4. Materials and Methods
4.1. Plant Materials and Genotyping
4.2. Genetic Diversity Analysis
4.3. Population Structure Analysis
4.4. Phylogenetic Analysis
4.5. Effective Population Size and Migration
4.6. Extraction and Determination of TPC
4.7. SOD Activity Measurement
4.8. Association Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Locus | Ng a | Na b | I c | Ho d | H e | Fst f | PIC g | MAF h |
---|---|---|---|---|---|---|---|---|
SSR-31 | 3 | 3 | 0.83 | 0 | 0.5185 | 0.5083 | 0.4277 | 0.5952 |
SSR-67 | 5 | 5 | 0.3864 | 0 | 0.1568 | 0.5596 | 0.1527 | 0.917 |
SSR-70 | 4 | 4 | 0.269 | 0 | 0.1208 | 0.211 | 0.1154 | 0.936 |
SSR-71 | 3 | 3 | 0.1518 | 0 | 0.0575 | 0.1335 | 0.0566 | 0.9706 |
SSR-82 | 6 | 6 | 0.4553 | 0 | 0.1926 | 0.4387 | 0.1857 | 0.8962 |
SSR-85 | 3 | 3 | 0.1527 | 0 | 0.0606 | 0.0957 | 0.0593 | 0.9689 |
SSR-86 | 2 | 2 | 0.1387 | 0 | 0.0603 | 0.119 | 0.0585 | 0.9689 |
SSR-92 | 3 | 3 | 0.5072 | 0 | 0.2864 | 0.6762 | 0.2534 | 0.8304 |
SSR-100 | 4 | 4 | 0.313 | 0 | 0.1341 | 0.0523 | 0.1294 | 0.9291 |
SSR-109 | 3 | 3 | 0.2646 | 0 | 0.1237 | 0.1991 | 0.1175 | 0.9343 |
SSR-120 | 5 | 5 | 0.6157 | 0 | 0.2895 | 0.4262 | 0.2723 | 0.8356 |
SSR-121 | 2 | 2 | 0.0803 | 0 | 0.0307 | 0.0705 | 0.0302 | 0.9844 |
SSR-127 | 3 | 3 | 0.1354 | 0 | 0.0508 | 0.0765 | 0.05 | 0.974 |
SSR-128 | 3 | 3 | 0.3346 | 0 | 0.1809 | 0.6783 | 0.1651 | 0.8997 |
SSR-129 | 3 | 3 | 0.2078 | 0 | 0.0837 | 0.0707 | 0.0819 | 0.9567 |
SSR-131 | 5 | 5 | 0.1612 | 0 | 0.0544 | 0.1865 | 0.0539 | 0.9723 |
SSR-142 | 3 | 3 | 0.1067 | 0 | 0.0375 | 0.1257 | 0.0371 | 0.981 |
SSR-143 | 5 | 5 | 0.0898 | 0 | 0.0274 | 0.0521 | 0.0273 | 0.9862 |
SSR-144 | 8 | 7 | 0.3365 | 0.0017 | 0.1199 | 0.5294 | 0.12 | 0.9369 |
SSR-146 | 4 | 4 | 0.0948 | 0 | 0.0308 | 0.0724 | 0.0306 | 0.9844 |
SSR-182 | 3 | 3 | 0.2275 | 0 | 0.0934 | 0.0609 | 0.0912 | 0.9516 |
SSR-195 | 3 | 3 | 0.5953 | 0 | 0.3512 | 0.6687 | 0.3024 | 0.7803 |
SSR-203 | 8 | 7 | 1.0966 | 0.0017 | 0.5816 | 0.4101 | 0.5086 | 0.545 |
SSR-232 | 17 | 6 | 1.2808 | 0.0657 | 0.6305 | 0.5055 | 0.5944 | 0.5536 |
SSR-331 | 4 | 4 | 0.5478 | 0 | 0.2672 | 0.4275 | 0.2511 | 0.8495 |
SSR-357 | 8 | 5 | 0.3716 | 0.0052 | 0.1535 | 0.3719 | 0.1491 | 0.9187 |
SSR-365 | 7 | 7 | 1.436 | 0 | 0.7331 | 0.4282 | 0.6884 | 0.3789 |
SSR-384 | 10 | 6 | 0.5456 | 0.0104 | 0.2291 | 0.2318 | 0.2178 | 0.878 |
SSR-386 | 6 | 6 | 0.1698 | 0.0035 | 0.0641 | 0.0604 | 0.0648 | 0.9663 |
SSR-394 | 4 | 4 | 0.7938 | 0.0017 | 0.52 | 0.5587 | 0.4107 | 0.5433 |
SSR-404 | 5 | 4 | 0.1716 | 0.0017 | 0.0672 | 0.3127 | 0.0642 | 0.9663 |
SSR-409 | 4 | 3 | 0.1446 | 0.0104 | 0.0636 | 0.0642 | 0.062 | 0.9671 |
SSR-420 | 4 | 3 | 0.0873 | 0.0087 | 0.034 | 0.0575 | 0.0287 | 0.9853 |
SSR-430 | 4 | 4 | 0.8734 | 0 | 0.4998 | 0.3517 | 0.44 | 0.6574 |
SSR-448 | 3 | 3 | 0.0885 | 0 | 0.0307 | 0.047 | 0.0304 | 0.9844 |
SSR-458 | 5 | 4 | 0.1054 | 0.0035 | 0.0375 | 0.0452 | 0.0371 | 0.981 |
SSR-460 | 5 | 3 | 0.1505 | 0.0035 | 0.0575 | 0.0742 | 0.0533 | 0.9723 |
Mean | 4.7838 | 4.0811 | 0.387 | 0.0032 | 0.19 | 0.4545 | 0.1735 | 0.874 |
St. Dev | 2.7226 | 1.3829 | 0.3434 | 0.0108 | 0.1954 | 0.1928 | 0.1705 | 0.1561 |
Origin | Ng a | Na b | I c | Ho d | H e | PIC f | MAF g |
---|---|---|---|---|---|---|---|
South Korea | 3.919 ± 1.402 | 3.73 ± 1.223 | 0.312 ± 0.338 | 0.002 ± 0.006 | 0.156 ± 0.192 | 0.145 ± 0.156 | 0.892 ± 0.154 |
North Korea | 1.486 ± 0.683 | 1.486 ± 0.683 | 0.077 ± 0.231 | 0 ± 0 | 0.051 ± 0.149 | 0.148 ± 0.201 | 0.858 ± 0.197 |
China | 3.108 ± 0.98 | 3.054 ± 0.928 | 0.188 ± 0.298 | 0.004 ± 0.013 | 0.333 ± 0.147 | 0.299 ± 0.13 | 0.857 ± 0.151 |
Mongolia | 2.324 ± 1.275 | 2.27 ± 1.106 | 0.248 ± 0.254 | 0.005 ± 0.018 | 0.13 ± 0.14 | 0.151 ± 0.175 | 0.893 ± 0.155 |
Uzbekistan | 1.243 ± 0.488 | 1.243 ± 0.488 | 0.068 ± 0.196 | 0.007 ± 0.041 | 0.047 ± 0.137 | 0.079 ± 0.153 | 0.912 ± 0.176 |
Thailand | 1.541 ± 0.682 | 1.541 ± 0.682 | 0.142 ± 0.338 | 0.003 ± 0.016 | 0.081 ± 0.191 | 0.103 ± 0.134 | 0.92 ± 0.124 |
India | 1.973 ± 1.174 | 1.919 ± 1.075 | 0.198 ± 0.338 | 0.002 ± 0.008 | 0.099 ± 0.18 | 0.094 ± 0.138 | 0.932 ± 0.116 |
Nepal | 1.27 ± 0.684 | 1.243 ± 0.633 | 0.174 ± 0.353 | 0.007 ± 0.044 | 0.097 ± 0.196 | 0.044 ± 0.112 | 0.969 ± 0.079 |
Turkey | 2.811 ± 1.135 | 2.811 ± 1.135 | 0.375 ± 0.409 | 0.004 ± 0.013 | 0.198 ± 0.225 | 0.255 ± 0.176 | 0.817 ± 0.146 |
Russia | 2.892 ± 2.576 | 2.568 ± 1.516 | 0.417 ± 0.324 | 0.008 ± 0.031 | 0.215 ± 0.183 | 0.131 ± 0.193 | 0.892 ± 0.185 |
Ukraine | 2 ± 1.115 | 1.973 ± 1.078 | 0.42 ± 0.436 | 0.01 ± 0.045 | 0.247 ± 0.247 | 0.198 ± 0.191 | 0.848 ± 0.164 |
AZE | BOL | CHN | CSK | FRA | IND | IRN | KAZ | KOR | MNG | NPL | PRK | RUS | THA | TJK | TUR | UKR | UZB | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
BOL | 0.078 *** | - | ||||||||||||||||
CHN | 0.133 *** | 0.16 *** | - | |||||||||||||||
CSK | 0.189 *** | 0.232 *** | 0.104 *** | - | ||||||||||||||
FRA | 0.081 *** | 0.124 *** | 0.156 *** | 0.162 *** | - | |||||||||||||
IND | 0.093 *** | 0.114 *** | 0.071 *** | 0.115 *** | 0.096 *** | - | ||||||||||||
IRN | 0.133 *** | 0.179 *** | 0.065 *** | 0.098 *** | 0.191 *** | 0.087 *** | - | |||||||||||
KAZ | 0.162 *** | 0.205 *** | 0.089 *** | 0.027 *** | 0.135 *** | 0.092 *** | 0.098 *** | - | ||||||||||
KOR | 0.127 *** | 0.143 *** | 0.055 *** | 0.114 *** | 0.13 *** | 0.038 *** | 0.081 *** | 0.089 *** | - | |||||||||
MNG | 0.135 *** | 0.145 *** | 0.088 *** | 0.136 *** | 0.132 *** | 0.063 *** | 0.127 *** | 0.109 *** | 0.041 *** | - | ||||||||
NPL | 0.165 *** | 0.186 *** | 0.121 *** | 0.117 *** | 0.145 *** | 0.082 *** | 0.126 *** | 0.09 *** | 0.065 *** | 0.078 *** | - | |||||||
PRK | 0.162 *** | 0.206 *** | 0.07 *** | 0.096 *** | 0.189 *** | 0.11 *** | 0.079 *** | 0.086 *** | 0.088 *** | 0.126 *** | 0.134 *** | - | ||||||
RUS | 0.085 *** | 0.094 *** | 0.07 *** | 0.128 *** | 0.096 *** | 0.025 *** | 0.103 *** | 0.104 *** | 0.031 *** | 0.032 *** | 0.073 *** | 0.109 *** | - | |||||
THA | 0.116 *** | 0.122 *** | 0.096 *** | 0.125 *** | 0.114 *** | 0.045 *** | 0.12 *** | 0.098 *** | 0.057 *** | 0.063 *** | 0.099 *** | 0.111 *** | 0.052 *** | - | ||||
TJK | 0.054 *** | 0.105 *** | 0.15 *** | 0.216 *** | 0.108 *** | 0.121 *** | 0.16 *** | 0.189 *** | 0.15 *** | 0.158 *** | 0.17 *** | 0.198 *** | 0.107 *** | 0.158 *** | - | |||
TUR | 0.208 *** | 0.248 *** | 0.1 *** | 0.215 ** | 0.27 *** | 0.172 *** | 0.114 *** | 0.226 *** | 0.145 *** | 0.181 *** | 0.225 *** | 0.133 *** | 0.17 *** | 0.207 *** | 0.238 *** | - | ||
UKR | 0.111 *** | 0.146 *** | 0.074 *** | 0.143 *** | 0.133 *** | 0.067 *** | 0.124 *** | 0.118 *** | 0.054 *** | 0.047 *** | 0.09 *** | 0.118 *** | 0.04 *** | 0.08 *** | 0.134 *** | 0.159 *** | - | |
UZB | 0.06 *** | 0.051 *** | 0.11 *** | 0.174 *** | 0.13 *** | 0.088 *** | 0.116 *** | 0.147 *** | 0.094 *** | 0.096 *** | 0.117 *** | 0.133 *** | 0.06 *** | 0.104 *** | 0.097 *** | 0.181 *** | 0.102 *** | - |
Pop18 | 0.341 *** | 0.272 *** | 0.253 *** | 0.137 ** | 0.212 *** | 0.111 ** | 0.131 *** | 0.157 *** | 0.313 *** | 0.221 *** | 0.313 *** | 0.215 *** | 0.119 | 0.307 *** | 0.237 *** | 0.324 *** | 0.431 *** | 0.101 *** |
No | Cluster | Sub-Cluster | NB/P a | HD b | HT c | PL d | PW e | SD f | PH g |
---|---|---|---|---|---|---|---|---|---|
1 | A | A1 | 8.74 ± 1.98 | 31.99 ± 3.95 | 93.84 ± 5.84 | 29.81 ± 3.91 | 8.34 ± 1.9 | 2.75 ± 0.39 | 106.55 ± 14.2 |
1 | A2 | 7.73 ± 1.94 | 27.13 ± 5.6 | 92.56 ± 6.71 | 25.73 ± 7.56 | 7.3 ± 3.34 | 2.23 ± 0.67 | 84.02 ± 31.64 | |
2 | B | B1 | 7.58 ± 2.15 | 23.34 ± 5.23 | 93.34 ± 5.32 | 19 ± 6.37 | 5.14 ± 2.65 | 1.68 ± 0.63 | 54.76 ± 28.67 |
2 | B2 | 8.16 ± 2.13 | 29.83 ± 5.27 | 94.78 ± 5.19 | 26.45 ± 6.02 | 7.93 ± 3.18 | 2.43 ± 0.57 | 92.78 ± 27.58 | |
3 | C | C1 | 8.1 ± 2.04 | 29.39 ± 5.93 | 94.09 ± 5.94 | 26.78 ± 7.28 | 7.1 ± 2.64 | 2.37 ± 0.68 | 89.06 ± 30.08 |
3 | C2 | 8.71 ± 2.18 | 26.81 ± 3.79 | 99.32 ± 5.36 | 22.42 ± 5.51 | 4.76 ± 1.59 | 1.71 ± 0.63 | 80.4 ± 21.59 |
Trait | Marker Name | p-Value | r2 | Genotype | Count | Corresponding Value (Average) |
---|---|---|---|---|---|---|
TPC (μg/g) | SSR-31 | 1.88E-04 | 0.07084 | 278/278 | 30 | 10.12 |
287/287 | 344 | 12.89 | ||||
297/297 | 204 | 19.41 |
Name | Forward Primer | Reverse Primer | Annealing Temp. (°C) |
---|---|---|---|
SSR-31 | ACTTCCCTAGAGTTCCAGT | TTCTGAAACTGTTCTATTGG | 45 |
SSR-67 | ACTAGGTAATTACAGGGGAG | GGCATGTGGAGTAGTAGTAT | 46 |
SSR-70 | ACTCATCTGACAAACTATGG | ATAGAACTGTGTGTTGGTGT | 45 |
SSR-71 | ACTCATGATTAAAGGGTGAT | TGTGACAACATTGTGAATAG | 46 |
SSR-82 | ACCAGCCCCAACTAC | ATTGTTTATGTGATCTCAGG | 45 |
SSR-85 | ACCAGTACGGCAACC | ATTTCTCTTTGATCTTCTCC | 45 |
SSR-86 | ACCAGTACGGCAACC | TTGATCTTCTCCTTAATGC | 45 |
SSR-92 | ACCCACCCAACCAGT | TACTTTGTCCTTTTCCAGTA | 46 |
SSR-100 | ACCTAGACAAATGCGTACT | CAAAACCAAACCCTCTC | 45 |
SSR-109 | ACCTTAAGGATTGGAATATC | GTTGAGTAAGTTTCTCCTCA | 46 |
SSR-120 | ACGACCATGATCTCATAAC | GAGGATGATGAGTAGGAAGT | 45 |
SSR-121 | ACGACGATGATGATGAC | TCTGGTCAAGTACTCAATTC | 46 |
SSR-127 | ACGAGGAGATGGATCAG | CTCTCTGTCCGTGGTC | 46 |
SSR-128 | ACGATGATGAAGAAGCA | GAACTGGCAGAAGCAC | 46 |
SSR-129 | ACGATGGGGTCTACG | AGCTTAACCCTGAACTTCT | 45 |
SSR-131 | ACGCAGCCTCATCAT | TAAGAAGCTGAGATTTGGT | 45 |
SSR-142 | ACTAAGAGGAAGCCTATGTT | AACTGCAGCTACATTGTATT | 45 |
SSR-143 | ACTAAGAGGAAGCCTATGTT | TACAGCAGTGCAGATATTTA | 45 |
SSR-144 | ACTAAGAGGAAGCCTATGTT | TTAAGCTGGAAAGTAATCAG | 45 |
SSR-146 | ACTACAAGAGCAAGTCCAC | AAATACAACATTGCAAGACT | 45 |
SSR-182 | ACAACAGATTTCTAAACCAA | TCTCGGAGAACATCAAG | 45 |
SSR-195 | ACAAGTAATTTCCGTATCAA | AGTCAGAAGAGTCAACAACA | 45 |
SSR-203 | ACACAAACTTGATACTCTGG | GTGTTGTATGCAACTGAAG | 45 |
SSR-232 | ACAGTAATCTACGCAACAAT | ATTTTTCCCTTTTGTTCTAT | 45 |
SSR-331 | AAGCAGCTGAGGATAAAG | GTACACTCCGAACTCAAAG | 45 |
SSR-357 | AAGGTGATCATGTAATGAGA | GTGTCATATTGGCAGTAAGT | 45 |
SSR-365 | AAGTACGAGAACCTGATTG | AGTTTCTTACCCTTTTCAAC | 53 |
SSR-384 | AAGTTCAGCGACTTAAGATA | TGATATTGTCCTCAAATGAC | 45 |
SSR-386 | AAGTTTCTACCCTTTTCAAC | AAGTACGAGAACCTGATTG | 53 |
SSR-394 | AATAATCAACAACCGAATTA | CTCCTATCCATTACTGATGA | 45 |
SSR-404 | AAGAGAAAGAACGGCTATT | ACAGAGCTCACAATATGTTC | 53 |
SSR-409 | AAGAGTAGGAGACCCATTAC | AGGTAAAAATATGCCTGAAT | 53 |
SSR-420 | AAGAAGGGTAGTGATGGAT | TTGTTTTAGACTCTCCTCAA | 53 |
SSR-430 | AACTCTGTCATATGGTTACG | AGGGGATTCTTCAGATAAT | 45 |
SSR-448 | AAGAAATCAGAGAGGACAGT | ACAAGAAAAACTCGAGTACA | 53 |
SSR-458 | AACTACGTACAAAAATGGAA | CATAAATAGCGAGCATACAT | 50 |
SSR-460 | AACTAGCAATAGGTTGAACA | GACTGGTACATTTTCAAAGA | 45 |
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Wang, X.-H.; Lee, M.-C.; Choi, Y.-M.; Kim, S.-H.; Han, S.; Desta, K.T.; Yoon, H.-M.; Lee, Y.-J.; Oh, M.-A.; Yi, J.-Y.; et al. Phylogeography and Antioxidant Activity of Proso Millet (Panicum miliaceum L.). Plants 2021, 10, 2112. https://doi.org/10.3390/plants10102112
Wang X-H, Lee M-C, Choi Y-M, Kim S-H, Han S, Desta KT, Yoon H-M, Lee Y-J, Oh M-A, Yi J-Y, et al. Phylogeography and Antioxidant Activity of Proso Millet (Panicum miliaceum L.). Plants. 2021; 10(10):2112. https://doi.org/10.3390/plants10102112
Chicago/Turabian StyleWang, Xiao-Han, Myung-Chul Lee, Yu-Mi Choi, Seong-Hoon Kim, Seahee Han, Kebede Taye Desta, Hye-Myeong Yoon, Yoon-Jung Lee, Mi-Ae Oh, Jung-Yoon Yi, and et al. 2021. "Phylogeography and Antioxidant Activity of Proso Millet (Panicum miliaceum L.)" Plants 10, no. 10: 2112. https://doi.org/10.3390/plants10102112
APA StyleWang, X.-H., Lee, M.-C., Choi, Y.-M., Kim, S.-H., Han, S., Desta, K. T., Yoon, H.-M., Lee, Y.-J., Oh, M.-A., Yi, J.-Y., & Shin, M.-J. (2021). Phylogeography and Antioxidant Activity of Proso Millet (Panicum miliaceum L.). Plants, 10(10), 2112. https://doi.org/10.3390/plants10102112