Epigenetic Variation Induced by Gamma Rays, DNA Methyltransferase Inhibitors, and Their Combination in Rice
Abstract
:1. Introduction
2. Results
2.1. Evaluation of Polymorphisms Detected by MSAP and TMD Marker Systems
2.2. Methylation Changes Induced by Treatment with GRs and DNMTis
2.3. Analysis of Molecular Variance
2.4. Population Structure and Phylogenetic Analysis
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Genomic DNA Extraction
4.2. Molecular Marker Analysis
4.3. Data Analysis
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Marker Type and Groups | No. of Samples | No. of Primer Sets | No. of Loci | No. of Polymorphic Loci (%) | Nei’s Gene Diversity (H) | Shannon’s Information Index (I) | PIC 1 |
---|---|---|---|---|---|---|---|
MSAP | |||||||
Control | 5 | 6 | 102 | 23 (22.55) | 0.292 | 0.433 | |
GR 2 | 24 | 6 | 102 | 41 (40.20) | 0.341 | 0.498 | |
DNMTi 3 | 16 | 6 | 102 | 39 (38.24) | 0.357 | 0.538 | |
DNMTi + GR 4 | 48 | 6 | 102 | 61 (59.80) | 0.366 | 0.549 | |
Total | 93 | 6 | 102 | 66 (64.71) | 0.340 | 0.500 | 0.63 |
TMD | |||||||
Control | 5 | 4 | 60 | 15 (25.00) | 0.438 | 0.627 | |
GR 2 | 24 | 4 | 60 | 24 (40.00) | 0.465 | 0.657 | |
DNMTi 3 | 16 | 4 | 60 | 29 (48.33) | 0.484 | 0.677 | |
DNMTi + GR 4 | 48 | 4 | 60 | 34 (56.67) | 0.497 | 0.679 | |
Total | 93 | 4 | 60 | 41 (68.33) | 0.420 | 0.660 | 0.65 |
Band Type | M 1 | H 1 | Treatment Groups | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Control | G100 | G150 | G250 | A80 | Z80 | A80 + G100 | A80 + Z150 | Z80 + G100 | Z80 + G150 | |||
I | 1 | 1 | 221 | 336 | 337 | 338 | 363 | 362 | 573 | 580 | 550 | 586 |
II | 1 | 0 | 70 | 100 | 67 | 84 | 57 | 59 | 90 | 92 | 96 | 102 |
III | 0 | 1 | 102 | 126 | 97 | 84 | 54 | 48 | 83 | 78 | 82 | 46 |
IV | 0 | 0 | 142 | 246 | 317 | 288 | 331 | 324 | 498 | 512 | 485 | 503 |
Total methylated (%) 2,3 | 58.69 | 58.42 | 58.8 | 57.43 | 54.91 | 54.35 | 53.94 | 54.04 | 54.66 | 52.63 | ||
Fully methylated (%) 2,4 | 13.08 | 12.38 | 8.19 | 10.58 | 7.08 | 7.44 | 7.23 | 7.29 | 7.91 | 8.25 | ||
Hemi-methylated (%) 2,5 | 19.07 | 15.59 | 11.86 | 10.58 | 6.71 | 6.05 | 6.67 | 6.18 | 6.76 | 3.72 | ||
Non-methylated (%)2,6 | 41.31 | 41.58 | 41.2 | 42.57 | 45.09 | 45.65 | 46.06 | 45.96 | 45.34 | 47.37 |
Band Type | M 1 | H 1 | Treatment Groups | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Control | G100 | G150 | G250 | A80 | Z80 | A80 + G100 | A80 + Z150 | Z80 + G100 | Z80 + G150 | |||
I | 1 | 1 | 97 | 148 | 162 | 164 | 166 | 167 | 254 | 266 | 287 | 299 |
II | 1 | 0 | 53 | 54 | 52 | 55 | 51 | 49 | 44 | 43 | 44 | 41 |
III | 0 | 1 | 16 | 45 | 46 | 48 | 66 | 64 | 115 | 121 | 121 | 130 |
IV | 0 | 0 | 61 | 119 | 126 | 127 | 115 | 112 | 127 | 132 | 133 | 121 |
Total methylated (%) 2,3 | 57.27 | 59.56 | 58.03 | 58.38 | 58.29 | 57.40 | 52.96 | 52.67 | 50.94 | 49.41 | ||
Fully methylated (%) 2,4 | 23.35 | 14.75 | 13.47 | 13.96 | 12.81 | 12.50 | 8.15 | 7.65 | 7.52 | 6.94 | ||
Hemi-methylated (%) 2,5 | 7.05 | 12.30 | 11.92 | 12.18 | 16.58 | 16.33 | 21.30 | 21.53 | 20.68 | 22.00 | ||
Non-methylated (%) 2,6 | 42.73 | 40.44 | 41.97 | 41.62 | 41.71 | 42.60 | 47.04 | 47.33 | 49.06 | 50.59 |
Source | Df 1 | SS 2 | MS 3 | Est. Var. 4 | % 5 | P (rand ≥ data) 6 |
---|---|---|---|---|---|---|
MSAP | ||||||
Among groups | 3 | 174.551 | 58.184 | 2.592 | 26% | 0.001 |
Within groups | 89 | 641.363 | 7.206 | 7.206 | 74% | |
TMD | ||||||
Among groups | 3 | 161.269 | 53.756 | 2.473 | 33% | 0.001 |
Within groups | 89 | 454.688 | 5.109 | 5.109 | 67% | |
MSAP + TMD | ||||||
Among groups | 3 | 335.821 | 111.940 | 5.065 | 29% | 0.001 |
Within groups | 89 | 1431.871 | 12.315 | 12.315 | 71% |
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Lee, S.-I.; Park, J.W.; Kwon, S.-J.; Jo, Y.D.; Hong, M.J.; Kim, J.-B.; Choi, H.-I. Epigenetic Variation Induced by Gamma Rays, DNA Methyltransferase Inhibitors, and Their Combination in Rice. Plants 2020, 9, 1088. https://doi.org/10.3390/plants9091088
Lee S-I, Park JW, Kwon S-J, Jo YD, Hong MJ, Kim J-B, Choi H-I. Epigenetic Variation Induced by Gamma Rays, DNA Methyltransferase Inhibitors, and Their Combination in Rice. Plants. 2020; 9(9):1088. https://doi.org/10.3390/plants9091088
Chicago/Turabian StyleLee, Sung-Il, Jae Wan Park, Soon-Jae Kwon, Yeong Deuk Jo, Min Jeong Hong, Jin-Baek Kim, and Hong-Il Choi. 2020. "Epigenetic Variation Induced by Gamma Rays, DNA Methyltransferase Inhibitors, and Their Combination in Rice" Plants 9, no. 9: 1088. https://doi.org/10.3390/plants9091088