Table 2. Analysis of DNA methylation patterns under salinity stress with respect to control condition in the shoot and root of seedlings of rice varieties, IR29, Nipponbare (Nipp), Pokkali (Pokk), and Geumgangbyeo (Geum).
Description of Pattern | Class | Banding Pattern | Shoot | Root | |||||||||
Control | Salinity | ||||||||||||
HpaII | MspI | HpaII | MspI | IR29 | Nipp | Pokk | Geum | IR29 | Nipp | Pokk | Geum | ||
A | 1 | 0 | 1 | 0 | 20 | 62 | 42 | 17 | 3 | 7 | 4 | 3 | |
No change | B | 0 | 1 | 0 | 1 | 108 | 44 | 30 | 12 | 54 | 55 | 54 | 51 |
C | 1 | 1 | 1 | 1 | 505 | 541 | 287 | 775 | 1238 | 1168 | 1131 | 1240 | |
D | 0 | 0 | 0 | 0 | 184 | 180 | 373 | 282 | 188 | 131 | 153 | 153 | |
Total | 817(50.0%) | 827(50.6%) | 732(44.9%) | 1086(66.7%) | 1483(90.9%) | 1361(85.8%) | 1342(84.8%) | 1447(88.7%) | |||||
E | 1 | 0 | 1 | 1 | 62 | 70 | 17 | 80 | 3 | 17 | 21 | 5 | |
F | 0 | 1 | 1 | 1 | 136 | 53 | 42 | 105 | 39 | 26 | 28 | 30 | |
Demethylation | G | 0 | 0 | 1 | 1 | 85 | 27 | 19 | 107 | 34 | 49 | 52 | 43 |
H | 0 | 1 | 1 | 0 | 25 | 37 | 30 | 16 | 3 | 7 | 3 | 4 | |
I | 0 | 0 | 1 | 0 | 50 | 49 | 43 | 56 | 10 | 13 | 5 | 5 | |
J | 0 | 0 | 0 | 1 | 127 | 50 | 36 | 44 | 22 | 16 | 22 | 17 | |
Total | 485(29.7%) | 286(17.5%) | 187(11.5%) | 408(25.1%) | 111(6.8%) | 128(8.1%) | 131(8.3%) | 104(6.4%) | |||||
K | 1 | 1 | 1 | 0 | 18 | 142 | 202 | 30 | 7 | 12 | 22 | 7 | |
L | 1 | 1 | 0 | 1 | 113 | 98 | 75 | 16 | 7 | 7 | 38 | 29 | |
Methylation | M | 1 | 1 | 0 | 0 | 29 | 96 | 134 | 17 | 21 | 46 | 37 | 32 |
N | 1 | 0 | 0 | 1 | 77 | 43 | 17 | 21 | 1 | 5 | 0 | 0 | |
O | 1 | 0 | 0 | 0 | 42 | 71 | 217 | 24 | 0 | 5 | 7 | 2 | |
P | 0 | 1 | 0 | 0 | 53 | 71 | 68 | 27 | 2 | 21 | 5 | 10 | |
Total | 332(20.3%) | 521(31.9%) | 713(43.6%) | 135(8.2%) | 38(2.3%) | 96(6.1%) | 109(6.9%) | 80(4.9%) |
A score of 1 and 0 represents presence and absence of bands, respectively. Values in parentheses indicate percentage of bands in each pattern which was determined by dividing number of bands in each pattern by total number of bands in all three patterns.