Table 2.
Genetic regions significantly associated with resistance to the Magnaporthe oryzae isolate 12YL-DL3-2
| No. | Population | Phenotype | Chr. | Rangea | Physical position (bp)b | Highest marker informationb | Known R genes/QTLs | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Marker ID | Allele | MAF (%)c | − Log10(P) | R2d | |||||||
| Y-01 | indica | DLA | 1 | id1013754–id1014034 | 23,732,729–23,934,283 | id1013942 | T/G | 36 | 4.47 | 0.21 | AQCT001, AQEN001, LABR_10 |
| Y-02 | indica | DLA | 1 | id1015101–id1015282 | 25,284,622–25,681,092 | id1015101 | A/G | 35.06 | 6.83 | 0.31 | AQAH002, AQCT001, AQEN001, Pitp(t) |
| LT | 35.06 | 4.85 | 0.28 | ||||||||
| Y-03 | indica | DLA | 2 | id2007485–id2007516 | 18,977,320–19,192,422 | id2007494 | G/T | 41.09 | 5.37 | 0.26 | – |
| Y-04 | indica | DLA | 2 | id2008594–id2008644 | 21,493,161–21,607,823 | id2008601 | A/G | 39.24 | 4.88 | 0.22 | Pid(t)1 |
| Y-05 | indica | DLA | 2 | id2009379–id2009403 | 23,397,267–23,466,199 | id2009379 | T/C | 34.21 | 4.42 | 0.21 | – |
| Y-06 | indica | DLA | 3 | id3017643–id3017725 | 35,480,048–35,558,427 | id3017643 | C/G | 33.33 | 4.19 | 0.19 | – |
| Y-07 | indica | DLA | 5 | id5002016-id5002075 | 3,483,482-3,586,560 | id5002075 | C/T | 30 | 4.06 | 0.18 | – |
| Y-08 | indica | DLA | 5 | wd5001198–wd5001344 | 10,351,569–10,848,969 | id5004839, id5004859 | C/T | 22.79 | 4.15 | 0.19 | AQEN004, Pi23 |
| A/G | 23.75 | 0.18 | |||||||||
| Y-09 | indica | DLA | 6 | id6004112–id6004235 | 6,458,990–6,636,955 | id6004212 | C/T | 46.15 | 4.37 | 0.20 | AQCT004, AQEN005, Pii1, Pi8, Pi59(t), Pi27(t) |
| Y-10 | indica | DLA | 8 | id8000511–id8000544 | 1,744,391–1,839,119 | id8000544 | A/G | 32.88 | 4.66 | 0.23 | – |
| Y-11 | indica | DLA | 8 | id8000658–id8000695 | 2,130,616–2,184,609 | id8000663 | C/T | 26.67 | 4.47 | 0.21 | – |
| Y-12 | indica | DLA | 12 | id12002136–id12002219 | 4,731,647–4,872,049 | id12002210 | A/G | 11.54 | 4.52 | 0.21 | Pi6(t), Pi62(t) |
| Y-13 | japonica | DLA | 12 | id12003134–id12003432 | 7,827,050–8,296,350 | id12003144 | T/C | 7.64 | 4.09 | 0.10 | AQCT008, AQEN010, AQEN017, Pi6(t), Pi12, Pi20, Pi31(t), Pi58(t), Pi62(t) |
| Y-14 | japonica | DLA | 12 | ud12000485–id12003608 | 8,383,596–8,874,826 | id12003547 | C/T | 7.9 | 4.04 | 0.10 | AQCT008, AQEN010, AQEN017, Pi6(t), Pi12, Pi19(t), Pi20, Pi31(t), Pi58(t), Pi62(t), Pi157 |
| id12003562 | A/T | 7.9 | 4.04 | 0.10 | |||||||
| Y-15 | japonica | DLA | 12 | id12003642–ud12000566 | 8,914,661–9,231,272 | id12003728 | T/A | 8.1 | 3.93 | 0.10 | AQCT008, AQEN010, AQEN017, Pi6(t), Pi12, Pi19(t), Pi20, Pi31(t), Pi58(t),, Pi62(t), Pi157 |
| Y-16e | Full | LT | 12 | id12003919–id12004113 | 10,058,758–10,669,467 | id12004093 | G/A | 10 | 5.67 | 0.11 | AQCT008, AQEN010, AQEN017, LABR_87, LABR_88, LABR_89, Pi6(t), Pi12, Pi19(t), Pi20, Pi31(t), Pi58(t), Pi62(t), Pi157, Pita2, Pita |
| japonica | LT | id12004007 | A/T | 7 | 4.82 | 0.02 | |||||
| japonica | DLA | wd12001025 | T/A | 8.2 | 4.62 | 0.13 | |||||
| Y-17f | Full | LT | 12 | id12004251–wd12001183 | 11,060,008–11,555,556 | id12004284 | C/G | 8.52 | 5.87 | 0.11 | AQCT008, AQEN010, AQEN017, CQAC4, LABR_90, Pi6(t), Pi12, Pi19(t), Pi31(t), Pi58(t), Pi62(t), Pi157, Pita2 |
| Y-18 | Full | LT | 12 | id12004546–id12004685 | 12,567,686–13,060,942 | id12004554 | C/A | 42.11 | 5.4 | 0.10 | AQCT008, AQCT009, AQEN010, AQEN017, CQAC4, Pi6(t), Pi12, Pi19(t), Pi51(t), Pi62(t), Pi157, Pita2 |
aThe left-border marker and right-border marker of the QTL
bThe physical map position is based on MSU version 7.0 Nipponbare rice reference genome
cMAF: minor allele frequency
dR2 represents the proportion of the phenotypic variation explained by the single nucleotide polymorphism
e, fSame or largely overlapped genetic region identified by using D41-2 and 12YL-DL3-2