Table 1.
Genetic regions significantly associated with resistance to the Magnaporthe oryzae isolate D41-2
| No. | Population | Phenotype | Chr. | Rangea | Physical position (bp)b | Highest marker information | Known R genes/QTLs | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Marker ID | Allele | MAF (%)c | − Log10(P) | R2d | |||||||
| D-01 | indica | LT | 1 | id1010103–id1010205 | 15,438,604–15,649,252 | id1010164 | T/C | 19.6 | 4.55 | 0.16 | AQCT001, AQEN001, AQEN011, AQEN018 |
| D-02 | indica | DLA | 1 | id1011342–id1011401 | 18,821,356–18,925,916 | id1011349 | C/A | 9.28 | 3.96 | 0.18 | AQCT001, AQEN001, AQEN011, AQEN018 |
| D-03 | Full | DLA | 2 | id2003636–id2003653 | 7,104,193–7,129,000 | id2003651 | C/T | 11.59 | 4.88 | 0.07 | – |
| D-04 | Full | DLA | 2 | id2006540-id2006687 | 16,209,277–16,648,368 | id2006548 | G/T | 8.28 | 4.38 | 0.06 | – |
| D-05 | Full | DLA | 3 | id3010758–ud3001344 | 23,818,976–24,280,279 | id3010813 | C/T | 32.01 | 4.86 | 0.06 | AQAF029 |
| ud3001342 | T/C | 31.91 | 0.06 | ||||||||
| D-06 | Full | DLA | 3 | id3016979–id3017136 | 34,609,998–34,809,786 | id3017114 | G/A | 12.37 | 5.41 | 0.08 | – |
| D-07 | Full | DLA | 4 | id4008106–id4008335 | 24,437,545–24,950,637 | id4008148 | T/A | 46.8 | 5.30 | 0.07 | CQAC2, Pikur1 |
| D-08 | Full | DLA | 4 | id4008360–id4008522 | 25,043,111–25,696,775 | id4008464 | G/A | 7.01 | 4.87 | 0.07 | CQAC2, Pikur1 |
| D-09 | Full | DLA | 4 | id4008601–id4008681 | 26,300,907–26,575,531 | id4008636 | G/A | 5.92 | 4.29 | 0.06 | CQAC2, Pikur1 |
| D-10 | Full | DLA | 5 | id5009568–id5009958 | 22,335,609–22,650,069 | id5009818 | G/T | 5.96 | 4.13 | 0.06 | AQAQ024 |
| D-11 | Full | DLA | 5 | id5009967–id5010294 | 22,654,409–23,102,774 | id5010176 | A/T | 10.2 | 3.72 | 0.05 | – |
| D-12 | Full | DLA | 8 | id8005634–ud8001357 | 20,708,815–20,937,247 | id8005717 | A/G | 34.65 | 5.21 | 0.07 | Pizh |
| D-13e | indica | LT | 12 | ud12000652–id12004102 | 10,218,678–10,611,754 | wd12001025 | T/A | 38.04 | 4.77 | 0.19 | AQCT008, AQEN010, AQEN017, LABR_87, LABR_88, LABR_89, Pi6(t), Pi12, Pi19(t), Pi20, Pi31(t), Pi58(t), Pi62(t), Pi157, Pita2, Pita |
| D-14 | Full | LT | 12 | id12004113–id12004234 | 10,669,467–10,900,950 | id12004183 | A/G | 35.64 | 4.64 | 0.07 | AQCT008, AQEN010, AQEN017, Pi6(t), Pi12, Pi19(t), Pi31(t), Pi58(t), Pi62(t), Pi157, Pita2, Ptr |
| Full | DLA | ||||||||||
| indica | LT | id12004196 | G/A | 15.46 | 5.03 | 0.07 | |||||
| id12004196 | G/A | 37.5 | 5.09 | 0.12 | |||||||
| D-15f | Full | DLA | 12 | id12004251–wd12001183 | 11,060,008–11,555,556 | id12004303 | A/G | 15.43 | 5.31 | 0.08 | AQCT008, AQEN010, AQEN017, CQAC4, LABR_90, Pi6(t), Pi12, Pi19(t), Pi31(t), Pi58(t), Pi62(t), Pi157, Pita2 |
| D-16 | Full | DLA | 12 | id12004432–id12004540 | 12,065,937–12,565,383 | id12004538 | G/A | 16.33 | 5.37 | 0.08 | 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