Trait | SNP ID | Chr. | Position (IRGSP-1.0) | Statistical model | P-value | Known QTL | Known gene | Â |
---|---|---|---|---|---|---|---|---|
NPQ | id1003509 | 1 | 4,209,827 | All - P | 4.17E-07 | QKr1.1 [28]; qRNC-1, qRRNC4, qRKC1, qRRKC1, qRNa/K1–1, qRRNa/K1–1 [29] |  |  |
F0 | id1004960 | 1 | 6,508,269 | IND - K | 2.17E-04 | qRL-1, qNAUP-1b [30] | Â | Â |
qL | id1016791 | 1 | 28,594,265 | All - P + K | 7.95E-05 |  |  | |
 | id1016825 | 1 | 28,599,615 | All - K | 8.10E-04 |  |  |  |
NPQ | id1024223 | 1 | 38,162,791 | All - P | 4.95E-05 | Â | Â | Â |
ΦPSII | id1026852 | 1 | 41,787,616 | All - P | 3.99E-05 | qSH1–3 [31] | Ygl8 (LOC_Os01g73450, Zhu et al. [32]) |  |
 | id1027309 | 1 | 42,134,803 | All - K | 2.20E-04 |  |  |  |
NPQ | id1026852 | 1 | 41,787,616 | All - P | 4.67E-06 | qSH1–3 [31] |  |  |
F0 | id1027269 | 1 | 42,082,183 | All - K | 1.01E-04 | qSH1–3 [31] |  |  |
 |  |  |  | JPN - K | 7.39E-04 |  |  |  |
 | id1027563 | 1 | 42,339,408 | All - P | 7.63E-06 | qSH1–3 [31] |  |  |
 |  |  |  | All - P + K | 1.53E-04 |  |  |  |
qL | id1027309 | 1 | 42,134,803 | All - P | 4.26E-05 | qSH1–3 [31] |  |  |
 |  |  |  | All - K | 5.44E-04 |  |  |  |
Fm | id1027821 | 1 | 42,581,986 | All - P | 1.55E-05 | qSH1–3 [31] |  |  |
ΦPSII | id2001842 | 2 | 3,253,759 | All - P | 7.78E-05 |  |  |  |
 |  |  |  | All - K | 3.05E-04 |  |  |  |
 |  |  |  | All - P + K | 2.35E-04 |  |  |  |
qL | id2001842 | 2 | 3,253,759 | All - K | 7.90E-04 | qSST2 [33] | Â | Â |
NPQ | id2006687 | 2 | 16,648,368 | All - P | 4.10E-05 | Â | Â | |
NPQ | id2007192 | 2 | 17,927,911 | All - P | 5.81E-05 | Â | Â | |
F0 | id2008158 | 2 | 20,817,846 | All - P | 7.91E-05 | QDss2a, QSkc2, QKna2 [34] | Â | Â |
 |  |  |  | All - K | 2.06E-04 |  |  |  |
 |  |  |  | All - P + K | 1.41E-04 |  |  |  |
NPQ | id2008679 | 2 | 21,812,170 | All - P | 5.36E-05 | QDss2a, QSkc2, QKna2 [34] | Â | Â |
F0 | id2010410 | 2 | 24,565,561 | All - P + K | 2.62E-04 |  |  | |
 | id2010572 | 2 | 24,696,197 | All - P | 1.25E-05 |  |  |  |
 | id2010581 | 2 | 24,713,963 | All - K | 5.03E-04 |  |  |  |
NPQ | id2010932 | 2 | 25,236,351 | All - P | 5.50E-05 | Â | Â | |
Fm | id4000429 | 4 | 686,361 | All - P | 1.90E-05 | Â | Â | Â |
 |  |  |  | All - K | 7.32E-04 |  |  |  |
qL | id4002349 | 4 | 5,526,924 | IND - K | 3.61E-04 | qRL4 [30] | Â | Â |
Fm | id4002319 | 4 | 5,487,935 | IND - K | 5.13E-04 | Â | Â | Â |
F0 | id5001540 | 5 | 2,773,921 | All - P | 1.70E-06 | QKs5 [28] | OsNHX3 (LOC_Os05g05610, Fukuda et al. [35]) | Â |
 | id5001584 | 5 | 2,825,199 | All - K | 9.66E-05 |  |  |  |
 |  |  |  | All - P + K | 6.82E-06 |  |  |  |
 |  |  |  | JPN - K | 3.06E-04 |  |  |  |
Fm | id5001738 | 5 | 3,064,389 | IND - K | 2.25E-05 | QSst5, QDss5a, QDss5b [34] | Â | Â |
NPQ | Â | Â | Â | IND - K | 7.46E-04 | Â | Â | Â |
qL | id5012588 | 5 | 26,473,167 | All - P | 3.40E-06 | OsCBL4 (LOC_Os05g45810, Martinez-Atienza et al. [36]) | Â | |
 |  |  |  | All - K | 5.61E-04 |  |  |  |
 |  |  |  | All - P + K | 4.95E-04 |  |  |  |
ΦPSII | id6002261 | 6 | 2,930,916 | All - P | 8.97E-07 |  |  |  |
 |  |  |  | All - P + K | 4.12E-05 |  |  |  |
 | id6002494 | 6 | 3,113,730 | All - K | 6.48E-05 |  |  |  |
 |  |  |  | IND - K | 8.00E-04 |  |  |  |
Fm | id6002261 | 6 | 2,930,916 | All - P | 2.77E-05 | Â | Â | Â |
 |  |  |  | All - K | 5.39E-04 |  |  |  |
 |  |  |  | All - P + K | 4.79E-04 |  |  |  |
qL | id6002261 | 6 | 2,930,916 | All - P | 3.90E-05 | Â | Â | Â |
 |  |  |  | All - P + K | 5.85E-04 |  |  |  |
 | id6002286 | 6 | 2,974,286 | All - K | 3.95E-04 |  |  |  |
NPQ | id6002389 | 6 | 3,042,568 | All - P | 2.10E-06 | Â | Â | Â |
 |  |  |  | All - P + K | 4.59E-04 |  |  |  |
NPQ | id6005326 | 6 | 8,187,911 | All - P | 1.31E-08 | qDRW6 [31] | Â | Â |
 |  |  |  | All - K | 3.98E-04 |  |  |  |
 |  |  |  | All - P + K | 2.35E-04 |  |  |  |
NPQ | id6006336 | 6 | 10,184,310 | All - P | 3.32E-05 | qDRW6 [31] | Â | Â |
 |  |  |  | All - K | 1.70E-04 |  |  |  |
 |  |  |  | All - P + K | 1.83E-04 |  |  |  |
 |  |  |  | JPN - K | 2.29E-04 |  |  |  |
NPQ | id7000336 | 7 | 1,865,306 | All - P | 3.43E-05 | Â | Â | Â |
F0 | id7003938 | 7 | 22,819,640 | All - P | 2.00E-05 | Â | Â | |
qL | id10000081 | 10 | 407,964 | JPN - K | 6.21E-04 | Â | Â | Â |
ΦPSII | id10003594 | 10 | 13,662,830 | All - K | 5.63E-04 |  |  |  |
 |  |  |  | All - P + K | 4.98E-04 |  |  |  |
 |  |  |  | JPN - K | 3.21E-04 |  |  |  |
Fm | id10003623 | 10 | 13,782,039 | All - P | 3.03E-05 | Â | Â | Â |
Fm | id10006610 | 10 | 20,943,116 | All - P | 1.43E-06 | Â | Â | Â |
NPQ | id11008520 | 11 | 22,516,795 | All - P | 6.39E-06 | qSNC11 [37] | Â | Â |
Fm | id11008950 | 11 | 23,178,265 | All - P | 4.04E-06 | qSNC11 [37] | Â | Â |
Fm | id12001261 | 12 | 3,059,845 | All - K | 4.65E-05 | Â | Â | Â |
 |  |  |  | All - P | 1.30E-06 |  |  |  |
 |  |  |  | JPN - K | 5.35E-05 |  |  |  |
 | id12001332 | 12 | 3,223,671 | All - P + K | 6.34E-05 |  |  |  |
NPQ | id12001256 | 12 | 3,027,442 | All - P | 1.23E-05 | Â | Â | Â |
qL | id12001769 | 12 | 4,044,980 | All - P + K | 6.57E-04 | qRRNC12 [29] |  |  |
ΦPSII | id12004053 | 12 | 10,470,139 | All - P | 5.14E-06 |  |  | |
 |  |  |  | All - K | 3.54E-04 |  |  |  |
ΦPSII | id12007270 | 12 | 21,906,089 | All - P | 1.48E-04 |  |  | |
ΦPSII | id12008292 | 12 | 23,734,278 | All - P | 2.45E-05 | qSH12.1, qSH12.2, qDSW12.1 [31]; qSUR12, qSES12, qCNL12 [38] |  |  |
 |  |  |  | All - K | 4.67E-04 |  |  |  |
qL | id12008234 | 12 | 23,663,599 | All - P | 5.21E-05 | qSH12.1, qSH12.2, qDSW12.1 [31]; qSUR12, qSES12, qCNL12 [38] | Â | Â |
 |  |  |  | All - K | 8.73E-04 |  |  |  |
ΦPSII | id12010084 | 12 | 27,378,310 | All - P | 1.65E-05 | qSUR12, qSES12, qCNL12 [38] |  |  |
 |  |  |  | All - K | 1.76E-04 |  |  |  |