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. 2019 Jun 27;9:9334. doi: 10.1038/s41598-019-45770-3

Table 2.

Identified significant SNP-trait associations in genome-wide study on the complex mapping population.

Trait SNP Chr Position QTL span (kb) 2015WS 2016DS Source: http://qtaro.abr.affrc.go.jp
p-value R2
(%)		 FDR p-value R2
(%)		 FDR Genes QTLs
RGR1 S1_37335658 1 37335658, 37335658–37605610 270 — — — 3.42 × 10−9 13 3.61 × 10−5 Lax39, moc240 —
RGR2 S1_37542157 1 37542157, 37542133–37542192 0.06a — — — 7.13 × 10−9 13 7.52 × 10−6 Lax39, moc240 —
RGR3 S1_42364262 1 42364262, 42364257–42906879 543 — — — 2.31 × 10−10 16 2.44 × 10−6 — —
NR1 S4_31903323 4 31903323–32251982 349 9.29 × 10−9 13 9.81 × 10−5 1.35 × 10−8 19 0.000143 nal1(nal5)41 rfw4a44, root thickness42,43, rooting depth42
NR2 S4_32664173 4 32664173, 31903323–32664173 761 1.70 × 10−8 16 0.000179 3.95 × 10−7 13 0.004172 nal1(nal5)41 rfw4a44, root thickness42,43, rooting depth42
RHL S5_18574046 5 18574046, 18574046–18574116 0.07a 7.88 × 10−10 13 2.59 × 10−6 3.99 × 10−7 10 0.001053 OsIPT3 45 —
RHD S2_24278920 2 24278920, 23246555–24278925 1032 1.55 × 10−7 10 0.000818 2.84 × 10−6 8 0.00998 EL5 46 , OsCKI1 47 , OsNAR2.1 48 —
FLA S2_24874074 2 24874074, 24874069–24874083 0.014a 9.22 × 10−8 13 0.000973 2.78 × 10−7 12 0.000978 — —
S5_27946781 5 27946781 — 5.52 × 10−6 11 0.001283 1.35 × 10−7 13 0.000739 — —
FLAngle S3_30920007 3 30920007 — 4.93 × 10−8 13 0.000520 5.12 × 10−9 19 5.40 × 10−5 OSH172, OsGRAS1961 —
S7_859891 7 859891 — 2.33 × 10−7 12 0.001231 2.65 × 10−7 17 0.000817 — —
S2_10388315 2 10388315 — 5.05 × 10−7 11 0.001775 — — — — —
S2_2772428 2

2772428,

2772428–2772461

 0.033a — — — 3.87 × 10−7 16 0.000817 — —
S5_23310970 5 23310970 — 8.17 × 10−6 9 0.021549 — — — — —
DTFirst S11_19839428 11 19839428, 19839399–19839440 0.041a 2.37 × 10−10 21 1.25 × 10−6 3.20 × 10−8 15 0.000169 — qGP-11, qGI-1153, yld11.1, gpl11.1, gw11.154
DTFull S11_28121354 11 28121354, 28121310–28121357 0.047a 3.36 × 10−8 19 0.000265 1.02 × 10−9 22 8.79 × 10−6 — —
SPAD S11_1639964 11

1639964,

1639964–1639983

 0.019a 6.31 × 10−8 13 0.000665 1.55 × 10−7 12 0.001633 OsNAC10 73 —
S2_5964826 2 5964826 4.61 × 10−7 12 0.001621 6.70 × 10−7 11 0.002359 CYP734A274, SPK2(SYG2)49 —
S3_9581723 3 9581723 — — — — 7.28 × 10−5 7 0.19204 —
BS S3_18257114 3 18257114, 18257114–18257152 0.038a 3.75 × 10−8 19 0.000396 — — — cwa1/bc1 75 —
BM S3_18257114 3 18257114, 18257114–18257152 0.038a 2.35 × 10−8 18 0.000248 — — — cwa1/bc1 75 —
CD S2_30984762 2 30984762, 30984762–32312089 1327 4.30 × 10−6 10 0.022673 — — — bc3 50 —
SD S3_28113794 3 28113794, 27926957–28113794 187 3.54 × 10−8 14 0.000187 1.10 × 10−7 13 0.000765 SCM3 5 —
1000 GW S10_11387999 10 11387999, 11387999–11388014 0.015a 1.92 × 10−7 14 0.000682 1.37 × 10−7 23 0.000721 — ssd1076, qSPBp10-277
S11_27252113 11 27252113 — 1.87 × 10−7 14 0.000682 2.13 × 10−7 22 0.000749 — —
PL S1_14102690 1 14102690, 13961627–14102698 141 2.96 × 10−10 18 1.21 × 10−6 3.44 × 10−7 16 0.000839 — —
S11_27831001 11 27831001 — — — — 2.97 × 10−7 16 0.000839 — —
NPT S11_4326232 11 4326232, 4326232–4326316 0.084a 1.75 × 10−7 17 0.000927 6.83 × 10−8 15 0.00024 — —
PHT S1_38286772 1 38286772, 35953453–38286810 2333 1.46 × 10−8 28 0.000154 1.68 × 10−8 39 0.000177 Sd151, qDTY1.152 —
DTF S3_31345368 3 31345368, 30831775–31345368 514 1.09 × 10−9 29 1.15 × 10−5 2.37 × 10−8 23 0.00025 MADS14 78 , pap2 79 , osmads34 80 —
S8_2061021 8 2061021 — — — — 5.35 × 10−7 21 0.002822 — —
GY S11_18903704 11 18903704, 16558222–18903704 2345 3.44 × 10−7 22 0.003506 2.00 × 10−7 21 0.001057 — qGP-11, qGI-11 53 , yld11.1, gpl11.1, gw11.1 54
S4_25915108 4 25915108, 25915108–25915179 0.071a — — — 4.65 × 10−6 19 0.008182 — —
Fe uptake S6_14891911 6 14891911–14891917 0.006a 7.96 × 10−7 79 0.004214 — — — OsPT9, OsPT1055, OsGLK156, nyc357 —
N uptake S2_20846594 2 20846594–20846633 0.039a 6.43 × 10−7 84 0.003402 — — — DP258, RCN259, OsAPX860, OsNAR2.148 —
P uptake S5_24675892 5 24675892, 24675892–24675951 0.059a 5.91 × 10−7 83 0.001308 — — — OsRPK181, OsCCaMK62, OsHAP3B63; OsTPS163, OsSTN864 —

RGR1: relative growth rate from 15 to 22 DAS, RGR2: relative growth rate from 22 to 29 DAS, RGR3: relative growth rate from 15 to 29 DAS, NR1: number of nodal roots at 15 DAS, NR2: number of nodal roots at 22 DAS, RHL: root hair length, RHD: root hair density, SPAD: chlorophyll content, FLA: flag-leaf area, FLAngle: flag-leaf angle, DTFirst: days to first emergence, DTFull: days to full emergence, SD: stem diameter, CD: culm diameter, BS: bending strength, BM: bending moment, 1000 GW: 1000-grain weight (g), PL: panicle length, NPT: number of productive tillers, PHT: plant height, DTF: days to 50% flowering, GY: grain yield, Fe uptake: iron uptake, N uptake: nitrogen uptake, P uptake: phosphorus uptake, DS: dry season, WS: wet season, R2: percent phenotypic variance explained by SNP, FDR: false discovery rate. aThe associated SNPs with very small intervals (≤14 kb) can be considered as the same locus.