Supplementary Table1Descriptive statistics and percentage of phenotypic variation explained by population structure for grain color and nutritional quality traits

Traits / Mean  SD / Range / R2 a
L* / 51.8±9.5 / 14.1~67.4 / 8.5
a* / 3.46±2.90 / –12.9~13.8 / 21.1
b* / 14.3±2.1 / –1.8~18.7 / 6.7
C / 15.1±1.4 / 9.48~19.7 / 9.5
H° / 72.5±31.0 / –193.3~101.4 / 7.0
Phenoliccontent
(mg GAE/100 g) / 208.1±155.6 / 108.1~1244.9 / 8.0
Flavonoidcontent
(mg RE/100 g) / 134.6±20.6 / 88.51~286.29 / 5.0
Antioxidant capacity (mMTAEC) / 0.474±0.752 / 0.0120~5.533 / 8.4

aPercentage of phenotypic variation explained by population structure.

These data were adapted from Jin et al. (2010).

Supplementary Table 2The marker loci identified to be associated with grain color, phenolic content, flavonoid content, and antioxidant capacity traits among the total rice panelbased on population structure (Q) performed using general linear model (GLM) in TASSELusing 50,000-time permutations for the correction of multiple testing.

Trait / Locus a / Chro. No. / Position
(cM) / P-adjust / R2 b
L* / Ra / 4 / 113.2 / 2.00E-05 / 0.1860
SS1 / 6 / 23.5 / 0.0451 / 0.0385
Rc / 7 / 43.8-44.4 / 2.00E-05 / 0.3742
RM228 / 10 / 96.3 / 0.0329 / 0.0562
a*
RM297 / 1 / 155.9 / 0.0356 / 0.0334
Ra / 4 / 113.2 / 2.00E-05 / 0.3194
Rc / 7 / 43.8-44.4 / 2.00E-05 / 0.0695
RM337 / 8 / 1.1 / 0.0239 / 0.0363
RM339 / 8 / 72.2 / 0.0193 / 0.0542
RM316 / 9 / 1.8 / 2.00E-05 / 0.1344
RM224 / 11 / 120.1 / 0.0037 / 0.0460
RM309 / 12 / 74.5 / 0.0302 / 0.0297
b*
Ra / 4 / 113.2 / 2.00E-05 / 0.5647
RM30 / 6 / 125.4 / 2.00E-05 / 0.0714
fgr / 8 / 71.7-72.2 / 2.00E-05 / 0.0503
RM339 / 8 / 72.2 / 0.0011 / 0.0830
RM316 / 9 / 1.8 / 2.00E-05 / 0.1348
RM228 / 10 / 96.3 / 0.0012 / 0.0745
RM215 / 9 / 99.4 / 0.0475 / 0.0345
C
RM507 / 4 / 0.0 / 0.018 / 0.0301
Ra / 4 / 113.2 / 2.00E-05 / 0.0630
fgr / 8 / 71.7-72.2 / 0.0071 / 0.0315
RM339 / 8 / 72.2 / 0.0058 / 0.0661
RM171 / 10 / 73.0 / 0.0112 / 0.0290
RM228 / 10 / 96.3 / 2.00E-05 / 0.0849
H°
Ra / 4 / 113.2 / 2.00E-05 / 0.8761
RM30 / 6 / 125.4 / 2.00E-05 / 0.0648
fgr / 8 / 71.7-72.2 / 2.00E-05 / 0.0544
RM339 / 8 / 72.2 / 2.00E-05 / 0.0913
RM316 / 9 / 1.8 / 2.00E-05 / 0.2168
Phenolic content
Ra / 4 / 113.2 / 2.00E-05 / 0.4443
SS1 / 6 / 23.5 / 0.0461 / 0.0359
Rc / 7 / 43.8-44.4 / 2.00E-05 / 0.2739
RM339 / 8 / 72.2 / 0.026 / 0.0660
RM316 / 9 / 1.8 / 2.00E-05 / 0.1236
Flavonoid content
Ra / 4 / 113.2 / 2.00E-05 / 0.4457
Rc / 7 / 43.8-44.4 / 2.00E-05 / 0.0528
fgr / 8 / 71.7-72.2 / 0.0094 / 0.0349
RM316 / 9 / 1.8 / 2.00E-05 / 0.1246
RM228 / 10 / 96.3 / 0.0424 / 0.0592
Antioxidant capcity
Ra / 4 / 113.2 / 2.00E-05 / 0.4632
SS1 / 6 / 23.5 / 0.0365 / 0.0372
Rc / 7 / 43.8-44.4 / 2.00E-05 / 0.2309
fgr / 8 / 71.7-72.2 / 0.0367 / 0.0281
RM339 / 8 / 72.2 / 0.0023 / 0.0766
RM316 / 9 / 1.8 / 2.00E-05 / 0.1065
RM228 / 10 / 96.3 / 0.0294 / 0.0579

aMarkers with the adjust P value <0.05 were reported as significant.

bR2 indicates the percentage of the total variation explained

Supplementary Table 3The marker loci identified to be associated with grain color, phenolic content, flavonoid content, and antioxidant capacity traits among the white rice (non-pigmented) panel based on population structure (Q) performed using general linear model (GLM) in TASSELusing 50,000-time permutations for the correction of multiple testing.

Trait a / Locus a / Chro. No. / Position
(cM) / P-adjust / R2 b
L*
RM317 / 4 / 118.3 / 0.0261 / 0.0262
RM161 / 5 / 96.9 / 4.20E-04 / 0.0357
WxSNP / 6 / 7.4 / 2.00E-05 / 0.0745
WxSSR / 6 / 7.4 / 2.00E-05 / 0.0911
SS1 SSR / 6 / 23.5 / 0.0061 / 0.0338
SS2a / 6 / 37.8 / 0.0477
RM105 / 9 / 32.1 / 0.0011 / 0.0363
a*
RM252 / 4 / 99.0 / 0.0042 / 0.0349
RM454 / 6 / 99.3 / 2.00E-05 / 0.0284
WxSSR / 6 / 7.4 / 0.0116 / 0.0424
RM447 / 8 / 124.6 / 2.00E-05 / 0.0459
RM219 / 9 / 11.7 / 0.028 / 0.0290
RM167 / 11 / 37.5 / 0.033 / 0.0205
RM206 / 11 / 102.9 / 0.0117 / 0.0332
RM286 / 11 / 0.0 / 2.00E-05 / 0.0428
b*
RM507 / 4 / 0.0 / 0.0088 / 0.0373
SB1STS / 6 / 143.7-149.7 / 0.014 / 0.0333
RM346 / 7 / 47 / 0.0478 / 0.052
RM201 / 9 / 81.2 / 0.0029 / 0.0508
RM171 / 10 / 73.0 / 0.0209 / 0.0314
C
SB1SSR / 6 / 143.7-149.7 / 0.0453 / 0.0495
SB1STS / 6 / 143.7-149.7 / 0.0039 / 0.0392
RM346 / 7 / 47 / 0.0105 / 0.0596
RM339 / 8 / 72.2 / 0.007 / 0.0784
RM201 / 9 / 81.2 / 0.016 / 0.0451
RM171 / 10 / 73.0 / 0.0016 / 0.0425
RM228 / 10 / 96.3 / 0.0458 / 0.0636
Ho
RM297 / 1 / 155.9 / 0.0326 / 0.0240
RM252 / 4 / 99.0 / 0.0371 / 0.0297
RM454 / 6 / 99.3 / 2.00E-05 / 0.0298
WxSSR / 6 / 7.4 / 0.0043 / 0.0445
RM447 / 8 / 124.6 / 2.00E-05 / 0.0520
RM219 / 9 / 11.7 / 0.0056 / 0.0321
RM167 / 11 / 37.5 / 0.0027 / 0.0247
RM224 / 11 / 120.1 / 0.0216 / 0.0279
RM206 / 11 / 102.9 / 0.0109 / 0.0330
RM286 / 11 / 0.0 / 2.00E-05 / 0.0393
Phenolic content
RM237 / 1 / 115.2 / 0.0041 / 0.0469
RM153 / 2 / 0.0 / 0.0161 / 0.0609
RM218 / 3 / 67.8 / 0.005 / 0.0609
RM346 / 7 / 47.0 / 0.0061 / 0.0631
RM339 / 8 / 72.2 / 0.0319 / 0.0716
Flavonoid content
Wx SNP / 6 / 7.4 / 0.0337 / 0.0325
Antioxidant capacity
RM447 / 8 / 124.6 / 0.0346 / 0.0429
RM251 / 3 / 79.1 / 2.00E-05 / 0.0610

aMarkers with the adjust P value <0.05 were reported as significant.

bR2 indicates the percentage of the total variation explained.