* Defined by ADMIXTURE (Alexander Et Al. 2009) When K = 2

Supplementary Table 1 Country of origin, type, and subpopulation designation of rice germplasm accessions included in this study. Code Accessions Country Type Subpopulation* CS001 Nam-Seon 34 South Korea Breeding line Japonica CS002 Nam Seon 52 South Korea Breeding line Japonica CS003 Nam Seon 126 South Korea Breeding line Japonica CS004 Milyang 42 South Korea Breeding line Indica CS006 Suwon 159 South Korea Breeding line Japonica CS007 Suwon 255 South Korea Breeding line Indica CS008 Young Poong Byoe South Korea Breeding line Indica CS009 Suwon 301 South Korea Breeding line Japonica CS010 IRI 336 South Korea Breeding line Indica CS011 Suwon 347 South Korea Breeding line Indica CS012 Mi Hyang Byoe South Korea Breeding line Japonica CS013 Mi Hyang 88 Ho South Korea Breeding line Japonica CS014 T9993 5 10 1 1 Colombia Introduction Indica CS020 Moroberekan Nepal Introduction Indica CS023 Rathal Sri lanka Introduction Admixture CS024 Tchampa Iran Introduction Japonica CS034 Jeju collection South Korea Weedy Japonica CS035 Jeju collection South Korea Weedy Japonica CS036 Jeju collection South Korea Weedy Indica CS037 Jeju collection South Korea Weedy Japonica CS038 Jeju collection South Korea Weedy Japonica CS039 Jeju collection South Korea Weedy Indica CS040 Jeju collection South Korea Weedy Japonica CS041 Jeju collection South Korea Weedy Japonica CS043 Kang Hwa Do Collection South Korea Weedy Japonica CS044 Mu An Do South Korea Landrace Japonica CS045 Hwyen Da Dack South Korea Landrace Japonica CS046 Jo Ta Jo South Korea Landrace Japonica CS047 Po Chun Jang Mang Mae Byoe South Korea Landrace Japonica CS048 Dong Oh Byoe South Korea Landrace Japonica CS049 Da Da Jo South Korea Landrace Japonica CS050 Seu Ri Anjin Baeng Iee South Korea Landrace Japonica CS051 Ok Chung South Korea Landrace Japonica CS052 Neul Byoe South Korea Landrace Japonica CS053 San do South Korea Landrace Japonica CS054 Baat Na Rak South Korea Landrace Japonica CS055 Jui Ip Pari Byoe South Korea Landrace Japonica CS056 Jung Jong Hwa South Korea Landrace Japonica CS057 So Du Jo South Korea Landrace Japonica CS058 Oh Ri Do South Korea Landrace Japonica CS059 Sa Du Cho South Korea Landrace Indica CS060 Sun South Korea Landrace Indica CS061 Han yang Cho South Korea Landrace Indica CS062 In Bu Ji Do South Korea Landrace Japonica CS063 Bup Pan Hwa South Korea Landrace Japonica CS064 Jan Mo Chal South Korea Landrace Japonica CS065 Pyo Do South Korea Landrace Japonica CS066 San do South Korea Landrace Japonica CS067 Bo Ri Byoe South Korea Landrace Japonica CS068 Yuel Jo Jo South Korea Landrace Japonica CS069 San Kyung Cho South Korea Landrace Japonica CS070 Du Do South Korea Landrace Japonica CS071 Nayng Cho South Korea Landrace Japonica CS072 Baek Gok Na South Korea Landrace Indica CS073 Mongdon Jae Rae South Korea Landrace Admixture CS074 Agbede Nigeria Introduction Japonica CS075 Anbaw C7 Brunei Introduction Japonica CS076 Bala India Introduction Indica CS077 Bellardone Egypt Introduction Japonica CS078 Bikom Nigeria Introduction Admixture CS079 British Honduras Creale Honduras Introduction Japonica CS080 Cartuna USA Introduction Japonica CS081 Chiem Chank Vietnam Introduction Indica CS083 Dharial Surinam Introduction Indica CS084 Dular India Introduction Indica CS085 IR28 Philippines Introduction Indica CS086 IR40 Philippines Introduction Indica CS087 Magnolia USA Introduction Japonica CS088 Mala Bangladesh Introduction Indica CS089 Mushkan Pakistan Introduction Admixture CS090 Pukhi Pakistan Introduction Indica CS091 Redrice Iran Introduction Indica CS092 Sahak Puerto rico Introduction Indica CS093 Taichung-Woo-Tsan Taiwan Introduction Indica CS094 Tun Sart Vietnam Introduction Japonica CS095 Victoria F A Afghanistan Introduction Japonica CS096 Zilanica Surinam Introduction Admixture CS097 Baek Gak Whara Taiwan Introduction Indica CS098 So Baek Mang Su Do Taiwan Introduction Japonica CS099 Yang Myun Taiwan Introduction Indica CS100 Joe Gak Oh Chum Taiwan Introduction Indica CS101 Belle Pantna USA Introduction Indica CS102 Pyung Book 3 North Korea Introduction Japonica CS103 Spin Mere Afghanistan Introduction Indica CS104 Yupul Liberia Introduction Japonica CS106 Liman Belozernij Russia Introduction Japonica CS108 Kagi India Introduction Indica CS109 Hatadani Sri lanka Introduction Indica CS110 TAI Mochito Thailand Introduction Japonica CS111 Woe Gak Ja Taiwan Introduction Indica CS112 Upland Nigeria Introduction Japonica CS113 Newrex USA Introduction Japonica CS115 Dan Kwang Hwa Ra Taiwan Introduction Japonica CS116 Oh gak Taiwan Introduction Indica CS117 Binato Philippines Introduction Indica CS118 Avangard Uzbekistan Introduction Japonica CS119 Debzera Uzbekistan Introduction Japonica CS122 Hawm Supan Thailand Introduction Indica CS123 SSAL Byeo 22 South Korea Weedy Japonica CS125 Urasan Japan Introduction Japonica CS126 Norin 22 Japan Introduction Japonica CS127 SSal Byeo 16 South Korea Weedy Japonica CS128 Nain Chi Shi China Introduction Indica CS129 X- Gua Bai China Introduction Japonica CS130 Yung Yuen Chuen Zim China Introduction Indica CS131 Keng Chi Ju China Introduction Indica CS132 Sung Pan Tao China Introduction Japonica CS133 Qua 77 Wuan Dau China Introduction Indica CS134 Tsong Gan Shun China Introduction Indica CS135 San Li Shun China Introduction Indica CS136 Chih-Tsao-he China Introduction Indica CS137 Hsiang-Ha-Tsan China Introduction Indica CS138 Yang Sha Tsan China Introduction Indica CS139 Chungdo 23 South Korea Weedy Indica CS140 Chungdo Hwayang 12 South Korea Weedy Indica CS141 Chungdo Hwayang 14 South Korea Weedy Indica CS142 Chungdo Dongkok 4 South Korea Weedy Indica CS143 Sung Ju 3 South Korea Weedy Indica CS144 Jang Sung 1 South Korea Weedy Indica CS145 Soonchun 5 South Korea Weedy Indica CS146 Daegu Damti 6 2 South Korea Weedy Japonica CS147 Gue Chang South Korea Weedy Japonica CS148 Ko Ryeong 2 South Korea Weedy Japonica CS149 Ko Ryeong 6 South Korea Weedy Japonica CS150 Dan Yang 7 South Korea Weedy Japonica CS151 Dan Yang 9 South Korea Weedy Japonica CS152 Dan Yang 38 South Korea Weedy Japonica CS153 Hwa Sung 5 South Korea Weedy Japonica CS154 Chung Song Aeng Mi South Korea Weedy Japonica CS155 Gou 405 Japan Introduction Japonica CS156 Back Sa Mi China Introduction Japonica CS157 Su Hyung Han Do China Introduction Indica CS158 So Jo Hwang China Introduction Japonica CS159 Akaine Japan Introduction Japonica CS163 Sha Re Byeo 61 1 B South Korea Weedy Japonica CS164 Sha Re Byeo 94 B South Korea Weedy Japonica CS165 Sha Re Byeo 163 1 B South Korea Weedy Japonica * Defined by ADMIXTURE (Alexander et al. 2009) when K = 2. Supplementary Table 2 Summary of BLUPs for tocochromanol contents between indica and japonica groups across 2 years. T T T3 T3 T3 Total T Total T3 Total TT3 Indica Maximum 0.53 4.55 0.05 1.40 6.43 0.64 4.45 3.32 Minimum -7.54 -1.10 -5.33 -0.77 -3.42 -6.36 -4.38 -10.11 Mean -3.64 1.30 -3.08 0.28 1.53 -2.07 -0.59 -2.71 Japonic Maximum 7.43 1.09 6.47 0.47 3.86 6.37 6.18 10.49 a Minimum -2.32 -1.78 -2.43 -0.81 -4.41 -2.03 -3.20 -5.08 Mean 2.51 -0.89 2.19 -0.22 -1.08 1.43 0.41 1.87 Supplementary Table 3 Mean square values from analysis of variance for tocochromanol contents in 2 years. Source T T T3 T3 T3 Total T Total T3 Total TT3 Year 3.8419* 0.3886* 4.9686* 0.2966* 7.5849* 5.2762* 16.2162* 37.546* Geno 20.4993** 2.3047** 12.9616** 0.34096** 10.6494** 11.832** 7.8104** 23.234** Year×Geno 0.2008* 0.1222* 0.00517** 0.20746** 0.1594** 0.2672* 0.4116** 1.393** Residual 1.8031* 0.1067* 0.5194* 0.04688** 2.0839** 1.768* 4.5322** 11.615** *: significant at  = 0.05, **: significant at  = 0.01, Supplementary Table 4 Summary of Type Ⅲ test of fixed effects (CDs haplotype of OsTMT) a Source Numerator df Denominator df F Significance Intercept 1 116.201 108.720 .000 CDs haplotype 1 130.001 13.088 .000 Pop b 1 130.118 1.595 .207 a dependent variable : T content. b: population structure represented by principle components Supplementary Table 5 Summary of Type Ⅲ test of fixed effects (promoter haplotype of OsTMT) a Source Numerator df Denominator df F Significance Intercept 1 120.375 88.386 .000 Promoter haplotype 9 122.194 2.208 0.026 Pop b 1 122.125 1.198 0.305 a: dependent variable : T content. b: population structure represented by principle components Supplementary Table 6 Pearson’s correlation efficiency between the T content and OsTMT RNA level. OsTMT RNA level T content OsTMT RNA level 1 0.641* T content 0.641* 1 ∗Correlation is significant at  = 0.05 (two-tailed). Supplementary Fig. 1 Scree plot with parallel analysis for genetic data. The most obvious change in slope in the scree plot occurs at component 2, suggesting that the number of components is two. Supplementary Fig. 2 Scree plot with parallel analysis. Both the results for the principal component analysis (PCA) and exploratory factor analysis (EFA) are shown. Parallel analysis suggests that the number of factors is three and the number of components is two.