Table S1 Functional annotation of the 10 non-R-genes non-R-loci Gene functional annotation Reference Sh4 Reducing shattering Li et al. 2005 Sp17 Heat stress transcription factor Yano et al. 2002 MSP1 Restriction of cell number entering into Nonomura et al. 2003 male and femal sporogenesis and initiation of anther wall formation sbe1 Starch branching enzyme Qu and Takaiwa, 2004 Gigantea Regulate photoperiodic flowering Fowler et al. 1999 qSH-1 Controlling seed shattering habit Konishi et al. 2006 EMF1 Control of shoot architecture Aubert et al. 2001 HKT1 Sodium ion transporter Horie et al. 2001 COC1 Circadian oscillator component Xiong et al. 2003 Vatp A neutrally-evolved gene in rice Londo et al. 2006

Reference:

Li C, Zhou A, Sang T. (2006). Rice domestication by reducing shattering. Science 311: 1936- 1939.

Yano M, Yamauchi U. (2002) Gene Sp17 inhibiting lesion formation in plant and utilization thereof. Patent, JP 2002125672-A

Nonomura K, Miyoshi K, Eiguchi M, Suzuki T, et al. (2003) The MSP1 gene is necessary to restriction the number of cells entering into male and femal sporogenesis and to initiate of anther wall formation in rice. Plant Cell 15: 1728-1739.

Qu LQ, Takaiwa F. (2004) Evaluation of tissue specificity and expression strength of rice seed component gene promoters in transgenic rice. Plant Biotechnol J 2: 113-125.

Fowler S, Lee K, Onouchi H, Samach A, et al. (1999) GIGANTEA: a circadian clock-controlled gene that regulates photoperiodic flowering in Arabidopsis and encodes a protein with several possible membrane-spanning domains. EMBO J 18: 4679-4688.

Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y, Sasaki T, Yano M. (2006) An SNP caused loss of seed shattering during rice domestication. Science 312: 1392-1396.

Aubert D, Chen L, Moon YH, Martin D, et al. (2001) EMF1, a novel protein involved in the control of shoot architecture and flowering. Plant Cell 13: 1865-1875.

Horie T, Yoshida K, Nakayama H, Yamada K et al. (2001) Two types of HKT transporters with different properties of Na+ and K+ transport in Oryza sativa. Plant J 27: 129-138.

Xiong L, Yang Y. (2003) Disease resistance and abiotic stress tolerance in rice are inversely modulated by an abscisic acid-inducible mitogen-activated protein kinase. Plant Cell 15: 745-759. Londo JP, Chiang YC, Huang KH, Chiang TY, Schaal BA. (2006) Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc Natl Acad Sci USA 103: 9578-9583. Table S2 Analysis of genetic structure between cultivated and wild rice or indica and japonica

Loci Genetic Differentiation Between W and C Genetic Differentiation Between Ind and Jap

Snn Fst Chi-square statistic Snn Fst Chi-square statisti

χ2 df P χ2 df P

R Loci

Os01g2338 0.52 0.13 19.1 16 0.260 0.56 0.02 9.00 5 0.109 0

Os07g2982 0.71*** 0.18 16.5 9 0.058 0.76*** 0.56*** 6.43 1 0.011* 0

AL006613 0.46 0.15 15.0 8 0.058 0.77*** 0.69*** 9.75 1 0.002**

Os02g2590 0.48 0.11 11.6 10 0.316 0.54 0.17 6.87 4 0.146 0

Os01g7239 0.45 0.06 9.27 9 0.414 0.04 0.10 1.54 2 0.462 0

Os01g1639 0.76*** 0.24*** 23.4 13 0.037* 0.44 0.17 3.66 2 0.159 0

Os01g1640 0.62 0.09 12.5 8 0.130 0.48 0.01 2.59 2 0.278 0

Os08g0943 0.60 0.06 18.4 13 0.147 0.35 0.07 6.63 4 0.157 0

Os06g4852 0.67* 0.14 1.37 5 0.018* 0.49 0.10 2.44 2 0.296 0

Os04g0211 0.63 0.04 12.5 11 0.321 0.53 0.04 6.16 5 0.291 0

Os02g1851 0.50 0.06 9.94 8 0.270 0.38 0.07 2.14 4 0.708 0

Os07g0889 0.70* 0.36*** 40.7 32 0.139 0.70* 0.04 27.6 21 0.153 0

Os07g4081 0.61 0.10 13.1 9 0.160 0.52 0.06 5.19 6 0.479 0

Os10g2248 0.58 0.07 24.9 18 0.125 0.043 0.02 16.65 11 0.126 4 Os12g2825 0.55 0.06 11.6 6 0.069 0.470 0.01 1.02 1 0.310 0

Pita 0.47 0.02 6.94 7 0.435 0.48 0.00 3.175 4 0.529

Pib 0.33 0.09 27.0 20 0.135 0.334 0.20 14.7 12 0.260

Os06g0638 0.97*** 0.34*** 32.0 13 0.002** ─ ─ ─ ─ 1.000 0

Os06g0639 0.98*** 0.45*** 32.0 7 <0.001*** ─ ─ ─ ─ 1.000 0

Os06g0640 0.67*** 0.10 9.5 6 0.062 ─ ─ ─ ─ 1.000 0

Os01g3369 0.48 0.11 5.58 2 0.068 ─ ─ ─ ─ 1.000 0

Os12g3374 0.69*** 0.26*** 21.8 10 0.016* ─ ─ ─ ─ 1.000 0

Average 36.3% 22.7% 22.7% 13.6% 9.1% 9.1%

Non-R Loci

Vatp 0.76*** 0.14*** 48.2 31 0.025* 0.93*** 0.78*** 15.0 4 0.005**

Sh4 0.87*** 0.64*** 31.1 5 <0.001*** ─ ─ ─ ─ 1.000

COC1 0.71** 0.08* 29.1 12 0.004** 0.89*** 0.64*** 20.5 5 0.001**

EMF1 0.53 0.02 11.1 9 0.267 0.81** 0.39*** 16.5 4 0.002**

Gigantea 0.54 0.03 13.2 9 0.15 0.69** 0.35*** 11.9 3 0.008**

HKT1 0.65*** 0.12** 18.6 10 0.045* 0.77** 0.60*** 13.7 4 0.008**

MSP1 0.74*** 0.13*** 24.5 8 0.002** 0.59** 0.23* 7.47 2 0.024*

qSH-1 0.58* 0.08* 13.55 6 0.035* 0.72** 0.46*** 12.6 2 0.002**

Sbe1 0.54* 0.15* 6.42 2 0.046* 0.64* 0.47*** 8.24 1 0.004**

Sp17 0.56* 0.06* 7.55 6 0.273 0.48 0.04 0.74 1 0.389

AK100970 a 0.51 0.02 5.49 5 0.365 0.66** 0.52*** 7.59 1 0.006**

AK105540 a 0.75*** 0.11** 23.79 11 0.018* 0.46 0.02 10.91 11 0.451

AK102890 a 0.46 0.02 11.10 11 0.435 0.72*** 0.27*** 13.42 4 0.009**

AF411133 a 0.57 0.01 14.66 11 0.198 0.73*** 0.62*** 14.58 7 0.040*

AK069589 a 0.52 0.051 23.04 18 0.189 0.76*** 0.33** 16.15 8 0.040* AK071112 a 0.66** 0.10* 24.21 14 0.0433* 0.60* 0.38*** 9.68 3 0.012*

AK100849 a 0.60* 0.29*** 15.79 7 0.027* 0.83*** 0.78*** 17.65 4 0.001**

AK068671 a 0.71*** 0.14** 35.03 21 0.028* 0.59* 0.34** 17.24 9 0.035*

AK069480 a 0.73*** 0.13** 28.13 17 0.043* 0.91*** 0.49*** 23.00 10 0.011*

AK064267 a 0.75*** 0.09* 29.25 13 0.006** 0.78*** 0.22* 14.29 6 0.026*

Average 70.0% 70.0% 65.0% 85.0% 85.0% 85.0%

C, Cultivars; W, Wild rice; Ind, Indica; Jap, Japonica.

Haplotype diversity (Nei 1987).

Snn, the nearest-neighbor statistic (Hudson 2000).

Fst (Weir 1996).

Chi-square statistic (Hudson et al. 1992).

*, 0.01< P <0.05; **, 0.001< P <0.01; ***, P <0.001 a These 10 non-R-genes from Tang et al. (2006) Table S3 Test for selection on R-genes and non-R genes.

Loci C (%) W (%) All (%) Mutations Between W and C RM

πs πa πs πa πs πa Fixe In W In C Shared C W All d

R-Loci

Os01g233 0.6 0.25 1.1 0.4 1.2 0.3 0 10(7) 9(4) 13(5) 1 1 5 6 80 6 8 1 8

Os07g298 0.4 0.18 0.9 0.3 0.7 0.3 0 17(9) 1(1) 4(2) 2 0 2 2 9 7 20 5 0

AL006613 0.0 0.11 0.3 0.2 0.2 0.1 0 8(5) 0(0) 1(1) 0 0 0 0 9 2 1 9

Os02g259 0.1 0.24 0.1 0.2 0.1 0.2 0 8(6) 2(1) 2(2) 1 0 1 00 9 4 8 7 7

Os01g723 0.8 0.11 0.7 0.2 0.7 0.1 0 5(5) 3(0) 3(1) 1 1 2 90 1 2 4 7 8

Os01g163 0.6 0.36 4.0 1.0 2.2 0.6 0 41(21) 2(2) 10(6) 0 4 4 90 2 4 4 5 8

Os01g164 0.7 0.26 2.4 0.5 1.5 0.4 0 9(4) 0(0) 8(2) 0 0 1 00 4 8 6 5 2

Os08g094 0.0 0.64 0.2 0.8 0.1 0.7 0 3(2) 0(0) 5(5) 2 2 2 30 0 6 7 2 7

Os06g485 0.4 0.43 0.5 0.4 0.5 0.4 0 2(1) 1(0) 4(2) 0 0 0 20 4 4 2 2 9

Os04g021 0.0 0.69 0.3 0.7 0.1 0.6 0 8(7) 1(0) 9(8) 0 1 1 10 7 2 5 8 9

Os02g185 1.3 0.48 1.0 0.5 1.2 0.5 0 6(4) 1(1) 19(11) 0 0 1 10 5 6 8 7 4

Os07g088 1.2 0.55 2.8 1.2 2.2 0.8 0 25(19) 1(1) 25(11) 6 0 8 90 9 8 7 9 5

Os07g408 2.1 0.32 2.2 0.4 2.2 0.3 0 4(2) 3(1) 14(5) 1 0 2 10 1 4 1 5 6

Os10g224 1.7 1.17 1.3 0.9 1.6 1.1 0 5(2) 6(4) 27(21) 3 2 4 4 8 5 9 5 84

Os12g282 3.7 0.70 5.3 4.6 4.6 3.8 0 6(2) 0 40(25) 0 2 2 50 6 6 9 5 8

Pita 0.1 0.08 0.1 0.1 0.1 0.1 0 5(5) 4(2) 8(5) 0 0 0 4 9 4 7 2

Pib 8.1 5.86 5.7 4.3 7.7 5.6 0 15(10) 74(29) 83(42) 21 4 25 8 1 1 3 6

Os06g063 0.0 0.00 1.8 0.1 1.1 0.0 1(0) 18(6) 0(0) 0(0) 0 1 1 80 0 7 9 1 9

Os06g063 0.0 0.00 2.6 0.0 1.4 1.0 1(1) 19(3) 0(0) 0(0) 0 1 1 90 0 2 5 2 4

Os06g064 0.0 0.00 0.7 0.2 0.3 0.1 0 12(6) 0(0) 0(0) 0 0 0 00 0 4 4 4 1

Os01g336 0.0 0.00 0.9 0.4 0.4 0.2 0 7(4) 0(0) 0(0) 0 0 0 90 0 9 6 7 3

Os12g337 0.0 0.00 1.2 0.5 0.4 0.2 0 22(11) 0(0) 0(0) 0 0 1 40 0 0 8 5 1

Average 1.0 0.55 1.7 0.8 1.4 0.8 11.6(6. 4.9(2.2) 12.5(7. 1. 0. 3. 2 1 7 4 5 4) 0) 7 9 2

Non-R-Loci

Vatp 0.3 ─ 0.4 ─ 0.4 ─ 0 5 22 8 1 1 2 9 0 3

Sh4 0.0 0.00 0.2 0.0 0.1 0.1 0 6(3) 0(0) 0(0) 0 0 0 0 2 7 4 1

COC1 0.4 0.13 0.6 0.1 0.5 0.1 0 13(6) 1(1) 3(1) 0 0 0 5 6 6 8 5

EMF1 0.3 0.09 0.7 0.2 0.5 0.1 0 18(8) 1(1) 4(2) 0 1 1 8 6 6 7 7

Gigantea 0.2 0.11 0.3 0.1 0.3 0.1 0 8(1) 0(0) 3(3) 0 0 0 1 7 2 0 1

HKT1 0.7 0.02 0.6 0.0 0.7 0.0 0 5(4) 1(1) 3(0) 0 0 0 6 1 7 5 4

MSP1 0.0 0.08 0.8 0.3 0.4 0.2 0 24(12) 2(2) 0(0) 0 0 0 0 6 1 1 1 qSH-1 0.4 0.06 0.6 0.1 0.5 0.0 0 8(4) 0(0) 2(0) 0 1 1 1 0 1 3 8

sbe1 0.3 0.00 0.2 0.0 0.3 0.0 0 1(0) 0(0) 1(0) 0 0 0 3 6 0 2 0

Sp17 0.0 0.02 0.7 0.0 0.3 0.0 0 16(5) 1(1) 0(0) 0 0 0 0 3 8 9 5

Average 0.2 0.05 0.5 0.1 0.4 0.1 10.4(4. 2.8(0.6 2.4(0.6 0. 0. 0. 9 7 5 3 4 0 8) 6) 6) 1 3 4

C, Cultivars; W, Wild rice; All, Cultivars and Wild rice.

πs, Nucleotide diversity with Jukes and Cantor correction calculated on synonymous substitution sites.

πa, Nucleotide diversity with Jukes and Cantor correction calculated on nonsynonymous substitution sites.

Tajima’s D (Tajima 1989).

Fixed, the number of fixed differences between cultivars and wild rice; In W, Mutations that are polymorphic in wild rice, but monomorphic in cultivars; In C, Mutations that are polymorphic in cultivars, but monomorphic in wild rice; Shared, the total number of shared mutations. The numbers in parentheses denote the nonsynonymous substitution sites.

RM, the minimum number of recombination events (Hudson and Kaplan 1985).

*, 0.01< P <0.05; **, 0.001< P <0.01; ***, P <0.001 Table S4. the list the world-wide rice cultivars and wild rice accessions

Accession name Species Subspecies Country of origin Lemont Oryza sativa Japonica USA Calrose Oryza sativa Japonica USA Nipponbare Oryza sativa Japonica Japan Dadaotou Oryza sativa Japonica Jiangsu, East China Yunjing1 Oryza sativa Japonica Yunnan, South-west China C416 Oryza sativa Japonica Liaoning, North-east China Beiguang Oryza sativa Japonica Japan Hokuriku Oryza sativa Japonica Japan Shin 2 Oryza sativa Japonica Japan K3 Oryza sativa Japonica Japan K59 Oryza sativa Japonica Japan Bl1 Oryza sativa Japonica Japan Dular Oryza sativa Indica India IR24 Oryza sativa Indica IRRI, Philippines Tadukan Oryza sativa Indica Philippines 93-11 Oryza sativa Indica Jiangsu, East China Milyang Oryza sativa Indica Korea NJ11 Oryza sativa Indica Jiangsu, East China PA64 Oryza sativa Indica Hunan, Central China Minghui 63 Oryza sativa Indica Fujian, South-east China Tianxiang 313 Oryza sativa Indica Hubei, Central China Tetep Oryza sativa Indica Taiwan, South-east China ZhenSha97 Oryza sativa Indica South-east China S4542A3-49B-2-12 Oryza sativa ND. Arkansas, USA Grassy Oryza sativa ND. Haiti Vintula Oryza sativa ND. Guyana WC 2634 Oryza sativa ND. Tanzania W0106 Oryza rufipogon Wild rice Orissa, India S03005 Oryza rufipogon Wild rice Fujian, South-east China S01169 Oryza rufipogon Wild rice Jiangxi, Central China S1010 Oryza rufipogon Wild rice Guangdong, South China S6222 Oryza rufipogon Wild rice Hainan, South China A100912-R Oryza rufipogon Wild rice Arkansas, USA W0120 Oryza rufipogon Wild rice Cuttack, Orissa, India W2003 Oryza rufipogon Wild rice Pajani to Bombay, India W0630 Oryza rufipogon Wild rice Magwe, Burma W0593 Oryza rufipogon Wild rice Binjai Rendah, Malaya W1852 Oryza rufipogon Wild rice Chiang Saen, Thailand W1551 Oryza rufipogon Wild rice Saraburi, Thailand W1807 Oryza rufipogon Wild rice Sri Lanka S2061 Oryza rufipogon Wild rice Zhanjiang, South China W2263 Oryza rufipogon Wild rice Near air port, Cambodia W0107 Oryza rufipogon Wild rice Pahala, Orissa, India RE 551 Oryza glaberrima - Zaire NSGC 5935 Oryza nivara Wild rice India