Table S1Functional annotation of the 10 non-R-genes
non-R-loci / Gene functional annotation / ReferenceSh4 / Reducing shattering / Li et al. 2005
Sp17 / Heat stress transcription factor / Yano et al. 2002
MSP1 / Restriction of cell number entering into male and femal sporogenesis and initiation of anther wall formation / Nonomura et al. 2003
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, YamauchiU. (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 S2Analysis of genetic structurebetween cultivated and wild rice or indica and japonica
Loci / Genetic Differentiation Between W and C / Genetic Differentiation Between Ind and JapSnn / Fst / Chi-square statistic / Snn / Fst / Chi-square statisti
χ2 / df / P / χ2 / df / P
R Loci
Os01g23380 / 0.52 / 0.13 / 19.1 / 16 / 0.260 / 0.56 / 0.02 / 9.00 / 5 / 0.109
Os07g29820 / 0.71*** / 0.18 / 16.5 / 9 / 0.058 / 0.76*** / 0.56*** / 6.43 / 1 / 0.011*
AL006613 / 0.46 / 0.15 / 15.0 / 8 / 0.058 / 0.77*** / 0.69*** / 9.75 / 1 / 0.002**
Os02g25900 / 0.48 / 0.11 / 11.6 / 10 / 0.316 / 0.54 / 0.17 / 6.87 / 4 / 0.146
Os01g72390 / 0.45 / 0.06 / 9.27 / 9 / 0.414 / 0.04 / 0.10 / 1.54 / 2 / 0.462
Os01g16390 / 0.76*** / 0.24*** / 23.4 / 13 / 0.037* / 0.44 / 0.17 / 3.66 / 2 / 0.159
Os01g16400 / 0.62 / 0.09 / 12.5 / 8 / 0.130 / 0.48 / 0.01 / 2.59 / 2 / 0.278
Os08g09430 / 0.60 / 0.06 / 18.4 / 13 / 0.147 / 0.35 / 0.07 / 6.63 / 4 / 0.157
Os06g48520 / 0.67* / 0.14 / 1.37 / 5 / 0.018* / 0.49 / 0.10 / 2.44 / 2 / 0.296
Os04g02110 / 0.63 / 0.04 / 12.5 / 11 / 0.321 / 0.53 / 0.04 / 6.16 / 5 / 0.291
Os02g18510 / 0.50 / 0.06 / 9.94 / 8 / 0.270 / 0.38 / 0.07 / 2.14 / 4 / 0.708
Os07g08890 / 0.70* / 0.36*** / 40.7 / 32 / 0.139 / 0.70* / 0.04 / 27.6 / 21 / 0.153
Os07g40810 / 0.61 / 0.10 / 13.1 / 9 / 0.160 / 0.52 / 0.06 / 5.19 / 6 / 0.479
Os10g22484 / 0.58 / 0.07 / 24.9 / 18 / 0.125 / 0.043 / 0.02 / 16.65 / 11 / 0.126
Os12g28250 / 0.55 / 0.06 / 11.6 / 6 / 0.069 / 0.470 / 0.01 / 1.02 / 1 / 0.310
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
Os06g06380 / 0.97*** / 0.34*** / 32.0 / 13 / 0.002** / ─ / ─ / ─ / ─ / 1.000
Os06g06390 / 0.98*** / 0.45*** / 32.0 / 7 / <0.001*** / ─ / ─ / ─ / ─ / 1.000
Os06g06400 / 0.67*** / 0.10 / 9.5 / 6 / 0.062 / ─ / ─ / ─ / ─ / 1.000
Os01g33690 / 0.48 / 0.11 / 5.58 / 2 / 0.068 / ─ / ─ / ─ / ─ / 1.000
Os12g33740 / 0.69*** / 0.26*** / 21.8 / 10 / 0.016* / ─ / ─ / ─ / ─ / 1.000
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
AK100970a / 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
aThese 10 non-R-genes from Tang et al. (2006)
TableS3Test for selection on R-genes and non-R genes.
Loci / C (%) / W (%) / All (%) / Mutations Between W and C / RMπs / πa / πs / πa / πs / πa / Fixed / In W / In C / Shared / C / W / All
R-Loci
Os01g23380 / 0.66 / 0.25 / 1.16 / 0.48 / 1.21 / 0.38 / 0 / 10(7) / 9(4) / 13(5) / 1 / 1 / 5
Os07g29820 / 0.42 / 0.18 / 0.99 / 0.37 / 0.75 / 0.30 / 0 / 17(9) / 1(1) / 4(2) / 2 / 0 / 2
AL006613 / 0.00 / 0.11 / 0.39 / 0.22 / 0.21 / 0.19 / 0 / 8(5) / 0(0) / 1(1) / 0 / 0 / 0
Os02g25900 / 0.19 / 0.24 / 0.14 / 0.28 / 0.17 / 0.27 / 0 / 8(6) / 2(1) / 2(2) / 1 / 0 / 1
Os01g72390 / 0.81 / 0.11 / 0.72 / 0.24 / 0.77 / 0.18 / 0 / 5(5) / 3(0) / 3(1) / 1 / 1 / 2
Os01g16390 / 0.62 / 0.36 / 4.04 / 1.04 / 2.25 / 0.68 / 0 / 41(21) / 2(2) / 10(6) / 0 / 4 / 4
Os01g16400 / 0.74 / 0.26 / 2.48 / 0.56 / 1.55 / 0.42 / 0 / 9(4) / 0(0) / 8(2) / 0 / 0 / 1
Os08g09430 / 0.00 / 0.64 / 0.26 / 0.87 / 0.12 / 0.77 / 0 / 3(2) / 0(0) / 5(5) / 2 / 2 / 2
Os06g48520 / 0.44 / 0.43 / 0.54 / 0.42 / 0.52 / 0.49 / 0 / 2(1) / 1(0) / 4(2) / 0 / 0 / 0
Os04g02110 / 0.07 / 0.69 / 0.32 / 0.75 / 0.18 / 0.69 / 0 / 8(7) / 1(0) / 9(8) / 0 / 1 / 1
Os02g18510 / 1.35 / 0.48 / 1.06 / 0.58 / 1.27 / 0.54 / 0 / 6(4) / 1(1) / 19(11) / 0 / 0 / 1
Os07g08890 / 1.29 / 0.55 / 2.88 / 1.27 / 2.29 / 0.85 / 0 / 25(19) / 1(1) / 25(11) / 6 / 0 / 8
Os07g40810 / 2.11 / 0.32 / 2.24 / 0.41 / 2.25 / 0.36 / 0 / 4(2) / 3(1) / 14(5) / 1 / 0 / 2
Os10g22484 / 1.74 / 1.17 / 1.38 / 0.95 / 1.69 / 1.15 / 0 / 5(2) / 6(4) / 27(21) / 3 / 2 / 4
Os12g28250 / 3.76 / 0.70 / 5.36 / 4.69 / 4.65 / 3.88 / 0 / 6(2) / 0 / 40(25) / 0 / 2 / 2
Pita / 0.14 / 0.08 / 0.19 / 0.14 / 0.17 / 0.12 / 0 / 5(5) / 4(2) / 8(5) / 0 / 0 / 0
Pib / 8.18 / 5.86 / 5.71 / 4.31 / 7.73 / 5.66 / 0 / 15(10) / 74(29) / 83(42) / 21 / 4 / 25
Os06g06380 / 0.00 / 0.00 / 1.87 / 0.19 / 1.11 / 0.09 / 1(0) / 18(6) / 0(0) / 0(0) / 0 / 1 / 1
Os06g06390 / 0.00 / 0.00 / 2.62 / 0.05 / 1.42 / 1.04 / 1(1) / 19(3) / 0(0) / 0(0) / 0 / 1 / 1
Os06g06400 / 0.00 / 0.00 / 0.74 / 0.24 / 0.34 / 0.11 / 0 / 12(6) / 0(0) / 0(0) / 0 / 0 / 0
Os01g33690 / 0.00 / 0.00 / 0.99 / 0.46 / 0.47 / 0.23 / 0 / 7(4) / 0(0) / 0(0) / 0 / 0 / 0
Os12g33740 / 0.00 / 0.00 / 1.20 / 0.58 / 0.45 / 0.21 / 0 / 22(11) / 0(0) / 0(0) / 0 / 0 / 1
Average / 1.02 / 0.55 / 1.71 / 0.87 / 1.44 / 0.85 / 11.6(6.4) / 4.9(2.2) / 12.5(7.0) / 1.7 / 0.9 / 3.2
Non-R-Loci
Vatp / 0.39 / ─ / 0.40 / ─ / 0.43 / ─ / 0 / 5 / 22 / 8 / 1 / 1 / 2
Sh4 / 0.00 / 0.00 / 0.22 / 0.07 / 0.14 / 0.11 / 0 / 6(3) / 0(0) / 0(0) / 0 / 0 / 0
COC1 / 0.45 / 0.13 / 0.66 / 0.16 / 0.58 / 0.15 / 0 / 13(6) / 1(1) / 3(1) / 0 / 0 / 0
EMF1 / 0.38 / 0.09 / 0.76 / 0.26 / 0.57 / 0.17 / 0 / 18(8) / 1(1) / 4(2) / 0 / 1 / 1
Gigantea / 0.21 / 0.11 / 0.37 / 0.12 / 0.30 / 0.11 / 0 / 8(1) / 0(0) / 3(3) / 0 / 0 / 0
HKT1 / 0.76 / 0.02 / 0.61 / 0.07 / 0.75 / 0.04 / 0 / 5(4) / 1(1) / 3(0) / 0 / 0 / 0
MSP1 / 0.00 / 0.08 / 0.86 / 0.31 / 0.41 / 0.21 / 0 / 24(12) / 2(2) / 0(0) / 0 / 0 / 0
qSH-1 / 0.41 / 0.06 / 0.60 / 0.11 / 0.53 / 0.08 / 0 / 8(4) / 0(0) / 2(0) / 0 / 1 / 1
sbe1 / 0.33 / 0.00 / 0.26 / 0.00 / 0.32 / 0.00 / 0 / 1(0) / 0(0) / 1(0) / 0 / 0 / 0
Sp17 / 0.00 / 0.02 / 0.73 / 0.08 / 0.39 / 0.05 / 0 / 16(5) / 1(1) / 0(0) / 0 / 0 / 0
Average / 0.29 / 0.057 / 0.55 / 0.13 / 0.44 / 0.10 / 10.4(4.8) / 2.8(0.66) / 2.4(0.66) / 0.1 / 0.3 / 0.4
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 parenthesesdenote 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 originLemont / 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