1. F B Allele group II E G U S V W Rec OS1 Substitution Rec OS2 Rec OS3 A B C Rec OS1 Rec OS2 Rec OS3 (-530 ~ -86) (-86 ~ +49) Fig. S1 Intragenic recombination in Hd1 among cultivated rice. (a) The structure of Hd1. White and gray boxes indicate UTR and coding regions, respectively. The positions of recombination points are shown by bars. (b, c) The process of recombinations between alleles. Representative polymorphisms of the alleles are shown.

2. Q N O M L P K R S J V W F G Gin I H A D B C E W0106 (O. rufipogon) U T W0652 (O. barthii) W1169 (O. glumaepatura) W1413 (O. longistaminata) 99 98 94 75 85 59 71 81 84 74 63 98 56 94 98 57 52 0.001 II IV I III Fig. S2 Neighbor-joining (NJ) tree of 23 alleles of cultivated rice and 4 accessions of its wild relatives carrying AA genomes; O. rufipogon (W0106), O. glumaepatula (W1169), O. barthii (W0652), and O. longistaminata (W1413). Bootstrap analysis values from 1,000 replications are shown at the nodal branches. The indicated scale represents 0.001 substitutions per site. This analysis was conducted using MEGA version 3.1 software (Kumar 2004).

3. Fig. S3 Haplotype patterns of the chromosomal regions surrounding Hd1 in 60 cultivated rice varieties. Graphical representation of haplotype patterns of the chromosomal region. Letters indicate the haplotype of each region with the colors of haplotype blocks. In Hd1 alleles, red indicates loss-of-function alleles and bold boxes indicate the 2-bp deletion. Information of accessions is referred from Table S1.

4. 5 6 7 3 9 10 13 19 26 28 U1 37 18 27 8 30 31 Rec1 Rec2 Rec3 Rec4 Rec5 Rec6 Rec7 A B Rec1 Rec2 Rec3 Rec4 Rec5 Rec6 Rec7 (+1205 ~ +1570) (+1131 ~ +1205) (+1131 ~ +1181) (+1131 ~ +1524) (+1531 ~ +1566) (+1630 ~ +1714) (+1181 ~ +1205) Fig. S4 Intragenic recombination in Hd1 among O. rufipogon. (a) The structure of Hd1. White and gray boxes indicate UTR and coding regions, respectively. The positions of recombination points are shown by bars. (b) The processes of recombination between alleles. Representative polymorphisms of the alleles are shown.

5. Fig. S5 Hypothetical process of the evolution of Hd1 among O. rufipogon and cultivated rice varieties. This model was constructed by step-by-step coalescence based on polymorphisms in the 725-bp region of Hd1, which are shown in supplemental Table S4. The number in the box indicates the haplotype. Numbers beside arrows indicate the mutation event in supplemental Table S4. Haplotype U1 was an unidentified haplotype in this population. Intragenic recombinations are shown as R1 to R7.

6. A B C D E H J P R SNLVWQ B B R O J R J MVVM C C C P G L U K B M T I B F OMO Fig. S6 Distribution of Hd1 alleles among cultivated rice. Letters in boxes indicate Hd1 alleles. Bars under the letters and red circles indicate alleles with FNPs and the 2-bp deletion, respectively. Boxes are colored according to the Hd1 allele groups.

7. Table S1

8. Table S2

9. Table S3

10. Table S4

11. Table S5