Fortuna

Tropical japonica

Aromatic (GroupV)

Aus

Indica

Temperate japonica

Basmati 217

Dom-Sufid

Dhala Shaita

Champa Tong 54

Jhona

349

DV 85

Chau

Taducan

Dee Geo Woo Gen

Guan Yin Tsan

Wells

Della

Trembese

Rikuti Norin 21

Ta Hung Ku

Norin

20

Koshihikari

Nipponbare

IR64

583

Creole

Chuan 4

NSF-TV 13

Sera

toes H

ari

Supplemental Fig. S1. Unrooted neighbor-joining tree based on Nei (1973) minimum genetic distance calculated from 409 genotypes using 36 SSR

markers. The five major clusters corresponding to aus, indica, temperate japonica, tropical japonica and aromatic (Group V) subpopulations are labeled

and the names of reference cultivars for the different subpopulations are identified by a larger font and arrow. Three accessions identified as admixtures,

K-65, 923 and Berenj, are not grouped with a subpopulation. Most of the other accessions classified as admixtures are positioned at borders of the

clusters (names not shown).

Sadri Belyi NSF-TV 160 NSF-TV 260 Dom Zard Dom Sofid Kitrana 508 Lambayeque NSF-TV 5 Firooz Bico Branco Gerdeh PanKhari 203 Basmati N12 Basmati 217

Supplemental Fig. S2.1. Dendrogram of 15 aromatic (Group V) rice accessions developed by cluster

analysis following Nei 1973 distance and neighbor-joining methods based on 36 SSR markers. Brackets

on the right side indicate the two subclusters and describe the geographic region that the accessions

originated from.

I. Western Asia (5),

other regions (3)

and unknown (3)

II. South Asia

Aromatic (Group V)

Supplemental Fig. S2.2. Dendrogram of 59 aus rice accessions developed by cluster analysis following Nei 1973

distance and neighbor-joining methods based on 36 SSR markers. Brackets on the right side indicate the five

subclusters and describe the geographic region that the accessions originated from.

DM 59CTG 1516SurjamKuhiPaung MalungDJ 24DV 123DM 56ARC 10376KaukauDK 12Black GoraPTB 30GhorbhaiDhala ShaitaDularCA 902 B 2 1KachilonDZ78Khao Tot Long 227DZ 193DJ 123KalamkatiDD 62NSF-TV 4MehrKaao GaewARC 7229PhudugeyChuan 4T26T 1SarayaNSF-TV 13Halwa Gose RedDNJ 140Champa Tong 54ARC 6578SufaidKarkati 87Jhona 349ShirkatiSanthi SufaidGhati kamma Nagarhar9524Shim BalteSathiKalubala VeeThavaluKhao Pahk MawP 737CoarseAswina 330KasalathGoriaDV 85DM 43BJ 1JamirFR13A

I. South Asia –

Bangladesh (12)

India (5) ;

and other regions (4)

IV. South Asia (2), other regions (3)

and unknown (1)

V. South Asia –

Bangladesh (6),

India (5),

Pakistan (4),

Sri Lanka (2)

Afghanistan (2);

and other regions (2)

II. South Asia (4), other regions (2)

and unknown (1)

III. South Asia (3) and East Asia (1)

Pakistan (South Asia)

Aus

Supplemental Fig. S2.3. Dendrogram of 90 indica

rice accessions developed by cluster analysis

following Nei 1973 distance and neighbor-joining

methods based on 36 SSR markers. Brackets on

the right side indicate the eight subclusters and

describe the geographic region that the

accessions originated from.

I. Southeast Asia (10), East Asia (8),

South Asia (4), South America (3)

and other regions (5)

VI. East Asia –

China (8) and

Taiwan (2);

South Asia (3),

Southeast Asia (3) and

other regions (4)

VIII. South Asia (3) ,Southeast Asia (2)

and unknown (1)

III. Southeast Asia (2), Africa (2)

and South Asia (1)

SL 22 613BinulawanRT0034IRGA 409Oryzica Llanos 5JayaIR 8SundensisECIA76 S89 1Jing 185 185-7IR 36Leung PratewIR64RathuweeBR24Jasmine85SigadisShufeng 121-165 1655Rondo (4484-1693)Minghui 63Ming HuiRTS12JM70TaducanChiem ChanhShai KuhShort GrainPappakuHonChim519Shuang ChiangLD 24Sintane DioforRadin Ebos 33DjimoronSeratoes HariBaguamon 14Tam Cau 9AChauMudgoJC149Tsipala 421MTU 9I Geo TzeDee Geo Woo GenLA 110Taichung Native-1IR 44595Peh KuhPeh Kuh Tsao TuPagaiyahanNSF-TV 57DawebyanZhenshan 97BZhenshan 2TchibangaHunan Early Dwarf No 3Zhe 733TeQingYang Dao 693-11SML 242China 1039AijiaonanteSabharajParaiba Chines NovaYodanyaAi Chiao HongGuan Yin TsanEmata A 16 3ANiraChang Ch'sang Hsu TaoO Luen CheungKiang Chou ChiuRTS14JC 117Sze Guen ZimPao Tou HungPai Hok GlutinousSLO 17Criollo La FriaKun Min Tsieh HunanByakkoku Y 5006 SelnHsia Chioh Keh TuC101A51BalaTKM6CO18RTS4NSF-TV 34

II. East Asia and South Asia

IV. South Asia (3), Southeast Asia (2)

and Africa (1)

V. East Asia –

China (7) and

Taiwan (6)

other regions (4) and

unknown (1)

VII. East Asia (2) and Oceania (1)

Indica

Supplemental Fig. S2.4. Dendrogram of 108

temperate japonica rice accessions developed

by cluster analysis following Nei 1973 distance

and neighbor-joining methods based on 36

SSR markers. Brackets on the right side

indicate the subclusters and describe the

geographic region that the accessions

originated from.

I. Europe (24),

East Asia (7),

Cent. & S. America (6)

and other regions (6)

II. East Asia and Southeast Asia

IV. Europe (3) and Africa (2)

VIII. East Asia –

Japan (11), S. Korea (7),

China (3) Taiwan (4) ;

Europe (4), Africa (3)

and other regions (10)

VI. East Asia (2) and other regions (2)

III. East Asia (2), Oceania (2) and

N. America & Caribbean (2)

V. East Asia and N. America & Caribbean

VII. Southeast Asia and Europe

Temperature japonica

Austria (Europe)

Argentina (S. America)

VialoneBreviaristataRikuto Norin 21OsogovkaRinaldo BersaniDoble Carolina Rinaldo BarsaniSML KapuriTa Mao TsaoHu Lo TaoVictoria FAWIR 3764Kon SuitoSab IniStegaru 65LusitanoItalica CarolinaTa Hung KuAzerbaidjanicaRomeoRazza 77Lomello68-2NortaiNorin 20DesvauxiiBombonToploea 70/76PatnaM BlatecBaldoMaratelliAgostanoOroNiquenBiser 1KarabaschakASD 1Pirinae 69RomanicaVaviloviNucleoryzaTropical RiceAgusitaKibiGotak GatikShiroganePI 298967 1Jouiku 393GCS-M3Pato De GallinazoM-202CaucasicaDoselKihogoGambiaka SebelaBahiaSuweonC1 6 5 3OstigliaSitpwaBenllokTainan Iku No 512Early WataribuneSri Malaysia DuaBellardoneBergreisNipponbareAichi AsahiShoemedBaghlani NangarharKawLuyoengBeonjoGyehwa 3Bul ZoChineseTaipei 309Tainan Iku 487Luk TakharYabani Montakhab 7ShinrikiKiuki No 46ChibicaTriomphe du MarocTainung 67GeumobyedAmpostaSung Liao 2Edomen Scented56 122 23KoshihikariUzbeksku 2Shangyu 394KamenooHatsunishikiErythroceros HokkaidoBulgareHaginomae MochiEh 1A ChiuDeokjeokjodoZerawchanica KaratalskiWIR 3039BombillaMansakuLeuang hawnRikuto kemochiARC 10086HeukgyeongChodongji

Supplemental Fig. S2.5. Dendrogram of 104

tropical japonica rice accessions developed by

cluster analysis following Nei 1973 distance and

neighbor-joining methods based on 36 SSR

markers. Brackets on the right side indicate the ten

subclusters and describe the geographic region

that the accessions originated from.

LaGrueFrancisWellsKaybonnetDelrexSpringS4542A3 49B 2B12KatySaberRosemontJeffersonLemontCypressCybonnetL 202CocodrieEarlyC57 5043PandaCuba 65B6616A4 22 Bk 5 4SinaguingFortuna583CoppocinaSinampaga SelectionPadi PagalongLlanero 501Keriting TingiiAriasPadi kasalleAsse Y PungAzucenaTia BuraCAAWA/Fortuna6-103-15TrembeseGogo LempukPate Blanc MN 1MoroberekanLigeritoFossa AvJambuKaniranga325PecosDellaR 101LeahSultaniSaturnWC 3397GuineandaoEstrelaSakuIRAT 44WAB 502 13 4 1WAB 501 11 5 1BengalWC 4419H256 76 1 1 1NovaKU115EdithLady Wright SelnBlue rose SupremeCreoleUplandHondurasCarolina Gold SelCarolina Gold 12033PR 304Canella De FerroNSF-TV 199Guatemala 1021OS 6 (WC10296)LAC 23ManzanoOS6Priano GuairaNSF-TV 107IAC 25PrataoDourado AgulhaTox 782 20 1NSF-TV 116IRAT 177IRAT 13NSF-TV 27NSF-TV 95Iguape Cateto318NSF-TV 89IITA 135WAB56 104RT 1031 69WC 4443Boa VistaPalmyraCenitBritish Honduras Creole27KinastanoWanicaCarolina Gold 12034

I. N. America & Caribbean -

USA (21) and Caribbean (1)

and other regions (2)

II. Southeast Asia (12),

Africa (3)

and other regions (4).

III. N. America & Carribean (3),

Africa (2) and Europe (1)

IV. Africa (4), Cent. & S. America (1)

and East Asia (1).

V. N. America & Caribbean (2), S.

America (1) and Southeast Asia (1)

VI. N. America & Caribbean

VII. N. America & Caribbean (2),

Cent. & S. America (2) and Oceania (1)

VIII. Cent. & S. America (9), Africa (9),

N. America & Caribbean (2),

unknown (6) and

other regions (1)

IX. S. America (2) and N. America (1)

X. N. America and Caribbean (2),

S. America (1) and Southeast Asia (1)

Jamaica (Caribbean)

Tropical japonica

Bulgaria (Europe)