<p>Table S1: List of the Vietnamese accessions, with their province of origin, varietal type, population assignments based on DArT and GBS markers, and phenotypic characteristics</p><p>L/ PRC GBS Gr Gr Gr W rat ID Name No Province Type Eco GBS P length width type io TEP HAI G1 11 HAIPHONG T IR y Im M N B NG PHONG TAM SON G10 216 NAM DINH T IR y I4 M N B NG NAM DINH KHAU QUAI G100 6969 TUYEN QUANG T UP y J1 L M A NG DANG 2 G101 DIEO KBIN 7295 DAK LAK T UP y J1 L L C G TZO KOH G102 7303 THUA THIEN-HUE T u y Im L M A NG DANG 2 CU PUA G103 7304 THUA THIEN-HUE T u y Jm L N A NG DANG 1 CU PUA G104 7305 THUA THIEN-HUE T u y I6 M M B NG DANG 2 NEP THAI G105 7312 HA GIANG & TUYEN QUANG T IR y I3 L N A G LAN NEP HAI G106 7316 NINH BINH T IR y J2 S M C G HAU NEP THAI G107 7317 NINH BINH T IR y J2 S M C G BINH LUN G108 TAM AP BE 7318 NINH BINH T IR y m M N A NG G109 MANH GIE 7349 QUANG BINH T UP y Im M M B NG TAM TRON G11 219 HAI DUONG T u y I4 S N B NG HAI DUONG G110 RAN TRANG 7823 BINH THUAN T UP y Im M M B NG G111 NEP RAY 7824 BINH THUAN T UP y Im VL N A G G112 NEP LUA 7826 VUNG TAU T IR n L N A na NANG G113 7827 VUNG TAU T IR y I2 M N A NG THIET G114 NEP QUA 7830 KHANH HOA T UP n VL M A na L/ PRC GBS Gr Gr Gr W rat ID Name No Province Type Eco GBS P length width type io G115 KOI LOI 7910 HA NOI T IR y I1 M M C NG G116 KOI PU 7913 THUA THIEN HUE T u n VL M A NG KHAO G117 7930 QUANG TRI T UP y J1 VL L B G SANG G118 L03 9175 HA NOI I IR n VL L C G G119 L26 9198 HA NOI I IR y I1 VL M A G TAM CAO G12 226 VINH PHUC T IR y I4 M N A NG VINH PHUC BAY G120 9219 CA MAU T IR y I2 L N A NG THANH G121 CA RO 9246 TAY NINH T IR y I2 M M B NG NEP LAO G122 9252 DAC LAC T UP n L L C na TRANG BAO THAI G123 9353 QUANG NINH T IR n S M C na LUN G124 NEP DEN 9355 QUANG NINH T IR y J2 S L C G G125 NEP NUONG 9356 QUANG NINH T u y Im M M C G KHAU DAM G126 9466 NGHE AN T UP y J1 VL L B G DOI KHAU BAO G127 9470 NGHE AN T IR n S M C na THAI G128 KHAU DAM 9476 NGHE AN T UP y J1 L L C G G129 LC93-2 9507 KHANH HOA T UP y Im L M B NG TAM DEN G13 253 HAIPHONG T IR n S N B NG HAI PHONG G130 LUA DA BO 9509 KHANH HOA T UP y J3 L L C NG PADAI G131 LONG 9517 KHANH HOA T UP y J3 VL L A NG KHANH PADAI TLIG G132 9520 KHANH HOA T UP y Im VL M A G JUG L/ PRC GBS Gr Gr Gr W rat ID Name No Province Type Eco GBS P length width type io G133 A 330 9524 KHANH HOA I IR y I1 VL M A NG PADAI G134 9530 KHANH HOA T UP y J3 M L C NG CALOC PADAI G135 9532 KHANH HOA T UP n L L C NG DLUC PHUOC G136 9541 KHANH HOA T UP y Im M M B NG LONG G137 NEP NGHE 9554 BEN TRE T RL n L L C G NANG G138 9563 BEN TRE T RL y Im L N A NG QUAT LUA NANG G139 9568 BEN TRE T RL y I2 M M C NG DEN TAM NHO G14 318 BAC NINH T IR y I4 M N A NG BAC NINH LUA BAY G140 9570 BEN TRE T RL y I2 L M B NG DANH LUA NANG G141 9573 BEN TRE T RL y I2 M M B NG NIEU CHUM LUA THANH G142 9574 BEN TRE T RL y I2 VL N A NG TRA NEP TROI G143 9576 BEN TRE T RL y I2 L M A NG CHO LUA MUA G144 DIA 9578 BEN TRE T RL y I2 S M B NG PHUONG G145 BA RIA 9580 BEN TRE T RL y J1 M M B NG NANG G146 LOAN HAT 9584 BEN TRE T RL y I2 L M B NG TRON LUA NANG G147 LOAN HAT 9585 BEN TRE T IR y I2 VL N A NG DAI G148 TRANG TEP 9588 BEN TRE T RL n L M B NG L/ PRC GBS Gr Gr Gr W rat ID Name No Province Type Eco GBS P length width type io MOT TEP G149 9593 BEN TRE T RL n M N A na AN GIANG NEP DIA G150 9595 BEN TRE T IR y I2 M M B G PHUONG G152 LOC SOM 9871 BAC GIANG T IR y J1 M L C G G153 TE NUONG 9874 SON LA T UP y I3 VL M A G G154 NEP THOM 9878 HA TAY T IR y J2 S L C G KHAU PE G155 9908 SON LA T UP y I3 VL M B G LANH G156 LUA K 9967 HA NOI T IR y Im L M B NG SO G157 9984 SEKONG T u y Jm L L C G CRIOONG VA TAI ANA G158 12049 NINH THUAN T UP y J3 L L C NG ACU NEP VAN G16 RUONG 384 HOA BINH T u y J2 M M C G HOA BINH G160 JASMINE 12059 AN GIANG I UP y I1 VL M A NG G161 BN1 12066 AN GIANG I IR y Im VL N A NG NEANG G162 12068 AN GIANG T UP y I2 S N B NG CON CA CHOCH G163 12071 AN GIANG T UP y I2 VL N A G CHAP GIONG 90 G165 12083 KIEN GIANG T RL y I1 VL N A NG NGAY G166 CHIN TEO 12086 KIEN GIANG T IR y I2 L N A NG THAN G167 12088 KIEN GIANG T RL y I2 L N A NG NONG MUA G168 OM1490 12101 KIEN GIANG I IR y I1 L N A NG G169 JASMINE 95 12102 KIEN GIANG I IR y I1 VL N A NG G17 NEP GA 394 HAI DUONG T IR y Im M N A NG GAY HAI L/ PRC GBS Gr Gr Gr W rat ID Name No Province Type Eco GBS P length width type io DUONG OM 504 G170 12103 KIEN GIANG I IR y I1 L N A NG JAPAN G171 NEP THAI 12104 KIEN GIANG T IR y I1 VL N A G G172 VND 95-20 12105 KIEN GIANG I IR y I1 L N A NG TAM THOM G173 TRUNG 12107 KIEN GIANG T IR y Im M N A NG QUOC G177 CHAM HOM 12563 HOA BINH T u y J1 L M A NG KHAU G178 12573 HOA BINH T u y J1 L L C G CHINH PHU BLAO PU G179 12581 HOA BINH T u y J1 L M A NG LAU NEP QUYT G18 407 HAI DUONG T IR y I4 M N A G HAI DUONG CA DUNG G180 12637 HA NOI T IR y I2 M M B NG HAT BLAU PLAN G181 12970 SON LA T UP y I6 M L C G PIENG G182 KHAU MO 13008 SON LA T UP y I6 S M B NG KHAU PE G183 13076 SON LA T UP y Im L M A G LANH KHAU PE G185 u SON LA T UP n L M B na LANH G186 KHAU NO 13309 SON LA T UP y I6 L M B NG KHAU G187 DUONG 13320 SON LA T UP y J1 L L C G PHUONG KHAU NAM G189 13362 DIEN BIEN T UP y I3 L M A G RINH G19 ON 509 HA NOI T IR y Im M M B NG G190 PLE PHMA 13363 DIEN BIEN T UP y I6 M M B NG L/ PRC GBS Gr Gr Gr W rat ID Name No Province Type Eco GBS P length width type io CHUA G191 KHAU TAN 13422 DIEN BIEN T RL y J2 S L C G KHAU BAO G192 13423 DIEN BIEN T RL y Im S M C NG THAI G193 BLE PE XA 13424 DIEN BIEN T UP y J1 VL L C G BLE BLAU G194 13425 DIEN BIEN T UP y J1 VL L B G LIA G195 BLE BDE 13426 DIEN BIEN T UP y J1 L M A NG G196 BLE CO PON 13427 DIEN BIEN T UP y m L M B NG BLE BLAU G197 u DIEN BIEN T UP n L L B na BLAU BLE BLAU G198 13429 DIEN BIEN T UP n VL L B G DA TA CO LAO G2 58 LAO CAI T u y Im M M B NG CAI TE LE HOA G20 553 HOA BINH T u y I4 M N B NG BINH G200 CHA FU NU 13431 LAI CHAU T UP y J1 L L C G CHA XU G201 13435 LAI CHAU T UP y Im M N A NG PHU LU G202 NONG TO 13442 LAI CHAU T UP y J1 L M B NG PLAU CA G203 14212 DIEN BIEN T UP y J1 L M A NG BANH G204 PLE DO 14215 DIEN BIEN T UP y J1 L M A NG BLE BLAU G205 14251 SON LA T UP y I3 VL N A G CHO BLE BLAU G206 14252 SON LA T UP y J1 VL L B G DO G207 KHAU LUA 14278 SON LA T RL y m VL M A G KHAU G208 BOONG 14279 SON LA T RL y Im M L C G LAM L/ PRC GBS Gr Gr Gr W rat ID Name No Province Type Eco GBS P length width type io G209 BLE CHO 14386 LAI CHAU T UP y I6 S M C NG GIE TRANG G21 614 HOA BINH T u y I4 M N A NG HOA BINH G210 KHAU LECH 14408 LAO CAI T UP y J1 L L C G PLAU G211 NGOANG 14587 LAO CAI T UP y Im L M B G PLAC PLAU G212 14589 LAO CAI T UP y J1 M L C NG BULAT PLAU CA G213 u LAO CAI T UP n S M C NG CHAT BLE BLAU G214 14596 LAO CAI T RL y Jm M L C G DO BLE BLAU G215 u LAO CAI T UP n L L B G XA TOM BEO G216 14607 LAO CAI T RL y J1 M M B NG BUA BLE BLAU G217 14615 LAO CAI T RL y J1 VL L B G SOA KHAU LA G219 14792 SON LA T RL y Im L L B NG LANH TRUNG TRANG G22 760 TUYEN QUANG T u y I4 M N B NG TUYN QUANG G220 PLE LA T5300 LAI CHAU T UP y J1 L M B NG KHAU MAC G221 T5455 LAI CHAU T UP y J1 VL L B G CO G222 PLE MA MU T6404 YEN BAI T UP y J1 L L B NG BLE BLAU G223 T6794 LAO CAI T UP y J1 L L B G TAN TAM XOAN G24 1048 NAM DINH T IR y m S N B NG HAI HAU L/ PRC GBS Gr Gr Gr W rat ID Name No Province Type Eco GBS P length width type io NEP VANG G25 ONG LAC 1058 HOA BINH T u y J2 S L C G SON HB KHAU CAI G26 1325 TAY BAC T u y J1 L L C G NOI G27 DOAN KET 1421 CAO BANG T u n M N B NG KHAU PE G28 u BAC THAI T u n L M B na LANH G29 NEP CON 1427 BAC THAI T UP n M M C G CTO VIND G295 u u T u n na na na NG IET6155 BA CHO G297 3525 BINH DINH T UP n na na na na KTE G298 TAN NGAN 3588 YEN BAI T RL n na na na na BLAO SINH G299 4806 HOA BINH T UP y J1 na na na G SAI AN TU VO G3 85 HA NOI T IR y I4 M N A NG DO TIEU CHET G30 1625 CAN THO T u y I2 L N A NG 5 NANG G300 u BAC LIEU T u y I2 na na na NG QUOT BIEN G31 NANG CHI 1629 CAN THO T u y I2 M M B NG G32 NANG DUM 1633 CAN THO T u y Im S M C NG G33 CHET CUT u CAN THO T u n S N B na G34 NANG DUM u CAN THO T u n S N B na G35 SANAKI 1638 CAN THO na u y I2 S M C NG G36 NANG TAY 1643 CAN THO T u y I2 S M C NG G37 NEP CAM 1845 HA GIANG T RL y Im VL N A G G38 NEP NUONG 1849 HA GIANG T UP y J1 L L C G G39 NEP CAM 1851 HA GIANG T RL y Im VL M B G L/ PRC GBS Gr Gr Gr W rat ID Name No Province Type Eco GBS P length width type io NHONG DO G4 135 HAI DUONG T u y I4 M M B NG HAI DUONG G40 NEP DO 2307 KIEN GIANG T RL y I2 L N A G G41 LUA DO 2310 KIEN GIANG T RL y I2 M N A NG LUA HON G42 2313 KIEN GIANG T RL y I2 M M B NG COI G43 THANH TUA 2315 KIEN GIANG T RL y I2 M N A NG G44 MOT BUI 2332 KIEN GIANG T RL n L N A NG G45 NEP CUC 2367 NINH BINH T RL y J4 S L C G NEP BA G46 2368 NAM DINH T MG y J4 M M C G LAO NEP ONG G47 2369 NAM DINH T MG y J4 M M B G LAO G48 LUA NGOI 2371 NAM DINH T MG y J4 S M C NG G49 DT10 2395 u I u y I1 L M A NG NHONG G5 TRANG HAI 149 HAIPHONG T u y I4 M N A NG PHONG LUA NEP G50 BA THANG 3323 QUANG NAM T UP y J2 M L C G DANG 1 BA TRANG G51 3332 QUANG NAM T UP y I5 S N B NG HUONG BA TRANG G52 3334 QUANG NAM T UP y I5 M N B NG HUONG LUA CAN G53 3351 u T u y I6 M M B NG DO LUA LOC G54 3360 QUANG NAM T RL y I6 M M B NG DO G56 LUA MAN 3363 QUANG NAM T RL y I5 S M B NG NEP GHIM G57 3364 QUANG NAM T RL y I6 L M B G HUONG L/ PRC GBS Gr Gr Gr W rat ID Name No Province Type Eco GBS P length width type io NEP HUONG G58 3368 QUANG NAM DA NANG T MG y I6 S M C G LANG G59 NEP MAM 3371 QUANG NAM DA NANG T u y I6 L M B G SOM GIAI G6 170 u T u y I4 L M B NG HUNG YEN G60 NEP CAU 3400 QUANG BINH T RL n S M C G G61 NEP RAN 3402 QUANG BINH T u y J2 S L C G QUANG G62 3426 QUANG TRI T IR y I5 S M C NG TRANG G63 CHIEM DO 3429 QUANG TRI T u y I4 M M B NG G64 VEN DO 3433 QUANG TRI T IR y I5 S N B NG NUOC MAN G65 3443 QUANG TRI T RL y I5 M M B NG DANG 1 G66 LUA MUOI 3483 QUANG NGAI T RL n M M B NG LUA TRI DO G67 3485 BINH DINH T RL y Im S M C NG DANG 2 NEP 3 G68 3487 BINH DINH T IR y m S M C G THANG COC MOI G69 3488 BINH DINH T RL y I6 M M B NG DANG 1 TE TRANG G7 172 HOA BINH T u y I4 M N B NG HOA BINH COC MOI G70 3489 BINH DINH T RL y I6 M M B NG DANG 2 G71 LUA THOM 3493 BINH DINH T RL n M M C NG LUA CANG G72 3494 BINH DINH T RL y Im M M C NG DANG 1 LUA CANG G73 3495 BINH DINH T RL y I6 M M C NG DANG 1 NEP QUA G74 CO RAU 3497 BINH DINH T RL y I6 M M C NG DANG 2 L/ PRC GBS Gr Gr Gr W rat ID Name No Province Type Eco GBS P length width type io G75 NEP QUA 3498 BINH DINH T RL n L M A G CANG KIEN G77 3506 BINH DINH T RL y I6 M M C NG DANG 1 CANG KIEN G78 3507 BINH DINH T RL y I6 M M C NG DANG 2 LUA DA G79 3508 BINH DINH T RL y I6 S M C NG DANG 2 CHON TU G8 502 HOC 175 u T u y I4 M N B NG VIEN G80 BA KTONG 3517 QUANG NGAI T UP y J3 VL M A NG BA DO G81 3519 QUANG NGAI T UP y m M M B NG DANG 1 BA DU G82 u QUANG NGAI T UP n L L C na DANG 2 G83 NEP VANG 3522 QUANG NGAI T UP y Jm L L C G BA CHO G84 3525 BINH DINH T u y J3 L L B NG KTE CHANH G85 3550 THANH HOA T MG y J4 M M B NG CHUI G86 TAN NGAN 3588 YEN BAI T u y J2 S L C G KHAU PAN G87 3886 u T u y J1 L L C G PUA BLE MA G88 3895 u T u y J1 VL L B NG MUA KHAU BO G89 3947 u T u y J1 VL L B G KHA LOC TRANG G9 SOM PLAY 200 u T u y I4 M N B NG CAU G90 BLAO CLIA 4812 HOA BINH T UP y J1 L L B G BLAO CO G91 4815 HOA BINH T UP y J1 L L B NG KEN L/ PRC GBS Gr Gr Gr W rat ID Name No Province Type Eco GBS P length width type io BLAO CO G92 4820 HOA BINH T UP y J1 L L C G CAM PO LE PO G93 5034 NGHE AN T UP y I5 L L B G LAU XA G94 LUA DO 5111 THUA THIEN-HUE T UP y I5 M M B NG G95 LUA CHAM 5127 NAM DINH T RL y I4 L M B NG CHIEM G96 6191 NAM DINH T IR y I5 M N A NG RONG G97 TAM THOM 6199 NAM DINH T IR n S N B NG G98 NGOI TIA 6203 NAM DINH T RL y J4 S M C NG LUA CHAM G99 6234 NINH BINH T RL y I4 L M B NG BIEN u = unknown; na = not analyzed; Zone: NE = Northeast; NW = Northwest; RRD = Red River Delta; NCC = North Central Coast; SSC = South Central Coast; CH = Central Highands; SE = Southeast; MRD = Mekong River Delta; Type: T = traditional, I = improved; Ecosystem: IR = irrigated, RL = rainfed lowland; MG = mangrove; UP = upland; DArT P: population assignments based on Structure results using the DArT markers; GBS: accession genotyped by GBS (y) or not (n); GBS P: population assignments based on Structure results using the GBS markers; Maturity class: E = early, M = medium, L= late; Grain length (L): S = short, M = medium, L = long; Grain width (W): N = narrow, M = medium, L = large; Grain type: G = glutinous; NG = non-glutinous</p><p>Table S2: List of the reference accessions included in the analyses</p><p>Structure ID Name Genebank no Country Source Ecos. EG DArT GBS G224 APO ORYTAGE_1 PHILIPPINES Cirad CC UP 1 1 n G225 ASD 1 IRGC_6267 INDIA Cirad CC IR? 1 1 n G226 FANDRAPOTSY 104 IRGC_10984 MADAGASCAR Cirad CC IR 1 1 n G228 IR64 IRGC_66970 PHILIPPINES Cirad CC IR 1 1 y G229 KHAO DAWK MALI 105 IRGC_27748 THAILAND Cirad CC RL 1 1 n G230 MAKALIOKA 34 IRGC_6087 MADAGASCAR Cirad CC IR 1 1 n G231 NONA BOKRA IRGC_22710 INDIA Cirad CC IR? 1 1 n G232 PETA IRGC_32571 INDONESIA Cirad CC IR 1 1 n G233 POKKALI IRGC_8948 SRI LANKA Cirad CC IR 1 1 n G237 TAICHUNG NATIVE 1 IRGC_105 TAIWAN Cirad CC IR 1 1 n G238 TE QING IRGC_81093 CHINA Cirad CC IR 1 1 n G239 BARAN BORO IRGC_27509 BANGLADESH Cirad CC IR 2 m n G240 BLACK GORA IRGC_40275 INDIA Cirad CC UP 2 1 n G241 DULAR IRGC_32561 INDIA Cirad CC UP 2 1 n G242 KASALATH IRGC_117617 INDIA Cirad CC UP? 2 1 n G244 BASMATI 1 IRGC_27798 PAKISTAN Cirad CC IR 5 m n G246 DOM SOFID IRGC_12880 IRAN Cirad CC IR 5 m n G247 KAUKKYI ANI IRGC_33188 MYANMAR Cirad CC RL? 5 m n G248 PANKHARI 203 IRGC_5999 INDIA Cirad CC IR? 5 m n G249 AZUCENA IRGC_328 PHILIPPINES Cirad CC UP 6 2 y G251 CHUAN 4 IRGC_17052 TAIWAN Cirad CC IR? 6 2 n G252 IRAT 216 CIRAD COTE D'IVOIRE Cirad CC UP 6 2 n G253 GIZA 171 IRGC_50750 EGYPT Cirad CC IR 6 2 n G255 IAC 165 GERVEX_8508 BRAZIL Cirad CC UP 6 2 n G256 IGUAPE CATETO IRGC_4122 BRAZIL Cirad CC UP 6 2 n G257 IRAT 13 IRGC_28508 CÔTE D'IVOIRE Cirad CC UP 6 2 n G258 KHAO DAM IRGC_23385 LAO Cirad CC UP 6 2 n G259 KINANDANG PATONG IRGC_23364 PHILIPPINES Cirad CC UP 6 2 n G260 M 202 IRGC_77142 USA Cirad CC IR 6 2 n G261 MOROBEREKAN IRGC_12048 GUINEA Cirad CC UP 6 2 n G262 NIPPONBARE IRGC_12731 JAPAN Cirad CC IR 6 2 y G263 ARIETE EURIGEN_97 ITALY Cirad CC IR 6 2 n G265 CG14 IRD SENEGAL Cirad CC IR Og m n G266 SO 1 u u AGI u u 1 n G267 HCL u u AGI u u 1 n G268 KDS u u AGI u u 1 n G269 RD6 u THAILAND AGI RL u 1 n G270 XNX u u AGI u u 1 n G271 FL u u AGI u u 2 n G272 SP u u AGI u u 1 n G273 SO 3 u u AGI u u 1 n G276 SM u u AGI u u 1 n G277 RRHD u INDIA AGI u u 1 n G279 LE HUONG 9520 u u AGI u u 1 n G280 VLD HAND 64 u u AGI u u 1 n G281 IET 8616 u INDIA AGI u u 1 n Structure ID Name Genebank no Country Source Ecos. EG DArT GBS G282 SANBAIKE u CHIU AGI u u 1 n G283 AMERICA u LAO PDR? AGI u u 2 n G284 IR 6279 u PHILIPPINES AGI u u 1 n G287 RR654 u INDIA AGI u u m n G288 MT 125 u u AGI u u 1 n G290 IET 17021 u INDIA AGI u u m n G291 PD12 u INDIA AGI IR u 1 n G292 MTU 7029 u INDIA AGI IR u 1 n G293 MTU 1010 u INDIA AGI IR u 1 n G294 M26 u u AGI u u 1 n u=unknown; Ecos.= ecosystem; EG = enzymatic group; IR= irrigated, RL = rainfed lowland; MG= mangrove; UP= upland; Table S3: List of the accessions used to build the DArT library</p><p>ID Variety name Country of Varietal origin group 1 63-83 Senegal trop jap 2 Apo Philippines indica 3 Arborio Itlay temp jap 4 Azucena Philippines trop jap 5 Baldo 363 Italy temp jap 6 Bomba Italy temp jap 7 Cigalon France temp jap 8 Gambiaka Mali indica 9 IAC 165 Brazil trop jap 10 IR64 Philippines indica 11 Kalinga III India indica 12 Khao Dam Thailand trop jap 13 Khao Dawk Mali 105 Thailand indica 14 Koral Portugal temp jap 15 Makalioka 34 Madagascar indica 16 Miara Italy temp jap 17 Moroberekan Guinea trop jap 18 Nipponbare Japan temp jap 19 Oryzica Llanos 5 Colombia indica 20 Ribe Jaune Italy temp jap 21 Swarna India indica 22 Tequing China indica 23 Thaibonnet USA temp jap 24 Vandana India indica 25 Viale Spain temp jap trop jap = tropical japonica; temp jap = temperate japonica</p>