Table S1Oryza rufipogonand weedy rice accessions, locations and habitats in this study

Region / Oryza rufipogonaccession / Habitat condition / UTM / Weedy rice
accession / UTM
Upper North / UN1 / ditch near rice fields / N 20.26765 E 100.40667
UN2 / deep marsh / N 20.27500 E 100.08833
UN3 / irrigation canal / N 18.89999 E 099.01756
UN4 / small marsh in rice field / N 18.57297 E 098.98835
UN5 / canal in longgan orchard / N 18.57335 E 098.99501
Lower North / LN1 / abandon fields, marsh / N 16.56934 E 100.20102 / LNWE1 / N 16.89376 E 100.21043
LN2 / marsh / N 16.48659 E 100.21312 / LNWE2 / N 16.17005 E 100.12967
LN3 / marsh / N 16.42549 E 100.31940
LN4 / abandoned field near rice field / N 16.87597 E 099.79168
LN5 / abandon fields / N 16.44356 E 101.14987
Central / CT1 / ditch near rice field / N 14.62251 E 100.47722 / CTWE1 / N 13.92987 E 099.74348
CT2 / swamp / N 14.50177 E 100.39212 / CTWE2 / N 13.88761 E 099.73245
CT3 / abandoned rice field / N 14.48885 E 100.47448 / CTWE3 / N 14.32981 E 100.11988
CT4 / abandoned field near rice field / N 14.06215 E 101.18994 / CTWE4 / N 14.34322 E 100.12340
CT5 / abandoned fields / N 14.87305 E 100.45166 / CTWE5 / N 14.38126 E 100.12912
CT6 / swamp / N 14.33751 E 100.12694
CT7 / small canal near rice fields / N 13.92453 E 099.74987
CT8 / abandoned field near rice fields / N 13.87653 E 099.71267
CT9 / deep swamp, in situ conservation area / N 13.99543 E 101.22135
Northeast / NE1 / abandoned fields / N 14.09166 E 102.69646 / NEWE1 / N 15.72180 E 104.24088
NE2 / small ditch / N 14.99367 E 103.16792 / NEWE2 / N 14.78988 E 103.83912
NE3 / abandoned fields / N 14.68020 E 102.55420 / NEWE3 / N 14.95359 E 104.20601
NE4 / shallow ditch / N 14.66321 E 102.61402 / NEWE4 / N 14.87909 E 103.30641
NE5 / swamp / N 14.62856 E 103.06692 / NEWE5 / N 14.62856 E 103.24280
NE6 / near rice field / N 14.62856 E 103.24828
NE7 / shallow ditch / N 14.94486 E 102.16223
NE8 / ditch near rice fields / N 16.15832 E 103.78356
NE9 / shallow ditch near rice fields / N 16.07418 E 103.61746
NE10 / shallow ditch near rice fields / N 16.03048 E 103.86951
NE11 / shallow field near rice fields / N 17.36042 E 102.96401
NE12 / shallow swamp near rice fields / N 14.65276 E 102.85075
NE13 / shallow swamp near rice fields / N 14.84563 E 103.43521
NE14 / abandon field / N 14.62291 E 103.89379
NE15 / shallow ditch near rice fields / N 15.10498 E 105.16513
NE16 / ditch near rice fields / N 15.94862 E 104.04889
NE17 / ditch near rice field / N 15.79287 E 104.17415
NE18 / marsh / N 16.19982 E 103.26114
NE19 / shallow marsh / N 16.25317 E 103.03255
NE20 / deep swamp, in situ conservation area / N 17.20692 E 104.18535
NE21 / shallow ditch / N 15.00356 E 104.38245
NE22 / ditch / N 15.09111 E 104.33101
NE23 / ditch / N 17.76823 E 103.09652

Table S2 Name, abbreviation, and pedigree description of 37 cultivated rice in the present study

Variety / Abbreviation / Type* / Description
Doh Hawm 26 / DH26 / ITV / Pure line selection from traditional variety
Dawk Mali 3 / DML3 / ITV / Pure line selection from traditional variety
Kum Doi Sa Ket / KDK / ITV / Pure line selection from traditional variety
Khao Dawk Mali 105 / KDML105 / ITV / Pure line selection from traditional variety
Gam Pai / KP41 / ITV / Pure line selection from traditional variety
Khao Pahk Maw 148 / KPM148 / ITV / Pure line selection from traditional variety
Gow Ruang 88 / KR88 / ITV / Pure line selection from traditional variety
Muey Nawng 62M / MN62M / ITV / Pure line selection from traditional variety
Nahng Mon S-4 / NMS-4 / ITV / Pure line selection from traditional variety
Nam Sa-gui 19 / NSG19 / ITV / Pure line selection from traditional variety
Pra Deu Dang / PDD / ITV / Pure line selection from traditional variety
R258 / R258 / ITV / Pure line selection from traditional variety
RD 10 / RD10 / ITV / Improved by mutation breeding from irradiated RD1
RD 6 / RD6 / ITV / Improved by mutation breeding from irradiated KDML105
Chai Nat 1 / CNT1 / MV / IR13146-158-1/IR15314-43-2-3-3/BKN6995-16-1-1-2
Chai Nat 2 / CNT2 / MV / Hawm Phama (GS. No. 3780)/IR11418-19-2-3
Chai Nat 3 / CNT3 / MV / ---
Chai Nat 80 / CNT80 / MV / Derived from F1-SPR60/IR29692-99-3-2-1/IR11418-19-2-3
Hawm Khlong Luang 1 / HKL1 / MV / Nahng Mon S-4/IR841-85-1-1-2
Hawm Suphan Buri / HSP / MV / SPR84177-8-2-2-2-1/SPR85091-13-1-1-4//KDML105
IR68144 / IR68144 / MV / ---
Phitsanulok 1 / PSL1 / MV / KDML105/LA29’72NFU-14-3-1-1//IR58
Phitsanulok 2 / PSL2 / MV / CNTLR81122-PSL-37-2-1/SPRLR81041-195-2-1//IR56
Phitsanulok 3 / PSL3 / MV / RD27 / LA29’73-NF1U-14-13-1-1
Pathum Thani 1 / PTT1 / MV / BKNA6-18-3-2/PTT85061-86-3-2-1
Pathum Thani 2 / PTT2 / MV / ---
RD 1 / RD1 / MV / Leuang Tawng/IR8
RD 23 / RD23 / MV / RD7/IR32//RD1
RD 29 / RD29 / MV / Chai Nat 80
RD 4 / RD4 / MV / LueangTawng/IR8//W1252///RD2
RD 7 / RD7 / MV / C4-63/Gow Ruang 88//Sigadis
Sakon Nakhon / SKN / MV / Hawm Ohm/RD10
Suphan Buri 1 / SPR1 / MV / IR25393-57-2-3/RD23//IR27316-96-3-2-2///SRPLR77205-3-2-1-1/SPRLR79134-51-2-2
Suphan Buri 2 / SPR2 / MV / RD23/IR60
Suphan Buri 60 / SPR60 / MV / Leuang Tawng/C4-63//IR48
Suphan Buri 90 / SPR90 / MV / RD21/IR4422-98-3-6-1//RD11/RD23
San-pah-tawng 1 / SPT1 / MV / BKNLR75001-B3-CNT-B4-RST-36-2/RD2

Source: Department of Agriculture, Thailand

* ITV=Improved traditional variety; MV=Modern variety

Table S3 Average number of alleles, polymorphic information content (PIC)for each microsatellite locus of 37 Thai cultivated rice varieties

Locus / Average no. of allele / Total
Allele no. / PIC*
RM1 / 1 / 13 / 0.883
RM206 / 1 / 16 / 0.912
RM109 / 1 / 8 / 0.764
RM247 / 1 / 9 / 0.746
RM211 / 1 / 12 / 0.828
RM477 / 1 / 1 / 0.000
RM251 / 1 / 12 / 0.861
RM234 / 1 / 11 / 0.820
RM259 / 1 / 7 / 0.669
RM133 / 1 / 6 / 0.694
RM316 / 1 / 8 / 0.784
RM481 / 1 / 14 / 0.887
No. of private allele / 6
Average / 1 / 9.7 / 0.737
Total / 117

*Polymorphic information content (PIC)

§Average number of allele per locus per group

Table S4 Proportion of estimated assign populations (Q) of 11 selected cultivated rice varieties, 12 weedy rice populations and 42 wild rice populations (K=5)

Accession / n / Given inferred clusters (Q)
Cr1 / Cr2 / Cr3 / W1 / W2
CNT1 / 10 / 0.979 / 0.014 / 0.003 / 0.002 / 0.002
SPR1 / 10 / 0.990 / 0.003 / 0.003 / 0.002 / 0.002
PSL1 / 10 / 0.002 / 0.993 / 0.002 / 0.002 / 0.002
PSL2 / 10 / 0.003 / 0.987 / 0.004 / 0.003 / 0.003
PSL3 / 10 / 0.002 / 0.992 / 0.002 / 0.002 / 0.002
PTT1 / 10 / 0.003 / 0.992 / 0.002 / 0.002 / 0.002
PTT2 / 10 / 0.002 / 0.992 / 0.002 / 0.002 / 0.002
KDML105 / 10 / 0.004 / 0.002 / 0.989 / 0.002 / 0.002
RD6 / 10 / 0.003 / 0.003 / 0.990 / 0.002 / 0.002
SKN / 10 / 0.002 / 0.003 / 0.990 / 0.002 / 0.002
SPT1 / 10 / 0.003 / 0.003 / 0.989 / 0.003 / 0.002
LNWE1 / 10 / 0.054 / 0.002 / 0.471 / 0.451 / 0.012
LNWE1 / 10 / 0.030 / 0.647 / 0.014 / 0.283 / 0.026
CTWE1 / 10 / 0.987 / 0.003 / 0.003 / 0.003 / 0.005
CTWE2 / 10 / 0.949 / 0.002 / 0.030 / 0.003 / 0.015
CTWE3 / 10 / 0.632 / 0.015 / 0.011 / 0.050 / 0.293
CTWE4 / 10 / 0.987 / 0.004 / 0.003 / 0.003 / 0.003
CTWE5 / 10 / 0.986 / 0.006 / 0.003 / 0.002 / 0.002
NEWE1 / 10 / 0.008 / 0.003 / 0.007 / 0.830 / 0.152
NEWE2 / 10 / 0.002 / 0.364 / 0.438 / 0.203 / 0.003
NEWE3 / 10 / 0.065 / 0.002 / 0.356 / 0.569 / 0.009
NEWE4 / 10 / 0.014 / 0.027 / 0.214 / 0.058 / 0.697
NEWE5 / 10 / 0.019 / 0.002 / 0.283 / 0.261 / 0.671
UN1 / 10 / 0.004 / 0.003 / 0.003 / 0.982 / 0.008
UN2 / 10 / 0.003 / 0.004 / 0.263 / 0.710 / 0.019
UN3 / 10 / 0.008 / 0.010 / 0.005 / 0.960 / 0.016
UN4 / 10 / 0.003 / 0.013 / 0.003 / 0.950 / 0.032
UN5 / 10 / 0.016 / 0.003 / 0.074 / 0.904 / 0.003
LN1 / 10 / 0.003 / 0.003 / 0.003 / 0.987 / 0.004
LN2 / 10 / 0.015 / 0.003 / 0.005 / 0.972 / 0.005
LN3 / 10 / 0.017 / 0.005 / 0.007 / 0.967 / 0.004
LN4 / 10 / 0.029 / 0.004 / 0.005 / 0.956 / 0.006
LN5 / 10 / 0.118 / 0.005 / 0.003 / 0.552 / 0.322
CT1 / 10 / 0.004 / 0.009 / 0.003 / 0.980 / 0.005
CT2 / 10 / 0.021 / 0.005 / 0.006 / 0.918 / 0.049
CT3 / 10 / 0.017 / 0.005 / 0.015 / 0.914 / 0.049
CT4 / 10 / 0.052 / 0.019 / 0.056 / 0.760 / 0.114
CT5 / 10 / 0.020 / 0.008 / 0.025 / 0.941 / 0.007
CT6 / 10 / 0.115 / 0.019 / 0.002 / 0.848 / 0.016
CT7 / 10 / 0.015 / 0.003 / 0.033 / 0.936 / 0.013
CT8 / 10 / 0.353 / 0.008 / 0.005 / 0.583 / 0.051
CT9 / 10 / 0.007 / 0.005 / 0.030 / 0.949 / 0.009
NE1 / 10 / 0.008 / 0.003 / 0.008 / 0.029 / 0.952
NE2 / 10 / 0.005 / 0.012 / 0.005 / 0.318 / 0.659
NE3 / 10 / 0.030 / 0.008 / 0.094 / 0.030 / 0.838
NE4 / 10 / 0.005 / 0.004 / 0.008 / 0.003 / 0.979
NE5 / 10 / 0.007 / 0.004 / 0.005 / 0.969 / 0.015
NE6 / 10 / 0.027 / 0.008 / 0.003 / 0.921 / 0.040
NE7 / 10 / 0.027 / 0.013 / 0.006 / 0.006 / 0.948
NE8 / 10 / 0.059 / 0.004 / 0.009 / 0.540 / 0.388
NE9 / 10 / 0.002 / 0.020 / 0.139 / 0.801 / 0.037
NE10 / 10 / 0.052 / 0.003 / 0.039 / 0.122 / 0.785
NE11 / 10 / 0.004 / 0.010 / 0.003 / 0.975 / 0.010
NE12 / 10 / 0.134 / 0.020 / 0.041 / 0.014 / 0.791
NE13 / 10 / 0.061 / 0.012 / 0.122 / 0.579 / 0.235
NE14 / 10 / 0.003 / 0.002 / 0.881 / 0.014 / 0.100
NE15 / 10 / 0.003 / 0.006 / 0.003 / 0.006 / 0.983
NE16 / 10 / 0.029 / 0.008 / 0.467 / 0.423 / 0.074
NE17 / 10 / 0.048 / 0.002 / 0.007 / 0.007 / 0.936
NE18 / 10 / 0.014 / 0.005 / 0.133 / 0.033 / 0.815
NE19 / 10 / 0.014 / 0.002 / 0.083 / 0.073 / 0.848
NE20 / 10 / 0.033 / 0.004 / 0.027 / 0.922 / 0.015
NE21 / 10 / 0.046 / 0.005 / 0.024 / 0.921 / 0.004
NE22 / 10 / 0.007 / 0.004 / 0.007 / 0.324 / 0.660
NE23 / 10 / 0.004 / 0.003 / 0.004 / 0.971 / 0.019