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Table 1 DNA genotype of modern rice accessions examined in this study

From: Classification of archaic rice grains excavated at the Mojiaoshan site within the Liangzhu site complex reveals an Indica and Japonica chloroplast complex

Variety name/ Accession numbera Country Group/ Rice type/ Species Cultivation type Seedb source Chloroplast genomec Nuclear genomec
rps16 intron1 Orf100 In/deld trnI petNdtrnC qSH1 sh4 DJ6 In/deld
F1–R1 F1–R2 F1–R1 F1–R2
Gendjah ratji / T0624 Indonesia Japonica / Tropical Lowland 1 152 100 162 A 75 G T 315 102
Paid kasalle / T0642 Indonesia Japonica / Tropical Lowland 1 152 100 162 A 75 G T 315 102
Sinanpablo / T0220 Philippines Japonica / Tropical Lowland 1 152 100 162 A 75 G T 315 102
Malagkit sinaguing / T0221 Philippines Japonica / Tropical Lowland 1 152 100 162 A 75 G T 315 102
Macan menita / T0224 Philippines Japonica / Tropical Lowland 1 152 100 162 A 75 G T 315 102
Hsu-chou-san-pei / T0718 China Japonica / Tropical Lowland 1 152 100 162 A 75 G T 315 102
Koddi / T0757 China Japonica / Tropical Lowland 1 159 NA 93 A 75 G T 98 NA
Ta-pei-mang / T0708 China Japonica / Temperate Lowland 1 152 100 162 A 75 G T 98 NA
Tsao-siao-pei-tao / T0709 China Japonica / Temperate Lowland 1 152 100 162 A 75 G T 98 NA
Bohai / T0848 China Japonica / Temperate Lowland 1 152 100 162 A 75 G T 315 102
Kinoshita-mochi / T0563 Japan Japonica / Temperate Lowland 1 152 100 162 A 75 G T 98 NA
Akamochi / JP4424 Japan Japonica / Temperate Upland 2 152 100 162 A 75 G T 315 102
Abaremochi / JP5085 Japan Japonica / Temperate Upland 2 152 100 162 A 75 G T 315 102
Akayakan / JP4663 Japan Japonica / Temperate Upland 2 152 100 162 A 75 G T 315 102
P.T.B.10 / T0414 India Indica   Lowland 1 159 NA 93 G 107 G T 315 102
A.D.T. 4 / T0415 India Indica   Lowland 1 159 NA 93 G 107 G T 315 102
A.D.T. 14 / T0417 India Indica   Lowland 1 159 NA 93 G 107 G T 315 102
M.T.U. 9 / T0420 India Indica   Lowland 1 159 NA 93 G 107 G T 315 102
P.T.B. 8 / T0421 India Indica   Lowland 1 152 100 162 G 107 G T 315 102
Mugi of bogra / T0440 India Indica   Lowland 1 152 NA 93 G 107 G T 315 102
Pduhai perumal / T0435 Sri Lanka Indica   Lowland 1 159 NA 93 G 107 G T 315 102
70a som cau / T0001 Vietnam Indica   Lowland 1 159 NA 93 G 107 G T 315 102
He-nan-tsao / T0706 China Indica   Lowland 1 159 NA 93 G 107 G T 315 102
Mao-tŭ-tas / T0710 China Indica   Lowland 1 159 NA 93 G 107 G T 315 102
Chiang-si-wan / T0715 China Indica   Lowland 1 159 NA 93 G 107 G T 315 102
Chin sen / T0719 China Indica   Lowland 1 159 NA 93 G 107 G T 315 102
Kun-mih-tsieh-huan / T0724 China Indica   Lowland 1 159 NA 93 G 107 G T 315 102
Ming-hou-tsiu-tsao / T0729 China Indica   Lowland 1 159 NA 93 G 107 G T 315 102
Siao-chung-kuh / T0761 China Indica   Lowland 1 159 NA 93 G 107 G T 315 102
U-kuh-tsing-you / T0101 China Indica   Lowland 1 159 NA 93 G 107 G T 315 102
Peh-kuh / T0108 China Indica   Lowland 1 159 NA 93 G 107 G T 315 102
Tuan-Kuang-hwa-lo / T0130 China Indica   Lowland 1 159 NA 93 G 107 G T 315 102
Patpaku / T0868 China Indica   Lowland 1 159 NA 93 G 107 G T 315 102
  1. aAccession numbers refer to varieties registered in the National Institute of Genetics (NIG), Japan
  2. bSeeds were provided by three source institutes indicated by the following numbers: 1 = National Institute of Genetics (NIG), Japan, 2 = Genebank, Genetic Resources Center, NARO, Japan
  3. cElectrophoresis and sequencing were used to detect an expected DNA fragment in regions rps16 intron1, Orf100, trnI, petNtrnC, qSH1, sh4 and DJ6 and the size of each DNA fragment was used as the genotype name. “F1–R1” or “F1–R2” are primer set in Orf100 and DJ6. NA = Not amplification by specific primer set
  4. dGenotype data, except for “P.TB. 8” in orf100 region, are referred to the study of Castillo et al. (2016)