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Table 3 DNA genotype of archaic grains and modern rice accessions by specific primer set in the chloroplast genome

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

Site name/ Rice type No. of grains/a accessions rps16 intron1b Orf100 F1–R1b Orf100 F1–R2b trnIb petNtrnCb
152 159 NA 100 NA 93 162 NA A G NA 75 107 NA
West trench 120 4 1 115 5 115 0 8 120 11 2 107 0 0 120
South trench 50 0 0 50 0 50 0 0 50 0 0 50 0 0 50
Japonica/ Tropical/ Lowland 7 6 1 0 6 1 1 6 0 7 0 0 7 0 0
Japonica/ Temperate/ Lowland 4 4 0 0 4 0 0 4 0 4 0 0 4 0 0
Japonica/ Temperate/ Upland 3 3 0 0 3 0 0 3 0 3 0 0 3 0 0
Indica 19 2 17 0 1 18 18 1 0 0 19 0 0 19 0
  1. aNumerical number indicates number of accessions in modern rice accessions
  2. bElectrophoresis and sequencing were used to detect an expected DNA fragment in regions rps16 intron1, Orf100, trnI and petNtrnC and the size of each DNA fragment was used as the genotype name. “F1–R1” or “F1–R2” are primer set in Orf100. NA = Not amplification by specific primer set