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

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

Site name/ Rice type	No. of grains/^a accessions	rps16 intron1^b			Orf100 F1–R1^b		Orf100 F1–R2^b			trnI^b			petN–trnC^b
Site name/ Rice type	No. of grains/^a accessions	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

^aNumerical number indicates number of accessions in modern rice accessions
^bElectrophoresis and sequencing were used to detect an expected DNA fragment in regions rps16 intron1, Orf100, trnI and petN–trnC 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