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

Tanaka, Katsunori; Zhao, Chunfang; Wang, Ningyuan; Kubota, Shinji; Kanehara, Masaaki; Kamijo, Nobuhiko; Ishikawa, Ryuji; Tasaki, Hiroyuki; Kanehara, Minako; Liu, Bin; Chen, Minghui; Nakamura, Shin-ichi; Udatsu, Tetsuro; Wang, Cailin

doi:10.1186/s43014-020-00028-8

Food Production, Processing and Nutrition

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 number^a		Country	Group/ Rice type/ Species		Cultivation type	Seed^b source	Chloroplast genome^c					Nuclear genome^c
							rps16 intron1	Orf100 In/del^d		trnI	petN–^dtrnC	qSH1	sh4	DJ6 In/del^d
							rps16 intron1	F1–R1	F1–R2	trnI	petN–^dtrnC	qSH1	sh4	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
70^a 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

^aAccession numbers refer to varieties registered in the National Institute of Genetics (NIG), Japan
^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
^cElectrophoresis and sequencing were used to detect an expected DNA fragment in regions rps16 intron1, Orf100, trnI, petN–trnC, 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
^dGenotype data, except for “P.TB. 8” in orf100 region, are referred to the study of Castillo et al. (2016)

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ISSN: 2661-8974

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