Molecular and Evolutionary Analysis of the Hd6 Photoperiod Sensitivity Gene Within Genus Oryza

Yamane, Hiroko; Ito, Tomoko; Ishikubo, Harumi; Fujisawa, Masaki; Yamagata, Harumi; Kamiya, Kozue; Ito, Yukiyo; Hamada, Masao; Kanamori, Hiroyuki; Ikawa, Hiroshi; Katayose, Yuichi; Wu, Jianzhong; Sasaki, Takuji; Matsumoto, Takashi

doi:10.1007/s12284-008-9019-2

Rice

Table 3 Nucleotide Variations Detected in the Hd6 Region of O. sativa and its DNA Divergence with the Different Oryza Species

From: Molecular and Evolutionary Analysis of the Hd6 Photoperiod Sensitivity Gene Within Genus Oryza

	Number of sites	S	π	K _sat–ruf	K _sat–gla	K _sat–bar	K _sat–glu	K _sat–mer	K _sat–lon	K _sat–pun	K _{sat–min(BB)}	K _{sat–min(CC)}	K _sat–off	K _{sat–alt(DD)}	K _sat–aus	K _sat–bra	K _sat–gra
Entire genetic region	5,647	19	0.0018	0.0011	0.0014	0.0019	0.0024	0.0131	0.0212	0.0595	0.0590	0.0489	0.0492	0.0624	0.0675	0.1515	0.1662
Entire genetic region	5,647	19	0.0018	[5.00]	[6.40]	[8.40]	[11.00]	[58.40]	[94.40]	[257.60]	[255.60]	[213.40]	[214.40]	[269.80]	[290.80]	[618.20]	[671.80]
Exons	1,002	1	0.0004	0.0002	0.0002	0.0002	0.0022	0.0012	0.0032	0.0103	0.0103	0.0082	0.0103	0.0204	0.0184	0.0318	0.0308
Exons	1,002	1	0.0004	[0.20]	[0.20]	[0.20]	[2.20]	[1.20]	[3.20]	[10.20]	[10.20]	[8.20]	[10.20]	[20.20]	[18.20]	[31.20]	[30.20]
Synonymous	223.1	0	0.0000	0.0000	0.0000	0.0000	0.0045	0.0045	0.0136	0.0462	0.0462	0.0367	0.0415	0.0954	0.0803	0.1482	0.1481
Synonymous	223.1	0	0.0000	[0.00]	[0.00]	[0.00]	[1.00]	[1.00]	[3.00]	[10.00]	[10.00]	[8.00]	[9.00]	[20.00]	[17.00]	[30.00]	[30.00]
Nonsynonymous	778.9	1	0.0005	0.0003	0.0003	0.0003	0.0015	0.0003	0.0003	0.0003	0.0003	0.0003	0.0015	0.0003	0.0015	0.0015	0.0003
Nonsynonymous	778.9	1	0.0005	[0.20]	[0.20]	[0.20]	[1.20]	[0.20]	[0.20]	[0.20]	[0.20]	[0.20]	[1.20]	[0.20]	[1.20]	[1.20]	[0.20]
Introns	4,173	17	0.0022	0.0014	0.0018	0.0024	0.0026	0.0118	0.0270	0.0753	0.0742	0.0596	0.0589	0.0720	0.0798	0.1933	0.2159
Introns	4,173	17	0.0022	[4.27]	[5.60]	[7.60]	[8.20]	[36.60]	[82.60]	[223.40]	[220.40]	[178.60]	[176.60]	[214.00]	[236.00]	[531.40]	[585.00]
5′UTR	284	0	0.0000	0.0000	0.0000	0.0000	0.0000	0.0666	0.0161	0.0754	0.0798	0.0798	0.0798	0.1208	0.1208	0.1691	0.1494
5′UTR	284	0	0.0000	[0.00]	[0.00]	[0.00]	[0.00]	[16.00]	[4.00]	[18.00]	[19.00]	[19.00]	[19.00]	[28.00]	[28.00]	[38.00]	[34.00]
3′UTR	188	1	0.0032	0.0039	0.0044	0.0044	0.0044	0.0346	0.0346	0.0455	0.0455	0.0581	0.0661	0.0581	0.0661	0.1421	0.1879
3′UTR	188	1	0.0032	[0.53]	[0.60]	[0.60]	[0.60]	[4.60]	[4.60]	[6.00]	[6.00]	[7.60]	[8.60]	[7.60]	[8.60]	[17.60]	[22.60]

Average numbers of nucleotide differences are shown in parentheses
S and π number of substitutions (polymorphic sites) and nucleotide diversity within O. sativa (five varieties), K nucleotide divergence calculated by Jukes and Cantor method between each pair of species as shown in subscript, sat O. sativa, ruf O. rufipogon, gla O. glaberrima, bar O. barthii, glu O. glumaepatula, mer O. meridionalis, lon O. longistaminata, pun O. punctata, min O. minuta, off O. officinalis, alt O. alta, aus O. australiensis, bra O. brachyantha, gra O. granulata

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