Classification and Identification of indica P/TGMS Lines in China

doi:10.1016/j.rsci.2019.01.003

Abstract

Abstract:

SUMMARY Despite extensive studies on cultivated rice, the population structure and genetic diversity of the indica photoperiod- and thermo-sensitive genic male sterility (P/TGMS) lines in China remains unclear. Using 48 simple sequence repeat (SSR) markers, we genotyped a panel of 208 indica P/TGMS lines and confirmed three subgroups, named indica-I, indica-II and indica-III, in indica P/TGMS lines. Further diversity analysis indicated indica-II had the highest genetic diversity. The genetic differentiation between indica-II and indica-III was demonstrated as the largest among the three subgroups. Moreover, indica/japonica component identification was detected that five P/TGMS lines possess indica components less than 0.900. These results improve our knowledge on the genetic background for P/TGMS lines in China and will be beneficial for hybrid rice breeding programs.

Mengchen Zhang, Shan Wang, Jianfang Yan, Shuiyong Sun, Xin Xu, Qun Xu, Xiaoping Yuan, Xinghua Wei, Yaolong Yang. Classification and Identification of indica P/TGMS Lines in China[J]. Rice Science, 2019, 26(3): 195-198.

Figures/Tables 9

References 15

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Locus name	Labelled color	Forward primer (5’ - 3’)	Reverse primer (5’ - 3’)
RM583	VIC	AGATCCATCCCTGTGGAGAG	GCGAACTCGCGTTGTAATC
RM424	NED	TTTGTGGCTCACCAGTTGAG	TGGCGCATTCATGTCATC
RM85	FAM	CCAAAGATGAAACCTGGATTG	GCACAAGGTGAGCAGTCC
RM471	VIC	ACGCACAAGCAGATGATGAG	GGGAGAAGACGAATGTTTGC
RM598	FAM	GAATCGCACACGTGATGAAC	ATGCGACTGATCGGTACTCC
RM190	VIC	CTTTGTCTATCTCAAGACAC	TTGCAGATGTTCTTCCTGATG
RM336	VIC	CTTACAGAGAAACGGCATCG	GCTGGTTTGTTTCAGGTTCG
RM72	PET	CCGGCGATAAAACAATGAG	GCATCGGTCCTAACTAAGGG
RM219	FAM	CGTCGGATGATGTAAAGCCT	CATATCGGCATTCGCCTG
RM590	PET	CATCTCCGCTCTCCATGC	GGAGTTGGGGTCTTGTTCG
RM209	VIC	ATATGAGTTGCTGTCGTGCG	CAACTTGCATCCTCCCCTCC
RM19	PET	CAAAAACAGAGCAGATGAC	CTCAAGATGGACGCCAAGA
RM1195	FAM	ATGGACCACAAACGACCTTC	CGACTCCCTTGTTCTTCTGG
RM208	PET	TCTGCAAGCCTTGTCTGATG	TAAGTCGATCATTGTGTGGACC
RM232	PET	CCGGTATCCTTCGATATTGC	CCGACTTTTCCTCCTGACG
RM119	PET	CATCCCCCTGCTGCTGCTGCTG	CGCCGGATGTGTGGGACTAGCG
RM267	NED	TGCAGACATAGAGAAGGAAGTG	AGCAACAGCACAACTTGATG
RM253	PET	TCCTTCAAGAGTGCAAAACC	GCATTGTCATGTCGAAGCC
RM481	FAM	TAGCTAGCCGATTGAATGGC	CTCCACCTCCTATGTTGTTG
RM339	VIC	GTAATCGATGCTGTGGGAAG	GAGTCATGTGATAGCCGATATG
RM316	VIC	CTAGTTGGGCATACGATGGC	ACGCTTATATGTTACGTCAAC
RM258	FAM	TGCTGTATGTAGCTCGCACC	TGGCCTTTAAAGCTGTCGC
RM224	NED	ATCGATCGATCTTCACGAGG	TGCTATAAAAGGCATTCGGG
RM17	NED	TGCCCTGTTATTTTCTTCTCTC	GGTGATCCTTTCCCATTTCA
RM493	VIC	TAGCTCCAACAGGATCGACC	GTACGTAAACGCGGAAGGTG
RM561	FAM	GAGCTGTTTTGGACTACGGC	GAGTAGCTTTCTCCCACCCC
RM8277	NED	AGCACAAGTAGGTGCATTTC	ATTTGCCTGTGATGTAATAGC
RM551	FAM	AGCCCAGACTAGCATGATTG	GAAGGCGAGAAGGATCACAG
RM274	VIC	CCTCGCTTATGAGAGCTTCG	CTTCTCCATCACTCCCATGG
RM176	FAM	CGGCTCCCGCTACGACGTCTCC	AGCGATGCGCTGGAAGAGGTGC
RM432	PET	TTCTGTCTCACGCTGGATTG	AGCTGCGTACGTGATGAATG
RM331	NED	GAACCAGAGGACAAAAATGC	CATCATACATTTGCAGCCAG
OSR28	NED	AGCAGCTATAGCTTAGCTGG	ACTGCACATGAGCAGAGACA
RM311	VIC	TGGTAGTATAGGTACTAAACAT	TCCTATACACATACAAACATAC
RM21	FAM	ACAGTATTCCGTAGGCACGG	GCTCCATGAGGGTGGTAGAG
RM3331	VIC	CCTCCTCCATGAGCTAATGC	AGGAGGAGCGGATTTCTCTC
RM443	VIC	GATGGTTTTCATCGGCTACG	AGTCCCAGAATGTCGTTTCG
RM490	FAM	ATCTGCACACTGCAAACACC	AGCAAGCAGTGCTTTCAGAG
RM71	FAM	CTAGAGGCGAAAACGAGATG	GGGTGGGCGAGGTAATAATG
RM423	FAM	AGCACCCATGCCTTATGTTG	CCTTTTTCAGTAGCCCTCCC
RM571	FAM	GGAGGTGAAAGCGAATCATG	CCTGCTGCTCTTTCATCAGC
RM231	PET	CCAGATTATTTCCTGAGGTC	CACTTGCATAGTTCTGCATTG
RM567	PET	ATCAGGGAAATCCTGAAGGG	GGAAGGAGCAATCACCACTG
RM289	PET	TTCCATGGCACACAAGCC	CTGTGCACGAACTTCCAAAG
RM542	VIC	TGAATCAAGCCCCTCACTAC	CTGCAACGAGTAAGGCAGAG
RM278	NED	GTAGTGAGCCTAACAATAATC	TCAACTCAGCATCTCTGTCC
RM332	VIC	GCGAAGGCGAAGGTGAAG	CATGAGTGATCTCACTCACCC
RM7102	PET	TAGGAGTGTTTAGAGTGCCA	TCGGTTTGCTTATACATCAG

Locus name	Labelled color	Forward primer (5’ - 3’)	Reverse primer (5’ - 3’)
RM583	VIC	AGATCCATCCCTGTGGAGAG	GCGAACTCGCGTTGTAATC
RM424	NED	TTTGTGGCTCACCAGTTGAG	TGGCGCATTCATGTCATC
RM85	FAM	CCAAAGATGAAACCTGGATTG	GCACAAGGTGAGCAGTCC
RM471	VIC	ACGCACAAGCAGATGATGAG	GGGAGAAGACGAATGTTTGC
RM598	FAM	GAATCGCACACGTGATGAAC	ATGCGACTGATCGGTACTCC
RM190	VIC	CTTTGTCTATCTCAAGACAC	TTGCAGATGTTCTTCCTGATG
RM336	VIC	CTTACAGAGAAACGGCATCG	GCTGGTTTGTTTCAGGTTCG
RM72	PET	CCGGCGATAAAACAATGAG	GCATCGGTCCTAACTAAGGG
RM219	FAM	CGTCGGATGATGTAAAGCCT	CATATCGGCATTCGCCTG
RM590	PET	CATCTCCGCTCTCCATGC	GGAGTTGGGGTCTTGTTCG
RM209	VIC	ATATGAGTTGCTGTCGTGCG	CAACTTGCATCCTCCCCTCC
RM19	PET	CAAAAACAGAGCAGATGAC	CTCAAGATGGACGCCAAGA
RM1195	FAM	ATGGACCACAAACGACCTTC	CGACTCCCTTGTTCTTCTGG
RM208	PET	TCTGCAAGCCTTGTCTGATG	TAAGTCGATCATTGTGTGGACC
RM232	PET	CCGGTATCCTTCGATATTGC	CCGACTTTTCCTCCTGACG
RM119	PET	CATCCCCCTGCTGCTGCTGCTG	CGCCGGATGTGTGGGACTAGCG
RM267	NED	TGCAGACATAGAGAAGGAAGTG	AGCAACAGCACAACTTGATG
RM253	PET	TCCTTCAAGAGTGCAAAACC	GCATTGTCATGTCGAAGCC
RM481	FAM	TAGCTAGCCGATTGAATGGC	CTCCACCTCCTATGTTGTTG
RM339	VIC	GTAATCGATGCTGTGGGAAG	GAGTCATGTGATAGCCGATATG
RM316	VIC	CTAGTTGGGCATACGATGGC	ACGCTTATATGTTACGTCAAC
RM258	FAM	TGCTGTATGTAGCTCGCACC	TGGCCTTTAAAGCTGTCGC
RM224	NED	ATCGATCGATCTTCACGAGG	TGCTATAAAAGGCATTCGGG
RM17	NED	TGCCCTGTTATTTTCTTCTCTC	GGTGATCCTTTCCCATTTCA
RM493	VIC	TAGCTCCAACAGGATCGACC	GTACGTAAACGCGGAAGGTG
RM561	FAM	GAGCTGTTTTGGACTACGGC	GAGTAGCTTTCTCCCACCCC
RM8277	NED	AGCACAAGTAGGTGCATTTC	ATTTGCCTGTGATGTAATAGC
RM551	FAM	AGCCCAGACTAGCATGATTG	GAAGGCGAGAAGGATCACAG
RM274	VIC	CCTCGCTTATGAGAGCTTCG	CTTCTCCATCACTCCCATGG
RM176	FAM	CGGCTCCCGCTACGACGTCTCC	AGCGATGCGCTGGAAGAGGTGC
RM432	PET	TTCTGTCTCACGCTGGATTG	AGCTGCGTACGTGATGAATG
RM331	NED	GAACCAGAGGACAAAAATGC	CATCATACATTTGCAGCCAG
OSR28	NED	AGCAGCTATAGCTTAGCTGG	ACTGCACATGAGCAGAGACA
RM311	VIC	TGGTAGTATAGGTACTAAACAT	TCCTATACACATACAAACATAC
RM21	FAM	ACAGTATTCCGTAGGCACGG	GCTCCATGAGGGTGGTAGAG
RM3331	VIC	CCTCCTCCATGAGCTAATGC	AGGAGGAGCGGATTTCTCTC
RM443	VIC	GATGGTTTTCATCGGCTACG	AGTCCCAGAATGTCGTTTCG
RM490	FAM	ATCTGCACACTGCAAACACC	AGCAAGCAGTGCTTTCAGAG
RM71	FAM	CTAGAGGCGAAAACGAGATG	GGGTGGGCGAGGTAATAATG
RM423	FAM	AGCACCCATGCCTTATGTTG	CCTTTTTCAGTAGCCCTCCC
RM571	FAM	GGAGGTGAAAGCGAATCATG	CCTGCTGCTCTTTCATCAGC
RM231	PET	CCAGATTATTTCCTGAGGTC	CACTTGCATAGTTCTGCATTG
RM567	PET	ATCAGGGAAATCCTGAAGGG	GGAAGGAGCAATCACCACTG
RM289	PET	TTCCATGGCACACAAGCC	CTGTGCACGAACTTCCAAAG
RM542	VIC	TGAATCAAGCCCCTCACTAC	CTGCAACGAGTAAGGCAGAG
RM278	NED	GTAGTGAGCCTAACAATAATC	TCAACTCAGCATCTCTGTCC
RM332	VIC	GCGAAGGCGAAGGTGAAG	CATGAGTGATCTCACTCACCC
RM7102	PET	TAGGAGTGTTTAGAGTGCCA	TCGGTTTGCTTATACATCAG

Line	Model-based group (K = 3)			Group	Line	Model-based group (K = 3)			Group
Line	I	II	III	Group	Line	I	II	III	Group
602S	0.571	0.369	0.06	Admix (I, II)	A7S	0.007	0.899	0.094	Indica-II
L66S	0.572	0.422	0.006	Admix (I, II)	F133S	0.005	0.973	0.022	Indica-II
Y11S	0.693	0.295	0.012	Admix (I, II)	GD-1S	0.007	0.939	0.054	Indica-II
Y22S	0.682	0.295	0.023	Admix (I, II)	H750S	0.011	0.983	0.006	Indica-II
Z316S	0.71	0.281	0.009	Admix (I, II)	HD9802S	0.007	0.989	0.004	Indica-II
GuangmoS	0.696	0.296	0.008	Admix (I, II)	M103S	0.085	0.846	0.069	Indica-II
Guofeng 8S	0.7	0.289	0.011	Admix (I, II)	N28S	0.034	0.933	0.032	Indica-II
Jiafeng 68s	0.492	0.481	0.027	Admix (I, II)	N2S	0.012	0.888	0.099	Indica-II
Quan 2S	0.627	0.361	0.013	Admix (I, II)	N39S	0.016	0.947	0.037	Indica-II
QuanxiangnuoS	0.516	0.422	0.062	Admix (I, II)	N68S	0.267	0.727	0.007	Indica-II
QuanziS	0.662	0.313	0.025	Admix (I, II)	N9S	0.198	0.785	0.016	Indica-II
Tongchuang 01S	0.577	0.404	0.019	Admix (I, II)	RGD-7S（GD-7S）	0.013	0.98	0.007	Indica-II
XinerPS	0.671	0.314	0.015	Admix (I, II)	SE21S	0.004	0.955	0.041	Indica-II
Yi64S	0.694	0.3	0.006	Admix (I, II)	SG1S	0.011	0.888	0.102	Indica-II
T01S	0.67	0.01	0.319	Admix (I, III)	W9834S	0.138	0.818	0.044	Indica-II
W869S	0.525	0.004	0.471	Admix (I, III)	W9864S	0.007	0.925	0.067	Indica-II
Y20S	0.453	0.272	0.275	Admix (I, III)	Z69S	0.025	0.748	0.227	Indica-II
208S	0.39	0.581	0.028	Admix (II, I)	Z9S	0.005	0.989	0.006	Indica-II
6303S	0.306	0.687	0.007	Admix (II, I)	AnnongS-1	0.008	0.957	0.036	Indica-II
E56s	0.348	0.443	0.209	Admix (II, I)	AnxiangS	0.009	0.984	0.007	Indica-II
N714S	0.41	0.585	0.005	Admix (II, I)	Aolong 1S	0.003	0.992	0.005	Indica-II
Jiafeng 127s	0.31	0.643	0.047	Admix (II, I)	Biao 810S	0.015	0.975	0.01	Indica-II
Lubai 76S	0.407	0.499	0.094	Admix (II, I)	FengS	0.003	0.988	0.008	Indica-II
Lv 102S	0.297	0.441	0.262	Admix (II, I)	GuangfuS	0.007	0.983	0.01	Indica-II
Shuxin 6S-7	0.435	0.56	0.005	Admix (II, I)	Hua 201S	0.023	0.902	0.075	Indica-II
Xiansha 7S	0.472	0.487	0.041	Admix (II, I)	HuaM102S	0.006	0.784	0.21	Indica-II
Yangxian 1S	0.433	0.545	0.022	Admix (II, I)	Hui 007S	0.003	0.974	0.023	Indica-II
Zheng 67S	0.462	0.508	0.029	Admix (II, I)	JinshanS-1	0.014	0.972	0.014	Indica-II
1161S	0.004	0.645	0.351	Admix (II, III)	JinshanS-2	0.064	0.901	0.036	Indica-II
15S	0.008	0.607	0.385	Admix (II, III)	Jing 4155S	0.035	0.919	0.046	Indica-II
885S	0.015	0.63	0.354	Admix (II, III)	Kang 3418S	0.006	0.984	0.011	Indica-II
9771S	0.078	0.617	0.305	Admix (II, III)	LianjiuS	0.003	0.99	0.007	Indica-II
G38S	0.078	0.701	0.222	Admix (II, III)	LongS	0.007	0.926	0.067	Indica-II
Hs-3	0.082	0.718	0.2	Admix (II, III)	Lu 18S	0.005	0.989	0.006	Indica-II
W226S	0.169	0.518	0.313	Admix (II, III)	Mian 9S	0.007	0.983	0.01	Indica-II
De 1S	0.007	0.642	0.351	Admix (II, III)	MingnuoS-1	0.003	0.993	0.004	Indica-II
DeS	0.104	0.687	0.209	Admix (II, III)	Mingxiang 10S	0.004	0.991	0.005	Indica-II
Hua 68S	0.282	0.71	0.009	Admix (II, III)	Nong 1S	0.054	0.915	0.031	Indica-II
MengS	0.161	0.6	0.239	Admix (II, III)	QianS	0.002	0.99	0.007	Indica-II
Shuang 88S	0.012	0.517	0.471	Admix (II, III)	Shenhan 1S	0.066	0.919	0.015	Indica-II
Shuang 8S	0.008	0.528	0.464	Admix (II, III)	Shunnong 16S	0.024	0.966	0.009	Indica-II
Zheke 47S	0.071	0.647	0.282	Admix (II, III)	TannongS	0.007	0.98	0.013	Indica-II
Zheke 52S	0.007	0.617	0.376	Admix (II, III)	Tianyuan 903S	0.015	0.973	0.012	Indica-II
Zhongzhong 1023S	0.014	0.572	0.413	Admix (II, III)	TianfengS	0.013	0.91	0.077	Indica-II
B621S	0.234	0.159	0.607	Admix (III, I)	TianfengS-2	0.007	0.98	0.014	Indica-II
35s	0.019	0.319	0.662	Admix (III, II)	WanjinS	0.005	0.984	0.01	Indica-II
F136S	0.01	0.289	0.701	Admix (III, II)	Xiang 125S	0.016	0.965	0.019	Indica-II
F168S	0.01	0.323	0.667	Admix (III, II)	Xiangling 628S	0.027	0.965	0.008	Indica-II
H155S	0.02	0.291	0.688	Admix (III, II)	Xiangling 750S	0.007	0.985	0.008	Indica-II
H318S	0.004	0.278	0.718	Admix (III, II)	Xiangzhou 9S	0.008	0.802	0.19	Indica-II
K12S	0.009	0.414	0.577	Admix (III, II)	XingguangS	0.006	0.973	0.02	Indica-II
MPeiai64S	0.008	0.302	0.689	Admix (III, II)	Yan 161S	0.053	0.941	0.006	Indica-II
Chuang 06S	0.005	0.418	0.577	Admix (III, II)	Yu 11S	0.009	0.954	0.037	Indica-II
Longke 638S	0.01	0.351	0.639	Admix (III, II)	YuanguangS	0.008	0.969	0.024	Indica-II
Shen 51S	0.01	0.287	0.703	Admix (III, II)	Yuanjing 1S	0.014	0.971	0.015	Indica-II
Shuangdipei eS	0.007	0.361	0.632	Admix (III, II)	Zhu 1S	0.005	0.988	0.006	Indica-II
Zhongzhong 1014S	0.146	0.395	0.459	Admix (III, II)	Zhu 25S	0.005	0.988	0.006	Indica-II
ZitaiS	0.029	0.362	0.609	Admix (III, II)	Zhu 712S	0.007	0.987	0.006	Indica-II
033S	0.994	0.003	0.003	Indica-I	HuaiS	0.006	0.99	0.005	Indica-II
03S	0.989	0.004	0.007	Indica-I	035S	0.004	0.003	0.993	Indica-III
108S	0.941	0.05	0.009	Indica-I	1892S	0.003	0.003	0.994	Indica-III
2148S	0.751	0.185	0.064	Indica-I	5561S	0.005	0.013	0.982	Indica-III
6105S	0.883	0.078	0.039	Indica-I	7-163S	0.008	0.012	0.98	Indica-III
6311S	0.986	0.007	0.007	Indica-I	9311S	0.003	0.005	0.992	Indica-III
683S	0.988	0.007	0.004	Indica-I	C815S	0.003	0.029	0.968	Indica-III
Bph68s	0.925	0.055	0.02	Indica-I	C815S-34	0.003	0.004	0.992	Indica-III
T77S	0.871	0.121	0.008	Indica-I	CO23S	0.004	0.004	0.992	Indica-III
W052S	0.994	0.003	0.003	Indica-I	H153S	0.114	0.024	0.862	Indica-III
Y46S	0.995	0.003	0.003	Indica-I	H175S	0.006	0.021	0.973	Indica-III
Y68S	0.896	0.055	0.049	Indica-I	Li55S	0.005	0.009	0.986	Indica-III
Y9S	0.995	0.003	0.003	Indica-I	P88S	0.004	0.003	0.993	Indica-III
Feng 39S	0.995	0.003	0.003	Indica-I	P8hS	0.005	0.006	0.989	Indica-III
Feng 6S	0.994	0.003	0.003	Indica-I	T161S	0.005	0.275	0.72	Indica-III
FulongS2	0.882	0.067	0.05	Indica-I	Y18S	0.008	0.065	0.927	Indica-III
GuangxuanS	0.765	0.14	0.095	Indica-I	Y58S	0.031	0.018	0.951	Indica-III
Guangzhan 63-4S	0.995	0.003	0.003	Indica-I	YZ170667	0.004	0.003	0.993	Indica-III
Guangzhan 63S	0.994	0.003	0.003	Indica-I	YZ170882	0.004	0.049	0.947	Indica-III
Hua 1228S	0.961	0.031	0.009	Indica-I	Z236S	0.01	0.014	0.976	Indica-III
Hui 34S	0.786	0.135	0.078	Indica-I	Aiqing 34s	0.007	0.242	0.751	Indica-III
Jing 118S	0.994	0.003	0.003	Indica-I	Aizhan 43S	0.004	0.003	0.993	Indica-III
LvminS	0.786	0.187	0.027	Indica-I	AiziS	0.004	0.004	0.992	Indica-III
SanfengS	0.988	0.005	0.006	Indica-I	Anlong 3S	0.008	0.009	0.983	Indica-III
Shuxin 11S	0.761	0.233	0.005	Indica-I	Bang 191S	0.01	0.011	0.979	Indica-III
Tianhe 1S	0.992	0.005	0.003	Indica-I	Chuang 5S	0.003	0.003	0.994	Indica-III
Tianyuan 6S	0.96	0.022	0.018	Indica-I	FueS1	0.004	0.004	0.992	Indica-III
XinanS	0.995	0.003	0.003	Indica-I	Guangxiang 24S	0.014	0.234	0.751	Indica-III
XinerS	0.994	0.003	0.003	Indica-I	Gui 118S	0.012	0.243	0.745	Indica-III
XinhuaS	0.949	0.043	0.008	Indica-I	Haifeng 1S	0.007	0.009	0.984	Indica-III
Xinqiang 03S	0.973	0.009	0.018	Indica-I	Heyuan 02S	0.113	0.024	0.863	Indica-III
Xuan 69S	0.993	0.004	0.003	Indica-I	He 620S	0.131	0.009	0.861	Indica-III
Yan 221S	0.99	0.007	0.004	Indica-I	Hua 893S	0.008	0.009	0.983	Indica-III
Yan 582S	0.994	0.003	0.003	Indica-I	WeihanS	0.143	0.027	0.83	Indica-III
Zhongzhongxin 3S	0.995	0.003	0.003	Indica-I	JianS	0.005	0.006	0.989	Indica-III
Zhuxuan 63-8S	0.983	0.007	0.01	Indica-I	JinfengS	0.013	0.008	0.979	Indica-III
1103S	0.004	0.927	0.069	Indica-II	Ke 8S	0.009	0.009	0.982	Indica-III
228S	0.008	0.982	0.01	Indica-II	Lvhan 1S	0.113	0.024	0.863	Indica-III
2301S	0.045	0.917	0.038	Indica-II	Peiai-2S	0.008	0.021	0.971	Indica-III
33S	0.031	0.768	0.201	Indica-II	Peiai 64S	0.004	0.003	0.992	Indica-III
360S	0.007	0.988	0.005	Indica-II	Shen 08S	0.007	0.017	0.976	Indica-III
4127S	0.008	0.985	0.007	Indica-II	Shungeng 01S	0.006	0.005	0.988	Indica-III
45S	0.005	0.94	0.055	Indica-II	Xu 98S	0.059	0.011	0.93	Indica-III
8109S	0.006	0.987	0.008	Indica-II	YutuS	0.005	0.067	0.928	Indica-III
810S	0.004	0.992	0.004	Indica-II	Yuan 95S	0.028	0.233	0.739	Indica-III
86315S	0.01	0.76	0.23	Indica-II	ZhonglianS	0.005	0.255	0.74	Indica-III

Line	Model-based group (K = 3)			Group	Line	Model-based group (K = 3)			Group
Line	I	II	III	Group	Line	I	II	III	Group
602S	0.571	0.369	0.06	Admix (I, II)	A7S	0.007	0.899	0.094	Indica-II
L66S	0.572	0.422	0.006	Admix (I, II)	F133S	0.005	0.973	0.022	Indica-II
Y11S	0.693	0.295	0.012	Admix (I, II)	GD-1S	0.007	0.939	0.054	Indica-II
Y22S	0.682	0.295	0.023	Admix (I, II)	H750S	0.011	0.983	0.006	Indica-II
Z316S	0.71	0.281	0.009	Admix (I, II)	HD9802S	0.007	0.989	0.004	Indica-II
GuangmoS	0.696	0.296	0.008	Admix (I, II)	M103S	0.085	0.846	0.069	Indica-II
Guofeng 8S	0.7	0.289	0.011	Admix (I, II)	N28S	0.034	0.933	0.032	Indica-II
Jiafeng 68s	0.492	0.481	0.027	Admix (I, II)	N2S	0.012	0.888	0.099	Indica-II
Quan 2S	0.627	0.361	0.013	Admix (I, II)	N39S	0.016	0.947	0.037	Indica-II
QuanxiangnuoS	0.516	0.422	0.062	Admix (I, II)	N68S	0.267	0.727	0.007	Indica-II
QuanziS	0.662	0.313	0.025	Admix (I, II)	N9S	0.198	0.785	0.016	Indica-II
Tongchuang 01S	0.577	0.404	0.019	Admix (I, II)	RGD-7S（GD-7S）	0.013	0.98	0.007	Indica-II
XinerPS	0.671	0.314	0.015	Admix (I, II)	SE21S	0.004	0.955	0.041	Indica-II
Yi64S	0.694	0.3	0.006	Admix (I, II)	SG1S	0.011	0.888	0.102	Indica-II
T01S	0.67	0.01	0.319	Admix (I, III)	W9834S	0.138	0.818	0.044	Indica-II
W869S	0.525	0.004	0.471	Admix (I, III)	W9864S	0.007	0.925	0.067	Indica-II
Y20S	0.453	0.272	0.275	Admix (I, III)	Z69S	0.025	0.748	0.227	Indica-II
208S	0.39	0.581	0.028	Admix (II, I)	Z9S	0.005	0.989	0.006	Indica-II
6303S	0.306	0.687	0.007	Admix (II, I)	AnnongS-1	0.008	0.957	0.036	Indica-II
E56s	0.348	0.443	0.209	Admix (II, I)	AnxiangS	0.009	0.984	0.007	Indica-II
N714S	0.41	0.585	0.005	Admix (II, I)	Aolong 1S	0.003	0.992	0.005	Indica-II
Jiafeng 127s	0.31	0.643	0.047	Admix (II, I)	Biao 810S	0.015	0.975	0.01	Indica-II
Lubai 76S	0.407	0.499	0.094	Admix (II, I)	FengS	0.003	0.988	0.008	Indica-II
Lv 102S	0.297	0.441	0.262	Admix (II, I)	GuangfuS	0.007	0.983	0.01	Indica-II
Shuxin 6S-7	0.435	0.56	0.005	Admix (II, I)	Hua 201S	0.023	0.902	0.075	Indica-II
Xiansha 7S	0.472	0.487	0.041	Admix (II, I)	HuaM102S	0.006	0.784	0.21	Indica-II
Yangxian 1S	0.433	0.545	0.022	Admix (II, I)	Hui 007S	0.003	0.974	0.023	Indica-II
Zheng 67S	0.462	0.508	0.029	Admix (II, I)	JinshanS-1	0.014	0.972	0.014	Indica-II
1161S	0.004	0.645	0.351	Admix (II, III)	JinshanS-2	0.064	0.901	0.036	Indica-II
15S	0.008	0.607	0.385	Admix (II, III)	Jing 4155S	0.035	0.919	0.046	Indica-II
885S	0.015	0.63	0.354	Admix (II, III)	Kang 3418S	0.006	0.984	0.011	Indica-II
9771S	0.078	0.617	0.305	Admix (II, III)	LianjiuS	0.003	0.99	0.007	Indica-II
G38S	0.078	0.701	0.222	Admix (II, III)	LongS	0.007	0.926	0.067	Indica-II
Hs-3	0.082	0.718	0.2	Admix (II, III)	Lu 18S	0.005	0.989	0.006	Indica-II
W226S	0.169	0.518	0.313	Admix (II, III)	Mian 9S	0.007	0.983	0.01	Indica-II
De 1S	0.007	0.642	0.351	Admix (II, III)	MingnuoS-1	0.003	0.993	0.004	Indica-II
DeS	0.104	0.687	0.209	Admix (II, III)	Mingxiang 10S	0.004	0.991	0.005	Indica-II
Hua 68S	0.282	0.71	0.009	Admix (II, III)	Nong 1S	0.054	0.915	0.031	Indica-II
MengS	0.161	0.6	0.239	Admix (II, III)	QianS	0.002	0.99	0.007	Indica-II
Shuang 88S	0.012	0.517	0.471	Admix (II, III)	Shenhan 1S	0.066	0.919	0.015	Indica-II
Shuang 8S	0.008	0.528	0.464	Admix (II, III)	Shunnong 16S	0.024	0.966	0.009	Indica-II
Zheke 47S	0.071	0.647	0.282	Admix (II, III)	TannongS	0.007	0.98	0.013	Indica-II
Zheke 52S	0.007	0.617	0.376	Admix (II, III)	Tianyuan 903S	0.015	0.973	0.012	Indica-II
Zhongzhong 1023S	0.014	0.572	0.413	Admix (II, III)	TianfengS	0.013	0.91	0.077	Indica-II
B621S	0.234	0.159	0.607	Admix (III, I)	TianfengS-2	0.007	0.98	0.014	Indica-II
35s	0.019	0.319	0.662	Admix (III, II)	WanjinS	0.005	0.984	0.01	Indica-II
F136S	0.01	0.289	0.701	Admix (III, II)	Xiang 125S	0.016	0.965	0.019	Indica-II
F168S	0.01	0.323	0.667	Admix (III, II)	Xiangling 628S	0.027	0.965	0.008	Indica-II
H155S	0.02	0.291	0.688	Admix (III, II)	Xiangling 750S	0.007	0.985	0.008	Indica-II
H318S	0.004	0.278	0.718	Admix (III, II)	Xiangzhou 9S	0.008	0.802	0.19	Indica-II
K12S	0.009	0.414	0.577	Admix (III, II)	XingguangS	0.006	0.973	0.02	Indica-II
MPeiai64S	0.008	0.302	0.689	Admix (III, II)	Yan 161S	0.053	0.941	0.006	Indica-II
Chuang 06S	0.005	0.418	0.577	Admix (III, II)	Yu 11S	0.009	0.954	0.037	Indica-II
Longke 638S	0.01	0.351	0.639	Admix (III, II)	YuanguangS	0.008	0.969	0.024	Indica-II
Shen 51S	0.01	0.287	0.703	Admix (III, II)	Yuanjing 1S	0.014	0.971	0.015	Indica-II
Shuangdipei eS	0.007	0.361	0.632	Admix (III, II)	Zhu 1S	0.005	0.988	0.006	Indica-II
Zhongzhong 1014S	0.146	0.395	0.459	Admix (III, II)	Zhu 25S	0.005	0.988	0.006	Indica-II
ZitaiS	0.029	0.362	0.609	Admix (III, II)	Zhu 712S	0.007	0.987	0.006	Indica-II
033S	0.994	0.003	0.003	Indica-I	HuaiS	0.006	0.99	0.005	Indica-II
03S	0.989	0.004	0.007	Indica-I	035S	0.004	0.003	0.993	Indica-III
108S	0.941	0.05	0.009	Indica-I	1892S	0.003	0.003	0.994	Indica-III
2148S	0.751	0.185	0.064	Indica-I	5561S	0.005	0.013	0.982	Indica-III
6105S	0.883	0.078	0.039	Indica-I	7-163S	0.008	0.012	0.98	Indica-III
6311S	0.986	0.007	0.007	Indica-I	9311S	0.003	0.005	0.992	Indica-III
683S	0.988	0.007	0.004	Indica-I	C815S	0.003	0.029	0.968	Indica-III
Bph68s	0.925	0.055	0.02	Indica-I	C815S-34	0.003	0.004	0.992	Indica-III
T77S	0.871	0.121	0.008	Indica-I	CO23S	0.004	0.004	0.992	Indica-III
W052S	0.994	0.003	0.003	Indica-I	H153S	0.114	0.024	0.862	Indica-III
Y46S	0.995	0.003	0.003	Indica-I	H175S	0.006	0.021	0.973	Indica-III
Y68S	0.896	0.055	0.049	Indica-I	Li55S	0.005	0.009	0.986	Indica-III
Y9S	0.995	0.003	0.003	Indica-I	P88S	0.004	0.003	0.993	Indica-III
Feng 39S	0.995	0.003	0.003	Indica-I	P8hS	0.005	0.006	0.989	Indica-III
Feng 6S	0.994	0.003	0.003	Indica-I	T161S	0.005	0.275	0.72	Indica-III
FulongS2	0.882	0.067	0.05	Indica-I	Y18S	0.008	0.065	0.927	Indica-III
GuangxuanS	0.765	0.14	0.095	Indica-I	Y58S	0.031	0.018	0.951	Indica-III
Guangzhan 63-4S	0.995	0.003	0.003	Indica-I	YZ170667	0.004	0.003	0.993	Indica-III
Guangzhan 63S	0.994	0.003	0.003	Indica-I	YZ170882	0.004	0.049	0.947	Indica-III
Hua 1228S	0.961	0.031	0.009	Indica-I	Z236S	0.01	0.014	0.976	Indica-III
Hui 34S	0.786	0.135	0.078	Indica-I	Aiqing 34s	0.007	0.242	0.751	Indica-III
Jing 118S	0.994	0.003	0.003	Indica-I	Aizhan 43S	0.004	0.003	0.993	Indica-III
LvminS	0.786	0.187	0.027	Indica-I	AiziS	0.004	0.004	0.992	Indica-III
SanfengS	0.988	0.005	0.006	Indica-I	Anlong 3S	0.008	0.009	0.983	Indica-III
Shuxin 11S	0.761	0.233	0.005	Indica-I	Bang 191S	0.01	0.011	0.979	Indica-III
Tianhe 1S	0.992	0.005	0.003	Indica-I	Chuang 5S	0.003	0.003	0.994	Indica-III
Tianyuan 6S	0.96	0.022	0.018	Indica-I	FueS1	0.004	0.004	0.992	Indica-III
XinanS	0.995	0.003	0.003	Indica-I	Guangxiang 24S	0.014	0.234	0.751	Indica-III
XinerS	0.994	0.003	0.003	Indica-I	Gui 118S	0.012	0.243	0.745	Indica-III
XinhuaS	0.949	0.043	0.008	Indica-I	Haifeng 1S	0.007	0.009	0.984	Indica-III
Xinqiang 03S	0.973	0.009	0.018	Indica-I	Heyuan 02S	0.113	0.024	0.863	Indica-III
Xuan 69S	0.993	0.004	0.003	Indica-I	He 620S	0.131	0.009	0.861	Indica-III
Yan 221S	0.99	0.007	0.004	Indica-I	Hua 893S	0.008	0.009	0.983	Indica-III
Yan 582S	0.994	0.003	0.003	Indica-I	WeihanS	0.143	0.027	0.83	Indica-III
Zhongzhongxin 3S	0.995	0.003	0.003	Indica-I	JianS	0.005	0.006	0.989	Indica-III
Zhuxuan 63-8S	0.983	0.007	0.01	Indica-I	JinfengS	0.013	0.008	0.979	Indica-III
1103S	0.004	0.927	0.069	Indica-II	Ke 8S	0.009	0.009	0.982	Indica-III
228S	0.008	0.982	0.01	Indica-II	Lvhan 1S	0.113	0.024	0.863	Indica-III
2301S	0.045	0.917	0.038	Indica-II	Peiai-2S	0.008	0.021	0.971	Indica-III
33S	0.031	0.768	0.201	Indica-II	Peiai 64S	0.004	0.003	0.992	Indica-III
360S	0.007	0.988	0.005	Indica-II	Shen 08S	0.007	0.017	0.976	Indica-III
4127S	0.008	0.985	0.007	Indica-II	Shungeng 01S	0.006	0.005	0.988	Indica-III
45S	0.005	0.94	0.055	Indica-II	Xu 98S	0.059	0.011	0.93	Indica-III
8109S	0.006	0.987	0.008	Indica-II	YutuS	0.005	0.067	0.928	Indica-III
810S	0.004	0.992	0.004	Indica-II	Yuan 95S	0.028	0.233	0.739	Indica-III
86315S	0.01	0.76	0.23	Indica-II	ZhonglianS	0.005	0.255	0.74	Indica-III

Marker	Na	He	PIC	Marker	Na	He	PIC	Marker	Na	He	PIC
OSR28	4	0.2108	0.2002	RM274	2	0.4672	0.3581	RM493	10	0.8243	0.801
RM119	3	0.5893	0.5092	RM278	5	0.6098	0.5313	RM542	7	0.3194	0.3006
RM1195	5	0.3633	0.3407	RM289	4	0.3252	0.2787	RM551	6	0.3143	0.2806
RM17	8	0.488	0.4027	RM311	6	0.7265	0.6878	RM561	2	0.4319	0.3387
RM176	1	0	0	RM316	4	0.5832	0.5198	RM567	4	0.3975	0.3468
RM19	9	0.6325	0.566	RM331	2	0.019	0.0189	RM571	3	0.5006	0.38
RM190	4	0.5372	0.493	RM332	9	0.5404	0.5034	RM583	6	0.5369	0.4628
RM208	6	0.6872	0.6307	RM3331	6	0.7493	0.7058	RM590	6	0.5676	0.5217
RM209	9	0.6283	0.5721	RM336	7	0.5336	0.4811	RM598	5	0.6543	0.5831
RM21	9	0.4907	0.469	RM339	5	0.3847	0.3214	RM71	5	0.2117	0.2048
RM219	11	0.7607	0.7325	RM423	4	0.5308	0.4465	RM7102	6	0.6717	0.6228
RM224	8	0.6703	0.6121	RM424	7	0.7086	0.6589	RM72	6	0.2697	0.2549
RM231	6	0.5967	0.5676	RM432	3	0.4752	0.404	RM8277	5	0.5588	0.5078
RM232	9	0.767	0.7377	RM443	4	0.0749	0.0739	RM85	4	0.4472	0.4109
RM253	5	0.4476	0.41	RM471	3	0.3752	0.334	Mean	5.6	0.5038	0.4541
RM258	6	0.6402	0.5955	RM481	12	0.7751	0.7398
RM267	4	0.5291	0.4189	RM490	4	0.5575	0.4589