Analysis of Population Structure and Genetic Diversity in Rice Germplasm Using SSR Markers: An Initiative Towards Association Mapping of Agronomic Traits in Oryza Sativa

Nachimuthu, Vishnu Varthini; Muthurajan, Raveendran; Duraialaguraja, Sudhakar; Sivakami, Rajeswari; Pandian, Balaji Aravindhan; Ponniah, Govinthraj; Gunasekaran, Karthika; Swaminathan, Manonmani; K K, Suji; Sabariappan, Robin

doi:10.1186/s12284-015-0062-5

Rice

Table 2 Population structure group of accessions based on Inferred ancestry values

From: Analysis of Population Structure and Genetic Diversity in Rice Germplasm Using SSR Markers: An Initiative Towards Association Mapping of Agronomic Traits in Oryza Sativa

G. no.	Genotypes	Inferred ancestry		Structure group	Subtype
		Q1	Q2
RG1	Mapillai samba	0.977	0.023	SG1	Indica
RG2	CK 275	0.991	0.009	SG1	Indica
RG3	Senkar	0.992	0.008	SG1	Indica
RG4	Murugankar	0.964	0.036	SG1	Indica
RG5	CHIR 6	0.811	0.189	SG1	Indica
RG6	CHIR 5	0.989	0.011	SG1	Indica
RG7	Kudai vazhai	0.975	0.025	SG1	Indica
RG8	CHIR 8	0.759	0.241	SG1	Indica
RG9	Kuruvai kalanjiyam	0.971	0.029	SG1	Indica
RG10	Nava konmani	0.99	0.01	SG1	Indica
RG11	CHIR 10	0.869	0.131	SG1	Indica
RG12	Vellai chithiraikar	0.802	0.198	SG1	Indica
RG13	CHIR 2	0.983	0.017	SG1	Indica
RG14	Jothi	0.992	0.008	SG1	indica
RG15	Palkachaka	0.962	0.038	SG1	indica
RG16	Thooyala	0.934	0.066	SG1	indica
RG17	Chivapu chithiraikar	0.994	0.006	SG1	indica
RG18	CHIR 11	0.976	0.024	SG1	indica
RG19	Koolavalai	0.99	0.01	SG1	indica
RG20	Kalvalai	0.982	0.018	SG1	indica
RG21	Mohini samba	0.963	0.037	SG1	indica
RG22	IR 36	0.989	0.011	SG1	indica
RG23	Koombalai	0.975	0.025	SG1	indica
RG24	Tadukan	0.674	0.326	AD	indica
RG25	Sorna kuruvai	0.986	0.014	SG1	indica
RG26	Rascadam	0.637	0.363	AD	indica
RG27	Muzhi karuppan	0.991	0.009	SG1	indica
RG28	Kaatukuthalam	0.828	0.172	SG1	indica
RG29	Vellaikattai	0.987	0.013	SG1	indica
RG30	Poongar	0.987	0.013	SG1	indica
RG31	Chinthamani	0.985	0.015	SG1	indica
RG32	Thogai samba	0.975	0.025	SG1	indica
RG33	Malayalathan samba	0.701	0.299	AD	indica
RG34	RPHP 125	0.986	0.014	SG1	indica
RG35	CK 143	0.993	0.007	SG1	indica
RG36	Kattikar	0.913	0.087	SG1	indica
RG37	Shenmolagai	0.994	0.006	SG1	indica
RG38	Velli samba	0.887	0.113	SG1	indica
RG39	Kaatu ponni	0.975	0.025	SG1	indica
RG40	kakarathan	0.989	0.011	SG1	indica
RG41	Godavari samba	0.941	0.059	SG1	indica
RG42	Earapalli samba	0.978	0.022	SG1	indica
RG43	RPHP 129	0.01	0.99	SG2	indica
RG44	Mangam samba	0.968	0.032	SG1	indica
RG45	RPHP 105	0.943	0.057	SG1	indica
RG46	IG 4(EC 729639- 121695)	0.977	0.023	SG1	indica
RG47	Machakantha	0.976	0.024	SG1	indica
RG48	Kalarkar	0.992	0.008	SG1	indica
RG49	Valanchennai	0.972	0.028	SG1	indica
RG50	Sornavari	0.957	0.043	SG1	indica
RG51	RPHP 134	0.909	0.091	SG1	indica
RG52	ARB 58	0.987	0.013	SG1	indica
RG53	IR 68144-2B-2-2-3-1-127	0.708	0.292	AD	indica
RG54	PTB 19	0.981	0.019	SG1	indica
RG55	IG 67(EC 729050- 120988)	0.957	0.043	SG1	indica
RG56	RPHP 59	0.031	0.969	SG2	Aromatic
RG57	RPHP 103	0.656	0.344	AD	Aromatic
RG58	Kodaikuluthan	0.828	0.172	SG1	indica
RG59	RPHP 68	0.981	0.019	SG1	indica
RG60	Rama kuruvaikar	0.985	0.015	SG1	indica
RG61	Kallundai	0.939	0.061	SG1	indica
RG62	Purple puttu	0.994	0.006	SG1	indica
RG63	IG 71(EC 728651- 117588)	0.823	0.177	SG1	aus
RG64	Ottadaiyan	0.994	0.006	SG1	indica
RG65	IG 56(EC 728700- 117658	0.435	0.565	AD	Aromatic
RG66	Jeevan samba	0.876	0.124	SG1	indica
RG67	RPHP 106	0.915	0.085	SG1	indica
RG68	IG 63(EC 728711- 117674)	0.049	0.951	SG2	Tropical Japonica
RG69	RPHP 48	0.025	0.975	SG2	Aromatic
RG70	Karthi samba	0.987	0.013	SG1	indica
RG71	IG 27(IC 0590934- 121255)	0.444	0.556	AD	indica
RG72	Aarkadu kichili	0.99	0.01	SG1	indica
RG73	Kunthali	0.969	0.031	SG1	indica
RG74	ARB 65	0.83	0.17	SG1	indica
RG75	IG 21(EC 729334- 121355)	0.091	0.909	SG2	japonica
RG76	Matta kuruvai	0.934	0.066	SG1	indica
RG77	Karuthakar	0.994	0.006	SG1	indica
RG78	RPHP 165	0.99	0.01	SG1	indica
RG79	Manavari	0.704	0.296	AD	indica
RG80	IG 66(EC 729047- 120985)	0.992	0.008	SG1	indica
RG81	CB-07-701-252	0.977	0.023	SG1	indica
RG82	Thooyamalli	0.994	0.006	SG1	indica
RG83	RPHP 93	0.153	0.847	SG2	indica
RG84	Velsamba	0.99	0.01	SG1	indica
RG85	RPHP 104	0.898	0.102	SG1	indica
RG86	RPHP 102	0.993	0.007	SG1	indica
RG87	IG 40(EC 728740- 117705)	0.98	0.02	SG1	indica
RG88	Saranga	0.988	0.012	SG1	indica
RG89	IR 83294-66-2-2-3-2	0.125	0.875	SG2	japonica
RG90	IG 61(EC 728731- 117696)	0.843	0.157	SG1	indica
RG91	IG 23(EC 729391- 121419)	0.852	0.148	SG1	Aus
RG92	IG 49(EC 729102- 121052)	0.945	0.055	SG1	indica
RG93	uppumolagai	0.987	0.013	SG1	indica
RG94	Karthigai samba	0.993	0.007	SG1	indica
RG95	Jeeraga samba	0.685	0.315	SG1	indica
RG96	RP-BIO-226	0.833	0.167	SG1	indica
RG97	Varigarudan samba	0.975	0.025	SG1	indica
RG98	IG 5(EC 729642- 121698)	0.012	0.988	SG2	japonica
RG99	IG 31(EC 728844- 117829)	0.813	0.187	SG1	indica
RG100	IG 7(EC 729598- 121648)	0.008	0.992	SG2	japonica
RG101	RPHP 52	0.991	0.009	SG1	indica
RG102	Varakkal	0.958	0.042	SG1	indica
RG103	Mattaikar	0.732	0.268	AD	indica
RG104	IG 53(EC 728752- 117719)	0.005	0.995	SG2	Temperate japonica
RG105	IG 6(EC 729592- 121642)	0.204	0.796	SG2	Temperate japonica
RG106	Katta samba	0.872	0.128	SG1	indica
RG107	RH2-SM-1-2-1	0.606	0.394	AD	indica
RG108	Red sirumani	0.93	0.07	SG1	indica
RG109	Vadivel	0.977	0.023	SG1	indica
RG110	Norungan	0.991	0.009	SG1	indica
RG111	IG 20(EC 729293- 121310)	0.113	0.887	SG2	indica
RG112	IG 35(EC 728858- 117843)	0.027	0.973	SG2	japonica
RG113	IG 45(EC 728768- 117736)	0.017	0.983	SG2	japonica
RG114	RPHP 159	0.008	0.992	SG2	aromatic rice
RG115	IG 43(EC 728788- 117759)	0.992	0.008	SG1	indica
RG116	RPHP 27	0.52	0.48	AD	Tropical Japonica
RG117	IG 65(EC 729024- 120958)	0.974	0.026	SG1	indica
RG118	Ponmani samba	0.973	0.027	SG1	indica
RG119	Ganthasala	0.993	0.007	SG1	indica
RG120	Thattan samba	0.949	0.051	SG1	indica
RG121	IG 74(EC 728622- 117517)	0.16	0.84	SG2	japonica
RG122	Kaliyan samba	0.245	0.755	AD	indica
RG123	IG 2(EC 729808-121874)	0.56	0.44	AD	japonica
RG124	IG 29(EC 728925- 117920)	0.059	0.941	SG2	Tropical Japonica
RG125	RPHP 55	0.963	0.037	SG1	indica
RG126	Kallimadayan	0.984	0.016	SG1	indica
RG127	IG 10(EC 729686- 121743)	0.066	0.934	SG2	aromatic
RG128	IG 75(EC 728587- 117420)	0.008	0.992	SG2	japonica
RG129	IG 38(EC 728742 - 117707)	0.02	0.98	SG2	Tropical japonica
RG130	IG 39(EC 728779- 117750)	0.012	0.988	SG2	indica
RG131	RPHP 90	0.991	0.009	SG1	indica
RG132	IG 33(EC 728938- 117935)	0.162	0.838	SG2	Tropical Japonica
RG133	IG 42(EC 728798- 117774)	0.495	0.505	AD	indica
RG134	IG 9(EC 729682- 121739)	0.019	0.981	SG2	indica
RG135	RPHP 161	0.849	0.151	SG1	indica
RG136	IG 8(EC 729601- 121651)	0.883	0.117	SG1	indica
RG137	IG 37(EC 728715- 117678)	0.005	0.995	SG2	Tropical Japonica
RG138	Sigappu kuruvikar	0.979	0.021	SG1	indica
RG139	RPHP 138	0.917	0.083	SG1	indica
RG140	Raja mannar	0.989	0.011	SG1	indica
RG141	IG 44(EC 728762- 117729)	0.134	0.866	SG2	indica
RG142	Sasyasree	0.989	0.011	SG1	indica
RG143	IG 46(IC 471826- 117647)	0.073	0.927	SG2	indica
RG144	Chetty samba	0.993	0.007	SG1	indica
RG145	IG 60(EC 728730- 117695)	0.033	0.967	SG2	indica
RG146	IR 75862-206	0.013	0.987	SG2	Tropical Japonica
RG147	IG 58(EC 728725- 117689)	0.011	0.989	SG2	japonica
RG148	Chinna aduku nel	0.798	0.202	SG1	indica
RG149	RH2-SM-2-23	0.296	0.704	AD	indica
RG150	IG 14(IC 517381- 121422)	0.775	0.225	AD	indica
RG151	IG 32(EC 728838- 117823)	0.065	0.935	SG2	japonica
RG152	RPHP 47	0.989	0.011	SG1	indica
RG153	Sembilipiriyan	0.933	0.067	SG1	indica
RG154	IG 48(EC 729203- 121195)	0.006	0.994	SG2	indica
RG155	Sona mahsuri	0.889	0.111	SG1	indica
RG156	IG 12(EC 729626- 121681)	0.405	0.595	AD	indica
RG157	Karungan	0.602	0.398	AD	indica
RG158	IG 13(EC 729640- 121696)	0.143	0.857	SG2	indica
RG159	Sembala	0.934	0.066	SG1	indica
RG160	IG 72(EC 728650- 117587)	0.992	0.008	SG1	indica
RG161	Panamarasamba	0.978	0.022	SG1	indica
RG162	IR 64	0.995	0.005	SG1	indica
RG163	Mikuruvai	0.992	0.008	SG1	indica
RG164	Thillainayagam	0.939	0.061	SG1	indica
RG165	ARB 64	0.843	0.157	SG1	indica
RG166	RPHP 140	0.959	0.041	SG1	indica
RG167	IG 70(EC 729045- 120983)	0.989	0.011	SG1	indica
RG168	Haladichudi	0.993	0.007	SG1	indica
RG169	IG 24(EC 728751- 117718)	0.725	0.275	AD	Aus
RG170	RPHP 42	0.981	0.019	SG1	indica
RG171	RPHP 44	0.951	0.049	SG1	indica
RG172	IG 25(EC 729728- 121785)	0.903	0.097	SG1	Tropical Japonica
RG173	IG 73(EC 728627- 117527)	0.991	0.009	SG1	indica
RG174	IG 51(EC 728772- 117742)	0.008	0.992	SG2	Tropical Japonica
RG175	Vellai kudaivazhai	0.786	0.214	SG1	indica
RG176	Kodai	0.906	0.094	SG1	indica
RG177	Kallundaikar	0.951	0.049	SG1	indica
RG178	IG 17(EC 728900- 117889)	0.993	0.007	SG1	indica
RG179	Avasara samba	0.939	0.061	SG1	indica
RG180	IG 59(EC 728729- 117694)	0.093	0.907	SG2	Tropical Japonica
RG181	IG 52(EC 728756- 117723)	0.026	0.974	SG2	Tropical Japonica
RG182	ARB 59	0.779	0.221	SG1	indica
RG183	RPHP 163	0.995	0.005	SG1	indica
RG184	IG 18(EC 728892- 117880)	0.994	0.006	SG1	indica
RG185	RPHP 36	0.915	0.085	SG1	indica
RG186	IG 28(EC 728920- 117914)	0.009	0.991	SG2	Tropical Japonica
RG187	Vadakathi samba	0.986	0.014	SG1	indica
RG188	RPHP 80	0.986	0.014	SG1	indica
RG189	IG 41(EC 728800- 117776)	0.016	0.984	SG2	Tropical japonica
RG190	IG 26(IC 0590943- 121899)	0.422	0.578	SG2	aromatic
RG191	IG 15(EC 728910- 117901)	0.755	0.245	AD	indica
RG192	Nootri pathu	0.943	0.057	SG1	indica

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