Linkage disequilibrium mapping for grain Fe and Zn enhancing QTLs useful for nutrient dense rice breeding

Pradhan, S. K.; Pandit, E.; Pawar, S.; Naveenkumar, R.; Barik, S. R.; Mohanty, S. P.; Nayak, D. K.; Ghritlahre, S. K.; Sanjiba Rao, D.; Reddy, J. N.; Patnaik, S. S. C.

doi:10.1186/s12870-020-2262-4

BMC Plant Biology

Table 3 The inferred ancestry value and population structure in the panel population containing 102 genotypes with their Fe-Zn classification category

From: Linkage disequilibrium mapping for grain Fe and Zn enhancing QTLs useful for nutrient dense rice breeding

Sl. No.	Genotype name/National testing No.	Inferred ancestry at K = 2		Structure group	Inferred ancestry at K = 3			group	Classification of genotype based on Fe & Zn content
Sl. No.	Genotype name/National testing No.	Q1	Q2	Structure group	Q1	Q2	Q3	group	Classification of genotype based on Fe & Zn content
1	IET23829	0.111	0.889	SP2	0.053	0.745	0.202	SP2	H-Fe & M-Zn
2	IR64	0.004	0.996	SP2	0.006	0.985	0.009	SP2	H-Fe & M-Zn
3	IET23834	0.001	0.999	SP2	0.024	0.975	0.001	SP2	M-Fe & M-Zn
4	Kalanamak	0.001	0.999	SP2	0.489	0.51	0.001	SP2	H-Fe & H-Zn
5	IET23824	0.001	0.999	SP2	0.006	0.993	0.001	SP2	M-Fe & H-Zn
6	IET23832	0.002	0.998	SP2	0.001	0.998	0.001	SP2	H-Fe & M-Zn
7	Chittimuthyalu	0.001	0.999	SP2	0.002	0.998	0.001	SP2	H-Fe & H-Zn
8	IET24780	0.001	0.999	SP2	0.001	0.998	0.001	SP2	H-Fe & H-Zn
9	BPT5204	0.001	0.999	SP2	0.007	0.992	0.001	SP2	H-Fe & M-Zn
10	IET24771	0.001	0.999	SP2	0.002	0.997	0.001	SP2	M-Fe & M-Zn
11	IET24766	0.001	0.999	SP2	0.005	0.994	0.001	SP2	M-Fe & M-Zn
12	IET24316	0.001	0.999	SP2	0.057	0.938	0.004	SP2	H-Fe & M-Zn
13	IET24391	0.001	0.999	SP2	0.002	0.997	0.001	SP2	L-Fe & H-Zn
14	IET24777	0.002	0.998	SP2	0.154	0.843	0.003	SP2	L-Fe & L-Zn
15	IET24760	0.242	0.758	SP2	0.96	0.018	0.022	SP1	H-Fe & M-Zn
16	IET24775	0.311	0.689	SP2	0.886	0.005	0.108	SP1	H-Fe & M-Zn
17	IET24783	0.002	0.998	SP2	0.002	0.997	0.001	SP2	M-Fe & M-Zn
18	IET24544	0.001	0.999	SP2	0.003	0.996	0.002	SP2	L-Fe & M-Zn
19	IET24336	0.001	0.999	SP2	0.005	0.994	0.001	SP2	L-Fe & M-Zn
20	IET24772	0.001	0.999	SP2	0.003	0.996	0.001	SP2	M-Fe & M-Zn
21	IET24557	0.111	0.889	SP2	0.993	0.002	0.004	SP1	M-Fe & M-Zn
22	IET24779	0.009	0.991	SP2	0.997	0.002	0.001	SP1	H-Fe & M-Zn
23	IET24774	0.008	0.992	SP2	0.99	0.009	0.001	SP1	L-Fe & M-Zn
24	IET24787	0.032	0.968	SP2	0.996	0.002	0.002	SP1	M-Fe & M-Zn
25	IET25441	0.001	0.999	SP2	0.004	0.994	0.001	SP2	H-Fe & M-Zn
26	IET25443	0.001	0.999	SP2	0.015	0.984	0.001	SP2	M-Fe & M-Zn
27	IET25444	0.001	0.999	SP2	0.001	0.998	0.001	SP2	M-Fe & M-Zn
28	IET25445	0.001	0.999	SP2	0.002	0.997	0.001	SP2	M-Fe & L-Zn
29	IET25446	0.009	0.991	SP2	0.995	0.003	0.002	SP1	M-Fe & H-Zn
30	IET25447	0.001	0.999	SP2	0.002	0.997	0.001	SP2	M-Fe & M-Zn
31	IET25449	0.001	0.999	SP2	0.001	0.998	0.001	SP2	M-Fe & M-Zn
32	IET25450	0.001	0.999	SP2	0.341	0.658	0.002	SP2	H-Fe & H-Zn
33	IET25452	0.012	0.988	SP2	0.112	0.843	0.045	SP2	M-Fe & M-Zn
34	IET25453	0.001	0.999	SP2	0.067	0.93	0.003	SP2	M-Fe & M-Zn
35	IET25454	0.106	0.894	SP2	0.983	0.007	0.01	SP1	M-Fe & M-Zn
36	IET25457	0.001	0.999	SP2	0.002	0.997	0.001	SP2	L-Fe & M-Zn
37	IET25459	0.001	0.999	SP2	0.002	0.998	0.001	SP2	L-Fe & M-Zn
38	IET25460	0.001	0.999	SP2	0.004	0.995	0.001	SP2	M-Fe & L-Zn
39	IET25461	0.007	0.993	SP2	0.994	0.005	0.001	SP1	M-Fe & H-Zn
40	IET25463	0.002	0.998	SP2	0.032	0.965	0.004	SP2	M-Fe & M-Zn
41	IET25464	0.001	0.999	SP2	0.525	0.474	0.001	SP1	L-Fe & M-Zn
42	IET25465	0.001	0.999	SP2	0.009	0.988	0.002	SP2	H-Fe & H-Zn
43	Gontra Bidhan3	0.009	0.991	SP2	0.97	0.028	0.001	SP1	L-Fe & L-Zn
44	IET25469	0.001	0.999	SP2	0.038	0.959	0.003	SP2	M-Fe & M-Zn
45	IET25470	0.022	0.978	SP2	0.736	0.256	0.008	SP1	L-Fe & M-Zn
46	IET25471	0.001	0.999	SP2	0.004	0.994	0.002	SP2	M-Fe & M-Zn
47	DRRH3	0.001	0.999	SP2	0.004	0.992	0.003	SP2	L-Fe & L-Zn
48	IET25472	0.048	0.952	SP2	0.976	0.017	0.007	SP1	M-Fe & H-Zn
49	IET25473	0.042	0.958	SP2	0.996	0.002	0.002	SP1	M-Fe & M-Zn
50	IET25474	0.002	0.998	SP2	0.065	0.926	0.008	SP2	M-Fe & M-Zn
51	IET25475	0.05	0.95	SP2	0.997	0.002	0.001	SP1	M-Fe & H-Zn
52	IET25477	0.121	0.879	SP2	0.995	0.001	0.003	SP1	M-Fe & H-Zn
53	IET25478	0.006	0.994	SP2	0.998	0.001	0.001	SP1	L-Fe & M-Zn
54	IET25479	0.001	0.999	SP2	0.006	0.993	0.001	SP2	M-Fe & M-Zn
55	Lalmeeta	0.022	0.978	SP2	0.019	0.934	0.047	SP2	L-Fe & L-Zn
56	Abhimanyu	0.001	0.999	SP2	0.003	0.995	0.001	SP2	M-Fe & L-Zn
57	Kalobhutia	0.007	0.993	SP2	0.998	0.001	0.001	SP1	M-Fe & L-Zn
58	Sadakajam	0.103	0.897	SP2	0.94	0.016	0.044	SP1	H-Fe & M-Zn
59	Geetanjali	0.001	0.999	SP2	0.002	0.998	0.001	SP2	M-Fe & L-Zn
60	Kakhru	0.001	0.999	SP2	0.001	0.998	0.001	SP2	L-Fe & L-Zn
61	Boanti	0.001	0.999	SP2	0.001	0.998	0.001	SP2	M-Fe & L-Zn
62	Tulsimukul	0.008	0.992	SP2	0.998	0.002	0.001	SP1	M-Fe & L-Zn
63	Kokilpatri	0.001	0.999	SP2	0.001	0.998	0.001	SP2	L-Fe & L-Zn
64	Basmatikarnal	0.001	0.999	SP2	0.034	0.965	0.001	SP2	M-Fe & L-Zn
65	Kalonunia	0.001	0.999	SP2	0.534	0.465	0.001	SP1	M-Fe & L-Zn
66	SafedLuchai2	0.001	0.999	SP2	0.001	0.998	0.001	SP2	M-Fe & M-Zn
67	Bankra	0.001	0.999	SP2	0.051	0.946	0.003	SP2	L-Fe &L-Zn
68	Moongi	0.009	0.991	SP2	0.031	0.935	0.033	SP2	L-Fe & L-Zn
69	Swarnakranti	0.001	0.999	SP2	0.524	0.475	0.001	SP1	M-Fe & L-Zn
70	Kalojeera	0.001	0.999	SP2	0.53	0.47	0.001	SP1	M-Fe & L-Zn
71	Ketekijoha	0.999	0.001	SP1	0.015	0.001	0.984	SP3	L- Fe & M- Zn
72	Maudamani	0.999	0.001	SP1	0.002	0.001	0.997	SP3	L- Fe & L- Zn
73	Tarori Basmati	0.999	0.001	SP1	0.032	0.001	0.967	SP3	L- Fe & M- Zn
74	Mamihunger	0.998	0.002	SP1	0.226	0.001	0.773	SP3	L- Fe & H- Zn
75	Sneha	0.999	0.001	SP1	0.002	0.001	0.998	SP3	L-Fe & H-Zn
76	Savitri	0.999	0.001	SP1	0.002	0.001	0.997	SP3	L Fe & L-Zn
77	CR Dhan 101	0.999	0.001	SP1	0.003	0.001	0.996	SP3	L-Fe & L-Zn
78	CR Dhan 907	0.999	0.001	SP1	0.001	0.001	0.998	SP3	M- Fe & M-Zn
79	CR Dhan 801	0.999	0.001	SP1	0.001	0.001	0.998	SP3	L- Fe & L-Zn
80	Chinikamini	0.999	0.001	SP1	0.015	0.001	0.984	SP3	L- Fe & M-Zn
81	Nuakalajeera	0.989	0.011	SP1	0.422	0.001	0.577	SP3	L- Fe & M-Zn
82	Moti	0.999	0.001	SP1	0.002	0.001	0.997	SP3	L- Fe & M-Zn
83	Nuadhusura	0.999	0.001	SP1	0.169	0.001	0.83	SP3	M- Fe & M-Zn
84	Heera	0.999	0.001	SP1	0.002	0.001	0.997	SP3	L- Fe & M-Zn
85	Jalmagna	0.999	0.001	SP1	0.002	0.001	0.997	SP3	L- Fe & M-Zn
86	AC44756	0.999	0.001	SP1	0.001	0.001	0.998	SP3	L- Fe & M-Zn
87	AC44755	0.999	0.001	SP1	0.001	0.001	0.998	SP3	L- Fe & M-Zn
88	AC44754	0.999	0.001	SP1	0.001	0.001	0.998	SP3	L- Fe & M-Zn
89	AC44753	0.999	0.001	SP1	0.003	0.001	0.996	SP3	L- Fe & M- Zn
90	Swarna-Sub 1	0.999	0.001	SP1	0.004	0.001	0.995	SP3	L-Fe & M- Zn
91	Ranjit	0.999	0.001	SP1	0.002	0.001	0.997	SP3	L- Fe & L- Zn
92	Swarna	0.999	0.001	SP1	0.001	0.001	0.998	SP3	L- F & L- Zn
93	Jaya	0.999	0.001	SP1	0.002	0.001	0.998	SP3	L-Fe & M- Zn
94	Samalei	0.999	0.001	SP1	0.001	0.001	0.998	SP3	L- Fe & L- Zn
95	AC44752	0.999	0.001	SP1	0.001	0.001	0.998	SP3	L- Fe & M- Zn
96	Lalat	0.999	0.001	SP1	0.001	0.001	0.998	SP3	L- Fe & H- Zn
97	MTU1010	0.999	0.001	SP1	0.004	0.001	0.995	SP3	L- Fe & M- Zn
98	Naveen	0.999	0.001	SP1	0.002	0.001	0.997	SP3	L- Fe & L- Zn
99	Satabdi	0.999	0.001	SP1	0.001	0.001	0.999	SP3	L- Fe & M- Zn
100	Pooja	0.999	0.001	SP1	0.001	0.001	0.998	SP3	L- Fe & L- Zn
101	Sarala	0.999	0.001	SP1	0.002	0.001	0.997	SP3	L- Fe & L- Zn
102	Agnisar	0.999	0.001	SP1	0.001	0.001	0.998	SP3	L- Fe & L- Zn

L-Fe Low grain Fe content, M-Fe Medium grain Fe content, H-Fe High grain Fe content, L-Zn: L-Zn Low grain Zn content, M-Zn Medium grain Zn content, H-Zn High grain Zn content

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