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 2 Details of 100 SSR and direct marker loci used for genotyping a panel containing 102 rice genotypes and their genetic diversity parameters

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

Sl. No.	Marker Name	No. of alleles	Range of amplicon (bp)	Major allele frequency	Gene diversity	Hetero- zygosity	PIC value	inbreeding coefficient (f)
1	RM243	3.0000	100–140	0.6238	0.5331	0.1980	0.4705	0.6315
2	RM488	2.0000	190–210	0.7344	0.3901	0.0104	0.3140	0.9736
3	RM490	2.0000	95–115	0.6450	0.4580	0.0500	0.3531	0.8919
4	RM574	2.0000	150–160	0.8618	0.2381	0.0132	0.2098	0.9455
5	RM122	2.0000	240–260	0.6480	0.4562	0.1939	0.3521	0.5785
6	RM234	3.0000	150–160	0.6050	0.5407	0.0500	0.4704	0.9084
7	RM248	3.0000	95–115	0.3670	0.6626	0.1383	0.5884	0.7933
8	RM8007	2.0000	155–175	0.5479	0.4954	0.1809	0.3727	0.6381
9	RM17	2.0000	150–170	0.5990	0.4804	0.0521	0.3650	0.8927
10	RM260	2.0000	100–130	0.7407	0.3841	0.0370	0.3103	0.9053
11	RM7	3.0000	140–400	0.4516	0.6374	0.0000	0.5625	1.0000
12	RM517	2.0000	250–270	0.7590	0.3658	0.0000	0.2989	1.0000
13	RM501	2.0000	150–165	0.7611	0.3636	0.0556	0.2975	0.8488
14	OsZIP4	2.0000	310–310	0.6569	0.4508	0.0000	0.3492	1.0000
15	RM594	2.0000	295–310	0.8110	0.3066	0.1585	0.2596	0.4876
16	RM3412	3.0000	200–260	0.5506	0.5936	0.0225	0.5261	0.9626
17	RM5638	2.0000	200–250	0.5956	0.4817	0.0735	0.3657	0.8494
18	RM6712	3.0000	105–200	0.6071	0.5541	0.3878	0.4941	0.3049
19	RM168	2.0000	100–120	0.5700	0.4902	0.0200	0.3701	0.9596
20	RM5626	2.0000	190–210	0.8118	0.3056	0.0471	0.2589	0.8477
21	RM3392	4.0000	160–170	0.3416	0.6940	0.4653	0.6320	0.3339
22	RM1278	2.0000	130–140	0.7150	0.4076	0.1500	0.3245	0.6350
23	RM471	2.0000	110–130	0.7500	0.3750	0.1327	0.3047	0.6492
24	RM521	2.0000	240–270	0.9278	0.1340	0.0111	0.1250	0.9180
25	RM6209	2.0000	80–90	0.9798	0.0396	0.0000	0.0388	1.0000
26	RM80	2.0000	135–160	0.6198	0.4713	0.2604	0.3602	0.4516
27	OsZIP8	2.0000	0–100	0.6863	0.4306	0.0000	0.3379	1.0000
28	RM152	3.0000	140–180	0.4023	0.6585	0.5632	0.5845	0.1503
29	RM440	3.0000	150–205	0.7961	0.3438	0.0132	0.3150	0.9622
30	RM432	3.0000	170–350	0.7990	0.3399	0.0882	0.3121	0.7426
31	RM434	3.0000	150–290	0.7677	0.3706	0.0808	0.3233	0.7839
32	RM 3	3.0000	115–160	0.5337	0.5716	0.0337	0.4871	0.9417
33	RM 1	3.0000	75–120	0.7464	0.4101	0.0435	0.3730	0.8954
34	RM 144	3.0000	235–270	0.5000	0.5955	0.1000	0.5137	0.8343
35	RM 201	2.0000	140–160	0.8693	0.2272	0.0568	0.2014	0.7524
36	RM 205	4.0000	100–140	0.6325	0.5547	0.0843	0.5172	0.8497
37	RM 270	2.0000	300–370	0.9412	0.1107	0.0000	0.1046	1.0000
38	RM 335	2.0000	100–110	0.6616	0.4478	0.0303	0.3475	0.9330
39	RM154	3.0000	130–200	0.4765	0.6358	0.4471	0.5641	0.3022
40	RM211	3.0000	120–170	0.6534	0.4884	0.1591	0.4156	0.6774
41	RM202	3.0000	150–200	0.5150	0.6106	0.0900	0.5385	0.8540
42	RM293	2.0000	200–210	0.7557	0.3693	0.0114	0.3011	0.9696
43	RM85	3.0000	90–110	0.5058	0.6182	0.0814	0.5468	0.8698
44	RM407	6.0000	170–550	0.4892	0.7019	0.1290	0.6713	0.8180
45	RM237	2.0000	130–150	0.5345	0.4976	0.0115	0.3738	0.9772
46	RM259	4.0000	180–280	0.6867	0.4806	0.0400	0.4346	0.9178
47	RM421	2.0000	240–300	0.9521	0.0912	0.0532	0.0870	0.4209
48	RM235	3.0000	90–150	0.6462	0.4857	0.2462	0.4044	0.4990
49	RM1337	2.0000	120–140	0.6875	0.4297	0.5000	0.3374	######
50	RM3409	2.0000	304–340	0.7692	0.3550	0.0000	0.2920	1.0000
51	RM105	2.0000	130–145	0.6076	0.4768	0.0000	0.3632	1.0000
52	RM309	1.0000	190–190	1.0000	0.0000	0.0000	0.0000	NaN
53	RM452	1.0000	250–250	1.0000	0.0000	0.0000	0.0000	NaN
54	RM204	3.0000	120–170	0.4695	0.5741	0.0244	0.4807	0.9580
55	RM137	1.0000	250–250	1.0000	0.0000	0.0000	0.0000	NaN
56	RM1789	1.0000	180–180	1.0000	0.0000	0.0000	0.0000	NaN
57	RM6641	2.0000	140–150	0.7527	0.3723	0.0000	0.3030	1.0000
58	RM296	4.0000	140–410	0.5337	0.6233	0.0337	0.5673	0.9465
59	RM3331	2.0000	165–175	0.5306	0.4981	0.0000	0.3741	1.0000
60	RM31	3.0000	100–125	0.5000	0.6157	0.0455	0.5419	0.9270
61	RM429	2.0000	120–140	0.9511	0.0930	0.0326	0.0887	0.6527
62	RM556	2.0000	130–190	0.7157	0.4070	0.0196	0.3242	0.9523
63	RM585	4.0000	130–210	0.3824	0.6915	0.0196	0.6330	0.9719
64	RM23	2.0000	150–160	0.8713	0.2243	0.0000	0.1991	1.0000
65	RM34	2.0000	160–180	0.9188	0.1493	0.0875	0.1382	0.4191
66	RM53	2.0000	180–200	0.5714	0.4898	0.0000	0.3698	1.0000
67	RM300	3.0000	130–150	0.6344	0.5305	0.0000	0.4743	1.0000
68	RM315	2.0000	145–150	0.8687	0.2281	0.0000	0.2021	1.0000
69	RM339	3.0000	150–190	0.7475	0.4081	0.0707	0.3706	0.8283
70	RM400	4.0000	250–340	0.6571	0.5224	0.0000	0.4819	1.0000
71	RM528	2.0000	300–320	0.5464	0.4957	0.0000	0.3728	1.0000
72	RM486	2.0000	135–140	0.7526	0.3724	0.0206	0.3031	0.9452
73	RM340	6.0000	130–290	0.5215	0.6656	0.1828	0.6293	0.7279
74	RM1132	4.0000	95–140	0.5505	0.6145	0.0303	0.5617	0.9512
75	RM441	1.0000	170–170	1.0000	0.0000	0.0000	0.0000	NaN
76	RM590	1.0000	190–190	1.0000	0.0000	0.0000	0.0000	0.0000
77	RM258	1.0000	250–250	1.0000	0.0000	0.0000	0.0000	0.0000
78	GRMM9–1	2.0000	0–275	0.6961	0.4231	0.0000	0.3336	1.0000
79	GRMM9–2	2.0000	0–150	0.9216	0.1446	0.0000	0.1341	1.0000
80	OsNAC	2.0000	0–600	0.7917	0.3299	0.0000	0.2755	1.0000
81	OsZIP8A	2.0000	0–900	0.5882	0.4844	0.0000	0.3671	1.0000
82	OsZIP8C	2.0000	0–930	0.5980	0.4808	0.0000	0.3652	1.0000
83	OsYSL4E	3.0000	0–851	0.5000	0.6250	0.0000	0.5546	1.0000
84	OsMTP1A	2.0000	0–950	0.7451	0.3799	0.0000	0.3077	1.0000
85	OsNRAMP5G	2.0000	0–150	0.6373	0.4623	0.0000	0.3555	1.0000
86	IRMM9–1	2.0000	0–200	0.7059	0.4152	0.0000	0.3290	1.0000
87	OsYSL1	2.0000	0–230	0.6667	0.4444	0.0000	0.3457	1.0000
88	OsYSL2A	2.0000	0–150	0.9216	0.1446	0.0000	0.1341	1.0000
89	OsYSL2B	3.0000	0–330	0.4412	0.6353	0.0000	0.5590	1.0000
90	OsYSL5	2.0000	0–380	0.5098	0.4998	0.0000	0.3749	1.0000
91	OsYSL6	2.0000	0–166	0.5098	0.4998	0.0000	0.3749	1.0000
92	OsYSL11	2.0000	0–190	0.6569	0.4508	0.0000	0.3492	1.0000
93	OsZIP6A	3.0000	0–170	0.5098	0.5352	0.0000	0.4280	1.0000
94	OsZIP6B	2.0000	0–220	0.6078	0.4767	0.0000	0.3631	1.0000
95	OsZIP7	3.0000	0–180	0.6569	0.4796	0.0000	0.4025	1.0000
96	OsZIP8	2.0000	0–160	0.5294	0.4983	0.0000	0.3741	1.0000
97	OsNRAMP1A	3.0000	0–310	0.6667	0.4931	0.0000	0.4364	1.0000
98	OsNRAMP1B	2.0000	0–250	0.6471	0.4567	0.0000	0.3524	1.0000
99	OsFER1	3.0000	0–170	0.8431	0.2737	0.0000	0.2518	1.0000
100	OsFER2	3.0000	0–475	0.4804	0.5992	0.0000	0.5157	1.0000
	Mean	2.44		0.682038	0.414195	0.061385	0.348211	0.849347

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