A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array

Table 1 Mean linkage disequilibrium (LD) given as r ² and average LD decay distance ^a in kb per chromosome in 155 lines (all) and in six ^b subgroups as determined by ADMIXTURE

	All		Dent – BSSS		Dent – Non-BSSS		Iodent		Non-Northern Flint		Northern Flint		(Sub) Tropical
	(N = 155)		(N = 14)		(N = 32)		(N = 14)		(N = 18)		(N = 34)		(N = 34)
Chr.	mean r²	r²decay	mean r²	r²decay	mean r²	r²decay	mean r²	r²decay	mean r²	r²decay	mean r²	r²decay	mean r²	r²decay
1	0.029	119.14	0.202	14,411.28	0.049	156.32	0.212	15,949.23	0.133	4,007.83	0.049	197.98	0.037	43.38
2	0.027	126.13	0.260	30,329.28	0.048	178.63	0.177	9,411.84	0.133	4,211.89	0.059	332.88	0.039	64.29
3	0.034	199.62	0.263	31,772.64	0.057	306.29	0.170	8,340.20	0.199	15,545.48	0.055	352.29	0.044	96.22
4	0.031	192.41	0.207	16,123.82	0.054	319.43	0.310	50,389.31	0.128	3,114.28	0.063	404.96	0.037	83.82
5	0.027	119.91	0.224	18,692.30	0.047	172.69	0.154	5,681.66	0.144	4,626.09	0.056	262.24	0.038	57.22
6	0.025	106.65	0.198	14,001.18	0.049	188.22	0.170	8,886.16	0.099	955.38	0.049	206.58	0.036	40.20
7	0.033	176.04	0.214	16,901.24	0.057	246.89	0.228	18,945.94	0.141	3,737.87	0.060	379.57	0.042	75.11
8	0.033	183.72	0.257	28,937.29	0.053	254.27	0.280	37,984.38	0.120	1,537.13	0.052	322.23	0.039	81.56
9	0.033	167.58	0.309	53,758.98	0.057	263.68	0.263	28,009.93	0.151	5,020.05	0.056	314.73	0.041	61.48
10	0.033	192.64	0.396	136,831.20	0.057	303.38	0.256	11,899.95	0.130	2,916.32	0.054	343.07	0.041	96.65
Mean	0.031	158.38	0.253	36,175.92	0.053	238.98	0.222	19,549.86	0.138	4,567.23	0.055	311.65	0.039	69.99
Median	0.032	171.81	0.241	23,814.80	0.054	250.58	0.220	13,924.59	0.133	3,872.85	0.055	327.55	0.039	69.70