Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel

Table 2 Mean linkage disequilibrium among syntenic SNPs over different map distances, pooled over all autosomes.

Distance	N	Mean D'	SD (D')	Median D'	Mean r²	SD (r²)	Median r²	25th percentile r²	Min no SNP required to cover genome
0–1 kb	3856	0.99	0.09	1.00	0.767	0.335	0.989	0.496	3,000,000
1–10 kb	1475	0.95	0.16	1.00	0.592	0.374	0.619	0.205	300,000
10–20 kb	546	0.87	0.24	1.00	0.402	0.352	0.280	0.082	150,000
20–40 kb	1089	0.80	0.28	0.97	0.309	0.311	0.186	0.057	75,000
40–60 kb	829	0.66	0.33	0.71	0.196	0.235	0.114	0.027	50,000
60–100 kb	1529	0.61	0.34	0.64	0.153	0.210	0.066	0.015	30,000
100–200 kb	3899	0.54	0.33	0.52	0.108	0.156	0.047	0.013	15,000
200–500 kb	11202	0.46	0.31	0.41	0.073	0.106	0.034	0.009	6,000
0.5–1 Mb	18082	0.41	0.29	0.36	0.057	0.083	0.026	0.006	3,000
1–2 Mb	36272	0.38	0.28	0.33	0.049	0.076	0.022	0.005	1,500
2–5 Mb	103940	0.34	0.26	0.27	0.036	0.056	0.016	0.004	750
5–10 Mb	163439	0.27	0.23	0.21	0.024	0.038	0.010	0.002	300
10–20 Mb	285318	0.21	0.19	0.15	0.013	0.022	0.006	0.001	150
20–50	575734	0.14	0.14	0.10	0.006	0.010	0.002	0.001	60
> 50 Mb	359680	0.11	0.12	0.08	0.003	0.007	0.001	0.000	NA
Non-syntenic	365400	0.11	0.11	0.07	0.003	0.005	0.002	0.000

ISSN: 1471-2164