Table 1.

Summary of linkage disequilibrium across chromosomes and sub-genomes.

Chromosome*	Total number of marker pairs	% r2 > 0.1	Average LD at r2 > 0.1	LD decay below baseline r2 = 0.1 (in cM)
1A	2926	16.6	0.25	2
1B	1378	17.4	0.29	5
1D	2415	25.1	0.35	20
2A	3570	20.2	0.30	8
2B	8001	15.8	0.30	5
2D	1081	27.2	0.36	25
3A	11175	15.7	0.32	2
3B	11476	14.4	0.28	5
3D	210	16.6	0.35	15
4A	3916	21.4	0.32	5
4B	2850	18.4	0.35	5
5A	8778	33.2	0.39	20
5B	18721	27.6	0.28	15
6A	9730	19.3	0.30	12
6B	50403	16.2	0.28	5
6D	351	14.8	0.36	12
7A	5886	14.2	0.27	5
7B	7140	26.0	0.35	25
7D	946	28.3	0.39	35
A genome	6569	20.0	0.30	15
B genome	14281	19.4	0.30	10
D genome	1001	22.4	0.38	20

^*LD and LD decay on chromosomes 4D and 5D were not calculated due to fewer markers.