Sequence-based ultra-dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes

Table 2 Characteristics of the 26 linkage groups in allotetraploid cotton

Linkage group	No. bins	No. SSRs	cM^a	Inter-bin average distance (cM)	No. scaffolds	Size (Mb)	No. SNPs
A01	157	13	179	1.14	240	115.9	169,307
A02	125	13	122	0.98	368	110.8	245,157
A03	150	19	146	0.98	326	116.7	138,849
A04	119	19	115	0.97	333	93.0	194,383
A05	213	32	213	1.00	313	113.2	136,212
A06	144	24	154	1.07	448	132.3	295,265
A07	163	13	151	0.93	376	101.1	315,158
A08	162	18	168	1.04	444	130.9	294,517
A09	153	28	151	0.99	233	87.0	117,361
A10	175	15	163	0.93	362	121.8	255,072
A11	202	28	205	1.01	407	126.3	260,274
A12	165	16	160	0.97	431	112.6	371,191
A13	168	17	157	0.94	354	115.8	350,161
A subgenome	2,096	255	2,087	1.00	4,635	1477.4	3,142,907
D01	136	27	125	0.92	107	64.2	138,376
D02	143	19	128	0.90	124	71.1	245,387
D03	121	18	128	1.06	101	55.4	182,200
D04	111	12	118	1.06	75	57.1	77,329
D05	213	30	214	1.01	145	66.0	133,959
D06	141	24	145	1.03	117	67.4	208,772
D07	145	16	145	1.00	116	58.4	128,679
D08	144	18	136	0.95	115	69.4	144,574
D09	146	25	157	1.08	122	53.8	116,224
D10	167	18	156	0.94	142	68.2	149,762
D11	174	21	176	1.01	130	72.6	152,575
D12	169	17	174	1.03	121	63.0	94,876
D13	143	19	153	1.07	96	64.5	83,428
D subgenome	1,953	264	1,956	1.00	1,511	831.1	1,856,141
Total	4,049	519	4,043	1.00	6,146	2308.5	4,999,048

^aGenetic distance was calculated by JoinMap 3.0 [39] using the maximum likelihood mapping method