Table 1.
A summary of LD observed among marker pairs and the number of significant marker pairs per genome and chromosome
| Chromosome | Total | Landrace | Cultivar | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| TNSP | r 2 | Dis. (cM) | NSSP | TNSP | r 2 | Dis. (cM) | NSSP | TNSP | r 2 | Dis. (cM) | NSSP | |
| 1 A | 111,575 | 0.111829 | 1.333712 | 49,917 (44.74%) | 94,575 | 0.116906 | 1.568634 | 34,895 (36.9%) | 85,625 | 0.148069 | 1.736676 | 27,111 (31.66%) |
| 2 A | 137,150 | 0.251605 | 0.856962 | 79,772 (58.16%) | 125,450 | 0.289098 | 0.936772 | 68,972 (54.98%) | 119,450 | 0.288518 | 0.972951 | 57,769 (48.36%) |
| 3 A | 96,450 | 0.130453 | 2.27878 | 44,914 (46.57%) | 74,950 | 0.134097 | 2.933748 | 28,787 (38.41%) | 85,000 | 0.15728 | 2.574908 | 25,912 (30.48%) |
| 4 A | 130,500 | 0.317779 | 1.378513 | 79,428 (60.86%) | 110,850 | 0.369392 | 1.594492 | 66,016 (59.55%) | 116,700 | 0.36745 | 1.50704 | 58,086 (49.77%) |
| 5 A | 71,850 | 0.132927 | 2.005721 | 32,488 (45.22%) | 60,100 | 0.146486 | 2.402626 | 24,483 (40.74%) | 60,600 | 0.166755 | 2.38547 | 18,725 (30.9%) |
| 6 A | 99,050 | 0.158856 | 1.296073 | 52,549 (53.05%) | 85,850 | 0.178539 | 1.498357 | 40,739 (47.45%) | 86,550 | 0.178744 | 1.486057 | 29,651 (34.26%) |
| 7 A | 149,700 | 0.193545 | 1.164988 | 78,616 (52.52%) | 128,550 | 0.211862 | 1.358487 | 64,114 (49.87%) | 129,900 | 0.232161 | 1.343972 | 49,454 (38.07%) |
| 1B | 150,800 | 0.154279 | 0.932852 | 80,419 (53.33%) | 135,600 | 0.154625 | 1.035051 | 64,442 (47.52%) | 132,400 | 0.20421 | 1.063407 | 49,705 (37.54%) |
| 2B | 187,300 | 0.156885 | 0.764253 | 102,236 (54.58%) | 157,350 | 0.176011 | 0.910909 | 79,057 (50.24%) | 166,950 | 0.19665 | 0.858127 | 66,140 (39.62%) |
| 3B | 201,700 | 0.210733 | 0.771726 | 119,399 (59.2%) | 173,200 | 0.220043 | 0.89872 | 90,266 (52.12%) | 177,550 | 0.243607 | 0.876084 | 78,180 (44.03%) |
| 4B | 60,050 | 0.115027 | 2.20477 | 23,537 (39.2%) | 44,800 | 0.09777 | 2.968273 | 12,423 (27.73%) | 52,600 | 0.142347 | 2.516753 | 13,477 (25.62%) |
| 5B | 152,400 | 0.15014 | 1.292476 | 80,669 (52.93%) | 136,300 | 0.14202 | 1.445522 | 57,252 (42%) | 135,650 | 0.202818 | 1.431617 | 55,651 (41.03%) |
| 6B | 190,850 | 0.13708 | 0.658245 | 99,314 (52.04%) | 167,500 | 0.135522 | 0.750676 | 71,975 (42.97%) | 159,700 | 0.203568 | 0.787671 | 66,038 (41.35%) |
| 7B | 150,100 | 0.121987 | 0.987127 | 70,107 (46.71%) | 127,550 | 0.12878 | 1.153868 | 51,602 (40.46%) | 134,150 | 0.155388 | 1.102364 | 41,168 (30.69%) |
| 1D | 48,650 | 0.238268 | 3.477302 | 26,009 (53.46%) | 42,500 | 0.226198 | 3.808863 | 20,075 (47.24%) | 38,350 | 0.285881 | 4.409069 | 16,564 (43.19%) |
| 2D | 69,550 | 0.183692 | 1.586178 | 31,547 (45.36%) | 55,400 | 0.163933 | 1.999469 | 21,117 (38.12%) | 49,600 | 0.228564 | 2.23156 | 16,357 (32.98%) |
| 3D | 37,050 | 0.116765 | 4.639072 | 5460 (14.74%) | 31,800 | 0.165445 | 5.245984 | 11,619 (36.54%) | 26,800 | 0.137566 | 6.273779 | 5458 (20.37%) |
| 4D | 13,500 | 0.122822 | 9.104484 | 4560 (33.78%) | 11,800 | 0.130958 | 10.56137 | 3577 (30.31%) | 11,550 | 0.154924 | 10.56621 | 2312 (20.02%) |
| 5D | 31,750 | 0.130873 | 6.894582 | 12,308 (38.77%) | 26,250 | 0.134737 | 8.311197 | 9238 (35.19%) | 23,700 | 0.147915 | 9.317761 | 5518 (23.28%) |
| 6D | 38,300 | 0.123729 | 4.134238 | 15,652 (40.87%) | 34,900 | 0.136001 | 4.545476 | 12,619 (36.16%) | 29,750 | 0.137805 | 5.369092 | 6852 (23.03%) |
| 7D | 46,700 | 0.150286 | 4.409549 | 17,838 (38.2%) | 42,300 | 0.147515 | 4.882439 | 14,457 (34.18%) | 35,850 | 0.201644 | 5.778975 | 10,863 (30.3%) |
| A genome | 796,275 | 0.195029 | 1.397647 | 417,684 (52.45%) | 680,325 | 0.220024 | 1.631824 | 328,006 (48.21%) | 683,825 | 0.232699 | 1.61945 | 266,708 (39%) |
| B genome | 1,093,200 | 0.154972 | 0.95375 | 575,681 (52.66%) | 942,300 | 0.1588 | 1.106081 | 427,017 (45.32%) | 959,000 | 0.199661 | 1.084318 | 370,359 (38.62%) |
| D genome | 285,500 | 0.162046 | 4.054108 | 113,374 (39.71%) | 244,950 | 0.1634 | 4.684331 | 92,702 (37.85%) | 215,600 | 0.197637 | 5.369609 | 63,924 (29.65%) |
| Whole genomes | 2,174,975 | 0.170566 | 1.523235 | 1,106,739 (50.89%) | 1,867,575 | 0.181706 | 1.766921 | 847,725 (45.39%) | 1,858,425 | 0.211583 | 1.778371 | 700,991 (37.72%) |
Abbreviations: r2 average squared allele frequency correlation, TNSP Total number of SNP pairs, NSSP Number of significant SNP pairs (P < 0.001), Dis Distance