Supplementary materials

Supplementary Table 1: Total reads, reads aligned, total size in giga base pairs and expected coverage using a predicted genome size of 1.132 giga base pairs of the Brassica napus double haploid population.

Name / Total reads / Reads aligned / Total size in giga base pairs / Approximate coverage
TN1 / 83,346,750 / 29,145,852 / 8.335 / 7.363
TN2 / 29,084,468 / 9,012,570 / 2.908 / 2.569
TN3 / 30,187,974 / 7,526,864 / 3.019 / 2.667
TN4 / 18,559,924 / 5,845,642 / 1.856 / 1.640
TN5 / 14,549,744 / 4,518,946 / 1.455 / 1.285
TN7 / 10,567,506 / 3,381,254 / 1.057 / 0.934
TN8 / 44,585,238 / 10,393,986 / 4.459 / 3.939
TN9 / 20,355,656 / 6,257,678 / 2.036 / 1.798
TN10 / 8,745,736 / 2,813,032 / 0.875 / 0.773
TN11 / 11,582,370 / 3,080,908 / 1.158 / 1.023
TN12 / 32,544,574 / 10,870,436 / 3.254 / 2.875
TN14 / 10,019,548 / 3,248,464 / 1.002 / 0.885
TN15 / 12,010,074 / 3,966,942 / 1.201 / 1.061
TN16 / 71,880,264 / 23,112,148 / 7.188 / 6.350
TN17 / 12,800,938 / 4,297,484 / 1.280 / 1.131
TN18 / 11,296,632 / 3,887,826 / 1.130 / 0.998
TN19 / 9,203,792 / 2,853,746 / 0.920 / 0.813
TN20 / 12,534,978 / 3,633,774 / 1.253 / 1.107
TN21 / 6,118,646 / 1,903,526 / 0.612 / 0.541
TN22 / 7,992,800 / 2,375,938 / 0.799 / 0.706
TN23 / 40,204,364 / 11,220,930 / 4.020 / 3.552
TN24 / 45,514,168 / 12,466,914 / 4.551 / 4.021
TN25 / 9,005,082 / 2,804,668 / 0.901 / 0.796
TN26 / 42,655,064 / 12,131,920 / 4.266 / 3.768
TN27 / 36,915,918 / 9,679,092 / 3.692 / 3.261
TN28 / 30,529,976 / 5,982,230 / 3.053 / 2.697
TN29 / 27,209,648 / 7,758,778 / 2.721 / 2.404
TN30 / 31,257,302 / 8,571,744 / 3.126 / 2.761
TN31 / 32,732,720 / 8,924,364 / 3.273 / 2.892
TN32 / 32,942,618 / 9,970,628 / 3.294 / 2.910
TN33 / 52,371,782 / 15,854,004 / 5.237 / 4.626
TN34 / 32,277,834 / 9,418,240 / 3.228 / 2.851
TN35 / 59,089,314 / 18,401,108 / 5.909 / 5.220
TN36 / 35,912,532 / 9,714,642 / 3.591 / 3.172
TN37 / 38,010,416 / 11,907,270 / 3.801 / 3.358
TN38 / 39,419,092 / 12,255,652 / 3.942 / 3.482
TN39 / 26,364,882 / 8,397,706 / 2.636 / 2.329
TN40 / 27,140,146 / 8,618,194 / 2.714 / 2.398
TN41 / 25,817,684 / 8,130,838 / 2.582 / 2.281
TN42 / 21,026,508 / 6,191,244 / 2.103 / 1.857
TN43 / 11,525,524 / 3,679,228 / 1.153 / 1.018
TN44 / 16,133,154 / 5,000,456 / 1.613 / 1.425
TN45 / 12,479,978 / 3,878,124 / 1.248 / 1.102
TN46 / 10,782,268 / 3,403,622 / 1.078 / 0.952
TN47 / 40,099,414 / 12,143,344 / 4.010 / 3.542
TN48 / 34,053,412 / 10,059,588 / 3.405 / 3.008
TN49 / 29,908,066 / 9,051,540 / 2.991 / 2.642
TN50 / 36,941,216 / 10,737,098 / 3.694 / 3.263
TN51 / 31,888,046 / 9,096,010 / 3.189 / 2.817
TN52 / 18,790,054 / 5,566,016 / 1.879 / 1.660
TN53 / 18,740,704 / 5,380,400 / 1.874 / 1.656
TN54 / 9,731,884 / 2,854,702 / 0.973 / 0.860
TN55 / 13,543,926 / 3,461,156 / 1.354 / 1.196
TN56 / 12,419,898 / 3,122,620 / 1.242 / 1.097
TN57 / 7,649,058 / 2,405,988 / 0.765 / 0.676
TN58 / 15,582,398 / 3,885,032 / 1.558 / 1.377
TN59 / 15,279,778 / 4,570,932 / 1.528 / 1.350
TN60 / 41,523,704 / 13,104,946 / 4.152 / 3.668
TN61 / 48,896,516 / 16,121,744 / 4.890 / 4.319
TN62 / 21,163,462 / 6,437,630 / 2.116 / 1.870
TN63 / 21,946,320 / 6,691,150 / 2.195 / 1.939
TN64 / 11,247,122 / 3,208,062 / 1.125 / 0.994
TN65 / 10,451,186 / 3,043,228 / 1.045 / 0.923
TN66 / 13,051,134 / 4,010,550 / 1.305 / 1.153
TN67 / 13,176,348 / 3,502,962 / 1.318 / 1.164
TN68 / 12,522,858 / 3,245,910 / 1.252 / 1.106
TN69 / 11,645,412 / 3,114,460 / 1.165 / 1.029
TN70 / 13,639,458 / 3,507,734 / 1.364 / 1.205
TN71 / 83,217,150 / 28,520,384 / 8.322 / 7.351
TN72 / 62,815,266 / 19,390,062 / 6.282 / 5.549
TN73 / 60,727,876 / 20,835,228 / 6.073 / 5.365
TN74 / 57,259,586 / 19,142,000 / 5.726 / 5.058
TN75 / 78,694,534 / 25,618,626 / 7.869 / 6.952
TN76 / 65,706,838 / 19,586,042 / 6.571 / 5.804
TN77 / 36,104,112 / 10,441,472 / 3.610 / 3.189
TN78 / 2,228,266 / 656,216 / 0.223 / 0.197
TN80 / 577,604 / 155,234 / 0.058 / 0.051
TN82 / 1,240,224 / 341,686 / 0.124 / 0.110
TN83 / 2,215,066 / 669,264 / 0.222 / 0.196
TN84 / 36,907,818 / 11,971,246 / 3.691 / 3.260
TN85 / 8,527,290 / 2,809,150 / 0.853 / 0.753
TN86 / 19,021,548 / 6,365,474 / 1.902 / 1.680
TN87 / 19,327,974 / 6,323,106 / 1.933 / 1.707
TN88 / 19,194,414 / 6,268,936 / 1.919 / 1.696
TN89 / 17,627,570 / 5,802,128 / 1.763 / 1.557
TN90 / 13,395,728 / 4,120,910 / 1.340 / 1.183
TN93 / 9,824,804 / 2,743,210 / 0.982 / 0.868
TN94 / 15,527,892 / 4,452,714 / 1.553 / 1.372
TN97 / 10,805,130 / 3,272,604 / 1.081 / 0.955
TN98 / 10,381,212 / 3,228,084 / 1.038 / 0.917
TN99 / 9,500,042 / 3,125,790 / 0.950 / 0.839
TN100 / 1,542,248 / 494,298 / 0.154 / 0.136

Supplementary Table 2: Total reads, reads aligned, total size in giga base pairs and expected coverage using a predicted genome size of 0.74 giga base pairs of the Cicer arietinum RIL population.

Name / Total reads / Reads aligned / Total size in giga base pairs / Estimated Coverage
RIL1 / 3,684,872 / 1,125,674 / 0.368 / 0.498
RIL2 / 5,205,294 / 1,498,968 / 0.521 / 0.703
RIL3 / 2,747,662 / 766,704 / 0.275 / 0.371
RIL4 / 5,444,572 / 1,327,202 / 0.544 / 0.736
RIL5 / 4,591,078 / 1,356,696 / 0.459 / 0.620
RIL6 / 3,629,626 / 1,576,436 / 0.363 / 0.490
RIL7 / 2,320,068 / 665,690 / 0.232 / 0.314
RIL8 / 4,361,032 / 1,260,634 / 0.436 / 0.589
RIL10 / 2,796,146 / 664,656 / 0.280 / 0.378
RIL11 / 2,117,620 / 742,612 / 0.212 / 0.286
RIL12 / 962,922 / 314,116 / 0.096 / 0.130
RIL13 / 1,657,602 / 556,654 / 0.166 / 0.224
RIL14 / 1,595,262 / 491,804 / 0.160 / 0.216
RIL15 / 1,226,102 / 406,310 / 0.123 / 0.166
RIL16 / 3,740,960 / 1,102,118 / 0.374 / 0.506
RIL17 / 2,454,692 / 779,988 / 0.245 / 0.332
RIL18 / 2,820,084 / 990,180 / 0.282 / 0.381
RIL19 / 4,250,980 / 1,536,168 / 0.425 / 0.574
RIL20 / 6,495,916 / 2,271,592 / 0.650 / 0.878
RIL21 / 4,303,956 / 1,489,752 / 0.430 / 0.582
RIL22 / 3,205,260 / 1,077,182 / 0.321 / 0.433
RIL23 / 5,937,812 / 1,945,460 / 0.594 / 0.802
RIL24 / 4,271,118 / 1,487,938 / 0.427 / 0.577
RIL25 / 3,084,224 / 908,300 / 0.308 / 0.417
RIL26 / 4,431,488 / 1,364,528 / 0.443 / 0.599
RIL27 / 2,772,592 / 873,100 / 0.277 / 0.375
RIL28 / 3,471,898 / 1,114,198 / 0.347 / 0.469
RIL29 / 5,599,984 / 1,789,082 / 0.560 / 0.757
RIL30 / 3,599,042 / 1,290,388 / 0.360 / 0.486
RIL31 / 5,424,262 / 1,905,006 / 0.542 / 0.733
RIL32 / 3,485,042 / 1,293,948 / 0.349 / 0.471
RIL33 / 1,160,832 / 318,572 / 0.116 / 0.157
RIL34 / 4,481,104 / 1,497,334 / 0.448 / 0.606
RIL35 / 2,737,340 / 825,870 / 0.274 / 0.370
RIL36 / 4,967,114 / 1,578,860 / 0.497 / 0.671
RIL37 / 5,896,262 / 1,741,778 / 0.590 / 0.797
RIL39 / 3,055,534 / 1,244,680 / 0.306 / 0.413
RIL40 / 3,452,314 / 1,171,420 / 0.345 / 0.467
RIL41 / 3,386,416 / 1,021,398 / 0.339 / 0.458
RIL42 / 2,585,090 / 739,238 / 0.259 / 0.349
RIL43 / 2,403,796 / 3,417,224 / 0.240 / 0.325
RIL44 / 3,286,314 / 2,953,014 / 0.329 / 0.444
RIL45 / 4,609,384 / 3,403,208 / 0.461 / 0.623
RIL46 / 4,071,794 / 2,834,830 / 0.407 / 0.550
RIL47 / 2,637,320 / 2,752,250 / 0.264 / 0.356
RIL48 / 3,870,340 / 3,111,754 / 0.387 / 0.523
RIL49 / 4,522,322 / 3,232,826 / 0.452 / 0.611
RIL50 / 2,217,534 / 2,801,588 / 0.222 / 0.300

Supplementary Table 3: Count of crossovers, gene conversions, before filtering of overlapping recombination events for individuals of the Brassica napus DH population after filtering of non-double haploid individuals, split up into A and C genome.

Name of individual / A genome crossovers / A genome gene conversions / C genome crossovers / C genome gene conversions
TN1 / 150 / 705 / 165 / 263
TN2 / 111 / 418 / 91 / 149
TN3 / 114 / 544 / 85 / 412
TN4 / 126 / 785 / 65 / 253
TN5 / 122 / 477 / 64 / 162
TN7 / 212 / 1651 / 172 / 1074
TN8 / 121 / 629 / 70 / 240
TN9 / 138 / 808 / 87 / 453
TN10 / 100 / 365 / 64 / 227
TN11 / 97 / 451 / 49 / 179
TN12 / 137 / 788 / 131 / 238
TN14 / 106 / 605 / 53 / 277
TN15 / 113 / 775 / 69 / 208
TN16 / 125 / 572 / 118 / 390
TN17 / 116 / 514 / 90 / 322
TN18 / 123 / 618 / 74 / 221
TN19 / 119 / 483 / 59 / 216
TN20 / 143 / 584 / 67 / 204
TN21 / 85 / 307 / 37 / 125
TN22 / 126 / 597 / 64 / 275
TN24 / 125 / 604 / 127 / 424
TN25 / 116 / 621 / 42 / 244
TN26 / 99 / 391 / 111 / 258
TN27 / 87 / 387 / 119 / 222
TN28 / 176 / 1156 / 119 / 203
TN29 / 115 / 403 / 125 / 304
TN30 / 180 / 1056 / 130 / 348
TN31 / 131 / 672 / 153 / 432
TN32 / 123 / 439 / 145 / 339
TN34 / 154 / 847 / 163 / 493
TN35 / 149 / 594 / 183 / 303
TN36 / 149 / 581 / 141 / 271
TN37 / 131 / 505 / 143 / 304
TN38 / 119 / 528 / 112 / 300
TN39 / 123 / 590 / 94 / 305
TN40 / 150 / 866 / 102 / 243
TN41 / 107 / 354 / 111 / 249
TN42 / 98 / 434 / 54 / 200
TN43 / 144 / 683 / 55 / 217
TN44 / 135 / 910 / 79 / 382
TN45 / 129 / 552 / 68 / 211
TN46 / 129 / 539 / 72 / 272
TN47 / 144 / 585 / 146 / 465
TN48 / 195 / 1250 / 139 / 361
TN54 / 187 / 1377 / 106 / 1103
TN57 / 133 / 693 / 75 / 434
TN65 / 254 / 1816 / 204 / 1628
TN73 / 167 / 674 / 217 / 356
TN74 / 135 / 388 / 164 / 406
TN75 / 161 / 1166 / 165 / 595
TN76 / 128 / 986 / 166 / 434
TN78 / 316 / 421 / 181 / 307
TN80 / 160 / 76 / 126 / 93
TN82 / 220 / 201 / 217 / 218
TN83 / 512 / 552 / 268 / 328
TN85 / 122 / 366 / 65 / 157
TN86 / 153 / 1406 / 134 / 523
TN87 / 143 / 1243 / 128 / 598
TN88 / 121 / 769 / 88 / 696
TN89 / 119 / 980 / 119 / 546
TN90 / 130 / 733 / 87 / 659
TN93 / 111 / 471 / 76 / 295
TN94 / 143 / 817 / 91 / 334
TN97 / 156 / 688 / 92 / 283
TN98 / 239 / 1904 / 174 / 1313
TN99 / 91 / 354 / 54 / 158
TN100 / 536 / 452 / 337 / 413

Supplementary Table 4: Count of crossovers, gene conversions, after filtering of overlapping recombination events for individuals of the Brassica napus DH population after filtering of non-double haploid individuals, split up into A and C genome.

Name of individual / A genome crossovers / A genome gene conversions / C genome crossovers / C genome gene conversions
TN1 / 1 / 8 / 1 / 6
TN2 / 0 / 9 / 0 / 5
TN3 / 0 / 8 / 1 / 7
TN4 / 1 / 8 / 0 / 4
TN5 / 2 / 7 / 1 / 5
TN7 / 27 / 9 / 14 / 11
TN8 / 1 / 7 / 1 / 8
TN9 / 0 / 8 / 11 / 9
TN10 / 2 / 8 / 3 / 6
TN11 / 1 / 9 / 0 / 8
TN12 / 2 / 7 / 2 / 7
TN14 / 1 / 9 / 0 / 6
TN15 / 0 / 8 / 0 / 8
TN16 / 1 / 6 / 3 / 7
TN17 / 0 / 8 / 2 / 8
TN18 / 0 / 5 / 7 / 5
TN19 / 0 / 9 / 1 / 8
TN20 / 0 / 7 / 0 / 8
TN21 / 0 / 10 / 0 / 9
TN22 / 1 / 9 / 6 / 5
TN24 / 2 / 7 / 2 / 6
TN25 / 0 / 8 / 1 / 5
TN26 / 0 / 6 / 1 / 4
TN27 / 1 / 5 / 1 / 7
TN28 / 3 / 4 / 2 / 6
TN29 / 1 / 5 / 1 / 6
TN30 / 1 / 7 / 0 / 8
TN31 / 1 / 9 / 0 / 6
TN32 / 2 / 8 / 0 / 7
TN34 / 1 / 8 / 3 / 7
TN35 / 1 / 6 / 3 / 7
TN36 / 1 / 6 / 2 / 6
TN37 / 1 / 7 / 2 / 7
TN38 / 1 / 6 / 0 / 7
TN39 / 2 / 8 / 0 / 6
TN40 / 8 / 6 / 0 / 7
TN41 / 0 / 6 / 2 / 7
TN42 / 0 / 7 / 0 / 7
TN43 / 1 / 9 / 1 / 7
TN44 / 1 / 9 / 1 / 6
TN45 / 0 / 8 / 1 / 8
TN46 / 0 / 8 / 0 / 8
TN47 / 1 / 7 / 5 / 8
TN48 / 1 / 9 / 4 / 6
TN54 / 17 / 9 / 11 / 7
TN57 / 5 / 8 / 3 / 8
TN65 / 16 / 9 / 20 / 9
TN73 / 0 / 6 / 0 / 6
TN74 / 1 / 6 / 3 / 5
TN75 / 1 / 8 / 2 / 6
TN76 / 3 / 7 / 4 / 8
TN78 / 51 / 10 / 35 / 9
TN80 / 10 / 9 / 13 / 6
TN82 / 27 / 7 / 39 / 9
TN83 / 109 / 10 / 41 / 9
TN85 / 0 / 7 / 0 / 5
TN86 / 2 / 7 / 3 / 5
TN87 / 7 / 7 / 9 / 7
TN88 / 5 / 6 / 1 / 6
TN89 / 9 / 8 / 6 / 8
TN90 / 0 / 8 / 2 / 7
TN93 / 3 / 6 / 3 / 9
TN94 / 0 / 10 / 0 / 7
TN97 / 1 / 9 / 4 / 7
TN98 / 25 / 9 / 28 / 7
TN99 / 1 / 8 / 3 / 8
TN100 / 111 / 9 / 138 / 9

Supplementary Table 5: Count of crossovers, gene conversions, after filtering of overlapping recombination events for individuals of the Brassica napus DH population after filtering of non-double haploid individuals, counted per chromosome.

Chromo-some / Minimum crossovers / Maximum crossovers / Average crossovers / Minimum gene conversion / Maximum gene conversion / Average gene conversion
A01 / 0 / 12 / 0.67 / 0 / 1 / 0.78
A02 / 0 / 9 / 0.63 / 0 / 1 / 0.87
A03 / 0 / 32 / 1.3 / 0 / 2 / 0.85
A04 / 0 / 18 / 0.69 / 0 / 1 / 0.73
A05 / 0 / 17 / 0.6 / 0 / 1 / 0.79
A06 / 0 / 14 / 0.67 / 0 / 1 / 0.7
A07 / 0 / 14 / 0.64 / 0 / 1 / 0.45
A08 / 0 / 8 / 0.34 / 0 / 1 / 0.84
A09 / 0 / 26 / 0.99 / 0 / 1 / 0.79
A10 / 0 / 24 / 0.55 / 0 / 1 / 0.84
C1 / 0 / 15 / 0.87 / 0 / 1 / 0.79
C2 / 0 / 9 / 0.54 / 0 / 1 / 0.7
C3 / 0 / 21 / 0.93 / 0 / 1 / 0.79
C4 / 0 / 40 / 1.42 / 0 / 2 / 0.84
C5 / 0 / 7 / 0.28 / 0 / 1 / 0.81
C6 / 0 / 14 / 0.63 / 0 / 1 / 0.88
C7 / 0 / 5 / 0.45 / 0 / 2 / 0.61
C8 / 0 / 36 / 0.85 / 0 / 1 / 0.87
C9 / 0 / 11 / 0.81 / 0 / 1 / 0.67

Supplementary Table 6: Count of crossovers and gene conversions for individuals of the Cicer arietinum RIL population after filtering of heterozygous individuals and before and after filtering of overlapping recombinations.

Name of element / Crossovers before filtering / Gene conversions before filtering / Crossovers after filtering / Gene conversions after filtering
RIL1 / 85 / 120 / 2 / 8
RIL2 / 121 / 132 / 4 / 7
RIL3 / 146 / 98 / 8 / 7
RIL4 / 117 / 108 / 1 / 5
RIL5 / 134 / 105 / 3 / 7
RIL6 / 46 / 84 / 22 / 8
RIL7 / 68 / 34 / 0 / 7
RIL8 / 72 / 30 / 1 / 7
RIL10 / 65 / 68 / 3 / 9
RIL11 / 124 / 78 / 1 / 6
RIL12 / 102 / 34 / 2 / 6
RIL13 / 108 / 89 / 12 / 7
RIL14 / 98 / 42 / 4 / 5
RIL15 / 101 / 41 / 1 / 6
RIL16 / 87 / 80 / 2 / 5
RIL17 / 108 / 72 / 2 / 7
RIL18 / 116 / 98 / 3 / 7
RIL20 / 177 / 244 / 5 / 7
RIL21 / 134 / 222 / 8 / 7
RIL22 / 114 / 98 / 2 / 6
RIL24 / 133 / 132 / 1 / 7
RIL25 / 83 / 86 / 2 / 7
RIL26 / 97 / 121 / 1 / 8
RIL27 / 127 / 70 / 9 / 6
RIL29 / 212 / 1174 / 60 / 22
RIL30 / 121 / 154 / 5 / 7
RIL31 / 119 / 162 / 5 / 5
RIL32 / 109 / 173 / 6 / 7
RIL33 / 96 / 52 / 19 / 7
RIL34 / 114 / 109 / 1 / 8
RIL35 / 134 / 89 / 7 / 5
RIL36 / 103 / 150 / 3 / 7
RIL37 / 37 / 74 / 1 / 8
RIL40 / 140 / 101 / 7 / 7
RIL41 / 109 / 92 / 1 / 6
RIL42 / 103 / 59 / 5 / 5

Supplementary Table 7: Count of crossovers, gene conversions, after filtering of overlapping recombination events for individuals of the Brassica napus DH population after filtering of non-double haploid individuals, counted per chromosome.