Table 2.
Structural organization of the duplicated regions of AK blocks E, J, R, U, and W in B. napus genome.
| Expected sub-genome according to (Parkin et al., 2014) | LF | MF1 | MF2 | LF | MF1 | MF2 |
|---|---|---|---|---|---|---|
| E Block | ChrA07 | ChrA02 | ChrA07 | ChrC06 | ChrC02 | ChrC06 |
| Start (in pb) | 18912043 | 6525027 | 15644284 | 28782631 | 12353161 | 21211096 |
| End (in pb) | 24002405 | 12403698 | 18772016 | 37223546 | 23287093 | 28440230 |
| Interval length (in pb) | 5090362 | 5878671 | 3127732 | 8440915 | 10933932 | 7229134 |
| Number of B. napus genes | 1051 | 777 | 548 | 1324 | 908 | 802 |
| Gene density (nb genes/Mb) | 206 | 132 | 175 | 157 | 83 | 111 |
| Number of B. napus genes without an A. thaliana gene hit | 69 | 111 | 27 | 191 | 260 | 170 |
| Number of B. napus genes with an A. thaliana gene hit | 982 | 666 | 521 | 1133 | 648 | 632 |
| Number of conserved B. napus genes with the orthologous regions in A. thaliana genome | 798 | 500 | 440 | 849 | 430 | 450 |
| Number of SNP tested | 147 | 95 | 192 | 169 | 154 | 89 |
| Percentage of resistance associated SNP | 21.77 | 15.79 | 11.46 | 6.51 | 6.49 | 10.11 |
| J Block | ChrA05 | ChrA04 | ChrA03 | ChrC04 | BlocJ | ChrC03 |
| Start (in pb) | 699676 | 15016807 | 6917392 | 632943 | 43520171 | 9229126 |
| End (in pb) | 5838732 | 19149123 | 10194192 | 9495166 | 48900949 | 14528271 |
| Interval length (in pb) | 5139056 | 4132316 | 3276800 | 8862223 | 5380778 | 5299145 |
| Number of B. napus genes | 951 | 823 | 651 | 1142 | 856 | 789 |
| Gene density (nb genes/Mb) | 185 | 199 | 199 | 129 | 159 | 149 |
| Number of B. napus genes without an A. thaliana gene hit | 70 | 74 | 62 | 199 | 115 | 117 |
| Number of B. napus genes with an A. thaliana gene hit | 881 | 749 | 589 | 943 | 741 | 672 |
| Number of conserved B. napus genes with the orthologous regions in A. thaliana genome | 694 | 589 | 496 | 649 | 512 | 536 |
| Number of SNP tested | 172 | 123 | 177 | 135 | 95 | 133 |
| Percentage of resistance associated SNP | 0.58 | 0.00 | 9.60 | 2.96 | 5.26 | 0.00 |
| 1 | 0 | 17 | 4 | |||
| R Block | ChrA10 | ChrA02 | ChrA03 | ChrC09 | ChrC02 | ChrC03 |
| Start (in pb) | 11356437 | 990124 | 2231348 | 39930843 | 2882942 | 3138662 |
| End (in pb) | 13755613 | 2330220 | 3716463 | 44266268 | 5141051 | 5148532 |
| Interval length (in pb) | 2399176 | 1340096 | 1485115 | 4335425 | 2258109 | 2009870 |
| Number of B. napus genes | 499 | 295 | 340 | 635 | 381 | 417 |
| Gene density (nb genes/Mb) | 208 | 220 | 229 | 146 | 169 | 207 |
| Number of B. napus genes without an A. thaliana gene hit | 17 | 17 | 18 | 101 | 47 | 46 |
| Number of B. napus genes with an A. thaliana gene hit | 482 | 278 | 322 | 534 | 334 | 371 |
| Number of conserved B. napus genes with the orthologous regions in A. thaliana genome | 389 | 252 | 247 | 353 | 254 | 272 |
| Number of SNP tested | 237 | 27 | 104 | 83 | 34 | 45 |
| Percentage of resistance associated SNP | 0.84 | 3.70 | 8.65 | 0.00 | 8.82 | 0.00 |
| U Block | ChrA01 | ChrA03 | ChrA08 | ChrC01 | ChrC07 | ChrC03 |
| Start (in pb) | 342750 | 21617651 | 8000633 | 904490 | 36754713 | 50094421 |
| End (in pb) | 8931368 | 28404044 | 12976485 | 14682435 | 44511125 | 57998913 |
| Interval length (in pb) | 8588618 | 6786393 | 4975852 | 13777945 | 7756412 | 7904492 |
| Number of B. napus genes | 1644 | 1076 | 753 | 1925 | 1353 | 728 |
| Gene density (nb genes/Mb) | 191 | 159 | 151 | 140 | 174 | 92 |
| Number of B. napus genes without an A. thaliana gene hit | 121 | 121 | 77 | 271 | 167 | 145 |
| Number of B. napus genes with an A. thaliana gene hit | 1523 | 955 | 676 | 1654 | 1186 | 583 |
| Number of conserved B. napus genes with the orthologous regions in A. thaliana genome | 1213 | 751 | 545 | 1216 | 840 | 436 |
| Number of SNP tested | 267 | 311 | 125 | 256 | 111 | 198 |
| Percentage of resistance associated SNP | 3.00 | 0.64 | 51.20 | 16.02 | 6.31 | 3.54 |
| W block | ChrA10 | ChrA02 | ChrA03 | ChrC09 | ChrC02 | ChrC03 |
| Start (in pb) | 3385159 | 3848607 | 4036801–11110331 | 26106711 | 6797697 | 6146917 |
| End (in pb) | 9960308 | 6209759 | 6201708–11257398 | 39079875 | 11891907 | 8380744 |
| Interval length (in pb) | 6575149 | 2361152 | 1606719–147067 | 12973164 | 5094210 | 2233827 |
| Number of B. napus genes | 645 | 546 | 467–28 | 949 | 480 | 367 |
| Gene density (nb genes/Mb) | 98 | 231 | 216–190 | 73 | 94 | 164 |
| Number of B. napus genes without an A. thaliana gene hit | 110 | 62 | 32– 2 | 263 | 103 | 50 |
| Number of B. napus genes with an A. thaliana gene hit | 535 | 484 | 259–196 | 686 | 377 | 317 |
| Number of conserved B. napus genes with the orthologous regions in A. thaliana genome | 353 | 258 | 276 | 304 | 268 | 272 |
| Number of SNP tested | 537 | 131 | 81 | 6 | 28 | 126 |
| Percentage of resistance associated SNP | 0.19 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |