Table 2. Marker distributions of SNP markers associated with the swede vs. non-swede morphotype split in B. napus, along with the most closely associated markers from deep sequencing for the swede vs. non-swede split.
| Marker name | Chromosome | Position | non-swede allele | swede allele | located in gene | clear non-swede | clear swede | mixed | deletions | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| non-swede pop | swede pop | non-swede pop | swede pop | −log(p) | ||||||||
| split markers | nn | ss | sn | 00 | ||||||||
| chrA03_4639027 | chrA03 | 4639027 | 260 | 0 | 0 | 11 | 57.7 | Bna.VIN3.A03 | 260 | 11 | na | 0 |
| chrA04_12696607 | chrA04 | 12696607 | 0 | 8 | 260 | 3 | 55.8 | 263 | 8 | na | 0 | |
| chrA06_5607262 | chrA06 | 5607262 | 2 | 11 | 258 | 0 | 56.0 | Bna.CCR1.A06 | 257 | 6 | 8 | 0 |
| chrA06_5607744 | chrA06 | 5607744 | 0 | 9 | 260 | 2 | 56.3 | Bna.CCR1.A06 | ||||
| chrA06_5608016 | chrA06 | 5608016 | 1 | 11 | 259 | 0 | 56.9 | Bna.CCR1.A06 | ||||
| chrA06_5608089 | chrA06 | 5608089 | 1 | 11 | 259 | 0 | 56.9 | Bna.CCR1.A06 | ||||
| chrA06_5614815 | chrA06 | 5614815 | 0 | 8 | 260 | 3 | 55.8 | |||||
| chrA08_14983629 | chrA08 | 14983629 | 260 | 3 | 0 | 8 | 55.8 | Bna.TEM1.A08 | 263 | 8 | na | 0 |
| chrA09_11993194 | chrA09 | 11993194 | 0 | 8 | 260 | 3 | 55.8 | BnaA09g19070D | 263 | 8 | 0 | 0 |
| chrA09_11993662 | chrA09 | 11993662 | 0 | 8 | 260 | 3 | 55.8 | BnaA09g19070D | ||||
| chrA09_11995810 | chrA09 | 11995810 | 260 | 3 | 0 | 8 | 55.8 | |||||
| Bn-A09-p21922383 | chrA09 | 19312044 | 0 | 8 | 260 | 3 | 55.8 | 263 | 8 | na | 0 | |
| chrA09_32435440 | chrA09 | 32435440 | 2 | 11 | 258 | 0 | 56.0 | Bna.PHYA.A09 | 258 | 9 | 4 | 0 |
| chrA09_32435455 | chrA09 | 32435455 | 2 | 11 | 258 | 0 | 56.0 | Bna.PHYA.A09 | ||||
| chrA09_32437048 | chrA09 | 32437048 | 0 | 10 | 260 | 1 | 56.9 | Bna.PHYA.A09 | ||||
| chrA09_32441986 | chrA09 | 32441986 | 260 | 2 | 0 | 9 | 56.3 | BnaA09g48430D | ||||
| chrA10_17106726 | chrA10 | 17106726 | 0 | 8 | 260 | 3 | 55.8 | Bna.ELF7.A10 | 263 | 8 | 0 | 0 |
| chrA10_17106744 | chrA10 | 17106744 | 0 | 8 | 260 | 3 | 55.8 | Bna.ELF7.A10 | ||||
| chrA10_17108533 | chrA10 | 17108533 | 260 | 3 | 0 | 8 | 55.8 | Bna.ELF7.A10 | ||||
| chrC01_1447013 | chrC01 | 1447013 | 0 | 8 | 260 | 3 | 55.8 | 262 | 8 | 1 | 0 | |
| chrC01_1447235 | chrC01 | 1447235 | 0 | 9 | 260 | 2 | 56.3 | Bna.FD.C01 | ||||
| chrC01_1447273 | chrC01 | 1447273 | 260 | 2 | 0 | 9 | 56.3 | Bna.FD.C01 | ||||
| chrC01_1447516 | chrC01 | 1447516 | 0 | 9 | 260 | 2 | 56.3 | Bna.FD.C01 | ||||
| chrC01_1447693 | chrC01 | 1447693 | 260 | 2 | 0 | 9 | 56.3 | Bna.FD.C01 | ||||
| chrC01_1447972 | chrC01 | 1447972 | 0 | 9 | 260 | 2 | 56.3 | Bna.FD.C01 | ||||
| Bn-scaff_16770_1-p1357882 | chrC08 | 24087909 | 0 | 8 | 260 | 3 | 55.8 | 263 | 8 | na | 0 | |
| chrC08_36752901 | chrC08 | 36752901 | 260 | 1 | 0 | 10 | 56.9 | BnaC08g42670D | 259 | 9 | 3 | 0 |
| chrC08_36752954 | chrC08 | 36752954 | 0 | 10 | 260 | 1 | 56.9 | BnaC08g42670D | ||||
| chrC08_36753586 | chrC08 | 36753586 | 1 | 10 | 259 | 1 | 56.1 | |||||
| chrC08_36754224 | chrC08 | 36754224 | 0 | 9 | 260 | 2 | 56.3 | BnaC08g42680D | ||||
| chrC08_36755379 | chrC08 | 36755379 | 1 | 10 | 259 | 1 | 56.1 | |||||
| chrC08_36755562 | chrC08 | 36755562 | 0 | 9 | 260 | 2 | 56.3 | |||||
| Bn-scaff_16389_1-p12505 | chrC08 | 38113567 | 0 | 8 | 260 | 0 | 56.8 | 260 | 8 | na | 3 | |
| chrC09_43739821 | chrC09 | 43739821 | 0 | 8 | 260 | 3 | 55.8 | Bna.CO-li.C09 | 263 | 8 | na | 0 |
| Regions from deep sequencing | ||||||||||||
| chrA01_random_477115 | chrA01_random | 477115 | 5 | 8 | 255 | 3 | 51.6 | mads-box protein | ||||
| chrA03_6053137 | chrA03 | 6053137 | 8 | 9 | 252 | 2 | 49.6 | Bna.FRI.A03 | ||||
| chrA03_6243410 | chrA03 | 6243410 | 12 | 8 | 248 | 2 | 46.2 | Bna.FLC.A03 | ||||
| chrA04_12695445 | chrA04 | 12695445 | 3 | 8 | 257 | 3 | 53.3 | Bna.ELF3.A04 | ||||
| chrA05_5425314 | chrA05 | 5425314 | 1 | 8 | 259 | 3 | 55.0 | Bna.SPL3.A05 | ||||
| chrA05_9211460 | chrA05 | 9211460 | 4 | 9 | 256 | 2 | 52.9 | ubiquitin-conjugating enzyme family protein | ||||
| chrA07_23775522 | chrA07 | 23775522 | 3 | 8 | 257 | 3 | 53.3 | cinnamoyl- reductase 2-2 | ||||
| chrA10_1357187 | chrA10 | 1357187 | 1 | 8 | 259 | 3 | 55.0 | Bna.CRY2.A10 | ||||
| chrA10_13359226 | chrA10 | 13359226 | 1 | 9 | 259 | 2 | 55.4 | Bna.CO.A10 | ||||
| chrA10_14998679 | chrA10 | 14998679 | 3 | 10 | 257 | 1 | 54.4 | Bna.FLC.A10 | ||||
| chrAnn_random_610372 | chrAnn_random | 610372 | 10 | 11 | 250 | 0 | 49.4 | Bna.TFL1.Ann.random | ||||
| chrAnn_random_20504534 | chrAnn_random | 20504534 | 253 | 3 | 7 | 8 | 49.9 | Bna.VRN2.Ann.random | ||||
| chrC03_8403949 | chrC03 | 8403949 | 12 | 8 | 248 | 3 | 45.9 | Bna.FLC.C03 | ||||
| chrC03_random_5400150 | chrC03_random | 5400150 | 259 | 2 | 1 | 9 | 55.4 | Bna.FD.C03.random | ||||
The table shows the marker name, chromosomal position and the number of lines carrying either a non-swede or a swede allele in the respective non-swede and swede populations. The table also gives the −log(p-value) which used to determine the split markers, along with the gene ID or the name of the gene where the marker is located. If empty, the marker is non-genic. The markers with the highest −log(p-value) in each split region are shown in bold letters. The last four columns of the table show how many clear non-swede or swede haplotypes were counted, along with the number of mixed haplotypes and deletions. For regions only containing one marker, mixed haplotypes do not apply (na).