Table 3.
Single nucleotide polymorphism (SNP)-trait associations with P < 1.28e-05 (Bonferroni correction of α = 0.05) across the 214 inbreds of the winter trial.
| Trait | Abbrevation | SNP array code | Chr.a | Position (bp) | Allele 1/2 | P value | Effect allele 1/2 | PVb % |
|---|---|---|---|---|---|---|---|---|
| BLC | BLC.A1.w.1 | Bn-Scaffold000014-p848941 | A1 | 4971489 | C/T | 3.61e-07 | −0.25 | 11.54 |
| BLC.A9.w.1 | Bn-Scaffold000053-p927209 | A9 | 31325035 | G/T | 2.42e-06 | 0.46 | 27.72 | |
| BLC.A9.w.2 | Bn-Scaffold000077-p229981 | A9 | 32873917 | G/A | 2.56e-18 | −0.71 | 30.25 | |
| BLC.C5.w.1 | Bn-ctg7180011640898-p1781 | C5 | 8100723 | C/A | 1.67e-07 | −0.12 | 2.63 | |
| Simultaneous fit | 37.57 | |||||||
| BOF | BOF.A3.w.1 | Bn-Scaffold000090-p1008061 | A3 | 12037767 | C/T | 2.06e-06 | 1.04 | 14.67 |
| BOF.A0.w.1 | Bn-Scaffold000002-p4747623 | A0 | 43436688 | C/A | 2.02e-06 | −0.92 | 5.93 | |
| BOF.w.1 | Bn-ctg7180014734592-p70 | C/T | 5.00e-11 | −3.61 | 19.50 | |||
| BOF.w.1 | Bn-Scaffold000032-p1987471 | G/A | 1.88e-06 | 0.00 | 0.00 | |||
| Simultaneous fit | 34.04 | |||||||
| DAE | DAE.C2.w.1 | Bn-ctg7180014740377-p6847 | C2 | 8490346 | G/A | 3.00e-10 | −2.63 | 17.48 |
| DBH | DBH.A2.w.1 | Bn-Scaffold000041-p1259335 | A2 | 1420724 | C/T | 1.49e-06 | −2.41 | 9.09 |
| DBH.A3.w.1 | Bn-Scaffold000001-p1755819 | A3 | 9705421 | G/A | 1.16e-06 | 1.06 | 7.00 | |
| DBH.C2.w.1 | Bn-ctg7180014734362-p2505 | C2 | 43393890 | C/T | 4.00e-07 | 0.99 | 4.85 | |
| DBH.C8.w.1 | Bn-ctg7180014749298-p3202 | C8 | 36366606 | C/A | 1.26e-05 | 0.06 | 0.02 | |
| DBH.C8.w.2 | BN075005-0426 | C8 | 36713957 | C/T | 1.60e-06 | −4.76 | 10.70 | |
| DBH.w.1 | Bn-ctg7180014758607-p5732 | C/A | 3.16e-08 | 1.25 | 15.53 | |||
| Simultaneous fit | 37.89 | |||||||
| DTH | DTH.A9.w.1 | Bn-ctg7180014738208-p2460 | A9 | 2712534 | C/T | 5.72e-06 | 6.58 | 11.28 |
| EMR | EMR.C2.w.1 | Bn-ctg7180014740377-p6847 | C2 | 8490346 | G/A | 5.30e-08 | −2.41 | 13.80 |
| EMR.C5.w.1 | snp_BGA_4916 | C5 | 8326061 | G/A | 5.99e-13 | 2.63 | 28.40 | |
| Simultaneous fit | 28.76 | |||||||
| LOF | LOF.A7.w.1 | Bn-Scaffold000012-p2678894 | A7 | 10224576 | G/T | 9.45e-06 | 1.02 | 10.30 |
| LOF.C8.w.1 | Bn-ctg7180014749298-p3202 | C8 | 36366606 | C/A | 1.01e-06 | 0.02 | 0.00 | |
| LOF.C8.w.2 | Bn-ctg7180014732248-p707 | C8 | 36668359 | G/A | 1.01e-05 | −0.14 | 0.33 | |
| LOF.C9.w.1 | UQ03C0067042 | C9 | 3443632 | G/T | 4.01e-06 | 0.13 | 0.28 | |
| LOF.C9.w.2 | Bn-ctg7180014727337-p703 | C9 | 3705755 | G/A | 4.49e-06 | 1.52 | 11.34 | |
| LOF.C0.w.1 | Bn-ctg7180014738704-p1270 | C0 | 56734079 | C/T | 6.45e-07 | 1.40 | 12.25 | |
| Simultaneous fit | 29.69 | |||||||
| LOM | LOM.A0.w.1 | Bn-ctg7180014768425-p356 | A0 | 6888575 | G/A | 1.12e-05 | −1.08 | 9.34 |
| MYD | MYD.A6.w.1 | Bn-Scaffold000009-p1111712 | A6 | 18877680 | G/A | 5.55e-06 | −2.52 | 8.42 |
| PTH | PTH.C5.w.1 | Bn-ctg7180014734309-p3655 | C5 | 42616932 | G/T | 8.48e-10 | −17.55 | 15.77 |
| PTH.w.1 | Bn-Scaffold000002-p1766964 | G/A | 1.14e-06 | −3.28 | 2.07 | |||
| Simultaneous fit | 16.00 | |||||||
| SAW | SAW.C5.w.1 | Bn-ctg7180014771511-p3122 | C5 | 38132173 | C/T | 3.76e-06 | −0.57 | 9.50 |
| SAW.C7.w.1 | Bn-ctg7180011792923-p2625 | C7 | 39260815 | C/A | 1.24e-05 | −0.13 | 0.09 | |
| Simultaneous fit | 10.47 | |||||||
| WIH | WIH.A1.w.1 | Bn-Scaffold000033-p594082 | A1 | 19725610 | C/A | 2.63e-06 | 1.65 | 6.99 |
| WIH.A5.w.1 | Bn-Scaffold000075-p544803 | A5 | 14988536 | G/A | 9.93e-06 | 0.16 | 0.20 | |
| WIH.A7.w.1 | Bn-Scaffold000003-p6314140 | A7 | 19611453 | G/A | 1.85e-06 | 0.15 | 0.62 | |
| WIH.A7.w.2 | Bn-ctg7180014771687-p18821 | A7 | 22478215 | C/T | 1.29e-07 | 1.53 | 13.34 | |
| Simultaneous fit | 21.74 | |||||||
| ADL | ADL.A9.w.1 | Bn-Scaffold000393-p7477 | A9 | 28209051 | G/T | 7.92e-07 | 3.63 | 11.29 |
| AVA | AVA.A4.w.1 | Bn-Scaffold000060-p374024 | A4 | 7313760 | G/A | 4.14e-06 | −0.34 | 9.76 |
| CEL | CEL.A8.w.1 | Bn-ctg7180014734032-p1283 | A8 | 12795000 | G/A | 7.37e-07 | −0.19 | 11.77 |
| CEL.w.1 | Bn-ctg7180014725119-p15361 | C/T | 2.41e-06 | 0.07 | 1.19 | |||
| Simultaneous fit | 12.52 | |||||||
| ERA | ERA.A8.w.1 | Bn-Scaffold000015-p2264201 | A8 | 2155967 | G/A | 3.20e-09 | 12.67 | 14.56 |
| ERA.A8.w.2 | Bn-Scaffold000097-p710068 | A8 | 10137532 | C/A | 4.27e-07 | −15.03 | 16.10 | |
| ERA.A8.w.3 | Bn-ctg7180014771893-p599 | A8 | 10225801 | C/T | 1.39e-08 | −12.10 | 18.40 | |
| ERA.A9.w.1 | Bn-Scaffold000110-p349432 | A9 | 2949845 | G/A | 1.20e-13 | 23.58 | 30.54 | |
| ERA.C3.w.1 | Bn-ctg7180014717095-p1564 | C3 | 53048146 | G/T | 5.77e-25 | 22.79 | 39.38 | |
| ERA.C3.w.2 | Bn-ctg7180014745940-p4510 | C3 | 54189048 | C/A | 6.25e-09 | 10.57 | 10.28 | |
| ERA.C3.w.3 | Bn-ctg7180014734187-p1715 | C3 | 55135183 | C/A | 1.18e-12 | 6.63 | 4.34 | |
| ERA.C3.w.4 | Bn-ctg7180014745151-p4302 | C3 | 55545323 | C/T | 1.66e-07 | 17.84 | 29.75 | |
| Simultaneous fit | 73.96 | |||||||
| GSL | GSL.A2.w.1 | Bn-ctg7180014748062-p8451 | A2 | 23876499 | C/T | 8.15e-54 | −52.57 | 66.14 |
| GSL.A4.w.1 | Bn-Scaffold000070-p872779 | A4 | 10413384 | G/A | 8.74e-06 | 1.03 | 0.03 | |
| GSL.A8.w.1 | Bn-Scaffold000032-p328876 | A8 | 9593875 | G/A | 5.64e-09 | −0.68 | 0.01 | |
| GSL.A9.w.1 | Bn-Scaffold000051-p1490572 | A9 | 2505543 | C/T | 1.11e-05 | 24.99 | 27.04 | |
| GSL.A9.w.2 | Bn-Scaffold000040-p186360 | A9 | 2531260 | G/A | 2.27e-07 | 9.55 | 1.47 | |
| GSL.A9.w.3 | Bn-Scaffold000110-p573327 | A9 | 2744611 | C/T | 5.29e-20 | −4.74 | 0.55 | |
| GSL.A9.w.4 | BN049898-0393 | A9 | 30354078 | G/A | 5.87e-06 | 0.53 | 0.00 | |
| GSL.C1.w.1 | p5_8563_snp7 | C1 | 6390553 | G/A | 8.11e-07 | 9.46 | 0.43 | |
| GSL.C1.w.2 | Bn-ctg7180014746781-p3170 | C1 | 6421746 | G/A | 4.99e-06 | −8.77 | 0.47 | |
| GSL.C5.w.1 | Bn-ctg7180014774826-p5432 | C5 | 12122482 | C/T | 1.15e-08 | 1.47 | 0.02 | |
| GSL.C9.w.1 | Bn-ctg7180014767584-p2156 | C9 | 1664352 | C/T | 4.48e-07 | −1.87 | 0.06 | |
| GSL.C9.w.2 | Bn-Scaffold000118-p574793 | C9 | 1809481 | C/A | 5.32e-09 | 2.14 | 0.24 | |
| GSL.w.1 | Bn-Scaffold000092-p984593 | G/A | 8.45e-07 | 1.61 | 0.13 | |||
| GSL.w.2 | Bn-Scaffold000094-p109812 | G/A | 4.26e-06 | 7.72 | 3.06 | |||
| Simultaneous fit | 76.71 | |||||||
| HCL | HCL.A8.w.1 | Bn-Scaffold000106-p682998 | A8 | 1027180 | G/A | 1.28e-05 | 0.29 | 11.36 |
| HCL.A8.w.2 | Bn-Scaffold000010-p3026578 | A8 | 13719625 | G/T | 3.72e-07 | 0.39 | 16.83 | |
| HCL.C8.w.1 | Bn-ctg7180014732414-p9149 | C8 | 25746465 | G/A | 1.25e-05 | −0.37 | 3.85 | |
| HCL.w.1 | Bn-ctg7180014709967-p3714 | G/A | 2.52e-14 | −0.44 | 25.82 | |||
| HCL.w.2 | Bn-ctg7180014725119-p15361 | C/T | 1.04e-09 | 0.11 | 1.40 | |||
| HCL.w.3 | Bn-Scaffold000031-p674411 | C/T | 9.09e-06 | −0.09 | 0.15 | |||
| Simultaneous fit | 41.22 | |||||||
| LIA | LIA.A7.w.1 | Bn-Scaffold000018-p869005 | A7 | 278027 | G/A | 9.28e-06 | 0.81 | 12.16 |
| LIA.A8.w.1 | Bn-Scaffold000097-p710068 | A8 | 10137532 | C/A | 7.63e-06 | 1.44 | 18.55 | |
| LIA.A9.w.1 | Bn-Scaffold000110-p349432 | A9 | 2949845 | G/A | 2.52e-07 | −1.47 | 24.65 | |
| LIA.C2.w.1 | Bn-ctg7180014733329-p2936 | C2 | 44856112 | C/T | 5.22e-06 | −0.80 | 6.43 | |
| LIA.C3.w.1 | Bn-ctg7180014726380-p989 | C3 | 5337555 | C/A | 5.96e-17 | 1.39 | 28.96 | |
| Simultaneous fit | 43.87 | |||||||
| NDF | NDF.C2.w.1 | Bn-ctg7180014746332-p7435 | C2 | 45024709 | G/T | 1.03e-07 | 0.72 | 14.33 |
| NDF.C3.w.1 | Bn-Scaffold000032-p835836 | C3 | 53374601 | G/T | 6.60e-06 | −0.13 | 0.36 | |
| Simultaneous fit | 14.60 | |||||||
| OIL | OIL.A1.w.1 | Bn-Scaffold000011-p1364245 | A1 | 2717777 | G/A | 1.05e-05 | −1.57 | 5.06 |
| OIL.C3.w.1 | Bn-ctg7180014717095-p1564 | C3 | 53048146 | G/T | 5.02e-07 | 1.50 | 11.70 | |
| Simultaneous fit | 20.21 | |||||||
| OLA | OLA.A9.w.1 | Bn-Scaffold000110-p349432 | A9 | 2949845 | G/A | 1.98e-20 | 5.31 | 30.93 |
| OLA.A9.w.2 | BN049898-0393 | A9 | 30354078 | G/A | 3.04e-06 | 0.59 | 0.15 | |
| OLA.A9.w.3 | Bn-ctg7180014758772-p913 | A9 | 30359414 | C/A | 4.35e-06 | −0.41 | 0.11 | |
| OLA.C3.w.1 | Bn-ctg7180014717095-p2357 | C3 | 53047354 | C/T | 8.18e-08 | 4.40 | 19.63 | |
| OLA.C8.w.1 | Bn-ctg7180014732414-p9149 | C8 | 25746465 | G/A | 5.87e-06 | 1.58 | 0.77 | |
| OLA.A0.w.1 | Bn-Scaffold000010-p2545490 | A0 | 37536253 | G/T | 1.60e-08 | 4.62 | 24.24 | |
| OLA.w.1 | Bn-ctg7180014709374-p768 | C/T | 4.72e-06 | 0.82 | 0.61 | |||
| OLA.w.2 | Bn-ctg7180014709661-p1084 | C/A | 2.83e-07 | 1.62 | 0.87 | |||
| OLA.w.3 | Bn-ctg7180014724744-p69 | G/A | 6.64e-06 | 0.83 | 1.41 | |||
| Simultaneous fit | 39.86 | |||||||
| PRT | PRT.C6.w.1 | Bn-ctg7180014756759-p1575 | C6 | 1625464 | G/T | 1.69e-06 | 1.03 | 10.76 |
| SUL | SUL.A2.w.1 | Bn-ctg7180014748062-p8451 | A2 | 23876499 | C/T | 1.93e-52 | −0.34 | 67.34 |
| SUL.A9.w.1 | Bn-Scaffold000040-p186360 | A9 | 2531260 | G/A | 3.68e-06 | 0.01 | 0.04 | |
| SUL.A9.w.2 | Bn-Scaffold000110-p573327 | A9 | 2744611 | C/T | 3.49e-16 | 0.00 | 0.00 | |
| Simultaneous fit | 68.06 | |||||||
For abbreviations of the traits see Table 1.
a
Chr. is the chromosome of the respective SNP; SNPs marked with a A0 or C0 could only be assigned to the genome of B. oleracea or B. rapa but not to a specific chromosome.
b
PV is the proportion of the explained phenotypic variance (%).