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Table 3 Single nucleotide polymorphism (SNP)-trait/-gene associations with P < 0.0001 across all inbreds

From: Seedling development traits in Brassica napus examined by gene expression analysis and association mapping

Trait SNP array code Chr. a Position (bp) Allele 1/2 P value Effect allele P V b (%)
       1/2  
APL Bn-ctg7180014739201-p14151 C3 23542236 C/T 1.59e-05 4.16 4.10
  Bn-ctg7180014739201-p15057 C3 23543142 G/A 3.63e-05 3.93 3.54
Simultaneous fit      3.56
CEL16 Bn-Scaffold000020-p837037 A8 18471964 G/A 3.21e-05 2.45 3.52
FBP Bn-ctg7180014767990-p1760 A9 27053307 G/T 9.56e-05 1.33 2.96
  p8_2822_snp11 C2 2008764 G/A 3.33e-05 1.56 3.89
  Bn-ctg7180014769003-p8702 C7 23881203 C/A 8.25e-07 -1.88 5.56
  Bn-ctg7180014750397-p3915 C8 28994818 G/A 7.42e-05 1.56 3.37
  Bn-ctg7180014767990-p1760 C8 29012996 G/T 9.56e-05 1.33 2.96
  Bn-ctg7180014767990-p516 C8 29014240 C/T 8.61e-05 -1.30 3.03
Simultaneous fit      10.37
GER1 Bn-ctg7180014741426-p3290 C1 40791705 C/A 3.44e-05 2.54 3.53
  Bn-ctg7180014744563-p4387 C2 45592086 C/T 6.28e-06 2.43 4.38
  Bn-ctg7180014744563-p4646 C2 45592345 G/A 2.92e-06 2.54 4.72
Simultaneous fit      7.50
GRF1 Bn-Scaffold000031-p1055544 A2 24176291 C/T 2.68e-05 4.44 3.58
MyAP Bn-Scaffold000033-p1183872 A1 23083128 G/A 4.32e-05 2.54 3.46
  p5_8783_snp47 C2 16695448 G/A 3.99e-05 -4.28 4.01
  Bn-ctg7180014755468-p3376 C5 45992213 G/A 4.66e-05 -3.04 3.60
Simultaneous fit      9.66
NOI Bn-ctg7180014731124-p2983 C9 52425308 C/A 7.91e-06 -3.30 4.92
PECT Bn-ctg7180014744894-p12663 C4 5903754 G/T 2.75e-05 3.95 3.49
  Bn-ctg7180014772336-p17139 C7 38391732 C/A 2.93e-05 5.11 3.62
Simultaneous fit      7.03
PK Bn-Scaffold000031-p1055544 A2 24176291 C/T 5.64e-05 2.55 3.29
  Bn-Scaffold000005-p1543856 A3 1543856 G/A 9.96e-05 1.85 3.14
  p5_8783_snp47 C2 16695448 G/A 9.42e-05 -2.83 3.63
  Bn-ctg7180014730936-p7448 C7 43801848 G/T 6.03e-05 -2.36 3.25
Simultaneous fit      10.04
RBC Bn-Scaffold000060-p721650 A4 6466112 C/T 7.19e-17 -3.36 13.53
  BN051924-0307 A4 6928299 C/T 2.66e-06 -2.67 4.46
  BN051924-0307 C4 36645724 C/T 2.66e-06 -2.67 4.46
Simultaneous fit      13.68
SPS BN043454-0504 A9 27982958 G/A 4.52e-05 2.88 3.36
  p5_8783_snp47 C2 16695448 G/A 8.09e-05 -4.10 3.68
Simultaneous fit      6.57
UBP15 Bn-Scaffold000003-p3164670 A7 14616879 G/T 9.71e-06 2.34 3.93
VPS2 Bn-Scaffold000004-p4962830 A5 4962830 G/A 8.30e-05 -5.07 3.13
  Bn-ctg7180014738809-p1661 C9 46132950 C/T 6.46e-05 -2.76 3.22
Simultaneous fit      5.95
ASR UQ10A0010802 A10 11497630 C/T 7.41e-05 -0.10 3.67
  Bn-ctg7180014733191-p16993 C2 11324627 G/A 8.80e-05 -0.10 3.02
  Bn-ctg7180014737642-p1736 C2 11521447 C/T 4.55e-05 -0.11 3.48
  Bn-ctg7180014722959-p1362 C2 11538841 G/A 7.27e-05 -0.10 3.08
  Bn-ctg7180014722959-p3680 C2 11541159 C/T 9.48e-05 0.10 3.62
  Bn-ctg7180014761021-p763 C2 11545317 G/T 8.56e-05 0.10 3.00
  Bn-ctg7180014761021-p1313 C2 11545867 G/T 6.38e-05 0.11 3.82
  Bn-ctg7180014746007-p654 C2 11575760 G/A 8.93e-05 -0.11 3.86
  Bn-ctg7180014747519-p4930 C2 11581331 C/A 6.89e-05 -0.10 3.77
  Bn-ctg7180014733329-p2936 C2 50724670 C/T 5.31e-05 0.08 3.45
  Bn-ctg7180014744693-p3728 C3 13670419 C/T 3.76e-05 0.09 3.77
  Bn-ctg7180014758876-p10173 C5 41416666 C/T 4.60e-05 0.08 3.67
  Bn-ctg7180014715862-p5107 C7 20535180 C/T 5.26e-06 0.09 4.57
  Bn-ctg7180014711252-p832 C7 20577577 G/A 1.82e-05 0.08 3.78
  Bn-ctg7180014711906-p3935 C7 21407038 C/T 3.44e-05 0.10 4.21
  Bn-ctg7180014711906-p4070 C7 21407173 C/T 2.12e-05 0.10 4.42
  Bn-ctg7180014769003-p8702 C7 23881203 C/A 9.20e-05 0.09 3.42
  Bn-ctg7180014760120-p14495 C7 37894126 G/A 8.06e-05 -0.08 4.23
  Bn-ctg7180014765154-p10081 C9 1282177 C/T 1.57e-05 -0.08 4.28
  Bn-ctg7180014758656-p7160 C9 2835355 C/A 2.53e-06 0.09 4.87
  Bn-ctg7180014722956-p4266 Scaffold01930 3005 G/T 3.40e-05 -0.11 3.63
Simultaneous fit      20.31
CIR UQ10A0010802 A10 11497630 C/T 1.75e-05 0.03 4.16
  BN064849-0420 C5 12385920 C/T 5.14e-05 0.04 3.32
Simultaneous fit      7.65
H2O Bn-Scaffold000005-p1543856 A3 1543856 G/A 7.66e-05 0.31 3.68
LA08 UQ10C0016384 C7 32496339 C/T 4.04e-06 -0.31 4.34
LA10 UQ10C0016384 C7 32496339 C/T 2.18e-06 -0.60 4.46
LA12 UQ10C0016384 C7 32496339 C/T 4.16e-05 -0.83 3.36
MAD BN054115-0054 A3 2852962 G/A 8.42e-05 0.27 3.79
  BN054115-0054 C3 3505618 G/A 8.42e-05 0.27 3.79
  UQ10C0016384 C7 32496339 C/T 3.16e-05 -0.23 3.44
Simultaneous fit      6.75
MAJ BN054115-0054 A3 2852962 G/A 5.11e-05 0.26 3.96
  Bn-Scaffold000004-p5075668 A5 5075668 C/T 8.74e-05 0.23 3.40
  Bn-Scaffold000058-p205581 A9 9133931 G/A 7.34e-05 0.19 3.27
  BN054115-0054 C3 3505618 G/A 5.11e-05 0.26 3.96
  UQ10C0016384 C7 32496339 C/T 5.59e-05 -0.21 3.24
Simultaneous fit      10.14
MID UQ10C0016384 C7 32496339 C/T 5.63e-05 -0.13 3.25
PER UQ10C0016384 C7 32496339 C/T 1.93e-05 -0.93 3.57
PRA UQ10C0204660 C4 12991242 C/T 3.28e-05 -0.08 3.64
ROU UQ10A0010802 A10 11497630 C/T 1.49e-05 0.04 4.46
  Bn-ctg7180014761021-p1313 C2 11545867 G/T 9.46e-05 -0.04 3.83
  Bn-ctg7180014715862-p5107 C7 20535180 C/T 1.02e-05 -0.03 4.38
  Bn-ctg7180014711252-p832 C7 20577577 G/A 4.92e-05 -0.03 3.39
  Bn-ctg7180014711906-p3935 C7 21407038 C/T 3.21e-05 -0.04 4.57
  Bn-ctg7180014711906-p4070 C7 21407173 C/T 2.00e-05 -0.04 4.79
  Bn-ctg7180014765154-p10081 C9 1282177 C/T 1.78e-05 0.03 4.45
  Bn-ctg7180014758656-p7160 C9 2835355 C/A 1.49e-05 -0.03 4.44
  Bn-ctg7180014722956-p4266 Scaffold01930 3005 G/T 9.35e-05 0.03 3.33
Simultaneous fit      13.23
SOY Bn-Scaffold000024-p2080233 A6 10852718 G/T 7.56e-05 0.02 3.42
  UQ10A0010802 A10 11497630 C/T 4.70e-05 0.02 3.99
  Bn-ctg7180014715862-p5107 C7 20535180 C/T 4.27e-06 -0.02 4.48
  Bn-ctg7180014711252-p832 C7 20577577 G/A 6.05e-06 -0.02 4.21
  Bn-ctg7180014760120-p14233 C7 37893864 C/T 2.33e-05 0.02 3.78
  Bn-ctg7180014760120-p14495 C7 37894126 G/A 3.73e-05 0.02 4.53
  Bn-ctg7180014765154-p10081 C9 1282177 C/T 5.69e-05 0.02 3.76
Simultaneous fit      14.07
SPD Bn-Scaffold000034-p1847442 A1 24476947 G/A 9.46e-05 1.68 3.21
  Bn-Scaffold000017-p525526 A7 5241142 C/T 2.47e-05 -1.11 3.61
  snp_BGA_4772 A10 11407615 C/T 8.35e-05 2.47 3.88
  Bn-ctg7180014759380-p14755 C1 1310534 G/A 1.84e-05 -1.96 4.12
  p5_8783_snp47 C2 16695448 G/A 2.40e-05 1.88 4.21
  Bn-ctg7180014762070-p3737 C5 1112869 C/T 4.52e-05 -1.15 3.36
  Bn-ctg7180014771511-p3122 C5 40979968 C/T 3.38e-05 -1.37 3.44
  Bn-ctg7180014748477-p7622 C8 19334419 G/T 4.00e-05 -1.71 3.38
  Bn-ctg7180014710293-p19591 C8 19418083 C/T 4.89e-05 -1.83 3.43
Simultaneous fit      20.10
  1. For abbreviations of the traits see Tables 1 and 2.
  2. aChr. is the chromosome of the respective SNP.
  3. b P V is the proportion of the explained phenotypic variance.