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