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Table 1 Single-nucleotide polymorphisms (SNP) with genome-wide significant (p < 10–7) associations with weight gain (WG), relative weight gain (RG), atom % 13C muscle (AMC), atom % 15N muscle (AMN), atom % 13C liver (ALC), and atom % 15N liver (ALN)

From: Genomic regions and signaling pathways associated with indicator traits for feed efficiency in juvenile Atlantic salmon (Salmo salar)

Trait Chr SNP Base pair A1 A2 Freq b se p
WG 5 ctg7180001180119_4244_SCT 33597277 C T 0.141 1.063 0.190 2.28E−08
5 ctg7180001923117_1435_SAG 31819838 A G 0.097 1.153 0.215 7.63E−08
9 ctg7180001197157_4756_SAG 89517134 G A 0.356 − 1.016 0.166 9.54E−10
9 ctg7180001818540_14626_SGT 96172057 G T 0.233 0.991 0.163 1.23E−09
9 ctg7180001818540_11784_SCT 96174899 C T 0.234 0.976 0.163 1.98E−09
9 ctg7180001664612_2468_SCT 91842480 C T 0.234 0.967 0.163 3.00E−09
9 ctg7180001664612_1619_SAG 91841631 G A 0.234 0.958 0.163 4.19E−09
9 ctg7180001545661_2981_SGT 16416138 G T 0.402 0.819 0.140 4.53E−09
9 ctg7180001832507_11515_SCG 75470675 G C 0.448 − 0.847 0.145 5.35E−09
9 ctg7180001868348_9058_SAG 15945100 G A 0.492 − 0.781 0.137 1.18E−08
9 ctg7180001628780_1051_SAG 17214390 G A 0.414 − 0.871 0.153 1.20E−08
9 ctg7180001197157_4700_SAC 89517078 A C 0.311 0.859 0.151 1.40E−08
9 ctg7180001894494_11001_SAG 89556217 G A 0.310 0.851 0.152 2.08E−08
9 ctg7180001911598_32299_SCT 17106888 C T 0.436 − 0.808 0.146 2.88E−08
9 ctg7180001802227_6890_SAC 78211162 A C 0.216 0.972 0.176 3.34E−08
9 ctg7180001806806_477_SAC 78242149 A C 0.216 0.969 0.176 3.67E−08
9 ctg7180001588841_1060_SGT 86047894 G T 0.234 0.855 0.155 3.77E−08
9 ctg7180001926947_6570_SGT 81306559 T G 0.247 0.885 0.161 3.86E−08
9 ctg7180001380355_4100_SGT 96979010 G T 0.422 0.721 0.133 5.50E−08
9 ctg7180001921692_473_SGT 95413530 G T 0.212 0.946 0.175 6.46E−08
9 ctg7180001898405_11116 82286805 A C 0.312 0.818 0.152 7.65E−08
9 ctg7180001678561_512_SGT 90982168 T G 0.335 0.769 0.143 7.99E−08
9 GCR_cBin45958_Ctg1_101 19444985 G A 0.386 0.825 0.154 8.16E−08
9 ctg7180001859612_1950_SCT 106163425 T C 0.426 0.837 0.157 9.45E−08
20 ctg7180001900661_2996_SAG 29391087 A G 0.472 0.651 0.116 1.97E−08
20 ctg7180001900661_8312_SAC 29385772 A C 0.472 0.632 0.116 4.75E−08
20 ctg7180001403181_749_SGT 32398670 T G 0.413 0.701 0.131 7.97E−08
RG 9 ctg7180001820745_5080_SAG 23240272 G A 0.202 2.191 0.337 7.98E−11
9 ctg7180001604256_10823_SAG 23113694 G A 0.156 2.406 0.380 2.39E−10
9 GCR_cBin45958_Ctg1_101 19444985 G A 0.386 2.035 0.339 1.99E−09
9 ctg7180001789610_1630_SCT 25039628 C T 0.349 − 1.669 0.288 7.03E−09
9 ctg7180001841302_7054_SGT 21739717 G T 0.184 2.112 0.367 8.33E−09
9 ctg7180001841302_7076_SGT 21739695 T G 0.191 2.046 0.365 2.02E−08
9 ctg7180001809374_3372_SCT 19466507 C T 0.373 1.900 0.343 3.03E−08
9 ctg7180001847789_6042_SAG 16428841 A G 0.263 2.034 0.367 3.07E−08
9 ctg7180001857693_2711_SAG 85086045 G A 0.278 1.814 0.329 3.60E−08
9 ctg7180001545661_2981_SGT 16416138 G T 0.402 1.704 0.310 3.68E−08
9 ctg7180001468960_5703_SCT 14756989 C T 0.226 2.035 0.370 3.83E−08
9 ctg7180001931759_8478_SAG 16329499 G A 0.217 2.046 0.376 5.14E−08
9 ctg7180001898949_10269_SAG 22638682 A G 0.482 − 1.584 0.292 5.86E−08
AMC 9 ctg7180001628780_1051_SAG 17214390 G A 0.415 − 0.013 0.002 1.04E−09
9 ctg7180001820745_5080_SAG 23240272 G A 0.202 0.013 0.002 2.45E−09
9 ctg7180001789610_1630_SCT 25039628 C T 0.349 − 0.011 0.002 5.22E−09
9 ctg7180001763729_3905_SAG 15474718 A G 0.283 0.013 0.002 8.27E−09
9 ctg7180001763729_4055_SGT 15474568 T G 0.283 0.013 0.002 1.14E−08
9 ctg7180001872184_4046_SAC 59521565 A C 0.267 − 0.012 0.002 1.69E−08
9 ctg7180001847789_6042_SAG 16428841 A G 0.261 0.013 0.002 1.91E−08
9 ctg7180001903467_551_SGT 30327474 T G 0.175 − 0.013 0.002 2.06E−08
9 ctg7180001700380_482_SGT 15707203 G T 0.282 0.013 0.002 2.08E−08
9 GCR_cBin45958_Ctg1_101 19444985 G A 0.385 0.012 0.002 3.47E−08
9 ctg7180001911598_32299_SCT 17106888 C T 0.436 − 0.011 0.002 3.78E−08
9 ctg7180001903534_19011_SGT 13431163 T G 0.283 − 0.013 0.002 3.98E−08
9 ctg7180001872184_453_SCT 59517972 T C 0.265 − 0.012 0.002 4.40E−08
9 ctg7180001604256_10823_SAG 23113694 G A 0.157 0.013 0.002 4.58E−08
9 ctg7180001343223_1775_SCT 67759885 T C 0.411 0.011 0.002 5.85E−08
9 ctg7180001545661_2981_SGT 16416138 G T 0.401 0.011 0.002 6.44E−08
9 ctg7180001833924_2266_SCT 24557694 T C 0.429 0.011 0.002 6.65E−08
9 ctg7180001794986_4059_SAC 20044519 C A 0.262 − 0.012 0.002 6.93E−08
9 ctg7180001898949_10269_SAG 22638682 A G 0.481 − 0.010 0.002 7.33E−08
AMN 9 ctg7180001820745_5080_SAG 23240272 G A 0.202 0.034 0.005 3.24E−11
9 ctg7180001841302_7054_SGT 21739717 G T 0.184 0.036 0.006 1.47E−10
9 ctg7180001604256_10823_SAG 23113694 G A 0.157 0.037 0.006 1.87E−10
9 ctg7180001841302_7076_SGT 21739695 T G 0.192 0.033 0.006 1.33E−09
9 ctg7180001898949_10269_SAG 22638682 A G 0.481 − 0.027 0.004 1.51E−09
9 ctg7180001909530_3368_SAC 30671958 A C 0.289 0.032 0.006 1.69E−08
9 ctg7180001857693_2711_SAG 85086045 G A 0.278 0.028 0.005 2.38E−08
9 ctg7180001628780_1051_SAG 17214390 G A 0.415 − 0.028 0.005 2.78E−08
9 ctg7180001912930_10973_SAC 59822403 C A 0.446 − 0.026 0.005 4.30E−08
9 ctg7180001343223_1775_SCT 67759885 T C 0.411 0.026 0.005 4.62E−08
9 ctg7180001911598_32299_SCT 17106888 C T 0.436 − 0.026 0.005 8.19E−08
9 ctg7180001254975_135_SCT 30005989 T C 0.328 0.017 0.003 9.72E−08
ALC 12 ctg7180001233434_1518_SCT 45935004 C T 0.418 − 0.009 0.001 1.79E−10
12 ctg7180001878331_16006_SAG 67415693 A G 0.411 − 0.008 0.001 3.95E−10
12 ctg7180001589944_2780_SAC 67420787 C A 0.410 − 0.008 0.001 5.82E−10
12 ctg7180001917752_6118_SAG 68229784 A G 0.342 − 0.008 0.001 6.01E−09
12 ctg7180001926810_6994_SGT 59975663 T G 0.445 − 0.008 0.001 8.58E−09
12 ctg7180001924417_6623_SAC 66355729 A C 0.178 − 0.010 0.002 1.38E−08
12 ctg7180001863800_134_SAC 54013376 C A 0.495 − 0.008 0.001 1.71E−08
12 ctg7180001930970_12364_SCT 34715679 C T 0.460 0.007 0.001 1.86E−08
12 ctg7180001787629_3714_SGT 63703424 G T 0.441 − 0.008 0.001 1.92E−08
12 ctg7180001926810_5584_SCT 59974253 C T 0.435 − 0.008 0.001 2.17E−08
12 ctg7180001759831_1827_SCT 45916216 C T 0.364 − 0.007 0.001 2.33E−08
12 ctg7180001481690_187_SAG 73548289 G A 0.438 − 0.008 0.001 3.22E−08
12 ctg7180001912956_2486_SGT 36748230 T G 0.416 − 0.007 0.001 3.25E−08
12 ctg7180001926810_6801_SAG 59975470 A G 0.444 − 0.007 0.001 3.28E−08
12 ctg7180001899463_4736_SCT 45925520 C T 0.365 − 0.007 0.001 3.78E−08
12 ctg7180001874153_6984_SAC 59968424 C A 0.444 − 0.007 0.001 3.82E−08
12 ctg7180001903261_15275_SCT 36741726 T C 0.419 − 0.007 0.001 4.80E−08
12 ctg7180001802518_8127_SAG 38630722 G A 0.264 − 0.008 0.002 5.60E−08
12 ctg7180001895532_9980_SAC 52536172 C A 0.150 − 0.010 0.002 8.47E−08
ALN 9 ctg7180001820745_5080_SAG 23240272 G A 0.202 0.034 0.005 1.71E−10
9 ctg7180001604256_10823_SAG 23113694 G A 0.157 0.037 0.006 3.95E−10
9 ctg7180001902776_3165 44544043 A G 0.030 − 0.082 0.013 1.00E−09
9 ctg7180001297112_1053_SAC 44743511 C A 0.029 − 0.079 0.013 3.51E−09
9 ctg7180001846444_1581_SAG 27624708 G A 0.050 − 0.060 0.010 3.64E−09
9 ctg7180001898949_10269_SAG 22638682 A G 0.481 − 0.027 0.005 6.84E−09
9 ctg7180001841823_6182_SGT 27830435 G T 0.050 − 0.059 0.010 8.19E−09
9 ctg7180001841823_8622_SAG 27832875 A G 0.051 − 0.058 0.010 9.34E−09
9 ctg7180001897675_6237_SCG 26358698 C G 0.050 − 0.058 0.010 1.04E−08
9 ctg7180001841302_7076_SGT 21739695 T G 0.192 0.033 0.006 1.28E−08
9 ctg7180001841302_7054_SGT 21739717 G T 0.184 0.033 0.006 1.39E−08
9 ctg7180001516979_6848_SCT 26634813 T C 0.050 − 0.058 0.010 1.54E−08
9 ctg7180001905112_13597_SAC 25462494 C A 0.061 − 0.052 0.009 1.57E−08
9 ctg7180001516979_7200_SCT 26635165 C T 0.050 − 0.057 0.010 2.04E−08
9 GCR_cBin3500_Ctg1_117 27426856 C G 0.081 − 0.044 0.008 3.60E−08
9 ctg7180001927229_6536 84462126 A G 0.448 0.027 0.005 4.58E−08
9 ctg7180001905111_1804_SAC 25477875 C A 0.062 − 0.050 0.009 4.77E−08
9 ctg7180001322796_3617_SGT 50798901 G T 0.113 − 0.037 0.007 6.77E−08
9 ctg7180001796082_675_SAC 19872408 C A 0.148 − 0.035 0.006 7.31E−08
  1. SNPs are ranked within trait and chromosome. Significant associations that are common between traits are indicated in italic characters
  2. A1: reference allele; A2: alternative allele; Freq: frequency of A1; b: SNP effect (the effect of increasing the genotype with one extra reference allele) with associated standard error (se) and p-value (p)