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Table 3 Number of significant SNPs influencing direct genetic effects and inflation factor for body weight recorded at different ages

From: Genome-wide associations and detection of potential candidate genes for direct genetic and maternal genetic effects influencing dairy cattle body weight at different ages

Trait Dependent variable Polygenic effect FDRa Bonferronib λ
BW0 Phen \({\mathbf{A}}\) 1213 64 1.92
\({\mathbf{G}}\) 7 3 0.96
LOCO 2268 125 2.22
LOCO_pruned 394 43 1.97
LOCO_SEG40 1811 103 2.06
LOCO_SEG441 80 17 1.29
LOCO_SEG864 41 12 1.18
LOCO + PC20 1132 73 1.90
LOCO + CHR_PC20 16 7 0.93
dDRP \({\mathbf{A}}\) 1463 104 1.96
\({\mathbf{G}}\) 15 6 0.96
LOCO 2212 163 2.19
LOCO_pruned 414 54 1.91
LOCO_SEG40 1802 143 2.07
LOCO_SEG441 103 23 1.28
LOCO_SEG864 57 15 1.17
LOCO + PC20 1180 108 1.87
LOCO + CHR_PC20 13 8 0.90
BW23 Phen \({\mathbf{A}}\) 11 0 1.17
\({\mathbf{G}}\) 0 0 0.99
LOCO + CHR_PC20 0 0 0.66
LOCO + CHR_PC10 0 0 0.93
dDRP \({\mathbf{A}}\) 22 5 1.33
\({\mathbf{G}}\) 3 2 1.00
LOCO + CHR_PC20 0 0 0.70
LOCO + CHR_PC10 1 1 0.96
BW1314 Phen \({\mathbf{A}}\) 47 14 1.46
\({\mathbf{G}}\) 5 3 0.97
LOCO + CHR_PC20 2 2 0.72
LOCO + CHR_PC10 7 4 0.98
dDRP \({\mathbf{A}}\) 50 17 1.45
\({\mathbf{G}}\) 7 6 0.97
LOCO + CHR_PC20 3 3 0.72
LOCO + CHR_PC10 12 6 0.97
  1. FDR: false discovery rate; Bonferroni: Bonferroni correction; λ: inflation factor; BW0: body weight recorded at birth; BW23: body weight recorded at 2 to 3 month of age; BW1314: body weight recorded at 13 to 14 months of age; dDRP: de-regressed proofs for the direct genetic effect; mDRP: de-regressed proofs for the maternal genetic effect; LOCO_pruned: LOCO based on pruned SNPs
  2. aNumber of significant SNPs according to false discovery rate
  3. bNumber of significant SNPs according to Bonferroni-correction