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Table 2 Association statistics for candidate mutations at recessive loci

From: Non-additive QTL mapping of lactation traits in 124,000 cattle reveals novel recessive loci

Trait QTL Chr8_44 Mb Chr25_24-27 Mb Chr25_35 Mb Chr27_15 Mb Chr28_6-7 Mb
  Position g.8.44119667T>A g.25.24904939C>T g.25.25161613G>A g.25.26689392G>A g.35975573C>T g.27.15491451C>T g.28.7922207G>A
rsID rs483207034 rs453138457 rs471945767 rs1116814780 NA rs523126258 NA
Candidate gene DOCK8 IL4R KIAA0556 ITGAL LRCH4 SLC25A4 RBM34
VEP AA substitution AA substitution AA substitution Premature stop Premature stop AA substitution Premature stop
Protein impact p.His649Leu p.Pro151Leu p.Arg158His p.Trp731* p.Arg123* p.Thr197Met p.Arg55*
SIFT score 0 0.02 0.14 NA NA 0.01 NA
MAF (HF/J/ALL) 0.013/0.059/0.03 0.001/0.043/0.017 0.001/0.042/0.016 0.002/0.049/0.019 0.034/0.001/0.031 0.046/0.001/0.027 0.044/0.004/0.043
Milk (L/lactation) a ± sd − 129.181 ± 23.604 − 218.249 ± 39.988 − 279.656 ± 49.108 − 169.491 ± 37.441 − 153.832 ± 24.201 − 123.607 ± 25.598 − 106.454 ± 17.786
p 4.43E−08 4.82E−08 1.24E−08 5.99E−06 2.05E−10 1.38E−06 2.16E−09
d ± sd 109.644 ± 23.905 215.668 ± 40.648 269.952 ± 49.887 161.062 ± 37.587 97.084 ± 245.537 120.056 ± 25.895 106.246 ± 17.929
p 4.51E−06 1.12E−07 6.26E−08 1.83E−08 7.60E−05 3.55E+06 3.10E−09
k 0.849 0.988 0.965 0.95 0.63 0.971 0.998
Fat (kg/lactation) a ± sd − 5.643 ± 1.177 − 11.827 ± 2.109 − 15.569 ± 2.359 − 9.708 ± 1.870 − 6.849 ± 1.137 − 7.075 ± 1.201 − 5.170 ± 0.866
p 1.66E−06 2.05E−08 4.10E−11 2.09E−07 1.71E−09 3.84E−09 2.40E−09
d ± sd 5.110 ± 1.181 11.339 ± 2.087 14.744 ± 2.372 9.022 ± 1.910 4.412 ± 1.133 5.729 ± 1.249 5.546 ± 0.859
p 1.51E−05 5.56E−08 5.08E−10 2.33E−06 9.82E−05 4.48E−06 1.06E−10
k 0.906 0.959 0.947 0.929 0.64 0.809 1.073
Protein (kg/lactation) a ± sd − 4.981 ± 0.870 − 9.226 ± 1.616 − 11.885 ± 1.834 − 7.847 ± 1.374 − 5.498 ± 0.838 − 5.008 ± 0.944 − 3.539 ± 0.587
p 1.05E−08 1.12E−08 9.23E−11 1.11E−08 5.49E−11 1.14E−07 1.60E−09
d ± sd 4.308 ± 0.897 9.023 ± 1.631 11.435 ± 1.829 7.497 ± 1.389 4.067 ± 0.844 4.595 ± 0.949 3.695 ± 0.592
p 1.56E−06 3.14E−08 4.02E−10 6.77E−08 1.43E−06 1.30E−06 4.29E−10
k 0.865 0.978 0.962 0.955 0.74 0.917 1.044
  1. Linkage values with top variants are in Additional file 1: Table S1.
  2. VEP: variant effect predictor; NA: not applicable or unknown; AA substitution: amino-acid substitution; a: genotypic additive effect; d: genotypic dominance effect; k: dominance coefficient; sd: standard deviation; p: p-value; MAF: minor allele frequency; HF: Holstein–Friesian; J: Jersey; ALL: all animals