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Table 2 Peak variants for composite milk production traits with highly significant protein sequence association effects

From: Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle

Trait Chr Position Tag variant ID Iteration P-value Protein coding variant ID LD Gene Impact Description
FP 5 75698283 rs385866519 1 4.0e−19 rs207628090 0.979 CSF2RB M c.41 T > C
FP 11 103304757 rs109625649 0 4.3e−46 rs109625649 1 PAEP M c.401 T > C
FP 12 69608900 rs211406918 0 4.2e−33 rs208744187 0.951 TGDS M c.204A > C
FP 14 1732043 rs437406031 1 7.2e−37 rs450710918 0.990 ENS..39978 M c.352G > A
FP 14 1732043 rs437406031 1 7.2e−37 rs476736066 0.997 MROH1 M c.3549G > C
FP 14 1800439 rs209876151 0 8.9e−2225 rs109326954 0.9999 DGAT1 M c.695C > A
FP 14 1800439 rs209876151 0 8.9e−2225 rs134364612 0.9998 SLC52A2 M c.724A > G
LP 3 15433518 rs109749506 1 1.3e−20 rs382689947 0.995 TENT5A M c.1237 T > C
LP 3 15433518 rs109749506 1 1.3e−20 rs134844772 0.992 GBA M c.1080C > A
LP 3 15433518 rs109749506 1 1.3e−20 rs109330809 0.992 MTX1 L c.508-6 T > C
LP 3 15545091 rs379353107 0 2.2e−42 rs109816684 0.998 SLC50A1 L c.282 + 7G > A
LP 6 38027010 rs43702337 0 9.0e−717 rs43702337 1 ABCG2 M c.1742A > C
LP 16 24983926 rs110162358 2 1.0e−19 rs109896036 0.999 MTARC1 L c.628-5C > T
LP 16 24983926 rs110162358 2 1.0e−19 rs110899826 0.999 MTARC1 M c.581C > G
LP 19 43036265 rs210324533 3 9.4e−40 rs207799702 0.944 KAT2A L c.700-7C > G
LP 19 43036265 rs210324533 3 9.4e−40 rs209410283 0.945 KCNH4 M c.408C > G
LP 19 43036265 rs210324533 3 9.4e−40 rs377779402 0.945 KCNH4 H c.2663 + 2 T > C
PP 3 15550598 rs380597285 0 1.7e−37 rs109816684 0.994 SLC50A1 L c.282 + 7G > A
PP 5 75758989 rs210094995 0 3.3e−34 rs209394772 0.935 CSF2RB M c.227G > A
PP 5 75758989 rs210094995 0 3.3e−34 rs210937722 0.926 NCF4 M c.841G > C
PP 5 118239754 rs384479185 2 3.9e−32 rs456403270 0.976 TBC1D22A M c.1063C > T
PP 6 38027010 rs43702337 0 6.4e−115 rs43702337 1 ABCG2 M c.1742A > C
PP 14 1763380 rs135017891 0 5.9e−718 rs135258919 0.999 HSF1 M c.1031 T > C
PP 14 1802265 rs109234250 1 1.2e−61 rs109234250 1 DGAT1 M c.694G > A
PP 14 1802265 rs109234250 1 1.2e−61 rs134364612 0.999 SLC52A2 M c.724A > G
PP 15 53940444 rs382926661 1 2.9e−20 rs380220394 0.992 DNAJB13 L c.69-4 T > C
PP 19 43035006 rs209494359 0 1.6e−40 rs207799702 0.944 KAT2A L c.700-7C > G
PP 19 43035006 rs209494359 0 1.6e−40 rs209410283 0.945 KCNH4 M c.408C > G
PP 19 43035006 rs209494359 0 1.6e−40 rs377779402 0.945 KCNH4 H c.2663 + 2 T > C
  1. Peak variants for composite milk production traits with highly significant protein sequence effects whereby: the –log10(p-value) for the effect was greater than 1.5 × the Bonferroni threshold and the correlation between the tag variant and the protein sequence variant was in the range (0.975, 1]; or the –log10(p-value) for the effect was greater than 2 × the Bonferroni threshold and the correlation between the tag variant and the protein sequence variant was in the range (0.95, 0.975]; or the –log10(p-value) for the effect was greater than 2.5 × the Bonferroni threshold and the correlation between the tag variant and the protein sequence variant was in the range (0.925, 0.95]. Bonferroni threshold: –log10(6.2e–13). Iterations are defined relative to the base GWAS, with the base GWAS represented as iteration 0. FP Fat %, LP Lactose %, PP Protein %, L Low impact splice region variant, M Moderate impact missense variant, H High impact splice donor
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Genetics Selection Evolution

ISSN: 1297-9686