Table 3 Values of significant KEGG pathways, after adjusting for multiple testing
| Â | Pathway | Trait | Number of SNPs | \(\text {H}^{2}_{\text {set}}\) | p-value | LR |
|---|---|---|---|---|---|---|
Amino Acid Metabolism | Â | Â | Â | Â | Â | |
|  | Arginine and proline metabolism | Fat yield | 390 | 13.8 % | 6·10−9 | 44.3 |
Carbohydrate Metabolism | Â | Â | Â | Â | Â | |
|  | Pentose phosphate pathway | Mastitis 1.1 | 182 | 2.3 % | 4·10−2 | 11.6 |
Digestive System | Â | Â | Â | Â | Â | |
| Â | Fat digestion and absorption | Fat yield | 436 | 43.4 % | 0 | 317 |
| Â | Fat digestion and absorption | Milk yield | 436 | 31.5 % | 0 | 184 |
Excretory System | Â | Â | Â | Â | Â | |
|  | Excretory System | Mastitis 1.1 | 1639 | 3.6 % | 4·10−2 | 11.2 |
|  | Proximal tubule bicarbonate reclamation | Udder- health | 187 | 1.2 % | 8·10−2 | 11.9 |
|  | Proximal tubule bicarbonate reclamation | Mastitis 1.1 | 187 | 2.2 % | 1·10−4 | 24.1 |
|  | Proximal tubule bicarbonate reclamation | Protein yield | 187 | 1.5 % | 6·10−2 | 10.8 |
Glycan Biosynthesis and Metabolism | Â | Â | Â | Â | Â | |
|  | Glycosphingolipid biosynthesis - globo series | Fat yield | 91 | 1.4 % | 3·10−2 | 13.2 |
| Â | Glycosylphosphatidylinositol(GPI)-anchor biosynthesis | Fat yield | 157 | 14.4 % | 0 | 91.6 |
|  | Glycosylphosphatidylinositol(GPI)-anchor biosynthesis | Milk yield | 157 | 10.3 % | 2·10−12 | 60.6 |
Immune System | Â | Â | Â | Â | Â | |
|  | Chemokine signaling pathway | Milk yield | 2809 | 5.3 % | 3·10−3 | 16.8 |
|  | Leukocyte transendothelial migration | Milk yield | 2001 | 4.6 % | 5·10−3 | 15.6 |
|  | Leukocyte transendothelial migration | Fat yield | 2001 | 4.5 % | 6·10−3 | 16.4 |
Lipid Metabolism | Â | Â | Â | Â | Â | |
|  | Glycerolipid metabolism | Milk yield | 969 | 27.9 % | 7·10−12 | 57.4 |
| Â | Glycerolipid metabolism | Fat yield | 969 | 41.6 % | 0 | 157 |
Metabolism of Cofactors and Vitamins | Â | Â | Â | Â | Â | |
|  | Metabolism of Cofactors and Vitamins | Milk yield | 1796 | 21.9 % | 4·10−9 | 44.5 |
|  | Metabolism of Cofactors and Vitamins | Fat yield | 1796 | 32.0 % | 3·10−12 | 59.7 |
|  | Metabolism of Cofactors and Vitamins | Protein yield | 1796 | 3.4 % | 8·10−2 | 9.5 |
|  | Porphyrin and chlorophyll metabolism | Protein yield | 194 | 3.0 % | 6·10−2 | 10.4 |
| Â | Retinol metabolism | Fat yield | 231 | 38.1 % | 0 | 382 |
| Â | Retinol metabolism | Milk yield | 231 | 28.9 % | 0 | 259 |
|  | Retinol metabolism | Protein yield | 231 | 9.9 % | 2·10−9 | 45.5 |
Metabolism of Other Amino Acids | Â | Â | Â | Â | Â | |
|  | Glutathione metabolism | Milk yield | 231 | 2.9 % | 3·10−2 | 12 |
Xenobiotics Biodegration and Metabolism | Â | Â | Â | Â | Â | |
|  | Xenobiotics Biodegration and Metabolism | Protein yield | 860 | 1.9 % | 8·10−2 | 9.04 |