Table 3. Results of haplotype association analysis with milk fat yield (FY) (estimated breeding values (EBV) in bulls, yield deviations (YD) in cows).
| Regression model | |||||||||||||
| Popu-lation | SNP number | SNP ID | Block ID | Haplotype | fhpt | No Adjustment | DGAT1 | Population structure | DGAT1+ Population structure | β | µ±se (FY) | ||
| Model 1 | Model 2 | Model 3 | Model 4 | Model 4 | |||||||||
| A | 1 | ARS-BFGL-NGS-41145 | HTB6 | AA | 0.52 | n.s. | 0.0081 | 0.0058 | 0.0058 | −2.62 | 19.10±0.47 | ||
| 2 | Hapmap39651-BTA-42671 | GC | 0.37 | n.s. | n.s. | n.s. | n.s. | 1.90 | 20.61±0.58 | ||||
| GA | 0.08 | n.s. | n.s. | n.s. | n.s. | 2.65 | 21.14±1.22 | ||||||
| AC | 0.03 | n.s. | n.s. | n.s. | n.s. | 1.22 | 22.60±1.93 | ||||||
| A | 3 | ARS-BFGL-NGS-28677 | HTB7 | AA | 0.41 | n.s. | n.s. | n.s. | n.s. | 1.65 | 20.98±0.54 | ||
| 4 | Hapmap51449-BTA-42665 | GA | 0.34 | n.s. | n.s. | n.s. | n.s. | 0.69 | 20.25±0.62 | ||||
| GG | 0.26 | 0.0082 | 0.0002 | 0.0129 | 0.0129 | −2.79 | 17.82±0.67 | ||||||
| AG | 0.0009 | n.s. | n.s. | n.s. | n.s. | – | 21.70±13.27 | ||||||
| B | 1 | ARS-BFGL-NGS-41145 | HTB6 | AA | 0.46 | 0.0005 | 0.0012 | 0.0293 | 0.0897 | −4.49 | 0.75±1.53 | ||
| 2 | Hapmap39651-BTA-42671 | GC | 0.34 | 0.0161 | 0.0419 | n.s. | n.s. | 3.19 | 8.20±1.70 | ||||
| GA | 0.11 | n.s. | n.s. | n.s. | n.s. | 4.71 | 6.57±3.35 | ||||||
| AC | 0.09 | n.s. | 0.0403 | n.s. | n.s. | 1.02 | 9.55±3.49 | ||||||
| B | 3 | ARS-BFGL-NGS-28677 | HTB7 | AA | 0.44 | n.s. | n.s. | n.s. | n.s. | −2.96 | 4.19±1.58 | ||
| 4 | Hapmap51449-BTA-42665 | GA | 0.32 | 0.0092 | 0.0054 | 0.0182 | 0.0210 | 6.86 | 8.61±1.82 | ||||
| GG | 0.21 | 0.0432 | n.s. | n.s. | n.s. | −1.86 | 0.59±2.18 | ||||||
| AG | 0.03 | n.s. | n.s. | n.s. | n.s. | −5.93 | 0.81±5.69 | ||||||
Shown are p-values for haplotypes within the 2 Mb FTO region on chromosome BTA18 that are signifcantly associated with the mean EBV for fat yield (FY) over the first three lactations after applying model 4 in the bull-(A) and cow population (B). P-values for all four models (Table 1) are shown for comparison. Positions refer to the Btau 4.2 assembly. β = effect size (regression coefficient) giving the per haplotype change of the trait. µ ± se denotes the phenotypic mean with standard error of the haplotype class based on EBVs in bulls and YDs in cows. β and µ are given in kilogram fat as EBV units in bulls and YD units in cows. Since the correction for environmental effects differs between EBV and YD, the units are not identical. fhpt = haplotype population frequency. P-values >0.1 are labeled “n.s.”.