Table 6.
Genomic regions associated with a reduction in fertility and milk yield identified using runs of homozygosity
| Trait | Breed | Chr 1 | Interval 2 (Mb) | Number of ROH P <0.001 3 | Frequency of ROH 4 (%) | b (s.e) 5 | -log10 (P-value) |
|---|---|---|---|---|---|---|---|
| Fertility | Holsteins | 2 | 1.34–1.69 | 7 | 6% | 5.2 (1.5) | 3.37 |
| 2 | 13.0–13.5 | 2 | 5% | 6.0 (1.8) | 3.17 | ||
| 5 | 37.6–37.7 | 3 | 5% | 5.7 (1.6) | 3.37 | ||
| 8 | 88.0–88.5 | 5 | 6% | 5.1 (1.5) | 3.11 | ||
| 9 | 6.9–9.2 | 26 | 3% | 7.6 (2.1) | 3.57 | ||
| 15 | 24.7–28.6 | 6 | 4% | 6.0 (1.8) | 3.20 | ||
| 24 | 60.4–60.5 | 3 | 4% | 6.0 (1.8) | 3.09 | ||
| Jerseys | X | 60.4–62.1 | 14 | 4% | 12.5 (3.6) | 3.19 | |
| Milk | Holsteins | ||||||
| 7 | 60.3–60.5 | 1 | 4% | -216 (65) | 3.02 | ||
| 11 | 99.9 | 2 | 3% | -245 (74) | 3.03 | ||
| 14 | 41.09525 | 1 | 3% | -255 (77) | 3.00 | ||
| 16 | 64.9–66.2 | 22 | 6% | -212 (58) | 3.34 | ||
| 17 | 70.7–70.8 | 2 | 4% | -260 (74) | 3.34 | ||
| 20 | 35.7–35.8 | 2 | 10% | -161 (48) | 3.11 | ||
| 26 | 32.3–33.9 | 12 | 4% | -239 (67) | 3.29 | ||
| 28 | 7.29–8.03 | 17 | 4% | -240 (66) | 3.49 | ||
| Jerseys | 8 | 89.7–95.5 | 27 | 7% | -254 (75) | 3.16 | |
| 20 | 28.1–30.9 | 13 | 5% | -194 (55) | 3.31 | ||
| 24 | 19.3–19.5 | 3 | 5% | -234 (68) | 3.21 |
1Chr = chromosome; 2Interval = interval between the start and end of the cluster of run of homozygosity (ROH) of 50 or more SNP from UMD build 3.1 measured in Mb; 3Number of ROH = the count of significant (P <0.001) ROH within the interval; 4frequency of ROH (%) = the mean frequency of ROH present in the interval; 5b = the regression coefficient of the phenotype (fertility which was calving interval; d or lactation milk yield L) on ROH and associated standard errors (s.e.).