Table 4.

Regions with unfavourable genotypes within the runs of homozygosity (ROH) with P-values < 1.0e-05 for milk, protein and fat yield (MILK, PROT and FAT, respectively).

Trait	CHR	Number of ROH genotypes	Position (Mb)	b in kg	P-value	Frequency of ROH genotypes (min/max)
MILK	2	5	80.54–84.81	−269.3–−279.5	4.35e-06	0.02/0.02
MILK	3	3	52.83–56.18	−321.6–−329.0	3.11e-06	0.01/0.01
MILK	5	1	89.16–90.75	−218.0	6.36e-06	0.03
MILK	5	1	96.55–102.05	−329.9	6.29e-06	0.01
MILK	6	1	115.84–117.01	−354.2	5.19e-06	0.01
MILK	13	131	44.37–58.55	−145.52–−252.0	1.23e-07	0.03/0.08
MILK	16	2	42.21–44.99	−196.7–−215.9	4.45e-06	0.03/0.04
MILK	20	22	29.23–33.31	−141.9–−217.7	9.30e-08	0.04/0.07
MILK	22	1	58.68–59.46	−341.6	2.99e-06	0.01
PROT	3	1	1.55–2.91	−6.94	4.93e-06	0.03
PROT	3	5	52.83–56.18	−9.7–−11.7	1.32e-07	0.01/0.01
PROT	6	12	72.53–80.66	−6.7–−11.6	2.60e-07	0.01/0.03
PROT	6	1	93.08–94.46	−10.47	8.91e-06	0.01
PROT	8	3	79.50–81.57	−9.8–−10.0	3.51e-06	0.01/0.01
PROT	13	176	42.93–58.55	−4.7–−8.8	3.60e-10	0.02/0.08
PROT	14	11	68.03–73.41	−5.6–−6.6	3.00e-06	0.03/0.04
PROT	16	1	43.64–46.51	−11.1	7.43e-06	0.01
PROT	16	1	52.51–53.92	−9.7	8.71e-06	0.01
PROT	22	1	57.99–59.33	−10.9	7.17e-06	0.01
FAT	5	1	87.02–88.11	−15.7	8.60e-09	0.01
FAT	5	6	109.93–118.35	−7.0–−12.8	1.56e-06	0.01/0.04
FAT	8	46	11.74–20.81	−10.5–−14.8	6.34e-08	0.01/0.02
FAT	13	1	57.32–58.55	−6.6	8.55e-06	0.04
FAT	17	2	7.14–8.03	−11.4–−11.5	2.69e-06	0.01/0.01
FAT	29	5	36.76–37.96	−3.9–−4.5	5.41e-07	0.12/0.14

Estimate b represents the difference between animals with the ROH genotype and animals without the ROH, while the P-value represents the smallest P-value for the region.