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Table 6 Genomic regions associated with a reduction in fertility and milk yield identified using runs of homozygosity

From: Identification of genomic regions associated with inbreeding depression in Holstein and Jersey dairy cattle

Trait

Breed

Chr1

Interval2(Mb)

Number of ROH P <0.0013

Frequency of ROH4(%)

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

  1. 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.).