Table 3 Haplotype regions and carrier frequency for putatively lethal alleles in Nellore cattle population.

From: Identification of candidate lethal haplotypes and genomic association with post-natal mortality and reproductive traits in Nellore cattle

Potentially lethal haplotype1

BTA2

Haplotype

Expected homozygotes numbers and probabilities of observing zero homozygous

Distance between haplotypes (Mb)

Start position3

End position3

Length (Mb)

Number of carriers*

Haplotype %*

Simple4

Probabilities (Phh)5

Mating6

Probabilities7

25.1

1

–

21,773,327

22,571,004

0.79768

5,929

4.78

141

4,07E−16

69

2,39E−09

108.7

1

69.63095

92,201,954

93,179,359

0.97741

4,750

3.83

91

1,32E−10

123

4,29E−16

231.4

2

–

30,989,280

31,660,659

0.67138

4,998

4.03

101

1,15E−11

73

7,58E−10

346.2

2

93.94106

125,601,735

126,602,788

1.00105

11,771

9.49

560

1,93E−61

368

1,05E−46

396.34

3

–

27,103,538

27,639,143

0.53561

4,291

3.46

74

8,65E−09

7

1,33E−01

461.4

3

56.52740

84,166,546

84,882,788

0.71624

5,941

4.79

142

3,51E−16

96

1,01E−12

479.2

3

12.97973

97,862,526

98,537,136

0.67461

2,783

3.05

57

5,43E−07

60

3,19E−08

676.135

5

–

19,466,593

20,216,556

0.74996

4,130

3.33

69

3,40E−08

2

5,63E−01

769.3

5

79.20781

99,424,373

100,174,866

0.75049

4,143

3.34

69

3,07E−08

26

5,64E−04

966.2

7

–

19,468,345

20,417,099

0.94875

6,053

4.88

148

9,09E−17

58

5,67E−08

988.14

7

16.13788

36,554,986

37,251,910

0.69692

4,329

3.49

76

6,26E−09

26

5,64E−04

1045.24

7

43.68097

80,932,886

81,622,237

0.68935

4,564

3.68

84

7,57E−10

3

4,22E−01

1077.1

7

25.22425

106,846,493

107,525,464

0.67897

6,958

5.61

196

6,29E−22

170

5,76E−22

1184.1

8

–

78,277,928

79,262,115

0.98419

3,832

3.09

59

3,71E−07

37

2,38E−05

1192.1

8

5.68177

84,943,889

85,809,360

0.86547

12,441

10.03

625

1,48E−68

588

3,44E−74

1277.303

9

–

42,710,447

43,514,053

0.80361

4,056

3.27

66

6,29E−08

5

2,37E−01

1278.37

9

0.00169

43,515,752

44,346,392

0.83064

3,733

3.01

56

7,91E−07

4

3,16E−01

1283.33

9

3.79844

48,144,835

48,978,466

0.83363

3,981

3.21

63

1,15E−07

4

3,16E−01

1312.67

9

23.54260

72,521,066

73,292,804

0.77174

3,721

3

56

8,68E−07

4

3,16E−01

1457.2

10

–

85,722,335

86,530,381

0.80805

4,378

3.53

77

4,05E−09

55

1,34E−07

1655.2

12

–

31,305,864

32,200,052

0.89419

4,242

3.42

72

1,33E−08

79

1,35E−10

2213.8

17

–

65,952,250

66,468,921

0.51667

3,696

2.98

55

1,05E−06

9

7,51E−02

2237.1

18

–

9,785,118

10,380,109

0.59499

4,775

3.85

92

1,04E−10

4

3,16E−01

2270.1

18

25.88554

36,265,657

37,406,377

1.14072

3,795

3.06

58

4,94E−07

38

1,79E−05

2329.1

19

–

20,292,526

21,133,267

0.84074

5,358

4.32

116

2,69E−13

55

1,34E−07

2371.1

19

33.51829

54,651,560

55,237,521

0.58596

15,145

12.21

927

2,63E−101

1028

3,66E−129

2585.3

22

–

18,857,788

19,688,790

0.831

4,192

3.39

71

1,82E−08

78

1,80E−10

2620.22

22

27.00519

46,693,982

47,385,511

0.69153

4,180

3.37

70

2,25E−08

10

5,63E−02

2724.2

24

–

18,329,342

19,105,911

0.77657

4,651

3.75

87

3,38E−10

76

3,20E−10

3063.3

29

–

40,482,004

41,207,696

0.72569

6,189

4.99

154

1,69E−17

163

4,32E−21

  1. *The number of carriers and frequency of haplotype among the heterozygous animals was calculated on the number of genotyped animals: 62,022.
  2. 1Haplotypes are identified by DNA segment number and haplotype within segment (e.g., 2371.1 indicates segment 2371 and haplotype 1).
  3. 2Bos taurus Autosome.
  4. 3ARS-UCD1.2 Bos taurus genome assembly (Rosen et al., 2020)27.
  5. 4Number of individuals genotyped (62,022) divided by 4 and multiplied by square of carrier frequency. The simple expected number of homozygotes does not require dividing by 4 if the haplotype frequency is used directly instead of the carrier frequency.
  6. 5 \(Phh = {(1 - {C}^{2}/4)}^{N}\), where the probability of no homozygous animals \((Phh)\) depends on the carrier frequency of the heterozygous animals \((C)\) and the number of genotyped animals\((N)\).
  7. 6Number of carrier service sire × carrier maternal grandsire mattings divided by 4.
  8. 7Follows a Bernoulli process and is equal to 0.75 raised to the power of the observed number of carrier service sire × carrier maternal grandsire pairs.
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