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Table 2 Regions containing putative lethal recessive haplotypes with an effect on total number born using the S × D model

From: Use of haplotypes to identify regions harbouring lethal recessive variants in pigs

Region

Step 1A

Step 1B

Step 2, S × D model

\(P (O[ H ] = 0 | E[ H ])\)

\(P (O[ H ] = 0 | S,D \;Carriers)\)

P value of MS

\(R\)

Number of SE from the expectation of a lethal recessive effect

Number of SE from no effect

6.1

7.84 × 10−4

1.00 × 10−2

5.62 × 10−2

0.157

1.13

1.91

10.1

5.30 × 10−3

1.78 × 10−3

4.79 × 10−2

0.157

1.18

1.97

14.1

1.77 × 10 −3

1.34 × 10 −5

2.03 × 10 −5

0.190

1.34

4.24

14.2

1.50 × 10−2

5.64 × 10−3

9.71 × 10−4

0.196

0.91

3.31

14.1 and 14.2 †

  

1.02 × 10 −4

0.240

0.16

3.93

  1. Regions containing a putative lethal recessive haplotype are named based on the chromosome and their order along that chromosome, i.e. 6.1 refers to the first region containing a putative lethal recessive haplotype located along chromosome 6. P values are given for the probability of observing no homozygotes within the population given the number expected based on the frequency of the haplotype (\(P (O[ H ] = 0 |E[ H ])\)), the probability of observing no homozygous offspring given the expected number from matings between a carrier sire and a carrier dam (\(P\left( {O[ H ] = 0 | S, D\;Carriers} \right)\)) and the significance of mating status (MS) using the S × D model. \(R\) is the relative reduction in total number born as a result of matings between two carriers compared to matings between a carrier and a non-carrier. The number of standard errors that \(R\) was from the expectation of a lethal recessive effect and from no effect are given. P values are nominal, with the haplotypes that achieved Bonferroni corrected significance (P < 3.25 × 10−4) for MS highlighted in italics. Results arising from the concurrent assessment of two putative lethal recessive haplotypes are denoted by â€