Table 1 The phenotypic difference between haplotypes of MUC13

From: Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences

Trait

Hap1

Hap2

P Value

Additive effect

Dominance effect

N

Incidence Or Mean ± SD

N

Incidence Or Mean ± SD

ETEC F4ac adhesion

711

0.67

815

0.35

4.1 × 10-35

(OR = 3.75)

0.328***

0.130***

Carcass straight length (cm)

854

97.04 ± 6.87

1000

95.31 ± 7.52

2.3 × 10-07

1.823***

0.255

Carcass diagonal length (cm)

854

80.71 ± 5.89

1000

79.39 ± 6.41

3.9 × 10-06

1.384***

0.249

Small intestine length (m)

856

15.88  ± 1.93

1002

15.46  ± 2.33

3.2 × 10-05

0.429***

0.075

Fourth cervical vertebra length (cm)

854

2.03 ± 0.20

1002

1.98 ± 0.20

2.2 × 10-06

0.048***

0.001

Fifth cervical vertebra length (cm)

853

1.99 ± 0.19

997

1.95 ± 0.18

9.2 × 10-07

0.045***

0.007

Sixth cervical vertebra length (cm)

851

2.07 ± 0.20

995

2.03 ± 0.20

4.9 × 10-05

0.040***

0.006

Seventh cervical vertebra length (cm)

851

2.29 ± 0.21

999

2.23 ± 0.21

1.0 × 10-08

0.059***

0.004

Neck Bone Length (cm)

853

17.32 ± 1.41

1003

17.06 ± 1.49

9.1 × 10-05

0.272***

0.109

  1. N, sample size; ETEC F4ac adhesion, susceptible to Enterotoxigenic Escherichia coli F4ac; OR, Odds ratio; Neck Bone Length, total length of cervical vertebra; Hap1 or Hap2, haplotypes of MUC13. The significance (P Value) of ETEC F4ac phenotypic difference between Hap1 and Hap2 was calculated by Pearson’s Chi Squared test. The significances (P Value) of remaining phenotypic differences between Hap1 and Hap2 was calculated by Student’s t test (two-sided). Reported P Values are nominal (i.e. not corrected for multiple testing). Proxy SNP 13_135417839, its allele A (G) in complete linkage disequilibrium with the haplotype Hap1 (Hap2) of MUC13, was used to estimate the additive and dominance effects with model \(Y=B+A*X1+D*X2\). Y denotes the phenotypic value as 0 (resistance to ETEC F4ac) or 1 (susceptible to ETEC F4ac). B denotes intercept. X1 represents the genotypes (A/A, A/G, G/G) of SNP 13_135417839. A/A, A/G, and G/G were recoded as 2, 1, and 0. Coefficient A represents the estimated additive effect. To account for dominance, a new variable was constructed, X2, with values of 0, 1, and 0 for, respectively, genotypes A/A, A/G, and G/G. Coefficient D represents the estimated dominance effect. *** represents that the P Value is highly significant. The P Values for the additive effects of ETEC F4ac, carcass straight length, carcass diagonal length, small intestine length, fourth cervical vertebra length, fifth cervical vertebra length, sixth cervical vertebra length, seventh cervical vertebra length, and neck bone length are 5.9 × 10-40, 1.9 × 10-07, 3.7 × 10-06, 3.6 × 10-05, 1.2 × 10-06, 5.9 × 10-07, 4.2 × 10-05, 5.6 × 10-09, and 1.2 × 10-04, respectively. The P Value for the dominance effect of ETEC F4ac is 5.2 × 10-05.
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