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Table 3 Haplotype statistics and analysis of suggested QTL regions.

From: Genome-wide association scan and phased haplotype construction for quantitative trait loci affecting boar taint in three pig breeds

       Haplotype analysis
SSC# Trait HF SNP-set Haplotypes$ Percent$ Significance Fixed effect (μg/g)
Duroc        
3 log Skatole 68.9 10 5 93 0.05023 0.022
3 log Androstenone 33.7 12 10 97.4 0.03365 * 0.844
5 log S/I-index 81.6 5 2 99.4 0.00304 ** 0.015
6 log Androstenone 56.1 4 4 99.4 2.106e-4 *** 0.775
10a log Indole 55.4 10 13 78 6.92e-4 *** 0.012
10b log Indole 34.1 15 12 77.2 0.0225 * 0.008 (0.003*)a
12 log Androstenone 51.5 9 9 93.4 1.027e-4 *** 1.292
14 log Androstenone 82.8 12 4 94.9 7.4e-3 ** 1.183
Landrace        
1 log Androstenone 19.8S 6 8 99.2 3.35e-4 *** 1.279
2a log Androstenone 23.4 7 14 85.7 6.48e-3 ** 0.838
2b log Androstenone 54.9 6 6 94.2 0.02133 * 1.172
5 log S/I-index 44.5 10 9 79.6 6.138e-3 ** -0.031
6 log Indole 27.6 11 10 89.3 0.01616 * -0.012
7 log Androstenone 38.6 15 13 58.7 8.094e-3 ** 1.240
14 log S/I-index 52.4 24 9 92.2 3.86e-5 *** -0.038 (-0.011***)a
14 log Indole 30 24 7 93.3 8.815e-5 *** -0.013 (-0.004***)a
15 log Indole 48.1 18 7 96 5.451e-3 ** -0.056
Yorkshire        
6a log S/I-index 73.9 15 3 95.8 4.706e-5 *** 0.015 (0.004***)b
6b log S/I-index 30.6 10 7 94.4 0.01399 * 0.009
7 log S/I-index 44.8 16 5 97.2 3.538e-3 ** 0.013
8 log S/I-index 63 11 5 97.2 1.741e-3 ** 0.013 (0.003**)a
9 log Skatole 33.5 11 10 90.5 0.03686 * -0.012
11b log Androstenone 57.1 5 6 98.4 0.0125 * 0.838 (0.059**)a
12 log Androstenone 61 16 10 94.3 0.03257 * 0.827
14 log Indole 43.8 12 8 95.1 1.028e-3 ** -0.007
  1. ***,**,* = p < 0.001, 0.01, 0.05, # = Sus scrofa chromosome
  2. HF = Haplotype frequency of the most common haplotype,S = The second most common haplotype
  3. $ = Amount of haplotypes with a frequency above 1.5%
  4. a,b = Test including slaughter weight, slaughter weight and meat content as covariate