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. 2012 Nov 7;13:97. doi: 10.1186/1471-2156-13-97

Table 2.

Results of a genome scan for QTL associated with stress response using half-sib regression interval mapping

Omy cM Trait Sire-dam family4 LR1 F-value2 FChromWide P=0.053 FExperWide P=0.054 P-value5 PGenomeWide 6 hq27 Left flanking marker Right flanking marker
6
 32.0
 BLUP3
 Dam
 21.14
 3.14*
 2.85
 4.16
 0.00350
 0.736
 0.26
 OMY105DU
 OMM5254
10
 70.0
 BLUP3
 Dam
 18.41
 2.72
 2.91
 4.16
 0.01002
 0.978
 0.21
 OMM1544
 OMM5108
10
 72.0
 EBV
 Dam
 23.19
 3.46*
 2.88
 4.15
 0.00155
 0.445
 0.30
 OMM1544
 OMM3102
12
 36.0
 EBV
 Dam
 19.83
 2.93*
 2.75
 4.15
 0.00594
 0.896
 0.24
 OMM1096
 OMM11308
12
 60.0
 EBV
 Sire
 19.88
 4.14*
 2.71
 4.48
 0.00129
 0.388
 0.27
 OMM1341
 OMM1711
14
 95.0
 EBV
 Sire
 15.8
 3.26*
 2.78
 4.48
 0.00733
 0.939
 0.20
 OMM1643
 OMM51538
16
 45.09
 BLUP3
 Sire
 17.4
 3.60*
 2.59
 4.53
 0.00108
 0.336
 0.23
 OMM1559
 OMM5162
16
 65.0
 BLUP3
 Dam
 20.44
 3.03*
 2.77
 4.16
 0.00462
 0.828
 0.25
 OMM1150
 OMM1221
16
 71.09
 BLUP3
 Sire
 22.64
 4.75**
 2.61
 4.53
 0.00005
 0.020
 0.32
 OMM1150
 OMM1221
19
 40.0
 EBV
 Sire
 14.33
 2.94*
 2.93
 4.48
 0.01365
 0.995
 0.17
 OMM1241
 OMM3067
19
 45.0
 BLUP3
 Sire
 14.59
 3.00*
 2.95
 4.53
 0.01215
 0.990
 0.18
 OMM1241
 OMM3067
19
 64.0
 BLUP3
 Dam
 18.34
 2.70
 2.77
 4.16
 0.01052
 0.982
 0.21
 OMM5327
 OMM5216
22
 35.0
 EBV
 Dam
 19.61
 2.90*
 2.54
 4.15
 0.00640
 0.913
 0.23
 OMM1292
 BX9130598
29
 50.010
 EBV
 Sire
 14.76
 3.04*
 2.73
 4.48
 0.01125
 0.986
 0.18
 OMM17728
 OMM1118
29 56.010 EBV Sire 14.6 3.01* 2.70 4.48 0.01192 0.990 0.18 OMM1118 OMM1405

1The likelihood ratio (LR) test statistic.

2Asymptotically F-test statistic with the degrees of freedom(DF) being the number of sires or dams included for the numerator, and the total number of offspring minus twice the number of sires or dams for the denominator. The QTL with F-value ≥ FChromWide P=0.05 was defined as suggestive QTL (*); and QTL with F-value ≥ FExperWide P=0.05 or PGenomeWide ≤ 0.05 was defined as significant QTL (**).

3Chromosome-wide F-value at P=0.05 was estimated using 10,000 permutations with software GridQTL.

4Experiment-wide F-value at P=0.05 was estimated using 10,000 bootstraps with re-sampling with software GridQTL.

5The nominal P-value was calculated assuming an F-value distributed with numerator DF equal to the number of sires or dams, and denominator DF equal to the total number of offspring minus twice the number of sires or dams.

6The genome-wide significance level for detected QTL.

7The proportion of phenotypic variance explained by the QTL.

8The QTL flanking markers OMM1772, OMM1130, BX913059 and OMM5153 had significant Mendelian segregation distortion (P <0.01) in families 2, 4, 5 and 6, respectively.

9The Omy16 QTL had significant statistical support for two QTL segregating (F2QTL vs. 0QTL; DF=10=3.58; F1QTL vs. 0QTL; DF=5=3.60; LR2QTL vs. 0QTL = 33.62) for BLUP3 when fitting a two-QTL model with sire HS families.

10The Sex chromosome QTL had significant statistical support for two QTL segregating (F2QTL vs. 0QTL; DF=10=3.45; F1QTL vs. 0QTL; DF=5=3.10; LR2QTL vs. 0QTL = 32.50) for EBV when fitting a two-QTL model with sire HS families.