## Table 2 |
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Results of a genome scan for QTL associated with stress response using half-sib regression
interval mapping |
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Omy |
cM |
Trait |
Sire-dam family^{4} |
LR^{1} |
F-value^{2} |
F_{ChromWide P=0.05}^{3} |
F_{ExperWide P=0.05}^{4} |
P-value^{5} |
P_{GenomeWide }^{6} |
h_{q}^{2}^{7} |
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 | OMM1130^{8} |

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 | OMM5153^{8} |

16 | 45.0^{9} |
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 | 71.0^{9} |
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 | BX913059^{8} |

29 | 50.0^{10} |
EBV | Sire | 14.76 | 3.04* | 2.73 | 4.48 | 0.01125 | 0.986 | 0.18 | OMM1772^{8} |
OMM1118 |

29 | 56.0^{10} |
EBV | Sire | 14.6 | 3.01* | 2.70 | 4.48 | 0.01192 | 0.990 | 0.18 | OMM1118 | OMM1405 |

^{1}The likelihood ratio (LR) test statistic.

^{2}Asymptotically *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 ≥ *F*_{ChromWide P=0.05} was defined as suggestive QTL (*); and QTL with *F*-value ≥ *F*_{ExperWide P=0.05} or *P*_{GenomeWide} ≤ 0.05 was defined as significant QTL (**).

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

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

^{5}The 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.

^{6}The genome-wide significance level for detected QTL.

^{7}The proportion of phenotypic variance explained by the QTL.

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

^{9}The Omy16 QTL had significant statistical support for two QTL segregating (*F*_{2QTL vs. 0QTL; DF=10}=3.58; *F*_{1QTL vs. 0QTL; DF=5}=3.60; *LR*_{2QTL vs. 0QTL} = 33.62) for BLUP3 when fitting a two-QTL model with sire HS families.

^{10}The Sex chromosome QTL had significant statistical support for two QTL segregating
(*F*_{2QTL vs. 0QTL; DF=10}=3.45; *F*_{1QTL vs. 0QTL; DF=5}=3.10; *LR*_{2QTL vs. 0QTL} = 32.50) for EBV when fitting a two-QTL model with sire HS families.

Rexroad * et al.*

Rexroad * et al.* *BMC Genetics* 2012 **13**:97 doi:10.1186/1471-2156-13-97