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.

Rexroad et al.

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

Open Data