Table 5

Results of a genome scan for QTL associated with stress response using linkage disequilibrium and linkage analysis
Omy cM Trait LR1 P2 PGenomeWide 3 LOD score4 hu25 haddQTL26 hdomQTL27 Flanking markers
Left Right
3 79.0 EBV 173.77** 1.8E-38 6.6E-36 36.2 0.00 0.00 0.98 OMM3120 OMM5109
3 98.0 BLUP3 16.65* 2.4E-04 8.5E-02 2.6 0.00 0.00 0.84 OMM1263 OMM1391b
4 7.0 EBV 39.75** 2.3E-09 1.0E-06 7.5 0.00 0.03 0.81 OMM11948 OMM1211
5 90.0 BLUP3 58.23** 2.3E-13 8.3E-11 11.4 0.00 0.76 0.11 OMM5025 OMM1774
5 99.0 EBV 20.63** 3.3E-05 1.2E-02 3.5 0.00 0.00 0.70 OMM5025 OMM1774
6 67.0 EBV 53.03** 3.1E-12 1.1E-09 10.3 0.00 0.00 0.71 OMM1753 OMM1628
7 35.0 EBV 31.27** 1.6E-07 5.9E-05 5.7 0.43 0.00 0.48 OMM1468 OMM17408
8 55.0 EBV 46.24** 9.1E-11 3.3E-08 8.8 0.00 0.37 0.29 OMM1295 OMM1632
9 71.0 EBV 18.83** 8.1E-05 2.9E-02 3.1 0.00 0.10 0.36 OMM5179 OMM1089
10 100.0 EBV 81.7** 1.8E-18 6.6E-16 16.4 0.00 0.00 0.64 CR3729718 OMY1000UW
11 34.0 EBV 22.36** 1.4E-05 5.1E-03 3.8 0.00 0.00 0.61 OMM1333 OMM3042
12 33.0 EBV 50.87** 9.0E-12 3.3E-09 9.8 0.52 0.00 0.38 OMY105INRA OMM1096
13 50.0 EBV 26.45** 2.0E-06 6.6E-04 4.7 0.00 0.00 0.54 OMY1UoG OMM5165a
13 51.0 BLUP3 15.05* 5.4E-04 1.8E-01 2.3 0.16 0.00 0.35 OMY1UoG OMM5165a
14 46.0 EBV 16.05* 3.3E-04 1.1E-01 2.5 0.14 0.00 0.47 OMM1038 OMM1415
16 54.0 EBV 21.32** 2.3E-05 8.5E-03 3.6 0.18 0.13 0.34 OmyRGT6TUFa OMM1362
16 69.0 BLUP3 22.89** 1.1E-05 3.9E-03 3.9 0.00 0.61 0.00 OMM1150 OMM1221
17 75.0 EBV 49.57** 1.7E-11 6.3E-09 9.5 0.00 0.45 0.23 OMM3126 OMM1808
18 108.0 EBV 16.64* 2.4E-04 8.5E-02 2.6 0.48 0.00 0.42 OMM1352 BX873238
19 84.0 EBV 45.14** 1.6E-10 5.8E-08 8.6 0.47 0.00 0.46 OMM5106a8 OMM1412b
21 16.0 EBV 17.23* 1.8E-04 6.4E-02 2.8 0.00 0.00 0.54 OMM12568 OMM5298
25 0.0 EBV 19.97** 4.6E-05 1.7E-02 3.3 0.00 0.00 0.68 OMM3142 BX881655a
26 56.0 EBV 29.97** 3.1E-07 1.1E-04 5.4 0.00 0.00 0.83 OMY1189UWa OMM1752b
27 28.0 EBV 19.3** 6.4E-05 2.3E-02 3.2 0.33 0.00 0.49 OMM13158 OMM5309
28 48.0 EBV 19.71** 5.2E-05 1.9E-02 3.3 0.00 0.00 0.53 CR3734048 OMY1013UW
Sex 20.0 EBV 53.66** 2.2E-12 8.1E-10 10.4 0.00 0.28 0.48 OMM1026 OMM1461
Sex 44.0 BLUP3 16.56* 2.5E-04 8.8E-02 2.6 0.47 0.00 0.38 BX076085 OMM17728

1The likelihood ratio (LR) test statistic is defined as <a onClick="popup('http://www.biomedcentral.com/1471-2156/13/97/mathml/M3','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/13/97/mathml/M3">View MathML</a> where ln stands for natural logarithm, Î(z) is the likelihood function evaluated at the maximum likelihood estimate (MLE) for the full model that includes polygenic and QTL effects, and Îr(z) is the MLE for the restricted model under which r parameters of the full model are assigned fixed values. The QTL was declared as suggestive if it had a LR ≥ 13.82 or nominal P ≤ 0.001 (*), and as significant if it had a PGenomeWide ≤0.05 (**).

2The nominal P-value was estimated assuming the LR test statistic follows a chi-square distribution with two degrees of freedom.

3The genome-wide significance level for detected QTL was estimated as PGenomeWide = 1 − (1 − P)g[37] where P is the nominal P-value, and g = 365 STR loci used with LDLA method of QTL analysis.

4Logarithm of odds (LOD) score was calculated as LOD = log10[L(QTL)/L(polygenic)] where L = likelihood of the model.

5hu2 is the residual genetic variance or proportion of the total variance due to the polygenic component.

6haddQTL2 is the proportion of the total variance due to additive effect QTL.

7hdomQTL2 is the proportion of the total variance due to dominance effect QTL.

8These QTL flanking markers had significant Mendelian segregation distortion (P <0.01): OMM1194, OMM1740, OMM5106a and OMM1772 in family 2; CR372971 and CR373404 in family 3; OMM1256 in family 4; OMM1315 in family 5; and OMM1752b in family 7.

Rexroad et al.

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

Open Data