Table 5 |
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Results of a genome scan for QTL associated with stress response using linkage disequilibrium and linkage analysis | |||||||||||
Omy | cM | Trait | LR^{1} | P^{2} | P_{GenomeWide }^{3} | LOD score^{4} | h_{u}^{2}^{5} | h_{addQTL}^{2}^{6} | h_{domQTL}^{2}^{7} | 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 | OMM1194^{8} | 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 | OMM1740^{8} |
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 | CR372971^{8} | 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 | OMM5106a^{8} | OMM1412b |
21 | 16.0 | EBV | 17.23* | 1.8E-04 | 6.4E-02 | 2.8 | 0.00 | 0.00 | 0.54 | OMM1256^{8} | 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 | OMM1315^{8} | OMM5309 |
28 | 48.0 | EBV | 19.71** | 5.2E-05 | 1.9E-02 | 3.3 | 0.00 | 0.00 | 0.53 | CR373404^{8} | 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 | OMM1772^{8} |
^{1}The likelihood ratio (LR) test statistic is defined as 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 Î_{r}(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 P_{GenomeWide} ≤0.05 (**).
^{2}The nominal P-value was estimated assuming the LR test statistic follows a chi-square distribution with two degrees of freedom.
^{3}The genome-wide significance level for detected QTL was estimated as P_{GenomeWide} = 1 − (1 − P)^{g}[37] where P is the nominal P-value, and g = 365 STR loci used with LDLA method of QTL analysis.
^{4}Logarithm of odds (LOD) score was calculated as LOD = log_{10}[L(QTL)/L(polygenic)] where L = likelihood of the model.
^{5}h_{u}^{2} is the residual genetic variance or proportion of the total variance due to the polygenic component.
^{6}h_{addQTL}^{2} is the proportion of the total variance due to additive effect QTL.
^{7}h_{domQTL}^{2} is the proportion of the total variance due to dominance effect QTL.
^{8}These 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