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The block structure of close sites is visualised in a different way in Figure 3, which shows all the significant cases of linkage disequilibrium.
Moreover, some inversions have closely linked breakpoints producing extreme cases of linkage disequilibrium; thus, we repeated the analysis by grouping inversions in four 'inversion systems': 2R j/+, 2R b/ bc/+, 2R d/ u/+ and 2L a/+.
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To address the case of linkage studies for diseases with unknown mode of inheritance, we suggested Clerget-Darpoux et al., 1986 extending the lod score function to a so-called mod score function.
This formula is the same as for the case of linkage equilibrium in the founders [ 15, 26].
A special case of linkage class (16) is the following: (18) C 1 ⇌ C 2 Deletion of the complex C 2 in this case is equivalent to deletion of the linkage class from the network.
Distinguishing between linkage and pleiotropy is important for breeding because only in the case of linkage it would be possible to implement resistance without co-selection of a certain developmental type.
In case of linkage equilibrium, the accuracy of GEBVs is not necessarily zero but will approach the accuracy of pedigree-based BLUP-EBVs as the number of SNPs fitted in the model increases.
In the case of linkage analysis, the input are pedigrees of families that segregate a disease, genetic marker information such as SNP data and affection status of some or all family members.
We took into account multiple testing (in the case of HWE tests) and nonindependence between tests (in the case of linkage tests) by using the false discovery rate (Benjamini and Hochberg, 1995) and the sequential Bonferroni (Sokal and Rolf, 1995: p. 236) adjustments, respectively.
If answering this question would provide information concerning the underlying mechanisms controlling the traits, it would also provide information about whether an unfavourable genetic correlation between two characters can be broken (in the case of linkage) or whether this is impossible (in the case of pleiotropism).
In such cases, measurements of linkage either cannot be made or become highly inaccurate when extrapolated over the time between sample points.
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