For studies in which the researcher contacts the study participants and informed consent is relevant (eg, in case of linkages with individual questionnaires or biological data), the EA should include information on who informs the study participants of the study.
However, in case of tight linkage, there should be a significant deviation from the expected genotype combination frequencies due to reduced recombination between these markers.
If two SNPs segregated completely independent from each other, i.e. in case of no linkage disequilibrium (LD), one expects to find all possible genotype combinations according to the product of their single locus genotype frequencies.
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).
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.
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 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.
In case of the genome-wide linkage studies for a complex, multifactorial disease such as PD, the regions with high LOD scores are rarely smaller than 20 cM.
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.
