In the second test we used the IA, that is the most common measure of multi-locus linkage.
Union tests can be more powerful than single marker tests because they make fuller use of the information (i.e., genotype frequencies and multi-locus linkage disequilibrium [ 16]) in a multivariable framework.
With high-density single-nucleotide polymorphism (SNP) markers, it is possible to use multi-locus linkage disequilibrium (LD) between QTLs and markers across the whole genome to predict genetic values that can be used in predictive genomic selection (GS) methodologies.
The Kullback-Leibler divergence (KLD), an information theoretic measure of the 'distance' between two distributions, has been proposed for 2-group comparisons such as those used to evaluate ancestry informative markers [ 7- 9], as a multi-locus linkage disequilibrium (LD) measure to enable identification of TagSNPs [ 6] and for analytical visualization [ 4, 5].
Therefore, the larger data sets that have low haplotype diversities are expected to be solved with higher accuracy by biologically-oriented methods, such as XOR-HAPLOGEN which obtains its inference according to a multi-locus linkage disequilibrium (LD -based bLD -basedtification model.
***TGUMS marker with multi locus amplifications.
DJR performed and analysed the multi locus characterisation.
The association-enriched regions might represent probable intervals of QTL effects, that is, QTL or the cluster of QTL may reside in the multi-locus regions or in linkage with the loci in the regions.
Because our model does not involve complications that result from explicit multi-locus genetics (such as linkage disequilibrium between loci resulting from the model's initialization), we decided that running the model for 100 years prior to harvesting was sufficient to lessen the effects of transient population dynamics and of the initial genetic distribution of PMRN traits.
Markers were traced through the pedigree by linkage analysis using the linkage disequilibrium multi-locus iterative peeling (LDMIP) method [ 7] based on information from all genotyped marker loci and the entire pedigree (using parents from generation 5000 as base population).
Although it has been well established that skewed sampling from a population with a linkage equilibrium distribution of multi-locus genotypes may result in spurious linkage disequilibrium [ 26], there has not been a comprehensive investigation of the consequences of non-random samples on statistical inference of LD from populations under disequilibrium.
