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Higher marker density leads to better resolution of recombination breakpoints.
The increase in marker density leads to the detection of more deletions, thus resulting in higher resolution.
However, an increase in marker density leads to detection of smaller deletions which ultimately reduces the average size of deletions.
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As expected, higher marker density led to better performances for imputation, as shown in Figure 3.
Specifically, stronger LD, lower MAF, or higher marker density lead to better ARs; greater size of haplotypes in the reference sample resulted in higher ARs for MACH, IMPUTE, PLINK and Beagle, but had little influence on ARs for fastPHASE.
Increasing marker density led to higher accuracies of EBVs for all methods.
Further, we did not find that using higher marker densities led to an increase in the prediction accuracy (results not shown).
Theoretically, the large increase in marker density should not lead to the identification of many more associations because, in both the indica and the japonica panels, LD decay is much slower than the average distance between markers even in the two GBS datasets (Courtois et al. 2013; Lafarge et al. 2017).
A higher marker density would not lead to a higher mapping resolution in this pedigree [ 42].
The relatively high cost and limited marker density of these methods led to the use of single-nucleotide polymorphisms (SNPs) as the current preferred genotyping system.
In all cases, ESS/CPU increased with lower marker densities, since that leads to an inferential situation of more data information per marker (i.e., higher n/ m) or a greater level of determinedness [ 27].
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