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In addition, the recent small effective population size in Holstein Friesian cattle has led to useful LD extending for considerably larger distances than in humans for example, which increase the prospects of finding associations with the marker density used in this experiment [19] [21].
This assumption should not affect the overall results because of the relatively low marker density used (1 per 10 kb).
Also in agreement with [ 12], prediction accuracies generally increased with the marker density used (m = 600 versus m = 6,932), but only slightly (Table 4: all markers versus Table 6: subsets of random markers).
Thus, diversity at neighboring gene loci was not correlated with recombination distances in the study population and, with the marker density used, there is little evidence for extended reductions in diversity due to selective sweeps.
However, given the rapid decay of LD in this species (within a few hundred bp on average), the marker density used was probably too low to capture any localized decline in heterozygosity, if any occurred around selected loci.
The high marker density used to construct the population provides a level of resolution not yet seen in a NIL population, thus minimizing ambiguity in fine-mapping and QTL validation studies caused by unidentified chromosomal introgressions elsewhere in the genome.
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Ever since, attempts have been made to increase marker density using new SSRs and gene-based markers in RIL populations.
We corrected map lengths for each species for marker density using method 4 of Chakravarti et al. [ 52], as implemented by Hall and Willis [ 53] and Dumont and Payseur [ 54].
We selected 50, 100 and 200 SNPs from each of the 19 autosomes to create three different marker densities using pre-corrected body weight at 6 weeks as phenotypes.
Given the high marker density being used in this paper, the QTL position is restricted to the midpoint between adjacent markers.
Average marker density was used to calculate the expected binomial frequencies for each marker class per block interval for all the linkage groups.
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