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Firstly, WGS data allows complete resolution of LD structure, given the maximal marker density.
WGS provides the best possible resource for LD mapping due to the maximal marker density and lack of ascertainment bias.
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Even where maximal marker densities have been attained, larger sample sizes are likely to improve the population representativeness of the map.
As a result, there may be some founding effects within this study and large stretches of LD, but it is doubtful we were able to fully cover the genome as close to the maximal Fisher's Information given the marker density and coupled with the low power of this study.
As few as 5 K SNPs gives close to maximal accuracy within population, suggesting that only moderate marker density is likely to be suitable for GS breeding programs for similar highly heritable but polygenic traits where the discovery populations have close relationships with the selection candidates.
The average marker density was 5.6 SNP markers per cM or 3.3 SNP markers per recombination point.
Fig. 3 Effect of the marker density on the predictability.
Chromosome wise marker density varied from 6.21 cM/marker in chromosome 11 to 19.25 cM/marker on chromosome 3 (Table 3).
The accuracy increased with increasing marker density.
The entire marker density was 0.42.
The average marker density was 3.2 cM.
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