As expected, the power of all strategies is decreased as the error rates and the frequency of missing genotypes increase (Supporting Information Figure S2).
The presence of linkage disequilibrium between two markers can falsely inflate the LOD score and missing genotypes can increase this effect.
One way of obtaining more SNPs would be to allow greater levels of missing genotypes, although the increase in missing data are likely to have a negative effect on imputation accuracy.
In addition to observed genotypes, our approach allows estimation of missing genotypes, resulting in substantial increases in power when genotyping resources are limited.
This in turn would have caused a substantial increase in missing genotypes because of significantly reduced overlap of homologous fragments.
The imputation-based estimates of topology accuracy for four representative samples were generally reduced with increased levels of missing genotypes.
The estimates of topology accuracy for four representative samples of interested groups generally were reduced with increased levels of missing genotypes.
The imputation-based estimates of topology accuracy as reflected in four representative samples of interested groups were generally reduced with increased levels of missing genotypes and they were smaller than those from random missing without imputations.
Increasing allowed alignment mismatches helps overcome missing genotypes, inaccuracies in the reference genome, and errors in the sequence reads, but also results in increased erroneous sequence alignment, particularly when aligning shorter reads.
