Marker data obtained were filtered using the following criteria: 1) monomorphic markers were removed; 2) markers were deleted when the frequency of heterozygotes per marker was equal to or higher than 5%, and 3) markers were deleted when the frequency of no-calls (NC) was equal to or higher than 50%.
After calibration markers were removed, the task was explained to the participant.
From the 384 SNPs, data of 58 markers were removed because of recognisable variation between plates of 96 samples.
Redundancy dropped to 3.3% and 5.6% respectively when SSH-derived DArT markers were removed.
A further 725 markers were removed from analysis because they were not polymorphic between our 37 selected strains.
Sequences showing non-specific binding to general cell surface markers were removed by incubating the enriched pool with HeLa cells (rounds 2, 4, 5, 7, 8, 9, 12, 20, 21, 22).
Eleven of the 400 markers were removed from the analysis because they were in significant Hardy-Weinberg disequilibrium among the founders (p<0.0001), using the method of Montoya-Delgado et al. [48].
No markers were removed from the third or X-chromosomes.
These additional markers were removed after the initial static trial.
These markers were removed from the dataset for GS analyses.
Based on the genotypes of the parents, monomorphic markers were removed.
