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Third, we examine how the number of markers genotyped initially in the study sample affects the performance of the most diverse reference panel by varying the density of markers in the study sample, considering 200, 300, 400, 500, 600, and 1000 markers per 1-Mb region.
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Out of the 125 SSR markers genotyped in the 75 Malaysian genotypes, 119 (95.2%) were found to be polymorphic.
Initially, 60 polymorphic SSR markers were genotyped in the RIL population according to [ 71].
This genotyping initially utilized polymorphic microsatellite markers.
Genotyping initially utilized additional polymorphic microsatellite markers, following the procedure described above, and sequencing of known polymorphic SNPs identified from the Mouse Phenome Database (www.jax.org/phenome).org/phenome
A total of 443,816 markers were genotyped.
In total 960 molecular markers were genotyped.
All the markers were genotyped in duplicate.
The marker was genotyped using 190 individuals of a segregating F2 population derived from DM1 3 and M622.
Each marker was genotyped twice.
Each subcongenic strain was initially genotyped with three microsatellite markers per strain (Additional file 3) using DNA isolated from Proteinase K digested tail clips and genotyped as described by Farber and Medrano [ 30].
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