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With more markers genotyped, a genetic map for QTL identification has tended to be infinitely dense.
We also observe that the improvement in discordance rates for the most diverse reference panel over the randomly selected panels slightly decreases with more markers genotyped in the study sample.
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Different marker density and coverage of rare alleles among different regions in the genome may affect detection sensitivity, and a much better covered homozygous region with more rare markers genotyped may stand out compared to other regions, generating spurious positive results.
2 Anch.: anchor marker, genotyped in more than one cross 3 Conf.: confirmed neighboring marker 4 Polym.: polymorphic neighboring markers 5 The total does not include information from Chr. X. Whereas the linkage map constructed from the JL data consisted of 94 markers (Table 1), they were linked to 24 groups and assigned to 23 chromosomes in the JL map.
This was not due to the fact that we genotyped more markers than Bethesda, as restricting our panel to 10 markers still resulted in a sensitivity rate of 85% (data not shown).
This effect is unfortunate given that the ability to genotype more markers is fast increasing while sampling many individuals can be difficult for populations of conservation concern.
The cost of genotyping increases as more markers are included in the genotyping arrays and this could be a major restriction for large-scale application of genomic evaluation.
However, such pedigree mistakes result in a small loss of QTL detection power [25] and can be improved when individuals are genotyped with more markers for linkage analysis and QTL mapping purposes.
This also means that the estimates of average deletion size are likely to decrease further when these RH lines are genotyped with more markers.
An additional 113 F2 plants with GSH were genotyped with 3 more markers for fine mapping.
Because these recombinants will be genotyped with several more markers in subsequent steps, we suggest extracting DNA from the leaf samples set aside earlier at −80°C (step 4b).
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