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Position data of markers placed bilaterally on the trochanter major were measured by Optotrak cameras (Northern Digital, Waterloo, Canada).
For further validation of linkages among markers, the genotyping data of markers grouped by MAPMAKER were analyzed through JoinMap 4.1 (http://www.kyazma.nl/index.php/mc.JoinMap) at higher logarithm of odds (LOD) threshold (4.0 8.0) with Kosambi mapping function.
The QTL mapping was performed by integrating the genotyping data of markers mapped on LG of intra-specific genetic map with multi-location/years replicated SW field phenotyping data of 192 mapping individuals.
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We also had no data on markers of endothelial injury.
The mapping data of these markers shows that the marker loss frequency within a chromosome is homogeneous for all chromosomes except for chromosome 1D and 7D.
Hence, data of 1065 markers (697 SNPs and 368 previously mapped co-dominant markers) were compiled together for linkage analysis and map generation using JoinMap ver. 4.0.
In conclusion, our preliminary data of molecular markers do show a major potential role for MSI instability as prognostic marker, but await inclusion of more patients.
The segregation data of other markers with multiple entries whose segregation signatures were almost identical (>95%) were collapsed into single-marker entries with consensus segregation signatures.
From the 384 SNPs, data of 58 markers were removed because of recognisable variation between plates of 96 samples.
Besides phylogenetic reconstructions, we applied a principal component analysis (PCA) to allele frequency data of typed markers.
Alternatively, the issue of population stratification can be handled at the population level by studying population structures from genotype data of multiple markers [11] [17].
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