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All markers shared between different mapping populations were assigned to congruent linkage groups.
This leads to variation in QTL locations between different mapping populations, and can effectively prevent comparison of genomic features between different maize inbred lines.
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The most likely explanation for these differences is that we used different mapping populations.
Several factors may be responsible, including the genetic constitution of different mapping populations, mapping strategies, number and type of mapped loci, the choice of mapping software and ratio between number of markers and population size [ 64- 67].
Similarly, in the FW study, a comparison was made between the specific parental combinations used to develop two different mapping populations (with the same thresholds) to find TUSs with differential expression.
Total map length, average distance between adjacent markers, and the linkage map coverage of the genome constructed from reciprocal F2 and BC1F1 populations was variable in the different mapping populations (Table 1).
Although several genetic maps have been constructed, most of them used different mapping populations with different population sizes.
Four other maps from two different mapping populations were also used.
The SNPs were used to construct genetic maps in seven different mapping populations.
We mapped 397 loci, 81% of which were common to at least two different mapping populations.
The small number of common markers between various genetic maps limits the ability to infer comparative positions of QTL across germplasm [ 7, 9, 49] and to associate interesting candidate genes to QTL detected in different mapping populations [ 50].
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