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Likewise, having accumulated many more recombination events than bi-parental mapping populations, such panels ensure finer genetic resolution.
In mapping populations such as RILs, segregation of major QTLs like DRO1 often masks the presence of minor QTLs.
Reverting to classical mapping populations such as RILs deriving from two divergent parents will solve these problems of the confounding effect of population structure and low frequency alleles.
This correlation can be verified by analyzing advanced mapping populations, such as recombinant inbred lines, near isogenic lines, or double haploid lines.
More than 75% of the populations used for QTL analysis were primary mapping populations such as RILs, F2, doubled haploid lines (DHLs), BILs, and backcross populations of the F1 to the recurrent parent (BC1F1; Fig. 2a).
The QTL detection efficiency in primary mapping populations such as F2, where heterozygous alleles are segregated, should be lower than that in advanced progenies such as chromosome segment substitution lines and NILs, which have a more homogeneous genetic background.
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This may be done in a genetic reference population to exploit the breadth of existing data or a large experimental cross or mapping population such as the Diversity Outbred to improve mapping power and precision.
One advantage of linkage mapping in multiparent populations such as the DO is that we obtain estimates of the founder allele effects at each locus.
The heat maps of blebbed populations, such as the HGPS cell lines, have many red speckles, whereas the heat maps of unblebbed populations, such as the control cell line, have few red speckles.
Furthermore, many markers have been mapped in different populations such that their genetic positions are inconsistent.
Here, we expand these approaches to work with eQTL mapping in genetically complex populations, such as the Collaborative Cross or heterogenous stock mice.
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