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The MAGIC approach can be used to generate pre-breeding populations with increased genotypic diversity and reduced linkage drag.
Relative to bi-parental populations, MAGIC populations will have greater genotypic diversity, a higher level of recombination, and reduced linkage drag.
Positions within the window have the same linkage as in the CWR, while positions further apart have reduced linkage.
Our simulations began with several generations of neutral mixing, emulating laboratory procedures that use inbred founder lines to create larger experimental populations with increased genetic variation and reduced linkage disequilibrium (e.g., Turner and Miller 2012).
Furthermore, with reduced linkage disequilibrium observed at rare and low-frequency SNPs (in comparison to common variants), it is less likely that an association to such a variant will be detected through additional tag SNPs.
As the NILs and the NIL-derived population used for fine mapping in this study were all obtained from crosses between bread wheat (Triticum aestivum L). and T. spelta genotypes [ 9, 22], the relatively distant genetic relatedness between the parental genotypes likely contributed to the reduced linkage distances obtained in this study.
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The multiple cycles of meiosis is expected to break the tight linkages between favourable and unfavourable loci, hence reducing linkage drag.
These results indicated that without direct background selection, no further increases in %RGC were obtained during pseudo-backcrossing, whereas rigorous foreground marker-assisted selection tended to reduce linkage drag during pseudo-backcrossing.
In order to increase selection efficiency and to reduce linkage drag, three to six flanking markers for each qDTY were used in the recombinant selection (Hospital and Charcosset 1997; Neeraja et al. 2007).
We found that reducing linkage drag on the carrier chromosome was the most difficult part of the procedure.
Currently, the mouse quantitative trait loci (QTL) mapping community is focused on creating novel inbred-based mouse populations to increase recombination events and thereby reduce linkage disequilibrium (LD) to facilitate fine-mapping studies.
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