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Briefly, given genotyping data at multiple linked loci, we estimate the unobserved haplotypic phase and impute any missing calls by combining information about population haplotypic frequencies with information about the neighbouring loci.
As highlighted by Cornforth and Long (2003) and by Mackay et al. (2009), fine mapping may reveal multiple linked loci of small effects.
However, the LOD peaks for the FH and FP QTL over the 2 yr are sufficiently far apart to suggest that there may be multiple linked loci contributing to the effects for each trait.
We compared this approach to a prospective aproach, the QTDTM and also extended the QTDTM to allow analysis of multiple linked loci (including multi-locus haplotypes), parent-of-origin or maternal genotype effects.
Cordell et al. [2004] showed that the case/pseudocontrol approach can easily be extended to fit models for parent-of-origin effects, multiallelic markers, multiple linked loci in multiple unlinked regions, and gene-gene and gene-environment interactions, via an adjustment to the conditioning argument that results in differing numbers of pseudocontrols depending on the model being fitted.
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Several Setaria QTL intervals had multiple LOD peaks and were composed of multiple syntenic blocks, suggesting that observed QTL represent multiple tightly linked loci.
Due to high correlations between the examined traits, it is highly likely that these loci have pleiotropic effects on multiple characters, rather than closely linked loci affecting individual characters.
Several QTL, such as QTL 4.1, 5.1, and 8.1, had multiple LOD peaks along the QTL interval, suggesting that several tightly linked loci may underlie a single QTL region.
However, multiple peaks in the F ratio profile of a trait per chromosome may also result from linkage disequilibria among alleles of linked loci in F2 animals, whereby the linkage disequilibrium increases while the distances between the considered loci decrease.
Genetic draft is the effect on a locus by selection on linked loci.
Bayesian assignment analysis, a method for dividing a collection of isolates into multiple genetic clusters on the basis of difference in allelic frequency at multiple marker loci was performed using BAPS ver. 5.2 [16] on the basis of the "Codon linkage model," employing the option of "clustering with linked loci".
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