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One challenge of this model is that condensin II would need to generate linkages only within the same chromatid and not between different chromosomes.
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To generate linkage disequilibrium during the 1010 generations, the recombination rate between loci was set to 0.06.
It is more difficult to generate linkage maps for species that do not meet these criteria.
We used HapMap data (http://www.hapmap.org/) to generate linkage disequilibrium (LD) structure around rs719376, which indicated that it resides in an ∼56-kb block defined by markers rs9922666 and rs7205278 (chr16:29,605,876- 29,662,434) that contains the QPRT gene (data not shown).
Thus AFLP analysis is a useful tool to generate linkage maps [ 10].
The data are now used to generate linkage phase and Identity-By-Descent (IBD) estimations using the FlexQTL™ software [ 17].
Segregating SNPs, or those where one or both parents are heterozygous, can be used to generate linkage maps in these F1 populations.
Like individual selection models with multiplicative fitnesses, selection in this model does not generate linkage disequilibrium between the competition and policing loci.
The first stage uses telomeric and centromeric SNPs to identify recombinants, and to generate linkage data that map the causative locus approximately.
For instance, if DNA from a multigeneration pedigree is available, this can be used to a generate linkage map (e.g., Chagné et al. 2003).
We used the R package OneMap (Margarido et al. 2007) to generate linkage maps for informative markers in each parent (hereafter referred to as FvbPat for paternal and FvbMat for maternal, or Fvb for the set of linkage groups).
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