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This once more indicates the strength of using a hierarchical multi-locus strategy with rbcL as a backbone locus, as proposed by the CBOL Plant Working Group [4].
Because the majority of the published GWAS concentrate on single-locus strategies to identify novel breast cancer susceptibility loci, a candidate gene approach restricted to specific pathway related gene polymorphisms to more effectively mine GWAS data is presented considering moderately associated SNPs.
A draft 1000 1 framework map was then built with Carthagene software [ 14], using a stepwise locus adding strategy (data not shown).
A 1000 1 framework map was built with buildfw option using a stepwise locus adding strategy under an haploid model of fragment retention.
A framework map was built using buildfw option, which constructs a 1000 1 framework map by a stepwise locus adding strategy under the haploid model of fragment retention.
For each linkage group, a 1000 1 framework map (likelihood of the map at least 1000-fold higher than the next highest likelihood using the same markers in alternate orders) was also built by using a stepwise locus adding strategy (BuilFW command).
However, our simulations focus attention on an important caveat to the many-locus sampling strategy – the loss of information at short loci (0.5 kb in our simulations) when θ is small (0.001 in our simulations).
Note that theoretical predictions encourage sampling more loci even at small values of θ; a 20 loci sampling strategy produced the highest predicted accuracy for each value of θ when each individual was sequenced at 10 kb.
The alignment and corresponding single-gene tree characteristics (see below) served as a basis for several alternative locus selection strategies.
To generate a set of candidate genes for the listed loci, a strategy schematically represented in Figure 1 was followed.
This framework was constructed using a stepwise locus-adding strategy, starting from the triplet of markers whose order is the most likely ("buildfw" option).
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