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The optimal order and spacing of markers for each linkage group was determined using the DGmap software [27].
Similar simulations are available for the number and spacing of markers, and for number of BC cycles.
Average spacing of markers genome-wide was 1.99 cM/SNP.
First, we calculated s, the average spacing of markers, as the sum of the lengths of the 10 linkage maps within each family divided by the total number of mapped intervals (i.e., the total number of markers minus the number of linkage groups, 10).
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The bubble interfaces are described by a spectral mesh and is advected according to the fluid velocity in such a manner so as to preserve equal arc length spacing of marker points.
Each set of multiplex PCR primers were designed to give a logarithmic progression of DNA product sizes, ranging from 200 bp to 650 bp in length, which gave regular spacing of marker bands when products were size-separated by agarose gel electrophoresis.
In the Methods section we report a simulated annealing algorithm that performs an exploration of the space of markers assigned to drugs and drug-to-sample protocols with a gradual increased bias towards improvements on the overall response rate.
These markers were not generated using GBS, but the data set was chosen because the total number of SSRs and relative spacing of the markers approximate what could be expected per individual from a low-coverage deployment of GBS.
First, Genome Estimation size 1 (Ge1) was calculated to account for chromosome ends by adding two times the average spacing of framework markers to the length of each linkage group [ 52].
This allows the inclusion of these markers in the linkage map but it is unclear how this analysis may interact with the limited recombination in the male However, despite the spacing of these markers, overall the male map had more limited recombination than the female (see Figure 5).
This result could be further confirmed by using a more densely spaced set of markers.
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