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In addition analysis showed no difference in the loci order of SA-LG21 and SA-LG2 groups in spite of the assumption of different recombination rate between sexes.
Linkage groups were built assuming an equal recombination rate between sexes; however, the loci order was also checked (using the 'Flips' option of CRI-MAP), assuming different recombination rates between sexes.
One of the exceptions was the loci order between closely linked markers.
The loci order, locations, and sequences were obtained from the UCSC Genome Browser database.
This index will serve as identifier for each allele (and keep the genome loci order) (step 2).
A loci order at multipoint LOD 3 and the most likely order of loci were determined within each of these two groups.
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Loci ordered as presented in Table 2.
Loci ordered by decreasing effect size (odds ratio (OR)).
For marker grouping and linked loci ordering, a LOD score of 6.0 to 9.0 and a minimum recombination fraction of 0.30 were used.
Marker grouping and linked loci ordering were performed using a minimum LOD threshold value of 6.0 and a minimum recombination fraction of 0.35.
In the joint data process, segregation data from individual populations are pooled and loci orders and genetic map distances are computed based on mean recombination frequencies and combined LOD scores (implemented in JoinMap® 4) [ 17].
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