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We then recoded the 42 randomised trials according to these broader linkage categories for comparison of linkages against outcomes.
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The physical map was used for linkage analysis which enabled comparison of linkage maps of sub-populations.
A comparison of linkage maps constructed in different species is feasible and reliable, provided that a sufficient number of orthologous genes are mapped.
This approach is an alternative to the direct comparison of linkage positions used in the Arachis-Lotus comparison.
However, direct comparison of linkage maps has to be interpreted cautiously, given the low number of shared SSR markers between studies.
This method may have missed L. parva contigs that were not expressed in L. goodei, but these contigs are uninformative for the comparison of linkage maps.
Comparison of linkage analysis and GWAS has shown that GWAS, where all SNPs are fitted simultaneously as random effects, has greater power to discriminate linked QTL [ 40], especially those of limited or modest sized effects [ 41].
Pairwise comparisons of linkage disequilibrium (LD) among loci were computed with the dedicated procedure of the TASSEL software, using 1,000 permutations.
Investigations of linkage validity are rare [ 14], and comparisons of linkage strategies uncommon [ 15]; however, available assessments of matching strategies have shown that linkage with limited personal information can be useful in a number of areas [ 10- 16, 16- 18].
Table S1 (Additional File 3) provides complete information on the map locations of all markers, where it can also be seen that there was no disagreement in the order of shared markers in any of the six pairwise comparisons of linkage maps, or between the consensus map and any individual map.
Comparison of genetic linkage maps and the physical linkage map also pointed out a misassembly on the long arm of chromosome 12 (between 48.8 Mbp and 61.7 Mbp; Additional file 6) in version 2.4 of the tomato genome.
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