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The consequence of ignoring mutation is that even with physical linkage, the expected association between loci is incomplete and leads to an underestimation of r 2. This effect increases as historical time increases.
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This was done to avoid false linkages from the expected Mendelian segregation ratio.
Of the 3,023 F1D SNPs that were classified as PHR and that were parentally concordant, all but 14 (0.46%) were able to be incorporated into a linkage map of the expected seven linkage groups based upon segregation in the 21-member F2D population.
The number of linkage groups exceed the expected haploid number of linkage groups (18 linkage groups), suggesting that more markers are required to fill the gap between adjacent markers.
Using this methodology, amplicons targeted to gene sequences were screened across a B. napus mapping population and the resulting allele scoring strings for 24 markers linkage mapped to the expected regions of the genome.
As a control for centromere-unrelated linkage, we calculated the expected physical distance between two unlinked loci by using the average number of centimorgans per kilobase reported for each chromosome at http://www.yeastgenome.org/pgMaps/pgMap.shtml.shtml
The samples would not represent a panmictic population, causing deviations from the expected linkage disequilibria and a bias in the linkage disequilibrium estimation of Ne.
The observed genome length (Goa) was simply the addition of all observed linkage group lengths and the expected genome length (Ge) was calculated by multiplying the length (cM) of each linkage group by (m + 1)/(m - 1), where m is the number of loci in each linkage group see [ 28].
Thus, we could justifiably use relatively liberal criteria for linkage map construction, and any features of the linkage map that deviated from the expected pattern, such as the number of linkage groups or marker order within groups, we examined individually for confirmation.
This intraspecific A. batizocoi genetic map has nine major linkage groups instead of the expected 10.
For example, the expected linkage disequilibrium (LD) for the same recombination rate will be reduced by doubling the effective population size Ne.
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