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The R2 value of linkage disequilibrium was calculated for all possible marker pairs within each chromosome.
To detect the small-effect QTL, the threshold value of linkage was set as P = 0.05 (Chi-square test).
To identify these potential small-effect QTL, we reanalyzed the data using a lower threshold value of linkage (P = 0.05).
Most of these genomic regions did not reach a genome-wide significant threshold value of linkage, with P values between 0.05 and 0.001 [ 1- 5].
This suggests that there must be other susceptibility genes whose contributions were not big enough to reach the stringent significance threshold value of linkage analysis.
However, Cia2 contributed to only 16% of the phenotype variations, indicating that there should be some small-effect QTL whose contributions to CIA were not big enough to reach the significant threshold value of linkage.
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If, ultimately, the claims-reporting requirement for Medicare Advantage plans is not enforced, this may limit the value of linkages like the one described in this paper.
In the absence of recombination, linkage disequilibrium measures tend to reflect the shape of the tree (the tendency of mutations to appear on related branches [52]) and maximal absolute values of linkage disequilibrium tend to decrease with decreasing frequencies of the mutations.
In fact, the 1,403 comparisons of nuclear vs. mitochondrial sites yielded 772 significant values of linkage disequilibrium (see Additional File 1, Table S1).
The program Powermarker was also used to estimate linkage disequilibrium between the microsatellite loci, through the coefficients D' [ 27] and r 2 [ 28] and also to estimate the significance of the values of linkage disequilibrium between pairs of loci.
The boxes painted in black indicate values of linkage disequilibrium that are highly significant, present mainly in the superior portion of the graph, which represents the complete set of 485 accessions (thematic collection).
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