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There were two test linkages performed between the EMS and VSTORM datasets.
A minimum LOD ≥ 10.0 and a maximum distance ≤ 50 cM were used to test linkages among markers.
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We used GENEPOP version 4.2 to test linkage disequilibrium and Hardy Weinberg equilibrium (Rousset, 2008).
In addition, the joint use of LD and LA makes it possible to test linkage alone or linkage disequilibrium separately [ 1].
To test linkage of the tgr2 BTG-active phenotype with the candidate genes, 38 individuals were analyzed.
We performed the same simulation design using the non-parametric bootstrap test (Lebreton et al., 1998) adapted for association analysis to test linkage versus pleiotropy.
We also used this program to test linkage disequilibria and deviation from Hardy-Weinberg equilibrium (Markov chain parameters: 10,000 dememorization steps, 100 batches, and 5,000 iterations per batch).
All the SNP analyses, such as Hardy Weinberg equilibrium test, linkage disequlibrium and haplotype inference, were performed with SNP Alyze (version 5.1; DYNACOM).
QTL software was adapted to test linkage statistical significance of each unique Solexa paired-end sequences using the 465 bins on the genetic map.
When choosing the preferred E linkage strategy to use in other studies two issues need to be considered in addition to the levels of accuracy found in the test linkage.
To test if F was significantly different from zero and to test linkage disequilibrium, we used 1000 Monte Carlo permutations (alleles among individuals) and a Bonferroni correction (95%, α = 0.05).
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