A significant epistasis was identified between a marker at the QTL on chromosome 1, SNP 21607030 which is 1.3 Mbp above FLM, and a marker at the first chromosome 4 QTL, MSAT 4.39 which is 0.18 Mbp above the FRI locus.
We found a significant interaction between a marker at 3 15,342,299 and sex; inclusion of this interaction could increase the fit of our model by 2.4 LOD and capture an additional 2.4% of the variation (data not shown).
The loadings are then used to quantify local haplotype sharing between individuals at each marker.
We calculated the LOD of association between the genotypes at each marker (markers were simulated every 1.0 cM) and sleep-related phenotypes (the sleep duration, swimming distance, bout number, bout duration or waking activity) and using Haley-Knott regression, while including age at sampling (5- to 7-years old) as covariates.
Three-point and multi-point analyses were used to determine the order and interval distances between the markers at each LG.
The merging step utilized the cytogenetic data obtained as part of this study, as well as the 2-point Lod scores between the markers at the extremes of each linkage group.
In this figure, each horizontal line denotes the distance between the markers at the transition between heterozygosity and homozygosity.
The association between markers of interest at baseline, at M12, association between markers at baseline and the change between baseline and M12, were tested using Spearman's non parametric correlation to study association of two continuous variables and Mann-Whitney test to study association of one continuous variable and one categorical variable.
The overall physical coverage was 155.4 Mbp compared to the 207.3 Mbp of T1E (75.0%) and the 211.9 Mbp of T×E (73.3%), and there was low coverage between mapped markers at the extremes of certain linkage groups (compared to T1E): coverage of G4, G5, and G8 was only 32.4%, 36.4%, and 70.2%, respectively of the distance of the same groups in T1E.
Therefore, one expects to find some LD values greater between close markers than between distant markers at a given moment in the evolution of a population.
