The two main components of this layer are the map manager and the repository manager.
Map Manager QTX, vQTXb20 (Manly et al. 2001) was used for linkage map construction with Kosambi map function.
Among the polymorphic markers, four markers alone segregated in the expected ratio of 1 1 at 0.01 % probability, and were added to the previous linkage map by reconstruction of the map with a logarithm of odds (LOD) of 3.0 and a minimal distance of 50 cM, by Map Manager QTX software (Manly et al. 2001) using the Haldane mapping function.
To detect epistatic interaction, we performed two-locus interaction analysis for all possible markers using Map Manager QTXb20.
Initially, interval mapping using a least-squares regression method (Map Manager QTXb20) was performed on 236 F2 hybrids using 60 Mit markers (2 to 4 markers per chromosome).
With regard to the circadian ratio, QTL analysis using Map Manager QTXb20 revealed a significant QTL (Arrhythmicity; Arrh-1, LOD 5.26) on Chr 8 (Fig. 3A, Table 2).
The genotype data were analyzed with Map Manager QTb29ppc [75] to estimate intervals between loci using the Kosambi mapping function and to obtain the recombinant fraction (R) relative to the centromere.
The parental male mouse retains a heterozygous allele for loci (Fig. S1); therefore, we excluded the F2 mice produced by the B/C×B/B backcross from the QTL analysis using Map Manager QTXb20.
At the loci where the genotype of the parental variant male were B/B (Fig. S1), these markesr were excluded from the analyses using Map Manager QTXb20 and QTL Express.
First, the significance of the overall effect was established by 1000 runs of a permutation test using Map Manager QTXb20 and then, if the overall effect exceeded the genome-wide 5% significance level, the interaction was tested using approximate genome-wide thresholds obtained as described by Knott et al. [20].
