Fig. 1 | Nature Communications

Fig. 1

From: Gene-diet interactions associated with complex trait variation in an advanced intercross outbred mouse line

Fig. 1

Phenotyping, QTL identification, and fine mapping of dietary perturbations in an AIL mouse population. a Heatmap illustrating distribution (normalized between 1.5 to −1.5) of the investigated complex traits in AIL mice for the three dietary regimens in both sexes. Data were analyzed using Kruskal–Wallis test followed by Dunn’s test for multiple comparisons (P-value was adjusted by Sidak correction procedure). For binary phenotypes (ANA and NASH), chi-square test was performed followed by Fisher exact test for multiple comparisons where p-values were adjusted by Benjamini-Hochberg correction procedure. The asterisk (*) within each box indicates statistical significance (Padj < 0.05), whereas the different color codes indicate the association of the particular trait with either diet (yellow), sex (pink) or both (blue). Extension of the abbreviations of the traits and their sample size (n) are provided in Supplementary table 1. b Manhattan plot showing QTL (αgw < 0.05) in the AIL population associated with various complex traits. The x-axis describes chromosomes in the C57BL/6J mouse genome (reference mouse assembly mm10), while the y-axis represents the LOD score (log of odds ratios). The QTL marked with blue represent the additive model, while gold and pink represent diet- and sex-interacting QTL, respectively. c An overview of variants called from 4 founder mouse strains (BxD2/TyJ, MRL/MpJ, NZM2410J, and CAST/EiJ) compared to the C57BL/6J mouse genome reference assembly (mm10). Each track in the circle indicates the relative density of single nucleotide polymorphisms (SNPs) and insertions and deletions (indels) for four strains across mouse chromosomes. d Schematic representation of fine-mapped genes for weight (6 months) under the influence of diet using whole-genome sequencing. The uppermost panel shows founders coefficients for significant QTL in chromosome 5. The middle panel shows a line plot for QTL with a red line indicating a genome-wide significance level (αgw < 0.05). The lowermost panel shows the genes present within the QTL and variants differing between NZM2410/J and MRL/MpJ strains, leading to the exclusion of several candidate genes. Source data for (a) are provided in the Source Data file

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