Fig. 5 | Nature Communications

Fig. 5

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

Fig. 5

Fine mapping of diet-associated ANA QTL. a Stacked percent bar plot shows distribution of ANA between three dietary groups caloric restriction (nANA− = 239, nANA+ = 64), control (nANA− = 319, nANA+ = 192) and western diet (nANA− = 149, nANA+ = 145) in AIL mice. b The X-Y line plot depicts the log of the odds (LOD) ratios on the y-axis and positions on chromosome 17 (Mb) on the x-axis with the genome-wide threshold indicated in red. The insert below shows genes present in the ANA QTL. While genes highlighted in blue contain consequential variation derived from the genome of the NZM2410/J mice, genes shown in orange are also differentially expressed between ANA-positive and ANA-negative mice. c Stacked percent bar plot illustrating the distribution of ANA+ (n = 401) vs. ANA (n = 707) mice in the AIL population based on the allele within the peak SNP (UNC27797171; nAA = 104, nAG = 459 and nGG = 545) and diet (ncalorie restricted = 303, ncontrol = 511 and nwestern = 294). While the A allele is derived from NZM2410/J mice, the G allele is derived from the MRL/MpJ, BxD2/TyJ, or CAST/EiJ mice. Data for panels a and c were analyzed using the X2 test with Fischer exact test as a post hoc test. *p < 0.05, **p < 0.01, n.s., not significant. d PCoA plot showing differences in beta diversity in the microbiome (unweighted UniFrac distance, left panel) and mycobiome (Jaccard distance, right panel) between ANA positive (nmicrobiome = 16, nmycobiome = 16) and negative samples (nmicrobiome = 37, nmycobiome = 18). Statistical significance was assessed using the adonis function in R (permutations = 999). e Boxplot (the band indicates the median, the box indicates the first and third quartiles and whiskers indicate 1.5*interquartile range) illustrates significant functional microbial (FMC3 & FMC5) and fungal (FFC6) communities associated with ANA presence (nFMC = 16, nFFC = 16) or absence (nFMC = 37, nFFC = 18) (Mann–Whitney U test, *p < 0.05). f Heatmap showing the expression of genes that are differentially expressed for the ANA phenotype and present within the ANA QTL. g Five-way Venn diagram demonstrating a multi-omics strategy used to fine map a diet-regulated gene within the ANA QTL. Source data for (a, cf) are provided in the Source Data file

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