Treatment- and population-dependent activity patterns of behavioral and expression QTLs

Abstract

Genetic control of gene expression and higher-order phenotypes is almost invariably dependent on environment and experimental conditions. We use two families of recombinant inbred strains of mice (LXS and BXD) to study treatment- and genotype-dependent control of hippocampal gene expression and behavioral phenotypes. We analyzed responses to all combinations of two experimental perturbations, ethanol and restraint stress, in both families, allowing for comparisons across 8 combinations of treatment and population. We introduce the concept of QTL activity patterns to characterize how associations between genomic loci and traits vary across treatments. We identified several significant behavioral QTLs and many expression QTLs (eQTLs). The behavioral QTLs are highly dependent on treatment and population. We classified eQTLs into three groups: cis-eQTLs (expression variation that maps to within 5 Mb of the cognate gene), syntenic trans-eQTLs (the gene and the QTL are on the same chromosome but not within 5 Mb), and non-syntenic trans-eQTLs (the gene and the QTL are on different chromosomes). We found that most non-syntenic trans-eQTLs were treatment-specific whereas both classes of syntenic eQTLs were more conserved across treatments. We also found there was a correlation between regions along the genome enriched for eQTLs and SNPs that were conserved across the LXS and BXD families. Genes with eQTLs that co-localized with the behavioral QTLs and displayed similar QTL activity patterns were identified as potential candidate genes associated with the phenotypes, yielding identification of novel genes as well as genes that have been previously associated with responses to ethanol.

Figure 1. QTL heatmap for behavioral phenotypes.

QTL mapping results for two anxiety-related phenotypes, total activity count (TOTAL ACTCNT) and total time spent in open quadrants (TOTAL OPEN), during the time spent in an elevated zero-maze. For each phenotype, each row, from top to bottom, represents the treatment groups SC, EC, SR, ER, respectively. Red indicates a positive correlation between the phenotype and the ILS or DBA/2J genotype at the marker, while blue indicates positive correlation between the phenotype and the ISS or C57BL/6J genotype at the marker. ILS and ISS are the parental strains of the LXS panel. C57BL/6J and DBA/2J are the parental strains of the BXD panel.

Figure 2. Expression QTL mapping.

Significant (FDR <5%) eQTLs are shown for (a) LXS and (a) BXD RI panels. The x- and y-axes show the physical position of the marker and transcript, respectively. The vertical lines indicate the separation of the chromosomes, which are denoted at the top of the figure. Expression QTLs that are conserved in 3, 2, and 1 other treatment conditions are indicated by black, red, and green dots, respectively. Blue dots indicate treatment specific eQTLs.

Figure 3. Treatment dependence of eQTL activity.

The figure shows the percentage of cis-eQTLs [(a) LXS and (b) BXD], syntenic trans-eQTLs [(c) LXS and (d) BXD], and non-syntenic trans-eQTLs [(e) LXS and (f) BXD] that belong to each of the 15 possible QTL activity patterns. eQTLs are conserved if the LRS >24 for the LXS panel and 26 for the BXD panel for more than one treatment.

Figure 4. Conservation of eQTLs and SNPs between BXD and LXS populations.

The conservation ratio for eQTLs (solid blue line) and SNPs (dashed red line) is shown as a function of genome position. The conservation ratio was calculated from the ratio of the number of features (eQTLs or SNPs) in the BXD population in a sliding window of 50 Mb that were conserved in the LXS population to the expected number of conserved features, given the number of features in the window and the fraction of conserved features across the entire genome. Most locations with a high amount of conservation of eQTLs also have a high amount of conservation of SNPs.

Figure 5. eQTLs with conserved QTL activity patterns.

The figure shows the maximum likelihood ratio statistic (LRS) for association between selected traits and loci for each experimental treatment and RI population. The LRS values of eQTLs are color-coded from green (no association, LRS = 0) to red (significant association, LRS = 24 for LXS and LRS = 26 for BXD, FDR = 5%), indicating the strength of the association between the locus and the trait. Genes that have been previously associated with ethanol have a blue background.

Figure 6. QTL activity patterns.

The figure shows the maximum likelihood ratio statistic (LRS) for association between selected traits for each experimental treatment near 136 Mb on Chr 3 (a), 9 Mb on Chr 14 (b), and 25 Mb on Chr 1 (c), the locations of the three significant behavioral QTLs. All gene expression transcripts that had an eQTL activity pattern similar to the phenotype QTL activity pattern are shown. The LRS values of eQTLs are color-coded from green (no association, LRS = 0) to red (significant association, LRS = 24 for LXS and LRS = 26 for BXD, FDR = 5%), indicating the strength of the association between the locus and the trait. Genes that have been previously associated with ethanol have a blue background.

Figure 7. QTL activity pattern correlation network.

The correlation networks were created from the Pearson correlation between QTL activity patterns of behavioral phenotype and gene expression transcripts at three locations with treatment-dependent behavioral phenotype QTLs: Chr 3 from 126 to 142 Mb (a), which was associated with the ACTCNT phenotype in the LXS panel, Chr 14 from 0 to 24 Mb (b), which was associated with the OPEN phenotype in the LXS panel, and Chr 1 from 22 to 32 Mb (c), which was associated with ACTCNT in the BXD. Traits are connected in the network if the Pearson correlation coefficient of the QTL activity pattern is greater than 0.8. Nodes with yellow and blue backgrounds denote phenotypes and genes that have been previously associated with ethanol, respectively. Genes that had similar QTL activity patterns as the phenotypes (Figure 6) are in red text. Elliptical nodes identify genes that are located on different chromosomes than the behavioral QTLs.