Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies

Abstract

Sprague Dawley (SD) rats are among the most widely used outbred laboratory rat populations. Despite this, the genetic characteristics of SD rats have not been clearly described, and SD rats are rarely used for experiments aimed at exploring genotype-phenotype relationships. In order to use SD rats to perform a genome-wide association study (GWAS), we collected behavioral data from 4,625 SD rats that were predominantly obtained from two commercial vendors, Charles River Laboratories and Harlan Sprague Dawley Inc. Using double-digest genotyping-by-sequencing (ddGBS), we obtained dense, high-quality genotypes at 291,438 SNPs across 4,061 rats. This genetic data allowed us to characterize the variation present in Charles River vs. Harlan SD rats. We found that the two populations are highly diverged (FST > 0.4). Furthermore, even for rats obtained from the same vendor, there was strong population structure across breeding facilities and even between rooms at the same facility. We performed multiple separate GWAS by fitting a linear mixed model that accounted for population structure and using meta-analysis to jointly analyze all cohorts. Our study examined Pavlovian conditioned approach (PavCA) behavior, which assesses the propensity for rats to attribute incentive salience to reward-associated cues. We identified 46 significant associations for the various metrics used to define PavCA. The surprising degree of population structure among SD rats from different sources has important implications for their use in both genetic and non-genetic studies.

Genome-wide association study in a rat model of temperament identifies multiple loci for exploratory locomotion and anxiety-like traits

“…Both phenotypic and genetic correlations are also quite strong among these traits in the F 2 animals, with anxiety-related traits showing moderate correlations, indicating a similar genetic architecture for these behaviors. Although PavCA traits exhibit low SNP heritability as has been reported for Sprague-Dawley rats ( Gileta et al, 2022 ), they are strongly correlated with EL traits in our F 2 animals, and the genetic correlations are especially strong. This is notable as outbred rats have not shown such a relationship between EL and sign-tracking/goal-tracking behavior ( Robinson and Flagel, 2009 ; Flagel et al, 2010 ; Hughson et al, 2019 ).…”

Genome-Wide Association Study in a Rat Model of Temperament Identifies Multiple Loci for Exploratory Locomotion and Anxiety-Like Traits

“…Although PavCA traits exhibit low SNP heritability as has been reported for Sprague-Dawley rats (Gileta et al, 2022), they are strongly correlated with EL traits in our F 2 animals, and the genetic correlations are especially strong. This is notable as outbred rats have not shown such a relationship between EL and sign-tracking/goal-tracking behavior (Flagel et al, 2010;Hughson et al, 2019;Robinson & Flagel, 2009).…”

Basal Forebrain Chemogenetic Inhibition Converts the Attentional Control Mode of Goal-Trackers to That of Sign-Trackers

“…This finding reflected that, in this sample, females were more likely to be classified as STs and males as GTs. However, such a relationship between these two categories was not reliably observed in prior experiments ( Pitchers et al, 2015 ), perhaps reflecting considerable variations in the distribution of these phenotypes in cohorts obtained from different vendors, as well as from different breeding barriers of the same vendors, and associated genetic heterogeneity ( Fitzpatrick et al, 2013 ; Gileta et al, 2022 ). Furthermore, an ANOVA on the effects of sex and phenotype on PCA scores obtained from test day 5 indicated neither a main effect of sex nor an interaction between the effects of sex and phenotype (both p > 0.93).…”