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

Abstract

30Sprague Dawley (SD) rats are one of the most commonly used outbred rat strains. Despite 31 this, the genetic characteristics of SD are poorly understood. We collected behavioral data from 32 4,625 SD rats acquired predominantly from two commercial vendors, Charles River Laboratories 33 and Harlan Sprague Dawley Inc. Using double-digest genotyping-by-sequencing (ddGBS), we 34 obtained dense, high-quality genotypes at 234,887 SNPs across 4,061 rats. This genetic data 35 allowed us to characterize the variation present in Charles River vs. Harlan SD rats. We found that 36 the two populations are highly diverged (FST > 0.4). We also used these data to perform a genome-37 wide association study (GWAS) of Pavlovian conditioned approach (PavCA), which assesses the 38 propensity for rats to attribute motivational value to discrete, reward-associated cues. Due to the 39 genetic divergence between rats from Charles River and Harlan, we performed two separate 40 GWAS by fitting a linear mixed model that accounted for within vendor population structure and 41 using meta-analysis to jointly analyze the two studies. We identified 18 independent loci that were 42 significantly associated with one or more metrics used to describe PavCA; we also identified 3 43 loci that were body weight, which was only measured in a subset of the rats. The genetic 44 characterization of SD rats is a valuable resource for the rat community that can be used to inform 45 future study design. 46 AuthorSummary 47 Outbred Sprague Dawley rats are among the most commonly used rats for neuroscience, 48 physiology and pharmacological research. SD rats are sold by several commercial vendors, 49 including Charles River Laboratories and Harlan Sprague Dawley Inc. (now Envigo). Despite their 50wide spread use, little is known about the genetic diversity of SD. We genotyped more than 4,000 51 2 SD rats, which we used to characterize genetic differences between SD rats from Charles River 52 Laboratories and Harlan. Our analysis revealed that the two SD colonies are highly divergent. We 53 also performed a genome-wide association study (GWAS) for Pavlovian conditioned approach 54 (PavCA), which assesses the propensity for rats to attribute motivational value to discrete, reward-55 associated cues. Our results demonstrate that, despite sharing an identical name, SD rats are 56 obtained from different vendors are genetically very different. We conclude that results obtained 57 using SD rats should not be presented without also carefully noting the vendor. 58 Introduction 59Rats are among the most commonly used organisms for experimental psychology and 60 biomedical research. Whereas research using mice makes extensive use of inbred strains, in rats, 61 it is more common to use commercially available outbred populations. Among the commercially 62 available outbred rat populations, the Sprague Dawley strain (SD) is one of the most widely used. 63SD rats are distributed by several vendors. Each vendor has multiple breeding locations, and each 64 breeding locatio...

Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats

“…The protocol we present here is the culmination of careful testing and optimization of each step of the GBS protocol for rats. We have now applied the approach to 4,973 HS rats, as well as 4,608 Sprague Dawley rats (Gileta et al 2018).…”

“…Tissue samples and DNA extraction Samples for this study originated from three sources: an in-house advanced intercross line (AIL) derived from LG/J and SM/J mice (Gonzales et al 2018), Sprague Dawley (SD) rats from Charles River Laboratories and Harlan Sprague Dawley, Inc. (Gileta et al 2018), and an HS rat colony (Woods and Mott 2017;Chitre et al 2018). Early stages of ddGBS optimization utilized AIL genomic DNA extracted from spleen by a standard salting-out protocol.…”

Investigating the influence of perinatal nicotine and alcohol exposure on the genetic profiles of dopaminergic neurons in the VTA using miRNA–mRNA analysis

“…All experimental protocols and surgical procedures were approved by the Institutional Animal Care and Use Committee (IACUC) and the University of Houston Animal Care Operations (ACO) and were performed in accordance with accepted guidelines and regulations. Sprague Dawley (SD) rats are one of the most commonly used outbred rat strains for biomedical research, providing 95% or greater accuracy on timed-pregnant gestation and ideal for safety and efficacy testing, aging, behavior, reproduction and surgical modifications 124,125 . Pregnant female SD rats purchased from Charles River (Charles River, Wilmington, MA, USA) were housed in the animal facility and were maintained at 22 ± 2 °C with 65% humidity, on a 12-h light/12-h dark cycle.…”

An MRI-Derived Neuroanatomical Atlas of the Fischer 344 Rat Brain

“…among others, have been shown to affect genetic and phenotypic presentation in rodents, not to mention the thoroughly documented physiological differences within the same rat strain obtained from different vendors (i.e. Sprague-Dawley obtained from Charles River versus Envigo) [37][38][39][40][41] . While no studies exist that directly compare neuroanatomical differences between rats subjected to any of the above confounding variables, care should be taken when choosing the rat strain, vendor, housing conditions, etc., when attempting to use resources generated from a specific population having experienced a facility-specific environment.…”