Zhang-James Y, Middleton FA, Faraone SV. Genetic architecture of Wistar-Kyoto rat and spontaneously hypertensive rat substrains from different sources. Physiol Genomics 45: 528 -538, 2013. First published May 14, 2013 doi:10.1152/physiolgenomics.00002.2013.-The spontaneously hypertensive rat (SHR) has been widely used as a model for studies of hypertension and attention deficit/hyperactivity disorder. The inbred Wistar-Kyoto (WKY) rat, derived from the same ancestral outbred Wistar rat as the SHR, are normotensive and have been used as the closest genetic control for the SHR, although the WKY has also been used as a model for depression. Notably, however, substantial behavioral and genetic differences among the WKY substrains, usually from the different vendors and breeders, have been observed. These differences have often been overlooked in prior studies, leading to inconsistent and even contradictory findings. The complicated breeding history of the SHR and WKY rats and the lack of a comprehensive understanding of the genetic background of different commercial substrains make the selection of control rats a daunting task, even for researchers who are mindful of their genetic heterogeneity. In this study, we examined the genetic relationship of 16 commonly used WKY and SHR rat substrains using genome-wide SNP genotyping data. Our results confirmed a large genetic divergence and complex relationships among the SHR and WKY substrains. This understanding, although incomplete without the genome sequence, provides useful guidance in selecting substrains and helps to interpret previous reports when the source of the animals was known. Moreover, we found two closely related, yet distinct WKY substrains that may provide novel opportunities in modeling psychiatric disorders.WKY; SHR; autism; ADHD; inbred rat; animal models; SNP; behavior THE SPONTANEOUSLY HYPERTENSIVE rat (SHR) is an inbred strain established from outbred Wistar rats selected for high blood pressure (8a). Although the SHR develops hypertension spontaneously at the age of 7-15 wk (36), prior to this age they have been used and validated as a model for attention deficit/hyperactivity disorder (ADHD), demonstrating all three ADHD core symptoms: hyperactivity, impulsivity, and inattentiveness (25, 28). The Wistar-Kyoto (WKY) strain was established from the same parental Wistar stock as the SHR and as a result has been commonly used as a control strain for the SHR (8a). Notably, however, the sources of WKY rats often varies between studies, and significant variability in the comparative results that employed these substrains has been noted, probably because the WKY breeding stock was distributed to different breeders prior to being fully inbred (11,13,21). In addition, the littermate pairings that produced the inbred WKY from the Wistar rat were initiated Ͼ10 yr after the inbreeding for the SHR was initiated (13), thus increasing the heterogeneity between the WKY and SHR and leading some to question the validity of the WKY as a control strain for SHR (30). ...