Long-read whole-genome sequencing of SHR rat substrains with distinct substance use phenotypes

The Spontaneously Hypertensive Rat (SHR) is a widely used model for hypertension and, more recently, for neuropsychiatric disorders such as ADHD and Substance Use Disorder (SUD). Despite a common origin, SHR substrains from different vendors exhibit distinct behavioral phenotypes, particularly in models of SUD. This study characterizes the genomic landscape of two such substrains, SHR/NCrl and SHR/NHsd, using high-fidelity long-read sequencing to identify genetic variants associated with their phenotypic divergence. We identified over 5.8 million variants shared by both substrains compared to the reference genome. These include high-impact variants in genes involved in blood pressure regulation, such as Ramp2 and Npy1r, providing a potential genetic basis for their hypertensive phenotype. We also discovered 17,618 high-confidence variants unique to each substrain. From these, we selected 500 high-quality SNP markers suitable for genetic mapping studies, such as Reduced Complexity Crosses (RCCs). Computational predictions indicated moderate-impact variants in genes involved in neuroplasticity and synaptic function. Notably, the SHR/NHsd substrain carries unique missense variants in Ptpro and Tenm2, genes linked to glutamatergic synapses and SUD-related pathways. In contrast, the SHR/NCrl substrain has unique variants in genes such as Wwc1 and Pcdh10, which are involved in synaptic plasticity and neurotransmission. These findings provide a critical genomic resource for dissecting the heritable components of SUD-related behaviors.