Roof rats (Rattus rattus) are common invasive pests in both urban and agricultural sites as well as a significant public health threat. The use of anticoagulant rodenticides to help control the rodent population poses a risk of developing resistance to these products. Several reports have associated the non-synonymous Single Nucleotide Polymorphism (nsSNP) Tyr25Phe (Y25F) of the vitamin K epoxide reductase subcomponent 1 (Vkorc1) gene to anticoagulant rodenticide resistance (Diaz et al. 2021). We conducted a nsSNP screen in the population of Rattus spp. in Orange County to determine the prevalence of the Y25F nsSNP in the sampled rodents. Thirty-seven live rat traps were set throughout the county and the species of each trapped rat was determined by sequencing the cytochrome oxide I (COI) gene using primers previously described in Goulois et al. (2015). Twenty specimens were identified as R. rattus and 12 as R. tanezumi (Asian house rat); the other five specimens were non-Rattus species. To further evaluate the rat species, we used tree-based methods using sequence alignments for three mitochondrial DNA regions, cytochrome b, COI, and non-coding displacement (D) loop using a different set of primers used by Robins et al. (2007). Sequences were aligned by Geneious Prime (v.2020.2.4), and maximum-likelihood phylogeny using 1,000 bootstrap replications was constructed using Mega (10.2.6). Sequences were compared to reference sequences in Robins et al. (2007) and Rattus norvegicus (Norway rat) was used to root the tree. Phylogenetic analysis confirmed the presence of R. tanezumi in our collected samples as well as two haplotypes of R. rattus. In addition to the concatenated data set, each gene was examined individually, and all phylogenetic trees generally agreed on topology. The Y25F nsSNP was present in both R. rattus (40%; 8 of 20) and R. tanezumi (16.67%; 2 of 12). Further genetic testing in Orange County and other areas of Southern California are needed to determine the extent of these Rattus populations and their hybridization as well as the presence of this adaptive trait.
