Rectal Swab DNA Collection Protocol for PCR Genotyping in Rats

DNA collection is essential for genotyping laboratory animals. However, common collection methods require tissue amputation, causing discomfort and injury. Rectal swabbing has been proposed as an effective non-invasive alternative, but an evidence-backed protocol for the technique remains unavailable. We evaluate the effect of collection parameters on PCR result quality and present a genotyping protocol that can yield results for a litter of rats within 3-5 hours. We found that samples with 2-8 scrapes produced enough DNA to amplify targets up to ~1800bp long using PCR. Rectal swabbing produced PCR results with similar quality to ear clip samples, and results were unaffected by residual fecal matter or cell debris. Our protocol enables fast, non-invasive, and repeatable genotyping using commercial PCR reagents.