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Rectal swab DNA collection protocol for PCR genotyping in rats
Audrey E Kaye1, Jacob W Proctor-Bonbright1, Jai Y Yu1,2,3
1Neuroscience Institute, University of Chicago, Chicago, IL 60637, USA.
Biotechniques
|April 23, 2024
Summary
Rectal swabbing offers a minimally invasive method for collecting DNA from laboratory animals. This study presents a validated protocol for efficient and repeatable animal genotyping, reducing discomfort and injury.
Area of Science:
- Animal Science
- Molecular Biology
- Genetics
Background:
- Standard DNA collection methods for animal genotyping, such as tissue amputation, cause significant discomfort and injury.
- A minimally invasive alternative, rectal swabbing, has been proposed but lacks a standardized, evidence-based protocol.
- Efficient and ethical DNA collection is crucial for laboratory animal research.
Purpose of the Study:
- To evaluate the impact of various rectal swabbing parameters on DNA quality for Polymerase Chain Reaction (PCR) analysis.
- To develop and present a reliable protocol for genotyping laboratory rats using rectal swabs.
- To establish a fast, minimally invasive, and repeatable method for animal genotyping.
Main Methods:
- Investigated the effect of sample collection parameters (e.g., number of scrapes) on DNA yield and quality.
- Compared PCR results from rectal swabs with those from traditional ear clip samples.
- Assessed the influence of residual fecal matter on PCR amplification success.
Main Results:
- Samples obtained with 2-8 rectal scrapes yielded sufficient DNA for amplifying targets up to approximately 1800 base pairs using PCR.
- Rectal swabbing produced PCR results comparable in utility to those from ear clip samples.
- The presence of residual fecal matter or cellular debris did not negatively impact PCR results.
Conclusions:
- Rectal swabbing is an effective, minimally invasive technique for obtaining DNA for animal genotyping.
- The developed protocol allows for rapid (3-5 hours) and repeatable genotyping of rat litters.
- This method provides a humane alternative to tissue amputation for routine genetic analysis in laboratory animals.
