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More affordable and effective noninvasive single nucleotide polymorphism genotyping using high-throughput amplicon
Charlotte E Eriksson1, Joel Ruprecht1, Taal Levi1
1Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA.
Molecular Ecology Resources
|June 11, 2020
Summary
This study presents a cost-effective method for noninvasive wildlife genotyping using single nucleotide polymorphisms (SNPs) and amplicon sequencing. The new protocol significantly increases genotyping success rates for degraded DNA, aiding wildlife conservation efforts.
Area of Science:
- Wildlife genetics
- Molecular ecology
- Conservation biology
Background:
- Noninvasive genotyping is crucial for wildlife research but often hampered by high costs and low success rates.
- Traditional microsatellite markers can lead to genotyping errors and data loss, potentially misguiding conservation actions.
- Single nucleotide polymorphisms (SNPs) offer an alternative due to shorter DNA fragment amplification and reduced error rates.
Purpose of the Study:
- To develop and validate a cost-effective, accurate protocol for noninvasive SNP genotyping using multiplexed amplicon sequencing.
- To optimize the method for degraded DNA samples commonly found in wildlife research.
- To improve the efficiency and affordability of wildlife population monitoring.
Main Methods:
- Developed a protocol for noninvasive SNP genotyping using multiplexed amplicon sequencing, optimized for degraded DNA.
- Validated the method on coyote (Canis latrans) samples including scats, hairs, and tissues, using 26 SNPs.
- Assessed genotyping success rates, accuracy, and cost-effectiveness compared to traditional methods.
Main Results:
- Achieved high genotyping success rates: 93% for scats and 100% for hair and tissues.
- Demonstrated a low cost of under $5 per PCR replicate (excluding labor).
- Confirmed genotype accuracy through matching scat genotypes to known individuals' territories.
Conclusions:
- The developed protocol offers a significant improvement in noninvasive genotyping success, accuracy, and cost-effectiveness.
- This method can increase the utility of noninvasive techniques for monitoring and conserving free-ranging wildlife populations.
- Optimizing PCR product cleanup is important for maximizing genotyping success.
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