Next-Generation Snow Leopard Population Assessment Tool: Multiplex-PCR SNP Panel for Individual Identification From...

Area of Science:

• Conservation Genetics
• Wildlife Forensics
• Genomic Analysis

Background:

• Existing single nucleotide polymorphism (SNP) panel methods for non-invasive sample genotyping lack broad usability for international conservation.
• Key limitations include high cost, complex laboratory protocols, and inaccessible bioinformatics for panel design and analysis.

Purpose of the Study:

• To present a broadly applicable, cost-effective, and user-friendly method for SNP panel development and analysis.
• To develop and validate a multiplex PCR SNP panel for snow leopard (Panthera uncia) individual identification using fecal samples.

Main Methods:

• Development of a 144-SNP multiplex PCR panel utilizing next-generation sequencing technology.
• Validation using paired tissue and fecal samples from zoo individuals, assessing allele call accuracy.
• Application to 235 field-collected fecal samples from Pakistan to evaluate reliability with low-quality and contaminated samples.

Main Results:

• The developed SNP panel demonstrated a minimum of 96.7% accuracy in allele calls per run.
• Reliable individual identification was achieved from low-quality, aged, and contaminated field-collected snow leopard fecal samples.
• The panel successfully identified first-order relatives and provided insights into sample geographic origins.

Conclusions:

• The presented SNP panel development method is cost-effective, streamlined, and user-friendly, suitable for diverse conservation projects.
• This tool empowers snow leopard research for population assessment and can be adapted for other species with available genomic data.