Comparison of single nucleotide polymorphisms and microsatellites in non-invasive genetic monitoring of a wolf population

• Published in: Archives of biological sciences Vol. 64; no. 1; pp. 321 - 335
• Main Authors: Fabbri, Elena, Caniglia, R., Mucci, Nadia, Thomsen, H.P., Krag, K., Pertoldi, C., Loeschcke, V., Randi, E.
• Format: Journal Article
• Language: English
• Published: University of Belgrade, University of Novi Sad 2012
• Subjects: Canis lupus; fecal samples; genotyping errors; Pyrosequencing; SNaPshot; TaqMan® Assay
• ISSN: 0354-4664; 1821-4339
• DOI: 10.2298/ABS1201321F

Single nucleotide polymorphisms (SNPs) which represent the most widespread
source of sequence variation in genomes, are becoming a routine application
in several fields such as forensics, ecology and conservation genetics. Their
use, requiring short amplifications, may allow a more efficient genotyping of
degraded DNA. We provide the first application of SNP genotyping in an
Italian non-invasive genetic monitoring project of the wolf. We compared
three different techniques for genotyping SNPs: pyrosequencing, SNaPshot? and
TaqMan? Probe Assay in Real-Time PCR. We successively genotyped nine SNPs
using the TaqMan Probe Assay in 51 Italian wolves, 57 domestic dogs, 15 wolf
x dog hybrids and 313 wolf scats collected in the northern Apennines. The
obtained results were used to estimate genetic variability and PCR error
rates in SNP genotyping protocols compared to standard microsatellite
analysis. We evaluated the cost, laboratory effort and reliability of these
different markers and discuss the possible future use of VeraCode, SNPlex and
Fluidigm EP1 system in wild population monitoring.
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