Comparison of single nucleotide polymorphisms and microsatellites in non-invasive genetic monitoring of a wolf population
2012
Fabbri, E., Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia - Bologna (Italy). Laboratorio di Genetica | Caniglia, R., Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia - Bologna (Italy). Laboratorio di Genetica | Mucci, N., Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia - Bologna (Italy). Laboratorio di Genetica | Thomsen, H.P., University of Aarhus, Aarhus C (Denmark). Department of Biological Sciences | Krag, K., University of Aarhus, Aarhus C (Denmark). Department of Biological Sciences | Pertoldi, C., University of Aarhus, Aarhus C (Denmark). Department of Biological Sciences | Loeschcke, V., University of Aarhus, Aarhus C (Denmark). Department of Biological Sciences | Randi, E., Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia - Bologna (Italy). Laboratorio di Genetica
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(R) and TaqMan(R) 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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