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Harmoinen et al. BMC Genomics (2021) 22:473 https://doi.org/10.1186/s12864-021-07761-5 RESEARCH ARTICLE Open Access Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples Jenni Harmoinen1* , Alina von Thaden2,3, Jouni Aspi1, Laura Kvist1, Berardino Cocchiararo2,4, Anne Jarausch2,3, Andrea Gazzola5, Teodora Sin5,6, Hannes Lohi7,8,9, Marjo K. Hytönen7,8,9, Ilpo Kojola10, Astrid Vik Stronen11,12, Romolo Caniglia13, Federica Mattucci13, Marco Galaverni14, Raquel Godinho15,16, Aritz Ruiz-González13,17, Ettore Randi18,19, Violeta Muñoz-Fuentes2,20† and Carsten Nowak2,4† Abstract Background: Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected a panel of 96 ancestry informative markers for wolves and dogs, derived from the Illumina CanineHD Whole-Genome BeadChip (174 K). We designed very short amplicons for genotyping on a microfluidic array, thus making the method suitable also for non-invasively collected samples. Results: Genotypes based on 93 SNPs from wolves sampled throughout Europe, purebred and non-pedigree dogs, and suspected hybrids showed that the new panel accurately identifies parental individuals, first-generation hybrids and first-generation backcrosses to wolves, while second- and third-generation backcrosses to wolves were identified as advanced hybrids in almost all cases.
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