Balancing at the Borderline of a Breed: A Case Study of the Hungarian Short-Haired Vizsla Dog Breed, Definition of the Breed Profile Using Simple SNP-Based Methods

László Varga; Erika Meleg Edviné; Péter Hudák; István Anton; Nóra Pálinkás-Bodzsár; Attila Zsolnai

doi:10.3390/genes13112022

Balancing at the Borderline of a Breed: A Case Study of the Hungarian Short-Haired Vizsla Dog Breed, Definition of the Breed Profile Using Simple SNP-Based Methods

Genes (Basel). 2022 Nov 3;13(11):2022. doi: 10.3390/genes13112022.

Authors

László Varga^{1

2}, Erika Meleg Edviné², Péter Hudák², István Anton³, Nóra Pálinkás-Bodzsár², Attila Zsolnai^{2

3}

Affiliations

¹ Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent István Campus, 2100 Gödöllő, Hungary.
² Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, 2100 Gödöllő, Hungary.
³ Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, 2053 Herceghalom, Hungary.

Abstract

The aim of this study was to determine the breed boundary of the Hungarian Short-haired Vizsla (HSV) dog breed. Seventy registered purebred HSV dogs were genotyped on approximately 145,000 SNPs. Principal Component Analysis (PCA) and Admixture analysis certified that they belong to the same population. The outer point of the breed demarcation was a single Hungarian Wire-haired Vizsla (HWV) individual, which was the closest animal genetically to the HSV population in the PCA analysis. Three programs were used for the breed assignment calculations, including the widely used GeneClass2.0 software and two additional approaches developed here: the 'PCA-distance' and 'IBS-central' methods. Both new methods calculate a single number that represents how closely a dog fits into the actual reference population. The former approach calculates this number based on the PCA distances from the median of HSV animals. The latter calculates it from identity by state (IBS) data, measuring the distance from a central animal that is the best representative of the breed. Having no mixed-breed dogs with known HSV genome proportion, admixture animals were simulated by using data of HSV and HWV individuals to calibrate the inclusion/exclusion probabilities for the assignment. The numbers generated from these relatively simple calculations can be used by breeders and clubs to keep their populations under genetic supervision.

Keywords: Hungarian Short-haired Vizsla; IBS-central; PCA-distance; SNP-chip; breed assignment.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Dogs* / genetics
Genome
Genotype
Hungary
Polymorphism, Single Nucleotide*

Grants and funding

This research was supported by the Strategic Program for Genetic Conservation of the National Centre for Biodiversity and Gene Conservation in accordance with Government Decision 1049/2018 (20.II.).