Single-Nucleotide-Polymorphism-Based Association Mapping of Dog Stereotypes

Abstract

Phenotypic stereotypes are traits, often polygenic, that have been stringently selected to conform to specific criteria. In dogs, Canis familiaris, stereotypes result from breed standards set for conformation, performance (behaviors), etc. As a consequence, phenotypic values measured on a few individuals are representative of the breed stereotype. We used DNA samples isolated from 148 dog breeds to associate SNP markers with breed stereotypes. Using size as a trait to test the method, we identified six significant quantitative trait loci (QTL) on five chromosomes that include candidate genes appropriate to regulation of size (e.g., IGF1, IGF2BP2 SMAD2, etc.). Analysis of other morphological stereotypes, also under extreme selection, identified many additional significant loci. Less well-documented data for behavioral stereotypes tentatively identified loci for herding, pointing, boldness, and trainability. Four significant loci were identified for longevity, a breed characteristic not under direct selection, but inversely correlated with breed size. The strengths and limitations of the approach are discussed as well as its potential to identify loci regulating the within-breed incidence of specific polygenic diseases.

Complex population structure in African village dogs and its implications for inferring dog domestication history

“…One hundred sixty-eight village dogs, 102 mixed-breed dogs, and dogs from 126 breeds were genotyped using the sequenom iPLEX platform on a 321-SNP panel described in ref. 20. For each sample, 2 L of dog genomic DNA was aliquoted into 13 separate microtiter wells for PCR amplification.…”

LUPA: A European initiative taking advantage of the canine genome architecture for unravelling complex disorders in both human and dogs

“…The LUPA database, already containing genotypes from 10,000 dogs, can be used to perform GWAS across breeds, with the aim to identify variants underlying traits shared by several breeds, as has already been documented in other studies (Jones et al, 2008;Cadieu et al, 2009;Akey et al, 2010;Bannasch et al, 2010;Boyko et al, 2010). An alternative approach searches for selective sweeps: regions with reduced heterozygosity associated with a specific trait within a single or within a group of breeds that share the same trait (A. Vaysse personal communication).…”

Recovering Power in Association Mapping Panels with Variable Levels of Linkage Disequilibrium

“…Compared to linkage mapping, more markers are therefore needed to capture causal signals but with a much higher mapping resolution (Rafalski and Morgante 2004). Major genes were identified by this approach in human, animal, and plant genetics (Ozaki et al 2002;Beló et al 2007;Jones et al 2008). However, contrary to linkage mapping populations, LD in association mapping panels is not only due to genetic linkage, but can also be caused by population structure, relatedness, drift, and selection (Jannink and Walsh 2002;Flint-Garcia et al 2003).…”