Tracking footprints of artificial selection in the dog genome

Abstract

The size, shape, and behavior of the modern domesticated dog has been sculpted by artificial selection for at least 14,000 years. The genetic substrates of selective breeding, however, remain largely unknown. Here, we describe a genome-wide scan for selection in 275 dogs from 10 phenotypically diverse breeds that were genotyped for over 21,000 autosomal SNPs. We identified 155 genomic regions that possess strong signatures of recent selection and contain candidate genes for phenotypes that vary most conspicuously among breeds, including size, coat color and texture, behavior, skeletal morphology, and physiology. In addition, we demonstrate a significant association between HAS2 and skin wrinkling in the Shar-Pei, and provide evidence that regulatory evolution has played a prominent role in the phenotypic diversification of modern dog breeds. Our results provide a first-generation map of selection in the dog, illustrate how such maps can rapidly inform the genetic basis of canine phenotypic variation, and provide a framework for delineating the mechanistic basis of how artificial selection promotes rapid and pronounced phenotypic evolution.

Postembryonic staging of wild‐type goldfish, with brief reference to skeletal systems

“…This possibility is also supported by recent progress of genomic studies on domesticated mammals and birds (for example, dog, cat, cow, chicken, and pigeon) (Lindblad‐Toh et al, 2005; Wayne and Ostrander, 2007; Akey et al, 2010; Vonholdt et al, 2010; Shapiro et al, 2013). These studies explain the processes underlying fixation of genetic mutations through selective pressure on favorable morphological and/or physiological features, providing a more specific and promising framework for combined genomic and developmental biological approaches to investigate how fixed mutations altered ontogenetic processes to form the favorable morphological features in domestic animals in the context of evolutionary developmental biology (Cresko et al, 2007).…”

A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits

“…These results support our hypothesis that comparison of recently domesticated population with its wild founder population facilitates the discovery of candidate loci for traits under strong deliberate and accidental selection in the new hatchery environment. In dogs, phenotypes that vary most conspicuously among recently derived breeds, including size, limb length, coat color, coat texture, behavior, diet, skeletal morphology, and physiology have been used to identify the genomic regions that possess strong signatures of recent selection and contain major candidate genes (Akey et al., 2010; Axelsson et al., 2013; Pollinger et al., 2005; Von Holdt et al., 2010). …”

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).…”