The domestic dog: man's best friend in the genomic era

Abstract

The domestic dog genome--shaped by domestication, adaptation to human-dominated environments and artificial selection--encodes tremendous phenotypic diversity. Recent developments have improved our understanding of the genetics underlying this diversity, unleashing the dog as an important model organism for complex-trait analysis.

Figure 1

Phenotypic diversity across 9 of the approximately 400 modern dog breeds. From top left to bottom right: Basenji, Newfoundland, Chihuahua, Standard Poodle, Australian Cattle Dog, Afghan Hound, Bull Terrier, Greyhound, and English Mastiff. Photos are used under Creative Commons from fugzu, alicjap, Kjunstorm, greg westfall, 3Dobes, diveofficer, Just chaos, msmornington, and claudiogennari, respectively.

Figure 2

A simplified diagram of dog evolutionary history. Blue (wolf) and green (village dog) arrows represent separate evolutionary lineages, each one containing population substructure largely resulting from isolation by distance among local populations. Red arrows (breeds) represent an ancient (far left) and three modern breeds. Green/blue bar and arrows depict one (but possibly more) domestication events from Eurasian wolves followed by some small degree of localized dog-wolf introgression. Red/green bars depict founders from one or more breeds being drawn from village-dog populations, with a red horizontal arrow at the present time to show admixture with descents of breed dogs contaminating the gene pool of some village-dog populations. As globalization and modernization continue, these breed-descended migrants will become an even larger threat to the reservoirs of indigenous dog diversity.

Figure 3

Decay of linkage disequilibrium (LD) among dogs and gray wolves. Among dog breeds (black dotted line); among gray wolves (dashed black line); within a population of village dogs (solid black line); and within dog breeds (colored lines). R² is square of the coefficient of association of allele frequencies between two loci [76]. Between breeds and within village dogs, LD extends for approximately 100 kb (roughly the equivalent of LD in humans). LD tracks are somewhat shorter in wolves and at least ten-fold longer within breeds (adapted from [8]).

Figure 4

QTL mapping of body-size variants in the domestic dog. (a) Genome-wide single-locus significance for male-average breed body weight across 80 breeds at more than 60,000 markers. The blue dots indicate the -log₁₀ P-values of association for a trait at each marker after controlling for genetic relatedness among breeds. (b) Best-fit regression model using the top six markers explains 72% of the variance of breed-average size among breeds, 72% of the variance of individual body size among breeds, and 25% of the variance of individual body size in village dogs. Figure reproduced from [8].