Signatures of selection in dog breeds

10 breeds, 21,000 SNPs, breed-specific Fst.

Their most notable hits:
HMGA2 and IGF1R (size)
SILV, MITF (coat color and texture)
CDH9, DRD5, HTR2A (behavior)
SOX9 (skeletal morphology)
FTO, SLC2A9, SLC5A2 (physiology)

Unfortunately they only use Fst to detect evidence of selection. It would have been interesting to try out some haplotype or other tests of selection, but they were probably constrained by the total number of SNPs they had.

Most interestingly:

Similar to analyses of selection in natural populations (23), we find that genes involved in immunity and defense are also significantly overrepresented in the 155 candidate selection
regions. This is somewhat surprising, as natural and artificial selection would not necessarily be expected a priori to act on similar classes of genes, and suggests that immune related genes are pervasive targets of selection because of their critical role in pathogen defense or propensity for pleiotropic effects (24).

...also:

We note that as an initial foray into comparative selection mapping, of the 1,506 genes located in putatively selected regions in dogs, 169 overlap with genes located in well-supported selected regions in humans (10). Although this result should be interpreted with caution, as the specific targets of selection are generally not known with certainty in either dogs or humans, it does raise the intriguing possibility that recent selection has influenced common loci in both the human and dog lineages.

Tracking footprints of artificial selection in the dog genome
Joshua M. Akey, Alison L. Ruhe, Dayna T. Akey, Aaron K. Wong, Caitlin F. Connelly, Jennifer Madeoy, Thomas J. Nicholas, and Mark W. Neff
PNAS January 19, 2010 vol. 107 no. 3 1160-1165

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.