The CanMap Project: Population Genetics and Whole Genome Association Mapping of Morphological and Behavioral Differences among Domestic Dog (Canis familiaris) Breeds. C.D. Bustamante1, T. Spady2, H.G. Parker2, B. vonHoldt2,3, K. Bryc1, M.H. Wright1, N.B. Sutter2, A. Reynolds1, A.R. Boyko1, M. Castelhano1, E. Wang4, K. Zhao1,5, G. Johnson6, M. Nordborg5, R.K. Wayne3, M. Cargill4, E.A. Ostrander2 1) Cornell University, Ithaca, NY; 2) NHGRI/NIH, Bethesda, MD; 3) UCLA, Los Angeles, CA; 4) Affymetrix, Santa Clara, CA; 5) U. Southern California, Los Angeles, CA; 6) U. of Missouri, Columbia, MO.

   Domestic dog breeds exhibit great variation in behavior and morphology among breeds and low phenotypic and genetic diversity within breeds, making the dog an excellent genetic system for mapping traits of interest. Here, we present population genetic analyses and preliminary results for simultaneous whole-genome association mapping of morphological and behavioral trait differences among breeds using a panel of 1,000 dogs from 80 breeds genotyped on the Affymetrix Canine Array v.2.0 (~100,000 SNP). Population genetic analyses reveal clear genetic clustering of dogs into breeds with well defined boundaries, and shallow clustering of breeds into higher order groups. We use fine-scale recombination rate estimates across the genome to identify regions of unusually high linkage-disequilibrium within a breed, which may identify recent targets of selection during breed formation. We also estimate the domestication bottleneck size for dog as well as breed-specific bottleneck and inbreeding rates which account for dramatic differences in effective population size among popular breeds. Using a mapping strategy that accounts for expected high genetic relatedness within a breed, we aim to identify regions of the dog genome associated with skeletal conformation, hair pigmentation and texture, and behavioral trait differences including: body size, foreshortened limbs, foreshortened face, compact face and cranimum, proportional dwarfism, wire hair, curly hair, corded coat, face mask color, and prey drive. For several traits, overlying peaks of association with signatures of selection allows us to refine our signals to a just a few candidate genes. The approach we employ replicates previously identifies gene-trait association, including the link between IGF1 and body size.