Abstract
Domestic dog breeds are characterized by an unrivaled diversity of morphologic traits and breed-associated behaviors resulting from human selective pressures. To identify the genetic underpinnings of such traits, we analyze 722 canine whole genome sequences (WGS), documenting over 91 million single nucleotide and small indels, creating a large catalog of genomic variation for a companion animal species. We undertake both selective sweep analyses and genome wide association studies (GWAS) inclusive of over 144 modern breeds, 54 wild canids and a hundred village dogs. Our results identify variants of strong impact associated with 16 phenotypes, including body weight variation which, when combined with existing data, explain greater than 90% of body size variation in dogs. We thus demonstrate that GWAS and selection scans performed with WGS are powerful complementary methods for expanding the utility of companion animal systems for the study of mammalian growth and biology.
Highlights
Domestic dog breeds are characterized by an unrivaled diversity of morphologic traits and breed-associated behaviors resulting from human selective pressures
To comprehensively represent the diversity of modern canids, we obtained publicly available whole genome sequences (WGS) data from the genera Canis, Cuon, and Lycalopex (Sequence Read Archive: http://www.ncbi.nlm.nih.gov/sra; n = 314 unique individuals), as well as 128 unpublished genomes contributed by collaborators, previously catalogued WGS25 and data from 94 domestic dogs sequenced by the Ostrander lab of which 52 were previously unpublished and available on NCBI
We have generated an expansive catalog of canine genomic variation, identifying 91 million variants in 722 WGS
Summary
Domestic dog breeds are characterized by an unrivaled diversity of morphologic traits and breed-associated behaviors resulting from human selective pressures. To identify the genetic underpinnings of such traits, we analyze 722 canine whole genome sequences (WGS), documenting over 91 million single nucleotide and small indels, creating a large catalog of genomic variation for a companion animal species. We undertake both selective sweep analyses and genome wide association studies (GWAS) inclusive of over 144 modern breeds, wild canids and a hundred village dogs.
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