Gene

Whole genome sequencing

Biology

Selection (genetic algorithm)

Computer science

Computational biology

Evolutionary biology

Single-nucleotide polymorphism

Genetics

Genome

Genome-wide association study

Genetic association

Genotype

Breed

Genomics

Artificial intelligence

Morphology (biology)

Indel

Genetic variation

Phenotype

Nature Communications

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.

Whole genome sequencing of canids reveals genomic regions under selection and variants influencing morphology