Data from: Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies

Genomic resources for the domestic dog have improved with the widespread
adoption of a 173k SNP array platform and updated reference genome. SNP
arrays of this density are sufficient for detecting genetic associations
within breeds but are underpowered for finding associations across
multiple breeds or in mixed-breed dogs, where linkage disequilibrium
rapidly decays between markers, even though such studies would hold
particular promise for mapping complex diseases and traits. Here we
introduce an imputation reference panel, consisting of 365 diverse,
whole-genome sequenced dogs and wolves, which increases the number of
markers that can be queried in genome-wide association studies
approximately 130-fold. Using previously genotyped dogs, we show the
utility of this reference panel in identifying potentially novel
associations, including a locus on CFA20 significantly associated with
cranial cruciate ligament disease, and fine-mapping for canine body size
and blood phenotypes, even when causal loci are not in strong linkage
disequilibrium with any single array marker. This reference panel resource
will improve future genome-wide association studies for canine complex
diseases and other phenotypes.