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

• DOI: 10.1371/journal.pgen.1008003
• Publication Date: 2019-09-16T17:34:40Z
• Authors: Jessica J. Hayward; Michelle E. White; Michael Boyle; Laura M. Shannon; Margret L. Casal; Marta G. Castelhano; Sharon A. Center; Vicki N. Meyers-W...; Kenneth W. Simpson; Nathan B. Sutter; Rory J. Todhunter; Adam R. Boyko
• Keywords: Linkage Disequilibrium; Genome-wide Association Study; Imputation (statistics); Genetic Association; Association mapping; SNP; Tag SNP; SNP array

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