R-locus for roaned coat is associated with a tandem duplication in an intronic region of USH2A in dogs and also contributes to Dalmatian spotting ...

• Main Authors: Kawakami, Takeshi, Jensen, Meghan, Slavney, Andrea, Milano, Ausra, Raghavan, Vandana, Ford, Brett, Sams, Aaron, Boyko, Adam
• Format: Dataset
• Language: English
• Published: Dryad 2021
• Subjects: pigmentation; coat color; structural variation; Canis lupus familiaris; SNP array genotyping; Canis lupus
• Online Access: https://dx.doi.org/10.5061/dryad.qz612jmdt; https://datadryad.org/stash/dataset/doi:10.5061/dryad.qz612jmdt

Structural variations (SVs) represent a large fraction of all genetic diversity, but how this genetic diversity is translated into phenotypic and organismal diversity is unclear. Explosive diversification of dog coat color and patterns after domestication can provide a unique opportunity to explore this question; however, the major obstacle is to efficiently collect a sufficient number of individuals with known phenotypes and genotypes of hundreds of thousands of markers. Using customer-provided information about coat color and patterns of dogs tested on a commercial canine genotyping platform, we identified a genomic region on chromosome 38 that is strongly associated with a mottled coat pattern (roaning) by genome-wide association study. We identified a putative causal variant in this region, an 11-kb tandem duplication (11,131,835-11,143,237) characterized by sequence read coverage and discordant reads of whole-genome sequence data, microarray probe intensity data, and a duplication-specific PCR assay. ... : DNA was extracted from buccal swab samples collected by dog owners and extracted by Illumina, Inc. Genotypes of the dogs were collected by using custom Illumina Canine high-density SNP arrays (a total of 220,484 markers). ...