Abstract
Identifying regions of artificial selection within dog breeds may provide insights into genetic variation that underlies breed-specific traits or diseases—particularly if these traits or disease predispositions are fixed within a breed. In this study, we searched for runs of homozygosity (ROH) and calculated the d i statistic (which is based upon F ST) to identify regions of artificial selection in Standard Poodles using high-coverage, whole-genome sequencing data of 15 Standard Poodles and 49 dogs across seven other breeds. We identified consensus ROH regions ≥1 Mb in length and common to at least ten Standard Poodles covering 0.6 % of the genome, and d i regions that most distinguish Standard Poodles from other breeds covering 3.7 % of the genome. Within these regions, we identified enriched gene pathways related to olfaction, digestion, and taste, as well as pathways related to adrenal hormone biosynthesis, T cell function, and protein ubiquitination that could contribute to the pathogenesis of some Poodle-prevalent autoimmune diseases. We also validated variants related to hair coat and skull morphology that have previously been identified as being under selective pressure in Poodles, and flagged additional polymorphisms in genes such as ITGA2B, CBX4, and TNXB that may represent strong candidates for other common Poodle disorders.
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Acknowledgments
SGF is supported by a National Institutes of Health T32 training award (5T32OD011130-07). Funding for whole-genome sequencing was provided in part by the Poodle Club of America Foundation, the American Kennel Club Canine Health Foundation, the Morris Animal Foundation, and the NCSU Cardiac Genetics Laboratory. Some whole-genome sequencing data were graciously contributed by Drs. Natasha J. Olby and Theirry Olivry (10 dogs), and Dr. Leigh Anne-Clark (8 dogs).
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SGF collected samples, designed the study, analyzed the data, and wrote the manuscript. KMM collected samples and supervised the study. TFCM also supervised and provided guidance to the study. All authors have read and edited the manuscript.
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335_2016_9660_MOESM1_ESM.tiff
Supplementary material 1 (TIFF 10,979 kb) Figure 1. LOESS-smoothed di values derived from whole-genome sequencing of 15 Standard Poodles compared to 7 other dog breeds. The dashed red line represents the 99th percentile cutoff value for di and the purple bars represent the 17 consensus ROH regions in Standard Poodles >1 Mb in length
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Friedenberg, S.G., Meurs, K.M. & Mackay, T.F.C. Evaluation of artificial selection in Standard Poodles using whole-genome sequencing. Mamm Genome 27, 599–609 (2016). https://doi.org/10.1007/s00335-016-9660-9
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DOI: https://doi.org/10.1007/s00335-016-9660-9