Evaluation of artificial selection in Standard Poodles using whole-genome sequencing

Mamm Genome. 2016 Dec;27(11-12):599-609. doi: 10.1007/s00335-016-9660-9. Epub 2016 Aug 10.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Breeding*
  • Dogs
  • Genome / genetics*
  • High-Throughput Nucleotide Sequencing
  • Homozygote
  • Integrin alpha2 / genetics
  • Phenotype
  • Polycomb-Group Proteins / genetics
  • Polymorphism, Single Nucleotide / genetics
  • Selection, Genetic*
  • Tenascin / genetics

Substances

  • Integrin alpha2
  • Polycomb-Group Proteins
  • Tenascin
  • tenascin X