Genome-wide SNP analysis of Japanese Thoroughbred racehorses

PLoS One. 2019 Jul 24;14(7):e0218407. doi: 10.1371/journal.pone.0218407. eCollection 2019.


The domestication process of plants and animals typically involves intense inbreeding and directional selection for various traits. Here, we genotyped 370 Japanese Thoroughbred horses using the recently developed 670k SNP array and performed various genome-wide analysis also using genotype data of other horse breeds. We identified a number of regions showing interesting patterns of polymorphisms. For instance, the region containing the MC1R locus associated with chestnut coat color may have been targeted by selection for a different mutation much earlier on than the recent selection for chestnut color. We also identified regions that show signatures of selection specific to Thoroughbreds. In addition, we found that intense inbreeding early in the history of the Thoroughbred breed and also before the formation of the breed has a significant impact on the genomic architecture of modern Thoroughbreds. Our study demonstrates that the horse 670k array can be utilized to gain important insight into the domestication process of horses and to understand the genetic basis of the phenotypic diversity in horses.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Breeding
  • Domestication*
  • Genetic Variation
  • Genome / genetics*
  • Genotype
  • Horses / genetics*
  • Inbreeding
  • Japan
  • Phenotype
  • Polymorphism, Single Nucleotide / genetics
  • Selection, Genetic*

Grant support

This work was partly supported by Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area) 23114004 to HI and JSPS KAKENHI Grant Number 16K18470 to JAF. Hidaka Training and Research Center, Japan Racing Association provided support in the form of salary to FS. Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi provided support in the form of salary for TT. The specific roles of these authors are articulated in the ‘author contributions’ section. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.