Inbreeding depression and the probability of racing in the thoroughbred horse

Emmeline W Hill, Martin A Stoffel, Beatrice A McGivney, David E MacHugh, Josephine M Pemberton

Research output: Contribution to journalArticlepeer-review


Small effective population sizes and active inbreeding can lead to inbreeding depression due to deleterious recessive mutations exposed in the homozygous state. The Thoroughbred racehorse has low levels of population genetic diversity, but the effects of genomic inbreeding in the population are unknown. Here, we quantified inbreeding based on runs of homozygosity (ROH) using 297 K SNP genotypes from 6128 horses born in Europe and Australia, of which 13.2% were unraced. We show that a 10% increase in inbreeding ( F ROH) is associated with a 7% lower probability of ever racing. Moreover, a ROH-based genome-wide association study identified a haplotype on ECA14 which, in its homozygous state, is linked to a 32.1% lower predicted probability of ever racing, independent of F ROH. The haplotype overlaps a candidate gene, EFNA5, that is highly expressed in cartilage tissue, which when damaged is one of the most common causes of catastrophic musculoskeletal injury in racehorses. Genomics-informed breeding aiming to reduce inbreeding depression and avoid damaging haplotype carrier matings will improve population health and racehorse welfare.

Original languageEnglish
Number of pages7
JournalProceedings. Biological sciences
Issue number1977
Early online date29 Jun 2022
Publication statusPublished - 29 Jun 2022


  • genomics
  • runs of homozygosity
  • EFNA5
  • inbreeding
  • inbreeding depression
  • racing


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