Inbreeding depression and the probability of racing in the Thoroughbred horse

Abstract

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.

Inbreeding depression and durability in the North American Thoroughbred horse

“…The results obtained for the North American population contrast with results for European and Australasian horses (Hill et al, 2022). Among European and Australasian horses, F ROH was not associated with the number of race starts.…”

“…In the Australasian Thoroughbred, pedigree‐based estimates of inbreeding are associated with a strong negative effect on racing performance (Todd et al, 2018). In European and Australasian Thoroughbreds inbreeding, quantified based on runs of homozygosity (ROH) determined from genome‐wide SNP data, is associated with a lower probability of ever racing (Hill et al, 2022).…”

Unlocking Horse Y Chromosome Diversity

“…Genomic analyses recently showed several autosomal loci and mutations significantly associated with stallion fertility [ 106 ], and abnormalities in a number of X- and/or Y chromosomes have been shown to be causes for aberrant sexual development [ 107 ]. As previously reviewed [ 83 ], among all the above mutations associated with infertility, only the deletion in the sex-determining region (SRY) leads to infertility in horses, which was found in the 25% of horses with chromosomal aberrations, but it was not detected in other species [ 108 ]. All other alterations and rearrangements known to be associated with horse infertility are ascribed to loci not localized in the Y chromosome.…”

“…Inbreeding has caused reduced fertility and survival among offspring of related individuals, resulting in a decline in fitness [ 79 ] and the emergence of disadvantageous traits [ 27 , 80 ]. The increased knowledge about inbreeding depression and the genetic structure of breeds [ 81 , 82 ] have allowed breeders to select horses by avoiding mating closely related individuals [ 83 ].…”

The Social and Reproductive Challenges Faced by Free-Roaming Horse (Equus caballus) Stallions

“…They are asked to mate with any oestrous female, often one they are not familiar with. They can even be used in kin breeding if the breeders decide this is required (e.g., [ 167 , 168 , 169 ]). Although in most breeding facilities juvenile colts are reared together [ 2 ], the majority of them are gelded, and only a few chosen individuals are kept intact.…”