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Home / Equine Research Bank / Equine Vet J / Does inbreeding contribute to pregnancy loss in Thoroughbred...
Equine veterinary journal2024; doi: 10.1111/evj.14057

Does inbreeding contribute to pregnancy loss in Thoroughbred horses?

Abstract: Excessive inbreeding increases the probability of uncovering homozygous recessive genotypes and has been associated with an increased risk of retained placenta and lower semen quality. No genomic analysis has investigated the association between inbreeding levels and pregnancy loss. Objective: To compare genetic inbreeding coefficients (F) of naturally occurring Thoroughbred Early Pregnancy Loss (EPLs), Mid and Late term Pregnancy Loss (MLPL) and Controls. The F value was hypothesised to be higher in cases of pregnancy loss (EPLs and MLPLs) than Controls. Methods: Observational case-control study. Methods: Allantochorion and fetal DNA from EPL (n = 37, gestation age 14-65 days), MLPL (n = 94, gestational age 70 days-24 h post parturition) and Controls (n = 58) were genotyped on the Axiom Equine 670K SNP Genotyping Array. Inbreeding coefficients using Runs of Homozygosity (FROH) were calculated using PLINK software. ROHs were split into size categories to investigate the recency of inbreeding. Results: MLPLs had significantly higher median number of ROH (188 interquartile range [IQR], 180.8-197.3), length of ROH (3.10, IQR 2.93-3.33), and total number of ROH (590.8, IQR 537.3-632.3), and F (0.26, IQR 0.24-0.28) when compared with the Controls and the EPLs (p 10 Mb) ROH (2.5%, IQR 1.6-3.6) than the Controls (1.7%, IQR 0.6-2.5), p = 0.001. No unique ROHs were found in the EPL or MLPL populations. Conclusions: SNP-array data does not allow analysis of every base in the sequence. Conclusions: This first study of the effect of genomic inbreeding levels on pregnancy loss showed that inbreeding is a contributor to MLPL, but not EPL in the UK Thoroughbred population. Mating choices remain critical, because inbreeding may predispose to MLPL by increasing the risk of homozygosity for specific lethal allele(s).
© 2024 The Authors. Equine Veterinary Journal published by John Wiley & Sons Ltd on behalf of EVJ Ltd.
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Publication Date: 2024-01-14 PubMed ID: 38221707DOI: 10.1111/evj.14057Google Scholar: Lookup
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Summary

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This research aims to investigate if inbreeding contributes to pregnancy loss in Thoroughbred horses. The study finds that higher inbreeding levels are associated with mid and late-term pregnancy loss, but not early pregnancy loss, in these horses.

Research Objective and Hypothesis

  • The goal of the study was to determine the association between inbreeding levels and pregnancy loss in Thoroughbred horses. This research has not been conducted previously.
  • The researchers hypothesized that inbreeding coefficients would be higher in cases of pregnancy loss, both early and mid to late-term, compared to controls.

Methodology

  • This was an observational case-control study.
  • Allantochorion and fetal DNA from horses experiencing early pregnancy loss (gestation age between 14–65 days), mid and late-term pregnancy loss (gestational age from 70 days to 24 hours post-parturition), and controls were included in the study.
  • The samples were genotyped using the Axiom Equine 670K SNP Genotyping Array.
  • The software PLINK was used to calculate inbreeding coefficients using ‘Runs of Homozygosity’ (FROH).
  • The researchers split the runs of homozygosity into different size categories to understand the timing of inbreeding.

Results

  • The study found significantly higher median numbers of Runs of Homozygosity (ROH) in mid and late term pregnancy losses (MLPL) compared to controls and early pregnancy losses (EPL).
  • There was no significant difference in any of the inbreeding indices between early pregnancy losses and controls.
  • Mid and late-term losses had a higher proportion of long runs of homozygosity than the control group.
  • No unique runs of homozygosity were found in the early or mid to late-term pregnancy loss groups.

Conclusions

  • Despite the fact that the SNP-array data does not allow for the analysis of every sequence base, this first study on the effect of genomic inbreeding levels on pregnancy loss in Thoroughbred horses suggests that inbreeding contributes to mid and late-term pregnancy loss, but not to early pregnancy loss.
  • The findings underscore the importance of careful mating choices, as inbreeding may increase the risk of homozygosity for specific lethal alleles, leading to mid and late-term pregnancy loss.

Cite This Article

APA
Lawson JM, Shilton CA, Lindsay-McGee V, Psifidi A, Wathes DC, Raudsepp T, de Mestre AM. (2024). Does inbreeding contribute to pregnancy loss in Thoroughbred horses? Equine Vet J. https://doi.org/10.1111/evj.14057

Publication

Equine veterinary journal
ISSN: 2042-3306
NlmUniqueID: 0173320
Country: United States
Language: English

Researcher Affiliations

Lawson, Jessica M
  • Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, UK.
Shilton, Charlotte A
  • Department of Comparative Biomedical Sciences, The Royal Veterinary College, University of London, London, UK.
Lindsay-McGee, Victoria
  • Department of Clinical Science and Services, The Royal Veterinary College, University of London, London, UK.
Psifidi, Androniki
  • Department of Clinical Science and Services, The Royal Veterinary College, University of London, London, UK.
Wathes, D Claire
  • Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, UK.
Raudsepp, Terje
  • Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA.
de Mestre, Amanda M
  • Department of Comparative Biomedical Sciences, The Royal Veterinary College, University of London, London, UK.

Grant Funding

  • Horserace Betting Levy Board
  • Thoroughbred Breeders Association
  • Royal Veterinary College
  • The Alborada Trust

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