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BMC genomics2022; 23(1); 501; doi: 10.1186/s12864-022-08729-9

Runs of homozygosity in Sable Island feral horses reveal the genomic consequences of inbreeding and divergence from domestic breeds.

Abstract: Understanding inbreeding and its impact on fitness and evolutionary potential is fundamental to species conservation and agriculture. Long stretches of homozygous genotypes, known as runs of homozygosity (ROH), result from inbreeding and their number and length can provide useful population-level information on inbreeding characteristics and locations of signatures of selection. However, the utility of ROH for conservation is limited for natural populations where baseline data and genomic tools are lacking. Comparing ROH metrics in recently feral vs. domestic populations of well understood species like the horse could provide information on the genetic health of those populations and offer insight into how such metrics compare between managed and unmanaged populations. Here we characterized ROH, inbreeding coefficients, and ROH islands in a feral horse population from Sable Island, Canada, using ~41 000 SNPs and contrasted results with those from 33 domestic breeds to assess the impacts of isolation on ROH abundance, length, distribution, and ROH islands. Results: ROH number, length, and ROH-based inbreeding coefficients (F) in Sable Island horses were generally greater than in domestic breeds. Short runs, which typically coalesce many generations prior, were more abundant than long runs in all populations, but run length distributions indicated more recent population bottlenecks in Sable Island horses. Nine ROH islands were detected in Sable Island horses, exhibiting very little overlap with those found in domestic breeds. Gene ontology (GO) enrichment analysis for Sable Island ROH islands revealed enrichment for genes associated with 3 clusters of biological pathways largely associated with metabolism and immune function. Conclusions: This study indicates that Sable Island horses tend to be more inbred than their domestic counterparts and that most of this inbreeding is due to historical bottlenecks and founder effects rather than recent mating between close relatives. Unique ROH islands in the Sable Island population suggest adaptation to local selective pressures and/or strong genetic drift and highlight the value of this population as a reservoir of equine genetic variation. This research illustrates how ROH analyses can be applied to gain insights into the population history, genetic health, and divergence of wild or feral populations of conservation concern.
© 2022. The Author(s).
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Publication Date: 2022-07-12 PubMed ID: 35820826PubMed Central: PMC9275264DOI: 10.1186/s12864-022-08729-9Google Scholar: Lookup
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Summary

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This research investigates inbreeding in the feral horse population on Sable Island, Canada by examining long segments of homozygous genes, known as ‘runs of homozygosity’ (ROH), and compare these with 33 domestic horse breeds. It was found that the Sable Island horses tend to be more inbred, with the inbreeding mainly due to historical factors rather than recent closely related matings, and that the population features unique ROH indicative of local adaptation or genetic drift.

Understanding Runs of Homozygosity (ROH)

  • ROH refer to long stretches of identical genetic material inherited from both parents. These sequences result from inbreeding and can give insights into the genetic health of a population.
  • Information about the number and length of these sequences can show inbreeding characteristics and locations of selective breeding patterns.
  • The use of ROH for conservation is limited in natural populations due to lack of baseline data and genomic tools.

Comparison of ROH in Feral and Domestic Horses

  • Findings demonstrate that ROH, inbreeding coefficients, and ROH islands (blocks of ROH in multiple individuals) were greater in the Sable Island horses than in the 33 domestic breeds sampled.
  • Short ROH, often arising from distant shared ancestors, were more abundant than long ROH, suggesting the presence of more recent population bottlenecks in the Sable Island horses.

Unique Features of Sable Island Horses

  • Unlike the domestic breeds, the Sable Island horses showed nine unique ROH islands, indicating different selective pressures or strong genetic drift.
  • These unique ROH islands appear to be associated with three clusters of genes primarily involved with metabolism and immune function.

Overall Conclusions of the Study

  • The Sable Island horses are seemingly more inbred than their domestic counterparts, with the inbreeding largely being due to historical population events like bottlenecks and founder effects rather than recent interbreeding.
  • The unique ROH islands in the Sable Island horse population suggest local adaptation or strong genetic drift, indicating the species’ value as a source of equine genetic variation.
  • This research offers a possible method for evaluating the population history, genetic health, and divergence of wild or feral populations of interest for conservation.

Cite This Article

APA
Colpitts J, McLoughlin PD, Poissant J. (2022). Runs of homozygosity in Sable Island feral horses reveal the genomic consequences of inbreeding and divergence from domestic breeds. BMC Genomics, 23(1), 501. https://doi.org/10.1186/s12864-022-08729-9

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 23
Issue: 1
Pages: 501
PII: 501

Researcher Affiliations

Colpitts, Julie
  • Department of Biology, University of Saskatchewan, Saskatchewan, Canada. julie.colpitts@usask.ca.
McLoughlin, Philip Dunstan
  • Department of Biology, University of Saskatchewan, Saskatchewan, Canada.
Poissant, Jocelyn
  • Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada. jocelyn.poissant@ucalgary.ca.

MeSH Terms

  • Animals
  • Genome
  • Genomics
  • Homozygote
  • Horses / genetics
  • Inbreeding
  • Mustelidae

Conflict of Interest Statement

The authors declare that they have no competing interests.

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