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Genes2025; 16(9); 1054; doi: 10.3390/genes16091054

Insights into Genomic Patterns of Homozygosity in the Endangered Dülmen Wild Horse Population.

Abstract: Dülmen wild horses are kept in a fenced wooden and marsh area around Dülmen in Westphalia, Germany, since 1856. Previous analyses supported early genetic divergence from other domesticated horse populations and the Przewalski horse. Therefore, the objective of this study was to evaluate genetic diversity using high-density genomic data. Methods: We collected 337 one-year-old male Dülmen wild horses, captured at 12 annual auctions, for genotyping on the Illumina GGP Equine Plus Beadchip. All analyses were performed for 63,123 autosomal SNPs. Results: On average, each horse had 27.96 ROH with an average length of 8.237 Mb, resulting in an average genomic inbreeding coefficient F of 0.107. ROH with a length of 2-4 Mb were most frequent, and the next frequent ROH fall into the length categories of 4-8 and 8-16 Mb. The effective population size (N) steadily decreased in the last 100 generations by 4.57 individuals per generation from 498 to 41. We identified 10 ROH islands on equine chromosomes 1, 4, 5, 7, 9, and 10. Only one ROH island on ECA 1 was shared by 45% of the horses. Overrepresented genes of ROH islands were associated with glycerophospholipid catabolism through genes, skeletal muscle contraction (, ), synapse activity and structure (), regulation of inflammatory response ( genes), and genes, which are involved in many cellular processes and may also act as tumor suppressors and oncogenes. Conclusions: This study highlights the development of genomic inbreeding and shows the importance of the stallions selected for breeding on the genetic diversity of the Dülmen wild horses. The results of this study should be used to develop strategies to slow down increase in inbreeding and prevent transmitting unfavorable alleles from the stallions to the next generation.
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Publication Date: 2025-09-08 PubMed ID: 41009997PubMed Central: PMC12469691DOI: 10.3390/genes16091054Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

Overview

  • This study investigates the genetic diversity and patterns of genomic homozygosity in the endangered Dülmen wild horse population using high-density genomic data.
  • The research aims to understand inbreeding levels, population size changes, and the genetic regions under homozygosity to inform conservation management strategies.

Background and Objective

  • The Dülmen wild horses have been maintained in a restricted fenced habitat in Westphalia, Germany, since 1856.
  • Previous studies showed that Dülmen wild horses genetically diverged early from domesticated horses and the Przewalski horse, indicating a unique genetic lineage.
  • The primary goal was to assess genetic diversity and inbreeding using detailed genomic data to better understand population structure and risks.

Methods

  • Sampling: 337 one-year-old male Dülmen wild horses were sampled over 12 annual auctions for this study.
  • Genotyping: Horses were genotyped using the Illumina GGP Equine Plus Beadchip, covering 63,123 autosomal single nucleotide polymorphisms (SNPs).
  • Analysis focused on runs of homozygosity (ROH) to measure genomic inbreeding and identify regions of the genome consistent across horses.

Key Findings

  • Each horse carried an average of about 28 ROHs with an average ROH length of 8.237 megabases (Mb).
  • The average genomic inbreeding coefficient (F) across the population was 0.107, indicating moderate inbreeding levels.
  • More frequent ROHs were shorter (2-4 Mb), with many also occurring in length categories of 4-8 Mb and 8-16 Mb, suggesting a mix of recent and older inbreeding events.
  • Effective population size (Ne) steadily declined over the last 100 generations, decreasing by approximately 4.57 individuals each generation, from 498 to around 41.
  • Ten highly homozygous genomic regions known as ROH islands were detected on six chromosomes (ECA 1, 4, 5, 7, 9, and 10), with one island on chromosome 1 present in 45% of horses.

Functional Insights from ROH Islands

  • Genes in ROH islands were linked to important biological pathways and functions, including:
    • Glycerophospholipid catabolism – critical in membrane lipid metabolism.
    • Skeletal muscle contraction – relevant for horse mobility and strength.
    • Synapse activity and structure – involved in neuronal signaling and brain function.
    • Regulation of inflammatory response – important for immune system function.
    • Genes with roles in cellular processes that may act as tumor suppressors or oncogenes, indicating possible impacts on health and disease susceptibility.

Conclusions and Conservation Implications

  • The study demonstrates that genomic inbreeding in the Dülmen wild horse population is increasing due to a reduction in effective population size and possibly breeding choices.
  • Stallions have a considerable influence on genetic diversity, highlighting the need for careful selection to avoid propagating deleterious alleles.
  • Findings emphasize the importance of monitoring genomic inbreeding and incorporating genetic information into breeding programs to maintain diversity and reduce risks of genetic disorders.
  • These insights can help guide conservation strategies to slow down inbreeding and preserve the health and vitality of this endangered horse population.

Cite This Article

APA
Duderstadt S, Distl O. (2025). Insights into Genomic Patterns of Homozygosity in the Endangered Dülmen Wild Horse Population. Genes (Basel), 16(9), 1054. https://doi.org/10.3390/genes16091054

Publication

Genes
ISSN: 2073-4425
NlmUniqueID: 101551097
Country: Switzerland
Language: English
Volume: 16
Issue: 9
PII: 1054

Researcher Affiliations

Duderstadt, Silke
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559 Hannover, Germany.
Distl, Ottmar
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559 Hannover, Germany.

MeSH Terms

  • Animals
  • Horses / genetics
  • Male
  • Endangered Species
  • Homozygote
  • Polymorphism, Single Nucleotide
  • Inbreeding
  • Genome
  • Genomics / methods
  • Animals, Wild / genetics
  • Germany

Conflict of Interest Statement

The authors declare no conflicts of interest.

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