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Home / Equine Research Bank / Genes (Basel) / Genomic Patterns of Homozygosity and Genetic Diversity in th...
Genes2025; 16(3); 327; doi: 10.3390/genes16030327

Genomic Patterns of Homozygosity and Genetic Diversity in the Rhenish German Draught Horse.

Abstract: The Rhenish German draught horse is an endangered German horse breed, originally used as working horse in agriculture. Therefore, the objective of this study was to evaluate the breed's genetic diversity using pedigree and genomic data in order to analyze classical and ancestral pedigree-based inbreeding, runs of homozygosity, ROH islands, and consensus ROH. Methods: We studied the genome-wide genotype data of 675 Rhenish German draught horses and collated pedigree-based inbreeding coefficients for these horses. The final dataset contained 64,737 autosomal SNPs. Results: The average number of ROH per individual was 43.17 ± 9.459 with an average ROH length of 5.087 Mb ± 1.03 Mb. The average genomic inbreeding coefficient F was 0.099 ± 0.03, the pedigree-based classical inbreeding coefficient F 0.016 ± 0.021, and ancestral inbreeding coefficients ranged from 0.03 (F) to 0.51 (Ahc). Most ROH (55.85%) were classified into the length category of 2-4 Mb, and the minority (0.43%) into the length category of >32 Mb. The effective population size (N) decreased in the last seven generations (~65 years) from 189.43 to 58.55. Consensus ROH shared by 45% of the horses were located on equine chromosomes 3 and 7, while ROH islands exceeding the 99th percentile threshold were identified on chromosomes 2, 3, 5, 7, 9, 10, and 11. These ROH islands contained genes associated with morphological development ( cluster), fertility (, , and ), muscle growth, and skin physiology ( gene cluster). Conclusions: This study highlights how important it is to monitor genetic diversity in endangered populations with genomic data. The results of this study will help to develop breeding strategies to ensure the conservation of the German Rhenish draught horse population and show whether favorable alleles from the overrepresented candidate genes within ROH were transmitted to the next generation.
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Publication Date: 2025-03-11 PubMed ID: 40149478PubMed Central: PMC11942601DOI: 10.3390/genes16030327Google 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.

The study examines the genetic diversity and patterns of homozygosity in the endangered Rhenish German draught horse. It reveals valuable insights into the breed’s genetic makeup and provides guidance for the development of conservation strategies.

Methods

  • The research involved studying the genome-wide genotype data of 675 Rhenish German draught horses.
  • Pedigree-based inbreeding coefficients were collected for these horses.
  • The final data set was made up of 64,737 autosomal SNPs, which are variations in a single DNA sequence found within a population.

Findings

  • The average number of Runs of Homozygosity (ROH) per individual horse was found to be 43.17 with an average ROH length of 5.087 Mb.
  • The researchers found that the average genomic inbreeding coefficient (F) was 0.099; the pedigree-based classical inbreeding coefficient (F) was 0.016, with ancestral inbreeding coefficients ranging from 0.03 to 0.51.
  • Most of the ROH were classified into the length category of 2-4 Mb, with a small fraction (0.43%) into the length category of more than 32 Mb.
  • The study calculated that the effective population size (N) has decreased in the last seven generations (approximately 65 years) from 189.43 to 58.55.
  • The consensus ROH shared by 45% of the horses were located on equine chromosomes 3 and 7.

ROH Islands and Gene Associations

  • ROH islands exceeding the 99th percentile threshold were identified on chromosomes 2, 3, 5, 7, 9, 10, and 11. These islands contained genes associated with morphological development, fertility, muscle growth, and skin physiology.

Conclusions

  • The results underscore the importance of monitoring genetic diversity in endangered populations using genomic data.
  • The findings from this study will aid in the development of breeding strategies to ensure the conservation of the Rhenish German draught horse population.
  • The study also highlighted the potential for favorable alleles from the overrepresented candidate genes within ROH to be transmitted to the next generation.

Cite This Article

APA
Sievers J, Distl O. (2025). Genomic Patterns of Homozygosity and Genetic Diversity in the Rhenish German Draught Horse. Genes (Basel), 16(3), 327. https://doi.org/10.3390/genes16030327

Publication

Genes
ISSN: 2073-4425
NlmUniqueID: 101551097
Country: Switzerland
Language: English
Volume: 16
Issue: 3
PII: 327

Researcher Affiliations

Sievers, Johanna
  • 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
  • Homozygote
  • Pedigree
  • Inbreeding
  • Polymorphism, Single Nucleotide
  • Genetic Variation
  • Genomics / methods
  • Male
  • Genome
  • Female
  • Breeding
  • Genotype

Grant Funding

  • 17-02.04.01-14/2019 / Ministry for Environment, Agriculture, Conservation and Consumer Protection

Conflict of Interest Statement

The authors declare no conflicts of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

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