The Whole-Genome Analysis and Breed Evolution of Horses

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (20 January 2025) | Viewed by 849

Special Issue Editor


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Guest Editor
Institute for Animal Genomics, University of Veterinary Medicine Hannover, 30559 Hannover, Germany
Interests: domestic animals; domestication; ecotypes; selection signatures; resilience; climate change; genomics; breeding program; genomic evaluation
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Special Issue Information

Dear Colleagues,

The domestication and selection of horses in different environments for specific purposes has resulted in more than 500 horse breeds worldwide. Understanding genetic variation between and within horse breeds should increase our knowledge of the genetic mechanisms involved in the development of traits and their genomic architecture. The identification of the variants and genes involved in the determination of traits should shed light on how selection has shaped different horse breeds.

In this Special Issue, we invite papers focusing on genome-wide association studies using SNP-by-SNP and multimarker methods. We also welcome papers that highlight selection signatures in horse breeds and the effects of inbreeding on traits. These findings will contribute to the refinement of breeding programs, provide new insights into the history of breeds and open the way for new traits in horse breeding.

This Special Issue aims to publish papers that address breed traits and their underlying genetic or regulatory variants, as well as genomic architecture and its consequences in a variety of horse breeds. 

Original research articles, reviews and methods are welcome in this Special Issue. Research areas may include complex and Mendelian traits. Research may use different data types such as genomic, transcriptomic or proteomic data.

Prof. Dr. Ottmar Distl
Guest Editor

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Keywords

  • horse breeds
  • genome-wide association
  • selection signature
  • inbreeding
  • inbreeding depression
  • genome architecture

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Published Papers (1 paper)

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Research

19 pages, 9223 KiB  
Article
Genomic Patterns of Homozygosity and Genetic Diversity in the Rhenish German Draught Horse
by Johanna Sievers and Ottmar Distl
Genes 2025, 16(3), 327; https://doi.org/10.3390/genes16030327 - 11 Mar 2025
Viewed by 526
Abstract
Background/Objectives: 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 [...] Read more.
Background/Objectives: 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 FROH was 0.099 ± 0.03, the pedigree-based classical inbreeding coefficient FPED 0.016 ± 0.021, and ancestral inbreeding coefficients ranged from 0.03 (Fa_Kal) 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 (Ne) 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 (HOXB cluster), fertility (AURKC, NLRP5, and DLX3), muscle growth, and skin physiology (ZNF 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. Full article
(This article belongs to the Special Issue The Whole-Genome Analysis and Breed Evolution of Horses)
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