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Home / Equine Research Bank / Genes (Basel) / Genome-Wide Assessment of Runs of Homozygosity by Whole-Geno...
Genes2023; 14(6); 1211; doi: 10.3390/genes14061211

Genome-Wide Assessment of Runs of Homozygosity by Whole-Genome Sequencing in Diverse Horse Breeds Worldwide.

Abstract: In the genomes of diploid organisms, runs of homozygosity (ROH), consecutive segments of homozygosity, are extended. ROH can be applied to evaluate the inbreeding situation of individuals without pedigree data and to detect selective signatures via ROH islands. We sequenced and analyzed data derived from the whole-genome sequencing of 97 horses, investigated the distribution of genome-wide ROH patterns, and calculated ROH-based inbreeding coefficients for 16 representative horse varieties from around the world. Our findings indicated that both ancient and recent inbreeding occurrences had varying degrees of impact on various horse breeds. However, recent inbreeding events were uncommon, particularly among indigenous horse breeds. Consequently, the ROH-based genomic inbreeding coefficient could aid in monitoring the level of inbreeding. Using the Thoroughbred population as a case study, we discovered 24 ROH islands containing 72 candidate genes associated with artificial selection traits. We found that the candidate genes in Thoroughbreds were involved in neurotransmission (, , and ), muscle development ( and ), positive regulation of heart rate and heart contraction ( and ), regulation of insulin secretion (, , and ), and spermatogenesis (, , and ). Our findings provide insight into horse breed characteristics and future breeding strategies.
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Publication Date: 2023-06-01 PubMed ID: 37372391PubMed Central: PMC10298080DOI: 10.3390/genes14061211Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • Non-U.S. Gov't

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.

This research article investigates runs of homozygosity (ROH) in the genome sequencing of different breeds of horses. The study helps understand how both ancient and recent inbreeding has impacted various horse breeds and identifies genes associated with specific traits in Thoroughbreds.

Study Parameters and Methodology

  • The researchers analyzed data derived from whole-genome sequencing of 97 horses. Their goal was to study the distribution of genome-wide Runs of Homozygosity (ROH) patterns. ROH refers to extended, consecutive segments of homozygosity in the genomes of diploid organisms.
  • The analysis of the collected data was performed for 16 representative horse breeds from around the world, providing a diverse sample for the study.
  • The study also calculated the ROH-based inbreeding coefficients. These coefficients provide valuable estimates of the inbreeding level of individuals in a population and are useful when pedigree data is not available.

Key Findings

  • The findings of the study revealed that both ancient and recent inbreeding occurrences have impacted various horse breeds to different degrees.
  • Notably, recent inbreeding events were found to be uncommon, particularly among indigenous horse breeds.
  • The genomic inbreeding coefficient, based on ROH, could be effectively used to monitor the level of inbreeding, enhancing breeding strategies.

Case Study: Thoroughbred Population

  • The study used the Thoroughbred population as a case to further delve into the nature and implication of ROH.
  • Through this case study, researchers discovered 24 ROH islands containing 72 candidate genes. These genes are suspected to be associated with specific traits that have been selected artificially.
  • The candidate genes were involved in a variety of biological processes. These included neurotransmission, muscle development, positive regulation of heart rate and heart contraction, regulation of insulin secretion, and spermatogenesis.

Implications

  • The findings of the study provide valuable insights into the characteristics of horse breeds and offer the potential to enhance future breeding strategies.
  • By identifying the impact of inbreeding on horses and mapping ROH patterns across different breeds, this research contributes meaningful data to support the genetic health and diversity of horse populations worldwide.

Cite This Article

APA
Chen C, Zhu B, Tang X, Chen B, Liu M, Gao N, Li S, Gu J. (2023). Genome-Wide Assessment of Runs of Homozygosity by Whole-Genome Sequencing in Diverse Horse Breeds Worldwide. Genes (Basel), 14(6), 1211. https://doi.org/10.3390/genes14061211

Publication

Genes
ISSN: 2073-4425
NlmUniqueID: 101551097
Country: Switzerland
Language: English
Volume: 14
Issue: 6
PII: 1211

Researcher Affiliations

Chen, Chujie
  • Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China.
Zhu, Bo
  • Novogene Bioinformatics Institute, Beijing 100015, China.
Tang, Xiangwei
  • Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China.
Chen, Bin
  • Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China.
Liu, Mei
  • Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China.
Gao, Ning
  • Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China.
Li, Sheng
  • Maxun Biotechnology Institute, Changsha 410024, China.
Gu, Jingjing
  • Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China.

MeSH Terms

  • Male
  • Horses / genetics
  • Animals
  • Polymorphism, Single Nucleotide / genetics
  • Homozygote
  • Genome / genetics
  • Inbreeding
  • Genomics

Conflict of Interest Statement

The authors declare no conflict of interest.

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Citations

This article has been cited 1 times.
  1. Dementieva N, Nikitkina E, Shcherbakov Y, Nikolaeva O, Mitrofanova O, Ryabova A, Atroshchenko M, Makhmutova O, Zaitsev A. The Genetic Diversity of Stallions of Different Breeds in Russia.. Genes (Basel) 2023 Jul 24;14(7).
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