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G3 (Bethesda, Md.)2022; 12(12); jkac278; doi: 10.1093/g3journal/jkac278

Copy number variation of horse Y chromosome genes in normal equine populations and in horses with abnormal sex development and subfertility: relationship of copy number variations with Y haplogroups.

Abstract: Structural rearrangements like copy number variations in the male-specific Y chromosome have been associated with male fertility phenotypes in human and mouse but have been sparsely studied in other mammalian species. Here, we designed digital droplet PCR assays for 7 horse male-specific Y chromosome multicopy genes and SRY and evaluated their absolute copy numbers in 209 normal male horses of 22 breeds, 73 XY horses with disorders of sex development and/or infertility, 5 Przewalski's horses and 2 kulans. This established baseline copy number for these genes in horses. The TSPY gene showed the highest copy number and was the most copy number variable between individuals and breeds. SRY was a single-copy gene in most horses but had 2-3 copies in some indigenous breeds. Since SRY is flanked by 2 copies of RBMY, their copy number variations were interrelated and may lead to SRY-negative XY disorders of sex development. The Przewalski's horse and kulan had 1 copy of SRY and RBMY. TSPY and ETSTY2 showed significant copy number variations between cryptorchid and normal males (P < 0.05). No significant copy number variations were observed in subfertile/infertile males. Notably, copy number of TSPY and ETSTY5 differed between successive male generations and between cloned horses, indicating germline and somatic mechanisms for copy number variations. We observed no correlation between male-specific Y chromosome gene copy number variations and male-specific Y chromosome haplotypes. We conclude that the ampliconic male-specific Y chromosome reference assembly has deficiencies and further studies with an improved male-specific Y chromosome assembly are needed to determine selective constraints over horse male-specific Y chromosome gene copy number and their relation to stallion reproduction and male biology.
© The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America.
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Publication Date: 2022-10-14 PubMed ID: 36227030PubMed Central: PMC9713435DOI: 10.1093/g3journal/jkac278Google Scholar: Lookup
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  • Journal Article
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  • Non-U.S. Gov't
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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 research conducted genetic analysis to examine Y chromosome gene variations in horses, aiding our understanding of their relationship to male fertility. The paper highlighted the presence of copy number variations (CNVs) in seven male-specific multicopy genes across different horse breeds, their effect on fertility, and the possible inconsistencies in current Y-chromosome reference assembly.

Objective of Research

  • The study was designed to understand the structural variations, specifically, the copy number variations (CNVs) in the horse Y chromosome and its effects on male fertility. It aimed to establish a baseline copy number for these genes in horses.

Methodology

  • The researchers conducted digital droplet PCR assays for seven horse male-specific Y chromosome multicopy genes and SRY (sex determining region on the Y chromosome), evaluating their absolute copy numbers in 209 normal male horses of 22 breeds and 73 XY horses with disorders of sex development and/or infertility.
  • The study included five Przewalski’s horses and two kulans to provide a diverse genetic background.

Key Findings

  • It was observed that the TSPY gene had the highest copy number and the most copy number variability between individuals and breeds.
  • The SRY gene had only one copy in most horses but showed 2-3 copies in some indigenous breeds. This suggests that CNVs of surrounding genes could lead to SRY-negative XY disorders of sex development in horses.
  • The study found no significant copy number variations in subfertile/infertile males, though TSPY and ETSTY2 showed significant copy number variations between cryptorchid and normal males.
  • Interestingly, the TSPY and ETSTY5 copy number differences were observed between successive male generations and cloned horses, indicating germline and somatic mechanisms for the observed CNVs.

Implications and Conclusion

  • Notably, there was no correlation observed between male-specific Y chromosome gene copy number variations and male-specific Y chromosome haplotypes.
  • The researchers concluded that the horse Y chromosome reference assembly might have deficiencies, which needs to be addressed in future studies for a better understanding of the selective constraints over horse male-specific Y chromosome gene copy number.
  • Further research with an improved Y chromosome assembly is necessary to determine the relation of these gene copy numbers to stallion reproduction and male biology.

Cite This Article

APA
Castaneda C, Radović L, Felkel S, Juras R, Davis BW, Cothran EG, Wallner B, Raudsepp T. (2022). Copy number variation of horse Y chromosome genes in normal equine populations and in horses with abnormal sex development and subfertility: relationship of copy number variations with Y haplogroups. G3 (Bethesda), 12(12), jkac278. https://doi.org/10.1093/g3journal/jkac278

Publication

G3 (Bethesda, Md.)
ISSN: 2160-1836
NlmUniqueID: 101566598
Country: England
Language: English
Volume: 12
Issue: 12
PII: jkac278

Researcher Affiliations

Castaneda, Caitlin
  • Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA.
Radović, Lara
  • Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria.
  • Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria.
Felkel, Sabine
  • Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria.
  • Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria.
  • Department of Biotechnology, Institute of Computational Biology, BOKU University of Life Sciences and Natural Resources, Vienna 1190, Austria.
Juras, Rytis
  • Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA.
Davis, Brian W
  • Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA.
Cothran, Ernest Gus
  • Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA.
Wallner, Barbara
  • Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria.
Raudsepp, Terje
  • Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA.

MeSH Terms

  • Animals
  • Male
  • Disorders of Sex Development / genetics
  • DNA Copy Number Variations / genetics
  • Genes, Y-Linked / genetics
  • Horses / genetics
  • Infertility, Male / genetics
  • Infertility, Male / veterinary
  • Mammals / genetics
  • Sexual Development
  • Y Chromosome / genetics

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Citations

This article has been cited 3 times.
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