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PeerJ2024; 12; e17549; doi: 10.7717/peerj.17549

Mitochondrial DNA and Y chromosome reveal the genetic structure of the native Polish Konik horse population.

Abstract: Polish Konik remains one of the most important horse breeds in Poland. The primitive, native horses with a stocky body and mouse-like coat color are protected by a conservation program, while their Polish population consists of about 3,480 individuals, representing 16 dam and six sire lines. To define the population's genetic structure, mitochondrial DNA and Y chromosome sequence variables were identified. The mtDNA whole hypervariable region analysis was carried out using the Sanger sequencing method on 233 Polish Koniks belonging to all dam lines, while the Y chromosome analysis was performed with the competitive allele-specific PCR genotyping method on 36 horses belonging to all sire lines. The analysis of the mtDNA hypervariable region detected 47 SNPs, which assigned all tested horses to 43 haplotypes. Most dam lines presented more than one haplotype; however, five dam lines were represented by only one haplotype. The haplotypes were classified into six (A, B, E, J, G, R) recognized mtDNA haplogroups, with most horses belonging to haplogroup A, common among Asian horse populations. Y chromosome analysis allocated Polish Koniks in the Crown group, condensing all modern horse breeds, and divided them into three haplotypes clustering with coldblood breeds (28 horses), warmblood breeds (two horses), and Duelmener Pony (six horses). The clustering of all Wicek sire line stallions with Duelmener horses may suggest a historical relationship between the breeds. Additionally, both mtDNA and Y chromosome sequence variability results indicate crossbreeding before the studbooks closure or irregularities in the pedigrees occurred before the DNA testing introduction.
© 2024 Musiał et al.
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Publication Date: 2024-06-20 PubMed ID: 38912049PubMed Central: PMC11193968DOI: 10.7717/peerj.17549Google Scholar: Lookup
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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.

Overview

  • This study investigates the genetic diversity and structure of the native Polish Konik horse population by analyzing their mitochondrial DNA (mtDNA) and Y chromosome sequences.
  • The research aims to understand the maternal and paternal lineage diversity and possible historical breeding influences within this conservation-priority horse breed.

Background and Importance

  • The Polish Konik horse is a native breed important to Poland’s cultural and biological heritage, known for its primitive features, such as a stocky body and mouse-gray coat color.
  • The current population comprises approximately 3,480 horses, organized into 16 maternal (dam) lines and six paternal (sire) lines.
  • Preserving the genetic diversity of this population is crucial, as the horses are protected through a conservation program.

Research Objectives

  • To determine the genetic structure of the Polish Konik horse population using maternal and paternal genetic markers.
  • To analyze mitochondrial DNA hypervariable regions to assess maternal lineage variability.
  • To analyze Y chromosome variation to assess paternal lineage diversity.
  • To evaluate whether historical crossbreeding or pedigree errors have affected genetic diversity.

Methods

  • Sample Collection:
    • 233 Polish Konik horses sampled from all 16 dam lines for mtDNA analysis.
    • 36 Polish Konik horses sampled from all six sire lines for Y chromosome analysis.
  • Mitochondrial DNA Analysis:
    • Sanger sequencing was applied to analyze the whole hypervariable region of mtDNA.
    • Single nucleotide polymorphisms (SNPs) were identified and used to define haplotypes.
  • Y Chromosome Analysis:
    • Competitive allele-specific PCR genotyping was employed to analyze Y chromosome sequences, which determine paternal lineage.

Key Genetic Findings

  • Mitochondrial DNA Diversity:
    • Analysis revealed 47 SNPs in the hypervariable region.
    • These SNPs defined 43 distinct mtDNA haplotypes within the tested horses.
    • Most dam lines showed multiple haplotypes, indicating maternal genetic diversity within lines.
    • Five dam lines displayed only one haplotype each, suggesting some maternal line uniformity.
    • Haplotypes fell into six recognized mtDNA haplogroups (A, B, E, J, G, R), with majority in haplogroup A, which is common in Asian horses.
  • Y Chromosome Diversity:
    • Y chromosome haplotypes grouped all Polish Koniks in the “Crown group,” which includes modern horse breeds.
    • The samples divided into three haplotypes:
      • 28 horses clustered with coldblood breeds.
      • 2 horses clustered with warmblood breeds.
      • 6 horses clustered with the Duelmener Pony, a breed known for ancient origins.
    • The Wicek sire line stallions specifically clustered with the Duelmener Pony group, suggesting a historical relationship or shared ancestry with this breed.

Interpretations and Implications

  • Both the mtDNA and Y chromosome results reveal substantial genetic diversity in the Polish Konik horse population, important for conservation planning.
  • The presence of multiple haplotypes within most dam lines suggests a multifaceted maternal ancestry rather than a strict single-line descent.
  • Clustering of paternal lines with various breed groups indicates historical crossbreeding or gene flow before formal studbook closures.
  • The alignment of some sire lines with breeds like Duelmener Pony points toward unexpected relationships or shared heritage that may have been underappreciated.
  • The detection of irregularities or mixing before DNA testing highlights the importance of molecular tools in validating and possibly correcting pedigree records.
  • Overall, this genetic insight supports the effectiveness of conservation strategies and can inform selective breeding to maintain or enhance genetic variation.

Conclusion

  • The study successfully characterized the genetic structure of the Polish Konik horse using mtDNA and Y chromosome markers.
  • Results emphasize the existence of diverse maternal and paternal lineages within this native population.
  • This genetic information is valuable for guiding conservation efforts to preserve the breed’s unique genetic legacy.

Cite This Article

APA
Musiał AD, Radović L, Stefaniuk-Szmukier M, Bieniek A, Wallner B, Ropka-Molik K. (2024). Mitochondrial DNA and Y chromosome reveal the genetic structure of the native Polish Konik horse population. PeerJ, 12, e17549. https://doi.org/10.7717/peerj.17549

Publication

PeerJ
ISSN: 2167-8359
NlmUniqueID: 101603425
Country: United States
Language: English
Volume: 12
Pages: e17549
PII: e17549

Researcher Affiliations

Musiał, Adrianna Dominika
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland.
Radović, Lara
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria.
  • Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, Vienna, Austria.
Stefaniuk-Szmukier, Monika
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland.
Bieniek, Agnieszka
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland.
Wallner, Barbara
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria.
Ropka-Molik, Katarzyna
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland.

MeSH Terms

  • Animals
  • Horses / genetics
  • DNA, Mitochondrial / genetics
  • Poland
  • Y Chromosome / genetics
  • Haplotypes / genetics
  • Male
  • Polymorphism, Single Nucleotide
  • Female
  • Breeding

Conflict of Interest Statement

The authors declare that they have no competing interests.

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Citations

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