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Frontiers in genetics2020; 11; 467; doi: 10.3389/fgene.2020.00467

Ancient Patrilineal Lines and Relatively High ECAY Diversity Preserved in Indigenous Horses Revealed With Novel Y-Chromosome Markers.

Abstract: Extremely low nucleotide diversity of modern horse Y-chromosome has been reported, and only poor phylogenetic resolution could be resulted from limited Y-chromosome markers. In this study, three types of horse Y-chromosome markers, including Single-nucleotide polymorphisms (SNPs), copy number variants (CNVs), and allele-specific CNVs, were developed by screening more than 300 male horses from 23 indigenous Chinese horse populations and 4 imported horse breeds. Fourteen segregating sites including a novel SNP in the AMELY gene were found in approximately 53 kb of male-specific Y-chromosome sequences. CNVs were detected at 11 of 14 sites, while allele-specific CNVs at 6 polymorphic sites in repeated fragments were also determined. The phylogenetic analyses with the SNPs identified in this study and previously published 51 SNPs obtained mainly from European horses showed that indigenous Chinese horses exhibit much deeper divergence than European and Middle Eastern horses, while individuals of Chinese horses with the C allele of the AMELY gene constituted the most ancient group. Via SNPs, CNVs, and allele-specific CNVs, much higher diversity of paternal lines can be detected than those identified with merely SNPs. Our results indicated that there are ancient paternal horse lines preserved in southwestern China, which sheds new light on the domestication and immigration of horses, and suggest that the priorities of the conservation should be given to the ancient and rare paternal lines. These three marker types provided finer phylogenetic resolution of horse patrilineal lines, and the strategies used in the present study also provide valuable reference for the genetic studies of other mammalian patrilineages.
Copyright © 2020 Liu, Yang, Pan, Sun, Ma, Liu, Wang, Zhao and Wu.
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Publication Date: 2020-05-21 PubMed ID: 32508879PubMed Central: PMC7253630DOI: 10.3389/fgene.2020.00467Google 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.

This study reveals that indigenous Chinese horses show more diversity from a genetic standpoint than their European and Middle Eastern counterparts. Through advanced genetic testing methods, previously unidentified ancient patrilineal lines were discovered, providing greater insight into the domestication and migration history of horses.

Research Methodology

  • The research involved a comprehensive screening of over 300 male horses. The subjects were divided into 23 indigenous Chinese horse populations and 4 imported horse breeds.
  • The screening focused on three types of horse Y-chromosome markers. These markes are:
    • Single-nucleotide polymorphisms (SNPs), which involve changes in individual genetic building blocks.
    • Copy number variants (CNVs), referring to regions of the genome where the number of copies of a particular section varies between individuals.
    • Allele-specific CNVs, which involve differences observed in the same genetic locus.
  • The researchers identified 14 segregating sites, including an unidentified SNP in the AMELY gene (found on male-specific Y-chromosomes). CNVs were detected at 11 of these sites, with allele-specific CNVs present in 6 polymorphic areas of repeated fragments.

Research Findings

  • The phylogenetic analyses (study of evolutionary relationships) was executed, using both the SNPs identified in this study, and 51 SNPs previously derived mostly from European horses.
  • The study revealed that indigenous Chinese horses show a deeper genetic divergence than European and Middle Eastern horses. A group of Chinese horses with a specific genetic trait (the C allele of the AMELY gene) were identified as the most ancient group.
  • Through the combination of SNPs, CNVs, and allele-specific CNVs, a higher diversity of paternal horse lines was identified.
  • Powerful evidence was identified for the existence of ancient paternal horse lines in southwestern China, shining new light on horse domestication and migration history.

Implications and Further Studies

  • The study suggests that conservation priorities should be reoriented towards protecting these ancient and rare paternal lines.
  • The techniques and strategies utilised in this study could be used to gain further understandings in genetic studies of other mammalian patrilineages, indicating the potential of these methods for broader use.

Cite This Article

APA
Liu S, Yang Y, Pan Q, Sun Y, Ma H, Liu Y, Wang M, Zhao C, Wu C. (2020). Ancient Patrilineal Lines and Relatively High ECAY Diversity Preserved in Indigenous Horses Revealed With Novel Y-Chromosome Markers. Front Genet, 11, 467. https://doi.org/10.3389/fgene.2020.00467

Publication

Frontiers in genetics
ISSN: 1664-8021
NlmUniqueID: 101560621
Country: Switzerland
Language: English
Volume: 11
Pages: 467
PII: 467

Researcher Affiliations

Liu, Shuqin
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
  • Equine Center, China Agricultural University, Beijing, China.
Yang, Yunzhou
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
  • Equine Center, China Agricultural University, Beijing, China.
Pan, Qingjie
  • School of Animal Science and Technology, Qingdao Agricultural University, Shandong, China.
Sun, Yujiang
  • School of Animal Science and Technology, Qingdao Agricultural University, Shandong, China.
Ma, Hongying
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
  • Equine Center, China Agricultural University, Beijing, China.
Liu, Yu
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
  • Equine Center, China Agricultural University, Beijing, China.
Wang, Min
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
  • Equine Center, China Agricultural University, Beijing, China.
Zhao, Chunjiang
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
  • Equine Center, China Agricultural University, Beijing, China.
  • National Engineering Laboratory for Animal Breeding, Beijing, China.
  • Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China.
  • Beijing Key Laboratory for Animal Genetic Improvement, Beijing, China.
Wu, Changxin
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
  • Equine Center, China Agricultural University, Beijing, China.
  • National Engineering Laboratory for Animal Breeding, Beijing, China.
  • Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China.
  • Beijing Key Laboratory for Animal Genetic Improvement, Beijing, China.

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