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G3 (Bethesda, Md.)2021; 11(2); jkab008; doi: 10.1093/g3journal/jkab008

Current genetic conservation of Chinese indigenous horses revealed with Y-chromosomal and mitochondrial DNA polymorphisms.

Abstract: To investigate the genetic diversity of Chinese indigenous horses and determine the genetic status of extant horse breeds, novel Y chromosomal microsatellite markers and known Y chromosomal SNPs and mtDNA loop sequences, were employed to study the genetic diversity levels of 13 Chinese indigenous horse populations and four introduced breeds. Sixteen Y-chromosomal microsatellite markers, including seven newly identified loci, were used in the genotyping. The results showed that 4 out of the 16 loci were highly polymorphic in Chinese indigenous horse populations, in which the polymorphisms of 3 loci, ECAYP12, ECAYP13, and ECAYCAU3, were first reported in the present study. The polymorphic Y chromosomal microsatellite markers result in 19 haplotypes in the studied horses and formed 24 paternal lines when merged with the 14 Y chromosomal SNPs reported previously. The haplotypes CHT18 and SS24 harboring AMELY gene mutation were the ancestral haplotypes, and other haplotypes were derived from them by one or more mutation steps. The horse populations in mountainous and remote areas of southwestern China have the most ancient paternal lines, which suggests that ancient paternal lines preserved in local populations attributed to less human interventions. Our results also showed that the northern local breeds had higher mtDNA diversity than the southern ones in China. The frequency of haplogroup B, F, and G of mtDNA in Chinese indigenous horses has declined in recent years, and some breeds are in endangered status mainly due to small population sizes. Urgent actions should be taken to conserve the genetic diversity of the indigenous horse populations, especially the rare paternal lines. Our findings help to elucidate the genetic diversity and evolutionary history of Chinese domestic horses, which will facilitate the conservation of the indigenous horses in the future.
© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.
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Publication Date: 2021-02-20 PubMed ID: 33604674PubMed Central: PMC8022964DOI: 10.1093/g3journal/jkab008Google Scholar: Lookup
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  • 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 investigated the genetic diversity of indigenous horse breeds in China, using Y-chromosomal and mitochondrial DNA markers. The study found that certain breeds, especially those in remote areas, carry rare and ancient paternal lines. Due to dwindling population sizes, some breeds are endangered, highlighting the urgent need for conservation efforts.

Study Design and Methods

  • The researchers selected 13 indigenous Chinese horse populations and 4 introduced breeds for the study. They used 16 Y-chromosomal microsatellite markers, including 7 newly identified, to genotype the selected horse populations.
  • Known Y chromosomal SNPs (Single Nucleotide Polymorphisms) and mtDNA (mitochondrial DNA) loop sequences were also employed to study the genetic diversity levels of the selected populations.

Findings

  • Four of the 16 Y-chromosomal microsatellite markers showed high polymorphism in Chinese indigenous horse populations. The polymorphisms of 3 markers, ECAYP12, ECAYP13, and ECAYCAU3, were first reported in this study.
  • The polymorphic Y chromosomal microsatellite markers yielded 19 different haplotypes in the studied horses. When combined with the 14 Y chromosomal SNPs reported earlier, these haplotypes gave rise to 24 unique paternal lines.
  • Two particular haplotypes, CHT18 and SS24, were identified as ancestral due to their harboring of the AMELY gene mutation. All other haplotypes were derived from these two through one or more mutation steps.

Historical and Conservation Implications

  • The most ancient paternal lines were found in horse populations inhabiting mountainous and isolated regions of southwestern China, suggesting these lines were preserved due to minimal human intervention.
  • Mounting evidence indicated that northern local horse breeds possess greater mtDNA diversity than those from the south. Additionally, the frequency of three specific haplogroups of mtDNA (B, F, and G) in the indigenous horses has been decreasing in recent years, indicating genetic loss over time.
  • Some horse breeds are currently threatened with extinction mainly due to small population sizes, emphasizing the urgent need for effective conservation strategies, particularly for the preservation of rare paternal lines.

Conclusion

  • The findings from this study contribute significantly to understanding the genetic diversity and evolutionary history of domestic horses in China. The data generated provide valuable insights that can be used to design effective conservation strategies for preserving the genetic wealth of indigenous horses locally.

Cite This Article

APA
Liu S, Fu C, Yang Y, Zhang Y, Ma H, Xiong Z, Ling Y, Zhao C. (2021). Current genetic conservation of Chinese indigenous horses revealed with Y-chromosomal and mitochondrial DNA polymorphisms. G3 (Bethesda), 11(2), jkab008. https://doi.org/10.1093/g3journal/jkab008

Publication

G3 (Bethesda, Md.)
ISSN: 2160-1836
NlmUniqueID: 101566598
Country: England
Language: English
Volume: 11
Issue: 2
PII: jkab008

Researcher Affiliations

Liu, Shuqin
  • Equine Center, China Agricultural University, Beijing, China.
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
  • College of Animal Science and Technology, Qingdao Agricultural University, Shandong, China.
Fu, Chunzheng
  • Equine Center, China Agricultural University, Beijing, China.
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
Yang, Yunzhou
  • Equine Center, China Agricultural University, Beijing, China.
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
Zhang, Yuanyuan
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
Ma, Hongying
  • Equine Center, China Agricultural University, Beijing, China.
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
Xiong, Zhiyao
  • Equine Center, China Agricultural University, Beijing, China.
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
Ling, Yao
  • Equine Center, China Agricultural University, Beijing, China.
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
  • Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, China.
  • Beijing Key Laboratory of Animal Genetic Improvement, Beijing, China.
Zhao, Chunjiang
  • Equine Center, China Agricultural University, Beijing, China.
  • College of Animal Science and Technology, China Agricultural University, Beijing, China.
  • Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, China.
  • Beijing Key Laboratory of Animal Genetic Improvement, Beijing, China.
  • National Engineering Laboratory for Animal Breeding. Beijing, China.

MeSH Terms

  • Animals
  • China
  • DNA, Mitochondrial
  • Genetic Variation
  • Haplotypes
  • Horses
  • Phylogeny
  • Y Chromosome

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