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Home / Equine Research Bank / Anim Genet / Whole-genome identification of transposable elements reveals...
Animal genetics2022; 54(2); 144-154; doi: 10.1111/age.13277

Whole-genome identification of transposable elements reveals the equine repetitive element insertion polymorphism in Chinese horses.

Abstract: Transposable elements (TEs) are diverse, abundant, and complicated in genomes. They not only can drive the genome evolution process but can also act as special resources for adaptation. However, little is known about the evolutionary processes that shaped horses. In this work, 126 horse assemblages involved in most horse breeds in China were used to investigate the patterns of TE variation for the first time. By using RepeatMasker and melt software, we found that the horse-specific short interspersed repetitive elements family, equine repetitive elements (ERE1), exhibited polymorphisms in horse genomes. Phylogenetic analysis based on these ERE1 loci (minor allele frequency ≥0.05) revealed three major horse groups, namely, those in northern China, southern China, and Qinghai-Tibetan, which mirrors the result determined by SNPs to some extent. The present ERE1 family emerged ~0.26 to 1.77 Mya ago, with an activity peak at ~0.49 Mya, which matches the early stage of the horse lineage and decreases after the divergence of Equus caballus and Equus ferus przewalskii. To detect the functional ERE1(s) associated with adaptation, locus-specific branch length, genome-wide association study, and absolute allele frequency difference analyses were conducted and resulted in two common protein-coding genes annotated by candidate ERE1s. They were clustered into the vascular smooth muscle contraction (p = 0.01, EDNRA) and apelin signalling pathways (p = 0.02, NRF1). Notably, ERE1 insertion into the EDNRA gene showed a higher association with adaptation among southern China horses and other horses in 15 populations and 451 individuals (p = 4.55 e-8). Our results provide a comprehensive understanding of TE variations to analyse the phylogenetic relationships and traits relevant to adaptive evolution in horses.
© 2022 Stichting International Foundation for Animal Genetics.
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Publication Date: 2022-12-05 PubMed ID: 36464985DOI: 10.1111/age.13277Google 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 research study explores the patterns of variation in transposable elements (TEs) in the Chinese horse genome. Results indicate that these TEs can reflect patterns of adaptability and evolution. The study contributes to an understanding of how these elements have influenced the divergence and development of different horse breeds.

Overview of the Research Study

  • The focus of the study lies on Transposable Elements (TEs), highly complex genome components that help drive evolution and offer resources for adaptation. In this study, TEs found in Chinese horse breeds were analyzed for their variations and effects on horse development and evolution.
  • To gather data, the scientists sourced 126 assembled genomes of most horse breeds in China. These specimens were then studied using RepeatMasker and melt software to identify the TEs and their variations.
  • Furthermore, the study concentrated on a specific type of TE known as Equine Repetitive Elements (EREs) which were found to show polymorphisms, or genetic variations, in horse genomes.

Key Findings

  • Phylogenetic analysis, the study of evolutionary relationships, was conducted by the researchers on the ERE1 sites showing a minor allele frequency greater than or equal to 0.05. This analysis revealed three major genetic groups of horses in northern China, southern China, and Qinghai-Tibetan – a result that is somewhat similar to previous findings based on SNPs.
  • The ERE1 family was found to have emerged between 0.26 to 1.77 million years ago with peak activity around 0.49 million years ago. This timeline coincides with the early stage of horse lineage and shows a decrease after the divergence of two horse species i.e., Equus caballus and Equus ferus przewalskii.
  • Further analysis was conducted to identify functional ERE1s that might be related to adaptation. The results showed two common protein-coding genes influenced by candidate ERE1s – EDNRA and NRF1 – which were linked to the vascular smooth muscle contraction and apelin signalling pathways, respectively.
  • Notably, ERE1 insertion into the EDNRA gene was strongly associated with adaptation among southern Chinese horses and other horses in 15 different populations. This finding adds new insights into understanding the adaptive evolution and genomic diversity of horses.

Contribution to the Field

  • This investigation provides a comprehensive understanding of TE variations in the horse genome. It uncovers the phylogenetic relationships among different horse breeds and elucidates factors driving adaptive evolution.
  • The identification of the specific genes influenced by ERE1 insertions, and their involvement in smooth muscle contractions and signalling pathways, opens new avenues for further research into the physiological and genetic adaptations in horses.

Cite This Article

APA
Liu X, Zhang Y, Pu Y, Ma Y, Jiang L. (2022). Whole-genome identification of transposable elements reveals the equine repetitive element insertion polymorphism in Chinese horses. Anim Genet, 54(2), 144-154. https://doi.org/10.1111/age.13277

Publication

Animal genetics
ISSN: 1365-2052
NlmUniqueID: 8605704
Country: England
Language: English
Volume: 54
Issue: 2
Pages: 144-154

Researcher Affiliations

Liu, Xuexue
  • National Germplasm Centre of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
  • Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France.
Zhang, Yanli
  • National Germplasm Centre of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
  • CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
Pu, Yabin
  • National Germplasm Centre of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
  • CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
Ma, Yuehui
  • National Germplasm Centre of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
  • CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
Jiang, Lin
  • National Germplasm Centre of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
  • CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.

MeSH Terms

  • Animals
  • DNA Transposable Elements
  • Gene Frequency
  • Genome-Wide Association Study
  • Horses / genetics
  • Phylogeny

Grant Funding

  • 20190102 / International Postdoctoral Exchange Fellowship Program
  • 32002144 / National Natural Science Foundation of China
  • 31972530 / National Natural Science Foundation of China
  • 31772553 / National Natural Science Foundation of China
  • ASTIP-IAS01 / the Agricultural Science and Technology Innovation Program of China
  • 101027750 / the European Union's Horizon 2020 research and Innovation programme under the Marie Sklodowska

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