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Advanced science (Weinheim, Baden-Wurttemberg, Germany)2025; 12(16); e2413023; doi: 10.1002/advs.202413023

Genomic Insights into Post-Domestication Expansion and Selection of Body Size in Ponies.

Abstract: Horse domestication revolutionizes human civilization by transforming transportation, agriculture, and warfare patterns. Despite extensive studies on modern domestic horse origins, the intricate demographic history and genetic signatures underlying pony size remain unexplored. Here, a high-quality genome assembly of the Chinese Debao pony is presented, and 452 qualified individuals from 64 horse breeds worldwide are extensively analyzed. The authors' results reveal the conservation of ancient components in East Asian horses and close relationships between Asian horses and Western pony lineages. Genetic analyses suggest an Asian paternal origin for European pony breeds. These pony-sized horses share close genetic affinities, potentially attributed to their early expansion and adaptation to local environments. In addition, promising cis-regulatory elements influencing horse withers height by regulating genes such as RFLNA and FOXO1 are identified. Overall, this study provides insightful perspectives on the dispersal history and genetic determinants underlying body size in ponies, offering broader implications for horse population management and improvement.
© 2025 The Author(s). Advanced Science published by Wiley‐VCH GmbH.
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Publication Date: 2025-02-26 PubMed ID: 40009528PubMed Central: PMC12021115DOI: 10.1002/advs.202413023Google 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 presents a thorough examination of the genetic history of pony size, revealing connections between Asian and Western pony breeds and identifying potential genetic elements influencing pony body size.

Overview of the Study

  • The researchers created a high-quality genome assembly from the Chinese Debao pony, and thoroughly analyzed the genomes of 452 individual horses from 64 different breeds worldwide.
  • Previous studies have explored the origins of domestic horses, but little research has explored the genetic history and demographic factors underlying the size of ponies.
  • This study aimed to fill in these gaps in our knowledge and provide insight into the genetic determinants that influence the body size of ponies.

Key Findings

  • The researchers found that ancient genetic components are conserved in East Asian horses, and that there are close genetic relationships between Asian horses and Western pony breeds.
  • The authors suggest an Asian paternal origin for European pony breeds, indicating a shared ancestry and potential migration paths.
  • It was identified that these smaller-sized horses share a close genetic affinity which can possibly be attributed to their early expansion and adaptation to various local environments.

Identification of Regulatory Elements

  • In addition to these findings, the researchers also identified promising cis-regulatory elements that might influence the size of horses.
  • These elements accomplish this by regulating the expression of certain genes, including RFLNA and FOXO1, which have been associated with size regulation in various organisms.

Implications of the Study

  • The findings of this study have broader implications for the management and improvement of horse populations.
  • A deeper understanding of the genetic determinants of body size in ponies could aid in breeding programs and the preservation of various pony breeds.
  • This research could also lead to better understanding of horse domestication and regional adaptations.

Cite This Article

APA
Li X, Wang Z, Zhu M, Wang B, Teng S, Yan J, Wang H, Yuan P, Cao S, Qu X, Wang Z, Zhan K, Choudhury MP, Yang X, Bao Q, He S, Liu L, Zhao P, Jiang J, Xiang H, Fang L, Tang Z, Liao Y, Yi G. (2025). Genomic Insights into Post-Domestication Expansion and Selection of Body Size in Ponies. Adv Sci (Weinh), 12(16), e2413023. https://doi.org/10.1002/advs.202413023

Publication

Advanced science (Weinheim, Baden-Wurttemberg, Germany)
ISSN: 2198-3844
NlmUniqueID: 101664569
Country: Germany
Language: English
Volume: 12
Issue: 16
Pages: e2413023

Researcher Affiliations

Li, Xingzheng
  • Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
Wang, Zihao
  • Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning, 530002, China.
Zhu, Min
  • Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning, 530002, China.
Wang, Binhu
  • Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
Teng, Shaohua
  • Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning, 530002, China.
Yan, Jing
  • Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning, 530002, China.
Wang, Haoyu
  • Nanning Capitano Equestrian Club Co., Ltd, Nanning, 530000, China.
Yuan, Pengxiang
  • Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
Cao, Shuwei
  • Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning, 530002, China.
Qu, Xiaolu
  • Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
Wang, Zhen
  • Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
Zhan, Kai
  • Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
Choudhury, Md Panir
  • Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
Yang, Xintong
  • Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
Bao, Qi
  • Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
He, Sang
  • Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
Liu, Lei
  • Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
Zhao, Pengju
  • Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China.
Jiang, Jicai
  • Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA.
Xiang, Hai
  • Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
Fang, Lingzhao
  • Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark.
Tang, Zhonglin
  • Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
  • Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan, 528226, China.
Liao, Yuying
  • Guangxi Veterinary Research Institute, Nanning, 530001, China.
Yi, Guoqiang
  • Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
  • Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan, 528226, China.
  • Bama Yao Autonomous County Rural Revitalization Research Institute, Bama, 547500, China.

MeSH Terms

  • Horses / genetics
  • Animals
  • Body Size / genetics
  • Domestication
  • Genomics / methods
  • Genome / genetics
  • Breeding

Grant Funding

  • AA17204024 / Guangxi Special Project for Innovation-Driven Development
  • CAAS-ASTIP / Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences
  • AB23026156 / Guangxi Key Research and Development Program
  • XM2402 / Program of Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety

Conflict of Interest Statement

The authors declare no conflict of interest.

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Citations

This article has been cited 1 times.
  1. Lewczuk D, Wypchło M, Hecold M, Buczkowska R, Korwin-Kossakowska A. Connections Between Gene Polymorphism and Fetlock and Hock Measurements in Polish Sport Horses. Int J Mol Sci 2025 Oct 2;26(19).
    doi: 10.3390/ijms26199645pubmed: 41096909google scholar: lookup
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