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BMC genomics2025; 26(1); 292; doi: 10.1186/s12864-025-11484-2

Genomic insights into the genetic diversity and genetic basis of body height in endangered Chinese Ningqiang ponies.

Abstract: Genetic diversity in livestock and poultry is critical for adapting production systems to future challenges. However, inadequate management practices, particularly in developing countries, have led to the extinction or near extinction of several species. Understanding the genetic composition and historical background of local breeds is essential for their effective conservation and sustainable use. This study compared the genomes of 30 newly sequenced Ningqiang ponies with those of 56 other ponies and 104 horses to investigate genetic diversity, genetic differentiation, and the genetic basis of body height differences. Results: Population structure and genetic diversity analyses revealed that Ningqiang ponies belong to southwestern Chinese ponies. They exhibit a moderate level of inbreeding compared to other pony and horse breeds. Mitochondrial DNA analysis indicated that Ningqiang and Debao ponies share the dominant haplogroups A and C, suggesting a likely common maternal origin. Our study identified low genetic differentiation and detectable gene flow between Ningqiang ponies and Datong horses. The study also indicated the effective population size of Ningqiang ponies showed a downward trend. These findings potentially reflect the historical formation of Ningqiang ponies and population size changes. A selection signal scan (CLR and θπ) within Ningqiang ponies detected several key genes associated with bone development (ANKRD11, OSGIN2, JUNB, and RPL13) and immune response (RIPK2). The combination of genome-wide association analysis and selective signature analysis (F) revealed significant single nucleotide polymorphisms and selective genes associated with body height, with the most prominent finding being the TBX3 gene on equine chromosome (ECA) 8. Additionally, TBX5, ASAP1, CDK12, CA10, and CSMD1 were identified as important candidate genes for body height differences between ponies and horses. Conclusions: The results of this study elucidate the genetic diversity, genetic differentiation, and effective population size of Ningqiang ponies compared to other ponies and horses, further deepen the understanding of their small stature, and provide valuable insights into the conservation and breeding of local horse breeds in China.
© 2025. The Author(s).
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Publication Date: 2025-03-24 PubMed ID: 40128652PubMed Central: PMC11934595DOI: 10.1186/s12864-025-11484-2Google 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 dives into the deeper understanding of genetic diversity and the genetic basis of body height in endangered Chinese Ningqiang ponies by studying and comparing their genomes to those of other ponies and horses. The results provide insights into their levels of inbreeding, genetic differentiation, effective population size, and genetic contributors to their small stature.

Objective and Methodology

  • The researchers aim to understand the genetic composition and historical background of Ningqiang ponies in order to ensure their effective conservation and sustainable use.
  • Their method involved comparing the genomes of 30 newly sequenced Ningqiang ponies with those of 56 other ponies and 104 horses.

Findings and Significance

  • Population structure and genetic diversity analyses revealed that Ningqiang ponies belong to southwestern Chinese ponies and exhibit a moderate level of inbreeding compared to other pony and horse breeds.
  • Analysis of mitochondrial DNA suggested common maternal origin between Ningqiang and Debao ponies, as they share the dominant haplogroups A and C.
  • The study also revealed low levels of genetic differentiation and detectable gene flow between Ningqiang ponies and Datong horses.
  • The effective population size of Ningqiang ponies is decreasing. These findings potentially reflect the historical formation of Ningqiang ponies and population size changes.
  • Genes associated with bone development (ANKRD11, OSGIN2, JUNB, and RPL13) and immune response (RIPK2) were detected.
  • Genome-wide association analysis and selective signature analysis (F) revealed significant single nucleotide polymorphisms and selective genes associated with body height.
  • The TBX3 gene was highlighted as fundamental in determining the body height in horses and ponies; other relevant genes included TBX5, ASAP1, CDK12, CA10, and CSMD1.

Conclusion and Future Recommendations

  • The study provides substantial insight into the genetic diversity, genetic differentiation, and effective population size of Ningqiang ponies compared to other ponies and horses.
  • The understanding of their smaller stature is deepened by identifying the genetic contributors.
  • The findings contribute to the ongoing efforts to conserve and breed local horse breeds in China.
  • Future research should focus on further exploring the impact of the detected genes on body height variations among horse and pony breeds.

Cite This Article

APA
Han J, Shao H, Sun M, Gao F, Hu Q, Yang G, Jafari H, Li N, Dang R. (2025). Genomic insights into the genetic diversity and genetic basis of body height in endangered Chinese Ningqiang ponies. BMC Genomics, 26(1), 292. https://doi.org/10.1186/s12864-025-11484-2

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 26
Issue: 1
Pages: 292
PII: 292

Researcher Affiliations

Han, Jiale
  • Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100, Yangling, China.
Shao, Hanrui
  • College of Information Engineering, Northwest A&F University, Yangling, 712100, China.
Sun, Minhao
  • Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100, Yangling, China.
Gao, Feng
  • Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100, Yangling, China.
Hu, Qiaoyan
  • Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100, Yangling, China.
Yang, Ge
  • Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100, Yangling, China.
Jafari, Halima
  • Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100, Yangling, China.
Li, Na
  • Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100, Yangling, China.
Dang, Ruihua
  • Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100, Yangling, China. dangruihua@nwsuaf.edu.cn.

MeSH Terms

  • Animals
  • Horses / genetics
  • Genetic Variation
  • Endangered Species
  • Body Height / genetics
  • Genomics / methods
  • Polymorphism, Single Nucleotide
  • China
  • Phylogeny
  • Genetics, Population
  • East Asian People

Conflict of Interest Statement

Declarations. Ethics approval and consent to participate: This study was approved by the Institutional Animal Care and Use Committee of Northwest A&F University (FAPWCNWAFU, Protocol number, NWAFAC 1008) following the recommendation of the Regulations for the Administration of Affairs Concerning Experimental Animals of China. All methods were carried out in accordance with relevant guidelines and regulations. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.

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Citations

This article has been cited 1 times.
  1. Salek Ardestani S, Mohandesan E. GENOVIS: a Python package for the visualization of population genetic analyses. BMC Genomics 2026 Feb 10;27(1):190.
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