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Home / Equine Research Bank / BMC Genomics / Comparative population genomic analysis uncovers novel genom...
BMC genomics2020; 21(1); 496; doi: 10.1186/s12864-020-06887-2

Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony.

Abstract: Body size is considered as one of the most fundamental properties of an organism. Due to intensive breeding and artificial selection throughout the domestication history, horses exhibit striking variations for heights at withers and body sizes. Debao pony (DBP), a famous Chinese horse, is known for its small body size and lives in Guangxi mountains of southern China. In this study, we employed comparative population genomics to study the genetic basis underlying the small body size of DBP breed based on the whole genome sequencing data. To detect genomic signatures of positive selection, we applied three methods based on population comparison, fixation index (F), cross population composite likelihood ratio (XP-CLR) and nucleotide diversity (θπ), and further analyzed the results to find genomic regions under selection for body size-related traits. Results: A number of protein-coding genes in windows with the top 1% values of F (367 genes), XP-CLR (681 genes), and log (θπ ratio) (332 genes) were identified. The most significant signal of positive selection was mapped to the NELL1 gene, probably underlies the body size and development traits, and may also have been selected for short stature in the DBP population. In addition, some other loci on different chromosomes were identified to be potentially involved in the development of body size. Conclusions: Results of our study identified some positively selected genes across the horse genome, which are possibly involved in body size traits. These novel candidate genes may be useful targets for clarifying our understanding of the molecular basis of body size and as such they should be of great interest for future research into the genetic architecture of relevant traits in horse breeding program.
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Publication Date: 2020-07-20 PubMed ID: 32689947PubMed Central: PMC7370493DOI: 10.1186/s12864-020-06887-2Google 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 research explores the genetic factors behind small body size in the Debao pony (DBP), a Chinese horse breed known for its diminutive stature. Using population genomics, the study identified certain genes that may have undergone selection leading to the small size.

Methods

  • The researchers collected whole genome sequencing data from the DBP breed, which lives in the mountains of Guangxi, southern China, to understand the genetic basis of their small body size.
  • They applied three methods to detect genomic signs of positive selection, specifically methods based on population comparison, the fixation index (F), the cross population composite likelihood ratio (XP-CLR), and nucleotide diversity (θπ).
  • They further analyzed the results to pinpoint genomic regions that have been selected for body size-related traits.

Results

  • The study identified protein-coding genes that showed the top 1% values of F, XP-CLR, and log (θπ ratio). These genes were found in 367, 681, and 332 windows respectively.
  • The most significant sign of positive selection was found in the NELL1 gene. This gene is theorized to underlie body size and development traits and may have been selected for its role in creating the short stature seen in the DBP population.
  • Other genes found on different chromosomes were also suspected to be involved in the development of body size.

Conclusion

  • The study identified a number of genes across the horse genome that likely play a role in determining body size.
  • These newly discovered candidate genes could potentially improve our understanding of the molecular basis of body size. As such, they are of great relevance for future research into the genetic structure of traits seen in horse breeding programs.

Cite This Article

APA
Asadollahpour Nanaei H, Esmailizadeh A, Ayatollahi Mehrgardi A, Han J, Wu DD, Li Y, Zhang YP. (2020). Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony. BMC Genomics, 21(1), 496. https://doi.org/10.1186/s12864-020-06887-2

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 21
Issue: 1
Pages: 496
PII: 496

Researcher Affiliations

Asadollahpour Nanaei, Hojjat
  • Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB, 76169-133, Iran.
Esmailizadeh, Ali
  • Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB, 76169-133, Iran. aliesmaili@uk.ac.ir.
  • State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan, China. aliesmaili@uk.ac.ir.
Ayatollahi Mehrgardi, Ahmad
  • Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB, 76169-133, Iran.
Han, Jianlin
  • CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
  • Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya.
Wu, Dong-Dong
  • State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan, China.
  • State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China.
Li, Yan
  • State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China. liyan0910@ynu.edu.cn.
Zhang, Ya-Ping
  • State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan, China. zhangyp@mail.kiz.ac.cn.
  • State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China. zhangyp@mail.kiz.ac.cn.

MeSH Terms

  • Animals
  • Body Size / genetics
  • China
  • Genomics
  • Horses / genetics
  • Metagenomics
  • Polymorphism, Single Nucleotide
  • Selection, Genetic

Grant Funding

  • 91531303 / Innovative Research Group Project of the National Natural Science Foundation of China (CN)
  • GJHZ1559 / International cooperation program of bureau of international cooperation of Chinese Academy of Sciences
  • XDA2004010302 / CAS Key Laboratory of Receptor Research

Conflict of Interest Statement

The authors declare that they have no competing interests.

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