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Genes2023; 14(10); 1934; doi: 10.3390/genes14101934

Genome-Wide Detection of Copy Number Variations Associated with Miniature Features in Horses.

Abstract: Copy number variations (CNVs) are crucial structural genomic variants affecting complex traits in humans and livestock animals. The current study was designed to conduct a comprehensive comparative copy number variation analysis among three breeds, Debao (DB), Baise (BS), and Warmblood (WB), with a specific focus on identifying genomic regions associated with miniature features in horses. Using whole-genome next-generation resequencing data, we identified 18,974 CNVs across 31 autosomes. Among the breeds, we found 4279 breed-specific CNV regions (CNVRs). Baise, Debao, and Warmblood displayed 2978, 986, and 895 distinct CNVRs, respectively, with 202 CNVRs shared across all three breeds. After removing duplicates, we obtained 1545 CNVRs from 26 horse genomes. Functional annotation reveals enrichment in biological functions, including antigen processing, cell metabolism, olfactory conduction, and nervous system development. Debao horses have 970 genes overlapping with CNVRs, possibly causing their small size and mountainous adaptations. We also found that the genes GHR, , and may be responsible for the miniature features of the Debao horse by analyzing their overlapping CNVRs. Overall, this study offers valuable insights into the widespread presence of CNVs in the horse genome. The findings contribute to mapping horse CNVs and advance research on unique miniature traits observed in the Debao horse.
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Publication Date: 2023-10-13 PubMed ID: 37895283PubMed Central: PMC10606273DOI: 10.3390/genes14101934Google 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 article presents a study examining the role of copy number variations (CNVs) in the genetic development of miniature traits in horses. Researchers examined three different horse breeds – Debao (DB), Baise (BS), and Warmblood (WB), and identified key regions in the horse genome associated with smaller features, particularly in the Debao breed. The findings could advance our understanding of horse genetics.

Understanding Copy Number Variations (CNVs)

  • Copy number variations (CNVs) represent structural changes in the genome, involving sections which are duplicated or deleted. They are significant because they can affect complex traits and cause variations in species.
  • The researchers in this study used whole-genome next-generation resequencing data to identify these CNVs to get insights on the breeds’ unique features.

Comparative Analysis among Three Horse Breeds

  • Using the genomic data, the team identified a total of 18,974 CNVs, spread across 31 autosomes (non-sex chromosomes).
  • They found 4279 CNV regions (CNVRs) that varied between the three breeds. Of these, Baise had the most at 2978, followed by Debao with 986, and Warmblood with 895.
  • Interestingly, 202 of these CNVRs were found in all three breeds. Once duplicates were removed, a total of 1545 unique CNVRs were identified.

Functional Annotation of CNVRs

  • The study went on to annotate the functions of the identified CNVs. This revealed that they are majorly enriched in biological functions like antigen processing, cell metabolism, olfactory conduction, and nervous system development.
  • Specifically, the Debao horses had 970 genes that overlapped with the CNVRs, which might be responsible for their small size and adaptations to mountainous regions.

Genes Associated with Miniature Features

  • The genes GHR, , and were found overlapping with the CNVRs in Debao horses, which suggests that these genes may influence the miniature features observed in this breed.

Conclusion

  • This study provides valuable understanding into the prevalence of CNVs in the horse genome and how they affect physical traits.
  • By identifying the genes that overlap with these CNVs, researchers can gain crucial insights into the unique miniature traits associated with horse breeds like Debao. This contributes to mapping horse CNVs and propels research into horse genetics.

Cite This Article

APA
Choudhury MP, Wang Z, Zhu M, Teng S, Yan J, Cao S, Yi G, Liu Y, Liao Y, Tang Z. (2023). Genome-Wide Detection of Copy Number Variations Associated with Miniature Features in Horses. Genes (Basel), 14(10), 1934. https://doi.org/10.3390/genes14101934

Publication

Genes
ISSN: 2073-4425
NlmUniqueID: 101551097
Country: Switzerland
Language: English
Volume: 14
Issue: 10
PII: 1934

Researcher Affiliations

Choudhury, Md Panir
  • Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 518124, China.
  • Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
  • Bangladesh Livestock Research Institute, Ministry of Fisheries and Livestock, Savar, Dhaka 1341, Bangladesh.
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.
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.
Cao, Shuwei
  • Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning 530002,China.
Yi, Guoqiang
  • Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 518124, China.
  • Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
Liu, Yuwen
  • Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 518124, China.
  • Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
Liao, Yuying
  • Guangxi Veterinary Research Institute, Nanning 530001, China.
Tang, Zhonglin
  • Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 518124, China.
  • Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.

MeSH Terms

  • Humans
  • Horses / genetics
  • Animals
  • DNA Copy Number Variations / genetics
  • Genome / genetics
  • Genomics
  • Phenotype
  • Polymorphism, Single Nucleotide

Conflict of Interest Statement

The authors declare that there are no conflict of interest concerning the authorship or publication of this article.

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