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Genes2022; 13(4); 603; doi: 10.3390/genes13040603

Genome-Wide Detection of Copy Number Variants in Chinese Indigenous Horse Breeds and Verification of CNV-Overlapped Genes Related to Heat Adaptation of the Jinjiang Horse.

Abstract: In the present study, genome-wide CNVs were detected in a total of 301 samples from 10 Chinese indigenous horse breeds using the Illumina Equine SNP70 Bead Array, and the candidate genes related to adaptability to high temperature and humidity in Jinjiang horses were identified and validated. We determined a total of 577 CNVs ranging in size from 1.06 Kb to 2023.07 Kb on the 31 pairs of autosomes. By aggregating the overlapping CNVs for each breed, a total of 495 CNVRs were detected in the 10 Chinese horse breeds. As many as 211 breed-specific CNVRs were determined, of which 64 were found in the Jinjiang horse population. By removing repetitive CNV regions between breeds, a total of 239 CNVRs were identified in the Chinese indigenous horse breeds including 102 losses, 133 gains and 4 of both events (losses and gains in the same region), in which 131 CNVRs were novel and only detected in the present study compared with previous studies. The total detected CNVR length was 41.74 Mb, accounting for 1.83% of the total length of equine autosomal chromosomes. The coverage of CNVRs on each chromosome varied from 0.47% to 15.68%, with the highest coverage on ECA 12, but the highest number of CNVRs was detected on ECA1 and ECA24. A total of 229 genes overlapping with CNVRs were detected in the Jinjiang horse population, which is an indigenous horse breed unique to the southeastern coast of China exhibiting adaptability to high temperature and humidity. The functional annotation of these genes showed significant relation to cellular heat acclimation and immunity. The expression levels of the candidate genes were validated by heat shock treatment of various durations on fibroblasts of horses. The results show that the expression levels of were significantly increased among the different heat shock durations. The expression level of and declined from the beginning of heat shock to 2 h after heat shock and then showed a gradual increase until it reached the highest value at 6 h and 10 h of heat shock, respectively. Breed-specific CNVRs of Chinese indigenous horse breeds were revealed in the present study, and the results facilitate mapping CNVs on the whole genome and also provide valuable insights into the molecular mechanisms of adaptation to high temperature and humidity in the Jinjiang horse.
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Publication Date: 2022-03-28 PubMed ID: 35456409PubMed Central: PMC9033042DOI: 10.3390/genes13040603Google 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.

The study focuses on identifying and verifying genome-wide copy number variants (CNVs) associated with heat adaptation traits in Chinese indigenous horse breeds, particularly the Jinjiang breed which is known for its adaptability to high temperature and humidity conditions.

Methodology and Approach

  • The researchers selected a total of 301 samples from 10 different Chinese indigenous horse breeds for the study.
  • They applied the Illumina Equine SNP70 Bead Array technology, a genotype scanning method designed specifically for horse genome investigations to detect CNVs.
  • A total of 577 CNVs, varying in size, were identified in the 31 pairs of autosomes of the breeds studied.
  • The overlapping CNVs for each breed were aggregated, leading to the detection of 495 CNVRs (Copy Number Variant Regions) among all the breeds studied.
  • The breed-specific CNVRs were separated out, among which 64 were specific to the Jinjiang horse breed.

Detection of Copy Number Variant Regions (CNVRs)

  • Reports show 211 breed-specific CNVRs, with Jinjiang horse breed having 64 of them.
  • Repetitive CNV regions between breeds were removed, leading to the identification of 239 CNVRs in the Chinese indigenous horse breeds.
  • These CNVRs included unique losses, gains and bimodal events (both loss and gain in the same region).
  • There were 131 novel CNVRs only detected in this study entrails previously unidentified.
  • The total detected CNVR length accounted for 1.83% of the total length of equine autosomal chromosomes, with variances in coverage across different chromosomes.

Validation and Implication of Findings

  • They identified and analyzed a total of 229 genes overlapping with CNVRs in the Jinjiang horse breed.
  • These genes showed a significant correlation with cellular heat acclimation and immunity, which reinforce the breed’s adaptability to high temperature and humidity.
  • The expression levels of these candidate genes were validated by heat shock treatment of various durations on horse fibroblasts (a type of cell).
  • The results indicated fluctuating expression levels of certain genes during different durations of the heat shock treatment, providing insights into cellular response to heat stress.

Conclusion

  • This study unveils the breed-specific CNVRs of Chinese indigenous horse breeds.
  • The research not only provides a comprehensive genome map for these breeds but also sheds light on the molecular mechanisms related to adaptation to high temperature and humidity in the Jinjiang horse.

Cite This Article

APA
Wang M, Liu Y, Bi X, Ma H, Zeng G, Guo J, Guo M, Ling Y, Zhao C. (2022). Genome-Wide Detection of Copy Number Variants in Chinese Indigenous Horse Breeds and Verification of CNV-Overlapped Genes Related to Heat Adaptation of the Jinjiang Horse. Genes (Basel), 13(4), 603. https://doi.org/10.3390/genes13040603

Publication

Genes
ISSN: 2073-4425
NlmUniqueID: 101551097
Country: Switzerland
Language: English
Volume: 13
Issue: 4
PII: 603

Researcher Affiliations

Wang, Min
  • College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
  • Equine Center, China Agricultural University, Beijing 100193, China.
  • Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing 100193, China.
  • National Engineering Laboratory for Animal Breeding, Beijing 100193, China.
  • Beijing Key Laboratory for Genetic Improvement of Livestock and Poultry, Beijing 100193, China.
Liu, Yu
  • College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
  • Equine Center, China Agricultural University, Beijing 100193, China.
  • Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing 100193, China.
  • National Engineering Laboratory for Animal Breeding, Beijing 100193, China.
  • Beijing Key Laboratory for Genetic Improvement of Livestock and Poultry, Beijing 100193, China.
Bi, Xiaokun
  • College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
  • Equine Center, China Agricultural University, Beijing 100193, China.
  • Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing 100193, China.
  • National Engineering Laboratory for Animal Breeding, Beijing 100193, China.
  • Beijing Key Laboratory for Genetic Improvement of Livestock and Poultry, Beijing 100193, China.
Ma, Hongying
  • Shaanxi Key Laboratory for Animal Conservation, Shaanxi Institute of Zoology, Xi'an 710032, China.
Zeng, Guorong
  • Jinjiang Animal Husbandry and Veterinary Station, Quanzhou 362200, China.
Guo, Jintu
  • Jinjiang Animal Husbandry and Veterinary Station, Quanzhou 362200, China.
Guo, Minghao
  • Jinjiang Animal Husbandry and Veterinary Station, Quanzhou 362200, China.
Ling, Yao
  • College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Zhao, Chunjiang
  • College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
  • Equine Center, China Agricultural University, Beijing 100193, China.
  • Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing 100193, China.
  • National Engineering Laboratory for Animal Breeding, Beijing 100193, China.
  • Beijing Key Laboratory for Genetic Improvement of Livestock and Poultry, Beijing 100193, China.

MeSH Terms

  • Adaptation, Physiological / genetics
  • Animals
  • China
  • DNA Copy Number Variations / genetics
  • Genome
  • Horses / genetics
  • Thermotolerance / genetics

Conflict of Interest Statement

The authors declare no conflict of interest.

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