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BMC genomics2025; 26(1); 88; doi: 10.1186/s12864-025-11240-6

A comprehensive allele specific expression resource for the equine transcriptome.

Abstract: Allele-specific expression (ASE) analysis provides a nuanced view of cis-regulatory mechanisms affecting gene expression. Results: An equine ASE analysis was performed, using integrated Iso-seq and short-read RNA sequencing data from four healthy Thoroughbreds (2 mares and 2 stallions) across 9 tissues from the Functional Annotation of Animal Genomes (FAANG) project. Allele expression was quantified by haplotypes from long-read data, with 42,900 allele expression events compared. Within these events, 635 (1.48%) demonstrated ASE, with liver tissue containing the highest proportion. Genetic variants within ASE events were located in histone modified regions 64.2% of the time. Validation of allele-specific variants, using a set of 66 equine liver samples from multiple breeds, confirmed that 97% of variants demonstrated ASE. Conclusions: This valuable publicly accessible resource is poised to facilitate investigations into regulatory variation in equine tissues. Our results highlight the tissue-specific nature of allelic imbalance in the equine genome.
© 2025. The Author(s).
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Publication Date: 2025-01-30 PubMed ID: 39885415PubMed Central: PMC11780778DOI: 10.1186/s12864-025-11240-6Google 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 detailed analysis of Allele-Specific Expression (ASE) in horses, using data from the Functional Annotation of Animal Genomes project. It’s a significant step in understanding gene regulation in equine tissues, with potential applications in horse breeding and animal genetics research.

Methodology and Experiment

  • The researchers performed an ASE analysis on four healthy thoroughbred horses (2 mares and 2 stallions), spanning 9 different tissues. The analysis is based on Integrated Iso-Seq and short-read RNA sequencing data sourced from the Functional Annotation of Animal Genomes (FAANG) project.
  • To quantify allele expression, the researchers used haplotypes from long-read data. They compared a total of 42,900 allele expression events during the analysis.

Key Results

  • Out of 42,900 allele expression events, 635 (or 1.48%) demonstrated ASE. The majority of these ASE events were identified in liver tissue.
  • The research found that genetic variants involved in ASE events were predominantly located in histone-modified regions, accounting for about 64.2% of the time.

Validation

  • To validate the allele-specific variants resulting from the ASE events, the research team utilized a set of 66 horse liver samples which were sourced from multiple breeds.
  • The validation process confirmed that 97% of detected variants demonstrated ASE, lending strong support to the results of the main experiment.

Conclusion and Implications

  • The outcome of the research establishes a robust, publicly accessible resource for further investigation of regulatory variation in equine tissues.
  • The findings also highlight the tissue-specific nature of allelic imbalance in the equine genome, underscoring the specific roles that different tissues play in genetic expression and potential phenotypic outcomes.

Wider Impact

  • This research provides vital information about the intricate genetic regulatory mechanisms affecting horses. Comprehensive studies like these have the potential to inform and improve horse breeding and health management strategies.
  • In the broader field of animal genetics, this study could serve as a model for studies into gene expression and regulation in other species.

Cite This Article

APA
Heath HD, Peng S, Szmatola T, Ryan S, Bellone RR, Kalbfleisch T, Petersen JL, Finno CJ. (2025). A comprehensive allele specific expression resource for the equine transcriptome. BMC Genomics, 26(1), 88. https://doi.org/10.1186/s12864-025-11240-6

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 26
Issue: 1
Pages: 88
PII: 88

Researcher Affiliations

Heath, Harrison D
  • Department of Population Health and Reproduction, Davis School of Veterinary Medicine, University of California, Room 4206 Vet Med3A One Shields Ave, Davis, CA, 95616, USA.
Peng, Sichong
  • Department of Population Health and Reproduction, Davis School of Veterinary Medicine, University of California, Room 4206 Vet Med3A One Shields Ave, Davis, CA, 95616, USA.
  • Present address: Eclipsebio, San Diego, CA, 92121, USA.
Szmatola, Tomasz
  • Department of Population Health and Reproduction, Davis School of Veterinary Medicine, University of California, Room 4206 Vet Med3A One Shields Ave, Davis, CA, 95616, USA.
  • Centre of Experimental and Innovative Medicine, University of Agriculture in Kraków, Al. Mickiewicza 24/28, 30-059, Kraków, Poland.
Ryan, Stephanie
  • Department of Population Health and Reproduction, Davis School of Veterinary Medicine, University of California, Room 4206 Vet Med3A One Shields Ave, Davis, CA, 95616, USA.
Bellone, Rebecca R
  • Department of Population Health and Reproduction, Davis School of Veterinary Medicine, University of California, Room 4206 Vet Med3A One Shields Ave, Davis, CA, 95616, USA.
  • Veterinary Genetics Laboratory, University of California, Davis School of Veterinary Medicine, Davis, CA, 95616, USA.
Kalbfleisch, Theodore
  • Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY, 40546, USA.
Petersen, Jessica L
  • Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
Finno, Carrie J
  • Department of Population Health and Reproduction, Davis School of Veterinary Medicine, University of California, Room 4206 Vet Med3A One Shields Ave, Davis, CA, 95616, USA. cjfinno@ucdavis.edu.

MeSH Terms

  • Animals
  • Horses / genetics
  • Alleles
  • Transcriptome
  • Liver / metabolism
  • Haplotypes
  • Gene Expression Profiling
  • Female
  • Male
  • Sequence Analysis, RNA
  • Polymorphism, Single Nucleotide

Grant Funding

  • L40 TR001136 / NCATS NIH HHS
  • 2019-67015-29340 / National Institute of Food and Agriculture
  • 21-04 / UC Davis Center for Equine Health

Conflict of Interest Statement

Declarations. Ethics approval and consent to participate: All protocols were approved by the University of California Davis Institutional Animal Care and Use Committee (Protocol #19037). Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.

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