A comprehensive allele specific expression resource for the equine transcriptome

Harrison D. Heath; Sichong Peng; Tomasz Szmatola; Stephanie Ryan; Rebecca R. Bellone; Theodore Kalbfleisch; Jessica L. Petersen; Carrie J. Finno

doi:10.1186/s12864-025-11240-6

A comprehensive allele specific expression resource for the equine transcriptome

Harrison D. Heath
, Sichong Peng
, Tomasz Szmatola
, Stephanie Ryan
, Rebecca R. Bellone
, Theodore Kalbfleisch
, Jessica L. Petersen
, Carrie J. Finno

Research output: Contribution to journal › Article › peer-review

Abstract

Background: 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.

Original language	English
Article number	88
Journal	BMC Genomics
Volume	26
Issue number	1
DOIs	https://doi.org/10.1186/s12864-025-11240-6
State	Published - Dec 2025

Bibliographical note

Publisher Copyright:
© The Author(s) 2025.

Funding

This project was supported by the Grayson-Jockey Club Research Foundation (C.J.F., J.L.P, R.R.B.), USDA National Institute of Food and Agriculture Animal Breeding and Functional Annotation of Genomes (A1201) Grant 2019–67015-29340 (J.L.P, C.J.F., R.B.) as well as NRSP-8 Species Coordinator Funds from the USDA National Institute of Food and Agriculture (C.J.F., J.L.P, R.R.B.), and the UC Davis Center for Equine Health with funds provided by the State of California pari-mutuel fund and contributions by private donors (C.J.F., J.L.P, R.R.B.). Additional support for S.R. was provided by the Foundation for the Horse Young Investigators Research Grant and the Ann T. Bowling Fellowship from the Veterinary Genetics Laboratory at UC Davis. C.J.F. was provided by NIH NCATS L40 TR001136. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Funders	Funder number
Grayson Jockey Club Research Foundation Inc
UC Davis Veterinary Genetics Laboratory
University of California Davis
US Department of Agriculture National Institute of Food and Agriculture, Agriculture and Food Research Initiative	A1201, 2019–67015-29340
US Department of Agriculture National Institute of Food and Agriculture, Agriculture and Food Research Initiative
National Center for Advancing Translational Sciences (NCATS)	L40 TR001136
National Center for Advancing Translational Sciences (NCATS)

Keywords

Epigenetics
FAANG
Haplotype
Horse
RNA-sequencing

ASJC Scopus subject areas

Biotechnology
Genetics

Access to Document

10.1186/s12864-025-11240-6

Cite this

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title = "A comprehensive allele specific expression resource for the equine transcriptome",

abstract = "Background: 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.",

keywords = "Epigenetics, FAANG, Haplotype, Horse, RNA-sequencing",

author = "Heath, \{Harrison D.\} and Sichong Peng and Tomasz Szmatola and Stephanie Ryan and Bellone, \{Rebecca R.\} and Theodore Kalbfleisch and Petersen, \{Jessica L.\} and Finno, \{Carrie J.\}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2025.",

year = "2025",

month = dec,

doi = "10.1186/s12864-025-11240-6",

language = "English",

volume = "26",

number = "1",

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AU - Heath, Harrison D.

AU - Peng, Sichong

AU - Szmatola, Tomasz

AU - Ryan, Stephanie

AU - Bellone, Rebecca R.

AU - Kalbfleisch, Theodore

AU - Petersen, Jessica L.

AU - Finno, Carrie J.

N1 - Publisher Copyright: © The Author(s) 2025.

PY - 2025/12

Y1 - 2025/12

N2 - Background: 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.

AB - Background: 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.

KW - Epigenetics

KW - FAANG

KW - Haplotype

KW - Horse

KW - RNA-sequencing

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SN - 1471-2164

VL - 26

JO - BMC Genomics

JF - BMC Genomics

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ER -

A comprehensive allele specific expression resource for the equine transcriptome

Abstract

Bibliographical note

Funding

Keywords

ASJC Scopus subject areas

Access to Document

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