A Comprehensive Allele Specific Expression Resource for the Equine Transcriptome

Area of Science:

• Genomics
• Molecular Biology
• Animal Science

Background:

• Allele-specific expression (ASE) analysis offers insights into cis-regulatory mechanisms influencing gene expression.
• Understanding gene regulation is crucial for animal breeding and health.
• Equine genomics research benefits from detailed expression analysis.

Approach:

• Integrated Iso-seq and short-read RNA sequencing data from four Thoroughbred horses (2 mares, 2 stallions) across nine tissues.
• Quantified allele expression using haplotypes from long-read data, comparing 42,900 events.
• Validated allele-specific variants in 66 equine liver samples from multiple breeds.

Key Points:

• Identified 635 (1.48%) allele expression events exhibiting ASE.
• Liver tissue showed the highest proportion of ASE events.
• Genetic variants within ASE events were frequently located in histone-modified regions (64.2%).
• Confirmed 97% of variants demonstrated ASE in validation samples.

Conclusions:

• This study establishes a valuable, publicly accessible resource for investigating regulatory variation in equine tissues.
• Results underscore the tissue-specific nature of allelic imbalance in the equine genome.
• Facilitates future research into the functional impact of genetic variants on gene expression in horses.