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Epistasis Analysis

Epistasis Analysis

Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...

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Related Experiment Video

Updated: Jan 16, 2026

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

A New Family-Based Approach for Detecting Allele-Specific Expression and for Mapping Possible eQTLs.

Maher Alnajjar¹, Zsófia Fekete², Tibor Nagy^1,3

¹Department of Genetics and Genomics, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi A. u. 4, H-2100 Gödöllő, Hungary.

Animals : an Open Access Journal From MDPI

|September 27, 2025

Summary

This study introduces a family-based approach using RNA-seq and whole-genome sequencing to detect allele-specific expression (ASE) and regulatory elements. The method effectively identifies ASE genes and potential cis-regulatory elements in pedigrees.

Keywords:

allele-specific expression cis-regulatory elements meat rabbit transcription factor binding sites

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Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis

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Published on: August 12, 2019

Area of Science:

Genomics
Molecular Biology
Quantitative Genetics

Background:

Allele-specific expression (ASE) reveals functional genetic variants impacting gene regulation.
Traditional ASE detection methods face limitations due to reliance on heterozygous variants or large population sizes.

Purpose of the Study:

To develop and validate a family-based strategy for detecting ASE and cis-regulatory elements.
To leverage RNA-seq and whole-genome sequencing (WGS) data from a pedigree for ASE analysis.

Main Methods:

Utilized a rabbit family (2 parents, 8 offspring) with RNA-seq and WGS data.
Analyzed gene expression inheritance patterns and RNA read counts to identify ASE genes.
Integrated genotype data to pinpoint transcription factor binding sites (TFBS) with regulatory potential (eQTLs).

Main Results:

Identified 913 ASE genes by classifying expression levels (high, medium, low) across family members.
Detected ASE even in genes lacking heterozygous exonic variants.
Found conserved TFBS variants with inheritance patterns suggesting regulatory roles (eQTLs).
Differential gene expression analysis between parents identified candidate genes for meat production traits.

Conclusions:

The family-based strategy using RNA-seq and WGS is a powerful approach for exploring ASE.
This method facilitates the mapping of potential expression quantitative trait loci (eQTLs).
The study provides insights into gene regulation relevant to economically important traits.