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A New Family-Based Approach for Detecting Allele-Specific Expression and for Mapping Possible eQTLs
by
, , , ,
Maher Alnajjar
1,
Zsófia Fekete
2,
Tibor Nagy
1,3,
Zoltán Német
4,
Agshin Sakif
1,
Nóra Ninausz
1,
Péter Fehér
1,
Viktor Stéger
1 and
Endre Barta
1,3,*
1
Department 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
2
Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistokatu 2, 80100 Joensuu, Finland
3
Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
4
Department of Pathology, University of Veterinary Medicine, István u. 2, H-1078 Budapest, Hungary
*
Author to whom correspondence should be addressed.
Animals 2025, 15(18), 2766; https://doi.org/10.3390/ani15182766
Submission received: 15 July 2025
/
Revised: 16 September 2025
/
Accepted: 17 September 2025
/
Published: 22 September 2025
(This article belongs to the Special Issue Livestock Genetic Evaluation and Selection)
Simple Summary
Allele-specific expression (ASE) is a valuable tool for finding different traits on the gene expression level. However, existing research often relies on heterozygous transcribed variants or sequencing large cohorts, which can be costly and sometimes limited. To address these challenges, we developed a novel family-based approach that combines RNA sequencing and whole-genome sequencing (WGS) in a family model to detect ASE and infer cis-regulatory variants without relying on population data or heterozygous SNPs in the exonic region. We applied this method to a hybrid rabbit family consisting of two genetically distinct parents and eight offspring. We identified 913 ASE genes by estimating the inheritance patterns of gene expression levels, even in the absence of heterozygous variants in the transcriptomes. Expression levels were categorized into three states—high, medium, and low—and genes were classified into seven expression patterns. We also identified conserved transcription factor binding sites (TFBS) near genes that showed consistent genotype patterns, supporting their role as cis-acting elements. Furthermore, differential expression analysis between parents revealed genes that are potentially relevant for meat production traits.
Abstract
Allele-specific expression (ASE) reflects the unequal expression of the parental alleles and can imply functional variants in cis-regulatory elements. The conventional ASE detection methods often depend on the presence of heterozygous variants in transcripts or sequencing a large number of individuals, both of which are often limited. In this study, we present a family-based strategy for detecting ASE and potential cis-regulatory elements utilizing both RNA-seq and whole-genome sequencing (WGS) from a pedigree. Using a rabbit family consisting of two divergent parents and their eight offspring, we identified 913 ASE genes by analyzing inheritance patterns of gene expression levels. Expression was classified into three levels—high, medium, and low—and used to define seven distinct expression groups across the family (e.g., H_L: high in the mother, low in the father, and intermediate in the offspring). Many ASE genes lacked heterozygous exonic variants, and inference was achieved via RNA read count patterns. We also pinpointed conserved transcription factor binding sites (TFBS) with sequence variants showing similar inherited genotypic patterns (e.g., AAxBB), suggesting their regulatory roles as eQTLs. Differential gene expression (DEG) analysis between the parents highlighted some candidate genes related to meat production and quality traits. Our findings show that the family-based method using RNA-seq and WGS data is promising for exploring ASE and mapping possible eQTLs.
