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Egg-laying ChickenGTEx resource deciphers context-specific regulatory effects on fertility traits
1State Key Laboratory of Animal Biotech Breeding, National Research Facility for Phenotypic and Genotypic Analysis of Model Animals, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
Nature Communications
|December 7, 2025
Summary
Understanding chicken egg production requires studying gene regulation. This research reveals stage-specific gene effects and their links to reproductive traits in multiple species, aiding genetic improvement.
Area of Science:
- Genomics
- Animal Breeding
- Molecular Biology
Background:
- Improving chicken egg production relies on understanding genetic and molecular factors.
- Artificial selection requires detailed knowledge of regulatory effects across different egg-laying stages.
Purpose of the Study:
- To explore the dynamic landscape of regulatory effects on egg-laying stages in chickens.
- To identify genes and regulatory mechanisms influencing egg production traits.
Main Methods:
- Generated 1272 RNA-seq samples from four tissues (hypothalamic-pituitary-ovarian axis, liver) and whole-genome sequence data from 358 hens.
- Detected stage-specific regulatory effects in 1008 genes across laying stages.
- Analyzed regulatory effects mediated by cell type composition, transcriptional factor activity, and gene co-expression networks.
Main Results:
- Identified 1008 genes with stage-specific regulatory effects, primarily in the ovary and liver.
- Found that cell type composition, transcriptional factor activity, and gene co-expression networks mediate these effects.
- Discovered that 37 and 5 significant loci associated with egg production traits colocalized with shared and stage-specific regulatory effects, respectively.
- Orthologues of colocalized genes are enriched for heritability of reproductive traits in pigs, cattle, and humans.
Conclusions:
- Provides a valuable resource for understanding reproduction-relevant gene regulation in chickens.
- Highlights the critical role of context-specific regulatory effects in complex traits like egg production.
- Suggests conserved regulatory mechanisms for reproductive traits across different species.
