Egg-laying ChickenGTEx resource deciphers context-specific regulatory effects on fertility traits

Characterization of the genetic and molecular architecture underlying egg production traits in chickens is essential for improving the rate of genetic gain through intensive artificial selection. Here, to explore the dynamic landscape of regulatory effects across egg-laying stages in chickens, we generated 1272 RNA-seq samples of four tissues, i.e., the hypothalamic-pituitary-ovarian axis and liver, and paired whole-genome sequence data from 358 hens. We detected 1008 genes with stage-specific regulatory effects in at least one tissue excluding the pituitary. Out of them, 12.60, 52.78 and 32.84% were mediated by alterations in cell type composition, transcriptional factor activity, and gene co-expression networks among laying stages, respectively. Out of 80 significant loci associated with egg production traits that were detected in a large population (n = 12,952), 37 and 5 colocalized by shared and stage-specific regulatory effects, respectively. Furthermore, orthologues of these colocalized genes are enriched for the heritability of reproductive traits in pigs, cattle, and humans. In summary, we provide a resource for understanding reproduction-relevant gene regulation and highlight the importance of context-specific regulatory effects in deciphering complex traits.

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Publication Details

Journal
Nature Communications
Published
2025-12-07
DOI
https://doi.org/10.1038/s41467-025-67245-y
Citations
2
Primary Topic
Hypothalamic control of reproductive hormones
Type
article
Field-Weighted Citation Impact
3.40
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article

Egg-laying ChickenGTEx resource deciphers context-specific regulatory effects on fertility traits

Yiqiang Zhao, Qing Lin, Baoliang Fan, Lingzhao Fang et al.
2 citations
Nature Communications
Hypothalamic control of reproductive hormones
3.40
article

Egg-laying ChickenGTEx resource deciphers context-specific regulatory effects on fertility traits

Yiqiang Zhao, Qing Lin, Baoliang Fan, Lingzhao Fang, Zhonghao Bai, Dingming Shu, Zhangyuan Pan, Conghao Zhong, Xiaoxiang Hu, Qinghua Nie, Xiquan Zhang, Yidan Yan, Xiaoning Zhu, Houcheng Li, Zi-Qin Jiang, Di Zhu, Hao Qu, Lizhi Tan, George E. Liu, Dailu Guan, Ning Yang, Haihan Zhang, Jinyan Teng, Wei Luo, Kai Shi, Chungang Feng, Chong Li, Bingjie Li, Yahui Gao, Yuzhe Wang, Zhenhui Li, Shuli Liu, Huaijun Zhou, Zhenqiang Xu, Chenglong Luo
article en
2 citations

Abstract

Characterization of the genetic and molecular architecture underlying egg production traits in chickens is essential for improving the rate of genetic gain through intensive artificial selection. Here, to explore the dynamic landscape of regulatory effects across egg-laying stages in chickens, we generated 1272 RNA-seq samples of four tissues, i.e., the hypothalamic-pituitary-ovarian axis and liver, and paired whole-genome sequence data from 358 hens. We detected 1008 genes with stage-specific regulatory effects in at least one tissue excluding the pituitary. Out of them, 12.60, 52.78 and 32.84% were mediated by alterations in cell type composition, transcriptional factor activity, and gene co-expression networks among laying stages, respectively. Out of 80 significant loci associated with egg production traits that were detected in a large population (n = 12,952), 37 and 5 colocalized by shared and stage-specific regulatory effects, respectively. Furthermore, orthologues of these colocalized genes are enriched for the heritability of reproductive traits in pigs, cattle, and humans. In summary, we provide a resource for understanding reproduction-relevant gene regulation and highlight the importance of context-specific regulatory effects in deciphering complex traits.

Nature CommunicationsVol. 17(1)
South China Agricultural University (CN), Hebei Agricultural University (CN), Nanjing Agricultural University (CN), Agricultural Research Service (US), Roslin Institute (GB), Aarhus University (DK), Scotland's Rural College (GB), Westlake University (CN), Guangdong Academy of Agricultural Sciences (CN), Ministère de l'Agriculture et de la Souveraineté alimentaire (FR), Beltsville Agricultural Research Center (US), Wen's Food Group (China) (CN), Chinese Academy of Agricultural Sciences (CN), China Agricultural University (CN), Hunan Agricultural University (CN), University of California, Davis (US)
Openalex Percentile: Top 7%
Hypothalamic control of reproductive hormones
3.40
DOIOpen Access PDFOpenAlex
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