数字农科院2.0

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

文献类型： 外文期刊

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

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期刊名称： Nature Communications

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年卷期： 2025 年 17 卷 1 期

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收录情况： SCIE（2025版） ; ; Nature Index（2023版）

摘要： 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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