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The ChickenGTEx portal: a pan-tissue catalogue of regulatory variants shaping transcriptomic and phenotypic diversity

文献类型： 外文期刊

作者： Hou, Yali 1 ; Zou, Dong 3 ; Chu, Qin 5 ; Zhan, Bujie 6 ; Wang, Ruizhen 7 ; Guan, Dailu 8 ; Wang, Wannian 9 ; Feng, Xiao 10 ; Li, Xin 1 ; Zhu, Xiaoning 10 ; Bai, Zhonghao 11 ; Gao, Yahui 12 ; Yin, Hongwei 13 ; Xu, Tianyi 3 ; Yuan, Zhixiang 3 ; Hu, Xiaoxiang 11 ; Yang, Ning 1 ; Zhou, Huaijun 8 ; Fang, Lingzhao 14 ; Zhang, Zhang 3 ;

作者机构： 1.Chinese Acad Agr Sci, State Key Lab Anim Biotech Breeding, Beijing 100193, Peoples R China

2.Chinese Acad Agr Sci, Inst Anim Sci, Natl Germplasm Ctr Domest Anim Resources, Beijing 100193, Peoples R China

3.China Natl Ctr Bioinformat, Natl Genom Data Ctr, Beijing 100101, Peoples R China

4.Chinese Acad Sci, Beijing Inst Genom, Beijing 100101, Peoples R China

5.Beijing Acad Agr & Forestry Sci, Inst Anim Husb & Vet Med, Beijing 100097, Peoples R China

6.Longdong Univ, Med Coll, Dept Basic Med Sci, Qingyang 745000, Peoples R China

7.Henan Univ Chinese Med, Acad Chinese Med Sci, Zhengzhou 450046, Peoples R China

8.Univ Calif Davis, Dept Anim Sci, Davis, CA 95616 USA

9.Shanxi Agr Univ, Dept Anim Sci, Taigu 030801, Peoples R China

10.China Agr Univ, Coll Anim Sci & Technol, Beijing 100193, Peoples R China

11.China Agr Univ, Coll Biol Sci, State Key Lab Anim Biotech Breeding, Beijing 100193, Peoples R China

12.South China Agr Univ, Coll Anim Sci, State Key Lab Livestock & Poultry Breeding, Guangdong Prov Key Lab Agroanim Genom & Mol Breed, Guangzhou 510642, Peoples R China

13.Chinese Acad Agr Sci, Shenzhen Branch,Agr Genom Inst Shenzhen, Guangdong Lab Lingnan Modern Agr, Key Lab Livestock & Poultry Multiom MARA, Shenzhen 518124, Peoples R China

14.Aarhus Univ, Ctr Quantitat Genet & Genom QGG, DK-8000 Aarhus, Denmark

期刊名称：NUCLEIC ACIDS RESEARCH （ 影响因子：13.1； 五年影响因子：16.8 ）

ISSN： 0305-1048

年卷期： 2025 年

页码：

收录情况： SCI

摘要： A systematic dissection of the functional impacts of non-coding variations across diverse tissues and cell types is essential for deciphering the molecular architecture underlying complex traits. Given the significance of chickens as both a key livestock species and a fundamental model organism, the development of an integrative genomics resource is imperative. Leveraging SNP-to-gene-to-trait linking strategies-including molecular quantitative trait loci (molQTL), regulatory elements, and context- or environment-dependent regulatory heterogeneity-we developed the ChickenGTEx portal (http://chicken.farmgtex.org), which provides a comprehensive catalogue of regulatory effects on transcriptomic and phenotypic diversity across tissues, cell types, and sexes. Key features of the resource include a genotype imputation panel of 2869 chickens from 123 breeds worldwide, five types of molecular phenotypes across 28 tissues, similar to 2.2 million molQTL, 806 229 fine-mapped molQTL, 1956 context-dependent molQTL, 257 genome-wide profiles of 7 epigenetic marks (representing 15 chromatin states) from 23 tissues, 185 376 single-cell expression profiles across 191 cell clusters from 9 tissues, and 96 386 gene-trait associations covering 108 economically important traits. In summary, the ChickenGTEx portal will serve as an invaluable resource for advancing research in fundamental and evolutionary biology, chicken precision breeding, and eventually human biomedicine.

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