文献类型： 外文期刊

作者： Guan, Dailu ¹ ; Bai, Zhonghao ² ; Zhu, Xiaoning ³ ; Zhong, Conghao ⁴ ; Hou, Yali ⁶ ; Zhu, Di ² ; Li, Houcheng ² ; Lan, Fangren ⁴ ; Diao, Shuqi ⁷ ; Yao, Yuelin ⁸ ; Zhao, Bingru ¹⁰ ; Li, Xiaochang ⁴ ; Pan, Zhangyuan ⁶ ; Gao, Yahui ⁷ ; Wang, Yuzhe ³ ; Zou, Dong ¹³ ; Wang, Ruizhen ¹³ ; Xu, Tianyi ¹³ ; Sun, Congjiao ⁴ ; Yin, Hongwei ¹⁶ ; Teng, Jinyan ⁷ ; Xu, Zhiting ⁷ ; Lin, Qing ⁷ ; Shi, Shourong ¹⁷ ; Shao, Dan ¹⁷ ; Degalez, Fabien ¹⁸ ; Lagarrigue, Sandrine ¹⁸ ; Wang, Ying ¹ ; Wang, Mingshan ¹⁹ ; Peng, Minsheng ¹⁹ ; Rocha, Dominique ²¹ ; Charles, Mathieu ²¹ ; Smith, Jacqueline ²² ; Watson, Kellie ²² ; Buitenhuis, Albert Johannes ² ; Sahana, Goutam ² ; Lund, Mogens Sando ² ; Warren, Wesley ²³ ; Frantz, Laurent ²⁴ ; Larson, Greger ²⁶ ; Lamont, Susan J. ²⁷ ; Si, Wei ⁶ ; Zhao, Xin ²⁸ ; Li, Bingjie ²⁹ ; Zhang, Haihan ³⁰ ; Luo, Chenglong ³¹ ; Shu, Dingming ³¹ ; Qu, Hao ³¹ ; Luo, Wei ³¹ ; Li, Zhenhui ⁷ ; Nie, Qinghua ⁷ ; Zhang, Xiquan ⁷ ; Xiang, Ruidong ³⁴ ; Liu, Shuli ³⁷ ; Zhang, Zhe ⁷ ; Zhang, Zhang ¹³ ; Liu, George E. ¹¹ ; Cheng, Hans ³⁸ ; Yang, Ning ⁴ ; Hu, Xiaoxiang ³ ; Zhou, Huaijun ¹ ; Fang, Lingzhao ² ;

作者机构： 1.Univ Calif Davis, Dept Anim Sci, Davis, CA 95616 USA

2.Aarhus Univ, Ctr Quantitat Genet & Genom QGG, Aarhus, Denmark

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

4.China Agr Univ, Coll Anim Sci & Technol, State Key Lab Anim Biotech Breeding, Beijing, Peoples R China

5.China Agr Univ, Coll Anim Sci & Technol, Frontier Sci Ctr Mol Design Breeding, Beijing, Peoples R China

6.Chinese Acad Agr Sci, Inst Anim Sci, Beijing, Peoples R China

7.South China Agr Univ, Coll Anim Sci, State Key Lab Swine & Poultry Breeding Ind, Guangdong Prov Key Lab Agroanim Genom & Mol Breedi, Guangzhou, Peoples R China

8.Univ Edinburgh, Inst Genet & Canc, MRC Human Genet Unit, Edinburgh, Scotland

9.Univ Edinburgh, Sch Informat, Edinburgh, Scotland

10.Nanjing Agr Univ, Coll Anim Sci & Technol, Jiangsu Livestock Embryo Engn Lab, Nanjing, Peoples R China

11.ARS, Anim Genom & Improvement Lab, Henry A Wallace Beltsville Agr Res Ctr, USDA, Beltsville, MD USA

12.Univ Maryland, Dept Anim & Avian Sci, College Pk, MD USA

13.Chinese Acad Sci, Beijing Inst Genom, Beijing, Peoples R China

14.China Natl Ctr Bioinformat, Beijing, Peoples R China

15.Univ Chinese Acad Sci, Beijing, Peoples R China

16.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Shenzhen Branch, Guangdong Lab Lingnan Modern Agr,Key Lab Livestock, Shenzhen, Peoples R China

17.Chinese Acad Agr Sci, Poultry Inst, Yangzhou 225003, Peoples R China

18.Inst Agro, PEGASE, INRAE, St Gilles, France

19.Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Evolut & Anim Models, Kunming, Peoples R China

20.Chinese Acad Sci, Kunming Inst Zool, Yunnan Key Lab Mol Biol Domest Anim, Kunming, Peoples R China

21.Univ Paris Saclay, INRAE, AgroParistech, GABI, Jouy En Josas, France

22.Univ Edinburgh, Roslin Inst, Royal Dick Sch Vet Studies, Edinburgh, Midlothian, Scotland

23.Univ Missouri, Data Sci & Informat Inst, Dept Anim Sci, Columbia, MO USA

24.Ludwig Maximilians Univ Munchen, Dept Vet Sci, Palaeogen Grp, Munich, Germany

25.Queen Mary Univ London, Sch Biol & Behav Sci, London, England

26.Univ Oxford, Sch Archaeol, Palaeogen & Bioarchaeol Res Network, Oxford, England

27.Iowa State Univ, Dept Anim Sci, Ames, IA USA

28.McGill Univ, Dept Anim Sci, Montreal, PQ, Canada

29.Scotlands Rural Coll SRUC, Roslin Inst Bldg, Edinburgh, Midlothian, Scotland

30.Hunan Agr Univ, Coll Anim Sci & Technol, Changsha, Peoples R China

31.Guangdong Acad Agr Sci, Inst Anim Sci, State Key Lab Swine & Poultry Breeding Ind, Guangdong Key Lab Anim Breeding & Nutr, Guangzhou, Peoples R China

32.South China Agr Univ, Coll Anim Sci, Guangdong Prov Key Lab Agroanim Genom & Mol Breedi, Minist Agr, Guangzhou, Peoples R China

33.South China Agr Univ, Coll Anim Sci, Key Lab Chicken Genet Breeding & Reprod, Minist Agr, Guangzhou, Peoples R China

34.Ctr AgriBiosci, Agr Victoria, Agribio, Bundoora, Vic, Australia

35.Baker Heart & Diabet Inst, Cambridge Baker Syst Genom Initiat, Melbourne, Vic, Australia

36.Univ Melbourne, Sch Agr Food & Ecosyst Sci, Parkville, Vic, Australia

37.Westlake Univ, Sch Life Sci, Hangzhou, Peoples R China

38.ARS, Avian Dis & Oncol Lab, USDA, USNPRC, E Lansing, MI USA

期刊名称：NATURE GENETICS （ 影响因子：29.0； 五年影响因子：37.4 ）

ISSN： 1061-4036

年卷期： 2025 年 57 卷 5 期

页码：

收录情况： SCI

摘要： The chicken is a valuable model for understanding fundamental biology and vertebrate evolution and is a major global source of nutrient-dense and lean protein. Despite being the first non-mammalian amniote to have its genome sequenced, a systematic characterization of functional variation on the chicken genome remains lacking. Here, we integrated bulk RNA sequencing (RNA-seq) data from 7,015 samples, single-cell RNA-seq data from 127,598 cells and 2,869 whole-genome sequences to present a pilot atlas of regulatory variants across 28 chicken tissues. This atlas reveals millions of regulatory effects on primary expression (protein-coding genes, long non-coding RNA and exons) and post-transcriptional modifications (alternative splicing and 3 '-untranslated region alternative polyadenylation). We highlighted distinct molecular mechanisms underlying these regulatory variants, their context-dependent behavior and their utility in interpreting genome-wide associations for 39 chicken complex traits. Finally, our comparative analyses of gene regulation between chickens and mammals demonstrate how this resource can facilitate cross-species gene mapping of complex traits.