数字农科院2.0

Construction of a Multitissue Cell Atlas Reveals Cell-Type-Specific Regulation of Molecular and Complex Phenotypes in Pigs

文献类型： 外文期刊

作者： Chen, Lijuan;Li, Houcheng;Teng, Jinyan;Wang, Zhen;Qu, Xiaolu;Chen, Zhe;Cai, Xiaodian;Zeng, Haonan;Bai, Zhonghao;Li, Jinghui;Pan, Xiangchun;Yan, Leyan;Wang, Fei;Lin, Lin;Luo, Yonglun;Sahana, Goutam;Lund, Mogens Sando;Ballester, Maria;Crespo-piazuelo, Daniel;Karlskov-mortensen, Peter;Fredholm, Merete;Clop, Alex;Amills, Marcel;Loving, Crystal;Tuggle, Christopher K.;Madsen, Ole;Li, Jiaqi;Zhang, Zhe;Liu, George E.;Jiang, Jicai;Fang, Lingzhao;Yi, Guoqiang

作者机构：

关键词： （1-1-1）cell-type-trait association;cellular deconvolution;gene regulation;PigGTEx;single-nucleus RNA-seq

期刊名称： ADVANCED SCIENCE

ISSN：

年卷期： 2025 年

页码：

收录情况： SCIE（2025版） ; ; EI（2025版）

摘要： The systematic characterization of cellular heterogeneity among tissues and cell-type-specific regulation underlying complex phenotypes remains elusive in pigs. Within the Pig Genotype-Tissue Expression (PigGTEx) project, this work presents a single-cell transcriptome atlas of adult pigs encompassing 229 268 high-quality nuclei from 19 tissues, annotated to 67 major cell types. Besides cellular heterogeneity within and across tissues, this work further characterizes prominent tissue-specific features and functions of muscle, epithelial, and immune cells. Through deconvoluting 3921 bulk RNA-seq samples from 17 matching tissues, this work dissects thousands of genetic variants with cell-type interaction effects on gene expression (ieQTL). By colocalizing these ieQTL with variants associated with 268 complex traits, new insights into the cellular mechanisms behind these traits are provided. Moreover, this work highlights that orthologous genes with cell-type-specific regulation in pigs exhibit significant heritability enrichment for some human complex phenotypes. Altogether, this work provides a valuable resource and highlights novel insights in cellular regulation of complex traits for accelerating pig precision breeding and human biomedical research.

分类号：

  • 相关文献

[1]Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of 232 complex traits in pigs. Zhiting Xu,Qing Lin,Xiaodian Cai,Zhanming Zhong,Jinyan Teng,Bingjie Li,Haonan Zeng,Yahui Gao,Zexi Cai,Xiaoqing Wang,Liangyu Shi,Xue Wang,Yi Wang,Zipeng Zhang,Yu Lin,Shuli Liu,Hongwei Yin,Zhonghao Bai,Chen Wei,Jun Zhou,Wenjing Zhang,Xiaoke Zhang,Shaolei Shi,Jun Wu,Shuqi Diao,Yuqiang Liu,Xiangchun Pan,Xueyan Feng,Ruiqi Liu,Zhanqin Su,Chengjie Chang,Qianghui Zhu,Yuwei Wu,Zhongyin Zhou,Lijing Bai,Kui Li,Qishan Wang,Yuchun Pan,Zhong Xu,Xianwen Peng,Shuqi Mei,Delin Mo,Xiaohong Liu,Hao Zhang,Xiaolong Yuan,Yang Liu,George E. Liu,Guosheng Su,Goutam Sahana,Mogens Sandø Lund,Li Ma,Ruidong Xiang,Xia Shen,Pinghua Li,Ruihua Huang,Maria Ballester,Daniel Crespo-Piazuelo,Marcel Amills,Alex Clop,Peter Karlskov-Mortensen,Merete Fredholm,Guoqing Tang,Mingzhou Li,Xuewei Li,Xiangdong Ding,Jiaqi Li,Yaosheng Chen,Qin Zhang,Yunxiang Zhao,Fuping Zhao,Lingzhao Fang,Zhe Zhang. 2025

[2]Multi-Tissue Genetic Regulation of RNA Editing in Pigs. Pan, Xiangchun,Gong, Wentao,Cai, Xiaodian,Teng, Jinyan,Cai, Jiali,Zeng, Haonan,Ayalew, Wondossen,Shen, Qingpeng,Zhong, Zhanming,Wang, Yifei,Zhang, Wenjing,Tian, Yuhan,Xu, Dantong,Gao, Yahui,Yin, Hongwei,Zhang, Yuebo,Hou, Jiahui,Zhou, Tianru,Li, Jiaqi,Fang, Lingzhao,Yuan, Xiaolong,Zhang, Zhe. 2026

[3]In rice, Oryzalin and abscisic acid differentially affect tubulin mRNA and protein levels. Giani, S,Qin, XQ,Faoro, F,Breviario, D. 1998

[4]Arabidopsis C3H14 and C3H15 have overlapping roles in the regulation of secondary wall thickening and anther development. Chai, Guohua,Zhu, Ming,Yu, Li,Qi, Guang,Tang, Xianfeng,Wang, Zengguang,Cao, Yingping,Yu, Changjiang,Zhou, Gongke,Kong, Yingzhen.

[5]Global characterization of microRNAs in Trichomonas gallinae. Xu, Min-Jun,Qiu, Shen-Ben,Fu, Jing-Hua,Zhu, Xing-Quan,Nisbet, Alasdair J.,Qiu, Shen-Ben,Fu, Jing-Hua,Shao, Chang-Chun. 2014

[6]Functional analysis of a putative regulatory gene, tadR, involved in aniline degradation in Delftia tsuruhatensis AD9. Geng, Lizhao,Chen, Ming,Liu, Wei,Zhang, Wei,Ping, Shuzhen,Lu, Wei,Yan, Yongliang,Wang, Weiwei,Lin, Min,Liang, Quanfeng,Takeo, Masahiro. 2009

[7]Foxtail Millet NF-Y Families: Genome-Wide Survey and Evolution Analyses Identified Two Functional Genes Important in Abiotic Stresses. Feng, Zhi-Juan,He, Guan-Hua,Lu, Pan-Pan,Chen, Ming,Ma, You-Zhi,Xu, Zhao-Shi,Feng, Zhi-Juan,Gong, Ya-Ming,Zheng, Wei-Jun. 2015

[8]Functions and Application of the AP2/ERF Transcription Factor Family in Crop Improvement. Xu, Zhao-Shi,Chen, Ming,Li, Lian-Cheng,Ma, You-Zhi. 2011

[9]Toxic effects of the combined cadmium and Cry1Ab protein exposure on the protective and transcriptomic responses of Pirata subpiraticus. Yong Peng,Bo Lv,Zi yan Lei,Yuan de Peng,Li jun Chen,Zhi Wang. 2022

[10]Exogenous Activation of the Ethylene Signaling Pathway Enhances the Freezing Tolerance of Young Tea Shoots by Regulating the Plant’s Antioxidant System. Yao Chen,Junwei Tang,Hengze Ren,Yuteng Li,Congcong Li,Haoqian Wang,Lu Wang,Yajun Yang,Xinchao Wang,Xinyuan Hao. 2023

[11]Integrative analysis identifies the safety of transgenic Cry1Ab rice to non-target spider Pardosa pseudoannulata. Bo Lv,Ying Zhou,Yuan de Peng,Zhi Wang,Qi sheng Song. 2022

[12]An extracytoplasmic function sigma/anti-sigma factor system regulates hypochlorous acid resistance and impacts expression of the type IV secretion system in brucella melitensis. Huoming Li,Sen Hu,Xin Yan,Yan Yang,Wenxing Liu,Zhigao Bu,Ganwu Li,Wentong Cai. 2021

[13]A Long Non-Coding Rna Regulates C.adherin Transcription And Susceptibility T o Bt Toxin Cry1Ac In Pink Bollworm, Pectinophora Gossypiella. Gu, Shaohua,Li, Xianchun,Hussain, Fiaz,Ni, Xinzhi,Unnithan, Gopalan C.,Hussain, Fiaz,Li, Shengyun,Li, Shengyun,Li, Shengyun,Tabashnik, Bruce E.,Carriere, Yves,Mathew, Lolita G.,Dong, Shuanglin,Fabrick, Jeffrey A.,UlAbdin, Zain. 2019

[14]Regulation of DNA methylation on key parasitism genes of Cysticercus cellulosae revealed by integrative epigenomic-transcriptomic analyses. Xinrui Wang,Weiyi Song,Guanyu Ji,Yining Song,Xiaolei Liu,Xuenong Luo,Mingyuan Liu,Shumin Sun. 2021

[15]The novel LysR-family transcriptional regulator BvtR is involved in the resistance of Brucella abortus to nitrosative stress, detergents and virulence through the genetic regulation of diverse pathways. Mingxing Tian,Zichen Li,Jing Qu,Tian Fang,Yi Yin,Dong Zuo,Hosny Ahmed Abdelgawad,Hai Hu,Shaohui Wang,Jingjing Qi,Guijun Wang,Shengqing Yu. 2022

[16]Thermosensitive sex chromosome dosage compensation in ZZ/ZW softshell turtles, Apalone spinifera. Basanta Bista,Zhiqiang Wu,Robert Literman,Nicole Valenzuela. 2021

[17]Unearthing the Alleviatory Mechanisms of Brassinolide in Cold Stress in Rice. Xu, Qingshan,Wei, Qianqian,Kong, Yali,Zhu, Lianfeng,Tian, Wenhao,Huang, Jing,Pan, Lin,Jin, Qianyu,Zhang, Junhua,Zhu, Chunquan. 2022

[18]Global N6-Methyladenosine Profiling Revealed the Tissue-Specific Epitranscriptomic Regulation of Rice Responses to Salt Stress. Yinxiao Wang,Fengping Du,Yingbo Li,Juan Wang,Xiuqin Zhao,Zhikang Li,Jianlong Xu,Wensheng Wang,Binying Fu. 2022

[19]Comparative analysis of cadmium-induced toxicity and survival responses in the wolf spider Pirata subpiraticus under low-temperature treatment. Lv, Bo,Zhuo, Jun-zhe,Peng, Yuan-de,Wang, Zhi. 2022

[20]Conserved and variable heat stress responses of the Heat Shock Factor transcription factor family in maize and Setaria viridis. Zachary A. Myers,Clair M. Wootan,Zhikai Liang,Peng Zhou,Julia Engelhorn,Thomas Hartwig,Springer M. Nathan. 2023

作者其他论文 更多>>