Comprehensive analysis of 1,771 transcriptomes from 7 tissues enhance genetic and biological interpretations of maize complex traits
文献类型： 外文期刊
作者： Lei, Mengyu 1 ; Si, Huan 1 ; Zhu, Mingjia 3 ; Han, Yu 4 ; Liu, Wei 4 ; Dai, Yifei 6 ; Ji, Yan 1 ; Liu, Zhengwen 1 ; Hao, Fan 7 ; Hao, Ran 8 ; Zhao, Jiarui 1 ; Ye, Guoyou 9 ; Zan, Yanjun 1 ;
作者机构： 1.Chinese Acad Agr Sci, Tobacco Res Inst, Qingdao 266000, Peoples R China
2.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Shenzhen 518120, Peoples R China
3.Lanzhou Univ, Coll Ecol, Lanzhou 730000, Peoples R China
4.Sichuan Univ, Minist Educ, Key Lab Bioresource & Ecoenvironm, Chengdu 610065, Peoples R China
5.Sichuan Univ, Coll Life Sci, Sichuan Zoige Alpine Wetland Ecosyst Natl Observat, Chengdu 610065, Peoples R China
6.Univ Michigan, Sch Publ Hlth, Biostat Dept, Ann Arbor, MI 48105 USA
7.Northwest Agr & Forestry Univ, Coll Forestry, Xianyang 712100, Peoples R China
8.Northwest Agr & Forestry Univ, Coll Informat Engn, Xianyang 712100, Peoples R China
9.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, CAAS IRRI Joint Lab Genom Assisted Germplasm Enhan, Shenzhen 518120, Peoples R China
10.Umea Univ, Umea Plant Sci Ctr, Dept Plant Physiol, S-90187 Umea, Sweden
11.Umea Univ, Integrated Sci Lab, S-90187 Umea, Sweden
关键词： GWAS; regulatory variants; integrative genomics; complex trait
期刊名称：G3-GENES GENOMES GENETICS （ 影响因子：2.2； 五年影响因子：2.5 ）
ISSN： 2160-1836
年卷期： 2025 年 15 卷 9 期
页码：
收录情况： SCI
摘要： By reanalyzing 1,771 RNA-seq datasets from 7 tissues in a maize diversity panel, we explored the landscape of multi-tissue transcriptome variation, evolution patterns of tissue-specific genes, and built a comprehensive multi-tissue gene regulation atlas to understand the genetic regulation of maize complex traits. Through an integrative analysis of tissue-specific gene regulatory variation with genome-wide association studies, we detected relevant tissue types and several candidate genes for a number of agronomic traits, including leaf during the day for the anthesis-silking interval, leaf during the day for kernel Zeinoxanthin level, and root for ear height, highlighting the potential contribution of tissue-specific gene expression to variation in agronomic traits. Using transcriptome-wide association and colocalization analysis, we associated tissue-specific expression variation of 74 genes to agronomic traits variation. Our findings provide novel insights into the genetic and biological mechanisms underlying maize complex traits, and the multi-tissue regulatory atlas serves as a primary source for biological interpretation, functional validation, and genomic improvement of maize.
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