Lei Mengyu, Si Huan, Zhu Mingjia, Han Yu, Liu Wei, Dai Yifei, Ji Yan, Liu Zhengwen, Hao Fan, Hao Ran, Zhao Jiarui, Ye Guoyou, Zan Yanjun
Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, CN 266000, China.
Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
G3 (Bethesda). 2025 Sep 3;15(9). doi: 10.1093/g3journal/jkaf140.
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.
通过重新分析来自玉米多样性群体中7个组织的1771个RNA测序数据集，我们探索了多组织转录组变异的全景、组织特异性基因的进化模式，并构建了一个全面的多组织基因调控图谱，以了解玉米复杂性状的遗传调控。通过对组织特异性基因调控变异与全基因组关联研究的综合分析，我们检测到了一些农艺性状的相关组织类型和几个候选基因，包括开花吐丝间隔期的白天叶片、籽粒玉米黄质水平的白天叶片以及穗位高的根部，突出了组织特异性基因表达对农艺性状变异的潜在贡献。利用全转录组关联和共定位分析，我们将74个基因的组织特异性表达变异与农艺性状变异相关联。我们的研究结果为玉米复杂性状的遗传和生物学机制提供了新的见解，并且多组织调控图谱是玉米生物学解释、功能验证和基因组改良的主要来源。
