Comprehensive analysis of 1,771 transcriptomes from 7 tissues enhance genetic and biological interpretations of maize complex traits.

IF 2.2 3区生物学 Q3 GENETICS & HEREDITY

G3: Genes|Genomes|Genetics Pub Date : 2025-07-22 DOI:10.1093/g3journal/jkaf140

Mengyu Lei, Huan Si, Mingjia Zhu, Yu Han, Wei Liu, Yifei Dai, Yan Ji, Zhengwen Liu, Fan Hao, Ran Hao, Jiarui Zhao, Guoyou Ye, Yanjun Zan

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引用次数: 0

Abstract

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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对来自7个组织的1771个转录组的综合分析增强了对玉米复合性状的遗传和生物学解释。

通过对玉米多样性面板中来自7个组织的1771个RNA-seq数据集的重新分析，我们探索了多组织转录组变异的格局和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，我们检测到一些农艺性状的相关组织类型和几个候选基因，包括白天叶片对花期-吐丝期的影响，白天叶片对籽粒玉米黄质水平的影响，以及根对穗高的影响，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联系起来。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，多组织调控图谱可作为玉米生物学解释、功能验证和基因组改良的主要来源。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

G3: Genes|Genomes|Genetics GENETICS & HEREDITY-

CiteScore

5.10

自引率

3.80%

发文量

305

审稿时长

3-8 weeks

期刊介绍： G3: Genes, Genomes, Genetics provides a forum for the publication of high‐quality foundational research, particularly research that generates useful genetic and genomic information such as genome maps, single gene studies, genome‐wide association and QTL studies, as well as genome reports, mutant screens, and advances in methods and technology. The Editorial Board of G3 believes that rapid dissemination of these data is the necessary foundation for analysis that leads to mechanistic insights. G3, published by the Genetics Society of America, meets the critical and growing need of the genetics community for rapid review and publication of important results in all areas of genetics. G3 offers the opportunity to publish the puzzling finding or to present unpublished results that may not have been submitted for review and publication due to a perceived lack of a potential high-impact finding. G3 has earned the DOAJ Seal, which is a mark of certification for open access journals, awarded by DOAJ to journals that achieve a high level of openness, adhere to Best Practice and high publishing standards.