Spatial transcriptome analysis reveals de novo regeneration of poplar roots

IF 8.7 1区农林科学 Q1 Agricultural and Biological Sciences

Horticulture Research Pub Date : 2024-08-21 DOI:10.1093/hr/uhae237

Kaiwen Lv, Naixu Liu, Yani Niu, Xiehai Song, Yongqi Liu, Zhiliang Yue, Muhammad Ali, Qiuyue Guo, Chunyu Lv, Dongdong Lu, Shaoman Zhang, Yangyan Zhou, Bosheng Li

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引用次数: 0

Abstract

Propagation through cuttings is a well-established and effective technique for plant multiplication. This study explores the regeneration of poplar roots using spatial transcriptomics to map a detailed developmental trajectory. Mapping of the time-series transcriptome data revealed notable alterations in gene expression during root development, particularly in the activation of cytokinin-responsive genes. Our analysis identified six distinct clusters during the second and third stages, each corresponding to specific anatomical regions with unique gene expression profiles. Auxin response cis-elements (AuxREs) were prevalent in the promoters of these cytokinin-responsive genes, indicating a regulatory interplay between auxin and cytokinin. Pseudo-temporal trajectory analysis mapped the differentiation from cambium cells to root primordium cells, revealing a complex pattern of cell differentiation. SAC56 and LOS1 emerged as potential novel biomarkers for enhancing root regeneration, with distinct spatial expression patterns confirmed by in situ hybridization. This comprehensive spatial analysis enhances our understanding of the molecular interactions driving root regeneration and provides insights for improving plant propagation techniques.

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空间转录组分析揭示了杨树根系的新生

扦插繁殖是一种行之有效的植物繁殖技术。本研究利用空间转录组学绘制详细的发育轨迹，探索杨树根系的再生过程。时间序列转录组数据图谱显示，根系发育过程中基因表达发生了显著变化，尤其是细胞分裂素响应基因的激活。我们的分析在第二和第三阶段发现了六个不同的群组，每个群组都对应于具有独特基因表达谱的特定解剖区域。在这些细胞分裂素响应基因的启动子中，普遍存在叶绿素响应顺式元件（AuxREs），这表明叶绿素和细胞分裂素之间存在相互调控作用。伪时序轨迹分析绘制了从骨皮层细胞到根原基细胞的分化图，揭示了复杂的细胞分化模式。SAC56 和 LOS1 成为促进根再生的潜在新型生物标记物，其独特的空间表达模式得到了原位杂交的证实。这种全面的空间分析增强了我们对驱动根再生的分子相互作用的理解，并为改进植物繁殖技术提供了启示。

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

Horticulture Research Biochemistry, Genetics and Molecular Biology-Biochemistry

CiteScore

11.20

自引率

6.90%

发文量

367

审稿时长

20 weeks

期刊介绍： Horticulture Research, an open access journal affiliated with Nanjing Agricultural University, has achieved the prestigious ranking of number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2022. As a leading publication in the field, the journal is dedicated to disseminating original research articles, comprehensive reviews, insightful perspectives, thought-provoking comments, and valuable correspondence articles and letters to the editor. Its scope encompasses all vital aspects of horticultural plants and disciplines, such as biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.