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基于空间转录组技术解析大豆种胚对X射线辐射的响应机制

许睿1，何妙华1，王昊1，李卫2，任杰2，夏志强1,*    

  1. 1 海南大学南繁学院(三亚南繁研究院) / 海南大学热带农林学院 / 热带作物生物育种全国重点实验室, 海南三亚 572025; 2 三亚鸣遥种质创新科技有限公司, 海南三亚 572025
  • 收稿日期:2025-07-03 修回日期:2025-09-10 接受日期:2025-09-10 网络出版日期:2025-09-22
  • 通讯作者: 夏志强, E-mail: zqiangx@gmail.com
  • 基金资助:
    本研究由农业生物育种国家科技重大专项(2023ZD04073), 海南省崖州湾种子实验室(B23YQ0002)和崖州湾科技城先进计算中心超算平台项目资助。

Spatial transcriptomic analysis of soybean embryonic responses to X-ray irradiation

XU Rui1,HE Miao-Hua1,WANG Hao1,LI Wei2,REN Jie2,XIA Zhi-Qiang1,*   

  1. 1 School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University / School of Tropical Agriculture and Forestry, Hainan University / National Key Laboratory for Tropical Crop Breeding, Sanya 572025, Hainan, China; 2 Sanya Mingyao Electron Accelerator Mutation Breeding Laboratory, Sanya 572025, Hainan, China
  • Received:2025-07-03 Revised:2025-09-10 Accepted:2025-09-10 Published online:2025-09-22
  • Contact: 夏志强, E-mail: zqiangx@gmail.com
  • Supported by:
    This study was supported by the Biological Breeding-National Science and Technology Major Project (2023ZD04073), the Hainan Yazhou Bay Seed Lab (B23YQ0002), and the High-performance Computing Platform of YZBSTCACC.

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摘要：

辐射诱变育种在大豆品种改良中被广泛使用，但辐射诱变的分子机制尚未完全阐明。空间转录组学作为近几年在各个生物研究领域中的热门技术，能够解析基因表达的空间异质性，然而其在辐射诱变大豆种胚研究中的应用尚未见报道。本研究利用空间转录组技术分析X射线辐射处理的大豆种胚基因表达特征及其空间调控模式。结果显示，未处理和辐射处理的大豆种胚共划分为13个细胞簇(Cluster)，并成功构建了其空间转录组图谱。差异表达分析鉴定出各细胞簇中的关键功能基因，包括参与DNA的合成和修复的GmW82.19G089600和GmW82.16G057600，响应非生物胁迫的GmW82.06G256600和GmW82.10G206900，以及参与茎的发育、结构维持、抗逆性及代谢调控的GmW82.13G274300。这些基因的空间表达分析表明，参与DNA的合成和修复以及非生物胁迫响应的基因在辐射处理的大豆种胚中高表达，参与茎的发育、结构维持、抗逆性及代谢调控的基因在未处理和辐射处理大豆种胚的上胚轴处均高表达，说明该基因可能在维持茎组织基本结构和功能中发挥重要作用。GO和KEGG富集分析进一步揭示，差异基因显著富集于细胞应激响应、DNA转录调控、氧化应激反应及谷胱甘肽代谢等通路，这些通路在植物逆境适应和胁迫耐受中具有关键作用。本研究通过空间转录组技术揭示了大豆种胚在辐射胁迫下的基因表达变化及其空间分布特征，识别出多个与DNA修复和胁迫响应相关的关键基因，反映了辐射对种胚细胞功能状态的影响，为理解辐射诱变过程中基因表达调控机制提供了基础数据支持。

关键词: 电离辐射, 空间转录组, 大豆, 差异表达基因

Abstract:

Radiation mutagenesis is widely applied in soybean breeding; however, its underlying molecular mechanisms remain poorly understood. Spatial transcriptomics has emerged as a powerful tool for resolving gene expression heterogeneity, yet its application in radiation-mutagenized soybean embryos has not been reported. In this study, spatial transcriptomics was employed to analyze gene expression patterns in non-irradiated and X-ray–irradiated soybean embryos. Both groups were classified into 13 distinct cellular clusters, and comprehensive spatial transcriptomic atlases were successfully constructed. Differential expression analysis identified several key functional genes, including DNA repair–related genes (GmW82.19G089600 and GmW82.16G057600), stress-responsive genes (GmW82.06G256600 and GmW82.10G206900), and GmW82.13G274300. These differentially expressed genes (DEGs) were associated with stem development and exhibited consistently high expression in the epicotyls of both irradiated and non-irradiated embryos. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed significant involvement of pathways related to cellular stress response, regulation of DNA-templated transcription, oxidative stress response, and glutathione metabolism This study presents the first spatial transcriptomic profiling of soybean embryos under radiation stress, identifies key genes involved in DNA repair and stress responses, and provides valuable insights into the regulatory mechanisms of underlying radiation-induced mutagenesis in plants.

Key words: ionizing radiation, spatial transcriptome, soybean, differentially expressed genes, abiotic stress response

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