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作物学报

作物学报 ›› 2025, Vol. 51 ›› Issue (12): 3121-3132.doi: 10.3724/SP.J.1006.2025.55043

• 作物遗传育种·种质资源·分子遗传学 •    下一篇

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 接受日期:2025-09-10 出版日期:2025-12-12 网络出版日期:2025-09-22
  • 通讯作者: *夏志强, E-mail: zqiangx@gmail.com
  • 作者简介:E-mail: ruixu0905@163.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项目(B23YQ0002);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. 1School 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
    2Sanya Mingyao Electron Accelerator Mutation Breeding Laboratory, Sanya 572025, Hainan, China
  • Received:2025-07-03 Accepted:2025-09-10 Published:2025-12-12 Published online:2025-09-22
  • Contact: *E-mail: zqiangx@gmail.com
  • Supported by:
    Biological Breeding-National Science and Technology Major Project(2023ZD04073);Hainan Yazhou Bay Seed Laboratory Project(B23YQ0002);High-performance Computing Platform Project 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, 非生物胁迫响应

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

图1

UMAP算法细胞聚类结果图 不同颜色标注的细胞簇代表不同的功能, 其空间距离代表表达模式的关联程度。"

图2

细胞类群在大豆种胚切片空间排布 A: 未辐射大豆胚根横切面; B: 未辐射大豆种胚纵切面; C: 辐射大豆胚根横切面; D: 辐射大豆种胚纵切面。红色部分表示各细胞簇在大豆种胚的分布位置。"

表1

差异表达基因功能注释"

簇
Cluster		 基因ID
Gene ID		 基因描述及注释
Gene description and annotation
Cluster0 GmW82.19G089600 核糖核苷二磷酸还原酶小亚基; 与DNA合成和修复有关, 通过提供dNTPs维持基因组稳定性Ribonucleoside-diphosphate reductase small chain; associated with DNA synthesis and repair, maintaining genome stability by providing dNTPs
GmW82.17G019100 胺氧化酶; 在植物生长发育、胁迫响应和信号转导中发挥关键作用
Amine oxidase; key roles in plant growth and development, stress response and signal transduction
Cluster1 GmW82.08G246300 UDP-葡萄糖6-脱氢酶; 可能在信号转导、细胞迁移中发挥作用
UDP-glucose 6-dehydrogenase; may play a role in signal transduction, cell migration
GmW82.03G052100 属于TPP酶家族(PDC1); 丙酮酸合成乙醇的关键酶
Belongs to the TPP enzyme family (PDC1); key enzyme in the synthesis of ethanol from pyruvate
Cluster2 GmW82.07G102700 可能作为生长素外排载体(PIN1)的组成成分发挥作用; 可能参与PIN1介导的生长素极性运输
May act as a component of the auxin efflux carrier (PIN1); may be involved in PIN1-mediated polar transport of growth hormones
GmW82.01G244100 通过细胞壁果胶的脱甲基酯化作用改变细胞壁
Acts in the modification of cell walls via demethylesterification of cell wall pectin
Cluster3 GmW82.17G019100 胺氧化酶; 在植物生长发育、胁迫响应和信号转导中发挥关键作用
Amine oxidase; key roles in plant growth and development, stress response and signal transduction
GmW82.10G297000 尿黑酸叶绿基转移酶1 (HPT1); 是催化生育酚生物合成分支途径中的关键酶
Homogentisate phytyltransferase 1 (HPT1); a key enzyme in the branch pathway that catalyses tocopherol biosynthesis
Cluster4 GmW82.06G256600 抗性蛋白
Resistance protein
GmW82.14G051900 富含甘氨酸蛋白家族; 植物富含甘氨酸蛋白家族, 在植物生长发育、逆境胁迫响应、激素信号传导等多个方面发挥着关键作用
Glycine rich protein family; plants are rich in the glycine protein family, which plays a key role in many aspects of plant growth and development, response to adversity stress, and hormone signaling
Cluster5 GmW82.13G344100 植物脂氧合酶可能参与多种生理过程, 包括生长发育、抗虫性、衰老及创伤响应(如LOX2)
Plant lipoxygenase may be involved in a number of diverse aspects of plant physiology including growth and development, pest resistance, and senescence or responses to wounding (LOX2)
GmW82.19G112900 金属离子结合; 金属离子结合是植物适应环境的关键
Metal ion binding; metal ion binding is key to plant adaptation
Cluster6 GmW82.17G019100 胺氧化酶; 在植物生长发育、胁迫响应和信号转导中发挥关键作用
Amine oxidase; key roles in plant growth and development, stress response and signal transduction
GmW82.03G114900 微管蛋白是微管的主要组成成分。它能结合两分子GTP: 一个位于β链的可交换位点, 另一个位于α链的不可交换位点; 参与微管的形成和维持、调控细胞分裂过程以及植物对环境的适应
Tubulin is the major constituent of microtubules. It binds two moles of GTP, one at an exchangeable site on the beta chain and one at a non-exchangeable site on the alpha chain; involved in microtubule formation and maintenance, regulation of cell division processes, and plant adaptation to the environment
Cluster7 GmW82.10G206900 AWPM-19-like蛋白家族; 是植物质膜蛋白家族, 该家族成员广泛参与植物对非生物胁迫的响应, 并在ABA信号传导、气孔调控、种子萌发等生理过程中发挥重要作用
AWPM-19-like family; it is a family of plant plasma membrane proteins, members of which are widely involved in plant responses to abiotic stresses and play important roles in physiological processes such as ABA signalling, stomatal regulation and seed germination
GmW82.13G235400 未知功能结构域1771; 一个蛋白质结构域, 属于DUF家族, 功能未知
DUF1771; a protein structural domain belonging to the DUF family, function unknown
Cluster8 GmW82.05G104300 属于过氧化物酶家族, 经典植物(III类)过氧化物酶亚家族; 参与维持细胞内活性氧(ROS)的稳态, 在植物生长代谢和逆境应答中发挥多种功能
Belongs to the peroxidase family. Classical plant (class III) peroxidase subfamily; involved in the maintenance of intracellular reactive oxygen species (ROS) homeostasis and plays multiple functions in plant growth and metabolism and in response to adversity
GmW82.10G212100 属于MIP水通道蛋白家族(TC 1.A.8); 水通道蛋白可以提高细胞质膜和液泡膜的通透性
Belongs to the MIP aquaporin (TC 1.A.8) family; water channel proteins increase the permeability of cytoplasmic and vesicular membranes
Cluster9 GmW82.11G076400 组蛋白H1; 组蛋白H1在表观调控、基因转录、DNA复制、DNA损伤修复、染色体重塑等方面发挥重要作用
Histone H1; histone H1 plays an important role in epistatic regulation, gene transcription, DNA replication, DNA damage repair, and chromosome remodelling
GmW82.13G274300 茎特异性蛋白; 参与茎的发育、结构维持、抗逆性及代谢调控等功能
Stem-specific protein; involved in stem development, structural maintenance, stress resistance and metabolic regulation
Cluster10 GmW82.16G057600 核糖核苷二磷酸还原酶小亚基; 对DNA合成和细胞增殖至关重要
Ribonucleoside-diphosphate reductase small; essential for DNA synthesis and cell proliferation
GmW82.17G143100 14 kD富含脯氨酸蛋白DC2.15同源蛋白; 可能与胚胎发生的开始或与生长素的去除所产生的代谢变化有关
14 kD proline-rich protein DC2.15-like; may be associated with the onset of embryogenesis or with metabolic changes resulting from the removal of growth hormone
Cluster11 GmW82.13G236200 RNA聚合酶II转录中介体亚基; 调节转录活性并募集激素信号传导模块和组蛋白修饰活性的中介
Mediator of RNA polymerase II transcription subunit; mediators that regulate transcriptional activity and recruit hormone signalling modules and histone modification activity
GmW82.14G010800 半乳糖醛-蔗糖半乳糖基转移酶; 主要参与棉子糖家族寡糖的生物合成, 棉子糖在种子成熟期积累, 保护细胞在脱水过程中保持稳定性, 延长种子寿命
Galactinol-sucrose galactosyltransferase; mainly involved in the biosynthesis of oligosaccharides of the cottonseed sugar family, cottonseed sugar accumulates during seed maturation, protects the cells to maintain stability during dehydration and prolongs seed life
Cluster12 GmW82.09G029800 乙酸丁酸-CoA连接酶AAE7 (AAE7); 影响植物的防御反应、能量代谢和次生代谢
Acetate butyrate-CoA ligase AAE7 (AAE7); influencing plant defence responses, energy metabolism and secondary metabolism
GmW82.18G248500 MYB相关蛋白; 参与植物的生长发育、次生代谢、胁迫响应以及激素信号转导等过程
Myb-related protein; involved in plant growth and development, secondary metabolism, stress response, and hormone signal transduction

图3

差异基因表达空间分布可视化图谱 颜色越浅表示该基因在该区域的表达越高。"

图4

差异表达基因的GO富集通路"

表2

差异表达基因GO功能注释"

簇
Cluster		 生物学过程
Biological process		 细胞组分
Cellular component		 分子功能
Molecular function
Cluster0 细胞对刺激的反应; 化学反应
Cellular response to stimulus; response to chemical		 — —
Cluster1 对异源物质的响应; 胁迫响应; 对化学物质的响应; 细胞对化学刺激的响应; 对非生物胁迫的响应
Response to xenobiotic stimulus; response to stress; response to chemical; cellular response to chemical stimulus; response to abiotic stimulus		 细胞壁; 细胞质
Cell wall; cytoplasm		 —
Cluster2 激素介导的信号通路; 维持稳态过程; 细胞对激素刺激的响应; 细胞对内源刺激的响应; 化学反应; 对激素的响应; 信号转导; 对内源刺激的响应
Hormone-mediated signaling pathway; homeostatic process; cellular response to hormone stimulus; cellular response to endogenous stimulus; response to chemical, response to hormone; signal transduction, response to endogenous stimulus		 细胞壁; 细胞膜外部的结构
Cell wall; external encapsulating structure		 —
Cluster3 — — —
Cluster4 细胞分化; 细胞发育过程; 大分子生物合成过程的调控; 生物合成过程的调控; 对刺激的反应
Cell differentiation; cellular developmental process; regulation of macromolecule biosynthetic process; regulation of biosynthetic process; response to stimulus		 — 蛋白结合
Protein binding
Cluster5 对酸性化学物质的反应; 对非生物胁迫的响应; 胚后发育; 调节生物合成过程
Response to acid chemical; response to abiotic stimulus; post-embryonic development; regulation of biosynthetic process		 叶绿体; 细胞壁Chloroplast thylakoid; cell wall 蛋白结合
Protein binding
Cluster6 对化学物质的响应Response to acid chemical — —
Cluster7 细胞对胁迫的反应; 核酸代谢过程
Cellular response to stimulus; nucleic acid metabolic process		 细胞核
Nucleus		 —
Cluster8 — — —
Cluster9 DNA模板转录的调控; 调节RNA生物合成过程
Regulation of DNA-templated transcription; regulation of RNA biosynthetic process		 — DNA结合转录因子活性
DNA-binding transcription factor activity
Cluster10 对含氧化合物的响应; 对酸性化学物质的响应; 细胞过程的调控Response to oxygen-containing compound; response to acid chemical; regulation of cellular process 细胞质膜
Plasma membrane		 —
Cluster11 — — —
Cluster12 对化学物质的响应; 发育过程
Response to chemical; developmental process		 — —

图5

差异表达基因的KEGG富集通路"

表3

细胞簇差异表达基因显著性富集的KEGG代谢途径"

簇
Cluster		 显著性富集的代谢通路
Significantly enriched metabolic pathways
Cluster0 谷胱甘肽代谢; 苯丙氨酸代谢; 嘧啶代谢; 嘌呤代谢; 核苷酸代谢
Glutathione metabolism; phenylalanine metabolism; pyrimidine metabolism; purine metabolism; nucleotide metabolism
Cluster1 半胱氨酸和蛋氨酸代谢; 抗坏血酸和醛酸代谢
Cysteine and methionine metabolism; ascorbate and aldarate metabolism
Cluster2 转录因子; 昼夜节律
Transcription factors; circadian rhythm-plant
Cluster3 泛醌和其他萜烯醌的生物合成; 苯丙烷生物合成
Ubiquinone and other terpenoid-quinone biosynthesis; phenylpropanoid biosynthesis
Cluster4 异喹啉生物碱生物合成; 托烷类、哌啶类和吡啶类生物碱合成; 苯丙氨酸代谢; 酪氨酸代谢
Isoquinoline alkaloid biosynthesis; tropane, piperidine and pyridine alkaloid biosynthesis; phenylalanine metabolism; tyrosine metabolism
Cluster5 亚油酸代谢; α-亚麻酸代谢
Linoleic acid metabolism; alpha-Linolenic acid metabolism
Cluster6 糖基转移酶; 异喹啉生物碱生物合成; 托烷类、哌啶类和吡啶类生物碱合成; 苯丙氨酸代谢; 酪氨酸代谢Glycosyltransferases; isoquinoline alkaloid biosynthesis; tropane, piperidine and pyridine alkaloid biosynthesis; phenylalanine metabolism; tyrosine metabolism
Cluster7 DNA修复和重组蛋白; 嘧啶代谢; 谷胱甘肽代谢; 嘌呤代谢; 非同源末端连接
DNA repair and recombination proteins; pyrimidine metabolism; glutathione metabolism; purine metabolism; non-homologous end-joining
Cluster8 异喹啉生物碱生物合成; 托烷类、哌啶类和吡啶类生物碱合成; 苯丙氨酸代谢; 酪氨酸代谢
Isoquinoline alkaloid biosynthesis; tropane, piperidine and pyridine alkaloid biosynthesis; phenylalanine metabolism; tyrosine metabolism
Cluster9 半乳糖代谢; 半胱氨酸和蛋氨酸代谢
Galactose metabolism; cysteine and methionine metabolism
Cluster10 嘌呤代谢; 谷胱甘肽代谢; 嘧啶代谢
Purine metabolism; glutathione metabolism; pyrimidine metabolism
Cluster11 核糖体Ribosome
Cluster12 苯丙烷生物合成; 脂肪酸延长; 氮代谢; 丙氨酸、天冬氨酸和谷氨酸代谢; 氰基氨基酸代谢
Phenylpropanoid biosynthesis; fatty acid elongation; nitrogen metabolism; alanine, aspartate and glutamate metabolism; cyanoamino acid metabolism

图6

差异表达基因的qRT-PCR验证结果 图中纵坐标代表相对表达量, 横坐标是不同辐射剂量处理的样本, ***表示在P < 0.001水平差异显著。"

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