Advances in the Application of Single-cell Transcriptomics in Plant Growth, Development and Stress Response

doi:10.11983/CBB24048

Abstract

Abstract: Single-cell transcriptomics has improved the spatiotemporal resolution from multi-cell to single-cell levels, and notable progress in this technique has facilitated the identification of new rare cell types, exploration of intercellular heterogeneity, and mapping of cell developmental trajectories. Single-cell transcriptomics is currently being widely used in various research fields such as plant growth and development, stress response, and environmental adaptability, which helps to more thoroughly and precisely uncover the molecular regulatory mechanisms underlying plant life processes. However, there are numerous challenges associated with the study and analysis of different plant species. In this review, we compare and evaluate various single-cell transcription techniques and processes, summarize plant single-cell studies in recent years, and explore new single-cell analysis tools to support researchers studying plant biology with high precision and dynamics. In addition, we propose future directions in using single-cell transcriptomics technologies to address some of the key challenges in plant research and breeding. Furthermore, some important methods for addressing plant research and breeding with single-cell transcriptomics are discussed, along with their difficulties and potential applications.

Key words: plant growth and development, stress response, single-cell RNA sequencing (scRNA-seq), 10× Genomics, cell type

Yaping Wang, Wenquan Bao, Yu’e Bai. Advances in the Application of Single-cell Transcriptomics in Plant Growth, Development and Stress Response[J]. Chinese Bulletin of Botany, 2025, 60(1): 101-113.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB24048

https://www.chinbullbotany.com/EN/Y2025/V60/I1/101

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References 78

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	Drop-seq (Dolomite Bio)	InDrop (1CellBio)	10× Genomics
珠型	脆性树脂	水凝胶	水凝胶
主要特点	温度控制; 无专有生化试剂	细胞捕获率非常高	乳液中的凝胶珠(GEM)液滴; 液滴内的反转录
每个样本捕获的细胞数	50000+	40000+	80000+
每次运行细胞数	最多8个	最多6个	最多8个
运行时间	20分钟	-	<9分钟
捕获效率	10%	>90%	高达65%
双峰率	6%-8%	4%	每捕获1000个细胞约0.9%; 每捕获10000个细胞约8%
成本	0.16美元(不包括测序)	0.65美元(不含反转录酶(RT), 含测序)	<0.35美元(包括测序)
分析流程	开源	OneCellPipe	Cell Ranger
参考文献	Macosko et al., 2015	Klein et al., 2015; Zilionis et al., 2017	Zheng et al., 2017; Zhang et al., 2019b

	Drop-seq (Dolomite Bio)	InDrop (1CellBio)	10× Genomics
珠型	脆性树脂	水凝胶	水凝胶
主要特点	温度控制; 无专有生化试剂	细胞捕获率非常高	乳液中的凝胶珠(GEM)液滴; 液滴内的反转录
每个样本捕获的细胞数	50000+	40000+	80000+
每次运行细胞数	最多8个	最多6个	最多8个
运行时间	20分钟	-	<9分钟
捕获效率	10%	>90%	高达65%
双峰率	6%-8%	4%	每捕获1000个细胞约0.9%; 每捕获10000个细胞约8%
成本	0.16美元(不包括测序)	0.65美元(不含反转录酶(RT), 含测序)	<0.35美元(包括测序)
分析流程	开源	OneCellPipe	Cell Ranger
参考文献	Macosko et al., 2015	Klein et al., 2015; Zilionis et al., 2017	Zheng et al., 2017; Zhang et al., 2019b

物种	器官/组织			研究方向	测序平台			细胞数量	参考文献
拟南芥(Arabidopsis thaliana)	根尖			转录图谱	10× Genomics			4727	Denyer et al., 2019
	根尖			转录图谱	10× Genomics			7522	Ryu et al., 2019
	根尖			转录图谱	10× Genomics			7695	Zhang et al., 2019a
	根尖			低磷响应机制	10× Genomics			5145	Wendrich et al., 2020
	侧根			侧根发育	10× Genomics			6658	Gala et al., 2021
	根尖			转录图谱	10× Genomics			110000	Shahan et al., 2022
	根			转录图谱	10× Genomics			3221	Jean-Baptiste et al., 2019
	根			转录图谱	Drop-seq			12198	Shulse et al., 2019
	根			木质部细胞亚型	Drop-seq			2400	Turco et al., 2019
	根			基因复制	10× Genomics			11470	Coate et al., 2020
	根			转录图谱	10× Genomics			5283	Dorrity et al., 2021
	叶片			转录图谱	10× Genomics			5230	Kim et al., 2021
	叶片			空间转录图谱	Stereo-seq			17406	Xia et al., 2022
	胚珠原基			雌性细胞发育	10× Genomics			16872	Hou et al., 2021
	叶片			细菌胁迫	10× Genomics			11000	Zhu et al., 2023
	愈伤组织			器官再生	10× Genomics			-	Zhai and Xu, 2021
	愈伤组织			茎顶端分生组织形成机制	Quartz-Seq2			-	Ogura et al., 2023
	愈伤组织			愈伤组织从头再生	10× Genomics			35669	Liu et al., 2022
水稻(Oryza sativa)	根尖			转录图谱	10× Genomics			20000	Liu et al., 2021b
	根和叶片			转录图谱	10× Genomics			237431	Wang et al., 2021c
	根			转录图谱	10× Genomics			27469	Zhang et al., 2021
	雌蕊			雌蕊发育	10× Genomics			6004	Li et al., 2023a
玉米(Zea mays)	根尖			氮胁迫	10× Genomics			7000	Li et al., 2022
	叶片			叶肉细胞发育	10× Genomics			14656	Tao et al., 2022
	叶片			生长高效机制	10× Genomics			7000	Bezrutczyk et al., 2021
	穗			转录图谱	10× Genomics			12525	Xu et al., 2021
	根			抗茎腐病	10× Genomics			29217	Cao et al., 2023
大豆(Glycine max)	根			根瘤发育	10× Genomics			52775	Sun et al., 2023a
	根瘤			根瘤发育	Spatial transcriptomic			26712	Liu et al., 2023
	根瘤			根瘤形成	10× Genomics			14639	Cervantes-Pérez et al., 2023
小麦(Triticum aestivum)	保卫细胞			脱落酸(ABA)胁迫	10× Genomics			8629	Wang et al., 2021a
小麦(Triticum aestivum)	根			转录图谱	10× Genomics			6875	Zhang et al., 2023
番茄(Solanum lycopersicum)	茎尖			转录图谱	10× Genomics			13377	Tian et al., 2020
	茎			茎生根和侧根启动调控机制	10× Genomics			3087	Omary et al., 2022
	愈伤组织			空间转录图谱	Spatial transcriptomic			6759	Song et al., 2023
比克氏棉(Gossypium bickii)	子叶			色素腺体发育	10× Genomics			12222	Sun et al., 2023c
陆地棉(G. hirsutum)	胚珠			纤维细胞类型	10× Genomics			21389	Wang et al., 2023
白菜型油菜(Brassica rapa)	叶片			转录图谱	10× Genomics			17372	郭新磊, 2021
白菜型油菜(Brassica rapa)	茎尖和叶片			热胁迫	Drop-seq			30000	Sun et al., 2022
花生(Arachis hypogaea)		叶片	转录图谱			10× Genomics	6815			Liu et al., 2021a
草莓(Fragaria vesca)		叶片	真菌胁迫			10× Genomics	50000			Bai et al., 2022
长春花(Catharanthus ros- eus)		叶片	长春碱生物合成			10× Genomics	25000			Sun et al., 2023b
毛竹(Phyllostachys edulis)		根尖	基根发育			10× Genomics	14279			Cheng et al., 2023
杨树(Populus trichocarpa)		茎	木质部单细胞图谱			Drop-seq	9798			Li et al., 2021
		茎	转录图谱			10× Genomics	12466			Xie et al., 2022
		茎	转录图谱			10× Genomics	6796			Chen et al., 2021
		茎	木质部发育及演化			10× Genomics+ MARS-seq2.0	25166			Tung et al., 2023
		茎	转录图谱			10× Genomics+ Spatial transcriptomic	19185			Li et al., 2023b
		茎	维管组织结构与发育			Spatial transcriptomic	-			Du et al., 2023
木棉(Bombax ceiba)		花及蒴果	纤维发育			10× Genomics	15567			Ding et al., 2023
龙眼(Dimocarpus longan)		愈伤组织	体胚发育			10× Genomics	28727			张舒婷, 2022
茶树(Camellia sinensis)		叶片	儿茶素酯代谢			10× Genomics	16977			Wang et al., 2022
橡胶树(Hevea brasiliensis)		叶片	真菌胁迫			10× Genomics	44102			Liang et al., 2023
红豆杉(Taxus mairei)		茎	紫杉烷合成调控机制			10× Genomics	10900000			Yu et al., 2023

物种	器官/组织			研究方向	测序平台			细胞数量	参考文献
拟南芥(Arabidopsis thaliana)	根尖			转录图谱	10× Genomics			4727	Denyer et al., 2019
	根尖			转录图谱	10× Genomics			7522	Ryu et al., 2019
	根尖			转录图谱	10× Genomics			7695	Zhang et al., 2019a
	根尖			低磷响应机制	10× Genomics			5145	Wendrich et al., 2020
	侧根			侧根发育	10× Genomics			6658	Gala et al., 2021
	根尖			转录图谱	10× Genomics			110000	Shahan et al., 2022
	根			转录图谱	10× Genomics			3221	Jean-Baptiste et al., 2019
	根			转录图谱	Drop-seq			12198	Shulse et al., 2019
	根			木质部细胞亚型	Drop-seq			2400	Turco et al., 2019
	根			基因复制	10× Genomics			11470	Coate et al., 2020
	根			转录图谱	10× Genomics			5283	Dorrity et al., 2021
	叶片			转录图谱	10× Genomics			5230	Kim et al., 2021
	叶片			空间转录图谱	Stereo-seq			17406	Xia et al., 2022
	胚珠原基			雌性细胞发育	10× Genomics			16872	Hou et al., 2021
	叶片			细菌胁迫	10× Genomics			11000	Zhu et al., 2023
	愈伤组织			器官再生	10× Genomics			-	Zhai and Xu, 2021
	愈伤组织			茎顶端分生组织形成机制	Quartz-Seq2			-	Ogura et al., 2023
	愈伤组织			愈伤组织从头再生	10× Genomics			35669	Liu et al., 2022
水稻(Oryza sativa)	根尖			转录图谱	10× Genomics			20000	Liu et al., 2021b
	根和叶片			转录图谱	10× Genomics			237431	Wang et al., 2021c
	根			转录图谱	10× Genomics			27469	Zhang et al., 2021
	雌蕊			雌蕊发育	10× Genomics			6004	Li et al., 2023a
玉米(Zea mays)	根尖			氮胁迫	10× Genomics			7000	Li et al., 2022
	叶片			叶肉细胞发育	10× Genomics			14656	Tao et al., 2022
	叶片			生长高效机制	10× Genomics			7000	Bezrutczyk et al., 2021
	穗			转录图谱	10× Genomics			12525	Xu et al., 2021
	根			抗茎腐病	10× Genomics			29217	Cao et al., 2023
大豆(Glycine max)	根			根瘤发育	10× Genomics			52775	Sun et al., 2023a
	根瘤			根瘤发育	Spatial transcriptomic			26712	Liu et al., 2023
	根瘤			根瘤形成	10× Genomics			14639	Cervantes-Pérez et al., 2023
小麦(Triticum aestivum)	保卫细胞			脱落酸(ABA)胁迫	10× Genomics			8629	Wang et al., 2021a
小麦(Triticum aestivum)	根			转录图谱	10× Genomics			6875	Zhang et al., 2023
番茄(Solanum lycopersicum)	茎尖			转录图谱	10× Genomics			13377	Tian et al., 2020
	茎			茎生根和侧根启动调控机制	10× Genomics			3087	Omary et al., 2022
	愈伤组织			空间转录图谱	Spatial transcriptomic			6759	Song et al., 2023
比克氏棉(Gossypium bickii)	子叶			色素腺体发育	10× Genomics			12222	Sun et al., 2023c
陆地棉(G. hirsutum)	胚珠			纤维细胞类型	10× Genomics			21389	Wang et al., 2023
白菜型油菜(Brassica rapa)	叶片			转录图谱	10× Genomics			17372	郭新磊, 2021
白菜型油菜(Brassica rapa)	茎尖和叶片			热胁迫	Drop-seq			30000	Sun et al., 2022
花生(Arachis hypogaea)		叶片	转录图谱			10× Genomics	6815			Liu et al., 2021a
草莓(Fragaria vesca)		叶片	真菌胁迫			10× Genomics	50000			Bai et al., 2022
长春花(Catharanthus ros- eus)		叶片	长春碱生物合成			10× Genomics	25000			Sun et al., 2023b
毛竹(Phyllostachys edulis)		根尖	基根发育			10× Genomics	14279			Cheng et al., 2023
杨树(Populus trichocarpa)		茎	木质部单细胞图谱			Drop-seq	9798			Li et al., 2021
		茎	转录图谱			10× Genomics	12466			Xie et al., 2022
		茎	转录图谱			10× Genomics	6796			Chen et al., 2021
		茎	木质部发育及演化			10× Genomics+ MARS-seq2.0	25166			Tung et al., 2023
		茎	转录图谱			10× Genomics+ Spatial transcriptomic	19185			Li et al., 2023b
		茎	维管组织结构与发育			Spatial transcriptomic	-			Du et al., 2023
木棉(Bombax ceiba)		花及蒴果	纤维发育			10× Genomics	15567			Ding et al., 2023
龙眼(Dimocarpus longan)		愈伤组织	体胚发育			10× Genomics	28727			张舒婷, 2022
茶树(Camellia sinensis)		叶片	儿茶素酯代谢			10× Genomics	16977			Wang et al., 2022
橡胶树(Hevea brasiliensis)		叶片	真菌胁迫			10× Genomics	44102			Liang et al., 2023
红豆杉(Taxus mairei)		茎	紫杉烷合成调控机制			10× Genomics	10900000			Yu et al., 2023