Single-cell nuclear transcriptomics reveal root tip adaptations to nitrogen scarcity in wheat
Roots play a critical role in acquisition and utilization of nitrogen in wheat, influencing nitrogen use efficiency (NUE), and ultimately determining yield. However, the detailed responses of root tips to fluctuations in nitrogen availability and the underlying regulatory mechanisms enabling adaptat...
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KeAi Communications Co., Ltd.
2025-08-01
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| Series: | Crop Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2214514125001400 |
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| author | Chuangbei Hai Yan Li Chaojun Peng Lin Hu Weigang Xu |
| author_facet | Chuangbei Hai Yan Li Chaojun Peng Lin Hu Weigang Xu |
| author_sort | Chuangbei Hai |
| collection | DOAJ |
| description | Roots play a critical role in acquisition and utilization of nitrogen in wheat, influencing nitrogen use efficiency (NUE), and ultimately determining yield. However, the detailed responses of root tips to fluctuations in nitrogen availability and the underlying regulatory mechanisms enabling adaptation to nitrogen-limited conditions, remain elusive. In this study, we used single-cell nuclear transcriptomics of the high-nitrogen utilization variety (HNV) Zhengmai 1860 (ZM1860) to construct a comprehensive map of root tip cells under both controlled and nitrogen starvation (N-starv) conditions. Identification of various cell types and their associated genes highlighted the diversity of cellular processes. Using single-nucleus consensus weighted gene co-expression network analysis (hdWGCNA), we identified key modules central to nitrogen metabolism. These identified the prominent role of epidermal cells (EC). The gene TaGS1.2, which is involved in glutamine synthesis, exhibited increased expression under nitrogen-deficient conditions, validating its functional significance in nutrient acquisition. Serving as a key functional gene that adapts to nitrogen-deficient conditions this gene also positively regulated root development. Analysis of the transcriptional regulatory network in EC further revealed the pivotal role of TaGS1.2 in the nitrogen metabolism network. We also uncovered mechanisms that enhance cell-to-cell communication in nitrogen-deficient environments by identifying specific receptors. Single-cell nuclear transcriptome mapping offers valuable insights into the complex responses of root tip cells to nitrogen scarcity and guides future breeding strategies aimed at developing more nitrogen-efficient wheat varieties. |
| format | Article |
| id | doaj-art-67f3361c740a43b9b5bf6ce99395ac33 |
| institution | Kabale University |
| issn | 2214-5141 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | KeAi Communications Co., Ltd. |
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| series | Crop Journal |
| spelling | doaj-art-67f3361c740a43b9b5bf6ce99395ac332025-08-22T04:56:32ZengKeAi Communications Co., Ltd.Crop Journal2214-51412025-08-011341156116710.1016/j.cj.2025.05.010Single-cell nuclear transcriptomics reveal root tip adaptations to nitrogen scarcity in wheatChuangbei Hai0Yan Li1Chaojun Peng2Lin Hu3Weigang Xu4College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Institute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory for Wheat Germplasm Resources Innovation and Genetic Improvement, Shennong Laboratory, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, ChinaInstitute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory for Wheat Germplasm Resources Innovation and Genetic Improvement, Shennong Laboratory, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, ChinaInstitute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory for Wheat Germplasm Resources Innovation and Genetic Improvement, Shennong Laboratory, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, ChinaInstitute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory for Wheat Germplasm Resources Innovation and Genetic Improvement, Shennong Laboratory, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, ChinaCollege of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Institute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory for Wheat Germplasm Resources Innovation and Genetic Improvement, Shennong Laboratory, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China; Corresponding author.Roots play a critical role in acquisition and utilization of nitrogen in wheat, influencing nitrogen use efficiency (NUE), and ultimately determining yield. However, the detailed responses of root tips to fluctuations in nitrogen availability and the underlying regulatory mechanisms enabling adaptation to nitrogen-limited conditions, remain elusive. In this study, we used single-cell nuclear transcriptomics of the high-nitrogen utilization variety (HNV) Zhengmai 1860 (ZM1860) to construct a comprehensive map of root tip cells under both controlled and nitrogen starvation (N-starv) conditions. Identification of various cell types and their associated genes highlighted the diversity of cellular processes. Using single-nucleus consensus weighted gene co-expression network analysis (hdWGCNA), we identified key modules central to nitrogen metabolism. These identified the prominent role of epidermal cells (EC). The gene TaGS1.2, which is involved in glutamine synthesis, exhibited increased expression under nitrogen-deficient conditions, validating its functional significance in nutrient acquisition. Serving as a key functional gene that adapts to nitrogen-deficient conditions this gene also positively regulated root development. Analysis of the transcriptional regulatory network in EC further revealed the pivotal role of TaGS1.2 in the nitrogen metabolism network. We also uncovered mechanisms that enhance cell-to-cell communication in nitrogen-deficient environments by identifying specific receptors. Single-cell nuclear transcriptome mapping offers valuable insights into the complex responses of root tip cells to nitrogen scarcity and guides future breeding strategies aimed at developing more nitrogen-efficient wheat varieties.http://www.sciencedirect.com/science/article/pii/S2214514125001400Single-nucleus RNA-seqRoot functionNitrogen scarcityEpidermal cell |
| spellingShingle | Chuangbei Hai Yan Li Chaojun Peng Lin Hu Weigang Xu Single-cell nuclear transcriptomics reveal root tip adaptations to nitrogen scarcity in wheat Crop Journal Single-nucleus RNA-seq Root function Nitrogen scarcity Epidermal cell |
| title | Single-cell nuclear transcriptomics reveal root tip adaptations to nitrogen scarcity in wheat |
| title_full | Single-cell nuclear transcriptomics reveal root tip adaptations to nitrogen scarcity in wheat |
| title_fullStr | Single-cell nuclear transcriptomics reveal root tip adaptations to nitrogen scarcity in wheat |
| title_full_unstemmed | Single-cell nuclear transcriptomics reveal root tip adaptations to nitrogen scarcity in wheat |
| title_short | Single-cell nuclear transcriptomics reveal root tip adaptations to nitrogen scarcity in wheat |
| title_sort | single cell nuclear transcriptomics reveal root tip adaptations to nitrogen scarcity in wheat |
| topic | Single-nucleus RNA-seq Root function Nitrogen scarcity Epidermal cell |
| url | http://www.sciencedirect.com/science/article/pii/S2214514125001400 |
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