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Yue H, Chen G, Zhang Z, Guo Z, Zhang Z, Zhang S, Turlings TCJ, Zhou X, Peng J, Gao Y, Zhang D, Shi X, Liu Y. Single-cell transcriptome landscape elucidates the cellular and developmental responses to tomato chlorosis virus infection in tomato leaf. PLANT, CELL & ENVIRONMENT 2024; 47:2660-2674. [PMID: 38619176 DOI: 10.1111/pce.14906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/14/2024] [Accepted: 03/23/2024] [Indexed: 04/16/2024]
Abstract
Plant viral diseases compromise the growth and yield of the crop globally, and they tend to be more serious under extreme temperatures and drought climate changes. Currently, regulatory dynamics during plant development and in response to virus infection at the plant cell level remain largely unknown. In this study, single-cell RNA sequencing on 23 226 individual cells from healthy and tomato chlorosis virus-infected leaves was established. The specific expression and epigenetic landscape of each cell type during the viral infection stage were depicted. Notably, the mesophyll cells showed a rapid function transition in virus-infected leaves, which is consistent with the pathological changes such as thinner leaves and decreased chloroplast lamella in virus-infected samples. Interestingly, the F-box protein SKIP2 was identified to play a pivotal role in chlorophyll maintenance during virus infection in tomato plants. Knockout of the SlSKIP2 showed a greener leaf state before and after virus infection. Moreover, we further demonstrated that SlSKIP2 was located in the cytomembrane and nucleus and directly regulated by ERF4. In conclusion, with detailed insights into the plant responses to viral infections at the cellular level, our study provides a genetic framework and gene reference in plant-virus interaction and breeding in the future research.
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Affiliation(s)
- Hao Yue
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
- Longping Branch, College of Biology, Hunan University, Changsha, China
| | - Gong Chen
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Zhuo Zhang
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Zhaojiang Guo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhanhong Zhang
- Institute of Vegetable, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Songbai Zhang
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Ted C J Turlings
- Laboratory of Fundamental and Applied Research in Chemical Ecology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, Kentucky, USA
| | - Jing Peng
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yang Gao
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Deyong Zhang
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
- Longping Branch, College of Biology, Hunan University, Changsha, China
| | - Xiaobin Shi
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
- Longping Branch, College of Biology, Hunan University, Changsha, China
| | - Yong Liu
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
- Longping Branch, College of Biology, Hunan University, Changsha, China
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2
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Lv Z, Jiang S, Kong S, Zhang X, Yue J, Zhao W, Li L, Lin S. Advances in Single-Cell Transcriptome Sequencing and Spatial Transcriptome Sequencing in Plants. PLANTS (BASEL, SWITZERLAND) 2024; 13:1679. [PMID: 38931111 PMCID: PMC11207393 DOI: 10.3390/plants13121679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/31/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
"Omics" typically involves exploration of the structure and function of the entire composition of a biological system at a specific level using high-throughput analytical methods to probe and analyze large amounts of data, including genomics, transcriptomics, proteomics, and metabolomics, among other types. Genomics characterizes and quantifies all genes of an organism collectively, studying their interrelationships and their impacts on the organism. However, conventional transcriptomic sequencing techniques target population cells, and their results only reflect the average expression levels of genes in population cells, as they are unable to reveal the gene expression heterogeneity and spatial heterogeneity among individual cells, thus masking the expression specificity between different cells. Single-cell transcriptomic sequencing and spatial transcriptomic sequencing techniques analyze the transcriptome of individual cells in plant or animal tissues, enabling the understanding of each cell's metabolites and expressed genes. Consequently, statistical analysis of the corresponding tissues can be performed, with the purpose of achieving cell classification, evolutionary growth, and physiological and pathological analyses. This article provides an overview of the research progress in plant single-cell and spatial transcriptomics, as well as their applications and challenges in plants. Furthermore, prospects for the development of single-cell and spatial transcriptomics are proposed.
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Affiliation(s)
- Zhuo Lv
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Z.L.); (S.J.); (S.K.); (X.Z.); (J.Y.); (W.Z.); (L.L.)
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
- College of Life Science, Nanjing Forestry University, Nanjing 210037, China
| | - Shuaijun Jiang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Z.L.); (S.J.); (S.K.); (X.Z.); (J.Y.); (W.Z.); (L.L.)
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
- College of Life Science, Nanjing Forestry University, Nanjing 210037, China
| | - Shuxin Kong
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Z.L.); (S.J.); (S.K.); (X.Z.); (J.Y.); (W.Z.); (L.L.)
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
- College of Life Science, Nanjing Forestry University, Nanjing 210037, China
| | - Xu Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Z.L.); (S.J.); (S.K.); (X.Z.); (J.Y.); (W.Z.); (L.L.)
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
- College of Life Science, Nanjing Forestry University, Nanjing 210037, China
| | - Jiahui Yue
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Z.L.); (S.J.); (S.K.); (X.Z.); (J.Y.); (W.Z.); (L.L.)
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
- College of Life Science, Nanjing Forestry University, Nanjing 210037, China
| | - Wanqi Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Z.L.); (S.J.); (S.K.); (X.Z.); (J.Y.); (W.Z.); (L.L.)
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
- College of Life Science, Nanjing Forestry University, Nanjing 210037, China
| | - Long Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Z.L.); (S.J.); (S.K.); (X.Z.); (J.Y.); (W.Z.); (L.L.)
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Shuyan Lin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Z.L.); (S.J.); (S.K.); (X.Z.); (J.Y.); (W.Z.); (L.L.)
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
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3
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Lian X, Zhong L, Bai Y, Guang X, Tang S, Guo X, Wei T, Yang F, Zhang Y, Huang G, Zhang J, Shao L, Lei G, Li Z, Sahu SK, Zhang S, Liu H, Hu F. Spatiotemporal transcriptomic atlas of rhizome formation in Oryza longistaminata. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1652-1668. [PMID: 38345936 PMCID: PMC11123419 DOI: 10.1111/pbi.14294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/22/2024]
Abstract
Rhizomes are modified stems that grow underground and produce new individuals genetically identical to the mother plant. Recently, a breakthrough has been made in efforts to convert annual grains into perennial ones by utilizing wild rhizomatous species as donors, yet the developmental biology of this organ is rarely studied. Oryza longistaminata, a wild rice species featuring strong rhizomes, provides a valuable model for exploration of rhizome development. Here, we first assembled a double-haplotype genome of O. longistaminata, which displays a 48-fold improvement in contiguity compared to the previously published assembly. Furthermore, spatiotemporal transcriptomics was performed to obtain the expression profiles of different tissues in O. longistaminata rhizomes and tillers. Two spatially reciprocal cell clusters, the vascular bundle 2 cluster and the parenchyma 2 cluster, were determined to be the primary distinctions between the rhizomes and tillers. We also captured meristem initiation cells in the sunken area of parenchyma located at the base of internodes, which is the starting point for rhizome initiation. Trajectory analysis further indicated that the rhizome is regenerated through de novo generation. Collectively, these analyses revealed a spatiotemporal transcriptional transition underlying the rhizome initiation, providing a valuable resource for future perennial crop breeding.
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Affiliation(s)
- Xiaoping Lian
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Liyuan Zhong
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Yixuan Bai
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Xuanmin Guang
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Sijia Tang
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Xing Guo
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Tong Wei
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Feng Yang
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Yujiao Zhang
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Guangfu Huang
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Jing Zhang
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Lin Shao
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Guijie Lei
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Zheng Li
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Shilai Zhang
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Huan Liu
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Fengyi Hu
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
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Cui Y, Su Y, Bian J, Han X, Guo H, Yang Z, Chen Y, Li L, Li T, Deng XW, Liu X. Single-nucleus RNA and ATAC sequencing analyses provide molecular insights into early pod development of peanut fruit. PLANT COMMUNICATIONS 2024:100979. [PMID: 38794796 DOI: 10.1016/j.xplc.2024.100979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/31/2024] [Accepted: 05/22/2024] [Indexed: 05/26/2024]
Abstract
Peanut (Arachis hypogaea L.) is an important leguminous oil and economic crop that produces flowers aboveground and fruits belowground. Subterranean fruit-pod development, which significantly affects peanut production, involves complex molecular mechanisms that likely require the coordinated regulation of multiple genes in different tissues. To investigate the molecular mechanisms that underlie peanut fruit-pod development, we characterized the anatomical features of early fruit-pod development and integrated single-nucleus RNA-sequencing (snRNA-seq) and single-nucleus assay for transposase-accessible chromatin with sequencing (snATAC-seq) data at the single-cell level. We identified distinct cell types, such as meristem, embryo, vascular tissue, cuticular layer, and stele cells within the shell wall. These specific cell types were used to examine potential molecular changes unique to each cell type during pivotal stages of fruit-pod development. snRNA-seq analyses of differentially expressed genes revealed cell-type-specific insights that were not previously obtainable from transcriptome analyses of bulk RNA. For instance, we identified MADS-box genes that contributes to the formation of parenchyma cells and gravity-related genes that are present in the vascular cells, indicating an essential role for the vascular cells in peg gravitropism. Overall, our single-nucleus analysis provides comprehensive and novel information on specific cell types, gene expression, and chromatin accessibility during the early stages of fruit-pod development. This information will enhance our understanding of the mechanisms that underlie fruit-pod development in peanut and contribute to efforts aimed at improving peanut production.
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Affiliation(s)
- Yuanyuan Cui
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Shandong 261325, China
| | - Yanning Su
- School of Advanced Agricultural Sciences, Peking University, Beijing 100083, China
| | - Jianxin Bian
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Shandong 261325, China
| | - Xue Han
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Shandong 261325, China
| | - Haosong Guo
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Shandong 261325, China; School of Advanced Agricultural Sciences, Peking University, Beijing 100083, China
| | - Zhiyuan Yang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Shandong 261325, China
| | - Yijun Chen
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Shandong 261325, China
| | - Lihui Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Shandong 261325, China
| | - Tianyu Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Shandong 261325, China
| | - Xing Wang Deng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Shandong 261325, China; School of Advanced Agricultural Sciences, Peking University, Beijing 100083, China
| | - Xiaoqin Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Shandong 261325, China.
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5
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Han E, Geng Z, Qin Y, Wang Y, Ma S. Single-cell network analysis reveals gene expression programs for Arabidopsis root development and metabolism. PLANT COMMUNICATIONS 2024:100978. [PMID: 38783601 DOI: 10.1016/j.xplc.2024.100978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/24/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Single-cell RNA-sequencing datasets of Arabidopsis roots have been generated, but related comprehensive gene co-expression network analyses are lacking. We conducted a single-cell gene co-expression network analysis with publicly available scRNA-seq datasets of Arabidopsis roots using a SingleCellGGM algorithm. The analysis identified 149 gene co-expression modules, which we considered to be gene expression programs (GEPs). By examining their spatiotemporal expression, we identified GEPs specifically expressed in major root cell types along their developmental trajectories. These GEPs define gene programs regulating root cell development at different stages and are enriched with relevant developmental regulators. As examples, a GEP specific for the quiescent center (QC) contains 20 genes regulating QC and stem cell niche homeostasis, and four GEPs are expressed in sieve elements (SEs) from early to late developmental stages, with the early-stage GEP containing 17 known SE developmental regulators. We also identified GEPs for metabolic pathways with cell-type-specific expression, suggesting the existence of cell-type-specific metabolism in roots. Using the GEPs, we discovered and verified a columella-specific gene, NRL27, as a regulator of the auxin-related root gravitropism response. Our analysis thus systematically reveals GEPs that regulate Arabidopsis root development and metabolism and provides ample resources for root biology studies.
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Affiliation(s)
- Ershang Han
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China
| | - Zhenxing Geng
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China
| | - Yue Qin
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China
| | - Yuewei Wang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China
| | - Shisong Ma
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China; School of Data Science, University of Science and Technology of China, Hefei 230027, China.
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6
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Cao S, Zhao X, Li Z, Yu R, Li Y, Zhou X, Yan W, Chen D, He C. Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification. PLANT DIVERSITY 2024; 46:372-385. [PMID: 38798726 PMCID: PMC11119547 DOI: 10.1016/j.pld.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 05/29/2024]
Abstract
Plant morphogenesis relies on precise gene expression programs at the proper time and position which is orchestrated by transcription factors (TFs) in intricate regulatory networks in a cell-type specific manner. Here we introduced a comprehensive single-cell transcriptomic atlas of Arabidopsis seedlings. This atlas is the result of meticulous integration of 63 previously published scRNA-seq datasets, addressing batch effects and conserving biological variance. This integration spans a broad spectrum of tissues, including both below- and above-ground parts. Utilizing a rigorous approach for cell type annotation, we identified 47 distinct cell types or states, largely expanding our current view of plant cell compositions. We systematically constructed cell-type specific gene regulatory networks and uncovered key regulators that act in a coordinated manner to control cell-type specific gene expression. Taken together, our study not only offers extensive plant cell atlas exploration that serves as a valuable resource, but also provides molecular insights into gene-regulatory programs that varies from different cell types.
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Affiliation(s)
- Shanni Cao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xue Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zhuojin Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ranran Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yuqi Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinkai Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
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Shanks CM, Rothkegel K, Brooks MD, Cheng CY, Alvarez JM, Ruffel S, Krouk G, Gutiérrez RA, Coruzzi GM. Nitrogen sensing and regulatory networks: it's about time and space. THE PLANT CELL 2024; 36:1482-1503. [PMID: 38366121 PMCID: PMC11062454 DOI: 10.1093/plcell/koae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/18/2024]
Abstract
A plant's response to external and internal nitrogen signals/status relies on sensing and signaling mechanisms that operate across spatial and temporal dimensions. From a comprehensive systems biology perspective, this involves integrating nitrogen responses in different cell types and over long distances to ensure organ coordination in real time and yield practical applications. In this prospective review, we focus on novel aspects of nitrogen (N) sensing/signaling uncovered using temporal and spatial systems biology approaches, largely in the model Arabidopsis. The temporal aspects span: transcriptional responses to N-dose mediated by Michaelis-Menten kinetics, the role of the master NLP7 transcription factor as a nitrate sensor, its nitrate-dependent TF nuclear retention, its "hit-and-run" mode of target gene regulation, and temporal transcriptional cascade identified by "network walking." Spatial aspects of N-sensing/signaling have been uncovered in cell type-specific studies in roots and in root-to-shoot communication. We explore new approaches using single-cell sequencing data, trajectory inference, and pseudotime analysis as well as machine learning and artificial intelligence approaches. Finally, unveiling the mechanisms underlying the spatial dynamics of nitrogen sensing/signaling networks across species from model to crop could pave the way for translational studies to improve nitrogen-use efficiency in crops. Such outcomes could potentially reduce the detrimental effects of excessive fertilizer usage on groundwater pollution and greenhouse gas emissions.
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Affiliation(s)
- Carly M Shanks
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Karin Rothkegel
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), 7500565 Santiago, Chile
- Center for Genome Regulation (CRG), Institute of Ecology and Biodiversity (IEB), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331010 Santiago, Chile
| | - Matthew D Brooks
- Global Change and Photosynthesis Research Unit, USDA-ARS, Urbana, IL 61801, USA
| | - Chia-Yi Cheng
- Department of Life Science, National Taiwan University, Taipei 10663, Taiwan
| | - José M Alvarez
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), 7500565 Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias, Universidad Andrés Bello, 8370035 Santiago, Chile
| | - Sandrine Ruffel
- Institute for Plant Sciences of Montpellier (IPSiM), Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l’Agriculture, l’Alimentation, et l'Environnement (INRAE), Université de Montpellier, Montpellier 34090, France
| | - Gabriel Krouk
- Institute for Plant Sciences of Montpellier (IPSiM), Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l’Agriculture, l’Alimentation, et l'Environnement (INRAE), Université de Montpellier, Montpellier 34090, France
| | - Rodrigo A Gutiérrez
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), 7500565 Santiago, Chile
- Center for Genome Regulation (CRG), Institute of Ecology and Biodiversity (IEB), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331010 Santiago, Chile
| | - Gloria M Coruzzi
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
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Dixon RA, Dickinson AJ. A century of studying plant secondary metabolism-From "what?" to "where, how, and why?". PLANT PHYSIOLOGY 2024; 195:48-66. [PMID: 38163637 PMCID: PMC11060662 DOI: 10.1093/plphys/kiad596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/15/2023] [Indexed: 01/03/2024]
Abstract
Over the past century, early advances in understanding the identity of the chemicals that collectively form a living plant have led scientists to deeper investigations exploring where these molecules localize, how they are made, and why they are synthesized in the first place. Many small molecules are specific to the plant kingdom and have been termed plant secondary metabolites, despite the fact that they can play primary and essential roles in plant structure, development, and response to the environment. The past 100 yr have witnessed elucidation of the structure, function, localization, and biosynthesis of selected plant secondary metabolites. Nevertheless, many mysteries remain about the vast diversity of chemicals produced by plants and their roles in plant biology. From early work characterizing unpurified plant extracts, to modern integration of 'omics technology to discover genes in metabolite biosynthesis and perception, research in plant (bio)chemistry has produced knowledge with substantial benefits for society, including human medicine and agricultural biotechnology. Here, we review the history of this work and offer suggestions for future areas of exploration. We also highlight some of the recently developed technologies that are leading to ongoing research advances.
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Affiliation(s)
- Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Alexandra Jazz Dickinson
- Department of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92093, USA
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Chen M, Dai Y, Liao J, Wu H, Lv Q, Huang Y, Liu L, Feng Y, Lv H, Zhou B, Peng D. TARGET OF MONOPTEROS: key transcription factors orchestrating plant development and environmental response. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2214-2234. [PMID: 38195092 DOI: 10.1093/jxb/erae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/04/2024] [Indexed: 01/11/2024]
Abstract
Plants have an incredible ability to sustain root and vascular growth after initiation of the embryonic root and the specification of vascular tissue in early embryos. Microarray assays have revealed that a group of transcription factors, TARGET OF MONOPTEROS (TMO), are important for embryonic root initiation in Arabidopsis. Despite the discovery of their auxin responsiveness early on, their function and mode of action remained unknown for many years. The advent of genome editing has accelerated the study of TMO transcription factors, revealing novel functions for biological processes such as vascular development, root system architecture, and response to environmental cues. This review covers recent achievements in understanding the developmental function and the genetic mode of action of TMO transcription factors in Arabidopsis and other plant species. We highlight the transcriptional and post-transcriptional regulation of TMO transcription factors in relation to their function, mainly in Arabidopsis. Finally, we provide suggestions for further research and potential applications in plant genetic engineering.
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Affiliation(s)
- Min Chen
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yani Dai
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Jiamin Liao
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Huan Wu
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Qiang Lv
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yu Huang
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Lichang Liu
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yu Feng
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Hongxuan Lv
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Bo Zhou
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, 438107, Huaihua, Hunan, China
- National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern China, 410004, Changsha, Hunan, China
- Forestry Biotechnology Hunan Key Laboratories, Hunan, China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, 410004, Changsha, Hunan, China
| | - Dan Peng
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, 438107, Huaihua, Hunan, China
- Forestry Biotechnology Hunan Key Laboratories, Hunan, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, 410004, Changsha, Hunan, China
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Ma Y, Wang Y, Zhou Z, Zhang R, Xie Y, Zhang Y, Bo Y, Lyu X, Yang J, Zhang M, Hu Z. A large presence/absence variation in the promotor of the ClLOG gene determines trichome elongation in watermelon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:98. [PMID: 38592431 DOI: 10.1007/s00122-024-04601-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/13/2024] [Indexed: 04/10/2024]
Abstract
KEY MESSAGE The ClLOG gene encoding a cytokinin riboside 5'-monophosphate phosphoribohydrolase determines trichome length in watermelon, which is associated with its promoter variations. Trichomes, which are differentiated from epidermal cells, are special accessory structures that cover the above-ground organs of plants and possibly contribute to biotic and abiotic stress resistance. Here, a bulked segregant analysis (BSA) of an F2 population with significant variations in trichome length was undertaken. A 1.84-Mb candidate region on chromosome 10 was associated with trichome length. Resequencing and fine-mapping analyses indicated that a 12-kb structural variation in the promoter of Cla97C10G203450 (ClLOG) led to a significant expression difference in this gene in watermelon lines with different trichome lengths. In addition, a virus-induced gene silencing analysis confirmed that ClLOG positively regulated trichome elongation. These findings provide new information and identify a potential target gene for controlling multicellular trichome elongation in watermelon.
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Affiliation(s)
- Yuyuan Ma
- Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China
| | - Yu Wang
- Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China
| | - Zhiqin Zhou
- Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China
| | - Runqin Zhang
- Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China
| | - Yiru Xie
- Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China
| | - Yihan Zhang
- Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
| | - Yongming Bo
- Key Laboratory of Vegetable Breeding, Ningbo Weimeng Seed Co., Ltd, Ningbo, 315100, People's Republic of China
| | - Xiaolong Lyu
- Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China
| | - Jinghua Yang
- Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China
| | - Mingfang Zhang
- Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China
- Key Laboratory of Vegetable Breeding, Ningbo Weimeng Seed Co., Ltd, Ningbo, 315100, People's Republic of China
| | - Zhongyuan Hu
- Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, People's Republic of China.
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China.
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China.
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11
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Bernal-Gallardo JJ, de Folter S. Plant genome information facilitates plant functional genomics. PLANTA 2024; 259:117. [PMID: 38592421 PMCID: PMC11004055 DOI: 10.1007/s00425-024-04397-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/20/2024] [Indexed: 04/10/2024]
Abstract
MAIN CONCLUSION In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Plant genome sequence information greatly facilitates the studies of plant biology, functional genomics, evolution of genomes and genes, domestication processes, phylogenetic relationships, among many others. More than two decades of sequencing efforts have boosted the number of available sequenced plant genomes. The first plant genome, of Arabidopsis, was published in the year 2000 and currently, 4604 plant genomes from 1482 plant species have been published. Various large sequence initiatives are running, which are planning to produce tens of thousands of sequenced plant genomes in the near future. In this review, we give an overview on the status of sequenced plant genomes and on the use of genome information in different research areas.
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Affiliation(s)
- Judith Jazmin Bernal-Gallardo
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico.
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12
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Adema K, Schon MA, Nodine MD, Kohlen W. Lost in space: what single-cell RNA sequencing cannot tell you. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00066-9. [PMID: 38570278 DOI: 10.1016/j.tplants.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/21/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
Abstract
Plant scientists are rapidly integrating single-cell RNA sequencing (scRNA-seq) into their workflows. Maximizing the potential of scRNA-seq requires a proper understanding of the spatiotemporal context of cells. However, positional information is inherently lost during scRNA-seq, limiting its potential to characterize complex biological systems. In this review we highlight how current single-cell analysis pipelines cannot completely recover spatial information, which confounds biological interpretation. Various strategies exist to identify the location of RNA, from classical RNA in situ hybridization to spatial transcriptomics. Herein we discuss the possibility of utilizing this spatial information to supervise single-cell analyses. An integrative approach will maximize the potential of each technology, and lead to insights which go beyond the capability of each individual technology.
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Affiliation(s)
- Kelvin Adema
- Laboratory of Cell and Developmental Biology, Cluster of Plant Developmental Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Michael A Schon
- Laboratory of Cell and Developmental Biology, Cluster of Plant Developmental Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands; Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Michael D Nodine
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Wouter Kohlen
- Laboratory of Cell and Developmental Biology, Cluster of Plant Developmental Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands; Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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13
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Grones C, Eekhout T, Shi D, Neumann M, Berg LS, Ke Y, Shahan R, Cox KL, Gomez-Cano F, Nelissen H, Lohmann JU, Giacomello S, Martin OC, Cole B, Wang JW, Kaufmann K, Raissig MT, Palfalvi G, Greb T, Libault M, De Rybel B. Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics. THE PLANT CELL 2024; 36:812-828. [PMID: 38231860 PMCID: PMC10980355 DOI: 10.1093/plcell/koae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/17/2023] [Accepted: 10/24/2023] [Indexed: 01/19/2024]
Abstract
Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidating the transcriptional changes across cell types in a specific tissue or organ, upon treatments, in response to biotic and abiotic stresses, or between genotypes. Despite the rapidly accelerating use of these technologies, collective and standardized experimental and analytical procedures to support the acquisition of high-quality data sets are still missing. In this commentary, we discuss common challenges associated with the use of single-cell transcriptomics in plants and propose general guidelines to improve reproducibility, quality, comparability, and interpretation and to make the data readily available to the community in this fast-developing field of research.
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Affiliation(s)
- Carolin Grones
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
- VIB Single Cell Core Facility, Ghent 9052, Belgium
| | - Dongbo Shi
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Manuel Neumann
- Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Lea S Berg
- Institute of Plant Sciences, University of Bern, 3012 Bern, Switzerland
| | - Yuji Ke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
| | - Rachel Shahan
- Department of Biology, Duke University, Durham, NC 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Kevin L Cox
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Fabio Gomez-Cano
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
| | - Jan U Lohmann
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Stefania Giacomello
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, 17165 Solna, Sweden
| | - Olivier C Martin
- Universities of Paris-Saclay, Paris-Cité and Evry, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay, Gif-sur-Yvette 91192, France
| | - Benjamin Cole
- DOE-Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Kerstin Kaufmann
- Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Michael T Raissig
- Institute of Plant Sciences, University of Bern, 3012 Bern, Switzerland
| | - Gergo Palfalvi
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Thomas Greb
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Marc Libault
- Division of Plant Science and Technology, Interdisciplinary Plant Group, College of Agriculture, Food, and Natural Resources, University of Missouri-Columbia, Columbia, MO 65201, USA
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Centre for Plant Systems Biology, Ghent 9052, Belgium
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14
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Zheng L, Hu Y, Yang T, Wang Z, Wang D, Jia L, Xie Y, Luo L, Qi W, Lv Y, Beeckman T, Xuan W, Han Y. A root cap-localized NAC transcription factor controls root halotropic response to salt stress in Arabidopsis. Nat Commun 2024; 15:2061. [PMID: 38448433 PMCID: PMC10917740 DOI: 10.1038/s41467-024-46482-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 02/28/2024] [Indexed: 03/08/2024] Open
Abstract
Plants are capable of altering root growth direction to curtail exposure to a saline environment (termed halotropism). The root cap that surrounds root tip meristematic stem cells plays crucial roles in perceiving and responding to environmental stimuli. However, how the root cap mediates root halotropism remains undetermined. Here, we identified a root cap-localized NAC transcription factor, SOMBRERO (SMB), that is required for root halotropism. Its effect on root halotropism is attributable to the establishment of asymmetric auxin distribution in the lateral root cap (LRC) rather than to the alteration of cellular sodium equilibrium or amyloplast statoliths. Furthermore, SMB is essential for basal expression of the auxin influx carrier gene AUX1 in LRC and for auxin redistribution in a spatiotemporally-regulated manner, thereby leading to directional bending of roots away from higher salinity. Our findings uncover an SMB-AUX1-auxin module linking the role of the root cap to the activation of root halotropism.
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Affiliation(s)
- Lulu Zheng
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Yongfeng Hu
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, Yichang, China
| | - Tianzhao Yang
- National Engineering Laboratory of Crop Stress Resistence Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Zhen Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Daoyuan Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Letian Jia
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yuanming Xie
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Long Luo
- National Engineering Laboratory of Crop Stress Resistence Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Weicong Qi
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Yuanda Lv
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Wei Xuan
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China.
| | - Yi Han
- National Engineering Laboratory of Crop Stress Resistence Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
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15
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Kaur H, Jha P, Ochatt SJ, Kumar V. Single-cell transcriptomics is revolutionizing the improvement of plant biotechnology research: recent advances and future opportunities. Crit Rev Biotechnol 2024; 44:202-217. [PMID: 36775666 DOI: 10.1080/07388551.2023.2165900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 11/04/2022] [Accepted: 12/08/2022] [Indexed: 02/14/2023]
Abstract
Single-cell approaches are a promising way to obtain high-resolution transcriptomics data and have the potential to revolutionize the study of plant growth and development. Recent years have seen the advent of unprecedented technological advances in the field of plant biology to study the transcriptional information of individual cells by single-cell RNA sequencing (scRNA-seq). This review focuses on the modern advancements of single-cell transcriptomics in plants over the past few years. In addition, it also offers a new insight of how these emerging methods will expedite advance research in plant biotechnology in the near future. Lastly, the various technological hurdles and inherent limitations of single-cell technology that need to be conquered to develop such outstanding possible knowledge gain is critically analyzed and discussed.
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Affiliation(s)
- Harmeet Kaur
- Division of Research and Development, Plant Biotechnology Lab, Lovely Professional University, Phagwara, Punjab, India
- Department of Biotechnology, Lovely Faculty of Technology and Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Priyanka Jha
- Department of Biotechnology, Lovely Faculty of Technology and Sciences, Lovely Professional University, Phagwara, Punjab, India
- Department of Research Facilitation, Division of Research and Development, Lovely Professional University, Phagwara, Punjab, India
| | - Sergio J Ochatt
- Agroécologie, InstitutAgro Dijon, INRAE, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Vijay Kumar
- Division of Research and Development, Plant Biotechnology Lab, Lovely Professional University, Phagwara, Punjab, India
- Department of Biotechnology, Lovely Faculty of Technology and Sciences, Lovely Professional University, Phagwara, Punjab, India
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16
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Wu R, Liu Z, Sun S, Qin A, Liu H, Zhou Y, Li W, Liu Y, Hu M, Yang J, Rochaix JD, An G, Herrera-Estrella L, Tran LSP, Sun X. Identification of bZIP Transcription Factors That Regulate the Development of Leaf Epidermal Cells in Arabidopsis thaliana by Single-Cell RNA Sequencing. Int J Mol Sci 2024; 25:2553. [PMID: 38473801 DOI: 10.3390/ijms25052553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
Epidermal cells are the main avenue for signal and material exchange between plants and the environment. Leaf epidermal cells primarily include pavement cells, guard cells, and trichome cells. The development and distribution of different epidermal cells are tightly regulated by a complex transcriptional regulatory network mediated by phytohormones, including jasmonic acid, and transcription factors. How the fate of leaf epidermal cells is determined, however, is still largely unknown due to the diversity of cell types and the complexity of their regulation. Here, we characterized the transcriptional profiles of epidermal cells in 3-day-old true leaves of Arabidopsis thaliana using single-cell RNA sequencing. We identified two genes encoding BASIC LEUCINE-ZIPPER (bZIP) transcription factors, namely bZIP25 and bZIP53, which are highly expressed in pavement cells and early-stage meristemoid cells. Densities of pavement cells and trichome cells were found to increase and decrease, respectively, in bzip25 and bzip53 mutants, compared with wild-type plants. This trend was more pronounced in the presence of jasmonic acid, suggesting that these transcription factors regulate the development of trichome cells and pavement cells in response to jasmonic acid.
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Affiliation(s)
- Rui Wu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Zhixin Liu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Susu Sun
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Aizhi Qin
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Hao Liu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Yaping Zhou
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Weiqiang Li
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Yumeng Liu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Mengke Hu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Jincheng Yang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Jean-David Rochaix
- Departments of Molecular Biology and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Guoyong An
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Luis Herrera-Estrella
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
| | - Xuwu Sun
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
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17
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Ali M, Yang T, He H, Zhang Y. Plant biotechnology research with single-cell transcriptome: recent advancements and prospects. PLANT CELL REPORTS 2024; 43:75. [PMID: 38381195 DOI: 10.1007/s00299-024-03168-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/05/2024] [Indexed: 02/22/2024]
Abstract
KEY MESSAGE Single-cell transcriptomic techniques have emerged as powerful tools in plant biology, offering high-resolution insights into gene expression at the individual cell level. This review highlights the rapid expansion of single-cell technologies in plants, their potential in understanding plant development, and their role in advancing plant biotechnology research. Single-cell techniques have emerged as powerful tools to enhance our understanding of biological systems, providing high-resolution transcriptomic analysis at the single-cell level. In plant biology, the adoption of single-cell transcriptomics has seen rapid expansion of available technologies and applications. This review article focuses on the latest advancements in the field of single-cell transcriptomic in plants and discusses the potential role of these approaches in plant development and expediting plant biotechnology research in the near future. Furthermore, inherent challenges and limitations of single-cell technology are critically examined to overcome them and enhance our knowledge and understanding.
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Affiliation(s)
- Muhammad Ali
- School of Agriculture, Sun Yat-Sen University, Shenzhen, 518107, China
- Peking University-Institute of Advanced Agricultural Sciences, Weifang, China
| | - Tianxia Yang
- School of Agriculture, Sun Yat-Sen University, Shenzhen, 518107, China
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Hai He
- School of Agriculture, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Yu Zhang
- School of Agriculture, Sun Yat-Sen University, Shenzhen, 518107, China.
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18
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Zeng J, Wang Y, Wu G, Sun Q, He X, Zhang X, Sun X, Zhao Y, Liu W, Xu D, Dai X, Ma W. Comparative Transcriptome Analysis Reveals the Genes and Pathways Related to Wheat Root Hair Length. Int J Mol Sci 2024; 25:2069. [PMID: 38396749 PMCID: PMC10889798 DOI: 10.3390/ijms25042069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/03/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Tube-like outgrowths from root epidermal cells, known as root hairs, enhance water and nutrient absorption, facilitate microbial interactions, and contribute to plant anchorage by expanding the root surface area. Genetically regulated and strongly influenced by environmental conditions, longer root hairs generally enhance water and nutrient absorption, correlating with increased stress resistance. Wheat, a globally predominant crop pivotal for human nutrition, necessitates the identification of long root hair genotypes and their regulatory genes to enhance nutrient capture and yield potential. This study focused on 261 wheat samples of diverse genotypes during germination, revealing noticeable disparities in the length of the root hair among the genotypes. Notably, two long root hair genotypes (W106 and W136) and two short root hair genotypes (W90 and W100) were identified. Transcriptome sequencing resulted in the development of 12 root cDNA libraries, unveiling 1180 shared differentially expressed genes (DEGs). Further analyses, including GO function annotation, KEGG enrichment, MapMan metabolic pathway analysis, and protein-protein interaction (PPI) network prediction, underscored the upregulation of root hair length regulatory genes in the long root hair genotypes. These included genes are associated with GA and BA hormone signaling pathways, FRS/FRF and bHLH transcription factors, phenylpropanoid, lignin, lignan secondary metabolic pathways, the peroxidase gene for maintaining ROS steady state, and the ankyrin gene with diverse biological functions. This study contributes valuable insights into modulating the length of wheat root hair and identifies candidate genes for the genetic improvement of wheat root traits.
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Affiliation(s)
- Jianbin Zeng
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Yongmei Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Gang Wu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Qingyi Sun
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Xiaoyan He
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Xinyi Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Xuelian Sun
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Yan Zhao
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Wenxing Liu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Dengan Xu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Xuehuan Dai
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Wujun Ma
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying 257347, China
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19
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Yan Y, Luo H, Qin Y, Yan T, Jia J, Hou Y, Liu Z, Zhai J, Long Y, Deng X, Cao X. Light controls mesophyll-specific post-transcriptional splicing of photoregulatory genes by AtPRMT5. Proc Natl Acad Sci U S A 2024; 121:e2317408121. [PMID: 38285953 PMCID: PMC10861865 DOI: 10.1073/pnas.2317408121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/29/2023] [Indexed: 01/31/2024] Open
Abstract
Light plays a central role in plant growth and development, providing an energy source and governing various aspects of plant morphology. Previous study showed that many polyadenylated full-length RNA molecules within the nucleus contain unspliced introns (post-transcriptionally spliced introns, PTS introns), which may play a role in rapidly responding to changes in environmental signals. However, the mechanism underlying post-transcriptional regulation during initial light exposure of young, etiolated seedlings remains elusive. In this study, we used FLEP-seq2, a Nanopore-based sequencing technique, to analyze nuclear RNAs in Arabidopsis (Arabidopsis thaliana) seedlings under different light conditions and found numerous light-responsive PTS introns. We also used single-nucleus RNA sequencing (snRNA-seq) to profile transcripts in single nucleus and investigate the distribution of light-responsive PTS introns across distinct cell types. We established that light-induced PTS introns are predominant in mesophyll cells during seedling de-etiolation following exposure of etiolated seedlings to light. We further demonstrated the involvement of the splicing-related factor A. thaliana PROTEIN ARGININE METHYLTRANSFERASE 5 (AtPRMT5), working in concert with the E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), a critical repressor of light signaling pathways. We showed that these two proteins orchestrate light-induced PTS events in mesophyll cells and facilitate chloroplast development, photosynthesis, and morphogenesis in response to ever-changing light conditions. These findings provide crucial insights into the intricate mechanisms underlying plant acclimation to light at the cell-type level.
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Affiliation(s)
- Yan Yan
- Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Haofei Luo
- Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Yuwei Qin
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
| | - Tingting Yan
- Key Laboratory of Tropical Fruit Tree Biology of Hainan Province, Institute of Tropical Fruit Trees, Hainan Academy of Agricultural Sciences, Haikou571100, China
| | - Jinbu Jia
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
| | - Yifeng Hou
- Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Zhijian Liu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
| | - Jixian Zhai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
| | - Yanping Long
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
| | - Xian Deng
- Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Xiaofeng Cao
- Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
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20
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Bawa G, Liu Z, Yu X, Tran LSP, Sun X. Introducing single cell stereo-sequencing technology to transform the plant transcriptome landscape. TRENDS IN PLANT SCIENCE 2024; 29:249-265. [PMID: 37914553 DOI: 10.1016/j.tplants.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 10/01/2023] [Accepted: 10/02/2023] [Indexed: 11/03/2023]
Abstract
Single cell RNA-sequencing (scRNA-seq) advancements have helped detect transcriptional heterogeneities in biological samples. However, scRNA-seq cannot currently provide high-resolution spatial transcriptome information or identify subcellular organs in biological samples. These limitations have led to the development of spatially enhanced-resolution omics-sequencing (Stereo-seq), which combines spatial information with single cell transcriptomics to address the challenges of scRNA-seq alone. In this review, we discuss the advantages of Stereo-seq technology. We anticipate that the application of such an integrated approach in plant research will advance our understanding of biological process in the plant transcriptomics era. We conclude with an outlook of how such integration will enhance crop improvement.
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Affiliation(s)
- George Bawa
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, PR China
| | - Zhixin Liu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, PR China
| | - Xiaole Yu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, PR China
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA.
| | - Xuwu Sun
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, PR China.
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21
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Clúa J, Montpetit J, Jimenez-Sandoval P, Naumann C, Santiago J, Poirier Y. A CYBDOM protein impacts iron homeostasis and primary root growth under phosphate deficiency in Arabidopsis. Nat Commun 2024; 15:423. [PMID: 38212368 PMCID: PMC10784552 DOI: 10.1038/s41467-023-43911-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 11/23/2023] [Indexed: 01/13/2024] Open
Abstract
Arabidopsis primary root growth response to phosphate (Pi) deficiency is mainly controlled by changes in apoplastic iron (Fe). Upon Pi deficiency, apoplastic Fe deposition in the root apical meristem activates pathways leading to the arrest of meristem maintenance and inhibition of cell elongation. Here, we report that a member of the uncharacterized cytochrome b561 and DOMON domain (CYBDOM) protein family, named CRR, promotes iron reduction in an ascorbate-dependent manner and controls apoplastic iron deposition. Under low Pi, the crr mutant shows an enhanced reduction of primary root growth associated with increased apoplastic Fe in the root meristem and a reduction in meristematic cell division. Conversely, CRR overexpression abolishes apoplastic Fe deposition rendering primary root growth insensitive to low Pi. The crr single mutant and crr hyp1 double mutant, harboring a null allele in another member of the CYDOM family, shows increased tolerance to high-Fe stress upon germination and seedling growth. Conversely, CRR overexpression is associated with increased uptake and translocation of Fe to the shoot and results in plants highly sensitive to Fe excess. Our results identify a ferric reductase implicated in Fe homeostasis and developmental responses to abiotic stress, and reveal a biological role for CYBDOM proteins in plants.
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Affiliation(s)
- Joaquín Clúa
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland
| | - Jonatan Montpetit
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland
| | - Pedro Jimenez-Sandoval
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland
| | - Christin Naumann
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany
| | - Julia Santiago
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland
| | - Yves Poirier
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland.
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22
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Konstantinova N, Mor E, Verhelst E, Nolf J, Vereecken K, Wang F, Van Damme D, De Rybel B, Glanc M. A precise balance of TETRASPANIN1/TORNADO2 activity is required for vascular proliferation and ground tissue patterning in Arabidopsis. PHYSIOLOGIA PLANTARUM 2024; 176:e14182. [PMID: 38618986 DOI: 10.1111/ppl.14182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 04/16/2024]
Abstract
The molecular mechanisms guiding oriented cell divisions in the root vascular tissues of Arabidopsis thaliana are still poorly characterised. By overlapping bulk and single-cell transcriptomic datasets, we unveiled TETRASPANIN1 (TET1) as a putative regulator in this process. TET1 is expressed in root vascular cells, and loss-of-function mutants contain fewer vascular cell files. We further generated and characterised a CRISPR deletion mutant and showed, unlike previously described mutants, that the full knock out is additionally missing endodermal cells in a stochastic way. Finally, we show that HA-tagged versions of TET1 are functional in contrast to fluorescent TET1 translational fusions. Immunostaining using HA-TET1 lines complementing the mutant phenotype suggested a dual plasma membrane and intracellular localisation in the root vasculature and a polar membrane localisation in the young cortex, endodermal and initial cells. Taken together, we show that TET1 is involved in both vascular proliferation and ground tissue patterning. Our initial results pave the way for future work to decipher its precise mode of action.
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Affiliation(s)
- Nataliia Konstantinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Eliana Mor
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Eline Verhelst
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Jonah Nolf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Kenzo Vereecken
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Feng Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Daniel Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Matouš Glanc
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
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23
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Liu H, Guo Z, Gangurde SS, Garg V, Deng Q, Du P, Lu Q, Chitikineni A, Xiao Y, Wang W, Hong Y, Varshney RK, Chen X. A Single-Nucleus Resolution Atlas of Transcriptome and Chromatin Accessibility for Peanut (Arachis Hypogaea L.) Leaves. Adv Biol (Weinh) 2024; 8:e2300410. [PMID: 37828417 DOI: 10.1002/adbi.202300410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/02/2023] [Indexed: 10/14/2023]
Abstract
The peanut is an important worldwide cash-crop for edible oil and protein. However, the kinetic mechanisms that determine gene expression and chromatin accessibility during leaf development in peanut represented allotetraploid leguminous crops are poorly understood at single-cell resolution. Here, a single-nucleus atlas of peanut leaves is developed by simultaneously profiling the transcriptome and chromatin accessibility in the same individual-cell using fluorescence-activated sorted single-nuclei. In total, 5930 cells with 50 890 expressed genes are classified into 18 cell-clusters, and 5315 chromatin fragments are enriched with 26 083 target genes in the chromatin accessible landscape. The developmental trajectory analysis reveals the involvement of the ethylene-AP2 module in leaf cell differentiation, and cell-cycle analysis demonstrated that genome replication featured in distinct cell-types with circadian rhythms transcription factors (TFs). Furthermore, dual-omics illustrates that the fatty acid pathway modulates epidermal-guard cells differentiation and providescritical TFs interaction networks for understanding mesophyll development, and the cytokinin module (LHY/LOG) that regulates vascular growth. Additionally, an AT-hook protein AhAHL11 is identified that promotes leaf area expansion by modulating the auxin content increase. In summary, the simultaneous profiling of transcription and chromatin accessibility landscapes using snRNA/ATAC-seq provides novel biological insights into the dynamic processes of peanut leaf cell development at the cellular level.
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Affiliation(s)
- Hao Liu
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, 510640, China
| | - Zenhua Guo
- Rice Research Institute of Heilongjiang Academy of Agriculture Sciences, Heilongjiang Province, Jiamusi, 154026, China
| | - Sunil S Gangurde
- USDA-ARS, Crop Genetics and Breeding Research Unit, Department of Plant Pathology, University of Georgia, Tifton, GA, 31793, USA
| | - Vanika Garg
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University (MU), Murdoch, Western Australia, 6150, Australia
| | - Quanqing Deng
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, 510640, China
| | - Puxuan Du
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, 510640, China
| | - Qing Lu
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, 510640, China
| | - Annapurna Chitikineni
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University (MU), Murdoch, Western Australia, 6150, Australia
| | - Yuan Xiao
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, 510640, China
| | - Wenyi Wang
- College of Agriculture, South China Agriculture University, Guangzhou, Guangdong Province, 510642, China
| | - Yanbin Hong
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, 510640, China
| | - Rajeev K Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University (MU), Murdoch, Western Australia, 6150, Australia
| | - Xiaoping Chen
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, 510640, China
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24
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Li Y, Ma H, Wu Y, Ma Y, Yang J, Li Y, Yue D, Zhang R, Kong J, Lindsey K, Zhang X, Min L. Single-Cell Transcriptome Atlas and Regulatory Dynamics in Developing Cotton Anthers. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2304017. [PMID: 37974530 PMCID: PMC10797427 DOI: 10.1002/advs.202304017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 10/08/2023] [Indexed: 11/19/2023]
Abstract
Plant anthers are composed of different specialized cell types with distinct roles in plant reproduction. High temperature (HT) stress causes male sterility, resulting in crop yield reduction. However, the spatial expression atlas and regulatory dynamics during anther development and in response to HT remain largely unknown. Here, the first single-cell transcriptome atlas and chromatin accessibility survey in cotton anther are established, depicting the specific expression and epigenetic landscape of each type of cell in anthers. The reconstruction of meiotic cells, tapetal cells, and middle layer cell developmental trajectories not only identifies novel expressed genes, but also elucidates the precise degradation period of middle layer and reveals a rapid function transition of tapetal cells during the tetrad stage. By applying HT, heterogeneity in HT response is shown among cells of anthers, with tapetal cells responsible for pollen wall synthesis are most sensitive to HT. Specifically, HT shuts down the chromatin accessibility of genes specifically expressed in the tapetal cells responsible for pollen wall synthesis, such as QUARTET 3 (QRT3) and CYTOCHROME P450 703A2 (CYP703A2), resulting in a silent expression of these genes, ultimately leading to abnormal pollen wall and male sterility. Collectively, this study provides substantial information on anthers and provides clues for heat-tolerant crop creation.
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Affiliation(s)
- Yanlong Li
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubei430070China
| | - Huanhuan Ma
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubei430070China
| | - Yuanlong Wu
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubei430070China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubei430070China
| | - Jing Yang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubei430070China
| | - Yawei Li
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubei430070China
| | - Dandan Yue
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubei430070China
| | - Rui Zhang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubei430070China
| | - Jie Kong
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiang830091China
| | - Keith Lindsey
- Department of BiosciencesDurham UniversityDurham27710UK
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubei430070China
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubei430070China
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25
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Liu X, Roszak P, Helariutta Y. The challenge of defining rare genetic programs by single-cell RNA sequencing: Insights from phloem studies. MOLECULAR PLANT 2024; 17:22-25. [PMID: 38115581 DOI: 10.1016/j.molp.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/21/2023]
Affiliation(s)
- Xiaomin Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; The Sainsbury Laboratory, University of Cambridge, CB2 1TN Cambridge, UK
| | - Pawel Roszak
- The Sainsbury Laboratory, University of Cambridge, CB2 1TN Cambridge, UK; Wood Development Group, University of Helsinki, 00100 Helsinki, Finland; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, 00100 Helsinki, Finland
| | - Ykä Helariutta
- The Sainsbury Laboratory, University of Cambridge, CB2 1TN Cambridge, UK; Wood Development Group, University of Helsinki, 00100 Helsinki, Finland; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, 00100 Helsinki, Finland.
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26
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Göbel M, Fichtner F. Functions of sucrose and trehalose 6-phosphate in controlling plant development. JOURNAL OF PLANT PHYSIOLOGY 2023; 291:154140. [PMID: 38007969 DOI: 10.1016/j.jplph.2023.154140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/28/2023]
Abstract
Plants exhibit enormous plasticity in regulating their architecture to be able to adapt to a constantly changing environment and carry out vital functions such as photosynthesis, anchoring, and nutrient uptake. Phytohormones play a role in regulating these responses, but sugar signalling mechanisms are also crucial. Sucrose is not only an important source of carbon and energy fuelling plant growth, but it also functions as a signalling molecule that influences various developmental processes. Trehalose 6-phosphate (Tre6P), a sucrose-specific signalling metabolite, is emerging as an important regulator in plant metabolism and development. Key players involved in sucrose and Tre6P signalling pathways, including MAX2, SnRK1, bZIP11, and TOR, have been implicated in processes such as flowering, branching, and root growth. We will summarize our current knowledge of how these pathways shape shoot and root architecture and highlight how sucrose and Tre6P signalling are integrated with known signalling networks in shaping plant growth.
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Affiliation(s)
- Moritz Göbel
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Plant Biochemistry, Germany; Cluster of Excellences on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Germany
| | - Franziska Fichtner
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Plant Biochemistry, Germany; Cluster of Excellences on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Germany.
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27
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Han X, Zhang Y, Lou Z, Li J, Wang Z, Gao C, Liu Y, Ren Z, Liu W, Li B, Pan W, Zhang H, Sang Q, Wan M, He H, Deng XW. Time series single-cell transcriptional atlases reveal cell fate differentiation driven by light in Arabidopsis seedlings. NATURE PLANTS 2023; 9:2095-2109. [PMID: 37903986 PMCID: PMC10724060 DOI: 10.1038/s41477-023-01544-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 09/19/2023] [Indexed: 11/01/2023]
Abstract
Light serves as the energy source for plants as well as a signal for growth and development during their whole life cycle. Seedling de-etiolation is the most dramatic manifestation of light-regulated plant development processes, as massive reprogramming of the plant transcriptome occurs at this time. Although several studies have reported about organ-specific development and expression induced by light, a systematic analysis of cell-type-specific differentiation and the associated transcriptional regulation is still lacking. Here we obtained single-cell transcriptional atlases for etiolated, de-etiolating and light-grown Arabidopsis thaliana seedlings. Informative cells from shoot and root tissues were grouped into 48 different cell clusters and finely annotated using multiple markers. With the determination of comprehensive developmental trajectories, we demonstrate light modulation of cell fate determination during guard cell specialization and vasculature development. Comparison of expression atlases between wild type and the pifq mutant indicates that phytochrome-interacting factors (PIFs) are involved in distinct developmental processes in endodermal and stomatal lineage cells via controlling cell-type-specific expression of target genes. These results provide information concerning the light signalling networks at the cell-type resolution, improving our understanding of how light regulates plant development at the cell-type and genome-wide levels. The obtained information could serve as a valuable resource for comprehensively investigating the molecular mechanism of cell development and differentiation in response to light.
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Affiliation(s)
- Xue Han
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China
| | - Yilin Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China
| | - Zhiying Lou
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Jian Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Zheng Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Chunlei Gao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Yi Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China
| | - Zizheng Ren
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Weimin Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Bosheng Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Wenbo Pan
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Huawei Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Qing Sang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Miaomiao Wan
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China
| | - Hang He
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China.
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China.
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China.
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China.
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28
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Sun Y, Yang B, De Rybel B. Hormonal control of the molecular networks guiding vascular tissue development in the primary root meristem of Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6964-6974. [PMID: 37343122 PMCID: PMC7615341 DOI: 10.1093/jxb/erad232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
Vascular tissues serve a dual function in plants, both providing physical support and controlling the transport of nutrients, water, hormones, and other small signaling molecules. Xylem tissues transport water from root to shoot; phloem tissues transfer photosynthates from shoot to root; while divisions of the (pro)cambium increase the number of xylem and phloem cells. Although vascular development constitutes a continuous process from primary growth in the early embryo and meristem regions to secondary growth in the mature plant organs, it can be artificially separated into distinct processes including cell type specification, proliferation, patterning, and differentiation. In this review, we focus on how hormonal signals orchestrate the molecular regulation of vascular development in the Arabidopsis primary root meristem. Although auxin and cytokinin have taken center stage in this aspect since their discovery, other hormones including brassinosteroids, abscisic acid, and jasmonic acid also take leading roles during vascular development. All these hormonal cues synergistically or antagonistically participate in the development of vascular tissues, forming a complex hormonal control network.
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Affiliation(s)
- Yanbiao Sun
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Centre for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Baojun Yang
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Centre for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Bert De Rybel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Centre for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
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29
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Barcenilla BB, Meyers AD, Castillo-González C, Young P, Min JH, Song J, Phadke C, Land E, Canaday E, Perera IY, Bailey SM, Aquilano R, Wyatt SE, Shippen DE. Arabidopsis telomerase takes off by uncoupling enzyme activity from telomere length maintenance in space. Nat Commun 2023; 14:7854. [PMID: 38030615 PMCID: PMC10686995 DOI: 10.1038/s41467-023-41510-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/07/2023] [Indexed: 12/01/2023] Open
Abstract
Spaceflight-induced changes in astronaut telomeres have garnered significant attention in recent years. While plants represent an essential component of future long-duration space travel, the impacts of spaceflight on plant telomeres and telomerase have not been examined. Here we report on the telomere dynamics of Arabidopsis thaliana grown aboard the International Space Station. We observe no changes in telomere length in space-flown Arabidopsis seedlings, despite a dramatic increase in telomerase activity (up to 150-fold in roots), as well as elevated genome oxidation. Ground-based follow up studies provide further evidence that telomerase is induced by different environmental stressors, but its activity is uncoupled from telomere length. Supporting this conclusion, genetically engineered super-telomerase lines with enhanced telomerase activity maintain wildtype telomere length. Finally, genome oxidation is inversely correlated with telomerase activity levels. We propose a redox protective capacity for Arabidopsis telomerase that may promote survivability in harsh environments.
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Affiliation(s)
- Borja Barbero Barcenilla
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Alexander D Meyers
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, 45701, USA
- NASA Postdoctoral Program, Oak Ridge Associated Universities, Kennedy Space Center FL, Merritt Island, FL, 32899, USA
| | - Claudia Castillo-González
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Pierce Young
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Ji-Hee Min
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Jiarui Song
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Chinmay Phadke
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Eric Land
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Emma Canaday
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, 45701, USA
| | - Imara Y Perera
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Susan M Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Roberto Aquilano
- National Technological University, Rosario Regional Faculty, Zeballos 1341, S2000, Rosario, Argentina
| | - Sarah E Wyatt
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA.
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, 45701, USA.
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA.
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30
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Minow MAA, Marand AP, Schmitz RJ. Leveraging Single-Cell Populations to Uncover the Genetic Basis of Complex Traits. Annu Rev Genet 2023; 57:297-319. [PMID: 37562412 PMCID: PMC10775913 DOI: 10.1146/annurev-genet-022123-110824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
The ease and throughput of single-cell genomics have steadily improved, and its current trajectory suggests that surveying single-cell populations will become routine. We discuss the merger of quantitative genetics with single-cell genomics and emphasize how this synergizes with advantages intrinsic to plants. Single-cell population genomics provides increased detection resolution when mapping variants that control molecular traits, including gene expression or chromatin accessibility. Additionally, single-cell population genomics reveals the cell types in which variants act and, when combined with organism-level phenotype measurements, unveils which cellular contexts impact higher-order traits. Emerging technologies, notably multiomics, can facilitate the measurement of both genetic changes and genomic traits in single cells, enabling single-cell genetic experiments. The implementation of single-cell genetics will advance the investigation of the genetic architecture of complex molecular traits and provide new experimental paradigms to study eukaryotic genetics.
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Affiliation(s)
- Mark A A Minow
- Department of Genetics, University of Georgia, Athens, Georgia, USA;
| | | | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, USA;
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31
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Kułak K, Wojciechowska N, Samelak-Czajka A, Jackowiak P, Bagniewska-Zadworna A. How to explore what is hidden? A review of techniques for vascular tissue expression profile analysis. PLANT METHODS 2023; 19:129. [PMID: 37981669 PMCID: PMC10659056 DOI: 10.1186/s13007-023-01109-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/10/2023] [Indexed: 11/21/2023]
Abstract
The evolution of plants to efficiently transport water and assimilates over long distances is a major evolutionary success that facilitated their growth and colonization of land. Vascular tissues, namely xylem and phloem, are characterized by high specialization, cell heterogeneity, and diverse cell components. During differentiation and maturation, these tissues undergo an irreversible sequence of events, leading to complete protoplast degradation in xylem or partial degradation in phloem, enabling their undisturbed conductive function. Due to the unique nature of vascular tissue, and the poorly understood processes involved in xylem and phloem development, studying the molecular basis of tissue differentiation is challenging. In this review, we focus on methods crucial for gene expression research in conductive tissues, emphasizing the importance of initial anatomical analysis and appropriate material selection. We trace the expansion of molecular techniques in vascular gene expression studies and discuss the application of single-cell RNA sequencing, a high-throughput technique that has revolutionized transcriptomic analysis. We explore how single-cell RNA sequencing will enhance our knowledge of gene expression in conductive tissues.
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Affiliation(s)
- Karolina Kułak
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
| | - Natalia Wojciechowska
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Anna Samelak-Czajka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Agnieszka Bagniewska-Zadworna
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
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32
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Su C, Lyu M, Mähönen AP, Helariutta Y, De Rybel B, Muranen S. Cella: 3D data visualization for plant single-cell transcriptomics in Blender. PHYSIOLOGIA PLANTARUM 2023; 175:e14068. [PMID: 38148248 DOI: 10.1111/ppl.14068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/20/2023] [Indexed: 12/28/2023]
Abstract
AIMS Recent advancements in single-cell transcriptomics have facilitated the possibility of acquiring vast amounts of data at single-cell resolution. This development has provided a broader and more comprehensive understanding of complex biological processes. The growing datasets require a visualization tool that transforms complex data into an intuitive representation. To address this challenge, we have utilized an open-source 3D software Blender to design Cella, a cell atlas visualization tool, which transforms data into 3D heatmaps that can be rendered into image libraries. Our tool is designed to support especially research on plant development. DATA RESOURCES GENERATED To validate our method, we have created a 3D model representing the Arabidopsis thaliana root meristem and mapped an existing single-cell RNA-seq dataset into the 3D model. This provided a user-friendly visual representation of the expression profiles of 21,489 genes from two perspectives (42,978 images). UTILITY OF THE RESOURCE This approach is not limited to single-cell RNA-seq data of the Arabidopsis root meristem. We provide detailed step-by-step instructions to generate 3D models and a script that can be customized to project data onto different tissues. KEY RESULTS Our tool provides a proof-of-concept method for how increasingly complex single-cell RNA-seq datasets can be visualized in a simple and cohesive manner.
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Affiliation(s)
- Chang Su
- Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology Research Program, University of Helsinki, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Finland
| | - Munan Lyu
- Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology Research Program, University of Helsinki, Finland
| | - Ari Pekka Mähönen
- Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology Research Program, University of Helsinki, Finland
| | - Ykä Helariutta
- Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology Research Program, University of Helsinki, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Finland
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Sampo Muranen
- Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology Research Program, University of Helsinki, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Finland
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Liu Z, Yang J, Long Y, Zhang C, Wang D, Zhang X, Dong W, Zhao L, Liu C, Zhai J, Wang E. Single-nucleus transcriptomes reveal spatiotemporal symbiotic perception and early response in Medicago. NATURE PLANTS 2023; 9:1734-1748. [PMID: 37749242 DOI: 10.1038/s41477-023-01524-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 08/25/2023] [Indexed: 09/27/2023]
Abstract
Establishing legume-rhizobial symbiosis requires precise coordination of complex responses in a time- and cell type-specific manner. Encountering Rhizobium, rapid changes of gene expression levels in host plants occur in the first few hours, which prepare the plants to turn off defence and form a symbiotic relationship with the microbes. Here, we applied single-nucleus RNA sequencing to characterize the roots of Medicago truncatula at 30 min, 6 h and 24 h after nod factor treatment. We found drastic global gene expression reprogramming at 30 min in the epidermis and cortex and most of these changes were restored at 6 h. Moreover, plant defence response genes are activated at 30 min and subsequently suppressed at 6 h in non-meristem cells. Only in the cortical cells but not in other cell types, we found the flavonoid synthase genes required to recruit rhizobia are highly expressed 30 min after inoculation with nod factors. A gene module enriched for symbiotic nitrogen fixation genes showed that MtFER (MtFERONIA) and LYK3 (LysM domain receptor-like kinase 3) share similar responses to symbiotic signals. We further found that MtFER can be phosphorylated by LYK3 and it participates in rhizobial symbiosis. Our results expand our understanding of dynamic spatiotemporal symbiotic responses at the single-cell level.
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Affiliation(s)
- Zhijian Liu
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Jun Yang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yanping Long
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Chi Zhang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Dapeng Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xiaowei Zhang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Wentao Dong
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Li Zhao
- School of Life Sciences, Division of Life Sciences and Medicine, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China
| | - Chengwu Liu
- School of Life Sciences, Division of Life Sciences and Medicine, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China
| | - Jixian Zhai
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, China.
| | - Ertao Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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34
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Wang X, Mäkilä R, Mähönen AP. From procambium patterning to cambium activation and maintenance in the Arabidopsis root. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102404. [PMID: 37352651 DOI: 10.1016/j.pbi.2023.102404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/08/2023] [Accepted: 05/20/2023] [Indexed: 06/25/2023]
Abstract
In addition to primary growth, which elongates the plant body, many plant species also undergo secondary growth to thicken their body. During primary vascular development, a subset of the vascular cells, called procambium and pericycle, remain undifferentiated to later gain vascular cambium and cork cambium identity, respectively. These two cambia are the lateral meristems providing secondary growth. The vascular cambium produces secondary xylem and phloem, which give plants mechanical support and transport capacity. Cork cambium produces a protective layer called cork. In this review, we focus on recent advances in understanding the formation of procambium and its gradual maturation to active cambium in the Arabidopsis thaliana root.
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Affiliation(s)
- Xin Wang
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Riikka Mäkilä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Ari Pekka Mähönen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
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35
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Oliva M, Lister R. Exploring the identity of individual plant cells in space and time. THE NEW PHYTOLOGIST 2023; 240:61-67. [PMID: 37483019 PMCID: PMC10952157 DOI: 10.1111/nph.19153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/17/2023] [Indexed: 07/25/2023]
Abstract
In recent years, single-cell genomics, coupled to imaging techniques, have become the state-of-the-art approach for characterising biological systems. In plant sciences, a variety of tissues and species have been profiled, providing an enormous quantity of data on cell identity at an unprecedented resolution, but what biological insights can be gained from such data sets? Using recently published studies in plant sciences, we will highlight how single-cell technologies have enabled a better comprehension of tissue organisation, cell fate dynamics in development or in response to various stimuli, as well as identifying key transcriptional regulators of cell identity. We discuss the limitations and technical hurdles to overcome, as well as future directions, and the promising use of single-cell omics to understand, predict, and manipulate plant development and physiology.
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Affiliation(s)
- Marina Oliva
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular SciencesUniversity of Western AustraliaPerthWA6009Australia
| | - Ryan Lister
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular SciencesUniversity of Western AustraliaPerthWA6009Australia
- The Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical ResearchThe University of Western AustraliaPerthWA6009Australia
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36
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Zhang J, Ahmad M, Gao H. Application of single-cell multi-omics approaches in horticulture research. MOLECULAR HORTICULTURE 2023; 3:18. [PMID: 37789394 PMCID: PMC10521458 DOI: 10.1186/s43897-023-00067-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/15/2023] [Indexed: 10/05/2023]
Abstract
Cell heterogeneity shapes the morphology and function of various tissues and organs in multicellular organisms. Elucidation of the differences among cells and the mechanism of intercellular regulation is essential for an in-depth understanding of the developmental process. In recent years, the rapid development of high-throughput single-cell transcriptome sequencing technologies has influenced the study of plant developmental biology. Additionally, the accuracy and sensitivity of tools used to study the epigenome and metabolome have significantly increased, thus enabling multi-omics analysis at single-cell resolution. Here, we summarize the currently available single-cell multi-omics approaches and their recent applications in plant research, review the single-cell based studies in fruit, vegetable, and ornamental crops, and discuss the potential of such approaches in future horticulture research.
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Affiliation(s)
- Jun Zhang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mayra Ahmad
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongbo Gao
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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37
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Jia Z, Giehl RFH, Hartmann A, Estevez JM, Bennett MJ, von Wirén N. A spatially concerted epidermal auxin signaling framework steers the root hair foraging response under low nitrogen. Curr Biol 2023; 33:3926-3941.e5. [PMID: 37699396 DOI: 10.1016/j.cub.2023.08.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/08/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023]
Abstract
As a major determinant of the nutrient-acquiring root surface, root hairs (RHs) provide a low-input strategy to enhance nutrient uptake. Although primary and lateral roots exhibit elongation responses under mild nitrogen (N) deficiency, the foraging response of RHs and underlying regulatory mechanisms remain elusive. Employing transcriptomics and functional studies revealed a framework of molecular components composing a cascade of auxin synthesis, transport, and signaling that triggers RH elongation for N acquisition. Through upregulation of Tryptophan Aminotransferase of Arabidopsis 1 (TAA1) and YUCCA8, low N increases auxin accumulation in the root apex. Auxin is then directed to the RH differentiation zone via the auxin transport machinery, AUXIN TRANSPORTER PROTEIN 1 (AUX1) and PIN-FORMED 2 (PIN2). Upon arrival to the RH zone, auxin activates the transcription factors AUXIN RESPONSE FACTOR 6 and 8 (ARF6/8) to promote the epidermal and auxin-inducible transcriptional module ROOT HAIR DEFECTIVE 6 (RHD6)-LOTUS JAPONICA ROOT HAIRLESS-LIKE 3 (LRL3) to steer RH elongation in response to low N. Our study uncovers a spatially defined regulatory signaling cascade for N foraging by RHs, expanding the mechanistic framework of hormone-regulated nutrient sensing in plant roots.
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Affiliation(s)
- Zhongtao Jia
- Molecular Plant Nutrition, Department of Physiology & Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany; State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
| | - Ricardo F H Giehl
- Molecular Plant Nutrition, Department of Physiology & Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
| | - Anja Hartmann
- Molecular Plant Nutrition, Department of Physiology & Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
| | - Jose M Estevez
- ANID - Millennium Science Initiative Program - Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile; Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Malcolm J Bennett
- Future Food Beacon and School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Nicolaus von Wirén
- Molecular Plant Nutrition, Department of Physiology & Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany.
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38
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Zhu X, Xu Z, Wang G, Cong Y, Yu L, Jia R, Qin Y, Zhang G, Li B, Yuan D, Tu L, Yang X, Lindsey K, Zhang X, Jin S. Single-cell resolution analysis reveals the preparation for reprogramming the fate of stem cell niche in cotton lateral meristem. Genome Biol 2023; 24:194. [PMID: 37626404 PMCID: PMC10463415 DOI: 10.1186/s13059-023-03032-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Somatic embryogenesis is a major process for plant regeneration. However, cell communication and the gene regulatory network responsible for cell reprogramming during somatic embryogenesis are still largely unclear. Recent advances in single-cell technologies enable us to explore the mechanism of plant regeneration at single-cell resolution. RESULTS We generate a high-resolution single-cell transcriptomic landscape of hypocotyl tissue from the highly regenerable cotton genotype Jin668 and the recalcitrant TM-1. We identify nine putative cell clusters and 23 cluster-specific marker genes for both cultivars. We find that the primary vascular cell is the major cell type that undergoes cell fate transition in response to external stimulation. Further developmental trajectory and gene regulatory network analysis of these cell clusters reveals that a total of 41 hormone response-related genes, including LAX2, LAX1, and LOX3, exhibit different expression patterns in the primary xylem and cambium region of Jin668 and TM-1. We also identify novel genes, including CSEF, PIS1, AFB2, ATHB2, PLC2, and PLT3, that are involved in regeneration. We demonstrate that LAX2, LAX1 and LOX3 play important roles in callus proliferation and plant regeneration by CRISPR/Cas9 editing and overexpression assay. CONCLUSIONS This study provides novel insights on the role of the regulatory network in cell fate transition and reprogramming during plant regeneration driven by somatic embryogenesis.
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Affiliation(s)
- Xiangqian Zhu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhongping Xu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Guanying Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yulong Cong
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Lu Yu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ruoyu Jia
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yuan Qin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Guangyu Zhang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Bo Li
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Wulumuqi, 830000, Xinjiang, China
| | - Daojun Yuan
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Lili Tu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xiyan Yang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Xianlong Zhang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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39
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Fehér A. A Common Molecular Signature Indicates the Pre-Meristematic State of Plant Calli. Int J Mol Sci 2023; 24:13122. [PMID: 37685925 PMCID: PMC10488067 DOI: 10.3390/ijms241713122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
In response to different degrees of mechanical injury, certain plant cells re-enter the division cycle to provide cells for tissue replenishment, tissue rejoining, de novo organ formation, and/or wound healing. The intermediate tissue formed by the dividing cells is called a callus. Callus formation can also be induced artificially in vitro by wounding and/or hormone (auxin and cytokinin) treatments. The callus tissue can be maintained in culture, providing starting material for de novo organ or embryo regeneration and thus serving as the basis for many plant biotechnology applications. Due to the biotechnological importance of callus cultures and the scientific interest in the developmental flexibility of somatic plant cells, the initial molecular steps of callus formation have been studied in detail. It was revealed that callus initiation can follow various ways, depending on the organ from which it develops and the inducer, but they converge on a seemingly identical tissue. It is not known, however, if callus is indeed a special tissue with a defined gene expression signature, whether it is a malformed meristem, or a mass of so-called "undifferentiated" cells, as is mostly believed. In this paper, I review the various mechanisms of plant regeneration that may converge on callus initiation. I discuss the role of plant hormones in the detour of callus formation from normal development. Finally, I compare various Arabidopsis gene expression datasets obtained a few days, two weeks, or several years after callus induction and identify 21 genes, including genes of key transcription factors controlling cell division and differentiation in meristematic regions, which were upregulated in all investigated callus samples. I summarize the information available on all 21 genes that point to the pre-meristematic nature of callus tissues underlying their wide regeneration potential.
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Affiliation(s)
- Attila Fehér
- Institute of Plant Biology, Biological Research Centre, 62 Temesvári Körút, 6726 Szeged, Hungary; or
- Department of Plant Biology, University of Szeged, 52 Közép Fasor, 6726 Szeged, Hungary
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40
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Chen C, Ge Y, Lu L. Opportunities and challenges in the application of single-cell and spatial transcriptomics in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1185377. [PMID: 37636094 PMCID: PMC10453814 DOI: 10.3389/fpls.2023.1185377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023]
Abstract
Single-cell and spatial transcriptomics have diverted researchers' attention from the multicellular level to the single-cell level and spatial information. Single-cell transcriptomes provide insights into the transcriptome at the single-cell level, whereas spatial transcriptomes help preserve spatial information. Although these two omics technologies are helpful and mature, further research is needed to ensure their widespread applicability in plant studies. Reviewing recent research on plant single-cell or spatial transcriptomics, we compared the different experimental methods used in various plants. The limitations and challenges are clear for both single-cell and spatial transcriptomic analyses, such as the lack of applicability, spatial information, or high resolution. Subsequently, we put forth further applications, such as cross-species analysis of roots at the single-cell level and the idea that single-cell transcriptome analysis needs to be combined with other omics analyses to achieve superiority over individual omics analyses. Overall, the results of this review suggest that combining single-cell transcriptomics, spatial transcriptomics, and spatial element distribution can provide a promising research direction, particularly for plant research.
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Affiliation(s)
- Ce Chen
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yining Ge
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Lingli Lu
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Agricultural Resource and Environment of Zhejiang Province, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
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41
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Zhu J, Moreno-Pérez A, Coaker G. Understanding plant pathogen interactions using spatial and single-cell technologies. Commun Biol 2023; 6:814. [PMID: 37542114 PMCID: PMC10403533 DOI: 10.1038/s42003-023-05156-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/18/2023] [Indexed: 08/06/2023] Open
Abstract
Plants are in contact with diverse pathogens and microorganisms. Intense investigation over the last 30 years has resulted in the identification of multiple immune receptors in model and crop species as well as signaling overlap in surface-localized and intracellular immune receptors. However, scientists still have a limited understanding of how plants respond to diverse pathogens with spatial and cellular resolution. Recent advancements in single-cell, single-nucleus and spatial technologies can now be applied to plant-pathogen interactions. Here, we outline the current state of these technologies and highlight outstanding biological questions that can be addressed in the future.
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Affiliation(s)
- Jie Zhu
- Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Alba Moreno-Pérez
- Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA.
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42
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Cheng Z, Mu C, Li X, Cheng W, Cai M, Wu C, Jiang J, Fang H, Bai Y, Zheng H, Geng R, Xu J, Xie Y, Dou Y, Li J, Mu S, Gao J. Single-cell transcriptome atlas reveals spatiotemporal developmental trajectories in the basal roots of moso bamboo ( Phyllostachys edulis). HORTICULTURE RESEARCH 2023; 10:uhad122. [PMID: 37554343 PMCID: PMC10405134 DOI: 10.1093/hr/uhad122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 06/01/2023] [Indexed: 08/10/2023]
Abstract
Roots are essential for plant growth and development. Bamboo is a large Poaceae perennial with 1642 species worldwide. However, little is known about the transcriptional atlas that underpins root cell-type differentiation. Here, we set up a modified protocol for protoplast preparation and report single-cell transcriptomes of 14 279 filtered single cells derived from the basal root tips of moso bamboo. We identified four cell types and defined new cell-type-specific marker genes for the basal root. We reconstructed the developmental trajectories of the root cap, epidermis, and ground tissues and elucidated critical factors regulating cell fate determination. According to in situ hybridization and pseudotime trajectory analysis, the root cap and epidermis originated from a common initial cell lineage, revealing the particularity of bamboo basal root development. We further identified key regulatory factors for the differentiation of these cells and indicated divergent root developmental pathways between moso bamboo and rice. Additionally, PheWOX13a and PheWOX13b ectopically expressed in Arabidopsis inhibited primary root and lateral root growth and regulated the growth and development of the root cap, which was different from WOX13 orthologs in Arabidopsis. Taken together, our results offer an important resource for investigating the mechanism of root cell differentiation and root system architecture in perennial woody species of Bambusoideae.
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Affiliation(s)
- Zhanchao Cheng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Changhong Mu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Xiangyu Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Wenlong Cheng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Miaomiao Cai
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Chongyang Wu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Jutang Jiang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Hui Fang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Yucong Bai
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Huifang Zheng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Ruiman Geng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Junlei Xu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Yali Xie
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Yuping Dou
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Juan Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Shaohua Mu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Jian Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
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43
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Tariq A, Ullah I, Sardans J, Graciano C, Mussarat S, Ullah A, Zeng F, Wang W, Al-Bakre DA, Ahmed Z, Ali S, Zhang Z, Yaseen A, Peñuelas J. Strigolactones can be a potential tool to fight environmental stresses in arid lands. ENVIRONMENTAL RESEARCH 2023; 229:115966. [PMID: 37100368 DOI: 10.1016/j.envres.2023.115966] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/01/2023] [Accepted: 04/19/2023] [Indexed: 05/21/2023]
Abstract
BACKGROUND Environmental stresses pose a significant threat to plant growth and ecosystem productivity, particularly in arid lands that are more susceptible to climate change. Strigolactones (SLs), carotenoid-derived plant hormones, have emerged as a potential tool for mitigating environmental stresses. METHODS This review aimed to gather information on SLs' role in enhancing plant tolerance to ecological stresses and their possible use in improving the resistance mechanisms of arid land plant species to intense aridity in the face of climate change. RESULTS Roots exude SLs under different environmental stresses, including macronutrient deficiency, especially phosphorus (P), which facilitates a symbiotic association with arbuscular mycorrhiza fungi (AMF). SLs, in association with AMF, improve root system architecture, nutrient acquisition, water uptake, stomatal conductance, antioxidant mechanisms, morphological traits, and overall stress tolerance in plants. Transcriptomic analysis revealed that SL-mediated acclimatization to abiotic stresses involves multiple hormonal pathways, including abscisic acid (ABA), cytokinins (CK), gibberellic acid (GA), and auxin. However, most of the experiments have been conducted on crops, and little attention has been paid to the dominant vegetation in arid lands that plays a crucial role in reducing soil erosion, desertification, and land degradation. All the environmental gradients (nutrient starvation, drought, salinity, and temperature) that trigger SL biosynthesis/exudation prevail in arid regions. The above-mentioned functions of SLs can potentially be used to improve vegetation restoration and sustainable agriculture. CONCLUSIONS Present review concluded that knowledge on SL-mediated tolerance in plants is developed, but still in-depth research is needed on downstream signaling components in plants, SL molecular mechanisms and physiological interactions, efficient methods of synthetic SLs production, and their effective application in field conditions. This review also invites researchers to explore the possible application of SLs in improving the survival rate of indigenous vegetation in arid lands, which can potentially help combat land degradation problems.
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Affiliation(s)
- Akash Tariq
- Xinjiang Key Desert Plant Roots Ecology and Vegetation Restoration Laboratory, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China.
| | - Ihteram Ullah
- Department of Plant Breeding & Genetics, Gomal University, Dera Ismail Khan, Pakistan
| | - Jordi Sardans
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Bellaterra, 08193, Barcelona, Catalonia, Spain; CREAF, Cerdanyola Del Vallès, 08193, Catalonia, Spain
| | - Corina Graciano
- Instituto de Fisiología Vegetal, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Sakina Mussarat
- Department of Botanical and Environmental Sciences, Faculty of Biological Sciences, Kohat University of Science and Technology, Kohat, Pakistan
| | - Abd Ullah
- Xinjiang Key Desert Plant Roots Ecology and Vegetation Restoration Laboratory, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China
| | - Fanjiang Zeng
- Xinjiang Key Desert Plant Roots Ecology and Vegetation Restoration Laboratory, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China.
| | - Weiqi Wang
- Key Laboratory of Humid Subtropical Eco-Geographical Process, Ministry of Education, Fujian Normal University, Fuzhou, 350007, China; Institute of Geography, Fujian Normal University, Fuzhou, 350007, China
| | - Dhafer A Al-Bakre
- Department of Biology, College of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Zeeshan Ahmed
- Xinjiang Key Desert Plant Roots Ecology and Vegetation Restoration Laboratory, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China
| | - Sikandar Ali
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Zhihao Zhang
- Xinjiang Key Desert Plant Roots Ecology and Vegetation Restoration Laboratory, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China
| | - Aftab Yaseen
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Josep Peñuelas
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Bellaterra, 08193, Barcelona, Catalonia, Spain; CREAF, Cerdanyola Del Vallès, 08193, Catalonia, Spain
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44
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Nobori T, Oliva M, Lister R, Ecker JR. Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap. NATURE PLANTS 2023; 9:1026-1033. [PMID: 37308583 PMCID: PMC10356616 DOI: 10.1038/s41477-023-01439-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 05/11/2023] [Indexed: 06/14/2023]
Abstract
Retrieving the complex responses of individual cells in the native three-dimensional tissue context is crucial for a complete understanding of tissue functions. Here, we present PHYTOMap (plant hybridization-based targeted observation of gene expression map), a multiplexed fluorescence in situ hybridization method that enables single-cell and spatial analysis of gene expression in whole-mount plant tissue in a transgene-free manner and at low cost. We applied PHYTOMap to simultaneously analyse 28 cell-type marker genes in Arabidopsis roots and successfully identified major cell types, demonstrating that our method can substantially accelerate the spatial mapping of marker genes defined in single-cell RNA-sequencing datasets in complex plant tissue.
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Affiliation(s)
- Tatsuya Nobori
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Marina Oliva
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Ryan Lister
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Joseph R Ecker
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA.
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45
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Nguyen TH, Thiers L, Van Moerkercke A, Bai Y, Fernández-Calvo P, Minne M, Depuydt T, Colinas M, Verstaen K, Van Isterdael G, Nützmann HW, Osbourn A, Saeys Y, De Rybel B, Vandepoele K, Ritter A, Goossens A. A redundant transcription factor network steers spatiotemporal Arabidopsis triterpene synthesis. NATURE PLANTS 2023; 9:926-937. [PMID: 37188853 DOI: 10.1038/s41477-023-01419-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023]
Abstract
Plant specialized metabolites modulate developmental and ecological functions and comprise many therapeutic and other high-value compounds. However, the mechanisms determining their cell-specific expression remain unknown. Here we describe the transcriptional regulatory network that underlies cell-specific biosynthesis of triterpenes in Arabidopsis thaliana root tips. Expression of thalianol and marneral biosynthesis pathway genes depends on the phytohormone jasmonate and is limited to outer tissues. We show that this is promoted by the activity of redundant bHLH-type transcription factors from two distinct clades and coactivated by homeodomain factors. Conversely, the DOF-type transcription factor DAG1 and other regulators prevent expression of the triterpene pathway genes in inner tissues. We thus show how precise expression of triterpene biosynthesis genes is determined by a robust network of transactivators, coactivators and counteracting repressors.
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Affiliation(s)
- Trang Hieu Nguyen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Louis Thiers
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Alex Van Moerkercke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Yuechen Bai
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Patricia Fernández-Calvo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Misión Biolóxica de Galicia, CSIC, Pontevedra, Spain
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Madrid, Spain
| | - Max Minne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Thomas Depuydt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Maite Colinas
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Kevin Verstaen
- VIB Single Cell Core, Ghent-Leuven, Belgium
- VIB Center for Inflammation Research, Data Mining and Modelling for Biomedicine, Ghent, Belgium
| | - Gert Van Isterdael
- VIB Flow Core, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Hans-Wilhelm Nützmann
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, UK
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, UK
| | - Anne Osbourn
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, UK
| | - Yvan Saeys
- VIB Center for Inflammation Research, Data Mining and Modelling for Biomedicine, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Andrés Ritter
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
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46
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Blanco-Touriñán N, Torres-Martínez HH, Augstein F, Champeyroux C, von der Mark C, Carlsbecker A, Dubrovsky JG, Rodriguez-Villalón A. The primary root procambium contributes to lateral root formation through its impact on xylem connection. Curr Biol 2023; 33:1716-1727.e3. [PMID: 37071995 DOI: 10.1016/j.cub.2023.03.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/21/2023] [Accepted: 03/21/2023] [Indexed: 04/20/2023]
Abstract
The postembryonic formation of lateral roots (LRs) starts in internal root tissue, the pericycle. An important question of LR development is how the connection of the primary root vasculature with that of the emerging LR is established and whether the pericycle and/or other cell types direct this process. Here, using clonal analysis and time-lapse experiments, we show that both the procambium and pericycle of the primary root (PR) affect the LR vascular connectivity in a coordinated manner. We show that during LR formation, procambial derivates switch their identity and become precursors of xylem cells. These cells, together with the pericycle-origin xylem, participate in the formation of what we call a "xylem bridge" (XB), which establishes the xylem connection between the PR and the nascent LR. If the parental protoxylem cell fails to differentiate, XB is still sometimes formed but via a connection with metaxylem cells, highlighting that this process has some plasticity. Using mutant analyses, we show that the early specification of XB cells is determined by CLASS III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIP III) transcription factors (TFs). Subsequent XB cell differentiation is marked by the deposition of secondary cell walls (SCWs) in spiral and reticulate/scalariform patterns, which is dependent on the VASCULAR-RELATED NAC-DOMAIN (VND) TFs. XB elements were also observed in Solanum lycopersicum, suggesting that this mechanism may be more widely conserved in plants. Together, our results suggest that plants maintain vascular procambium activity, which safeguards the functionality of newly established lateral organs by assuring the continuity of the xylem strands throughout the root system.
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Affiliation(s)
- Noel Blanco-Touriñán
- Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, 8092 Zurich, Switzerland.
| | - Héctor H Torres-Martínez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Frauke Augstein
- Department of Organismal Biology, Physiological Botany, Linnean Centre for Plant Biology, Uppsala University, Ullsv. 24E, 756 51 Uppsala, Sweden
| | - Chloé Champeyroux
- Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, 8092 Zurich, Switzerland
| | - Claudia von der Mark
- Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, 8092 Zurich, Switzerland
| | - Annelie Carlsbecker
- Department of Organismal Biology, Physiological Botany, Linnean Centre for Plant Biology, Uppsala University, Ullsv. 24E, 756 51 Uppsala, Sweden
| | - Joseph G Dubrovsky
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 2001, Cuernavaca 62250, Mexico.
| | - Antia Rodriguez-Villalón
- Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, 8092 Zurich, Switzerland.
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47
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Zhang L, He C, Lai Y, Wang Y, Kang L, Liu A, Lan C, Su H, Gao Y, Li Z, Yang F, Li Q, Mao H, Chen D, Chen W, Kaufmann K, Yan W. Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis. Genome Biol 2023; 24:65. [PMID: 37016448 PMCID: PMC10074895 DOI: 10.1186/s13059-023-02908-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/23/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Homoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs. Homoeolog expression bias, referring to the relative contribution of homoeologs to the transcriptome, is critical for determining the traits that influence wheat growth and development. Asymmetric transcription of homoeologs has been so far investigated in a tissue or organ-specific manner, which could be misleading due to a mixture of cell types. RESULTS Here, we perform single nuclei RNA sequencing and ATAC sequencing of wheat root to study the asymmetric gene transcription, reconstruct cell differentiation trajectories and cell-type-specific gene regulatory networks. We identify 22 cell types. We then reconstruct cell differentiation trajectories that suggest different origins between epidermis/cortex and endodermis, distinguishing bread wheat from Arabidopsis. We show that the ratio of asymmetrically transcribed triads varies greatly when analyzing at the single-cell level. Hub transcription factors determining cell type identity are also identified. In particular, we demonstrate that TaSPL14 participates in vasculature development by regulating the expression of BAM1. Combining single-cell transcription and chromatin accessibility data, we construct the pseudo-time regulatory network driving root hair differentiation. We find MYB3R4, REF6, HDG1, and GATAs as key regulators in this process. CONCLUSIONS Our findings reveal the transcriptional landscape of root organization and asymmetric gene transcription at single-cell resolution in polyploid wheat.
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Affiliation(s)
- Lihua Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuting Lai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yating Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lu Kang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ankui Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Handong Su
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuwen Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zeqing Li
- Wuhan Igenebook Biotechnology Co., Ltd, Wuhan, 430014, China
| | - Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität Zu Berlin, 10115, Berlin, Germany
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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48
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Sun Y, Han Y, Sheng K, Yang P, Cao Y, Li H, Zhu QH, Chen J, Zhu S, Zhao T. Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii. MOLECULAR PLANT 2023; 16:694-708. [PMID: 36772793 DOI: 10.1016/j.molp.2023.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/31/2022] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Comprehensive utilization of cottonseeds is limited by the presence of pigment glands and its inclusion gossypol. The ideal cotton has glandless seeds but a glanded plant, a trait found in only a few Australian wild cotton species, including Gossypium bickii. Introgression of this trait into cultivated species has proved to be difficult. Understanding the biological processes toward pigment gland morphogenesis and the associated underlying molecular mechanisms will facilitate breeding of cultivated cotton varieties with the trait of glandless seeds and glanded plant. In this study, single-cell RNA sequencing (scRNA-seq) was performed on 12 222 protoplasts isolated from cotyledons of germinating G. bickii seeds 48 h after imbibition. Clustered into 14 distinct clusters unsupervisedly, these cells could be grouped into eight cell populations with the assistance of known cell marker genes. The pigment gland cells were well separated from others and could be separated into pigment gland parenchyma cells, secretory cells, and apoptotic cells. By integrating the pigment gland cell developmental trajectory, transcription factor regulatory networks, and core transcription factor functional validation, we established a model for pigment gland formation. In this model, light and gibberellin were verified to promote the formation of pigment glands. In addition, three novel genes, GbiERF114 (ETHYLENE RESPONSE FACTOR 114), GbiZAT11 (ZINC FINGER OF ARABIDOPSIS THALIANA 11), and GbiNTL9 (NAC TRANSCRIPTION FACTOR-LIKE 9), were found to affect pigment gland formation. Collectively, these findings provide new insights into pigment gland morphogenesis and lay the cornerstone for future cotton scRNA-seq investigations.
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Affiliation(s)
- Yue Sun
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yifei Han
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Kuang Sheng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ping Yang
- Agricultural Experiment Station, Zhejiang University, Hangzhou 310058, China
| | - Yuefen Cao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Huazu Li
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Jinhong Chen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Institute of Hainan, Zhejiang University, Hangzhou 310058, China
| | - Shuijin Zhu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Institute of Hainan, Zhejiang University, Hangzhou 310058, China.
| | - Tianlun Zhao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Institute of Hainan, Zhejiang University, Hangzhou 310058, China.
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49
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Li C, Zhang S, Yan X, Cheng P, Yu H. Single-nucleus sequencing deciphers developmental trajectories in rice pistils. Dev Cell 2023; 58:694-708.e4. [PMID: 37028425 DOI: 10.1016/j.devcel.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 01/25/2023] [Accepted: 03/07/2023] [Indexed: 04/08/2023]
Abstract
Angiosperms possess a life cycle with an alternation of sporophyte and gametophyte generations, which happens in plant organs like pistils. Rice pistils contain ovules and receive pollen for successful fertilization to produce grains. The cellular expression profile in rice pistils is largely unknown. Here, we show a cell census of rice pistils before fertilization through the use of droplet-based single-nucleus RNA sequencing. The ab initio marker identification validated by in situ hybridization assists with cell-type annotation, revealing cell heterogeneity between ovule- and carpel-originated cells. A comparison of 1N (gametophyte) and 2N (sporophyte) nuclei identifies the developmental path of germ cells in ovules with typical resetting of pluripotency before the sporophyte-gametophyte transition, while trajectory analysis of carpel-originated cells suggests previously neglected features of epidermis specification and style function. These findings gain a systems-level view of cellular differentiation and development of rice pistils before flowering and lay a foundation for understanding female reproductive development in plants.
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Affiliation(s)
- Chengxiang Li
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore
| | - Songyao Zhang
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore
| | - Xingying Yan
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore; Biotechnology Research Center, Southwest University, Chongqing 400716, China
| | - Peng Cheng
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore
| | - Hao Yu
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore.
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50
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Lu H, Wang F, Wang Y, Lin R, Wang Z, Mao C. Molecular mechanisms and genetic improvement of low-phosphorus tolerance in rice. PLANT, CELL & ENVIRONMENT 2023; 46:1104-1119. [PMID: 36208118 DOI: 10.1111/pce.14457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/01/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Phosphorus (P) is a macronutrient required for plant growth and reproduction. Orthophosphate (Pi), the preferred P form for plant uptake, is easily fixed in the soil, making it unavailable to plants. Limited phosphate rock resources, low phosphate fertilizer use efficiency and high demands for green agriculture production make it important to clarify the molecular mechanisms underlying plant responses to P deficiency and to improve plant phosphate efficiency in crops. Over the past 20 years, tremendous progress has been made in understanding the regulatory mechanisms of the plant P starvation response. Here, we systematically review current research on the mechanisms of Pi acquisition, transport and distribution from the rhizosphere to the shoot; Pi redistribution and reuse during reproductive growth; and the molecular mechanisms of arbuscular mycorrhizal symbiosis in rice (Oryza sativa L.) under Pi deficiency. Furthermore, we discuss several strategies for boosting P utilization efficiency and yield in rice.
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Affiliation(s)
- Hong Lu
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya, Hainan, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Fei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yan Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Rongbin Lin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhiye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chuanzao Mao
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya, Hainan, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
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