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Lu Y, Fricke W. Salt Stress-Regulation of Root Water Uptake in a Whole-Plant and Diurnal Context. Int J Mol Sci 2023; 24:ijms24098070. [PMID: 37175779 PMCID: PMC10179082 DOI: 10.3390/ijms24098070] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
This review focuses on the regulation of root water uptake in plants which are exposed to salt stress. Root water uptake is not considered in isolation but is viewed in the context of other potential tolerance mechanisms of plants-tolerance mechanisms which relate to water relations and gas exchange. Plants spend between one third and half of their lives in the dark, and salt stress does not stop with sunset, nor does it start with sunrise. Surprisingly, how plants deal with salt stress during the dark has received hardly any attention, yet any growth response to salt stress over days, weeks, months and years is the integrative result of how plants perform during numerous, consecutive day/night cycles. As we will show, dealing with salt stress during the night is a prerequisite to coping with salt stress during the day. We hope to highlight with this review not so much what we know, but what we do not know; and this relates often to some rather basic questions.
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Affiliation(s)
- Yingying Lu
- School of Biology and Environmental Science, University College Dublin (UCD), Belfield, D04 N2E5 Dublin, Ireland
| | - Wieland Fricke
- School of Biology and Environmental Science, University College Dublin (UCD), Belfield, D04 N2E5 Dublin, Ireland
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2
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Duan Y, Lei T, Li W, Jiang M, Zhao Z, Yu X, Li Y, Yang L, Li J, Gao S. Enhanced Na + and Cl - sequestration and secretion selectivity contribute to high salt tolerance in the tetraploid recretohalophyte Plumbago auriculata Lam. PLANTA 2023; 257:52. [PMID: 36757459 DOI: 10.1007/s00425-023-04082-7] [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: 08/29/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Enhanced secretion of Na+ and Cl- in leaf glands and leaf vacuolar sequestration of Na+ or root retention of Cl-, combined with K+ retention, contribute to the improved salt tolerance of tetraploid recretohalophyte P. auriculata. Salt stress is one of the major abiotic factors threatening plant growth and development, and polyploids generally exhibit higher salt stress resistance than diploids. In recretohalophytes, which secrete ions from the salt gland in leaf epidermal cells, the effects of polyploidization on ion homeostasis and secretion remain unknown. In this study, we compared the morphology, physiology, and ion homeostasis regulation of diploid and autotetraploid accessions of the recretohalophyte Plumbago auriculata Lam. after treatment with 300 mM NaCl for 0, 2, 4, 6, and 8 days. The results showed that salt stress altered the morphology, photosynthetic efficiency, and chloroplast structure of diploid P. auriculata to a greater extent than those of its tetraploid counterpart. Moreover, the contents of organic osmoregulatory substances (proline and soluble sugars) were significantly higher in the tetraploid than in the diploid, while those of H2O2 and malondialdehyde (MDA) were significantly lower. Analysis of ion homeostasis revealed that the tetraploid cytotype accumulated more Na+ in stems and leaves and more Cl- in roots but less K+ loss in roots compared with diploid P. auriculata. Additionally, the rate of Na+ and Cl- secretion from the leaf surface was higher, while that of K+, Mg2+, and Ca2+ secretion was lower in tetraploid plants. X-ray microanalysis of mesophyll cells revealed that Na+ mainly accumulated in different cellular compartments in the tetraploid (vacuole) and diploid (cytoplasm) plants. Our results suggest that polyploid recretohalophytes require the ability to sequester Na+ and Cl-(via accumulation in leaf cell vacuoles or unloading by roots) and selectively secrete these ions (through salt glands) together with the ability to prevent K+ loss (by roots). This mechanism required to maintain K+/Na+ homeostasis in polyploid recretohalophytes under high salinity provides new insights in the improved maintenance of ion homeostasis in polyploids under salt stress.
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Affiliation(s)
- Yifan Duan
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ting Lei
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wenji Li
- Chongqing Industry Polytechnic College, Chongqing, 401120, China
| | - Mingyan Jiang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zi'an Zhao
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaofang Yu
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yirui Li
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lijuan Yang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiani Li
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Suping Gao
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China.
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Alle J, Gruber R, Wörlein N, Uhlmann N, Claußen J, Wittenberg T, Gerth S. 3D segmentation of plant root systems using spatial pyramid pooling and locally adaptive field-of-view inference. FRONTIERS IN PLANT SCIENCE 2023; 14:1120189. [PMID: 37082341 PMCID: PMC10110838 DOI: 10.3389/fpls.2023.1120189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/13/2023] [Indexed: 05/03/2023]
Abstract
Background The non-invasive 3D-imaging and successive 3D-segmentation of plant root systems has gained interest within fundamental plant research and selectively breeding resilient crops. Currently the state of the art consists of computed tomography (CT) scans and reconstruction followed by an adequate 3D-segmentation process. Challenge Generating an exact 3D-segmentation of the roots becomes challenging due to inhomogeneous soil composition, as well as high scale variance in the root structures themselves. Approach (1) We address the challenge by combining deep convolutional neural networks (DCNNs) with a weakly supervised learning paradigm. Furthermore, (2) we apply a spatial pyramid pooling (SPP) layer to cope with the scale variance of roots. (3) We generate a fine-tuned training data set with a specialized sub-labeling technique. (4) Finally, to yield fast and high-quality segmentations, we propose a specialized iterative inference algorithm, which locally adapts the field of view (FoV) for the network. Experiments We compare our segmentation results against an analytical reference algorithm for root segmentation (RootForce) on a set of roots from Cassava plants and show qualitatively that an increased amount of root voxels and root branches can be segmented. Results Our findings show that with the proposed DCNN approach combined with the dynamic inference, much more, and especially fine, root structures can be detected than with a classical analytical reference method. Conclusion We show that the application of the proposed DCNN approach leads to better and more robust root segmentation, especially for very small and thin roots.
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Affiliation(s)
- Jonas Alle
- Fraunhofer Institut für Integrierte Schaltungen (IIS), Fraunhofer Institute for Integrated Circuits Institut für Integrierte Schaltungen (IIS), Division Development Center X-Ray Technology, Fürth, Germany
| | - Roland Gruber
- Fraunhofer Institut für Integrierte Schaltungen (IIS), Fraunhofer Institute for Integrated Circuits Institut für Integrierte Schaltungen (IIS), Division Development Center X-Ray Technology, Fürth, Germany
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Chair for Visual Computing, Erlangen, Germany
| | - Norbert Wörlein
- Fraunhofer Institut für Integrierte Schaltungen (IIS), Fraunhofer Institute for Integrated Circuits Institut für Integrierte Schaltungen (IIS), Division Development Center X-Ray Technology, Fürth, Germany
| | - Norman Uhlmann
- Fraunhofer Institut für Integrierte Schaltungen (IIS), Fraunhofer Institute for Integrated Circuits Institut für Integrierte Schaltungen (IIS), Division Development Center X-Ray Technology, Fürth, Germany
| | - Joelle Claußen
- Fraunhofer Institut für Integrierte Schaltungen (IIS), Fraunhofer Institute for Integrated Circuits Institut für Integrierte Schaltungen (IIS), Division Development Center X-Ray Technology, Fürth, Germany
| | - Thomas Wittenberg
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Chair for Visual Computing, Erlangen, Germany
- Fraunhofer Institut für Integrierte Schaltungen (IIS), Fraunhofer Institute for Integrated Circuits Institut für Integrierte Schaltungen (IIS), Division Smart Sensors and Electronics, Erlangen, Germany
| | - Stefan Gerth
- Fraunhofer Institut für Integrierte Schaltungen (IIS), Fraunhofer Institute for Integrated Circuits Institut für Integrierte Schaltungen (IIS), Division Development Center X-Ray Technology, Fürth, Germany
- *Correspondence: Stefan Gerth,
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Geng L, Li Q, Jiao L, Xiang Y, Deng Q, Zhou DX, Zhao Y. WOX11 and CRL1 act synergistically to promote crown root development by maintaining cytokinin homeostasis in rice. THE NEW PHYTOLOGIST 2023; 237:204-216. [PMID: 36208055 DOI: 10.1111/nph.18522] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Crown root (CR) morphogenesis is critical for normal growth and nutrition absorption in cereals. In rice, WUSCHEL-RELATED HOMEOBOX11 (WOX11) and CROWN ROOTLESS1 (CRL1) play vital roles in controlling CR development. Despite their importance, whether and how the two regulators coordinate CR formation remains unclear. Electrophoretic mobility shift assays, transient expression, and chromatin immunoprecipitation qPCR suggested that WOX11 and CRL1 directly bind to OsCKX4 to regulate its expression during CR development. CRL1 enhances OsCKX4 activation through direct interaction with WOX11 at root emergence and elongation stages. Genetic dissection showed that the wox11/crl1 double mutant exhibits a more severe root phenotype. OsCKX4 knockout plants generated by CRISPR/Cas9 exhibited fewer CRs and higher cytokinin levels in the root meristem. Increased expression of OsCKX4 could partially complement the CR phenotypes of both crl1 and wox11 mutants. Furthermore, cytokinin can promote WOX11 protein accumulation in the root meristem. Together, these findings show that cytokinin accumulation is tightly regulated by the WOX11-CRL1 complex during CR elongation by counteracting the negative regulatory effects of cytokinin on root development. Importantly, these results reveal an intrinsic link between WOX11 protein accumulation and cytokinin to maintain CR growth.
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Affiliation(s)
- Leping Geng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qi Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lele Jiao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yimeng Xiang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiyu Deng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Institute of Plant Science Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, Orsay, 91405, France
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
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Comparative Analysis of Physiological, Hormonal and Transcriptomic Responses Reveal Mechanisms of Saline-Alkali Tolerance in Autotetraploid Rice ( Oryza sativa L.). Int J Mol Sci 2022; 23:ijms232416146. [PMID: 36555786 PMCID: PMC9783840 DOI: 10.3390/ijms232416146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/09/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Saline-alkali soil has posed challenges to the growth of agricultural crops, while polyploidy often show greater adaptability in diverse and extreme environments including saline-alkali stress, but its defense mechanisms in rice remain elusive. Herein, we explored the mechanisms of enhanced saline-alkali tolerance of autotetraploid rice 93-11T relative to diploid rice 93-11D, based on physiological, hormonal and transcriptomic profilings. Physiologically, the enhanced saline-alkali tolerance in 93-11T was manifested in higher soluble sugar accumulation and stronger superoxide dismutase (SOD) and peroxidase (POD) activities in leaves during 24 h after saline-alkali shock. Furthermore, various hormone levels in leaves of 93-11T altered greatly, such as the negative correlation between salicylic acid (SA) and the other four hormones changed to positive correlation due to polyploidy. Global transcriptome profiling revealed that the upregulated differentially expressed genes (DEGs) in leaves and roots of 93-11T were more abundant than that in 93-11D, and there were more DEGs in roots than in leaves under saline-alkali stress. Genes related to phytohormone signal transduction of auxin (AUX) and SA in roots, lignin biosynthesis in leaves or roots, and wax biosynthesis in leaves were obviously upregulated in 93-11T compared with 93-11D under saline-alkali condition. Collectively, 93-11T subjected to saline-alkali stress possibly possesses higher osmotic regulation ability due to cuticular wax synthesis, stronger negative regulation of reactive oxygen species (ROS) production by increasing the SA levels and maintaining relative lower levels of IAA, and higher antioxidant capacity by increasing activities of SOD and POD, as well as lignin biosynthesis. Our research provides new insights for exploring the mechanisms of saline-alkali tolerance in polyploid rice and discovering new gene targets for rice genetic improvement.
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Bai J, Xie Y, Shi M, Yao S, Lu W, Xiao K. TaMPK2B, a member of the MAPK family in T. aestivum, enhances plant low-Pi stress tolerance through modulating physiological processes associated with phosphorus starvation defensiveness. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111375. [PMID: 35820548 DOI: 10.1016/j.plantsci.2022.111375] [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: 03/01/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
The mitogen-activated protein kinase (MAPK) cascades are present in plant species and modulate plant growth and stress responses. This study characterizes TaMPK2B, a MAPK family gene in T. aestivum that regulates plant adaptation to low-Pi stress. TaMPK2B harbors the conserved domains involving protein phosphorylation and protein-protein interaction. A yeast two-hybrid assay reveals an interaction between TaMPK2B and TaMPKK2 and between the latter and TaMPKKK;A, suggesting that all comprise a MAPK signaling cascade TaMPKKK;A-TaMPKK2-TaMPK2B. TaMPK2B expression levels were elevated in roots and leaves under a Pi starvation (PS) condition. Additionally, the induced TaMPK2B transcripts under PS in tissues were gradually restored following the Pi normal recovery condition. TaMPK2B overexpression conferred on plants improved PS adaptation; the tobacco lines with TaMPK2B overexpression enhanced the plant's dry mass production, Pi uptake capacity, root system architecture (RSA) establishment, and ROS homeostasis relative to wild type under PS treatment. Moreover, the transcripts of genes in phosphate transporter (PT), PIN-FORMED, and antioxidant enzyme (AE) families, including NtPT3 and NtPT4, NtPIN9, and NtMnSOD1 and NtPOD1;7, were elevated in Pi-deprived lines overexpressing TaMPK2B. Transgene analyses validated their functions in regulating Pi uptake, RSA establishment, and AE activities of plants treated by PS. These results suggest that TaMPK2B-mediated plant PS adaptation is correlated with the modified transcription of distinct PT, PIN, and AE genes. Our investigation suggests that TaMPK2B is one of the crucial regulators in plant low-Pi adaptation by improving Pi uptake, RSA formation, and ROS homeostasis via transcriptionally regulating genes associated with the above physiological processes.
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Affiliation(s)
- Jinghua Bai
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding 071001, PR China; College of Life Sciences, Hebei Agricultural University, Baoding 071001, PR China
| | - Yameng Xie
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding 071001, PR China; College of Life Sciences, Hebei Agricultural University, Baoding 071001, PR China
| | - Meihua Shi
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding 071001, PR China; College of Life Sciences, Hebei Agricultural University, Baoding 071001, PR China
| | - Sufei Yao
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding 071001, PR China; College of Life Sciences, Hebei Agricultural University, Baoding 071001, PR China
| | - Wenjing Lu
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding 071001, PR China; College of Life Sciences, Hebei Agricultural University, Baoding 071001, PR China.
| | - Kai Xiao
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding 071001, PR China; College of Agronomy, Hebei Agricultural University, Baoding 071001, PR China.
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7
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Li S, Li Q, Tian X, Mu L, Ji M, Wang X, Li N, Liu F, Shu J, Crawford NM, Wang Y. PHB3 regulates lateral root primordia formation via NO-mediated degradation of AUXIN/INDOLE-3-ACETIC ACID proteins. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4034-4045. [PMID: 35303089 DOI: 10.1093/jxb/erac115] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/16/2022] [Indexed: 05/21/2023]
Abstract
We have previously shown that Arabidopsis thaliana Prohibitin 3 (PHB3) controls auxin-stimulated lateral root (LR) formation; however, the underlying molecular mechanism is unknown. Here, we demonstrate that PHB3 regulates lateral root (LR) development mainly through influencing lateral root primordia (LRP) initiation, via affecting nitric oxide (NO) accumulation. The reduced LRP in phb3 mutant was largely rescued by treatment with a NO donor. The decreased NO accumulation in phb3 caused a lower expression of GATA TRANSCRIPTION FACTOR 23 (GATA23) and LATERAL ORGAN BOUNDARIES DOMAIN 16 (LBD16) through inhibiting the degradation of INDOLE-3-ACETIC ACID INDUCIBLE 14/28 (IAA14/28). Overexpression of either GATA23 or LBD16 in phb3 mutant background recovered the reduced density of LRP. These results indicate that PHB3 regulates LRP initiation via NO-mediated auxin signalling, by modulating the degradation of IAA14/28.
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Affiliation(s)
- Shuna Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Qingqing Li
- College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
| | - Xiao Tian
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Lijun Mu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Meiling Ji
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Xiaoping Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Na Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Fei Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Jing Shu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
- College of Agriculture Science and Technology, Shandong Agriculture and Engineering University, Jinan Shandong, China
| | - Nigel M Crawford
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, USA
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
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Cai B, Wang T, Sun H, Liu C, Chu J, Ren Z, Li Q. Gibberellins regulate lateral root development that is associated with auxin and cell wall metabolisms in cucumber. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 317:110995. [PMID: 35193752 DOI: 10.1016/j.plantsci.2021.110995] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/05/2021] [Accepted: 07/17/2021] [Indexed: 06/14/2023]
Abstract
Cucumber is an economically important crop cultivated worldwide. Gibberellins (GAs) play important roles in the development of lateral roots (LRs), which are critical for plant stress tolerance and productivity. Therefore, it is of great importance for cucumber production to study the role of GAs in LR development. Here, the results showed that GAs regulated cucumber LR development in a concentration-dependent manner. Treatment with 1, 10, 50 and 100 μM GA3 significantly increased secondary root length, tertiary root number and length. Of these, 50 μM GA3 treatment had strong effects on increasing root dry weight and the root/shoot dry weight ratio. Pairwise comparisons identified 417 down-regulated genes enriched for GA metabolism-related processes and 447 up-regulated genes enriched for cell wall metabolism-related processes in GA3-treated roots. A total of 3523 non-redundant DEGs were identified in our RNA-Seq data through pairwise comparisons and linear factorial modeling. Of these, most of the genes involved in auxin and cell wall metabolisms were up-regulated in GA3-treated roots. Our findings not only shed light on LR regulation mediated by GA but also offer an important resource for functional studies of candidate genes putatively involved in the regulation of LR development in cucumber and other crops.
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Affiliation(s)
- Bingbing Cai
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071001, China.
| | - Ting Wang
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China.
| | - Hong Sun
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China.
| | - Cuimei Liu
- National Centre for Plant Gene Research (Beijing), Innovation Academy for Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Innovation Academy for Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China.
| | - Zhonghai Ren
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huang-Huai Region, Ministry of Agriculture, Tai'an, Shandong, 271018, China.
| | - Qiang Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071001, China.
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9
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Daryani P, Darzi Ramandi H, Dezhsetan S, Mirdar Mansuri R, Hosseini Salekdeh G, Shobbar ZS. Pinpointing genomic regions associated with root system architecture in rice through an integrative meta-analysis approach. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:81-106. [PMID: 34623472 DOI: 10.1007/s00122-021-03953-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Applying an integrated meta-analysis approach led to identification of meta-QTLs/ candidate genes associated with rice root system architecture, which can be used in MQTL-assisted breeding/ genetic engineering of root traits. Root system architecture (RSA) is an important factor for facilitating water and nutrient uptake from deep soils and adaptation to drought stress conditions. In the present research, an integrated meta-analysis approach was employed to find candidate genes and genomic regions involved in rice RSA traits. A whole-genome meta-analysis was performed for 425 initial QTLs reported in 34 independent experiments controlling RSA traits under control and drought stress conditions in the previous twenty years. Sixty-four consensus meta-QTLs (MQTLs) were detected, unevenly distributed on twelve rice chromosomes. The confidence interval (CI) of the identified MQTLs was obtained as 0.11-14.23 cM with an average of 3.79 cM, which was 3.88 times narrower than the mean CI of the original QTLs. Interestingly, 52 MQTLs were co-located with SNP peak positions reported in rice genome-wide association studies (GWAS) for root morphological traits. The genes located in these RSA-related MQTLs were detected and explored to find the drought-responsive genes in the rice root based on the RNA-seq and microarray data. Multiple RSA and drought tolerance-associated genes were found in the MQTLs including the genes involved in auxin biosynthesis or signaling (e.g. YUCCA, WOX, AUX/IAA, ARF), root angle (DRO1-related genes), lateral root development (e.g. DSR, WRKY), root diameter (e.g. OsNAC5), plant cell wall (e.g. EXPA), and lignification (e.g. C4H, PAL, PRX and CAD). The genes located within both the SNP peak positions and the QTL-overview peaks for RSA are suggested as novel candidate genes for further functional analysis. The promising candidate genes and MQTLs can be used as basis for genetic engineering and MQTL-assisted breeding of root phenotypes to improve yield potential, stability and performance in a water-stressed environment.
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Affiliation(s)
- Parisa Daryani
- Department of Agronomy & Plant Breeding, University of Mohaghegh Ardabili, Ardabil, Iran
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), 31535-1897, Karaj, Iran
| | - Hadi Darzi Ramandi
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Sara Dezhsetan
- Department of Agronomy & Plant Breeding, University of Mohaghegh Ardabili, Ardabil, Iran.
| | - Raheleh Mirdar Mansuri
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), 31535-1897, Karaj, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), 31535-1897, Karaj, Iran
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), 31535-1897, Karaj, Iran.
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10
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Preliminary Application of Ground-Penetrating Radar for Reconstruction of Root System Architecture in Moso Bamboo. REMOTE SENSING 2021. [DOI: 10.3390/rs13142816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Root system architecture (RSA) refers to the geometric features and topology of the root system. Ground-penetrating radar (GPR) is a possible method of RSA reconstruction. However, because the topology of the root system is not directly accessible by GPR, GPR-based reconstruction must be complemented by manual connection of root points, resulting in limited accuracy. In this study, we used both GPR and direct excavation to obtain 3D coordinates (XYZ coordinates) and diameters of moso bamboo rhizomes on an orthogonal grid. A score function for selecting the best-connected root points was developed using rhizome diameter, depth, extension angle, and measured line spacing, which was then used to recover the topology of discrete root points. Based on the recovered topology, the 3D RSA of the rhizomes was reconstructed using a smoothing function. Based on the excavation data, the reconstructed RSA was generally consistent with the measured RSA, with 78.13% of root points correctly connected. The reconstructed RSA based on GPR data thus provided a rough approximation of the measured RSA, with errors arising due to missing root points and rhizome displacement. The proposed algorithm for reconstructing 3D RSA further enriches the application of ground-penetrating radar to root detection.
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Kumar V, Singh D, Majee A, Singh S, Asif MH, Sane AP, Sane VA. Identification of tomato root growth regulatory genes and transcription factors through comparative transcriptomic profiling of different tissues. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1173-1189. [PMID: 34177143 PMCID: PMC8212336 DOI: 10.1007/s12298-021-01015-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 05/07/2021] [Accepted: 05/27/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Tomato is an economically important vegetable crop and a model for development and stress response studies. Although studied extensively for understanding fruit ripening and pathogen responses, its role as a model for root development remains less explored. In this study, an Illumina-based comparative differential transcriptomic analysis of tomato root with different aerial tissues was carried out to identify genes that are predominantly expressed during root growth. Sequential comparisons revealed ~ 15,000 commonly expressed genes and ~ 3000 genes of several classes that were mainly expressed or regulated in roots. These included 1069 transcription factors (TFs) of which 100 were differentially regulated. Prominent amongst these were members of families encoding Zn finger, MYB, ARM, bHLH, AP2/ERF, WRKY and NAC proteins. A large number of kinases, phosphatases and F-box proteins were also expressed in the root transcriptome. The major hormones regulating root growth were represented by the auxin, ethylene, JA, ABA and GA pathways with root-specific expression of certain components. Genes encoding carbon metabolism and photosynthetic components showed reduced expression while several protease inhibitors were amongst the most highly expressed. Overall, the study sheds light on genes governing root growth in tomato and provides a resource for manipulation of root growth for plant improvement. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01015-0.
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Affiliation(s)
- Vinod Kumar
- Plant Gene Expression Lab, Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Deepika Singh
- Plant Gene Expression Lab, Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001 India
- Integral University, Lucknow, 226026 India
| | - Adity Majee
- Plant Gene Expression Lab, Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Shikha Singh
- Plant Gene Expression Lab, Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001 India
| | - Mehar Hasan Asif
- Plant Gene Expression Lab, Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Aniruddha P. Sane
- Plant Gene Expression Lab, Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Vidhu A. Sane
- Plant Gene Expression Lab, Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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12
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Gerth S, Claußen J, Eggert A, Wörlein N, Waininger M, Wittenberg T, Uhlmann N. Semiautomated 3D Root Segmentation and Evaluation Based on X-Ray CT Imagery. PLANT PHENOMICS (WASHINGTON, D.C.) 2021; 2021:8747930. [PMID: 33644765 PMCID: PMC7903318 DOI: 10.34133/2021/8747930] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 12/11/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Computed X-ray tomography (CTX) is a high-end nondestructive approach for the visual assessment of root architecture in soil. Nevertheless, in order to evaluate high-resolution CTX data of root architectures, manual segmentation of the depicted root systems from large-scale volume data is currently necessary, which is both time consuming and error prone. The duration of such a segmentation is of importance, especially for time-resolved growth analysis, where several instances of a plant need to be segmented and evaluated. Specifically, in our application, the contrast between soil and root data varies due to different growth stages and watering situations at the time of scanning. Additionally, the root system itself is expanding in length and in the diameter of individual roots. OBJECTIVE For semiautomated and robust root system segmentation from CTX data, we propose the RootForce approach, which is an extension of Frangi's "multi-scale vesselness" method and integrates a 3D local variance. It allows a precise delineation of roots with diameters down to several μm in pots with varying diameters. Additionally, RootForce is not limited to the segmentation of small below-ground organs, but is also able to handle storage roots with a diameter larger than 40 voxels. RESULTS Using CTX volume data of full-grown bean plants as well as time-resolved (3D + time) growth studies of cassava plants, RootForce produces similar (and much faster) results compared to manual segmentation of the regarded root architectures. Furthermore, RootForce enables the user to obtain traits not possible to be calculated before, such as total root volume (V root), total root length (L root), root volume over depth, root growth angles (θ min, θ mean, and θ max), root surrounding soil density D soil, or form fraction F. Discussion. The proposed RootForce tool can provide a higher efficiency for the semiautomatic high-throughput assessment of the root architectures of different types of plants from large-scale CTX. Furthermore, for all datasets within a growth experiment, only a single set of parameters is needed. Thus, the proposed tool can be used for a wide range of growth experiments in the field of plant phenotyping.
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Affiliation(s)
- Stefan Gerth
- Development Center X-Ray Technology (EZRT), Fraunhofer Institute for Integrated Systems (IIS), Flugplatzstraße 75, 90768 Fürth, Germany
| | - Joelle Claußen
- Development Center X-Ray Technology (EZRT), Fraunhofer Institute for Integrated Systems (IIS), Flugplatzstraße 75, 90768 Fürth, Germany
| | - Anja Eggert
- Development Center X-Ray Technology (EZRT), Fraunhofer Institute for Integrated Systems (IIS), Flugplatzstraße 75, 90768 Fürth, Germany
| | - Norbert Wörlein
- Development Center X-Ray Technology (EZRT), Fraunhofer Institute for Integrated Systems (IIS), Flugplatzstraße 75, 90768 Fürth, Germany
| | - Michael Waininger
- Development Center X-Ray Technology (EZRT), Fraunhofer Institute for Integrated Systems (IIS), Flugplatzstraße 75, 90768 Fürth, Germany
| | - Thomas Wittenberg
- Development Center X-Ray Technology (EZRT), Fraunhofer Institute for Integrated Systems (IIS), Flugplatzstraße 75, 90768 Fürth, Germany
- Biomedical Engineering Department, Fraunhofer Institute for Integrated Systems (IIS), Am Wolfsmantel 33 11, 91058 Erlangen, Germany
| | - Norman Uhlmann
- Development Center X-Ray Technology (EZRT), Fraunhofer Institute for Integrated Systems (IIS), Flugplatzstraße 75, 90768 Fürth, Germany
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Villaécija-Aguilar JA, Struk S, Goormachtig S, Gutjahr C. Bioassays for the Effects of Strigolactones and Other Small Molecules on Root and Root Hair Development. Methods Mol Biol 2021; 2309:129-142. [PMID: 34028684 DOI: 10.1007/978-1-0716-1429-7_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Growth and development of plant roots are highly dynamic and adaptable to environmental conditions. They are under the control of several plant hormone signaling pathways, and therefore root developmental responses can be used as bioassays to study the action of plant hormones and other small molecules. In this chapter, we present different procedures to measure root traits of the model plant Arabidopsis thaliana. We explain methods for phenotypic analysis of lateral root development, primary root length, root skewing and straightness, and root hair density and length. We describe optimal growth conditions for Arabidopsis seedlings for reproducible root and root hair developmental outputs; and how to acquire images and measure the different traits using image analysis with relatively low-tech equipment. We provide guidelines for a semiautomatic image analysis of primary root length, root skewing, and root straightness in Fiji and a script to automate the calculation of root angle deviation from the vertical and root straightness. By including mutants defective in strigolactone (SL) or KAI2 ligand (KL) synthesis and/or signaling, these methods can be used as bioassays for different SLs or SL-like molecules. In addition, the techniques described here can be used for studying seedling root system architecture, root skewing, and root hair development in any context.
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Affiliation(s)
| | - Sylwia Struk
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent,, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent,, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Caroline Gutjahr
- Plant Genetics, TUM School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany.
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Echeverria A, Larrainzar E, Li W, Watanabe Y, Sato M, Tran CD, Moler JA, Hirai MY, Sawada Y, Tran LSP, Gonzalez EM. Medicago sativa and Medicago truncatula Show Contrasting Root Metabolic Responses to Drought. FRONTIERS IN PLANT SCIENCE 2021; 12:652143. [PMID: 33968107 PMCID: PMC8097159 DOI: 10.3389/fpls.2021.652143] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/19/2021] [Indexed: 05/16/2023]
Abstract
Drought is an environmental stressor that affects crop yield worldwide. Understanding plant physiological responses to stress conditions is needed to secure food in future climate conditions. In this study, we applied a combination of plant physiology and metabolomic techniques to understand plant responses to progressive water deficit focusing on the root system. We chose two legume plants with contrasting tolerance to drought, the widely cultivated alfalfa Medicago sativa (Ms) and the model legume Medicago truncatula (Mt) for comparative analysis. Ms taproot (tapR) and Mt fibrous root (fibR) biomass increased during drought, while a progressive decline in water content was observed in both species. Metabolomic analysis allowed the identification of key metabolites in the different tissues tested. Under drought, carbohydrates, abscisic acid, and proline predominantly accumulated in leaves and tapRs, whereas flavonoids increased in fibRs in both species. Raffinose-family related metabolites accumulated during drought. Along with an accumulation of root sucrose in plants subjected to drought, both species showed a decrease in sucrose synthase (SUS) activity related to a reduction in the transcript level of SUS1, the main SUS gene. This study highlights the relevance of root carbon metabolism during drought conditions and provides evidence on the specific accumulation of metabolites throughout the root system.
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Affiliation(s)
- Andres Echeverria
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra, Pamplona, Spain
| | - Estíbaliz Larrainzar
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra, Pamplona, Spain
| | - Weiqiang Li
- State Key Laboratory of Cotton Biology, Department of Biology, Institute of Plant Stress Biology, Henan University, Kaifeng, China
- Henan Joint International Laboratory for Crop Multi-Omics Research, Henan University, Kaifeng, China
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yasuko Watanabe
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Muneo Sato
- Metabolic System Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Cuong Duy Tran
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
| | - Jose A. Moler
- Department of Statistics, Computing and Mathematics, Public University of Navarra, Pamplona, Spain
| | - Masami Yokota Hirai
- Metabolic System Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yuji Sawada
- Metabolic System Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Lam-Son Phan Tran
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
- Lam-Son Phan Tran,
| | - Esther M. Gonzalez
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra, Pamplona, Spain
- *Correspondence: Esther M. Gonzalez,
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15
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Zhang C, Li X, Wang Z, Zhang Z, Wu Z. Identifying key regulatory genes of maize root growth and development by RNA sequencing. Genomics 2020; 112:5157-5169. [PMID: 32961281 DOI: 10.1016/j.ygeno.2020.09.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 09/08/2020] [Accepted: 09/14/2020] [Indexed: 01/31/2023]
Abstract
Root system architecture (RSA), the spatio-temporal configuration of roots, plays vital roles in maize (Zea mays L.) development and productivity. We sequenced the maize root transcriptome of four key growth and development stages: the 6th leaf stage, the 12th leaf stage, the tasseling stage and the milk-ripe stage. Differentially expressed genes (DEGs) were detected. 81 DEGs involved in plant hormone signal transduction pathway and 26 transcription factor (TF) genes were screened. These DEGs and TFs were predicted to be potential candidate genes during maize root growth and development. Several of these genes are homologous to well-known genes regulating root architecture or development in Arabidopsis or rice, such as, Zm00001d005892 (AtERF109), Zm00001d027925 (AtERF73/HRE1), Zm00001d047017 (AtMYC2, OsMYC2), Zm00001d039245 (AtWRKY6). Identification of these key genes will provide a further understanding of the molecular mechanisms responsible for maize root growth and development, it will be beneficial to increase maize production and improve stress resistance by altering RSA traits in modern breeding.
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Affiliation(s)
- Chun Zhang
- Beijing Agriculture Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xianglong Li
- Beijing Agriculture Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Zuoping Wang
- Beijing Agriculture Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Zhongbao Zhang
- Beijing Agriculture Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Zhongyi Wu
- Beijing Agriculture Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
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16
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Waidmann S, Sarkel E, Kleine-Vehn J. Same same, but different: growth responses of primary and lateral roots. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2397-2411. [PMID: 31956903 PMCID: PMC7178446 DOI: 10.1093/jxb/eraa027] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/15/2020] [Indexed: 05/20/2023]
Abstract
The root system architecture describes the shape and spatial arrangement of roots within the soil. Its spatial distribution depends on growth and branching rates as well as directional organ growth. The embryonic primary root gives rise to lateral (secondary) roots, and the ratio of both root types changes over the life span of a plant. Most studies have focused on the growth of primary roots and the development of lateral root primordia. Comparably less is known about the growth regulation of secondary root organs. Here, we review similarities and differences between primary and lateral root organ growth, and emphasize particularly how external stimuli and internal signals differentially integrate root system growth.
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Affiliation(s)
- Sascha Waidmann
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Elizabeth Sarkel
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Jürgen Kleine-Vehn
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
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17
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At-Hook Motif Nuclear Localised Protein 18 as a Novel Modulator of Root System Architecture. Int J Mol Sci 2020; 21:ijms21051886. [PMID: 32164240 PMCID: PMC7084884 DOI: 10.3390/ijms21051886] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/03/2020] [Accepted: 03/06/2020] [Indexed: 01/10/2023] Open
Abstract
The At-Hook Motif Nuclear Localized Protein (AHL) gene family encodes embryophyte-specific nuclear proteins with DNA binding activity. They modulate gene expression and affect various developmental processes in plants. We identify AHL18 (At3G60870) as a developmental modulator of root system architecture and growth. AHL18 is involved in regulation of the length of the proliferation domain and number of dividing cells in the root apical meristem and thereby, cell production. Both primary root growth and lateral root development respond according to AHL18 transcription level. The ahl18 knock-out plants show reduced root systems due to a shorter primary root and a lower number of lateral roots. This change results from a higher number of arrested and non-developing lateral root primordia (LRP) rather than from a decreased LRP initiation. The over-expression of AHL18 results in a more extensive root system, longer primary roots, and increased density of lateral root initiation events. AHL18 is thus involved in the formation of lateral roots at both LRP initiation and their later development. We conclude that AHL18 participates in modulation of root system architecture through regulation of root apical meristem activity, lateral root initiation and emergence; these correspond well with expression pattern of AHL18.
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18
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Pan J, Li Z, Wang Q, Yang L, Yao F, Liu W. An S-domain receptor-like kinase, OsESG1, regulates early crown root development and drought resistance in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110318. [PMID: 31779898 DOI: 10.1016/j.plantsci.2019.110318] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/15/2019] [Indexed: 05/19/2023]
Abstract
Plant receptor-like kinase (RLKs) are serine/threonine protein kinases that play fundamental roles in development, innate immunity, and abiotic stress response. Here, we identified an S-domain receptor-like kinase OsESG1 from rice (Oryza sativa), and identified its involvement in early crown root (CR) development and drought response. The OsESG1 kinase domain possessed auto-phosphorylation activity and was able to phosphorylate MBP and His proteins. OsESG1 was expressed ubiquitously in all tissues that were examined, with relatively higher expression in the embryo. And it could be induced to express by treating with PEG, NaCl and ABA. Transgenic plants carrying anti-sense (AS) OsESG1 were generated by knockdown of OsESG1 expression. At the early seedling stage, AS lines had fewer CRs and shorter shoot compared with wild type (WT) plants. IAA flux and the genes' expressions of the auxin responsive and efflux carrier were infected in the AS lines. These results indicated that auxin signaling and polar auxin transport (PAT) were disrupted. The AS lines were more sensitive to osmotic stress compared to WT, and showed excessive accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA), lower activities of antioxidant enzymes, and impaired expressions of stress-related genes under PEG treatment. Results above suggested that OsESG1 may regulate CR initiation and development by controlling auxin response and distribution, and participate in stress response by regulating the activities of antioxidants and expressions of stress-regulated genes.
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Affiliation(s)
- Jiaowen Pan
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan 250100, Shandong, China
| | - Zhen Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan 250100, Shandong, China
| | - Qingguo Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan 250100, Shandong, China
| | - Lianqun Yang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan 250100, Shandong, China
| | - Fangyin Yao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan 250100, Shandong, China.
| | - Wei Liu
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan 250100, Shandong, China.
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19
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Chen J, Li H, Yang K, Wang Y, Yang L, Hu L, Liu R, Shi Z. Melatonin facilitates lateral root development by coordinating PAO-derived hydrogen peroxide and Rboh-derived superoxide radical. Free Radic Biol Med 2019; 143:534-544. [PMID: 31520769 DOI: 10.1016/j.freeradbiomed.2019.09.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/10/2019] [Accepted: 09/10/2019] [Indexed: 10/26/2022]
Abstract
Melatonin, a phytochemical, can regulate lateral root (LR) formation, but the downstream signaling of melatonin remains elusive. Here we investigated the roles of hydrogen peroxide (H2O2) and superoxide radical (O2•‾) in melatonin-promoted LR formation in tomato (Solanum lycopersicum) roots by using physiological, histochemical, bioinformatic, and biochemical approaches. The increase in endogenous melatonin level stimulated reactive oxygen species (ROS)-dependent development of lateral root primordia (LRP) and LR. Melatonin promoted LRP/LR formation and modulated the expression of cell cycle genes (SlCDKA1, SlCYCD3;1, and SlKRP2) by stimulating polyamine oxidase (PAO)-dependent H2O2 production and respiratory burst oxidase homologue (Rboh)-dependent O2•‾ production, respectively. Screening of SlPAOs and SlRbohs gene family combined with gene expression analysis suggested that melatonin-promoted LR formation was correlated to the upregulation of SlPAO1, SlRboh3, and SlRboh4 in LR-emerging zone. Transient expression analysis confirmed that SlPAO1 was able to produce H2O2 while SlRboh3 and SlRboh4 were capable of producing O2•‾. Melatonin-ROS signaling cassette was also found in the regulation of LR formation in rice root and lateral hyphal branching in fungi. These results suggested that SlPAO1-H2O2 and SlRboh3/4-O2•‾ acted as downstream of melatonin to regulate the expression of cell cycle genes, resulting in LRP initiation and LR development. Such findings uncover one of the regulatory pathways for melatonin-regulated LR formation, which extends our knowledge for melatonin-regulated plant intrinsic physiology.
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Affiliation(s)
- Jian Chen
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Hui Li
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Kang Yang
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Yongzhu Wang
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Lifei Yang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Liangbin Hu
- Department of Food Science, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Ruixian Liu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Zhiqi Shi
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
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20
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Cejas CM, Hough LA, Beaufret R, Castaing JC, Frétigny C, Dreyfus R. Preferential Root Tropisms in 2D Wet Granular Media with Structural Inhomogeneities. Sci Rep 2019; 9:14195. [PMID: 31578384 PMCID: PMC6775086 DOI: 10.1038/s41598-019-50653-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 09/17/2019] [Indexed: 11/23/2022] Open
Abstract
We investigate certain aspects of the physical mechanisms of root growth in a granular medium and how these roots adapt to changes in water distribution induced by the presence of structural inhomogeneities in the form of solid intrusions. Physical intrusions such as a square rod added into the 2D granular medium maintain robust capillary action, pumping water from the more saturated areas at the bottom of the cell towards the less saturated areas near the top of the cell while the rest of the medium is slowly devoid of water via evaporation. The intrusion induces "preferential tropism" of roots by first generating a humidity gradient that attracts the root to grow towards it. Then it guides the roots and permits them to grow deeper into more saturated regions in the soil. This further allows more efficient access to available water in the deeper sections of the medium thereby resulting to increased plant lifetime.
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Affiliation(s)
- Cesare M Cejas
- Complex Assemblies of Soft Matter, CNRS-Solvay-UPenn UMI 3254, Bristol, PA, 19007-3624, USA.
- Microfluidics, MEMS, Nanostructures Laboratory, CNRS Chimie Biologie Innovation (CBI) UMR 8231, Institut Pierre Gilles de Gennes (IPGG), ESPCI Paris, PSL Research University, 6 rue Jean Calvin, Paris, 75005, France.
| | - Lawrence A Hough
- Complex Assemblies of Soft Matter, CNRS-Solvay-UPenn UMI 3254, Bristol, PA, 19007-3624, USA
| | - Raphaël Beaufret
- Complex Assemblies of Soft Matter, CNRS-Solvay-UPenn UMI 3254, Bristol, PA, 19007-3624, USA
| | | | - Christian Frétigny
- Sciences et Ingénierie de la Matière Molle (SIMM) CNRS UMR 7615 ESPCI, 10 rue Vauquelin, Paris, 75005, France
| | - Rémi Dreyfus
- Complex Assemblies of Soft Matter, CNRS-Solvay-UPenn UMI 3254, Bristol, PA, 19007-3624, USA
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Yoshida S, Kim S, Wafula EK, Tanskanen J, Kim YM, Honaas L, Yang Z, Spallek T, Conn CE, Ichihashi Y, Cheong K, Cui S, Der JP, Gundlach H, Jiao Y, Hori C, Ishida JK, Kasahara H, Kiba T, Kim MS, Koo N, Laohavisit A, Lee YH, Lumba S, McCourt P, Mortimer JC, Mutuku JM, Nomura T, Sasaki-Sekimoto Y, Seto Y, Wang Y, Wakatake T, Sakakibara H, Demura T, Yamaguchi S, Yoneyama K, Manabe RI, Nelson DC, Schulman AH, Timko MP, dePamphilis CW, Choi D, Shirasu K. Genome Sequence of Striga asiatica Provides Insight into the Evolution of Plant Parasitism. Curr Biol 2019; 29:3041-3052.e4. [PMID: 31522940 DOI: 10.1016/j.cub.2019.07.086] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/23/2019] [Accepted: 07/30/2019] [Indexed: 11/25/2022]
Abstract
Parasitic plants in the genus Striga, commonly known as witchweeds, cause major crop losses in sub-Saharan Africa and pose a threat to agriculture worldwide. An understanding of Striga parasite biology, which could lead to agricultural solutions, has been hampered by the lack of genome information. Here, we report the draft genome sequence of Striga asiatica with 34,577 predicted protein-coding genes, which reflects gene family contractions and expansions that are consistent with a three-phase model of parasitic plant genome evolution. Striga seeds germinate in response to host-derived strigolactones (SLs) and then develop a specialized penetration structure, the haustorium, to invade the host root. A family of SL receptors has undergone a striking expansion, suggesting a molecular basis for the evolution of broad host range among Striga spp. We found that genes involved in lateral root development in non-parasitic model species are coordinately induced during haustorium development in Striga, suggesting a pathway that was partly co-opted during the evolution of the haustorium. In addition, we found evidence for horizontal transfer of host genes as well as retrotransposons, indicating gene flow to S. asiatica from hosts. Our results provide valuable insights into the evolution of parasitism and a key resource for the future development of Striga control strategies.
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Affiliation(s)
- Satoko Yoshida
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan; Institute for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Seungill Kim
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul 151-742, Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-742, Korea
| | - Eric K Wafula
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Jaakko Tanskanen
- Production Systems, Luke Natural Resources Institute Finland, 00790 Helsinki, Finland; Luke/BI Plant Genomics Laboratory, Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Yong-Min Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon 305-806, Korea
| | - Loren Honaas
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA; U.S.D.A. ARS, Wenatchee, WA, USA
| | - Zhenzhen Yang
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Thomas Spallek
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; Institute of Plant Physiology and Biochemistry, University of Hohenheim, 70599 Stuttgart, Germany
| | - Caitlin E Conn
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Yasunori Ichihashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Kyeongchae Cheong
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul 151-742, Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-742, Korea
| | - Songkui Cui
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; Institute for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Joshua P Der
- Department of Biological Science, California State University, Fullerton, Fullerton, CA 92831, USA
| | - Heidrun Gundlach
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, Neuherberg 85764, Germany
| | - Yuannian Jiao
- Institute of Botany, The Chinese Academy of Sciences, Nanxincun, Xiangshan, Beijing, China
| | - Chiaki Hori
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; Research Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Juliane K Ishida
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroyuki Kasahara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu 183-8509, Japan
| | - Takatoshi Kiba
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Myung-Shin Kim
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul 151-742, Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-742, Korea
| | - Namjin Koo
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon 305-806, Korea
| | - Anuphon Laohavisit
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Yong-Hwan Lee
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul 151-742, Korea; Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Shelley Lumba
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S-3B2, Canada
| | - Peter McCourt
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S-3B2, Canada
| | - Jenny C Mortimer
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - J Musembi Mutuku
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, 00100 Nairobi, Kenya
| | - Takahito Nomura
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya 321-8505, Japan
| | - Yuko Sasaki-Sekimoto
- School of Life Science and Technology, Tokyo Institute of Technology, 226-8501, Yokohama, Kanagawa, Japan
| | - Yoshiya Seto
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan; Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Yu Wang
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
| | - Takanori Wakatake
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Taku Demura
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Shinjiro Yamaguchi
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan; Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Koichi Yoneyama
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya 321-8505, Japan
| | - Ri-Ichiroh Manabe
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - David C Nelson
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Alan H Schulman
- Production Systems, Luke Natural Resources Institute Finland, 00790 Helsinki, Finland; Luke/BI Plant Genomics Laboratory, Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
| | - Claude W dePamphilis
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Doil Choi
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul 151-742, Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-742, Korea
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan.
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22
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Colchado-López J, Cervantes RC, Rosas U. A Linear Model to Describe Branching and Allometry in Root Architecture. PLANTS (BASEL, SWITZERLAND) 2019; 8:plants8070218. [PMID: 31336829 PMCID: PMC6681317 DOI: 10.3390/plants8070218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 06/26/2019] [Accepted: 07/08/2019] [Indexed: 05/31/2023]
Abstract
Root architecture is a complex structure that comprises multiple traits of the root phenotype. Novel platforms and models have been developed to better understand root architecture. In this methods paper, we introduce a novel allometric model, named rhizochron index (m), which describes lateral root (LR) branching and elongation patterns across the primary root (PR). To test our model, we obtained data from 16 natural accessions of Arabidopsis thaliana at three stages of early root development to measure conventional traits of root architecture (e.g., PR and LR length), and extracted the rhizochron index (m). In addition, we tested previously published datasets to assess the utility of the rhizochron index (m) to distinguish mutants and environmental effects on root architecture. Our results indicate that rhizochron index (m) is useful to distinguish the natural variations of root architecture between A. thaliana accessions, but not across early stages of root development. Correlation analyses in these accessions showed that m is a novel trait that partially captures information from other root architecture traits such as total lateral root length, and the ratio between lateral root and primary root lengths. Moreover, we found that the rhizochron index was useful to distinguish ABA effect on root architecture, as well as the mutant pho1 phenotype. We propose the rhizochron index (m) as a new feature of the root architectural system to be considered, in addition to conventional traits in future investigations.
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Affiliation(s)
- Joel Colchado-López
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - R Cristian Cervantes
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - Ulises Rosas
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico.
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23
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Fakih M, Delenne JY, Radjai F, Fourcaud T. Root growth and force chains in a granular soil. Phys Rev E 2019; 99:042903. [PMID: 31108586 DOI: 10.1103/physreve.99.042903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Indexed: 06/09/2023]
Abstract
Roots provide basic functions to plants such as water and nutrient uptake and anchoring in soil. The growth and development of root systems contribute to colonizing the surrounding soil and optimizing the access to resources. It is generally known that the variability of plant root architecture results from the combination of genetic, physiological, and environmental factors, in particular soil mechanical resistance. However, this last factor has never been investigated at the soil grain scale for roots. In this paper, we are interested in the effect of the disordered texture of granular soils on the evolution of forces experienced by the root cap during its growth. We introduce a numerical model in which the root is modeled as a flexible self-elongating tube that probes a soil composed of solid particles. By means of extensive simulations, we show that the forces exerted on the root cap reflect interparticle force chains. Our simulations also show that the mean force declines exponentially with root flexibility, the highest force corresponding to the soil hardness. Furthermore, we find that this functional dependence is characterized by a single dimensionless parameter that combines granular structure and root bending stiffness. This finding will be useful to further address the biological issues of mechanosensing and thigmomorphogenesis in plant roots.
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Affiliation(s)
- Mahmoud Fakih
- LMGC, Université de Montpellier, CNRS, 163 rue Auguste Broussonnet, 34095 Montpellier, France
- AMAP, CIRAD, CNRS, INRA, IRD, University of Montpellier, TA A51/PS2, 34398 Montpellier, France
| | - Jean-Yves Delenne
- IATE, INRA, CIRAD, SupAgro, University of Montpellier, 2 place Pierre Viala, 34060 Montpellier, France
| | - Farhang Radjai
- LMGC, Université de Montpellier, CNRS, 163 rue Auguste Broussonnet, 34095 Montpellier, France
- ⟨MSE⟩2, UMI 3466 CNRS-MIT, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge 02139, USA
| | - Thierry Fourcaud
- AMAP, CIRAD, CNRS, INRA, IRD, University of Montpellier, TA A51/PS2, 34398 Montpellier, France
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24
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Proteome of rice roots treated with exogenous proline. 3 Biotech 2019; 9:101. [PMID: 30800612 DOI: 10.1007/s13205-019-1615-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 02/04/2019] [Indexed: 01/09/2023] Open
Abstract
Proteomic analysis was conducted to identify the rice root proteins induced by exogenous proline and their involvement in root growth. Proteins were extracted from the root tissues grown under two conditions, T1 (control) and T2 (10 mM proline), and profiled by two-dimensional polyacrylamide gel electrophoresis. Seventeen of 30 differentially expressed proteins were identified by mass spectrometry. Proline-treated rice roots showed up-regulation and down-regulation of nine and eight proteins, respectively, when compared to those in the control. Among the differentially expressed proteins, the down-regulation of glutathione reductase and peroxidase could be involved in the regulation of cellular hydrogen peroxide and reactive oxygen species levels that modulate the root cell wall structure. Differentially expressed proteins identified as pathogenesis-related proteins might be related to stress adaptive mechanisms in response to exogenous proline treatment. In addition, differentially expressed protein identified as the fructose-bisphosphate aldolases and cytochrome c oxidase might be associated with energy metabolism, which is needed during root developmental process. This is the first attempt to study the changes in rice root proteome treated with proline. The acquired information could open new avenues for further functional studies on the involvement of proline in modulating root development and its relation to stress adaptation of plants.
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25
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Kanwar MK, Yu J, Zhou J. Phytomelatonin: Recent advances and future prospects. J Pineal Res 2018; 65:e12526. [PMID: 30256447 DOI: 10.1111/jpi.12526] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/16/2018] [Accepted: 09/18/2018] [Indexed: 12/13/2022]
Abstract
Melatonin (MEL) has been revealed as a phylogenetically conserved molecule with a ubiquitous distribution from primitive photosynthetic bacteria to higher plants, including algae and fungi. Since MEL is implicated in numerous plant developmental processes and stress responses, the exploration of its functions in plant has become a rapidly progressing field with the new paradigm of involvement in plants growth and development. The pleiotropic involvement of MEL in regulating the transcripts of numerous genes confirms its vital involvement as a multi-regulatory molecule that architects many aspects of plant development. However, the cumulative research in plants is still preliminary and fragmentary in terms of its established functions compared to what is known about MEL physiology in animals. This supports the need for a comprehensive review that summarizes the new aspects pertaining to its functional role in photosynthesis, phytohormonal interactions under stress, cellular redox signaling, along with other regulatory roles in plant immunity, phytoremediation, and plant microbial interactions. The present review covers the latest advances on the mechanistic roles of phytomelatonin. While phytomelatonin is a sovereign plant growth regulator that can interact with the functions of other plant growth regulators or hormones, its qualifications as a complete phytohormone are still to be established. This review also showcases the yet to be identified potentials of phytomelatonin that will surely encourage the plant scientists to uncover new functional aspects of phytomelatonin in plant growth and development, subsequently improving its status as a potential new phytohormone.
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Affiliation(s)
- Mukesh Kumar Kanwar
- Department of Horticulture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Jingquan Yu
- Department of Horticulture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zijingang Campus, Zhejiang University, Hangzhou, China
- Key Laboratory of Horticultural Plants Growth, Development and Quality Improvement, Agricultural Ministry of China, Hangzhou, China
| | - Jie Zhou
- Department of Horticulture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zijingang Campus, Zhejiang University, Hangzhou, China
- Key Laboratory of Horticultural Plants Growth, Development and Quality Improvement, Agricultural Ministry of China, Hangzhou, China
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26
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Ristova D, Giovannetti M, Metesch K, Busch W. Natural genetic variation shapes root system responses to phytohormones in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:468-481. [PMID: 30030851 PMCID: PMC6220887 DOI: 10.1111/tpj.14034] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/13/2018] [Accepted: 07/02/2018] [Indexed: 05/21/2023]
Abstract
Plants adjust their architecture by modulating organ growth. This ability is largely dependent on phytohormones. While responses to phytohormones have been studied extensively, it remains unclear to which extent and how these responses are modulated in non-reference strains. Here, we assess variation of root traits upon treatment with auxin, cytokinin and abscisic acid (ABA) in 192 Arabidopsis accessions. We identify common response patterns, uncover the extent of their modulation by specific genotypes, and find that the Col-0 reference accession is not a good representative of the species in this regard. We conduct genome-wide association studies and identify 114 significant associations, most of them relating to ABA treatment. The numerous ABA candidate genes are not enriched for known ABA-associated genes, indicating that we largely uncovered unknown players. Overall, our study provides a comprehensive view of the diversity of hormone responses in the Arabidopsis thaliana species, and shows that variation of genes that are yet mostly not associated with such a role to determine natural variation of the response to phytohormones.
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Affiliation(s)
- Daniela Ristova
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr. Bohr‐Gasse 3Vienna1030Austria
| | - Marco Giovannetti
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr. Bohr‐Gasse 3Vienna1030Austria
| | - Kristina Metesch
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr. Bohr‐Gasse 3Vienna1030Austria
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr. Bohr‐Gasse 3Vienna1030Austria
- Salk Institute for Biological StudiesPlant Molecular and Cellular Biology Laboratory, and Integrative Biology Laboratory10010 N Torrey Pines RdLa JollaCA92037USA
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27
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Schlüter S, Blaser SRGA, Weber M, Schmidt V, Vetterlein D. Quantification of Root Growth Patterns From the Soil Perspective via Root Distance Models. FRONTIERS IN PLANT SCIENCE 2018; 9:1084. [PMID: 30087691 PMCID: PMC6066721 DOI: 10.3389/fpls.2018.01084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/05/2018] [Indexed: 05/21/2023]
Abstract
The rhizosphere, the fraction of soil altered by plant roots, is a dynamic domain that rapidly changes during plant growth. Traditional approaches to quantify root growth patterns are very limited in estimating this transient extent of the rhizosphere. In this paper we advocate the analysis of root growth patterns from the soil perspective. This change of perspective addresses more directly how certain root system architectures facilitate the exploration of soil. For the first time, we propose a parsimonious root distance model with only four parameters which is able to describe root growth patterns throughout all stages in the first 3 weeks of growth of Vicia faba measured with X-ray computed tomography. From these models, which are fitted to the frequency distribution of root distances in soil, it is possible to estimate the rhizosphere volume, i.e., the volume fraction of soil explored by roots, and adapt it to specific interaction distances for water uptake, rhizodeposition, etc. Through 3D time-lapse imaging and image registration it is possible to estimate root age dependent rhizosphere volumes, i.e., volumes specific for certain root age classes. These root distance models are a useful abstraction of complex root growth patterns that provide complementary information on root system architecture unaddressed by traditional root system analysis, which is helpful to constrain dynamic root growth models to achieve more realistic results.
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Affiliation(s)
- Steffen Schlüter
- Department of Soil System Science, Helmholtz-Centre for Environmental Research – UFZ, Halle, Germany
| | - Sebastian R. G. A. Blaser
- Department of Soil System Science, Helmholtz-Centre for Environmental Research – UFZ, Halle, Germany
| | | | | | - Doris Vetterlein
- Department of Soil System Science, Helmholtz-Centre for Environmental Research – UFZ, Halle, Germany
- Soil Science, Martin-Luther-University Halle-Wittenberg, Halle, Germany
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28
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Lee S, I. Sergeeva L, Vreugdenhil D. Natural variation of hormone levels in Arabidopsis roots and correlations with complex root architecture. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:292-309. [PMID: 29205819 PMCID: PMC5947113 DOI: 10.1111/jipb.12617] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 12/01/2017] [Indexed: 06/07/2023]
Abstract
Studies on natural variation are an important tool to unravel the genetic basis of quantitative traits in plants. Despite the significant roles of phytohormones in plant development, including root architecture, hardly any studies have been done to investigate natural variation in endogenous hormone levels in plants. Therefore, in the present study a range of hormones were quantified in root extracts of thirteen Arabidopsis thaliana accessions using a ultra performance liquid chromatography triple quadrupole mass spectrometer. Root system architecture of the set of accessions was quantified, using a new parameter (mature root unit) for complex root systems, and correlated with the phytohormone data. Significant variations in phytohormone levels among the accessions were detected, but were remarkably small, namely less than three-fold difference between extremes. For cytokinins, relatively larger variations were found for ribosides and glucosides, as compared to the free bases. For root phenotyping, length-related traits-lateral root length and total root length-showed larger variations than lateral root number-related ones. For root architecture, antagonistic interactions between hormones, for example, indole-3-acetic acid to trans-zeatin were detected in correlation analysis. These findings provide conclusive evidence for the presence of natural variation in phytohormone levels in Arabidopsis roots, suggesting that quantitative genetic analyses are feasible.
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Affiliation(s)
- Sangseok Lee
- Laboratory of Plant PhysiologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
- Gyeongsangbuk‐Do Agricultural Research & Extension Services Centre136 Gil‐14Chilgokjungang‐daeroDaeguSouth Korea
| | - Lidiya I. Sergeeva
- Laboratory of Plant PhysiologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
| | - Dick Vreugdenhil
- Laboratory of Plant PhysiologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
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29
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Parra-Londono S, Kavka M, Samans B, Snowdon R, Wieckhorst S, Uptmoor R. Sorghum root-system classification in contrasting P environments reveals three main rooting types and root-architecture-related marker-trait associations. ANNALS OF BOTANY 2018; 121:267-280. [PMID: 29351588 PMCID: PMC5808808 DOI: 10.1093/aob/mcx157] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 10/19/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Roots facilitate acquisition of macro- and micronutrients, which are crucial for plant productivity and anchorage in the soil. Phosphorus (P) is rapidly immobilized in the soil and hardly available for plants. Adaptation to P scarcity relies on changes in root morphology towards rooting systems well suited for topsoil foraging. Root-system architecture (RSA) defines the spatial organization of the network comprising primary, lateral and stem-derived roots and is important for adaptation to stress conditions. RSA phenotyping is a challenging task and essential for understanding root development. METHODS In this study, 19 traits describing RSA were analysed in a diversity panel comprising 194 sorghum genotypes, fingerprinted with a 90-k single-nucleotide polymorphism (SNP) array and grown under low and high P availability. KEY RESULTS Multivariate analysis was conducted and revealed three different RSA types: (1) a small root system; (2) a compact and bushy rooting type; and (3) an exploratory root system, which might benefit plant growth and development if water, nitrogen (N) or P availability is limited. While several genotypes displayed similar rooting types in different environments, others responded to P scarcity positively by developing more exploratory root systems, or negatively with root growth suppression. Genome-wide association studies revealed significant quantitative trait loci (P < 2.9 × 10-6) on chromosomes SBI-02, SBI-03, SBI-05 and SBI-09. Co-localization of significant and suggestive (P < 5.7 × 10-5) associations for several traits indicated hotspots controlling root-system development on chromosomes SBI-02 and SBI-03. CONCLUSIONS Sorghum genotypes with a compact, bushy and shallow root system provide potential adaptation to P scarcity in the field by allowing thorough topsoil foraging, while genotypes with an exploratory root system may be advantageous if N or water is the limiting factor, although such genotypes showed highest P uptake levels under the artificial conditions of the present study.
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Affiliation(s)
| | - Mareike Kavka
- Chair of Agronomy, University of Rostock, Rostock, Germany
| | - Birgit Samans
- Department of Plant Breeding, Justus Liebig University Gießen, Gießen, Germany
| | - Rod Snowdon
- Department of Plant Breeding, Justus Liebig University Gießen, Gießen, Germany
| | | | - Ralf Uptmoor
- Chair of Agronomy, University of Rostock, Rostock, Germany
- For correspondence. E-mail:
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30
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The activation of OsEIL1 on YUC8 transcription and auxin biosynthesis is required for ethylene-inhibited root elongation in rice early seedling development. PLoS Genet 2017; 13:e1006955. [PMID: 28829777 PMCID: PMC5581195 DOI: 10.1371/journal.pgen.1006955] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 09/01/2017] [Accepted: 08/04/2017] [Indexed: 11/21/2022] Open
Abstract
Rice is an important monocotyledonous crop worldwide; it differs from the dicotyledonous plant Arabidopsis in many aspects. In Arabidopsis, ethylene and auxin act synergistically to regulate root growth and development. However, their interaction in rice is still unclear. Here, we report that the transcriptional activation of OsEIL1 on the expression of YUC8/REIN7 and indole-3-pyruvic acid (IPA)-dependent auxin biosynthesis is required for ethylene-inhibited root elongation. Using an inhibitor of YUC activity, which regulates auxin biosynthesis via the conversion of IPA to indole-3-acetic acid (IAA), we showed that ethylene-inhibited primary root elongation is dependent on YUC-based auxin biosynthesis. By screening phenotypes of seedling primary root from mutagenesis libraries following ethylene treatment, we identified a rice ethylene-insensitive mutant, rein7-1, in which YUC8/REIN7 is truncated at its C-terminus. Mutation in YUC8/REIN7 reduced auxin biosynthesis in rice, while YUC8/REIN7 overexpression enhanced ethylene sensitivity in the roots. Moreover, YUC8/REIN7 catalyzed the conversion of IPA to IAA, truncated version at C-terminal end of the YUC8/REIN7 resulted in significant reduction of enzymatic activity, indicating that YUC8/REIN7 is required for IPA-dependent auxin biosynthesis and ethylene-inhibited root elongation in rice early seedlings. Further investigations indicated that ethylene induced YUC8/REIN7 expression and promoted auxin accumulation in roots. Addition of low concentrations of IAA rescued the ethylene response in the rein7-1, strongly demonstrating that ethylene-inhibited root elongation depends on IPA-dependent auxin biosynthesis. Genetic studies revealed that YUC8/REIN7-mediated auxin biosynthesis functioned downstream of OsEIL1, which directly activated the expression of YUC8/REIN7. Thus, our findings reveal a model of interaction between ethylene and auxin in rice seedling primary root elongation, enhancing our understanding of ethylene signaling in rice. Rice is an important crop worldwide and is grown in water-saturated environments during its life cycle. This unique feature confers that rice might have different aspects from Arabidopsis in ethylene signaling. Although the crosstalk between ethylene and auxin is well understood in Arabidopsis, however, the interaction in rice is largely unclear. Here, we show that YUC8/REIN7, a member of the YUC gene family, catalyzing the conversion of IPA to IAA in auxin biosynthesis, is transcriptionally modulated by ethylene signaling component OsEIL1, and mainly participates in auxin biosynthesis and ethylene-inhibited root growth. We first identified that ethylene-inhibited root elongation is suppressed by the inhibitor of YUC activity, and YUC8/REIN7 is required for IPA-dependent auxin biosynthesis, indicating that YUC8/REIN7 is involved in ethylene-inhibited root elongation in rice early seedlings. Moreover, ethylene induced YUC8/REIN7 transcription and promoted auxin accumulation in roots. Addition of low concentrations of IAA rescued the ethylene response in the rein7-1, demonstrating that ethylene stimulates auxin biosynthesis dependent on YUC8/REIN7 function. Further evidence revealed that OsEIL1 transcriptionally activates the expression of YUC8/REIN7, and YUC8/REIN7-mediated auxin biosynthesis genetically acts downstream of OsEIL1. Our data in the present report identified an interaction between ethylene and auxin in rice seedling primary root elongation, increasing our understanding of ethylene signaling in rice root growth.
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Hobecker KV, Reynoso MA, Bustos-Sanmamed P, Wen J, Mysore KS, Crespi M, Blanco FA, Zanetti ME. The MicroRNA390/TAS3 Pathway Mediates Symbiotic Nodulation and Lateral Root Growth. PLANT PHYSIOLOGY 2017; 174:2469-2486. [PMID: 28663332 PMCID: PMC5543954 DOI: 10.1104/pp.17.00464] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/24/2017] [Indexed: 05/19/2023]
Abstract
Legume roots form two types of postembryonic organs, lateral roots and symbiotic nodules. Nodule formation is the result of the interaction of legumes with rhizobia and requires the mitotic activation and differentiation of root cells as well as an independent, but coordinated, program that allows infection by rhizobia. MicroRNA390 (miR390) is an evolutionarily conserved microRNA that targets the Trans-Acting Short Interference RNA3 (TAS3) transcript. Cleavage of TAS3 by ARGONAUTE7 results in the production of trans-acting small interference RNAs, which target mRNAs encoding AUXIN RESPONSE FACTOR2 (ARF2), ARF3, and ARF4. Here, we show that activation of the miR390/TAS3 regulatory module by overexpression of miR390 in Medicago truncatula promotes lateral root growth but prevents nodule organogenesis, rhizobial infection, and the induction of two key nodulation genes, Nodulation Signaling Pathway1 (NSP1) and NSP2 Accordingly, inactivation of the miR390/TAS3 module, either by expression of a miR390 target mimicry construct or mutations in ARGONAUTE7, enhances nodulation and rhizobial infection, alters the spatial distribution of the nodules, and increases the percentage of nodules with multiple meristems. Our results revealed a key role of the miR390/TAS3 pathway in legumes as a modulator of lateral root organs, playing opposite roles in lateral root and nodule development.
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Affiliation(s)
- Karen Vanesa Hobecker
- Instituto de Biotecnología y Biología Molecular, FCE-UNLP CCT-CONICET, C.P. 1900 La Plata, Argentina
| | - Mauricio Alberto Reynoso
- Instituto de Biotecnología y Biología Molecular, FCE-UNLP CCT-CONICET, C.P. 1900 La Plata, Argentina
| | - Pilar Bustos-Sanmamed
- Institute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Universités Paris-Sud, Evry, Paris-Diderot, Université Paris-Saclay, 91405 Orsay, France
| | - Jiangqi Wen
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Kirankumar S Mysore
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Martín Crespi
- Institute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Universités Paris-Sud, Evry, Paris-Diderot, Université Paris-Saclay, 91405 Orsay, France
| | - Flavio Antonio Blanco
- Instituto de Biotecnología y Biología Molecular, FCE-UNLP CCT-CONICET, C.P. 1900 La Plata, Argentina
| | - María Eugenia Zanetti
- Instituto de Biotecnología y Biología Molecular, FCE-UNLP CCT-CONICET, C.P. 1900 La Plata, Argentina
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Fakih M, Delenne JY, Radjai F, Fourcaud T. Modeling root growth in granular soils: effects of root stiffness and packing fraction. EPJ WEB OF CONFERENCES 2017. [DOI: 10.1051/epjconf/201714014013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Prapagdee S, Tawinteung N. Effects of biochar on enhanced nutrient use efficiency of green bean, Vigna radiata L. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:9460-9467. [PMID: 28236199 DOI: 10.1007/s11356-017-8633-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 02/13/2017] [Indexed: 06/06/2023]
Abstract
Biochar is the carbonized material produced from biomass and is used in several environmental applications. The biochar characteristics depend on the carbonization conditions and feedstock. The suitability of a given biochar for soil improvement depends on the biochar characteristics, soil properties, and target plants. Biochar has been applied at 1-20% (w/w) in the soil, but currently there is a lack of information on what type and concentration of biochar are most suitable for a specific plant and soil quality. Too much biochar will reduce plant growth because of the high alkalinity of biochar, which will cause long-term soil alkalinity. In contrast, too little biochar might be insufficient to enhance plant productivity. In this study, a suitable concentration of cassava stem (an abundant agricultural waste in Thailand) biochar produced at 350 °C was evaluated for green bean (Vigna radiata L.) growth from germination to seed production in pots over 8 weeks. The soil fertility was increased with increasing biochar concentration. At 5% (w/w) biochar, the soil fertility and plant growth were significantly enhanced, while 10% (w/w) biochar significantly enhanced bean growth and bean pod production. The increased biochar concentration in the soil significantly increased the soil total nitrogen and extractable potassium (K) levels but did not affect the amount of available phosphorous. Biochar at 10% (w/w) significantly induced the accumulation of K in the stems, leaves, nut shells, and roots but not in nut seeds. Moreover, biochar not only increased the K concentration in soil but also increased the plant nutrient use efficiency of K, which is important for plant growth. Graphical abstract ᅟ.
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Affiliation(s)
- Songkrit Prapagdee
- Environmental Research Institute, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand.
| | - Nukoon Tawinteung
- Department of Plant Production Technology, Faculty of Agricultural Technology, King Mongkut's Institute of Technology Ladkrabang, Ladkrabang, Bangkok, 10520, Thailand
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Liang C, Li A, Yu H, Li W, Liang C, Guo S, Zhang R, Chu C. Melatonin Regulates Root Architecture by Modulating Auxin Response in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:134. [PMID: 28223997 PMCID: PMC5293752 DOI: 10.3389/fpls.2017.00134] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/23/2017] [Indexed: 05/17/2023]
Abstract
It has been suggested that melatonin acts as an important regulator in controlling root growth and development, but the underlying molecular mechanism driving this relationship remains undetermined. In this study, we demonstrated that melatonin acts as a potent molecule to govern root architecture in rice. Treatments with melatonin significantly inhibited embryonic root growth, and promoted lateral root formation and development. Genome-wide expression profiling by RNA-sequencing revealed auxin-related genes were significantly activated under melatonin treatment. Moreover, several transcription factors and candidate cis-regulatory elements involved in root growth and developments, as well as auxin-related processes, were over-represented in both co-up and -down differentially expressed genes, suggesting that melatonin-mediated root growth occurs in an auxin signal pathway-dependent manner. Further, gravitropic response analysis determined that melatonin affects auxin-regulated processes in rice root. These data show that melatonin shapes root architecture by directly or indirectly activating the auxin signaling pathway.
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Affiliation(s)
- Chengzhen Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
| | - Aifu Li
- National Center for Plant Gene Research (Beijing), State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Hua Yu
- National Center for Plant Gene Research (Beijing), State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Wenzhen Li
- National Center for Plant Gene Research (Beijing), State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Chengzhi Liang
- National Center for Plant Gene Research (Beijing), State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Sandui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
| | - Chengcai Chu
- National Center for Plant Gene Research (Beijing), State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
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Liu Z, Gao K, Shan S, Gu R, Wang Z, Craft EJ, Mi G, Yuan L, Chen F. Comparative Analysis of Root Traits and the Associated QTLs for Maize Seedlings Grown in Paper Roll, Hydroponics and Vermiculite Culture System. FRONTIERS IN PLANT SCIENCE 2017; 8:436. [PMID: 28424719 PMCID: PMC5371678 DOI: 10.3389/fpls.2017.00436] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/14/2017] [Indexed: 05/22/2023]
Abstract
Root system architecture (RSA) plays an important role in the acquisition of both nitrogen (N) and phosphorus (P) from the environment. Currently RSA is rarely considered as criteria for selection to improve nutrient uptake efficiency in crop breeding. Under field conditions roots can be greatly influenced by uncontrolled environment factors. Therefore, it is necessary to develop fast selection methods for evaluating root traits of young seedlings in the lab which can then be related to high nutrient efficiency of adult plants in the field. Here, a maize recombination inbred line (RILs) population was used to compare the genetic relationship between RSA and nitrogen and phosphorous efficiency traits. The phenotypes of eight RSA-related traits were evaluated in young seedlings using three different growth systems (i.e., paper roll, hydroponics and vermiculite), and then subjected to correlation analysis with N efficiency and P efficiency related traits measured under field conditions. Quantitative trait loci (QTL) of RSA were determined and QTL co-localizations across different growth systems were further analyzed. Phenotypic associations were observed for most of RSA traits among all three culture systems. RSA-related traits in hydroponics and vermiculite weakly correlated with Nitrogen (NupE) uptake efficiency (r = 0.17-0.31) and Phosphorus (PupE) uptake efficiency (r = 0.22-0.34). This correlation was not found in the paper roll growth system. A total of 14 QTLs for RSA were identified in paper rolls, 18 in hydroponics, and 14 in vermiculite. Co-localization of QTLs for RSA traits were identified in six chromosome regions of bin 1.04/1.05, 1.06, 2.04/2.05, 3.04, 4.05, and 5.04/5.05. The results suggest the problem of using the phenotype from one growth system to predict those in another growth system. Assessing RSA traits at the seedling stage using either hydroponics or a vermiculite system appears better suited than the paper roll system as an important index to accelerate the selection of high N and P efficient genotypes for maize breeding programs.
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Affiliation(s)
- Zhigang Liu
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural UniversityBeijing, China
| | - Kun Gao
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural UniversityBeijing, China
| | - Shengchen Shan
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural UniversityBeijing, China
| | - Riling Gu
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural UniversityBeijing, China
| | - Zhangkui Wang
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural UniversityBeijing, China
| | - Eric J. Craft
- Robert Holley Center for Agriculture and Health, USDA-ARSIthaca, NY, USA
| | - Guohua Mi
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural UniversityBeijing, China
| | - Lixing Yuan
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural UniversityBeijing, China
| | - Fanjun Chen
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural UniversityBeijing, China
- *Correspondence: Fanjun Chen
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Zanetti ME, Rípodas C, Niebel A. Plant NF-Y transcription factors: Key players in plant-microbe interactions, root development and adaptation to stress. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:645-654. [PMID: 27939756 DOI: 10.1016/j.bbagrm.2016.11.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 11/18/2016] [Accepted: 11/21/2016] [Indexed: 11/15/2022]
Abstract
NF-Ys are heterotrimeric transcription factors composed by the NF-YA, NF-YB and NF-YC subunits. In plants, NF-Y subunits are encoded by multigene families whose members show structural and functional diversifications. An increasing number of NF-Y genes has been shown to play key roles during different stages of root nodule and arbuscular mycorrhizal symbiosis, as well as during the interaction of plants with pathogenic microorganisms. Individual members of the NF-YA and NF-YB families have also been implicated in the development of primary and lateral roots. In addition, different members of the NF-YA and NF-YB gene families from mono- and di-cotyledonous plants have been involved in plant responses to water and nutrient scarcity. This review presents the most relevant and striking results concerning these NF-Y subunits. A phylogenetic analysis of the functionally characterized NF-Y genes revealed that, across plant species, NF-Y proteins functioning in the same biological process tend to belong to common phylogenetic groups. Finally, we discuss the forthcoming challenges of plant NF-Y research, including the detailed dissection of expression patterns, the elucidation of functional specificities as well as the characterization of the potential NF-Y-mediated epigenetic mechanisms by which they control the expression of their target genes. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.
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Affiliation(s)
- María Eugenia Zanetti
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CCT-La Plata, CONICET, calle 115 y 49 s/n, CP 1900, La Plata, Argentina.
| | - Carolina Rípodas
- LIPM, Université de Toulouse, Institut National de la Recherche Agronomique, Centre, National de la Recherche Scientifique, 31326 Castanet-Tolosan, France
| | - Andreas Niebel
- LIPM, Université de Toulouse, Institut National de la Recherche Agronomique, Centre, National de la Recherche Scientifique, 31326 Castanet-Tolosan, France.
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Rao IM, Miles JW, Beebe SE, Horst WJ. Root adaptations to soils with low fertility and aluminium toxicity. ANNALS OF BOTANY 2016; 118:593-605. [PMID: 27255099 PMCID: PMC5055624 DOI: 10.1093/aob/mcw073] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/18/2016] [Accepted: 03/01/2016] [Indexed: 05/21/2023]
Abstract
Background Plants depend on their root systems to acquire the water and nutrients necessary for their survival in nature, and for their yield and nutritional quality in agriculture. Root systems are complex and a variety of root phenes have been identified as contributors to adaptation to soils with low fertility and aluminium (Al) toxicity. Phenotypic characterization of root adaptations to infertile soils is enabling plant breeders to develop improved cultivars that not only yield more, but also contribute to yield stability and nutritional security in the face of climate variability. Scope In this review the adaptive responses of root systems to soils with low fertility and Al toxicity are described. After a brief introduction, the purpose and focus of the review are outlined. This is followed by a description of the adaptive responses of roots to low supply of mineral nutrients [with an emphasis on low availability of nitrogen (N) and phosphorus (P) and on toxic levels of Al]. We describe progress in developing germplasm adapted to soils with low fertility or Al toxicity using selected examples from ongoing breeding programmes on food (maize, common bean) and forage/feed (Brachiaria spp.) crops. A number of root architectural, morphological, anatomical and metabolic phenes contribute to the superior performance and yield on soils with low fertility and Al toxicity. Major advances have been made in identifying root phenes in improving adaptation to low N (maize), low P (common bean) or high Al [maize, common bean, species and hybrids of brachiariagrass, bulbous canarygrass (Phalaris aquatica) and lucerne (Medicago sativa)]. Conclusions Advanced root phenotyping tools will allow dissection of root responses into specific root phenes that will aid both conventional and molecular breeders to develop superior cultivars. These new cultivars will play a key role in sustainable intensification of crop-livestock systems, particularly in smallholder systems of the tropics. Development of these new cultivars adapted to soils with low fertility and Al toxicity is needed to improve global food and nutritional security and environmental sustainability.
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Affiliation(s)
- Idupulapati M. Rao
- Centro Internacional de Agricultura Tropical (CIAT), A. A. 6713, Cali, Colombia and
| | - John W. Miles
- Centro Internacional de Agricultura Tropical (CIAT), A. A. 6713, Cali, Colombia and
| | - Stephen E. Beebe
- Centro Internacional de Agricultura Tropical (CIAT), A. A. 6713, Cali, Colombia and
| | - Walter J. Horst
- Leibniz University of Hannover, Herrenhaeuser Str. 2, D-30419 Hannover, Germany
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Burridge J, Jochua CN, Bucksch A, Lynch JP. Legume shovelomics: High—Throughput phenotyping of common bean (Phaseolus vulgaris L.) and cowpea (Vigna unguiculata subsp, unguiculata) root architecture in the field. FIELD CROPS RESEARCH 2016; 192:21-32. [PMID: 0 DOI: 10.1016/j.fcr.2016.04.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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Araya T, Kubo T, von Wirén N, Takahashi H. Statistical modeling of nitrogen-dependent modulation of root system architecture in Arabidopsis thaliana. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:254-265. [PMID: 26425993 DOI: 10.1111/jipb.12433] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/28/2015] [Indexed: 06/05/2023]
Abstract
Plant root development is strongly affected by nutrient availability. Despite the importance of structure and function of roots in nutrient acquisition, statistical modeling approaches to evaluate dynamic and temporal modulations of root system architecture in response to nutrient availability have remained as widely open and exploratory areas in root biology. In this study, we developed a statistical modeling approach to investigate modulations of root system architecture in response to nitrogen availability. Mathematical models were designed for quantitative assessment of root growth and root branching phenotypes and their dynamic relationships based on hierarchical configuration of primary and lateral roots formulating the fishbone-shaped root system architecture in Arabidopsis thaliana. Time-series datasets reporting dynamic changes in root developmental traits on different nitrate or ammonium concentrations were generated for statistical analyses. Regression analyses unraveled key parameters associated with: (i) inhibition of primary root growth under nitrogen limitation or on ammonium; (ii) rapid progression of lateral root emergence in response to ammonium; and (iii) inhibition of lateral root elongation in the presence of excess nitrate or ammonium. This study provides a statistical framework for interpreting dynamic modulation of root system architecture, supported by meta-analysis of datasets displaying morphological responses of roots to diverse nitrogen supplies.
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Affiliation(s)
- Takao Araya
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Takuya Kubo
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Nicolaus von Wirén
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Hideki Takahashi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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Reinhardt H, Hachez C, Bienert MD, Beebo A, Swarup K, Voß U, Bouhidel K, Frigerio L, Schjoerring JK, Bennett MJ, Chaumont F. Tonoplast Aquaporins Facilitate Lateral Root Emergence. PLANT PHYSIOLOGY 2016; 170:1640-54. [PMID: 26802038 PMCID: PMC4775129 DOI: 10.1104/pp.15.01635] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 01/19/2016] [Indexed: 05/18/2023]
Abstract
Aquaporins (AQPs) are water channels allowing fast and passive diffusion of water across cell membranes. It was hypothesized that AQPs contribute to cell elongation processes by allowing water influx across the plasma membrane and the tonoplast to maintain adequate turgor pressure. Here, we report that, in Arabidopsis (Arabidopsis thaliana), the highly abundant tonoplast AQP isoforms AtTIP1;1, AtTIP1;2, and AtTIP2;1 facilitate the emergence of new lateral root primordia (LRPs). The number of lateral roots was strongly reduced in the triple tip mutant, whereas the single, double, and triple tip mutants showed no or minor reduction in growth of the main root. This phenotype was due to the retardation of LRP emergence. Live cell imaging revealed that tight spatiotemporal control of TIP abundance in the tonoplast of the different LRP cells is pivotal to mediating this developmental process. While lateral root emergence is correlated to a reduction of AtTIP1;1 and AtTIP1;2 protein levels in LRPs, expression of AtTIP2;1 is specifically needed in a restricted cell population at the base, then later at the flanks, of developing LRPs. Interestingly, the LRP emergence phenotype of the triple tip mutants could be fully rescued by expressing AtTIP2;1 under its native promoter. We conclude that TIP isoforms allow the spatial and temporal fine-tuning of cellular water transport, which is critically required during the highly regulated process of LRP morphogenesis and emergence.
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Affiliation(s)
- Hagen Reinhardt
- Institut des Sciences de la Vie, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium (H.R., C.H., F.C.);Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark (M.D.B., J.K.S.);Université de Bourgogne, UMR1347 Agroécologie IPM, F-21000 Dijon, France (A.B., K.B.);Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (K.S., U.V., M.J.B.); andSchool of Life Sciences, University of Warwick, Coventry CV47AL, United Kingdom (L.F.)
| | - Charles Hachez
- Institut des Sciences de la Vie, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium (H.R., C.H., F.C.);Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark (M.D.B., J.K.S.);Université de Bourgogne, UMR1347 Agroécologie IPM, F-21000 Dijon, France (A.B., K.B.);Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (K.S., U.V., M.J.B.); andSchool of Life Sciences, University of Warwick, Coventry CV47AL, United Kingdom (L.F.)
| | - Manuela Désirée Bienert
- Institut des Sciences de la Vie, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium (H.R., C.H., F.C.);Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark (M.D.B., J.K.S.);Université de Bourgogne, UMR1347 Agroécologie IPM, F-21000 Dijon, France (A.B., K.B.);Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (K.S., U.V., M.J.B.); andSchool of Life Sciences, University of Warwick, Coventry CV47AL, United Kingdom (L.F.)
| | - Azeez Beebo
- Institut des Sciences de la Vie, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium (H.R., C.H., F.C.);Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark (M.D.B., J.K.S.);Université de Bourgogne, UMR1347 Agroécologie IPM, F-21000 Dijon, France (A.B., K.B.);Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (K.S., U.V., M.J.B.); andSchool of Life Sciences, University of Warwick, Coventry CV47AL, United Kingdom (L.F.)
| | - Kamal Swarup
- Institut des Sciences de la Vie, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium (H.R., C.H., F.C.);Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark (M.D.B., J.K.S.);Université de Bourgogne, UMR1347 Agroécologie IPM, F-21000 Dijon, France (A.B., K.B.);Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (K.S., U.V., M.J.B.); andSchool of Life Sciences, University of Warwick, Coventry CV47AL, United Kingdom (L.F.)
| | - Ute Voß
- Institut des Sciences de la Vie, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium (H.R., C.H., F.C.);Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark (M.D.B., J.K.S.);Université de Bourgogne, UMR1347 Agroécologie IPM, F-21000 Dijon, France (A.B., K.B.);Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (K.S., U.V., M.J.B.); andSchool of Life Sciences, University of Warwick, Coventry CV47AL, United Kingdom (L.F.)
| | - Karim Bouhidel
- Institut des Sciences de la Vie, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium (H.R., C.H., F.C.);Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark (M.D.B., J.K.S.);Université de Bourgogne, UMR1347 Agroécologie IPM, F-21000 Dijon, France (A.B., K.B.);Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (K.S., U.V., M.J.B.); andSchool of Life Sciences, University of Warwick, Coventry CV47AL, United Kingdom (L.F.)
| | - Lorenzo Frigerio
- Institut des Sciences de la Vie, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium (H.R., C.H., F.C.);Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark (M.D.B., J.K.S.);Université de Bourgogne, UMR1347 Agroécologie IPM, F-21000 Dijon, France (A.B., K.B.);Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (K.S., U.V., M.J.B.); andSchool of Life Sciences, University of Warwick, Coventry CV47AL, United Kingdom (L.F.)
| | - Jan K Schjoerring
- Institut des Sciences de la Vie, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium (H.R., C.H., F.C.);Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark (M.D.B., J.K.S.);Université de Bourgogne, UMR1347 Agroécologie IPM, F-21000 Dijon, France (A.B., K.B.);Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (K.S., U.V., M.J.B.); andSchool of Life Sciences, University of Warwick, Coventry CV47AL, United Kingdom (L.F.)
| | - Malcolm J Bennett
- Institut des Sciences de la Vie, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium (H.R., C.H., F.C.);Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark (M.D.B., J.K.S.);Université de Bourgogne, UMR1347 Agroécologie IPM, F-21000 Dijon, France (A.B., K.B.);Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (K.S., U.V., M.J.B.); andSchool of Life Sciences, University of Warwick, Coventry CV47AL, United Kingdom (L.F.)
| | - Francois Chaumont
- Institut des Sciences de la Vie, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium (H.R., C.H., F.C.);Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark (M.D.B., J.K.S.);Université de Bourgogne, UMR1347 Agroécologie IPM, F-21000 Dijon, France (A.B., K.B.);Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (K.S., U.V., M.J.B.); andSchool of Life Sciences, University of Warwick, Coventry CV47AL, United Kingdom (L.F.)
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Cai XT, Xu P, Wang Y, Xiang CB. Activated expression of AtEDT1/HDG11 promotes lateral root formation in Arabidopsis mutant edt1 by upregulating jasmonate biosynthesis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:1017-30. [PMID: 25752924 DOI: 10.1111/jipb.12347] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 03/02/2015] [Indexed: 05/11/2023]
Abstract
Root architecture is crucial for plants to absorb water and nutrients. We previously reported edt1 (edt1D) mutant with altered root architecture that contributes significantly to drought resistance. However, the underlying molecular mechanisms are not well understood. Here we report one of the mechanisms underlying EDT1/HDG11-conferred altered root architecture. Root transcriptome comparison between the wild type and edt1D revealed that the upregulated genes involved in jasmonate biosynthesis and signaling pathway were enriched in edt1D root, which were confirmed by quantitative RT-PCR. Further analysis showed that EDT1/HDG11, as a transcription factor, bound directly to the HD binding sites in the promoters of AOS, AOC3, OPR3, and OPCL1, which encode four key enzymes in JA biosynthesis. We found that the jasmonic acid level was significantly elevated in edt1D root compared with that in the wild type subsequently. In addition, more auxin accumulation was observed in the lateral root primordium of edt1D compared with that of wild type. Genetic analysis of edt1D opcl1 double mutant also showed that HDG11 was partially dependent on JA in regulating LR formation. Taken together, overexpression of EDT1/HDG11 increases JA level in the root of edt1D by directly upregulating the expressions of several genes encoding JA biosynthesis enzymes to activate auxin signaling and promote lateral root formation.
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Affiliation(s)
- Xiao-Teng Cai
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Ping Xu
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Yao Wang
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Cheng-Bin Xiang
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
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42
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Hao L, Wen Y, Zhao Y, Lu W, Xiao K. Wheat mitogen-activated protein kinase gene TaMPK4 improves plant tolerance to multiple stresses through modifying root growth, ROS metabolism, and nutrient acquisitions. PLANT CELL REPORTS 2015; 34:2081-97. [PMID: 26275989 DOI: 10.1007/s00299-015-1853-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 07/14/2015] [Accepted: 07/29/2015] [Indexed: 05/04/2023]
Abstract
KEY MESSAGE Wheat MAPK member TaMPK4 responds to abiotic stresses of Pi and N deprivations and high salinity and is crucial in regulating plant tolerance to aforementioned stresses. Mitogen-activated protein kinase (MAPK) cascades are important signal transduction modules in regulating plant responses to various environmental stresses. In this study, a wheat MAPK member referred to TaMPK4 was characterized for its roles in mediating plant tolerance to diverse stresses. TaMPK4 shares conserved domains generally identified in plant MAPKs and possesses in vitro kinase activity. Under stresses of Pi and N deprivations and high salinity, TaMPK4 was strongly upregulated and its expressions were restored upon recovery treatments from above stresses. Sense- and antisense-expressing TaMPK4 in tobacco significantly modified plant growth under the stress conditions and dramatically modified the root architecture through transcriptional regulation of the auxin transport-associated genes NtPIN3 and NtPIN9, whose downregulated expressions dramatically reduced the root growth. Compared with wild type (WT), the antioxidant enzymatic activities under the stress conditions, P accumulation under P deprivation, and N amount under N deficiency were altered dramatically in the transgenic plants, showing higher in the TaMPK4-overexpressing and lower in the TaMPK4-knockout plants, which were in concordance with the modified expressions of a set of antioxidant enzyme genes (NtPOD2;1, NtPOD9, NtSOD2, NtFeSOD, and NtCAT), two phosphate transporter genes (NtPT and NtPT2), and two nitrate transporter genes (NtNRT1.1-s and NtNRT1.1-t), respectively. Downregulated expression of above genes in tobacco largely reduced the plant growth, and Pi and N acquisitions under the stress conditions. TaMPK4 also involved regulations of plant K(+) and osmolyte contents under high salinity. Thus, TaMPK4 is functional in regulating plant tolerance to diverse stresses through modifying various biological processes.
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Affiliation(s)
- Lin Hao
- College of Life Sciences, Agricultural University of Hebei, No. 289, Lingyusi Stresst, Baoding, 071001, People's Republic of China
| | - Yanli Wen
- College of Agronomy, Agricultural University of Hebei, No. 289, Lingyusi Stresst, Baoding, 071001, People's Republic of China
- College of Life Sciences, Agricultural University of Hebei, No. 289, Lingyusi Stresst, Baoding, 071001, People's Republic of China
| | - Yuanyuan Zhao
- College of Agronomy, Agricultural University of Hebei, No. 289, Lingyusi Stresst, Baoding, 071001, People's Republic of China
| | - Wenjing Lu
- College of Life Sciences, Agricultural University of Hebei, No. 289, Lingyusi Stresst, Baoding, 071001, People's Republic of China.
| | - Kai Xiao
- College of Agronomy, Agricultural University of Hebei, No. 289, Lingyusi Stresst, Baoding, 071001, People's Republic of China.
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43
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Root architecture, plant size and soil nutrient variation in natural populations of Arabidopsis thaliana. Evol Ecol 2015. [DOI: 10.1007/s10682-015-9808-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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44
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Airaki M, Leterrier M, Valderrama R, Chaki M, Begara-Morales JC, Barroso JB, del Río LA, Palma JM, Corpas FJ. Spatial and temporal regulation of the metabolism of reactive oxygen and nitrogen species during the early development of pepper (Capsicum annuum) seedlings. ANNALS OF BOTANY 2015; 116:679-93. [PMID: 25808658 PMCID: PMC4577988 DOI: 10.1093/aob/mcv023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 02/02/2015] [Indexed: 05/06/2023]
Abstract
BACKGROUND AND AIMS The development of seedlings involves many morphological, physiological and biochemical processes, which are controlled by many factors. Some reactive oxygen and nitrogen species (ROS and RNS, respectively) are implicated as signal molecules in physiological and phytopathological processes. Pepper (Capsicum annuum) is a very important crop and the goal of this work was to provide a framework of the behaviour of the key elements in the metabolism of ROS and RNS in the main organs of pepper during its development. METHODS The main seedling organs (roots, hypocotyls and green cotyledons) of pepper seedlings were analysed 7, 10 and 14 d after germination. Activity and gene expression of the main enzymatic antioxidants (catalase, ascorbate-glutathione cycle enzymes), NADP-generating dehydrogenases and S-nitrosoglutathione reductase were determined. Cellular distribution of nitric oxide ((·)NO), superoxide radical (O2 (·-)) and peroxynitrite (ONOO(-)) was investigated using confocal laser scanning microscopy. KEY RESULTS The metabolism of ROS and RNS during pepper seedling development was highly regulated and showed significant plasticity, which was co-ordinated among the main seedling organs, resulting in correct development. Catalase showed higher activity in the aerial parts of the seedling (hypocotyls and green cotyledons) whereas roots of 7-d-old seedlings contained higher activity of the enzymatic components of the ascorbate glutathione cycle, NADP-isocitrate dehydrogenase and NADP-malic enzyme. CONCLUSIONS There is differential regulation of the metabolism of ROS, nitric oxide and NADP dehydrogenases in the different plant organs during seedling development in pepper in the absence of stress. The metabolism of ROS and RNS seems to contribute significantly to plant development since their components are involved directly or indirectly in many metabolic pathways. Thus, specific molecules such as H2O2 and NO have implications for signalling, and their temporal and spatial regulation contributes to the success of seedling establishment.
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Affiliation(s)
- Morad Airaki
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Apartado 419, E-18080 Granada, Spain and
| | - Marina Leterrier
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Apartado 419, E-18080 Granada, Spain and
| | - Raquel Valderrama
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Biochemistry and Molecular Biology, Campus 'Las Lagunillas', University of Jaén, E-23071 Jaén, Spain
| | - Mounira Chaki
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Biochemistry and Molecular Biology, Campus 'Las Lagunillas', University of Jaén, E-23071 Jaén, Spain
| | - Juan C Begara-Morales
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Biochemistry and Molecular Biology, Campus 'Las Lagunillas', University of Jaén, E-23071 Jaén, Spain
| | - Juan B Barroso
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Biochemistry and Molecular Biology, Campus 'Las Lagunillas', University of Jaén, E-23071 Jaén, Spain
| | - Luis A del Río
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Apartado 419, E-18080 Granada, Spain and
| | - José M Palma
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Apartado 419, E-18080 Granada, Spain and
| | - Francisco J Corpas
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Apartado 419, E-18080 Granada, Spain and
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Rahaman MM, Chen D, Gillani Z, Klukas C, Chen M. Advanced phenotyping and phenotype data analysis for the study of plant growth and development. FRONTIERS IN PLANT SCIENCE 2015; 6:619. [PMID: 26322060 PMCID: PMC4530591 DOI: 10.3389/fpls.2015.00619] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 07/27/2015] [Indexed: 05/18/2023]
Abstract
Due to an increase in the consumption of food, feed, fuel and to meet global food security needs for the rapidly growing human population, there is a necessity to breed high yielding crops that can adapt to the future climate changes, particularly in developing countries. To solve these global challenges, novel approaches are required to identify quantitative phenotypes and to explain the genetic basis of agriculturally important traits. These advances will facilitate the screening of germplasm with high performance characteristics in resource-limited environments. Recently, plant phenomics has offered and integrated a suite of new technologies, and we are on a path to improve the description of complex plant phenotypes. High-throughput phenotyping platforms have also been developed that capture phenotype data from plants in a non-destructive manner. In this review, we discuss recent developments of high-throughput plant phenotyping infrastructure including imaging techniques and corresponding principles for phenotype data analysis.
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Affiliation(s)
- Md. Matiur Rahaman
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, HangzhouChina
| | - Dijun Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, HangzhouChina
- Leibniz Institute of Plant Genetics and Crop Plant Research, GaterslebenGermany
| | - Zeeshan Gillani
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, HangzhouChina
| | - Christian Klukas
- Leibniz Institute of Plant Genetics and Crop Plant Research, GaterslebenGermany
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, HangzhouChina
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46
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Bensmihen S. Hormonal Control of Lateral Root and Nodule Development in Legumes. PLANTS (BASEL, SWITZERLAND) 2015; 4:523-47. [PMID: 27135340 PMCID: PMC4844399 DOI: 10.3390/plants4030523] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/24/2015] [Accepted: 07/29/2015] [Indexed: 11/23/2022]
Abstract
Many plants can establish symbioses with nitrogen-fixing bacteria, some of which lead to nodulation, including legumes. Indeed, in the rhizobium/legume symbiosis, new root organs, called nodules, are formed by the plant in order to host the rhizobia in protective conditions, optimized for nitrogen fixation. In this way, these plants can benefit from the reduction of atmospheric dinitrogen into ammonia by the hosted bacteria, and in exchange the plant provides the rhizobia with a carbon source. Since this symbiosis is costly for the plant it is highly regulated. Both legume nodule and lateral root organogenesis involve divisions of the root inner tissues, and both developmental programs are tightly controlled by plant hormones. In fact, most of the major plant hormones, such as auxin, cytokinins, abscisic acid, and strigolactones, control both lateral root formation and nodule organogenesis, but often in an opposite manner. This suggests that the sensitivity of legume plants to some phytohormones could be linked to the antagonism that exists between the processes of nodulation and lateral root formation. Here, we will review the implication of some major phytohormones in lateral root formation in legumes, compare them with their roles in nodulation, and discuss specificities and divergences from non-legume eudicot plants such as Arabidopsis thaliana.
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Affiliation(s)
- Sandra Bensmihen
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326 Castanet-Tolosan, France.
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, F-31326 Castanet-Tolosan, France.
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47
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Fraas S, Lüthen H. Novel imaging-based phenotyping strategies for dissecting crosstalk in plant development. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4947-4955. [PMID: 26041318 DOI: 10.1093/jxb/erv265] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In an era of genomics, proteomics, and metabolomics a large number of mutants are available. The discovery of their phenotypes is fast becoming the bottleneck of molecular plant physiology. This crisis can be overcome by imaging-based phenotyping, an emerging, rapidly developing and innovative approach integrating plant and computer science. A tremendous amount of digital image data are automatically analysed using techniques of 'machine vision'. This minireview will shed light on the available imaging strategies and discuss standard methods for the automated analysis of images to give the non-bioinformatic reader an idea how the new technology works. A number of successful platforms will be described and the prospects that image-based phenomics may offer for elucidating hormonal cross-talk and molecular growth physiology will be discussed.
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Affiliation(s)
- Simon Fraas
- Biozentrum Hamburg der Universität, Physiology, Ohnhorststr. 18, D-22609 Hamburg, Germany
| | - Hartwig Lüthen
- Biozentrum Hamburg der Universität, Physiology, Ohnhorststr. 18, D-22609 Hamburg, Germany
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48
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Subramanian S, Han L, Dutilleul P, Smith DL. Computed tomography scanning can monitor the effects of soil medium on root system development: an example of salt stress in corn. FRONTIERS IN PLANT SCIENCE 2015; 6:256. [PMID: 25972876 PMCID: PMC4411998 DOI: 10.3389/fpls.2015.00256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 04/01/2015] [Indexed: 05/25/2023]
Abstract
Seeds and young seedlings often encounter high soluble salt levels in the upmost soil layers, impeding vigorous growth by affecting root establishment. Computed tomography (CT) scanning used at low X-ray doses can help study root development in such conditions non-destructively, because plants are allowed to grow throughout the experiment. Using a high-resolution Toshiba XVision CT scanner, we studied corn (Zea mays L.) root growth under optimal and salt-stressed conditions in 3D and on a weekly basis over 3 weeks. Two groups of three corn plants were grown in the controlled environment of a growth chamber, in mid-sized plastic pots filled with sieved and autoclaved sand. Seedlings were subjected to first CT scanning 1 week after seed planting. Our main research objectives concerning root systems were: (i) to quantify structural complexity from fractal dimensions estimated on skeletal 3-D images built from CT scanning data; (ii) to measure growth from volumes and lengths and the derived relative rates and increments, after isolating primary and secondary roots from the soil medium in CT scanning data; and (iii) to assess differences in complexity and growth per week and over Weeks 1-3 for groups of corn plants. Differences between groups were present from Week 1; starting in Week 2 secondary roots were present and could be isolated, which refined the complexity and growth analyses of root systems. Besides expected Week main effects (P < 0.01 or 0.05), Week × Group interaction (P < 0.05 or 0.10), and Group main effects were observed. Graphical, quantitative, and statistical analyses of CT scanning data were thus completed at an unprecedented level, and provided new and important insights regarding root system development. Repeated CT scanning is the key to a better understanding of the establishment in the soil medium of crop plants such as corn and the assessment of salt stress effects on developing root systems, in complexity, volume, and length.
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Affiliation(s)
| | | | | | - Donald L. Smith
- Department of Plant Science, McGill UniversityMontréal, QC, Canada
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49
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Marhavý P, Benková E. Real-time Analysis of Lateral Root Organogenesis in Arabidopsis. Bio Protoc 2015; 5:e1446. [PMID: 27331080 PMCID: PMC4910864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023] Open
Abstract
Plants maintain capacity to form new organs such as leaves, flowers, lateral shoots and roots throughout their postembryonic lifetime. Lateral roots (LRs) originate from a few pericycle cells that acquire attributes of founder cells (FCs), undergo series of anticlinal divisions, and give rise to a few short initial cells. After initiation, coordinated cell division and differentiation occur, giving rise to lateral root primordia (LRP). Primordia continue to grow, emerge through the cortex and epidermal layers of the primary root, and finally a new apical meristem is established taking over the responsibility for growth of mature lateral roots [for detailed description of the individual stages of lateral root organogenesis see Malamy and Benfey (1997)]. To examine this highly dynamic developmental process and to investigate a role of various hormonal, genetic and environmental factors in the regulation of lateral root organogenesis, the real time imaging based analyses represent extremely powerful tools (Laskowski et al., 2008; De Smet et al., 2012; Marhavý et al., 2013 and 2014). Herein, we describe a protocol for real time lateral root primordia (LRP) analysis, which enables the monitoring of an onset of the specific gene expression and subcellular protein localization during primordia organogenesis, as well as the evaluation of the impact of genetic and environmental perturbations on LRP organogenesis.
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Affiliation(s)
- Peter Marhavý
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Eva Benková
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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50
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Kumar P, Cai J, Miklavcic SJ. A complete system for 3D reconstruction of roots for phenotypic analysis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 823:249-70. [PMID: 25381112 DOI: 10.1007/978-3-319-10984-8_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Here we present a complete system for 3D reconstruction of roots grown in a transparent gel medium or washed and suspended in water. The system is capable of being fully automated as it is self calibrating. The system starts with detection of root tips in root images from an image sequence generated by a turntable motion. Root tips are detected using the statistics of Zernike moments on image patches centred on high curvature points on root boundary and Bayes classification rule. The detected root tips are tracked in the image sequence using a multi-target tracking algorithm. Conics are fitted to the root tip trajectories using a novel ellipse fitting algorithm which weighs the data points by its eccentricity. The conics projected from the circular trajectory have a complex conjugate intersection which are image of the circular points. Circular points constraint the image of the absolute conics which are directly related to the internal parameters of the camera. The pose of the camera is computed from the image of the rotation axis and the horizon. The silhouettes of the roots and camera parameters are used to reconstruction the 3D voxel model of the roots. We show the results of real 3D reconstruction of roots which are detailed and realistic for phenotypic analysis.
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Affiliation(s)
- Pankaj Kumar
- School of Information Technology and Mathematical Sciences, Phenomics and Bioinformatics Research Centre, Australian Centre for Plant Functional Genomics, University of South Australia, Mawson Lakes, SA, 5095, Australia,
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