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Pélissier PM, Parizot B, Jia L, De Knijf A, Goossens V, Gantet P, Champion A, Audenaert D, Xuan W, Beeckman T, Motte H. Nitrate and ammonium, the yin and yang of nitrogen uptake: a time-course transcriptomic study in rice. FRONTIERS IN PLANT SCIENCE 2024; 15:1343073. [PMID: 39246813 PMCID: PMC11377263 DOI: 10.3389/fpls.2024.1343073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 07/29/2024] [Indexed: 09/10/2024]
Abstract
Nitrogen is an essential nutrient for plants and a major determinant of plant growth and crop yield. Plants acquire nitrogen mainly in the form of nitrate and ammonium. Both nitrogen sources affect plant responses and signaling pathways in a different way, but these signaling pathways interact, complicating the study of nitrogen responses. Extensive transcriptome analyses and the construction of gene regulatory networks, mainly in response to nitrate, have significantly advanced our understanding of nitrogen signaling and responses in model plants and crops. In this study, we aimed to generate a more comprehensive gene regulatory network for the major crop, rice, by incorporating the interactions between ammonium and nitrate. To achieve this, we assessed transcriptome changes in rice roots and shoots over an extensive time course under single or combined applications of the two nitrogen sources. This dataset enabled us to construct a holistic co-expression network and identify potential key regulators of nitrogen responses. Next to known transcription factors, we identified multiple new candidates, including the transcription factors OsRLI and OsEIL1, which we demonstrated to induce the primary nitrate-responsive genes OsNRT1.1b and OsNIR1. Our network thus serves as a valuable resource to obtain novel insights in nitrogen signaling.
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Affiliation(s)
- Pierre-Mathieu Pélissier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Boris Parizot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Letian Jia
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and MOA Key Laboratory of Plant Nutrition and Fertilization in Lower Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, China
| | - Alexa De Knijf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Vera Goossens
- Center for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
- VIB Screening Core, Ghent, Belgium
| | - Pascal Gantet
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Antony Champion
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Dominique Audenaert
- Center for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
- VIB Screening Core, Ghent, Belgium
| | - Wei Xuan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and MOA Key Laboratory of Plant Nutrition and Fertilization in Lower Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, China
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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2
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Phukan UJ, Jindal S, Laldinsangi C, Singh PK, Longchar B. A microscopic scenario on recovery mechanisms under waterlogging and submergence stress in rice. PLANTA 2023; 259:9. [PMID: 38030751 DOI: 10.1007/s00425-023-04285-y] [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: 09/01/2023] [Accepted: 11/08/2023] [Indexed: 12/01/2023]
Abstract
MAIN CONCLUSION Adaptive traits in rice responding to flooding, a compound stress, are associated with morpho-anatomical and physiological changes which are regulated at the genetic level. Therefore, understanding submergence stress tolerance in rice will help development of adapted cultivars that can help mitigate agricultural losses. Rice is an important dietary component of daily human consumption and is cultivated as a staple crop worldwide. Flooding is a compound stress which imposes significant financial losses to farmers. Flood-affected rainfed rice ecosystems led to the development of various adaptive traits in different cultivars for their optimal growth and survival. Some cultivars can tolerate hypoxia by temporarily arresting elongation and conserving their energy sources, which they utilize to regrow after the stress conditions subside. However, few other cultivars rapidly elongate to escape hypoxia using carbohydrate resources. These contrasting characters are regulated at the genetic level through different quantitative trait loci that contain ERF transcription factors (TFs), Submergence and Snorkels. TFs can simultaneously activate the transcription of various genes involved in stress and development responses. These TFs are of prime importance because the introgressed and near-isogenic lines showed promising results with increased submergence tolerance without affecting yield or quality. However, the entire landscape of submergence tolerance is not entirely depicted, and further exploration in the field is necessary to understand the mechanism in rice completely. Therefore, this review will highlight the significant adaptive traits observed in flooded rice varieties and how they are regulated mechanistically.
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Affiliation(s)
- Ujjal J Phukan
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721-0036, USA
| | - Sunita Jindal
- Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic
| | - C Laldinsangi
- Department of Life Sciences, Pachhunga University College, Mizoram University, Aizawl, 796001, Mizoram, India
| | - Prashant Kumar Singh
- Department of Biotechnology, Pachhunga University College, Mizoram University, Aizawl, 796001, Mizoram, India
- Institute of Plant Sciences, Agricultural Research Organization (ARO), Volcani Center, 68 HaMacabim Road, 7505101, Rishon Lezion, Israel
| | - Bendangchuchang Longchar
- Department of Life Sciences, Pachhunga University College, Mizoram University, Aizawl, 796001, Mizoram, India.
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Wang Q, Zhang L, Wang L, Bu L. A practical method for predicting and analyzing the consequences of ammonium nitrate explosion accidents adjacent to densely populated areas. Heliyon 2023; 9:e15616. [PMID: 37159714 PMCID: PMC10163611 DOI: 10.1016/j.heliyon.2023.e15616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 04/09/2023] [Accepted: 04/17/2023] [Indexed: 05/11/2023] Open
Abstract
Several catastrophic ammonium nitrate (AN) explosion accidents have been reported during the last decades. Previous studies have been mainly focused on investigating adverse effects caused by the AN explosion, while only a few systematically analyzed the consequences and impacts of AN explosions. This study collects data from three typical AN explosions (accidental explosion of the US fertilizer plant in 2013; an accidental explosion of China's Tianjin port in 2015, and a recent explosion (2020) of the Beirut port in Lebanon). The consequences of accidental explosions were analyzed by mathematical equations that further provide scientific explanations for AN explosions. Based on the explosives' properties on-site, these accidental explosions were caused by condensed phase explosives. Comparison with the conditions at the explosion site indicated that blast overpressure was the primary factor in the loss of life and damage to the building, while ground shock was a secondary factor. The severity of loss of life and building damage from explosions decreased with increasing distance. These distances could be calculated by the scaling law, which was replaced by the equivalent TNT mass of the explosive and the damage scale's overpressure boundary value. In addition, mapping the damaged area on a map helped in the visual presentation of the consequence assessment. The long-term environmental and ecological impact due to the explosions was also an important issue that could not be ignored. Overall, this study establishes a simple and easy-to-use method to rapidly predict and assess the consequences of an explosion, and provides technical guidance for future emergency response to similar large-scale accidents.
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Affiliation(s)
- Qiang Wang
- Corresponding author. Chinese PLA Center for Disease Control and Prevention, 20 Dongda Street, Beijing, 100071, China.
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Theerawitaya C, Supaibulwatana K, Tisarum R, Samphumphuang T, Chungloo D, Singh HP, Cha-Um S. Expression levels of nitrogen assimilation-related genes, physiological responses, and morphological adaptations of three indica rice (Oryza sativa L. ssp. indica) genotypes subjected to nitrogen starvation conditions. PROTOPLASMA 2023; 260:691-705. [PMID: 36056227 DOI: 10.1007/s00709-022-01806-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Nitrogen (N) is an essential nutrient available to the plants in form of nitrate and ammonium. It is a macronutrient important for the plant growth and development, especially in cereal crops, which consume it for the production of amino acids, proteins/enzymes, nucleic acids, cell wall complexes, plant hormones, and vitamins. In rice production, 17 kg N uptake is required to produce 1 ton of rice. Considering this, many techniques have been developed to evaluate leaf greenness or SPAD value for assessing the amount of N application in the rice cultivar to maximize the grain yield. The aim of the present study was to investigate the morpho-physiological characteristics and relative expression level of N assimilation in three different rice genotypes (MT2, RD31, KDML105) under 1.00 × (full N), 0.50 × , 0.25 × (N depletion), and 0.00 × (N deficiency) at seedling stage and the morpho-physiological traits and the grain yield attributes under 1.00 × (full N) and 0.25 × (N depletion) were compared. Leaf chlorosis and growth inhibition in rice seedlings under N deficiency were evidently observed. Shoot height, number of leaves, shoot fresh weight, shoot dry weight, and root fresh weight in KDML105 under N deficiency were decreased by 27.65%, 42.11%, 65.44%, 47.90%, and 54.09% over the control (full N). Likewise, leaf greenness was lowest in KDML105 under N deficiency (78.57% reduction over the full N), leading to low photosynthetic abilities. In addition, expression of nitrogen assimilation-related genes, OsNR1, OsGln1;1, and OsGln2, in KDML105 under N depletion were increased within 3 h and then declined after the long incubation period, whereas those were unchanged in cvs. MT2 and RD31. Similarly, relative expression level of OsNADH-GOGAT, OsFd-GOGAT, and OsAspAt1 in KDML105 was peaked when subjected to 0.50 × N for 6 h and then declined after the long incubation period. Moreover, overall growth characters and physiological changes in cv. RD31 at vegetative stage under 0.25 × N were retained better than those in cvs. KDML105 and MT2, resulting in high yield at the harvesting process. In summary, N assimilated-related genes in rice seedlings under N depletion were rapidly regulated within 3-6 h, especially cv. KDML105 and MT2, then downregulated, resulting in physiological changes, growth inhibition, and yield reduction.
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Affiliation(s)
- Cattarin Theerawitaya
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Kanyaratt Supaibulwatana
- Department of Biotechnology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok, 10400, Thailand
| | - Rujira Tisarum
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Thapanee Samphumphuang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Daonapa Chungloo
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Harminder Pal Singh
- Department of Environment Studies, Faculty of Science, Panjab University, Chandigarh, 160014, India
| | - Suriyan Cha-Um
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand.
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Govindasamy P, Muthusamy SK, Bagavathiannan M, Mowrer J, Jagannadham PTK, Maity A, Halli HM, G. K. S, Vadivel R, T. K. D, Raj R, Pooniya V, Babu S, Rathore SS, L. M, Tiwari G. Nitrogen use efficiency-a key to enhance crop productivity under a changing climate. FRONTIERS IN PLANT SCIENCE 2023; 14:1121073. [PMID: 37143873 PMCID: PMC10151540 DOI: 10.3389/fpls.2023.1121073] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/20/2023] [Indexed: 05/06/2023]
Abstract
Nitrogen (N) is an essential element required for the growth and development of all plants. On a global scale, N is agriculture's most widely used fertilizer nutrient. Studies have shown that crops use only 50% of the applied N effectively, while the rest is lost through various pathways to the surrounding environment. Furthermore, lost N negatively impacts the farmer's return on investment and pollutes the water, soil, and air. Therefore, enhancing nitrogen use efficiency (NUE) is critical in crop improvement programs and agronomic management systems. The major processes responsible for low N use are the volatilization, surface runoff, leaching, and denitrification of N. Improving NUE through agronomic management practices and high-throughput technologies would reduce the need for intensive N application and minimize the negative impact of N on the environment. The harmonization of agronomic, genetic, and biotechnological tools will improve the efficiency of N assimilation in crops and align agricultural systems with global needs to protect environmental functions and resources. Therefore, this review summarizes the literature on nitrogen loss, factors affecting NUE, and agronomic and genetic approaches for improving NUE in various crops and proposes a pathway to bring together agronomic and environmental needs.
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Affiliation(s)
- Prabhu Govindasamy
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Muthukumar Bagavathiannan, ; Prabhu Govindasamy,
| | - Senthilkumar K. Muthusamy
- Division of Crop Improvement, Indian Council of Agricultural Research (ICAR)-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | - Muthukumar Bagavathiannan
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- *Correspondence: Muthukumar Bagavathiannan, ; Prabhu Govindasamy,
| | - Jake Mowrer
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | | | - Aniruddha Maity
- Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Hanamant M. Halli
- School of Soil Stress Management, Indian Council of Agricultural Research (ICAR)-National Institute of Abiotic Stress Management, Pune, India
| | - Sujayananad G. K.
- Crop Protection, Indian Council of Agricultural Research (ICAR)-Indian Institute of Pulse Research, Kanpur, India
| | - Rajagopal Vadivel
- School of Soil Stress Management, Indian Council of Agricultural Research (ICAR)-National Institute of Abiotic Stress Management, Pune, India
| | - Das T. K.
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Rishi Raj
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Vijay Pooniya
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Subhash Babu
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Sanjay Singh Rathore
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Muralikrishnan L.
- Division of Agricultural Extension, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Gopal Tiwari
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
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6
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Shanks CM, Huang J, Cheng CY, Shih HJS, Brooks MD, Alvarez JM, Araus V, Swift J, Henry A, Coruzzi GM. Validation of a high-confidence regulatory network for gene-to-NUE phenotype in field-grown rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1006044. [PMID: 36507422 PMCID: PMC9732682 DOI: 10.3389/fpls.2022.1006044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/01/2022] [Indexed: 05/03/2023]
Abstract
Nitrogen (N) and Water (W) - two resources critical for crop productivity - are becoming increasingly limited in soils globally. To address this issue, we aim to uncover the gene regulatory networks (GRNs) that regulate nitrogen use efficiency (NUE) - as a function of water availability - in Oryza sativa, a staple for 3.5 billion people. In this study, we infer and validate GRNs that correlate with rice NUE phenotypes affected by N-by-W availability in the field. We did this by exploiting RNA-seq and crop phenotype data from 19 rice varieties grown in a 2x2 N-by-W matrix in the field. First, to identify gene-to-NUE field phenotypes, we analyzed these datasets using weighted gene co-expression network analysis (WGCNA). This identified two network modules ("skyblue" & "grey60") highly correlated with NUE grain yield (NUEg). Next, we focused on 90 TFs contained in these two NUEg modules and predicted their genome-wide targets using the N-and/or-W response datasets using a random forest network inference approach (GENIE3). Next, to validate the GENIE3 TF→target gene predictions, we performed Precision/Recall Analysis (AUPR) using nine datasets for three TFs validated in planta. This analysis sets a precision threshold of 0.31, used to "prune" the GENIE3 network for high-confidence TF→target gene edges, comprising 88 TFs and 5,716 N-and/or-W response genes. Next, we ranked these 88 TFs based on their significant influence on NUEg target genes responsive to N and/or W signaling. This resulted in a list of 18 prioritized TFs that regulate 551 NUEg target genes responsive to N and/or W signals. We validated the direct regulated targets of two of these candidate NUEg TFs in a plant cell-based TF assay called TARGET, for which we also had in planta data for comparison. Gene ontology analysis revealed that 6/18 NUEg TFs - OsbZIP23 (LOC_Os02g52780), Oshox22 (LOC_Os04g45810), LOB39 (LOC_Os03g41330), Oshox13 (LOC_Os03g08960), LOC_Os11g38870, and LOC_Os06g14670 - regulate genes annotated for N and/or W signaling. Our results show that OsbZIP23 and Oshox22, known regulators of drought tolerance, also coordinate W-responses with NUEg. This validated network can aid in developing/breeding rice with improved yield on marginal, low N-input, drought-prone soils.
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Affiliation(s)
- Carly M. Shanks
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, United States
| | - Ji Huang
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, United States
| | - Chia-Yi Cheng
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, United States
- Department of Life Science, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Hung-Jui S. Shih
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, United States
| | - Matthew D. Brooks
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, United States
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture (USDA) Agricultural Research Service (ARS), Urbana, IL, United States
| | - José M. Alvarez
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, United States
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Agencia Nacional de Investigación y Desarrollo–Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Viviana Araus
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, United States
- Agencia Nacional de Investigación y Desarrollo–Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Joseph Swift
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, United States
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Amelia Henry
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Gloria M. Coruzzi
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, United States
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Kawai M, Tabata R, Ohashi M, Honda H, Kamiya T, Kojima M, Takebayashi Y, Oishi S, Okamoto S, Hachiya T, Sakakibara H. Regulation of ammonium acquisition and use in Oryza longistaminata ramets under nitrogen source heterogeneity. PLANT PHYSIOLOGY 2022; 188:2364-2376. [PMID: 35134987 PMCID: PMC8968255 DOI: 10.1093/plphys/kiac025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/18/2021] [Indexed: 05/31/2023]
Abstract
Oryza longistaminata, a wild rice, vegetatively reproduces and forms a networked clonal colony consisting of ramets connected by rhizomes. Although water, nutrients, and other molecules can be transferred between ramets via the rhizomes, inter-ramet communication in response to spatially heterogeneous nitrogen availability is not well understood. We studied the response of ramet pairs to heterogeneous nitrogen availability using a split hydroponic system that allowed each ramet root to be exposed to different conditions. Ammonium uptake was compensatively enhanced in the sufficient-side root when roots of the ramet pairs were exposed to ammonium-sufficient and ammonium-deficient conditions. Comparative transcriptome analysis revealed that a gene regulatory network for effective ammonium assimilation and amino acid biosynthesis was activated in the sufficient-side roots. Allocation of absorbed nitrogen from the nitrogen-sufficient to the nitrogen-deficient ramets was rather limited. Nitrogen was preferentially used for newly growing axillary buds on the sufficient-side ramets. Biosynthesis of trans-zeatin (tZ), a cytokinin, was upregulated in response to the nitrogen supply, but tZ appeared not to target the compensatory regulation. Our results also implied that the O. longistaminata putative ortholog of rice (Oryza sativa) C-terminally encoded peptide1 plays a role as a nitrogen-deficient signal in inter-ramet communication, providing compensatory upregulation of nitrogen assimilatory genes. These results provide insights into the molecular basis for efficient growth strategies of asexually proliferating plants growing in areas where the distribution of ammonium ions is spatially heterogeneous.
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Affiliation(s)
- Misato Kawai
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Ryo Tabata
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Miwa Ohashi
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Haruno Honda
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Takehiro Kamiya
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Yumiko Takebayashi
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Shunsuke Oishi
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya464-8602, Japan
| | - Satoru Okamoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Takushi Hachiya
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
- Department of Molecular and Function Genomics, Interdisciplinary Center for Science Research, Shimane University, Matsue 690-8504, Japan
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Mandal VK, Jangam AP, Chakraborty N, Raghuram N. Nitrate-responsive transcriptome analysis reveals additional genes/processes and associated traits viz. height, tillering, heading date, stomatal density and yield in japonica rice. PLANTA 2022; 255:42. [PMID: 35038039 DOI: 10.1007/s00425-021-03816-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/27/2021] [Indexed: 05/22/2023]
Abstract
Our transcriptomic analysis expanded the repertoire of nitrate-responsive genes/processes in rice and revealed their phenotypic association with root/shoot, stomata, tiller, panicle/flowering and yield, with agronomic implications for nitrogen use efficiency. Nitrogen use efficiency (NUE) is a multigenic quantitative trait, involving many N-responsive genes/processes that are yet to be fully characterized. Microarray analysis of early nitrate response in excised leaves of japonica rice revealed 6688 differentially expressed genes (DEGs), including 2640 hitherto unreported across multiple functional categories. They include transporters, enzymes involved in primary/secondary metabolism, transcription factors (TFs), EF-hand containing calcium binding proteins, hormone metabolism/signaling and methytransferases. Some DEGs belonged to hitherto unreported processes viz. alcohol, lipid and trehalose metabolism, mitochondrial membrane organization, protein targeting and stomatal opening. 1158 DEGs were associated with growth physiology and grain yield or phenotypic traits for NUE. We identified seven DEGs for shoot apical meristem, 66 for leaf/culm/root, 31 for tiller, 70 for heading date/inflorescence/spikelet/panicle, 144 for seed and 78 for yield. RT-qPCR validated nitrate regulation of 31 DEGs belonging to various important functional categories/traits. Physiological validation of N-dose responsive changes in plant development revealed that relative to 1.5 mM, 15 mM nitrate significantly increased stomatal density, stomatal conductance and transpiration rate. Further, root/shoot growth, number of tillers and grain yield declined and panicle emergence/heading date delayed, despite increased photosynthetic rate. We report the binding sites of diverse classes of TFs such as WRKY, MYB, HMG etc., in the 1 kb up-stream regions of 6676 nitrate-responsive DEGs indicating their role in regulating nitrate response/NUE. Together, these findings expand the repertoire of genes and processes involved in genomewide nitrate response in rice and reveal their physiological, phenotypic and agronomic implications for NUE.
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Affiliation(s)
- Vikas Kumar Mandal
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, India
| | - Annie Prasanna Jangam
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, India
| | - Navjyoti Chakraborty
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, India
| | - Nandula Raghuram
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, India.
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Zhang C, Luo JJ, Zuo JB, Zhang Z, Wang ST, Zhang XJ, Fu TS, Feng YL. Transcripts related with ammonium use and effects of gibberellin on expressions of the transcripts responding to ammonium in two invasive and native Xanthium species. FRONTIERS IN PLANT SCIENCE 2022; 13:1035137. [PMID: 36388472 PMCID: PMC9644049 DOI: 10.3389/fpls.2022.1035137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/11/2022] [Indexed: 05/22/2023]
Abstract
Soil nitrogen forms are important for exotic plant invasions. However, little effort has been made to study the molecular mechanisms underlying the utilization of different N forms in co-occurring invasive and native plants. The invasive plant Xanthium strumarium prefers nitrate relative to ammonium, and mainly invades nitrate-dominated environments, while it co-occurring native congener X. sibiricum prefers ammonium. Here, we addressed the genetic bases for the interspecific difference in ammonium use and the effects of gibberellin (GA). Twenty-six transcripts related with GA biosynthesis and ammonium utilization were induced by ammonium in X. sibiricum, while only ten in X. strumarium and none for ammonium uptake. XsiAMT1.1a, XsiGLN1.1 and XsiGLT1b may be crucial for the strong ability to absorb and assimilate ammonium in X. sibiricum. All tested transcripts were significantly up-regulated by GA1 and GA4 in X. sibiricum. XsiGA3OX1a, which was also induced by ammonium, may be involved in this regulation. Consistently, glutamine synthetase activity increased significantly with increasing ammonium-N/nitrate-N ratio for X. sibiricum, while decreased for X. strumarium. Our study is the first to determine the molecular mechanisms with which invasive and native plants use ammonium differently, contributing to understanding the invasion mechanisms of X. strumarium and its invasion habitat selection.
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Affiliation(s)
- Chang Zhang
- Liaoning Key Laboratory for Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Jia-Jun Luo
- Liaoning Key Laboratory for Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Jing-Bo Zuo
- Liaoning Key Laboratory for Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Zheng Zhang
- Liaoning Key Laboratory for Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Shi-Ting Wang
- Liaoning Key Laboratory for Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xiao-Jia Zhang
- Liaoning Key Laboratory for Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Tian-Si Fu
- Liaoning Key Laboratory for Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yu-Long Feng
- Liaoning Key Laboratory for Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
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10
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Guha T, Gopal G, Mukherjee A, Kundu R. Fe 3O 4-urea nanocomposites as a novel nitrogen fertilizer for improving nutrient utilization efficiency and reducing environmental pollution. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 292:118301. [PMID: 34626716 DOI: 10.1016/j.envpol.2021.118301] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 09/02/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
Almost 81% of nitrogen fertilizers are applied in form of urea but most of it is lost due to volatilization and leaching leading to environmental pollution. In this regard, slow-release nano fertilizers can be an effective solution. Here, we have synthesized different Fe3O4-urea nanocomposites with Fe3O4 NPs: urea ratio (1:1, 1:2, 1:3) ie. NC-1, 2, and 3 respectively, and checked their efficacy for growth and yield enhancement. Oryza sativa L. cv. Swarna seedlings were treated with different NCs for 14 days in hydroponic conditions and significant up-regulation of photosynthetic efficiency and nitrogen metabolism were observed due to increased availability of nitrogen and iron. The discriminant functional analysis confirmed that the NC3 treatment yielded the best results so further gene expression studies were performed for NC-3 treated seedlings. Significant changes in expression profiles of ammonia and nitrate transporters indicated that NC-3 treatment enhanced nitrogen utilization efficiency (NUE) due to sustained slow release of urea. From pot experiments, we found significant enhancement of growth, grain nutrient content, and NUE in NC supplemented sets. 1.45 fold increase in crop yield was achieved when 50% N was supplemented in form of NC-3 and the rest in form of ammonium nitrate. NC supplementation can also play a vital role in minimizing the use of bulk N fertilizers because, when 75% of the recommended N dose was supplied in form of NC-3, 1.18 fold yield enhancement was found. Thus our results highlight that, slow-release NC-3 can play a major role in increasing the NUE of rice.
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Affiliation(s)
- Titir Guha
- Centre of Advanced Study, Department of Botany, Calcutta University, 35, Ballygange Circular Road, Kolkata-19, India
| | - Geetha Gopal
- Centre for Nanobiotechnology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Amitava Mukherjee
- Centre for Nanobiotechnology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Rita Kundu
- Centre of Advanced Study, Department of Botany, Calcutta University, 35, Ballygange Circular Road, Kolkata-19, India.
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11
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Buoso S, Tomasi N, Said-Pullicino D, Arkoun M, Yvin JC, Pinton R, Zanin L. Characterization of physiological and molecular responses of Zea mays seedlings to different urea-ammonium ratios. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 162:613-623. [PMID: 33774466 DOI: 10.1016/j.plaphy.2021.03.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/16/2021] [Indexed: 05/14/2023]
Abstract
Despite the wide use of urea and ammonium as N-fertilizers, no information is available about the proper ratio useful to maximize the efficiency of their acquisition by crops. Ionomic analyses of maize seedlings fed with five different mixes of urea and ammonium indicated that after 7 days of treatment, the elemental composition of plant tissues was more influenced by ammonium in the nutrient solution than by urea. Within 24 h, similar high affinity influx rates of ammonium were measured in ammonium-treated seedlings, independently from the amount of the cation present in the nutrient solution (from 0.5 to 2.0 mM N), and it was confirmed by the similar accumulation of 15N derived from ammonium source. After 7 days, some changes in ammonium acquisition occurred among treatments, with the highest ammonium uptake efficiency when the urea-to-ammonium ratio was 3:1. Gene expression analyses of enzymes and transporters involved in N nutrition highlight a preferential induction of the cytosolic N-assimilatory pathway (via GS, ASNS) when both urea and ammonium were supplied in conjunction, this response might explain the higher N-acquisition efficiency when both sources are applied. In conclusion, this study provides new insights on plant responses to mixes of N sources that maximize the N-uptake efficiency by crops and thus could allow to adapt agronomic practices in order to limit the economic and environmental impact of N-fertilization.
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Affiliation(s)
- Sara Buoso
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy.
| | - Nicola Tomasi
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy.
| | - Daniel Said-Pullicino
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy.
| | - Mustapha Arkoun
- Laboratoire de Nutrition Végétale, Centre Mondial de l'Innovation, Groupe Roullier, Saint-Malo, France.
| | - Jean-Claude Yvin
- Laboratoire de Nutrition Végétale, Centre Mondial de l'Innovation, Groupe Roullier, Saint-Malo, France.
| | - Roberto Pinton
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy.
| | - Laura Zanin
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy.
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12
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Takehisa H, Sato Y. Transcriptome-based approaches for clarification of nutritional responses and improvement of crop production. BREEDING SCIENCE 2021; 71:76-88. [PMID: 33762878 PMCID: PMC7973498 DOI: 10.1270/jsbbs.20098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/01/2020] [Indexed: 06/12/2023]
Abstract
Genome-wide transcriptome profiling is a powerful tool for identifying key genes and pathways involved in plant development and physiological processes. This review summarizes studies that have used transcriptome profiling mainly in rice to focus on responses to macronutrients such as nitrogen, phosphorus and potassium, and spatio-temporal root profiling in relation to the regulation of root system architecture as well as nutrient uptake and transport. We also discuss strategies based on meta- and co-expression analyses with different attributed transcriptome data, which can be used for investigating the regulatory mechanisms and dynamics of nutritional responses and adaptation, and speculate on further advances in transcriptome profiling that could have potential application to crop breeding and cultivation.
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Affiliation(s)
- Hinako Takehisa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yutaka Sato
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
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13
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Marzec M, Situmorang A, Brewer PB, Brąszewska A. Diverse Roles of MAX1 Homologues in Rice. Genes (Basel) 2020; 11:E1348. [PMID: 33202900 PMCID: PMC7709044 DOI: 10.3390/genes11111348] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/30/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023] Open
Abstract
Cytochrome P450 enzymes encoded by MORE AXILLARY GROWTH1 (MAX1)-like genes produce most of the structural diversity of strigolactones during the final steps of strigolactone biosynthesis. The diverse copies of MAX1 in Oryza sativa provide a resource to investigate why plants produce such a wide range of strigolactones. Here we performed in silico analyses of transcription factors and microRNAs that may regulate each rice MAX1, and compared the results with available data about MAX1 expression profiles and genes co-expressed with MAX1 genes. Data suggest that distinct mechanisms regulate the expression of each MAX1. Moreover, there may be novel functions for MAX1 homologues, such as the regulation of flower development or responses to heavy metals. In addition, individual MAX1s could be involved in specific functions, such as the regulation of seed development or wax synthesis in rice. Our analysis reveals potential new avenues of strigolactone research that may otherwise not be obvious.
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Affiliation(s)
- Marek Marzec
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland;
| | - Apriadi Situmorang
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (A.S.); (P.B.B.)
| | - Philip B. Brewer
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (A.S.); (P.B.B.)
| | - Agnieszka Brąszewska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland;
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14
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To HTM, Le KQ, Van Nguyen H, Duong LV, Kieu HT, Chu QAT, Tran TP, Mai NTP. A genome-wide association study reveals the quantitative trait locus and candidate genes that regulate phosphate efficiency in a Vietnamese rice collection. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2267-2281. [PMID: 33268928 PMCID: PMC7688854 DOI: 10.1007/s12298-020-00902-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/12/2020] [Accepted: 10/17/2020] [Indexed: 05/21/2023]
Abstract
The crucial role of phosphate (Pi) for plant alongside the expected depletion of non-renewable phosphate rock have created an urgent need for phosphate-efficient rice varieties. In this study, 157 greenhouse-grown Vietnamese rice landraces were treated under Pi-deficient conditions to discover the genotypic variation among biochemical traits, including relative efficiency of phosphorus use (REP), relative root to shoot weight ratio (RRSR), relative physiological phosphate use efficiency (RPPUE), and relative phosphate uptake efficiency (RPUpE). Plants were grown in Yoshida nutrient media with either a full (320 μM) or a low Pi supply (10 μM) over six weeks. This genome-wide association study led to the discovery of 31 significant single nucleotide polymorphisms, 18 quantitative trait loci (QTLs), and 85 candidate genes. A common QTL named qRPUUE9.16 was found among the three investigated traits. Some interesting candidate genes, such as PLASMA MEMBRANE PROTEIN1 (OsPM1), CALMODULIN-RELATED CALCIUM SENSOR PROTEIN 15 (OsCML15), phosphatases 2C (PP2C), STRESS-ACTIVATED PROTEIN KINASE (OsSAPK2), and GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASES (GDPD13), were found strongly correlated to the Pi starvation. RNA sequencing transcriptomes revealed that 45 out of 85 candidate genes were significantly regulated under Pi starvation. Furthermore, nearly two-thirds of genotypes did not possess the OsPsTOL1 gene; however, no significant difference was observed in response to Pi deficiency between genotypes with or without this gene, suggesting that other QTLs in rice may resist Pi starvation. These results provide new information on the genetics of nutrient use efficiency in rice and may potentially assist with developing more phosphate-efficient rice plants.
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Affiliation(s)
- Huong Thi Mai To
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Khang Quoc Le
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Hiep Van Nguyen
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Linh Viet Duong
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Hanh Thi Kieu
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Quynh Anh Thi Chu
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Trang Phuong Tran
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Nga T. P. Mai
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
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15
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Shao CH, Qiu CF, Qian YF, Liu GR. Nitrate deficiency decreased photosynthesis and oxidation-reduction processes, but increased cellular transport, lignin biosynthesis and flavonoid metabolism revealed by RNA-Seq in Oryza sativa leaves. PLoS One 2020; 15:e0235975. [PMID: 32649704 PMCID: PMC7351185 DOI: 10.1371/journal.pone.0235975] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 06/26/2020] [Indexed: 11/19/2022] Open
Abstract
Rice cultivar "Weiyou916" (Oryza sativa L. ssp. Indica) were cultured with control (10 mM NO3-) and nitrate deficient solution (0 mM NO3-) for four weeks. Nitrogen (N) deficiency significantly decreased the content of N and P, dry weight (DW) of the shoots and roots, but increased the ratio of root to shoot in O. sativa. N deficiency decreased the photosynthesis rate and the maximum quantum yield of primary photochemistry (Fv/Fm), however, increased the intercellular CO2 concentration and primary fluorescence (Fo). N deficiency significantly increased the production of H2O2 and membrane lipid peroxidation revealed as increased MDA content in O. sativa leaves. N deficiency significantly increased the contents of starch, sucrose, fructose, and malate, but did not change that of glucose and total soluble protein in O. sativa leaves. The accumulated carbohydrates and H2O2 might further accelerate biosynthesis of lignin in O. sativa leaves under N limitation. A total of 1635 genes showed differential expression in response to N deficiency revealed by Illumina sequencing. Gene Ontology (GO) analysis showed that 195 DEGs were found to highly enrich in nine GO terms. Most of DEGs involved in photosynthesis, biosynthesis of ethylene and gibberellins were downregulated, whereas most of DEGs involved in cellular transport, lignin biosynthesis and flavonoid metabolism were upregulated by N deficiency in O. sativa leaves. Results of real-time quantitative PCR (RT-qPCR) further verified the RNA-Seq data. For the first time, DEGs involved oxygen-evolving complex, phosphorus response and lignin biosynthesis were identified in rice leaves. Our RNA-Seq data provided a global view of transcriptomic profile of principal processes implicated in the adaptation of N deficiency in O. sativa and shed light on the candidate direction in rice breeding for green and sustainable agriculture.
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Affiliation(s)
- Cai-Hong Shao
- Institute of Soil Fertilizer and Resources Environment, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Cai-Fei Qiu
- Institute of Soil Fertilizer and Resources Environment, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Yin-Fei Qian
- Institute of Soil Fertilizer and Resources Environment, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Guang-Rong Liu
- Institute of Soil Fertilizer and Resources Environment, Jiangxi Academy of Agricultural Sciences, Nanchang, China
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16
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Thi Nong H, Tateishi R, Suriyasak C, Kobayashi T, Oyama Y, Chen WJ, Matsumoto R, Hamaoka N, Iwaya-Inoue M, Ishibashi Y. Effect of Seedling Nitrogen Condition on Subsequent Vegetative Growth Stages and Its Relationship to the Expression of Nitrogen Transporter Genes in Rice. PLANTS (BASEL, SWITZERLAND) 2020; 9:E861. [PMID: 32646051 PMCID: PMC7412562 DOI: 10.3390/plants9070861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/23/2020] [Accepted: 07/03/2020] [Indexed: 11/17/2022]
Abstract
Nitrogen (N) deficiency is one of the most common problems in soils, limiting crop growth and production. However, the effects of N limitation in seedlings on vegetative growth remain poorly understood. Here, we show that N limitation in rice seedlings restricted vegetative growth but not yield. Aboveground parts were affected mainly during the period of tillering, but belowground parts were sensitive throughout vegetative growth, especially during panicle development. At the tillering stage, N-limited plants had a significantly lower N content in shoots, but not in roots. On the other hand, N content in roots during the panicle development stage was significantly lower in N-limited plants. This distinct response was driven by significant changes in expression of N transporter genes during growth. Under N limitation, N translocation from roots to shoots was greatly sped up by systemic expression of N transporter genes to obtain balanced growth. N limitation during the seedling stage did not reduce any yield components. We conclude that the N condition during the seedling stage affects physiological responses such as N translocation through the expression of N transporter genes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yushi Ishibashi
- Graduate school of Bioresource and Bioenviromental Sciences, Kyushu University, Mootoka 774, Fukuoka 819–0395, Japan; (H.T.N.); (R.T.); (C.S.); (T.K.); (Y.O.); (W.J.C.); (R.M.); (N.H.); (M.I.-I.)
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17
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Wang R, Qian J, Fang Z, Tang J. Transcriptomic and physiological analyses of rice seedlings under different nitrogen supplies provide insight into the regulation involved in axillary bud outgrowth. BMC PLANT BIOLOGY 2020; 20:197. [PMID: 32380960 PMCID: PMC7206722 DOI: 10.1186/s12870-020-02409-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/28/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND N is an important macronutrient required for plant development and significantly influences axillary bud outgrowth, which affects tillering and grain yield of rice. However, how different N concentrations affect axillary bud growth at the molecular and transcriptional levels remains unclear. RESULTS In this study, morphological changes in the axillary bud growth of rice seedlings under different N concentrations ranging from low to high levels were systematically observed. To investigate the expression of N-induced genes involved in axillary bud growth, we used RNA-seq technology to generate mRNA transcriptomic data from two tissue types, basal parts and axillary buds, of plants grown under six different N concentrations. In total, 10,221 and 12,180 DEGs induced by LN or HN supplies were identified in the basal parts and axillary buds, respectively, via comparisons to expression levels under NN level. Analysis of the coexpression modules from the DEGs of the basal parts and axillary buds revealed an abundance of related biological processes underlying the axillary bud growth of plants under N treatments. Among these processes, the activity of cell division and expansion was positively correlated with the growth rate of axillary buds of plants grown under different N supplies. Additionally, TFs and phytohormones were shown to play roles in determining the axillary bud growth of plants grown under different N concentrations. We have validated the functions of OsGS1;2 and OsGS2 through the rice transgenic plants with altered tiller numbers, illustrating the important valve of our transcriptomic data. CONCLUSION These results indicate that different N concentrations affect the axillary bud growth rate, and our study show comprehensive expression profiles of genes that respond to different N concentrations, providing an important resource for future studies attempting to determine how axillary bud growth is controlled by different N supplies.
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Affiliation(s)
- Rongna Wang
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
| | - Junjie Qian
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
| | - Zhongming Fang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China.
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Jihua Tang
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.
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18
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Yamazaki K, Ohmori Y, Fujiwara T. A Positive Tropism of Rice Roots toward a Nutrient Source. PLANT & CELL PHYSIOLOGY 2020; 61:546-553. [PMID: 31808938 DOI: 10.1093/pcp/pcz218] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
Plants take up water and nutrients through roots, and uptake efficiency depends on root behavior. Roots recognize the moisture gradient in the soil and grow toward the direction of high moisture. This phenomenon is called hydrotropism, and it contributes to efficient water uptake. As nutrients in soil are also unevenly distributed, it is beneficial for plants to grow their roots in the direction of increasing nutrient concentrations, but such a phenomenon has not been demonstrated. Here, we describe the directional growth of roots in response to a nutrient gradient. Using our assay system, the gradient of a nitrogen nutrient, NH4+, was sufficient to stimulate positive tropic responses of rice lateral roots. This phenomenon is a tropism of plant roots to nutrients; hence, we propose the name 'nutritropism'. As well as other tropisms, differential cell elongation was observed before the elongation zone during nutritropism, but the pattern promoting cell elongation preferentially on the non-stimulated side was opposite to those in root hydrotropism and gravitropism. Our evaluation of the NH4+ gradient suggested that the root tips responded to a sub-micromolar difference in NH4+ concentration on both sides of the root. Hydrotropism, gravitropism and phototropism were described in plants as the 'power of movement' by Charles and Francis Darwin in 1880, and these three tropisms have attracted the attention of plant scientists for more than 130 years. Our discovery of nutritropism represents the fourth 'power of movement' in plants and provides a novel root behavioral property used by plants to acquire nutrients efficiently.
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Affiliation(s)
- Kiyoshi Yamazaki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Yoshihiro Ohmori
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
- Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Toru Fujiwara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
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19
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Zhang F, Wang L, Bai P, Wei K, Zhang Y, Ruan L, Wu L, Cheng H. Identification of Regulatory Networks and Hub Genes Controlling Nitrogen Uptake in Tea Plants [ Camellia sinensis (L.) O. Kuntze]. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:2445-2456. [PMID: 31899627 DOI: 10.1021/acs.jafc.9b06427] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nitrogen (N) uptake, as the first step of N metabolism, is a key limiting factor for plant growth. To understand the gene expression networks that control N absorption and metabolism in tea plants, we analyzed transcriptomes in the young roots of two groups of tea plants with significantly different growth rates under different N treatments (0, 0.2, and 2 mM). Using pairwise comparisons and weighted gene co-expression network analyses (WGCNA), we successfully constructed 16 co-expression modules. Among them, a specific module (turquoise) that substantially responded to the low N treatment was identified. Based on KEGG analysis, the relative genes that enriched in the "N metabolism" pathways were used to construct gene co-expression networks of N metabolism. Finally, a high-affinity ammonium (NH4+) transporter designated CsAMT1.2 was identified as a hub gene in the N metabolism network in tea plant roots and the gene expression could be highly induced by N resupply. The gene functional analysis revealed that CsAMT1.2 could make functional complementation of MEP1, MEP2, and MEP3 genes in 31019b yeast cells and improve NH4+ uptake rate in 31019b at low NH4+ level. Thus, CsAMT1.2 was a key gene controlling N uptake in tea plants and might play a vital role in promoting NH4+ uptake from the environment in tea roots. This study provided a useful foundation for improving the NUE in tea plantations.
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Affiliation(s)
- Fen Zhang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute , Chinese Academy of Agricultural Sciences , 9 Meiling South Road , Hangzhou 310008 , China
| | - Liyuan Wang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute , Chinese Academy of Agricultural Sciences , 9 Meiling South Road , Hangzhou 310008 , China
| | - Peixian Bai
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute , Chinese Academy of Agricultural Sciences , 9 Meiling South Road , Hangzhou 310008 , China
| | - Kang Wei
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute , Chinese Academy of Agricultural Sciences , 9 Meiling South Road , Hangzhou 310008 , China
| | - Yazhen Zhang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute , Chinese Academy of Agricultural Sciences , 9 Meiling South Road , Hangzhou 310008 , China
| | - Li Ruan
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute , Chinese Academy of Agricultural Sciences , 9 Meiling South Road , Hangzhou 310008 , China
| | - Liyun Wu
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute , Chinese Academy of Agricultural Sciences , 9 Meiling South Road , Hangzhou 310008 , China
| | - Hao Cheng
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute , Chinese Academy of Agricultural Sciences , 9 Meiling South Road , Hangzhou 310008 , China
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20
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Ravazzolo L, Trevisan S, Forestan C, Varotto S, Sut S, Dall’Acqua S, Malagoli M, Quaggiotti S. Nitrate and Ammonium Affect the Overall Maize Response to Nitrogen Availability by Triggering Specific and Common Transcriptional Signatures in Roots. Int J Mol Sci 2020; 21:ijms21020686. [PMID: 31968691 PMCID: PMC7013554 DOI: 10.3390/ijms21020686] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/13/2020] [Accepted: 01/16/2020] [Indexed: 01/01/2023] Open
Abstract
Nitrogen (N) is an essential macronutrient for crops. Plants have developed several responses to N fluctuations, thus optimizing the root architecture in response to N availability. Nitrate and ammonium are the main inorganic N forms taken up by plants, and act as both nutrients and signals, affecting gene expression and plant development. In this study, RNA-sequencing was applied to gain comprehensive information on the pathways underlying the response of maize root, pre-treated in an N-deprived solution, to the provision of nitrate or ammonium. The analysis of the transcriptome shows that nitrate and ammonium regulate overlapping and distinct pathways, thus leading to different responses. Ammonium activates the response to stress, while nitrate acts as a negative regulator of transmembrane transport. Both the N-source repress genes related to the cytoskeleton and reactive oxygen species detoxification. Moreover, the presence of ammonium induces the accumulation of anthocyanins, while also reducing biomass and chlorophyll and flavonoids accumulation. Furthermore, the later physiological effects of these nutrients were evaluated through the assessment of shoot and root growth, leaf pigment content and the amino acid concentrations in root and shoot, confirming the existence of common and distinct features in response to the two nitrogen forms.
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Affiliation(s)
- Laura Ravazzolo
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Agripolis—V.le dell’Università, 16, 35020 Legnaro (PD), Italy; (L.R.); (S.T.); (C.F.); (S.V.); (S.S.); (M.M.)
| | - Sara Trevisan
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Agripolis—V.le dell’Università, 16, 35020 Legnaro (PD), Italy; (L.R.); (S.T.); (C.F.); (S.V.); (S.S.); (M.M.)
| | - Cristian Forestan
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Agripolis—V.le dell’Università, 16, 35020 Legnaro (PD), Italy; (L.R.); (S.T.); (C.F.); (S.V.); (S.S.); (M.M.)
| | - Serena Varotto
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Agripolis—V.le dell’Università, 16, 35020 Legnaro (PD), Italy; (L.R.); (S.T.); (C.F.); (S.V.); (S.S.); (M.M.)
| | - Stefania Sut
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Agripolis—V.le dell’Università, 16, 35020 Legnaro (PD), Italy; (L.R.); (S.T.); (C.F.); (S.V.); (S.S.); (M.M.)
| | - Stefano Dall’Acqua
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova—Via Marzolo 5, 35121 Padova, Italy;
| | - Mario Malagoli
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Agripolis—V.le dell’Università, 16, 35020 Legnaro (PD), Italy; (L.R.); (S.T.); (C.F.); (S.V.); (S.S.); (M.M.)
| | - Silvia Quaggiotti
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Agripolis—V.le dell’Università, 16, 35020 Legnaro (PD), Italy; (L.R.); (S.T.); (C.F.); (S.V.); (S.S.); (M.M.)
- Correspondence: ; Tel.: +39-049-8272913
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21
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Ou X, Li S, Liao P, Cui X, Zheng B, Yang Y, Liu D, Zheng Y. The transcriptome variations of Panaxnotoginseng roots treated with different forms of nitrogen fertilizers. BMC Genomics 2019; 20:965. [PMID: 31874632 PMCID: PMC6929466 DOI: 10.1186/s12864-019-6340-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 11/26/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The sensitivity of plants to ammonia is a worldwide problem that limits crop production. Excessive use of ammonium as the sole nitrogen source results in morphological and physiological disorders, and retarded plant growth. RESULTS In this study we found that the root growth of Panax notoginseng was inhibited when only adding ammonium nitrogen fertilizer, but the supplement of nitrate fertilizer recovered the integrity, activity and growth of root. Twelve RNA-seq profiles in four sample groups were produced and analyzed to identify deregulated genes in samples with different treatments. In comparisons to NH[Formula: see text] treated samples, ACLA-3 gene is up-regulated in samples treated with NO[Formula: see text] and with both NH[Formula: see text] and NO[Formula: see text], which is further validated by qRT-PCR in another set of samples. Subsequently, we show that the some key metabolites in the TCA cycle are also significantly enhanced when introducing NO[Formula: see text]. These potentially enhance the integrity and recover the growth of Panax notoginseng roots. CONCLUSION These results suggest that the activated TCA cycle, as demonstrated by up-regulation of ACLA-3 and several key metabolites in this cycle, contributes to the increased Panax notoginseng root yield when applying both ammonium and nitrate fertilizer.
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Affiliation(s)
- Xiaohong Ou
- Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Shipeng Li
- Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
- Yunnan Key Lab of Primate Biomedicine Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Peiran Liao
- Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xiuming Cui
- Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ye Yang
- Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Dahui Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China.
| | - Yun Zheng
- Yunnan Key Lab of Primate Biomedicine Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
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22
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Xuan YH, Kumar V, Han X, Kim SH, Jeong JH, Kim CM, Gao Y, Han CD. CBL-INTERACTING PROTEIN KINASE 9 regulates ammonium-dependent root growth downstream of IDD10 in rice (Oryza sativa). ANNALS OF BOTANY 2019; 124:947-960. [PMID: 30715138 PMCID: PMC6881222 DOI: 10.1093/aob/mcy242] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/02/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS INDETERMINATE DOMAIN 10 (IDD10) is a key transcription factor gene that activates the expression of a large number of NH4+-responsive genes including AMMONIUM TRANSPORTER 1;2 (AMT1;2). Primary root growth of rice (Oryza sativa) idd10 mutants is hypersensitive to NH4+. The involvement of CALCINEURIN B-LIKE INTERACTING PROTEIN KINASE (CIPK) genes in the action of IDD10 on NH4+-mediated root growth was investigated. METHODS Quantitative reverse transcription-PCR was used to analyse NH4+- and IDD10-dependent expression of CIPK genes. IDD10-regulated CIPK target genes were identified using electrophoretic mobility shift assays, chromatin immunoprecipitation and transient transcription assays. Root growth rate, ammonium content and 15N uptake of cipk mutants were measured to determine their sensitivity to NH4+ and to compare these phenotypes with those of idd10. The genetic relationship between CIPK9 OX and idd10 was investigated by crosses between the CIPK9 and IDD10 lines. KEY RESULTS AMT1;2 was overexpressed in idd10 to determine whether NH4+-hypersensitive root growth of idd10 resulted from limitations in NH4+ uptake or from low cellular levels of NH4+. High NH4+ levels in idd10/AMT1;2 OX did not rescue the root growth defect. Next, the involvement of CIPK genes in NH4+-dependent root growth and interactions between IDD10 and CIPK genes was investigated. Molecular analysis revealed that IDD10 directly activated transcription of CIPK9 and CIPK14. Expression of CIPK8, 9, 14/15 and 23 was sensitive to exogenous NH4+. Further studies revealed that cipk9 and idd10 had almost identical NH4+-sensitive root phenotypes, including low efficiency of 15NH4+ uptake. Analysis of plants containing both idd10 and CIPK9 OX showed that CIPK9 OX could rescue the NH4+-dependent root growth defects of idd10. CONCLUSIONS CIPK9 was involved in NH4+-dependent root growth and appeared to act downstream of IDD10. This information will be useful in future explorations of NH4+ signalling in plants.
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Affiliation(s)
- Yuan Hu Xuan
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
- For correspondence. E-mails: or
| | - Vikranth Kumar
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Korea
| | - Xiao Han
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Sung Hoon Kim
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Korea
| | - Jin Hee Jeong
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Korea
| | - Chul Min Kim
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Korea
| | - Yue Gao
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Chang-deok Han
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Korea
- For correspondence. E-mails: or
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23
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Hsieh PH, Kan CC, Wu HY, Yang HC, Hsieh MH. Early molecular events associated with nitrogen deficiency in rice seedling roots. Sci Rep 2018; 8:12207. [PMID: 30111825 PMCID: PMC6093901 DOI: 10.1038/s41598-018-30632-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/31/2018] [Indexed: 11/16/2022] Open
Abstract
Nitrogen (N) deficiency is one of the most common problems in rice. The symptoms of N deficiency are well documented, but the underlying molecular mechanisms are largely unknown in rice. Here, we studied the early molecular events associated with N starvation (−N, 1 h), focusing on amino acid analysis and identification of −N-regulated genes in rice roots. Interestingly, levels of glutamine rapidly decreased within 15 min of −N treatment, indicating that part of the N-deficient signals could be mediated by glutamine. Transcriptome analysis revealed that genes involved in metabolism, plant hormone signal transduction (e.g. abscisic acid, auxin, and jasmonate), transporter activity, and oxidative stress responses were rapidly regulated by −N. Some of the −N-regulated genes encode transcription factors, protein kinases and protein phosphatases, which may be involved in the regulation of early −N responses in rice roots. Previously, we used similar approaches to identify glutamine-, glutamate-, and ammonium nitrate-responsive genes. Comparisons of the genes induced by different forms of N with the −N-regulated genes identified here have provided a catalog of potential N regulatory genes for further dissection of the N signaling pathwys in rice.
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Affiliation(s)
- Ping-Han Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chia-Cheng Kan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Hsin-Yu Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Hsiu-Chun Yang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Ming-Hsiun Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan.
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