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Physiological and biochemical changes in Moroccan barley ( Hordeum vulgare L.) cultivars submitted to drought stress. Heliyon 2023; 9:e13643. [PMID: 36873157 PMCID: PMC9975271 DOI: 10.1016/j.heliyon.2023.e13643] [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: 05/21/2022] [Revised: 01/25/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Barley (Hordeum vulgare L.) is the second most consumed and cultivated cereal by the Moroccan population. However, it is predicted that frequent drought periods, caused by climate change, can cause problems in plant growth. Thus, the selection of drought-tolerant barley cultivars is essential to ensure the security of barley's needs. We aimed to screen drought stress tolerance in Moroccan barley cultivars. We tested the drought tolerance of nine Moroccan barley cultivars ('Adrar', 'Amalou', 'Amira', 'Firdaws', 'Laanaceur', 'Massine', 'Oussama', 'Taffa', and 'Tamellalt') based on physiological and biochemical parameters. Drought stress was applied by maintaining field capacity at 40% (90% for the control), and plants were randomly arranged in a greenhouse at 25 °C under natural light conditions. Drought stress decreased relative water content (RWC), shoot dry weight (SDW), and chlorophyll content (SPAD index), but significantly increased electrolyte leakage, hydrogen peroxide, malondialdehyde (MDA), water-soluble carbohydrates, and soluble protein contents, as well as catalase (CAT) and ascorbate peroxidase (APX) activities. High levels of SDW, RWC, CAT, and APX activities were recorded in 'Firdaws', 'Laanaceur', 'Massine', 'Taffa', and 'Oussama', which can be interpreted by high drought tolerance. On the other hand, 'Adrar', 'Amalou', 'Amira', and 'Tamellalt' showed higher values of MDA and H2O2 content, which can be linked with drought sensitivity. Physiological and biochemical parameter changes are discussed in terms of barley's tolerance to drought. Tolerant cultivars could be a good background for barley breeding in areas known for the alternative of long dry spells.
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Gao G, Zhang X, Zhao K, Zhao K, Cao D, Ma Q, Zhu S, Qu C, Ma Y, Gong F, Li Z, Ren R, Ma X, Yin D. Genome wide identification and expression analysis of patatin-like protein family members in peanut (Arachis hypogaea L.). REPRODUCTION AND BREEDING 2021. [DOI: 10.1016/j.repbre.2021.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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3
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Ding N, Huertas R, Torres‐Jerez I, Liu W, Watson B, Scheible W, Udvardi M. Transcriptional, metabolic, physiological and developmental responses of switchgrass to phosphorus limitation. PLANT, CELL & ENVIRONMENT 2021; 44:186-202. [PMID: 32822068 PMCID: PMC7821211 DOI: 10.1111/pce.13872] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/11/2020] [Accepted: 08/17/2020] [Indexed: 05/10/2023]
Abstract
Knowing how switchgrass (Panicum virgatum L.) responds and adapts to phosphorus (P)-limitation will aid efforts to optimize P acquisition and use in this species for sustainable biomass production. This integrative study investigated the impacts of mild, moderate, and severe P-stress on genome transcription and whole-plant metabolism, physiology and development in switchgrass. P-limitation reduced overall plant growth, increased root/shoot ratio, increased root branching at moderate P-stress, and decreased root diameter with increased density and length of root hairs at severe P-stress. RNA-seq analysis revealed thousands of genes that were differentially expressed under moderate and severe P-stress in roots and/or shoots compared to P-replete plants, with many stress-induced genes involved in transcriptional and other forms of regulation, primary and secondary metabolism, transport, and other processes involved in P-acquisition and homeostasis. Amongst the latter were multiple miRNA399 genes and putative targets of these. Metabolite profiling showed that levels of most sugars and sugar alcohols decreased with increasing P stress, while organic and amino acids increased under mild and moderate P-stress in shoots and roots, although this trend reversed under severe P-stress, especially in shoots.
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Affiliation(s)
- Na Ding
- Noble Research Institute LLCArdmoreOklahomaUSA
| | | | | | - Wei Liu
- Noble Research Institute LLCArdmoreOklahomaUSA
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Pfaff J, Denton AK, Usadel B, Pfaff C. Phosphate starvation causes different stress responses in the lipid metabolism of tomato leaves and roots. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158763. [DOI: 10.1016/j.bbalip.2020.158763] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 06/15/2020] [Accepted: 07/03/2020] [Indexed: 12/17/2022]
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Ma Q, Sun M, Lu J, Kang H, You C, Hao Y. An apple sucrose transporter MdSUT2.2 is a phosphorylation target for protein kinase MdCIPK22 in response to drought. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:625-637. [PMID: 30133123 PMCID: PMC6381786 DOI: 10.1111/pbi.13003] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 08/02/2018] [Accepted: 08/18/2018] [Indexed: 05/22/2023]
Abstract
Sugars increase with drought stress in plants and accumulate in the vacuole. However, the exact molecular mechanism underlying this process is not clear yet. In this study, protein interaction and phosphorylation experiments were conducted for sucrose transporter and CIPK kinase in apple. The specific phosphorylation site of sucrose transporter was identified with mass spectrometry. Transgenic analyses were performed to characterize their biological function. It was found that overexpression of sucrose transporter gene MdSUT2.2 in apple plants promoted sugar accumulation and drought tolerance. MdSUT2.2 protein was phosphorylated at Ser381 site in response to drought. A DUALmembrane system using MdSUT2.2 as bait through an apple cDNA library got a protein kinase MdCIPK22. Bimolecular fluorescence complementary (BiFC), pull-down and co-immunoprecipitation (Co-IP) assays further demonstrated that MdCIPK22 interacted with MdSUT2.2. A series of transgenic analysis showed that MdCIPK22 was required for the drought-induced phosphylation at Ser381 site of MdSUT2.2 protein, and that it enhanced the stability and transport activity of MdSUT2.2 protein. Finally, it was found that MdCIPK22 overexpression promoted sugar accumulation and improved drought tolerance in an MdSUT2.2-dependent manner in transgenic apple plants. MdCIPK22-MdSUT2.2 regulatory module shed light on the molecular mechanism by which plant accumulates sugars and enhances tolerance in response to drought stress.
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Affiliation(s)
- Qi‐Jun Ma
- National Key Laboratory of Crop BiologyMOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in Huanghuai RegionCollege of Horticulture Science and EngineeringShandong Agricultural UniversityTai‐AnShandongChina
| | - Mei‐Hong Sun
- National Key Laboratory of Crop BiologyMOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in Huanghuai RegionCollege of Horticulture Science and EngineeringShandong Agricultural UniversityTai‐AnShandongChina
| | - Jing Lu
- National Key Laboratory of Crop BiologyMOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in Huanghuai RegionCollege of Horticulture Science and EngineeringShandong Agricultural UniversityTai‐AnShandongChina
| | - Hui Kang
- National Key Laboratory of Crop BiologyMOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in Huanghuai RegionCollege of Horticulture Science and EngineeringShandong Agricultural UniversityTai‐AnShandongChina
| | - Chun‐Xiang You
- National Key Laboratory of Crop BiologyMOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in Huanghuai RegionCollege of Horticulture Science and EngineeringShandong Agricultural UniversityTai‐AnShandongChina
| | - Yu‐Jin Hao
- National Key Laboratory of Crop BiologyMOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in Huanghuai RegionCollege of Horticulture Science and EngineeringShandong Agricultural UniversityTai‐AnShandongChina
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Wang Y, Lysøe E, Armarego-Marriott T, Erban A, Paruch L, van Eerde A, Bock R, Liu-Clarke J. Transcriptome and metabolome analyses provide insights into root and root-released organic anion responses to phosphorus deficiency in oat. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3759-3771. [PMID: 29757407 DOI: 10.1093/jxb/ery176] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/09/2018] [Indexed: 05/23/2023]
Abstract
Roots and root-released organic anions play important roles in uptake of phosphorus (P), an essential macronutrient for food production. Oat, ranking sixth in the world's cereal production, contains valuable nutritional compounds and can withstand poor soil conditions. Our aim was to investigate root transcriptional and metabolic responses of oat grown under P-deficient and P-sufficient conditions. We conducted a hydroponic experiment and measured root morphology and organic anion exudation, and analysed changes in the transcriptome and metabolome. Oat roots showed enhanced citrate and malate exudation after 4 weeks of P deficiency. After 10 d of P deficiency, we identified 9371 differentially expressed transcripts with a 2-fold or greater change (P<0.05): 48 sequences predicted to be involved in organic anion biosynthesis and efflux were consistently up-regulated; 24 up-regulated transcripts in oat were also found to be up-regulated upon P starvation in rice and wheat under similar conditions. Phosphorylated metabolites (i.e. glucose-6-phosphate, myo-inositol phosphate) were reduced dramatically, while citrate and malate, some sugars and amino acids increased slightly in P-deficient oat roots. Our data are consistent with a strategy of increased organic anion efflux and a shift in primary metabolism in response to P deficiency in oat.
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Affiliation(s)
- Yanliang Wang
- Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Erik Lysøe
- Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | | | - Alexander Erban
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - Lisa Paruch
- Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - André van Eerde
- Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Ralph Bock
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
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Zhao P, Wang L, Yin H. Transcriptional responses to phosphate starvation in Brachypodium distachyon roots. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 122:113-120. [PMID: 29216498 DOI: 10.1016/j.plaphy.2017.11.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 11/16/2017] [Accepted: 11/16/2017] [Indexed: 06/07/2023]
Abstract
Brachypodium distachyon is a model plant that has recently emerged in grass research. Although the growth and photochemical efficiency of this species respond strongly to phosphate (Pi) availability, its Pi starvation response mechanism, which controls the Pi homeostasis, remains largely unknown. This study presents the transcriptomic response profiles of Pi-deficient roots at growth stages during which the plants were starved but obvious growth defects were absent. The results identify several phosphate transporters (i.e., PHO1), purple acid phosphatases, and SYG1/PHO81/XPR1 (SPX) domain-containing proteins out of a total of 1740 differentially expressed genes (DEGs). In particular, the transcription factor ethylene response factor (ERF), basic helix-loop-helix (bHLH), and WRKY family genes were the three most abundant DEG groups and the latter was significantly enriched. Comparative transcriptome analysis of Brachypodium versus Arabidopsis and rice revealed the presence of several common components in response to Pi fluctuations. Most significantly, jasmonic acid (JA) signaling-related genes were overrepresented in gene ontology (GO) enrichment tests. The presence of a possible link between low Pi response, inositol polyphosphates, and JA signaling is therefore discussed.
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Affiliation(s)
- Pengshan Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China; Shapotou Desert Research & Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Lirong Wang
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Hengxia Yin
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China.
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Nasr Esfahani M, Inoue K, Chu HD, Nguyen KH, Van Ha C, Watanabe Y, Burritt DJ, Herrera-Estrella L, Mochida K, Tran LSP. Comparative transcriptome analysis of nodules of two Mesorhizobium-chickpea associations with differential symbiotic efficiency under phosphate deficiency. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017. [PMID: 28628240 DOI: 10.1111/tpj.13616] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Phosphate (Pi) deficiency is known to be a major limitation for symbiotic nitrogen fixation (SNF), and hence legume crop productivity globally. However, very little information is available on the adaptive mechanisms, particularly in the important legume crop chickpea (Cicer arietinum L.), which enable nodules to respond to low-Pi availability. Thus, to elucidate these mechanisms in chickpea nodules at molecular level, we used an RNA sequencing approach to investigate transcriptomes of the nodules in Mesorhizobium mediterraneum SWRI9-(MmSWRI9)-chickpea and M. ciceri CP-31-(McCP-31)-chickpea associations under Pi-sufficient and Pi-deficient conditions, of which the McCP-31-chickpea association has a better SNF capacity than the MmSWRI9-chickpea association during Pi starvation. Our investigation revealed that more genes showed altered expression patterns in MmSWRI9-induced nodules than in McCP-31-induced nodules (540 vs. 225) under Pi deficiency, suggesting that the Pi-starvation-more-sensitive MmSWRI9-induced nodules required expression change in a larger number of genes to cope with low-Pi stress than the Pi-starvation-less-sensitive McCP-31-induced nodules. The functional classification of differentially expressed genes (DEGs) was examined to gain an understanding of how chickpea nodules respond to Pi starvation, caused by soil Pi deficiency. As a result, more DEGs involved in nodulation, detoxification, nutrient/ion transport, transcriptional factors, key metabolic pathways, Pi remobilization and signalling were found in Pi-starved MmSWRI9-induced nodules than in Pi-starved McCP-31-induced nodules. Our findings have enabled the identification of molecular processes that play important roles in the acclimation of nodules to Pi deficiency, ultimately leading to the development of Pi-efficient chickpea symbiotic associations suitable for Pi-deficient soils.
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Affiliation(s)
| | - Komaki Inoue
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Ha Duc Chu
- Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Pham Van Dong, North Tu Liem, Hanoi, Vietnam
| | - Kien Huu Nguyen
- Plant Abiotic Stress Research Group & Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, 70000, Vietnam
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Chien Van Ha
- Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Pham Van Dong, North Tu Liem, Hanoi, Vietnam
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Yasuko Watanabe
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - David J Burritt
- Department of Botany, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio)/Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, 36500 Irapuato, Guanajuato, Mexico
| | - Keiichi Mochida
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Okayama, 710-0046, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan
| | - Lam-Son Phan Tran
- Plant Abiotic Stress Research Group & Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, 70000, Vietnam
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
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Ma QJ, Sun MH, Lu J, Liu YJ, Hu DG, Hao YJ. Transcription Factor AREB2 Is Involved in Soluble Sugar Accumulation by Activating Sugar Transporter and Amylase Genes. PLANT PHYSIOLOGY 2017; 174:2348-2362. [PMID: 28600345 PMCID: PMC5543958 DOI: 10.1104/pp.17.00502] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/07/2017] [Indexed: 05/18/2023]
Abstract
Sugars play important roles in plant growth and development, crop yield and quality, as well as responses to abiotic stresses. Abscisic acid (ABA) is a multifunctional hormone. However, the exact mechanism by which ABA regulates sugar accumulation is largely unknown in plants. Here, we tested the expression profile of several sugar transporter and amylase genes in response to ABA treatment. MdSUT2 and MdAREB2 were isolated and genetically transformed into apple (Malus domestica) to investigate their roles in ABA-induced sugar accumulation. The MdAREB2 transcription factor was found to bind to the promoters of the sugar transporter and amylase genes and activate their expression. Both MdAREB2 and MdSUT2 transgenic plants produced more soluble sugars than controls. Furthermore, MdAREB2 promoted the accumulation of sucrose and soluble sugars in an MdSUT2-dependent manner. Our results demonstrate that the ABA-responsive transcription factor MdAREB2 directly activates the expression of amylase and sugar transporter genes to promote soluble sugar accumulation, suggesting a mechanism by which ABA regulates sugar accumulation in plants.
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Affiliation(s)
- Qi-Jun Ma
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Mei-Hong Sun
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Jing Lu
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Ya-Jing Liu
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Da-Gang Hu
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Yu-Jin Hao
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
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Zhou X, Zha M, Huang J, Li L, Imran M, Zhang C. StMYB44 negatively regulates phosphate transport by suppressing expression of PHOSPHATE1 in potato. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1265-1281. [PMID: 28338870 PMCID: PMC5441854 DOI: 10.1093/jxb/erx026] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Phosphorus is an important macronutrient for plant growth, but often deficient in soil. To understand the molecular basis of the complex responses of potato (Solanum tuberosum L.) to phosphate (Pi) deficiency stress, the RNA-Seq approach was taken to identify genes responding to Pi starvation in potato roots. A total of 359 differentially expressed genes were identified, among which the Solanum tuberosum transcription factor gene MYB44 (StMYB44) was found to be down-regulated by Pi starvation. StMYB44 was ubiquitously expressed in potato tissues and organs, and StMYB44 protein was exclusively localized in the nucleus. Overexpression of StMYB44 in potato resulted in lower accumulation of Pi in shoots. Transcriptomic analysis indicated that the abundance of S. tuberosum PHOSPHATE1 (StPHO1), a Pi transport-related gene, was reduced in StMYB44 overexpression lines. In contrast, knock-out of StMYB44 by a CRISPR/Cas9 system failed to increase transcription of StPHO1. Moreover, StMYB44 was found to interact in the nucleus with AtWRKY6, a known Arabidopsis transcription factor directly regulating PHO1 expression, and StWRKY6, indicating that StMYB44 could be a member of the regulatory complex controlling transcription of StPHO1. Taken together, our study demonstrates that StMYB44 negatively regulates Pi transport in potato by suppressing StPHO1 expression.
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Affiliation(s)
- Xiangjun Zhou
- Department of Agronomy, Purdue University, West Lafayette IN 47907, USA
| | - Manrong Zha
- Department of Agronomy, Purdue University, West Lafayette IN 47907, USA
| | - Jing Huang
- Department of Agronomy, Purdue University, West Lafayette IN 47907, USA
| | - Li Li
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Muhammad Imran
- Department of Agronomy, Purdue University, West Lafayette IN 47907, USA
- Department of Soil and Environmental Sciences, University College of Agriculture, University of Sargodha, Pakistan 40100
| | - Cankui Zhang
- Department of Agronomy, Purdue University, West Lafayette IN 47907, USA
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Sami F, Yusuf M, Faizan M, Faraz A, Hayat S. Role of sugars under abiotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 109:54-61. [PMID: 27639065 DOI: 10.1016/j.plaphy.2016.09.005] [Citation(s) in RCA: 245] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 08/25/2016] [Accepted: 09/05/2016] [Indexed: 05/21/2023]
Abstract
Sugars are the most important regulators that facilitate many physiological processes, such as photosynthesis, seed germination, flowering, senescence, and many more under various abiotic stresses. Exogenous application of sugars in low concentration promote seed germination, up regulates photosynthesis, promotes flowering, delayed senescence under various unfavorable environmental conditions. However, high concentration of sugars reverses all these physiological process in a concentration dependent manner. Thus, this review focuses the correlation between sugars and their protective functions in several physiological processes against various abiotic stresses. Keeping in mind the multifaceted role of sugars, an attempt has been made to cover the role of sugar-regulated genes associated with photosynthesis, seed germination and senescence. The concentration of sugars determines the expression of these sugar-regulated genes. This review also enlightens the interaction of sugars with several phytohormones, such as abscisic acid, ethylene, cytokinins and gibberellins and its effect on their biosynthesis under abiotic stress conditions.
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Affiliation(s)
- Fareen Sami
- Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh, 202002, India
| | - Mohammad Yusuf
- Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh, 202002, India
| | - Mohammad Faizan
- Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh, 202002, India
| | - Ahmad Faraz
- Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh, 202002, India
| | - Shamsul Hayat
- Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh, 202002, India.
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The nitrogen responsive transcriptome in potato (Solanum tuberosum L.) reveals significant gene regulatory motifs. Sci Rep 2016; 6:26090. [PMID: 27193058 PMCID: PMC4872257 DOI: 10.1038/srep26090] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/25/2016] [Indexed: 12/18/2022] Open
Abstract
Nitrogen (N) is the most important nutrient for the growth of potato (Solanum tuberosum L.). Foliar gene expression in potato plants with and without N supplementation at 180 kg N ha(-1) was compared at mid-season. Genes with consistent differences in foliar expression due to N supplementation over three cultivars and two developmental time points were examined. In total, thirty genes were found to be over-expressed and nine genes were found to be under-expressed with supplemented N. Functional relationships between over-expressed genes were found. The main metabolic pathway represented among differentially expressed genes was amino acid metabolism. The 1000 bp upstream flanking regions of the differentially expressed genes were analysed and nine overrepresented motifs were found using three motif discovery algorithms (Seeder, Weeder and MEME). These results point to coordinated gene regulation at the transcriptional level controlling steady state potato responses to N sufficiency.
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Mehra M, Gangwar I, Shankar R. A Deluge of Complex Repeats: The Solanum Genome. PLoS One 2015; 10:e0133962. [PMID: 26241045 PMCID: PMC4524691 DOI: 10.1371/journal.pone.0133962] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 07/06/2015] [Indexed: 12/18/2022] Open
Abstract
Repetitive elements have lately emerged as key components of genome, performing varieties of roles. It has now become necessary to have an account of repeats for every genome to understand its dynamics and state. Recently, genomes of two major Solanaceae species, Solanum tuberosum and Solanum lycopersicum, were sequenced. These species are important crops having high commercial significance as well as value as model species. However, there is a reasonable gap in information about repetitive elements and their possible roles in genome regulation for these species. The present study was aimed at detailed identification and characterization of complex repetitive elements in these genomes, along with study of their possible functional associations as well as to assess possible transcriptionally active repetitive elements. In this study, it was found that ~50-60% of genomes of S. tuberosum and S. lycopersicum were composed of repetitive elements. It was also found that complex repetitive elements were associated with >95% of genes in both species. These two genomes are mostly composed of LTR retrotransposons. Two novel repeat families very similar to LTR/ERV1 and LINE/RTE-BovB have been reported for the first time. Active existence of complex repeats was estimated by measuring their transcriptional abundance using Next Generation Sequencing read data and Microarray platforms. A reasonable amount of regulatory components like transcription factor binding sites and miRNAs appear to be under the influence of these complex repetitive elements in these species, while several genes appeared to possess exonized repeats.
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MESH Headings
- Base Sequence
- Binding Sites
- Chromosomes, Plant/genetics
- DNA, Plant/genetics
- Evolution, Molecular
- Exons/genetics
- Gene Expression Regulation, Plant/genetics
- Genome, Plant
- Humans
- INDEL Mutation
- Solanum lycopersicum/genetics
- MicroRNAs/genetics
- Molecular Sequence Data
- Phylogeny
- Plant Proteins/metabolism
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Plant/biosynthesis
- RNA, Plant/genetics
- Repetitive Sequences, Nucleic Acid
- Retroelements/genetics
- Sequence Alignment
- Solanum tuberosum/genetics
- Species Specificity
- Terminal Repeat Sequences
- Transcription Factors/metabolism
- Transcription, Genetic
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Affiliation(s)
- Mrigaya Mehra
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, 176061, HP, India
- Academy of Scientific & Innovative Research, Chennai, India
| | - Indu Gangwar
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, 176061, HP, India
- Academy of Scientific & Innovative Research, Chennai, India
| | - Ravi Shankar
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, 176061, HP, India
- Academy of Scientific & Innovative Research, Chennai, India
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Muneer S, Jeong BR. Proteomic Analysis Provides New Insights in Phosphorus Homeostasis Subjected to Pi (Inorganic Phosphate) Starvation in Tomato Plants (Solanum lycopersicum L.). PLoS One 2015; 10:e0134103. [PMID: 26222137 PMCID: PMC4519287 DOI: 10.1371/journal.pone.0134103] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/06/2015] [Indexed: 12/21/2022] Open
Abstract
Phosphorus is a major nutrient acquired by plants via high-affinity inorganic phosphate (Pi) transporters. To determine the adaptation and homeostasis strategy to Pi starvation, we compared the proteome analysis of tomato leaves that were treated with and without Pi (as KH2PO4) for 10 days. Among 600 reproducible proteins on 2-DE gels 46 of them were differentially expressed. These proteins were involved in major metabolic pathways, including photosynthesis, transcriptional/translational regulations, carbohydrate/energy metabolism, protein synthesis, defense response, and other secondary metabolism. The results also showed that the reduction in photosynthetic pigments lowered P content under -Pi treatments. Furthermore, high-affinity Pi transporters (lePT1 and lePT2) expressed in higher amounts under -Pi treatments. Also, the accumulation of Pi transporters was observed highly in the epidermis and palisade parenchyma under +Pi treatments compared to -Pi treatments. Our data suggested that tomato plants developed reactive oxygen species (ROS) scavenging mechanisms to cope with low Pi content, including the up-regulation of proteins mostly involved in important metabolic pathways. Moreover, Pi-starved tomato plants increased their internal Pi utilization efficiency by increasing the Pi transporter genes and their rational localization. These results thus provide imperative information about how tomato plants respond to Pi starvation and its homeostasis.
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Affiliation(s)
- Sowbiya Muneer
- Division of Applied Life Science (BK21 Plus), Graduate School, Gyeongsang National University, Jinju, 660–701, South Korea
| | - Byoung Ryong Jeong
- Division of Applied Life Science (BK21 Plus), Graduate School, Gyeongsang National University, Jinju, 660–701, South Korea
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 660–701, South Korea
- Research Institute of Life Science, Gyeongsang National University, Jinju, 660–701, South Korea
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15
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Pandey R, Zinta G, AbdElgawad H, Ahmad A, Jain V, Janssens IA. Physiological and molecular alterations in plants exposed to high [CO2] under phosphorus stress. Biotechnol Adv 2015; 33:303-16. [PMID: 25797341 DOI: 10.1016/j.biotechadv.2015.03.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/07/2015] [Accepted: 03/14/2015] [Indexed: 11/24/2022]
Abstract
Atmospheric [CO2] has increased substantially in recent decades and will continue to do so, whereas the availability of phosphorus (P) is limited and unlikely to increase in the future. P is a non-renewable resource, and it is essential to every form of life. P is a key plant nutrient controlling the responsiveness of photosynthesis to [CO2]. Increases in [CO2] typically results in increased biomass through stimulation of net photosynthesis, and hence enhance the demand for P uptake. However, most soils contain low concentrations of available P. Therefore, low P is one of the major growth-limiting factors for plants in many agricultural and natural ecosystems. The adaptive responses of plants to [CO2] and P availability encompass alterations at morphological, physiological, biochemical and molecular levels. In general low P reduces growth, whereas high [CO2] enhances it particularly in C3 plants. Photosynthetic capacity is often enhanced under high [CO2] with sufficient P supply through modulation of enzyme activities involved in carbon fixation such as ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). However, high [CO2] with low P availability results in enhanced dry matter partitioning towards roots. Alterations in below-ground processes including root morphology, exudation and mycorrhizal association are influenced by [CO2] and P availability. Under high P availability, elevated [CO2] improves the uptake of P from soil. In contrast, under low P availability, high [CO2] mainly improves the efficiency with which plants produce biomass per unit P. At molecular level, the spatio-temporal regulation of genes involved in plant adaptation to low P and high [CO2] has been studied individually in various plant species. Genome-wide expression profiling of high [CO2] grown plants revealed hormonal regulation of biomass accumulation through complex transcriptional networks. Similarly, differential transcriptional regulatory networks are involved in P-limitation responses in plants. Analysis of expression patterns of some typical P-limitation induced genes under high [CO2] suggests that long-term exposure of plants to high [CO2] would have a tendency to stimulate similar transcriptional responses as observed under P-limitation. However, studies on the combined effect of high [CO2] and low P on gene expression are scarce. Such studies would provide insights into the development of P efficient crops in the context of anticipated increases in atmospheric [CO2].
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Affiliation(s)
- Renu Pandey
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi 110012, India.
| | - Gaurav Zinta
- Department of Biology, University of Antwerp, 2610, Belgium
| | - Hamada AbdElgawad
- Department of Biology, University of Antwerp, 2610, Belgium; Department of Botany, Faculty of Science, University of Beni-Sueif, Beni-Sueif 62511, Egypt
| | - Altaf Ahmad
- Department of Botany, Aligarh Muslim University, Aligarh 201002, India
| | - Vanita Jain
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi 110012, India
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16
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van Maarschalkerweerd M, Husted S. Recent developments in fast spectroscopy for plant mineral analysis. FRONTIERS IN PLANT SCIENCE 2015; 6:169. [PMID: 25852719 PMCID: PMC4371691 DOI: 10.3389/fpls.2015.00169] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/02/2015] [Indexed: 05/07/2023]
Abstract
Ideal fertilizer management to optimize plant productivity and quality is more relevant than ever, as global food demands increase along with the rapidly growing world population. At the same time, sub-optimal or excessive use of fertilizers leads to severe environmental damage in areas of intensive crop production. The approaches of soil and plant mineral analysis are briefly compared and discussed here, and the new techniques using fast spectroscopy that offer cheap, rapid, and easy-to-use analysis of plant nutritional status are reviewed. The majority of these methods use vibrational spectroscopy, such as visual-near infrared and to a lesser extent ultraviolet and mid-infrared spectroscopy. Advantages of and problems with application of these techniques are thoroughly discussed. Spectroscopic techniques considered having major potential for plant mineral analysis, such as chlorophyll a fluorescence, X-ray fluorescence, and laser-induced breakdown spectroscopy are also described.
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Affiliation(s)
- Marie van Maarschalkerweerd
- Department of Plant and Environmental Sciences, University of CopenhagenFrederiksberg, Denmark
- Foss Analytical A/SHillerød, Denmark
| | - Søren Husted
- Department of Plant and Environmental Sciences, University of CopenhagenFrederiksberg, Denmark
- *Correspondence: Søren Husted, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
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17
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O'Rourke JA, Bolon YT, Bucciarelli B, Vance CP. Legume genomics: understanding biology through DNA and RNA sequencing. ANNALS OF BOTANY 2014; 113:1107-20. [PMID: 24769535 PMCID: PMC4030821 DOI: 10.1093/aob/mcu072] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 03/13/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND The legume family (Leguminosae) consists of approx. 17 000 species. A few of these species, including, but not limited to, Phaseolus vulgaris, Cicer arietinum and Cajanus cajan, are important dietary components, providing protein for approx. 300 million people worldwide. Additional species, including soybean (Glycine max) and alfalfa (Medicago sativa), are important crops utilized mainly in animal feed. In addition, legumes are important contributors to biological nitrogen, forming symbiotic relationships with rhizobia to fix atmospheric N2 and providing up to 30 % of available nitrogen for the next season of crops. The application of high-throughput genomic technologies including genome sequencing projects, genome re-sequencing (DNA-seq) and transcriptome sequencing (RNA-seq) by the legume research community has provided major insights into genome evolution, genomic architecture and domestication. SCOPE AND CONCLUSIONS This review presents an overview of the current state of legume genomics and explores the role that next-generation sequencing technologies play in advancing legume genomics. The adoption of next-generation sequencing and implementation of associated bioinformatic tools has allowed researchers to turn each species of interest into their own model organism. To illustrate the power of next-generation sequencing, an in-depth overview of the transcriptomes of both soybean and white lupin (Lupinus albus) is provided. The soybean transcriptome focuses on analysing seed development in two near-isogenic lines, examining the role of transporters, oil biosynthesis and nitrogen utilization. The white lupin transcriptome analysis examines how phosphate deficiency alters gene expression patterns, inducing the formation of cluster roots. Such studies illustrate the power of next-generation sequencing and bioinformatic analyses in elucidating the gene networks underlying biological processes.
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Affiliation(s)
- Jamie A O'Rourke
- United States Department of Agriculture, Agricultural Research Service, University of Minnesota, St. Paul, MN 55108, USA Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
| | - Yung-Tsi Bolon
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
| | - Bruna Bucciarelli
- United States Department of Agriculture, Agricultural Research Service, University of Minnesota, St. Paul, MN 55108, USA Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
| | - Carroll P Vance
- United States Department of Agriculture, Agricultural Research Service, University of Minnesota, St. Paul, MN 55108, USA Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
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18
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Zhang K, Liu H, Tao P, Chen H. Comparative proteomic analyses provide new insights into low phosphorus stress responses in maize leaves. PLoS One 2014; 9:e98215. [PMID: 24858307 PMCID: PMC4032345 DOI: 10.1371/journal.pone.0098215] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 04/30/2014] [Indexed: 12/03/2022] Open
Abstract
Phosphorus deficiency limits plant growth and development. To better understand the mechanisms behind how maize responds to phosphate stress, we compared the proteome analysis results of two groups of maize leaves that were treated separately with 1,000 µM (control, +P) and 5 µM of KH2PO4 (intervention group, -P) for 25 days. In total, 1,342 protein spots were detected on 2-DE maps and 15.43% had changed (P<0.05; ≥1.5-fold) significantly in quantity between the +P and -P groups. These proteins are involved in several major metabolic pathways, including photosynthesis, carbohydrate metabolism, energy metabolism, secondary metabolism, signal transduction, protein synthesis, cell rescue and cell defense and virulence. The results showed that the reduction in photosynthesis under low phosphorus treatment was due to the down-regulation of the proteins involved in CO2 enrichment, the Calvin cycle and the electron transport system. Electron transport and photosynthesis restrictions resulted in a large accumulation of peroxides. Maize has developed many different reactive oxygen species (ROS) scavenging mechanisms to cope with low phosphorus stress, including up-regulating its antioxidant content and antioxidase activity. After being subjected to phosphorus stress over a long period, maize may increase its internal phosphorus utilization efficiency by altering photorespiration, starch synthesis and lipid composition. These results provide important information about how maize responds to low phosphorus stress.
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Affiliation(s)
- Kewei Zhang
- School of Life Sciences, Shandong University, Ministry of Education Key Laboratory of Plant Cell Engineering and Germplasm Enhancement, Jinan, China
| | - Hanhan Liu
- School of Life Sciences, Shandong University, Ministry of Education Key Laboratory of Plant Cell Engineering and Germplasm Enhancement, Jinan, China
| | - Peilin Tao
- College of Agriculture Vocational, Xuzhou Biology Engineering Technical College, Xuzhou, China
| | - Huan Chen
- School of Life Sciences, Shandong University, Ministry of Education Key Laboratory of Plant Cell Engineering and Germplasm Enhancement, Jinan, China
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19
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Hosokawa M, Yamauchi T, Takahama M, Goto M, Mikano S, Yamaguchi Y, Tanaka Y, Ohno S, Koeda S, Doi M, Yazawa S. Phosphorus starvation induces post-transcriptional CHS gene silencing in Petunia corolla. PLANT CELL REPORTS 2013; 32:601-609. [PMID: 23397276 DOI: 10.1007/s00299-013-1391-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 01/16/2013] [Accepted: 01/18/2013] [Indexed: 06/01/2023]
Abstract
The corolla of Petunia 'Magic Samba' exhibits unstable anthocyanin expression depending on its phosphorus content. Phosphorus deficiency enhanced post-transcriptional gene silencing of chalcone synthase - A in the corolla. Petunia (Petunia hybrida) 'Magic Samba' has unstable red-white bicolored corollas that respond to nutrient deficiency. We grew this cultivar hydroponically using solutions that lacked one or several nutrients to identify the specific nutrient related to anthocyanin expression in corolla. The white area of the corolla widened under phosphorus (P)-deficient conditions. When the P content of the corolla grown under P-deficient conditions dropped to <2,000 ppm, completely white corollas continued to develop in >40 corollas until the plants died. Other elemental deficiencies had no clear effects on anthocyanin suppression in the corolla. After phosphate was resupplied to the P-deficient plants, anthocyanin was restored in the corollas. The expression of chalcone synthase-A (CHS-A) was suppressed in the white area that widened under P-suppressed conditions, whereas the expression of several other genes related to anthocyanin biosynthesis was enhanced more in the white area than in the red area. Reddish leaves and sepals developed under the P-deficient condition, which is a typical P-deficiency symptom. Two genes related to anthocyanin biosynthesis were enhanced in the reddish organs. Small interfering RNA analysis of CHS-A showed that the suppression resulted from post-transcriptional gene silencing (PTGS). Thus, it was hypothesized that the enhancement of anthocyanin biosynthetic gene expression due to P-deficiency triggered PTGS of CHS-A, which resulted in white corolla development.
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Affiliation(s)
- Munetaka Hosokawa
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.
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20
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Ha S, Tran LS. Understanding plant responses to phosphorus starvation for improvement of plant tolerance to phosphorus deficiency by biotechnological approaches. Crit Rev Biotechnol 2013; 34:16-30. [PMID: 23586682 DOI: 10.3109/07388551.2013.783549] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In both prokaryotes and eukaryotes, including plants, phosphorus (P) is an essential nutrient that is involved in various biochemical processes, such as lipid metabolism and the biosynthesis of nucleic acids and cell membranes. P also contributes to cellular signaling cascades by function as mediators of signal transduction and it also serves as a vital energy source for a wide range of biological functions. Due to its intensive use in agriculture, P resources have become limited. Therefore, it is critically important in the future to develop scientific strategies that aim to increase P use efficiency and P recycling. In addition, the biologically available soluble form of P for uptake (phosphate; Pi) is readily washed out of topsoil layers, resulting in serious environmental pollution. In addition to this environmental concern, the wash out of Pi from topsoil necessitates a continuous Pi supply to maintain adequate levels of fertilization, making the situation worse. As a coping mechanism to P stress, plants are known to undergo drastic cellular changes in metabolism, physiology, hormonal balance and gene expression. Understanding these molecular, physiological and biochemical responses developed by plants will play a vital role in improving agronomic practices, resource conservation and environmental protection as well as serving as a foundation for the development of biotechnological strategies, which aim to improve P use efficiency in crops. In this review, we will discuss a variety of plant responses to low P conditions and various molecular mechanisms that regulate these responses. In addition, we also discuss the implication of this knowledge for the development of plant biotechnological applications.
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Affiliation(s)
- Sukbong Ha
- Department of Plant Biotechnology, Chonnam National University , Buk-Gu, Gwangju , Korea and
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21
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O’Rourke JA, Yang SS, Miller SS, Bucciarelli B, Liu J, Rydeen A, Bozsoki Z, Uhde-Stone C, Tu ZJ, Allan D, Gronwald JW, Vance CP. An RNA-Seq transcriptome analysis of orthophosphate-deficient white lupin reveals novel insights into phosphorus acclimation in plants. PLANT PHYSIOLOGY 2013; 161:705-24. [PMID: 23197803 PMCID: PMC3561014 DOI: 10.1104/pp.112.209254] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 11/21/2012] [Indexed: 05/18/2023]
Abstract
Phosphorus, in its orthophosphate form (P(i)), is one of the most limiting macronutrients in soils for plant growth and development. However, the whole-genome molecular mechanisms contributing to plant acclimation to P(i) deficiency remain largely unknown. White lupin (Lupinus albus) has evolved unique adaptations for growth in P(i)-deficient soils, including the development of cluster roots to increase root surface area. In this study, we utilized RNA-Seq technology to assess global gene expression in white lupin cluster roots, normal roots, and leaves in response to P(i) supply. We de novo assembled 277,224,180 Illumina reads from 12 complementary DNA libraries to build what is to our knowledge the first white lupin gene index (LAGI 1.0). This index contains 125,821 unique sequences with an average length of 1,155 bp. Of these sequences, 50,734 were transcriptionally active (reads per kilobase per million reads ≥ 3), representing approximately 7.8% of the white lupin genome, using the predicted genome size of Lupinus angustifolius as a reference. We identified a total of 2,128 sequences differentially expressed in response to P(i) deficiency with a 2-fold or greater change and P ≤ 0.05. Twelve sequences were consistently differentially expressed due to P(i) deficiency stress in three species, Arabidopsis (Arabidopsis thaliana), potato (Solanum tuberosum), and white lupin, making them ideal candidates to monitor the P(i) status of plants. Additionally, classic physiological experiments were coupled with RNA-Seq data to examine the role of cytokinin and gibberellic acid in P(i) deficiency-induced cluster root development. This global gene expression analysis provides new insights into the biochemical and molecular mechanisms involved in the acclimation to P(i) deficiency.
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Affiliation(s)
- Jamie A. O’Rourke
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
| | - S. Samuel Yang
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
| | - Susan S. Miller
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
| | - Bruna Bucciarelli
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
| | - Junqi Liu
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
| | - Ariel Rydeen
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
| | - Zoltan Bozsoki
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
| | - Claudia Uhde-Stone
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
| | | | - Deborah Allan
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
| | - John W. Gronwald
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
| | - Carroll P. Vance
- United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, St. Paul, Minnesota 55108 (J.A.O., S.S.Y., S.S.M., B.B., J.W.G., C.P.V.); Department of Agronomy and Plant Genetics (J.A.O., S.S.M., B.B., J.L., A.R., J.W.G., C.P.V.), Supercomputing Institute for Advanced Computational Research (Z.J.T.), and Department Soil Water and Climate (D.A.), University of Minnesota, St. Paul, Minnesota 55108; Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary (Z.B.); and Department of Biological Sciences, California State University, East Bay, Hayward, California 94542 (C.U.-S.)
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Lambers H, Cawthray GR, Giavalisco P, Kuo J, Laliberté E, Pearse SJ, Scheible WR, Stitt M, Teste F, Turner BL. Proteaceae from severely phosphorus-impoverished soils extensively replace phospholipids with galactolipids and sulfolipids during leaf development to achieve a high photosynthetic phosphorus-use-efficiency. THE NEW PHYTOLOGIST 2012; 196:1098-1108. [PMID: 22937909 DOI: 10.1111/j.1469-8137.2012.04285.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 07/20/2012] [Indexed: 05/20/2023]
Abstract
Proteaceae species in south-western Australia occur on severely phosphorus (P)-impoverished soils. They have very low leaf P concentrations, but relatively fast rates of photosynthesis, thus exhibiting extremely high photosynthetic phosphorus-use-efficiency (PPUE). Although the mechanisms underpinning their high PPUE remain unknown, one possibility is that these species may be able to replace phospholipids with nonphospholipids during leaf development, without compromising photosynthesis. For six Proteaceae species, we measured soil and leaf P concentrations and rates of photosynthesis of both young expanding and mature leaves. We also assessed the investment in galactolipids, sulfolipids and phospholipids in young and mature leaves, and compared these results with those on Arabidopsis thaliana, grown under both P-sufficient and P-deficient conditions. In all Proteaceae species, phospholipid levels strongly decreased during leaf development, whereas those of galactolipids and sulfolipids strongly increased. Photosynthetic rates increased from young to mature leaves. This shows that these species extensively replace phospholipids with nonphospholipids during leaf development, without compromising photosynthesis. A considerably less pronounced shift was observed in A. thaliana. Our results clearly show that a low investment in phospholipids, relative to nonphospholipids, offers a partial explanation for a high photosynthetic rate per unit leaf P in Proteaceae adapted to P-impoverished soils.
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Affiliation(s)
- Hans Lambers
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Gregory R Cawthray
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Patrick Giavalisco
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany
| | - John Kuo
- Centre for Microscopy and Microanalysis, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Etienne Laliberté
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Stuart J Pearse
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Wolf-Rüdiger Scheible
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany
| | - François Teste
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Benjamin L Turner
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancón, Republic of Panama
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Identification of genes differentially expressed in the roots of rubber tree (Hevea brasiliensis Muell. Arg.) in response to phosphorus deficiency. Mol Biol Rep 2012; 40:1397-405. [PMID: 23076531 DOI: 10.1007/s11033-012-2183-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 10/09/2012] [Indexed: 10/27/2022]
Abstract
Phosphorus (P) is an essential macronutrient for plant growth and development. P deficiency could affect rubber tree productivity seriously, and understanding the mechanism responses of the rubber tree under the P deficiency will be helpful to improving rubber tree productivity. The molecular mechanism by which the rubber trees respond to a P-deficiency is a complex network involving many processes. To identify the genes differentially expressed in that response, we constructed subtractive suppression hybridization libraries for roots of plants growing under deficient or sufficient conditions. We identified 94 up-regulated genes from the forward library and 45 down-regulated from the reverse library. These differentially expressed genes were categorized into eight groups representing functions in metabolism, transcription, signal transduction, protein synthesis, transport, stress responses, photosynthesis, and development. We also performed quantitative real-time PCR to investigate the expression profiles of eight randomly selected clones. Our results provide useful information for further study of the molecular mechanism for adaptations to a P-deficiency in this species. Further characterization and functional analysis of these differentially expressed genes will help us improve its phosphorus utilization and overall productivity.
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