skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Transcriptional, metabolic, physiological and developmental responses of switchgrass to phosphorus limitation


Citation Formats

Ding, Na, Huertas, Raul, Torres‐Jerez, Ivone, Liu, Wei, Watson, Bonnie, Scheible, Wolf‐Rüdiger, and Udvardi, Michael. Transcriptional, metabolic, physiological and developmental responses of switchgrass to phosphorus limitation. United Kingdom: N. p., 2020. Web. doi:10.1111/pce.13872.
Ding, Na, Huertas, Raul, Torres‐Jerez, Ivone, Liu, Wei, Watson, Bonnie, Scheible, Wolf‐Rüdiger, & Udvardi, Michael. Transcriptional, metabolic, physiological and developmental responses of switchgrass to phosphorus limitation. United Kingdom. doi:10.1111/pce.13872.
Ding, Na, Huertas, Raul, Torres‐Jerez, Ivone, Liu, Wei, Watson, Bonnie, Scheible, Wolf‐Rüdiger, and Udvardi, Michael. Wed . "Transcriptional, metabolic, physiological and developmental responses of switchgrass to phosphorus limitation". United Kingdom. doi:10.1111/pce.13872.
@article{osti_1671137,
title = {Transcriptional, metabolic, physiological and developmental responses of switchgrass to phosphorus limitation},
author = {Ding, Na and Huertas, Raul and Torres‐Jerez, Ivone and Liu, Wei and Watson, Bonnie and Scheible, Wolf‐Rüdiger and Udvardi, Michael},
abstractNote = {},
doi = {10.1111/pce.13872},
journal = {Plant, Cell and Environment},
issn = {0140-7791},
number = ,
volume = ,
place = {United Kingdom},
year = {2020},
month = {10}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1111/pce.13872

Save / Share:

Works referenced in this record:

Morphological responses of wheat ( Triticum aestivum L.) roots to phosphorus supply in two contrasting soils
journal, July 2015

  • Yuan, H. M.; Blackwell, M.; Mcgrath, S.
  • The Journal of Agricultural Science, Vol. 154, Issue 1
  • DOI: 10.1017/S0021859615000702

Uncertainty budgeting in fold change determination and implications for non-targeted metabolomics studies in model systems
journal, January 2017

  • Ortmayr, Karin; Charwat, Verena; Kasper, Cornelia
  • The Analyst, Vol. 142, Issue 1
  • DOI: 10.1039/C6AN01342B

Nitrate Acts as a Signal to Induce Organic Acid Metabolism and Repress Starch Metabolism in Tobacco
journal, May 1997

  • Scheible, Wolf-Rudiger; Gonzalez-Fontes, Agustin; Lauerer, Marianne
  • The Plant Cell, Vol. 9, Issue 5
  • DOI: 10.2307/3870432

Water and energy footprints of bioenergy crop production on marginal lands: LAND MARGINALITY EFFECTS ON WATER AND ENERGY USE
journal, November 2010


Spatio-Temporal Transcript Profiling of Rice Roots and Shoots in Response to Phosphate Starvation and Recovery
journal, November 2013


The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA
journal, March 2009

  • El Yacoubi, B.; Lyons, B.; Cruz, Y.
  • Nucleic Acids Research, Vol. 37, Issue 9
  • DOI: 10.1093/nar/gkp152

Phospholipase C5 (NPC5) is involved in galactolipid accumulation during phosphate limitation in leaves of Arabidopsis
journal, October 2008


Lipid changes after leaf wounding in Arabidopsis thaliana : expanded lipidomic data form the basis for lipid co-occurrence analysis
journal, October 2014

  • Vu, Hieu Sy; Shiva, Sunitha; Roth, Mary R.
  • The Plant Journal, Vol. 80, Issue 4
  • DOI: 10.1111/tpj.12659

RNA-seq analysis identifies an intricate regulatory network controlling cluster root development in white lupin
journal, January 2014


Stars and Symbiosis: MicroRNA- and MicroRNA*-Mediated Transcript Cleavage Involved in Arbuscular Mycorrhizal Symbiosis
journal, May 2011

  • Devers, Emanuel A.; Branscheid, Anja; May, Patrick
  • Plant Physiology, Vol. 156, Issue 4
  • DOI: 10.1104/pp.111.172627

Phosphate Starvation Inducible Metabolism in Lycopersicon esculentum: I. Excretion of Acid Phosphatase by Tomato Plants and Suspension-Cultured Cells
journal, July 1988

  • Goldstein, Alan H.; Baertlein, Dawn A.; McDaniel, Robert G.
  • Plant Physiology, Vol. 87, Issue 3
  • DOI: 10.1104/pp.87.3.711

Differential analysis of gene regulation at transcript resolution with RNA-seq
journal, December 2012

  • Trapnell, Cole; Hendrickson, David G.; Sauvageau, Martin
  • Nature Biotechnology, Vol. 31, Issue 1
  • DOI: 10.1038/nbt.2450

Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method
journal, December 2001


Phosphorus nutrition in Proteaceae and beyond
journal, August 2015


Editing of the OsACS locus alters phosphate deficiency-induced adaptive responses in rice seedlings
journal, February 2019

  • Lee, Han Yong; Chen, Zhixiong; Zhang, Cankui
  • Journal of Experimental Botany, Vol. 70, Issue 6
  • DOI: 10.1093/jxb/erz074

Integrating transcriptional, metabolomic, and physiological responses to drought stress and recovery in switchgrass (Panicum virgatum L.)
journal, January 2014


The Impacts of Phosphorus Deficiency on the Photosynthetic Electron Transport Chain
journal, March 2018

  • Carstensen, Andreas; Herdean, Andrei; Schmidt, Sidsel Birkelund
  • Plant Physiology, Vol. 177, Issue 1
  • DOI: 10.1104/pp.17.01624

Multivariate analyses in microbial ecology: Multivariate analyses in microbial ecology
journal, November 2007


psRNATarget: a plant small RNA target analysis server (2017 release)
journal, April 2018

  • Dai, Xinbin; Zhuang, Zhaohong; Zhao, Patrick Xuechun
  • Nucleic Acids Research, Vol. 46, Issue W1
  • DOI: 10.1093/nar/gky316

Metabolic Adaptations of Phosphate-Starved Plants
journal, May 2011


An Integrative Systems Perspective on Plant Phosphate Research
journal, February 2019


The Challenge of Lignocellulosic Bioenergy in a Water-Limited World
journal, February 2013


BHLH32 modulates several biochemical and morphological processes that respond to Pi starvation in Arabidopsis
journal, June 2007

  • Chen, Zhi-Hui; Nimmo, Gillian A.; Jenkins, Gareth I.
  • Biochemical Journal, Vol. 405, Issue 1
  • DOI: 10.1042/BJ20070102

A simple and efficient method for isolating RNA from pine trees
journal, June 1993

  • Chang, Shujun; Puryear, Jeff; Cairney, John
  • Plant Molecular Biology Reporter, Vol. 11, Issue 2
  • DOI: 10.1007/BF02670468

ViennaRNA Package 2.0
journal, November 2011

  • Lorenz, Ronny; Bernhart, Stephan H.; Höner zu Siederdissen, Christian
  • Algorithms for Molecular Biology, Vol. 6, Issue 1
  • DOI: 10.1186/1748-7188-6-26

Sustainable bioenergy production from marginal lands in the US Midwest
journal, January 2013

  • Gelfand, Ilya; Sahajpal, Ritvik; Zhang, Xuesong
  • Nature, Vol. 493, Issue 7433
  • DOI: 10.1038/nature11811

Uncovering Small RNA-Mediated Responses to Phosphate Deficiency in Arabidopsis by Deep Sequencing
journal, October 2009

  • Hsieh, Li-Ching; Lin, Shu-I.; Shih, Arthur Chun-Chieh
  • Plant Physiology, Vol. 151, Issue 4
  • DOI: 10.1104/pp.109.147280

Evolution of microRNA827 targeting in the plant kingdom
journal, December 2017

  • Lin, Wei-Yi; Lin, Yen-Yu; Chiang, Su-Fen
  • New Phytologist, Vol. 217, Issue 4
  • DOI: 10.1111/nph.14938

Metabolic Changes of Amino Acids and Flavonoids in Tea Plants in Response to Inorganic Phosphate Limitation
journal, November 2018

  • Kc, Santosh; Liu, Meiya; Zhang, Qunfeng
  • International Journal of Molecular Sciences, Vol. 19, Issue 11
  • DOI: 10.3390/ijms19113683

Harvest Management of Switchgrass for Biomass Feedstock and Forage Production
journal, January 1999


Transcriptome analysis in roots and leaves of wheat seedlings in response to low-phosphorus stress
journal, December 2019


Root Phenes for Enhanced Soil Exploration and Phosphorus Acquisition: Tools for Future Crops
journal, May 2011


Long- and short-term phosphate deprivation in bean roots: Plasma membrane lipid alterations and transient stimulation of phospholipases
journal, June 2007


Vacuolar Ca 2+ /H + Transport Activity Is Required for Systemic Phosphate Homeostasis Involving Shoot-to-Root Signaling in Arabidopsis
journal, May 2011

  • Liu, Tzu-Yin; Aung, Kyaw; Tseng, Ching-Ying
  • Plant Physiology, Vol. 156, Issue 3
  • DOI: 10.1104/pp.111.175257

Genome-wide reprogramming of metabolism and regulatory networks of Arabidopsis in response to phosphorus
journal, January 2007


Root Architecture and Plant Productivity
journal, September 1995


Stimulation of root hair elongation in Arabidopsis thaliana by low phosphorus availability
journal, May 1996


In vivo regulatory phosphorylation of the phosphoenolpyruvate carboxylase AtPPC1 in phosphate-starved Arabidopsis thaliana
journal, April 2009

  • Gregory, Allison L.; Hurley, Brenden A.; Tran, Hue T.
  • Biochemical Journal, Vol. 420, Issue 1
  • DOI: 10.1042/BJ20082397

Biomass Yield and Nutrient Responses of Switchgrass to Phosphorus Application
journal, January 2012


WRKY75 Transcription Factor Is a Modulator of Phosphate Acquisition and Root Development in Arabidopsis
journal, February 2007

  • Devaiah, Ballachanda N.; Karthikeyan, Athikkattuvalasu S.; Raghothama, Kashchandra G.
  • Plant Physiology, Vol. 143, Issue 4
  • DOI: 10.1104/pp.106.093971

PHO2, MicroRNA399, and PHR1 Define a Phosphate-Signaling Pathway in Plants
journal, May 2006

  • Bari, Rajendra; Datt Pant, Bikram; Stitt, Mark
  • Plant Physiology, Vol. 141, Issue 3
  • DOI: 10.1104/pp.106.079707

A Novel Framework to Classify Marginal Land for Sustainable Biomass Feedstock Production
journal, January 2011

  • Gopalakrishnan, Gayathri; Cristina Negri, M.; Snyder, Seth W.
  • Journal of Environment Quality, Vol. 40, Issue 5
  • DOI: 10.2134/jeq2010.0539

Metabolic profiling of root exudates from two ecotypes of Sedum alfredii treated with Pb based on GC-MS
journal, January 2017

  • Luo, Qing; Wang, Shiyu; Sun, Li-na
  • Scientific Reports, Vol. 7, Issue 1
  • DOI: 10.1038/srep39878

Membrane Glycerolipid Remodeling Triggered by Nitrogen and Phosphorus Starvation in Phaeodactylum tricornutum
journal, December 2014

  • Abida, Heni; Dolch, Lina-Juana; Meï, Coline
  • Plant Physiology, Vol. 167, Issue 1
  • DOI: 10.1104/pp.114.252395

Metabolic Adaptations of White Lupin Roots and Shoots under Phosphorus Deficiency
journal, November 2015

  • Müller, Julia; Gödde, Victoria; Niehaus, Karsten
  • Frontiers in Plant Science, Vol. 6
  • DOI: 10.3389/fpls.2015.01014

mRNA-Seq Reveals a Comprehensive Transcriptome Profile of Rice under Phosphate Stress
journal, June 2011


The Switchgrass Genome: Tools and Strategies
journal, January 2011


The transcription factor PHR1 regulates lipid remodeling and triacylglycerol accumulation in Arabidopsis thaliana during phosphorus starvation
journal, February 2015

  • Pant, Bikram Datt; Burgos, Asdrubal; Pant, Pooja
  • Journal of Experimental Botany, Vol. 66, Issue 7
  • DOI: 10.1093/jxb/eru535

Phosphorus Nutrition of Proteaceae in Severely Phosphorus-Impoverished Soils: Are There Lessons To Be Learned for Future Crops?
journal, April 2011

  • Lambers, Hans; Finnegan, Patrick M.; Laliberté, Etienne
  • Plant Physiology, Vol. 156, Issue 3
  • DOI: 10.1104/pp.111.174318

Identification of Nutrient-Responsive Arabidopsis and Rapeseed MicroRNAs by Comprehensive Real-Time Polymerase Chain Reaction Profiling and Small RNA Sequencing
journal, May 2009

  • Pant, Bikram Datt; Musialak-Lange, Magdalena; Nuc, Przemyslaw
  • Plant Physiology, Vol. 150, Issue 3
  • DOI: 10.1104/pp.109.139139

Opportunities for improving phosphorus-use efficiency in crop plants: Tansley review
journal, June 2012


Biosynthesis and Function of the Sulfolipid Sulfoquinovosyl Diacylglycerol
journal, June 1998


miRNA alterations are important mechanism in maize adaptations to low-phosphate environments
journal, November 2016


A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation
journal, August 2005

  • Misson, J.; Raghothama, K. G.; Jain, A.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 33
  • DOI: 10.1073/pnas.0505266102

Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism
journal, December 2004

  • Broeckling, Corey D.; Huhman, David V.; Farag, Mohamed A.
  • Journal of Experimental Botany, Vol. 56, Issue 410
  • DOI: 10.1093/jxb/eri058

Transcriptome Profiling of Rust Resistance in Switchgrass Using RNA-Seq Analysis
journal, January 2015


Phosphate Source Interacts with Endophyte Strain to Influence Biomass and Root System Architecture in Tall Fescue
journal, March 2015

  • Ding, Na; Kupper, Joseph V.; McNear, David H.
  • Agronomy Journal, Vol. 107, Issue 2
  • DOI: 10.2134/agronj14.0135

Switchgrass for forage and bioenergy: harvest and nitrogen rate effects on biomass yields and nutrient composition
journal, April 2010


Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass ( Panicum virgatum L.)
journal, February 2013

  • Zhang, Ji-Yi; Lee, Yi-Ching; Torres-Jerez, Ivone
  • The Plant Journal, Vol. 74, Issue 1
  • DOI: 10.1111/tpj.12104

Genome-wide identification of microRNAs responding to early stages of phosphate deficiency in maize
journal, January 2016

  • Nie, Zhi; Ren, Zhiyong; Wang, Libo
  • Physiologia Plantarum, Vol. 157, Issue 2
  • DOI: 10.1111/ppl.12409

A Genome-Wide Survey of Switchgrass Genome Structure and Organization
journal, April 2012


MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis
journal, May 2015

  • Tsugawa, Hiroshi; Cajka, Tomas; Kind, Tobias
  • Nature Methods, Vol. 12, Issue 6
  • DOI: 10.1038/nmeth.3393

Early Transcriptomic Response to Phosphate Deprivation in Soybean Leaves as Revealed by RNA-Sequencing
journal, July 2018

  • Zeng, Houqing; Zhang, Xiajun; Zhang, Xin
  • International Journal of Molecular Sciences, Vol. 19, Issue 7
  • DOI: 10.3390/ijms19072145

Is root growth under phosphorus deficiency affected by source or sink limitations?
journal, May 2005

  • Wissuwa, Matthias; Gamat, Gloria; Ismail, Abdelbagi M.
  • Journal of Experimental Botany, Vol. 56, Issue 417
  • DOI: 10.1093/jxb/eri189

Widespread Translational Inhibition by Plant miRNAs and siRNAs
journal, May 2008

  • Brodersen, P.; Sakvarelidze-Achard, L.; Bruun-Rasmussen, M.
  • Science, Vol. 320, Issue 5880
  • DOI: 10.1126/science.1159151

The PILNCR1 -miR399 Regulatory Module Is Important for Low Phosphate Tolerance in Maize
journal, July 2018

  • Du, Qingguo; Wang, Kai; Zou, Cheng
  • Plant Physiology, Vol. 177, Issue 4
  • DOI: 10.1104/pp.18.00034

Plasma membrane H + -ATPase-dependent citrate exudation from cluster roots of phosphate-deficient white lupin
journal, May 2009


WinRHlZO™, a Root-measuring System with a Unique Overlap Correction Method
journal, July 1995


Genome-Wide Analysis of the Arabidopsis Leaf Transcriptome Reveals Interaction of Phosphate and Sugar Metabolism
journal, November 2006

  • Müller, Renate; Morant, Marc; Jarmer, Hanne
  • Plant Physiology, Vol. 143, Issue 1
  • DOI: 10.1104/pp.106.090167

Characterization of phosphorus-regulated miR399 and miR827 and their isomirs in barley under phosphorus-sufficient and phosphorus-deficient conditions
journal, January 2013


A simplified protocol for genetic transformation of switchgrass (Panicum virgatum L.)
journal, June 2012


The transcription factor PHR1 plays a key role in the regulation of sulfate shoot-to-root flux upon phosphate starvation in Arabidopsis
journal, January 2011


Performance and Limitations of Phosphate Quantification: Guidelines for Plant Biologists
journal, February 2016

  • Kanno, Satomi; Cuyas, Laura; Javot, Hélène
  • Plant and Cell Physiology, Vol. 57, Issue 4
  • DOI: 10.1093/pcp/pcv208

Gene Expression Changes in Phosphorus Deficient Potato (Solanum tuberosum L.) Leaves and the Potential for Diagnostic Gene Expression Markers
journal, September 2011


StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
journal, February 2015

  • Pertea, Mihaela; Pertea, Geo M.; Antonescu, Corina M.
  • Nature Biotechnology, Vol. 33, Issue 3
  • DOI: 10.1038/nbt.3122

Target mimicry provides a new mechanism for regulation of microRNA activity
journal, July 2007

  • Franco-Zorrilla, José Manuel; Valli, Adrián; Todesco, Marco
  • Nature Genetics, Vol. 39, Issue 8
  • DOI: 10.1038/ng2079

Phosphorus Stress in Common Bean: Root Transcript and Metabolic Responses
journal, April 2007

  • Hernández, Georgina; Ramírez, Mario; Valdés-López, Oswaldo
  • Plant Physiology, Vol. 144, Issue 2
  • DOI: 10.1104/pp.107.096958

An RNA-Seq Transcriptome Analysis of Orthophosphate-Deficient White Lupin Reveals Novel Insights into Phosphorus Acclimation in Plants
journal, November 2012

  • O’Rourke, Jamie A.; Yang, S. Samuel; Miller, Susan S.
  • Plant Physiology, Vol. 161, Issue 2
  • DOI: 10.1104/pp.112.209254

Phosphorus acquisition and utilisation in crop legumes under global change
journal, October 2018


Comparative transcript profiling of maize inbreds in response to long-term phosphorus deficiency stress
journal, December 2016


Global Changes in the Transcript and Metabolic Profiles during Symbiotic Nitrogen Fixation in Phosphorus-Stressed Common Bean Plants
journal, September 2009

  • Hernández, Georgina; Valdés-López, Oswaldo; Ramírez, Mario
  • Plant Physiology, Vol. 151, Issue 3
  • DOI: 10.1104/pp.109.143842

Developmental Physiology of Cluster-Root Carboxylate Synthesis and Exudation in Harsh Hakea. Expression of Phospho enol pyruvate Carboxylase and the Alternative Oxidase
journal, April 2004

  • Shane, Michael W.; Cramer, Michael D.; Funayama-Noguchi, Sachiko
  • Plant Physiology, Vol. 135, Issue 1
  • DOI: 10.1104/pp.103.035659

Chemical characteristics of phosphorus in alkaline soils from southern Australia
journal, January 2003

  • Bertrand, I.; Holloway, R. E.; Armstrong, R. D.
  • Soil Research, Vol. 41, Issue 1
  • DOI: 10.1071/SR02021

HISAT: a fast spliced aligner with low memory requirements
journal, March 2015

  • Kim, Daehwan; Langmead, Ben; Salzberg, Steven L.
  • Nature Methods, Vol. 12, Issue 4
  • DOI: 10.1038/nmeth.3317

Knock out of the PHOSPHATE 2 Gene TaPHO2-A1 Improves Phosphorus Uptake and Grain Yield under Low Phosphorus Conditions in Common Wheat
journal, July 2016

  • Ouyang, Xiang; Hong, Xia; Zhao, Xueqiang
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep29850