Home LiteratureArticle Details
PMID: 19117793 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Review

Functional genomics of root growth and development in Arabidopsis.

Current opinion in plant biology ·Vol. 12 ·No. 2 ·2009-04-00 ·Pages 165-71

Iyer-Pascuzzi A, Simpson J, Herrera-Estrella L, Benfey PN

Abstract

Roots are vital for the uptake of water and nutrients, and for anchorage in the soil. They are highly plastic, able to adapt developmentally and physiologically to changing environmental conditions. Understanding the molecular mechanisms behind this growth and development requires knowledge of root transcriptomics, proteomics, and metabolomics. Genomics approaches, including the recent publication of a root expression map, root proteome, and environment-specific root expression studies, are uncovering complex transcriptional and post-transcriptional networks underlying root development. The challenge is in further capitalizing on the information in these datasets to understand the fundamental principles of root growth and development. In this review, we highlight progress researchers have made toward this goal.

MeSH Terms
Arabidopsis/genetics,growth & development Genomics Metabolomics Oryza/genetics,growth & development Plant Roots/genetics,growth & development Zea mays/genetics,growth & development
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Iyer-Pascuzzi Anjali
Duke University, Department of Biology and Center for Systems Biology, United States.
Simpson June
Herrera-Estrella Luis
Benfey Philip N
References (54)
54 references, click to expand
  1. A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation.
    Proc Natl Acad Sci U S A. 2005 Aug 16;102(33):11934-9 PMID: 16085708
  2. Plant systems biology comes of age.
    Trends Plant Sci. 2008 Apr;13(4):165-71 PMID: 18329321
  3. A gene expression map of the Arabidopsis root.
    Science. 2003 Dec 12;302(5652):1956-60 PMID: 14671301
  4. Transcript profiling of Zea mays roots reveals gene responses to phosphate deficiency at the plant- and species-specific levels.
    J Exp Bot. 2008;59(9):2479-97 PMID: 18503042
  5. Biochemical networks and epistasis shape the Arabidopsis thaliana metabolome.
    Plant Cell. 2008 May;20(5):1199-216 PMID: 18515501
  6. The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling.
    Cell. 2000 May 26;101(5):555-67 PMID: 10850497
  7. Phospholipase DZ2 plays an important role in extraplastidic galactolipid biosynthesis and phosphate recycling in Arabidopsis roots.
    Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6765-70 PMID: 16617110
  8. The genetics of plant metabolism.
    Nat Genet. 2006 Jul;38(7):842-9 PMID: 16751770
  9. The Arabidopsis transcription factor MYB77 modulates auxin signal transduction.
    Plant Cell. 2007 Aug;19(8):2440-53 PMID: 17675404
  10. Isolation, characterization, and pericycle-specific transcriptome analyses of the novel maize lateral and seminal root initiation mutant rum1.
    Plant Physiol. 2005 Nov;139(3):1255-67 PMID: 16215225
  11. A global survey of gene regulation during cold acclimation in Arabidopsis thaliana.
    PLoS Genet. 2005 Aug;1(2):e26 PMID: 16121258
  12. Cell wall proteome in the maize primary root elongation zone. II. Region-specific changes in water soluble and lightly ionically bound proteins under water deficit.
    Plant Physiol. 2007 Dec;145(4):1533-48 PMID: 17951457
  13. Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis.
    Plant Cell. 2008 Aug;20(8):2160-76 PMID: 18757557
  14. Genome-wide reprogramming of primary and secondary metabolism, protein synthesis, cellular growth processes, and the regulatory infrastructure of Arabidopsis in response to nitrogen.
    Plant Physiol. 2004 Sep;136(1):2483-99 PMID: 15375205
  15. Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics.
    Science. 2008 May 16;320(5878):938-41 PMID: 18436743
  16. Proteomic analysis of shoot-borne root initiation in maize (Zea mays L.).
    Proteomics. 2006 Apr;6(8):2530-41 PMID: 16521151
  17. Intercellular movement of the putative transcription factor SHR in root patterning.
    Nature. 2001 Sep 20;413(6853):307-11 PMID: 11565032
  18. WRKY75 transcription factor is a modulator of phosphate acquisition and root development in Arabidopsis.
    Plant Physiol. 2007 Apr;143(4):1789-801 PMID: 17322336
  19. Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana.
    Proc Natl Acad Sci U S A. 2004 Jul 6;101(27):10205-10 PMID: 15199185
  20. A high-resolution root spatiotemporal map reveals dominant expression patterns.
    Science. 2007 Nov 2;318(5851):801-6 PMID: 17975066
  21. OsPTF1, a novel transcription factor involved in tolerance to phosphate starvation in rice.
    Plant Physiol. 2005 Aug;138(4):2087-96 PMID: 16006597
  22. A gene expression map of Arabidopsis thaliana development.
    Nat Genet. 2005 May;37(5):501-6 PMID: 15806101
  23. Root branching responses to phosphate and nitrate.
    Curr Opin Plant Biol. 2008 Feb;11(1):82-7 PMID: 18024148
  24. Cell identity mediates the response of Arabidopsis roots to abiotic stress.
    Science. 2008 May 16;320(5878):942-5 PMID: 18436742
  25. Cell-specific nitrogen responses mediate developmental plasticity.
    Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):803-8 PMID: 18180456
  26. Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets.
    Proc Natl Acad Sci U S A. 2005 Jun 14;102(24):8633-8 PMID: 15932943
  27. The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access.
    Plant J. 2008 Aug;55(3):526-42 PMID: 18419781
  28. Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression.
    Genome Biol. 2007;8(4):R49 PMID: 17408486
  29. A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies.
    Nat Genet. 2009 Feb;41(2):258-63 PMID: 19122662
  30. Approaches for extracting practical information from gene co-expression networks in plant biology.
    Plant Cell Physiol. 2007 Mar;48(3):381-90 PMID: 17251202
  31. Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis.
    Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6478-83 PMID: 17420480
  32. The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses.
    Plant J. 2007 Apr;50(2):347-63 PMID: 17376166
  33. Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1.
    Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4939-44 PMID: 18344319
  34. Bioinformatics and its applications in plant biology.
    Annu Rev Plant Biol. 2006;57:335-60 PMID: 16669765
  35. Comparative proteome analyses of phosphorus responses in maize (Zea mays L.) roots of wild-type and a low-P-tolerant mutant reveal root characteristics associated with phosphorus efficiency.
    Plant J. 2008 Sep;55(6):927-39 PMID: 18489707
  36. Comparative proteome analyses of maize (Zea mays L.) primary roots prior to lateral root initiation reveal differential protein expression in the lateral root initiation mutant rum1.
    Proteomics. 2006 Aug;6(15):4300-8 PMID: 16819721
  37. BHLH32 modulates several biochemical and morphological processes that respond to Pi starvation in Arabidopsis.
    Biochem J. 2007 Jul 1;405(1):191-8 PMID: 17376028
  38. Genome-wide reprogramming of metabolism and regulatory networks of Arabidopsis in response to phosphorus.
    Plant Cell Environ. 2007 Jan;30(1):85-112 PMID: 17177879
  39. The maize root transcriptome by serial analysis of gene expression.
    Plant Physiol. 2005 Jul;138(3):1700-10 PMID: 15965024
  40. Regulatory network of microRNA399 and PHO2 by systemic signaling.
    Plant Physiol. 2008 Jun;147(2):732-46 PMID: 18390805
  41. A prominent role for the CBF cold response pathway in configuring the low-temperature metabolome of Arabidopsis.
    Proc Natl Acad Sci U S A. 2004 Oct 19;101(42):15243-8 PMID: 15383661
  42. The regulatory code for transcriptional response diversity and its relation to genome structural properties in A. thaliana.
    PLoS Genet. 2007 Feb 9;3(2):e11 PMID: 17291162
  43. Systemic signaling of the plant nitrogen status triggers specific transcriptome responses depending on the nitrogen source in Medicago truncatula.
    Plant Physiol. 2008 Apr;146(4):2020-35 PMID: 18287487
  44. Phosphate homeostasis and root development in Arabidopsis are synchronized by the zinc finger transcription factor ZAT6.
    Plant Physiol. 2007 Sep;145(1):147-59 PMID: 17631527
  45. MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis.
    Plant J. 2008 Mar;53(5):731-8 PMID: 17988220
  46. Transcriptomic and proteomic analyses of pericycle cells of the maize primary root.
    Plant Physiol. 2007 Nov;145(3):575-88 PMID: 17766395
  47. Transcription profile analyses identify genes and pathways central to root cap functions in maize.
    Plant Mol Biol. 2006 Feb;60(3):343-63 PMID: 16514559
  48. A systems biology approach identifies a R2R3 MYB gene subfamily with distinct and overlapping functions in regulation of aliphatic glucosinolates.
    PLoS One. 2007 Dec 19;2(12):e1322 PMID: 18094747
  49. Double knockouts of phospholipases Dzeta1 and Dzeta2 in Arabidopsis affect root elongation during phosphate-limited growth but do not affect root hair patterning.
    Plant Physiol. 2006 Feb;140(2):761-70 PMID: 16384909
  50. Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis.
    PLoS Biol. 2006 May;4(5):e143 PMID: 16640459
  51. Systems rebalancing of metabolism in response to sulfur deprivation, as revealed by metabolome analysis of Arabidopsis plants.
    Plant Physiol. 2005 May;138(1):304-18 PMID: 15834012
  52. Decoding genes with coexpression networks and metabolomics - 'majority report by precogs'.
    Trends Plant Sci. 2008 Jan;13(1):36-43 PMID: 18160330
  53. Cell wall proteome in the maize primary root elongation zone. I. Extraction and identification of water-soluble and lightly ionically bound proteins.
    Plant Physiol. 2006 Jan;140(1):311-25 PMID: 16377746
  54. Hydrogen peroxide mediates plant root cell response to nutrient deprivation.
    Proc Natl Acad Sci U S A. 2004 Jun 8;101(23):8827-32 PMID: 15173595
Article Info
Journal
Current opinion in plant biology
Abbr.
Curr Opin Plant Biol
ISSN
1879-0356
DOI
10.1016/j.pbi.2008.11.002
Published
2009-04-00
Epub
2008-00-29
Pages
165-71
Language
English
Region
England
NLM ID
100883395
PMCID
PMC2683257
Subset
IM
Grants
NIGMS NIH HHS · P50 GM081883-010003 · United States
NIGMS NIH HHS · P50 GM081883-020003 · United States
NIGMS NIH HHS · R01 GM043778 · United States
NIGMS NIH HHS · 5 P50GM081883 · United States
NIGMS NIH HHS · P50 GM081883-01 · United States
NIGMS NIH HHS · R01 GM043778-18 · United States
NIGMS NIH HHS · P50 GM081883-02 · United States
NIGMS NIH HHS · P50 GM081883 · United States
NIGMS NIH HHS · R01-GM043778 · United States
NIGMS NIH HHS · R01 GM043778-19 · United States
External Links
PubMed source DOI: 10.1016/j.pbi.2008.11.002 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2