Home LiteratureArticle Details
PMID: 21406116 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

Genome-wide temporal-spatial gene expression profiling of drought responsiveness in rice.

BMC genomics ·Vol. 12 ·2011-03-16 ·Pages 149

Wang D, Pan Y, Zhao X, Zhu L, Fu B, Li Z

Abstract

Rice is highly sensitive to drought, and the effect of drought may vary with the different genotypes and development stages. Genome-wide gene expression profiling was used as the initial point to dissect molecular genetic mechanism of this complex trait and provide valuable information for the improvement of drought tolerance in rice. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice exposed to drought stress. The transcriptome from leaf, root, and young panicle at three developmental stages was comparatively analyzed combined with bioinformatics exploring drought stress related cis-elements. There were 5,284 genes detected to be differentially expressed under drought stress. Most of these genes were tissue- or stage-specific regulated by drought. The tissue-specific down-regulated genes showed distinct function categories as photosynthesis-related genes prevalent in leaf, and the genes involved in cell membrane biogenesis and cell wall modification over-presented in root and young panicle. In a drought environment, several genes, such as GA2ox, SAP15, and Chitinase III, were regulated in a reciprocal way in two tissues at the same development stage. A total of 261 transcription factor genes were detected to be differentially regulated by drought stress. Most of them were also regulated in a tissue- or stage-specific manner. A cis-element containing special CGCG box was identified to over-present in the upstream of 55 common induced genes, and it may be very important for rice plants responding to drought environment. Genome-wide gene expression profiling revealed that most of the drought differentially expressed genes (DEGs) were under temporal and spatial regulation, suggesting a crosstalk between various development cues and environmental stimuli. The identification of the differentially regulated DEGs, including TF genes and unique candidate cis-element for drought responsiveness, is a very useful resource for the functional dissection of the molecular mechanism in rice responding to environment stress.

MeSH Terms
Computational Biology Droughts Gene Expression Profiling Gene Expression Regulation, Developmental Gene Expression Regulation, Plant Genome, Plant Oligonucleotide Array Sequence Analysis Oryza/genetics Plant Leaves/genetics Plant Roots/genetics RNA, Plant/genetics Regulatory Elements, Transcriptional Stress, Physiological Transcription Factors/genetics
Chemicals
RNA, Plant Transcription Factors
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Wang Di
Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.
Pan Yajiao
Zhao Xiuqin
Zhu Linghua
Fu Binying
Li Zhikang
References (48)
48 references, click to expand
  1. Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses.
    Plant Cell. 2002 Mar;14(3):559-74 PMID: 11910004
  2. Gene networks involved in drought stress response and tolerance.
    J Exp Bot. 2007;58(2):221-7 PMID: 17075077
  3. A novel class of gibberellin 2-oxidases control semidwarfism, tillering, and root development in rice.
    Plant Cell. 2008 Oct;20(10):2603-18 PMID: 18952778
  4. Complex regulation of ABA biosynthesis in plants.
    Trends Plant Sci. 2002 Jan;7(1):41-8 PMID: 11804826
  5. CUT1, an Arabidopsis gene required for cuticular wax biosynthesis and pollen fertility, encodes a very-long-chain fatty acid condensing enzyme.
    Plant Cell. 1999 May;11(5):825-38 PMID: 10330468
  6. ACC synthase expression regulates leaf performance and drought tolerance in maize.
    Plant J. 2004 Dec;40(5):813-25 PMID: 15546363
  7. DRTF: a database of rice transcription factors.
    Bioinformatics. 2006 May 15;22(10):1286-7 PMID: 16551659
  8. Tissue-specific expression and drought responsiveness of cell-wall invertase genes of rice at flowering.
    Plant Mol Biol. 2005 Dec;59(6):945-64 PMID: 16307368
  9. Negative regulation of the Arabidopsis homeotic gene AGAMOUS by the APETALA2 product.
    Cell. 1991 Jun 14;65(6):991-1002 PMID: 1675158
  10. Genome-wide transcriptional analysis of salinity stressed japonica and indica rice genotypes during panicle initiation stage.
    Plant Mol Biol. 2007 Mar;63(5):609-23 PMID: 17160619
  11. AREB1 is a transcription activator of novel ABRE-dependent ABA signaling that enhances drought stress tolerance in Arabidopsis.
    Plant Cell. 2005 Dec;17(12):3470-88 PMID: 16284313
  12. Comparative transcriptome profiling of near-isogenic barley (Hordeum vulgare) lines differing in the allelic state of a major grain protein content locus identifies genes with possible roles in leaf senescence and nitrogen reallocation.
    New Phytol. 2008;177(2):333-349 PMID: 18028296
  13. Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle.
    Plant Mol Biol. 2007 Mar;63(5):591-608 PMID: 17225073
  14. LIPID-TRANSFER PROTEINS IN PLANTS.
    Annu Rev Plant Physiol Plant Mol Biol. 1996 Jun;47:627-654 PMID: 15012303
  15. Genetic basis of drought resistance at reproductive stage in rice: separation of drought tolerance from drought avoidance.
    Genetics. 2006 Feb;172(2):1213-28 PMID: 16272419
  16. Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice.
    Mol Genet Genomics. 2008 Dec;280(6):547-63 PMID: 18813954
  17. Salt stress affects glutamine synthetase activity and mRNA accumulation on potato plants in an organ-dependent manner.
    Plant Physiol Biochem. 2009 Sep;47(9):807-13 PMID: 19481951
  18. Plant glycoside hydrolases involved in cell wall polysaccharide degradation.
    Plant Physiol Biochem. 2006 Jul-Sep;44(7-9):435-49 PMID: 17023165
  19. Expression of a gibberellin 2-oxidase gene around the shoot apex is related to phase transition in rice.
    Plant Physiol. 2001 Mar;125(3):1508-16 PMID: 11244129
  20. Inhibition of photosynthesis and energy dissipation induced by water and high light stresses in rice.
    J Exp Bot. 2007;58(5):1207-17 PMID: 17283375
  21. Genome-wide introgression lines and their use in genetic and molecular dissection of complex phenotypes in rice (Oryza sativa L.).
    Plant Mol Biol. 2005 Sep;59(1):33-52 PMID: 16217600
  22. Gibberellin and abscisic acid regulate GAST1 expression at the level of transcription.
    Plant Mol Biol. 1998 Dec;38(6):1053-60 PMID: 9869411
  23. Gibberellin-GID1-DELLA: a pivotal regulatory module for plant growth and development.
    Plant Physiol. 2010 Oct;154(2):567-70 PMID: 20921186
  24. Root growth maintenance during water deficits: physiology to functional genomics.
    J Exp Bot. 2004 Nov;55(407):2343-51 PMID: 15448181
  25. Engineering drought tolerance in plants: discovering and tailoring genes to unlock the future.
    Curr Opin Biotechnol. 2006 Apr;17(2):113-22 PMID: 16495045
  26. Expression profiling of rice segregating for drought tolerance QTLs using a rice genome array.
    Funct Integr Genomics. 2005 Apr;5(2):104-16 PMID: 15480887
  27. Genome-wide analysis of NAC transcription factor family in rice.
    Gene. 2010 Oct 1;465(1-2):30-44 PMID: 20600702
  28. Role of AP2/EREBP transcription factors in gene regulation during abiotic stress.
    FEBS Lett. 2001 Jun 8;498(2-3):187-9 PMID: 11412854
  29. Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice.
    Plant Physiol. 2008 Feb;146(2):333-50 PMID: 18065552
  30. Molecular analysis of signals controlling dormancy and growth in underground adventitious buds of leafy spurge.
    Plant Physiol. 2002 Apr;128(4):1439-46 PMID: 11950992
  31. Mechanisms of cross talk between gibberellin and other hormones.
    Plant Physiol. 2007 Jul;144(3):1240-6 PMID: 17616507
  32. A role for Arabidopsis PUCHI in floral meristem identity and bract suppression.
    Plant Cell. 2009 May;21(5):1360-72 PMID: 19482972
  33. Salt-responsive genes in rice revealed by cDNA microarray analysis.
    Cell Res. 2005 Oct;15(10):796-810 PMID: 16246269
  34. Identification of functional candidate genes for drought tolerance in rice.
    Mol Genet Genomics. 2007 Dec;278(6):599-609 PMID: 17665216
  35. Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage.
    Plant Physiol. 2005 Oct;139(2):822-35 PMID: 16183841
  36. Monitoring large-scale changes in transcript abundance in drought- and salt-stressed barley.
    Plant Mol Biol. 2002 Mar-Apr;48(5-6):551-73 PMID: 11999834
  37. Regulation of cucumber class III chitinase gene expression.
    Mol Plant Microbe Interact. 1994 Jan-Feb;7(1):48-57 PMID: 8167370
  38. AINTEGUMENTA and AINTEGUMENTA-LIKE6 act redundantly to regulate Arabidopsis floral growth and patterning.
    Plant Physiol. 2009 Aug;150(4):1916-29 PMID: 19542297
  39. Microarray analysis reveals similarities and variations in genetic programs controlling pollination/fertilization and stress responses in rice (Oryza sativa L.).
    Plant Mol Biol. 2005 Sep;59(1):151-64 PMID: 16217609
  40. Microarray analysis of transcriptional responses to abscisic acid and osmotic, salt, and drought stress in the moss, Physcomitrella patens.
    New Phytol. 2007;176(2):275-287 PMID: 17696978
  41. A calmodulin-binding/CGCG box DNA-binding protein family involved in multiple signaling pathways in plants.
    J Biol Chem. 2002 Nov 22;277(47):45049-58 PMID: 12218065
  42. Genes commonly regulated by water-deficit stress in Arabidopsis thaliana.
    J Exp Bot. 2004 Nov;55(407):2331-41 PMID: 15448178
  43. Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes.
    Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W199-203 PMID: 15215380
  44. Genome-wide analysis of spatial and temporal gene expression in rice panicle development.
    Plant J. 2006 May;46(3):503-11 PMID: 16623909
  45. Comprehensive expression profiling of rice grain filling-related genes under high temperature using DNA microarray.
    Plant Physiol. 2007 May;144(1):258-77 PMID: 17384160
  46. The branching gene RAMOSUS1 mediates interactions among two novel signals and auxin in pea.
    Plant Cell. 2005 Feb;17(2):464-74 PMID: 15659639
  47. A network of rice genes associated with stress response and seed development.
    Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4945-50 PMID: 12684538
  48. Overexpression of an R1R2R3 MYB gene, OsMYB3R-2, increases tolerance to freezing, drought, and salt stress in transgenic Arabidopsis.
    Plant Physiol. 2007 Apr;143(4):1739-51 PMID: 17293435
Article Info
Journal
BMC genomics
Abbr.
BMC Genomics
ISSN
1471-2164
DOI
10.1186/1471-2164-12-149
Published
2011-03-16
Epub
2011-00-16
Pages
149
Language
English
Region
England
NLM ID
100965258
PMCID
PMC3070656
Subset
IM
External Links
PubMed source DOI: 10.1186/1471-2164-12-149 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