Identification of transcriptome induced in roots of maize seedlings at the late stage of waterlogging

Xiling Zou; Yuanyuan Jiang; Lei Liu; Zuxin Zhang; Yonglian Zheng
January 2010
BMC Plant Biology;2010, Vol. 10, p189
Academic Journal
Background: Plants respond to low oxygen stress, particularly that caused by waterlogging, by altering transcription and translation. Previous studies have mostly focused on revealing the mechanism of the response at the early stage, and there is limited information about the transcriptional profile of genes in maize roots at the late stage of waterlogging. The genetic basis of waterlogging tolerance is largely unknown. In this study, the transcriptome at the late stage of waterlogging was assayed in root cells of the tolerant inbred line HZ32, using suppression subtractive hybridization (SSH). A forward SSH library using RNA populations from four time points (12 h, 16 h, 20 h and 24 h) after waterlogging treatment was constructed to reveal up-regulated genes, and transcriptional and linkage data was integrated to identify candidate genes for waterlogging tolerance. Results: Reverse Northern analysis of a set of 768 cDNA clones from the SSH library revealed a large number of genes were up-regulated by waterlogging. A total of 465 ESTs were assembled into 296 unigenes. Bioinformatic analysis revealed that the genes were involved in complex pathways, such as signal transduction, protein degradation, ion transport, carbon and amino acid metabolism, and transcriptional and translational regulation, and might play important roles at the late stage of the response to waterlogging. A significant number of unigenes were of unknown function. Approximately 67% of the unigenes could be aligned on the maize genome and 63 of them were co-located within reported QTLs. Conclusion: The late response to waterlogging in maize roots involves a broad spectrum of genes, which are mainly associated with two response processes: defense at the early stage and adaption at the late stage. Signal transduction plays a key role in activating genes related to the tolerance mechanism for survival during prolonged waterlogging. The crosstalk between carbon and amino acid metabolism reveals that amino acid metabolism performs two main roles at the late stage: the regulation of cytoplasmic pH and energy supply through breakdown of the carbon skeleton.


Related Articles

  • Signal transduction pathway profiling of individual tumor samples. Breslin, Thomas; Krogh, Morten; Peterson, Carsten; Troein, Carl // BMC Bioinformatics;2005, Vol. 6, p163 

    Background: Signal transduction pathways convey information from the outside of the cell to transcription factors, which in turn regulate gene expression. Our objective is to analyze tumor gene expression data from microarrays in the context of such pathways. Results: We use pathways compiled...

  • Discriminating response groups in metabolic and regulatory pathway networks. Van Hemert, John L.; Dickerson, Julie A. // Bioinformatics;Apr2012, Vol. 28 Issue 7, p947 

    Motivation: Analysis of omics experiments generates lists of entities (genes, metabolites, etc.) selected based on specific behavior, such as changes in response to stress or other signals. Functional interpretation of these lists often uses category enrichment tests using functional annotations...

  • Metabolic regulation of Escherichia coli and its phoB and phoR genes knockout mutants under phosphate and nitrogen limitations as well as at acidic condition. Wal Marzan, Lolo; Shimizu, Kazuyuki // Microbial Cell Factories;2011, Vol. 10 Issue 1, p39 

    Background: The phosphorus compounds serve as major building blocks of many biomolecules, and have important roles in signal transduction. The phosphate is involved in many biochemical reactions by the transfer of phosphoryl groups. All living cells sophisticatedly regulate the phosphate uptake,...

  • Two Membrane-Associated Tyrosine Phosphatase Homologs Potentiate C. elegans AKT-1/PKB Signaling. Hu, Patrick J.; Jinling Xu; Ruvkun, Gary // PLoS Genetics;Jul2006, Vol. 3 Issue 1, pe99 

    Akt/protein kinase B (PKB) functions in conserved signaling cascades that regulate growth and metabolism. In humans, Akt/PKB is dysregulated in diabetes and cancer; in Caenorhabditis elegans, Akt/PKB functions in an insulin-like signaling pathway to regulate larval development. To identify...

  • Modulation of PI3K/Akt pathway by E1a mediates sensitivity to cisplatin. Guinea Viniegra, Juan; Hernandez Losa, Javier; Javier Sanchez-Arevalo, Victor; Parada Cobo, Carlos; Manuel Fernandez Soria, Victor; Ramon y Cajal, Santiago; Sanchez-Prieto, Ricardo // Oncogene;10/10/2002, Vol. 21 Issue 46, p7130 

    Presents a study that investigated which signal transduction pathways could be affected by the E1a gene in Human Normal Fibroblast in order to investigate the molecular mechanisms implicated in the induction of chemo sensitivity by adenovirus E1a gene expression. Absence of effect in Stress...

  • Reeling CASK into the nucleus. Bredt, David S. // Nature;3/16/2000, Vol. 404 Issue 6775, p241 

    Describes a cellular signaling pathway in which CASK, a structural girder of cell junctions, directly enters the nucleus and thereby regulates gene expression. CASK as a member of the membrane-associated guanylate kinase (MAGUK) family; Screening for proteins that would bind to the GUK domain...

  • Notch takes a short cut. Goodbourn, Stephen // Nature;9/28/1995, Vol. 377 Issue 6547, p288 

    Discusses the role of Notch genes in cellular signal transduction. Notch gene in lateral specification; Result of null mutations in Notch; Induction of E(spl) transcription in response to Notch activation; Notch signalling pathway in mice.

  • Data recovery and integration from public databases uncovers transformation-specific transcriptional downregulation of cAMP-PKA pathway-encoding genes. Balestrieri, Chiara; Alberghina, Lilia; Vanoni, Marco; Chiaradonna, Ferdinando // BMC Bioinformatics;2009 Supplement 12, Vol. 10, Special section p1 

    Background: The integration of data from multiple genome-wide assays is essential for understanding dynamic spatio-temporal interactions within cells. Such integration, which leads to a more complete view of cellular processes, offers the opportunity to rationalize better the high amount of...

  • Approximate Bayesian feature selection on a large meta-dataset offers novel insights on factors that effect siRNA potency. Jochen W. Klingelhoefer; Loukas Moutsianas; Chris Holmes // Bioinformatics;Jul2009, Vol. 25 Issue 13, p1594 

    Motivation: Short interfering RNA (siRNA)-induced RNA interference is an endogenous pathway in sequence-specific gene silencing. The potency of different siRNAs to inhibit a common target varies greatly and features affecting inhibition are of high current interest. The limited success in...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics