Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)

BMC Genomics

Research Article

Marta Simões¹  Rob Alba²  John M Bordeaux³  Yuan-Sheng Yu³  W Walter Lorenz³  Jeffrey FD Dean⁴ 

[1] Instituto de Biologia Experimental e Tecnológica (IBET)/Instituto de Tecnologia Química e Biológica-Universidade Nova de Lisboa (ITQB-UNL), Av. República (EAN), 2784-505, Oeiras, Portugal;Monsanto Company, Mailstop C1N, 800 N. Lindbergh Blvd., 63167, St. Louis, MO, USA;Warnell School of Forestry and Natural Resources, The University of Georgia, 30602, Athens, GA, USA;Warnell School of Forestry and Natural Resources, The University of Georgia, 30602, Athens, GA, USA;Department of Biochemistry & Molecular Biology, The University of Georgia, Life Sciences Building, 30602, Athens, GA, USA;

关键词: Drought Stress;    Differentially Express Gene;    Late Embryogenesis Abundant;    WRKY Gene;    Drought Response;   

DOI  :  10.1186/1471-2164-12-264

 received in 2010-11-30, accepted in 2011-05-24,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundGlobal transcriptional analysis of loblolly pine (Pinus taeda L.) is challenging due to limited molecular tools. PtGen2, a 26,496 feature cDNA microarray, was fabricated and used to assess drought-induced gene expression in loblolly pine propagule roots. Statistical analysis of differential expression and weighted gene correlation network analysis were used to identify drought-responsive genes and further characterize the molecular basis of drought tolerance in loblolly pine.ResultsMicroarrays were used to interrogate root cDNA populations obtained from 12 genotype × treatment combinations (four genotypes, three watering regimes). Comparison of drought-stressed roots with roots from the control treatment identified 2445 genes displaying at least a 1.5-fold expression difference (false discovery rate = 0.01). Genes commonly associated with drought response in pine and other plant species, as well as a number of abiotic and biotic stress-related genes, were up-regulated in drought-stressed roots. Only 76 genes were identified as differentially expressed in drought-recovered roots, indicating that the transcript population can return to the pre-drought state within 48 hours. Gene correlation analysis predicts a scale-free network topology and identifies eleven co-expression modules that ranged in size from 34 to 938 members. Network topological parameters identified a number of central nodes (hubs) including those with significant homology (E-values ≤ 2 × 10-30) to 9-cis-epoxycarotenoid dioxygenase, zeatin O-glucosyltransferase, and ABA-responsive protein. Identified hubs also include genes that have been associated previously with osmotic stress, phytohormones, enzymes that detoxify reactive oxygen species, and several genes of unknown function.ConclusionPtGen2 was used to evaluate transcriptome responses in loblolly pine and was leveraged to identify 2445 differentially expressed genes responding to severe drought stress in roots. Many of the genes identified are known to be up-regulated in response to osmotic stress in pine and other plant species and encode proteins involved in both signal transduction and stress tolerance. Gene expression levels returned to control values within a 48-hour recovery period in all but 76 transcripts. Correlation network analysis indicates a scale-free network topology for the pine root transcriptome and identifies central nodes that may serve as drivers of drought-responsive transcriptome dynamics in the roots of loblolly pine.

【 授权许可】

Unknown   
© Lorenz et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.