Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress

• Published in: PloS one Vol. 9; no. 1; p. e87499
• Main Authors: Priest, Henry D, Fox, Samuel E, Rowley, Erik R, Murray, Jessica R, Michael, Todd P, Mockler, Todd C
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 29.01.2014; Public Library of Science (PLoS)
• Subjects: Abiotic stress; Acclimatization; Agricultural production; Analysis; Arabidopsis; Arabidopsis thaliana; Barley; BASIC BIOLOGICAL SCIENCES; Bioinformatics; Biology; Brachypodium; Brachypodium - genetics; Brachypodium - metabolism; Brachypodium distachyon; Cell cycle; Cell walls; cellular stress response; Cereal crops; Cold; Correlation analysis; Crops; Deoxyribonucleic acid; DNA; DNA sequencing; DNA transcription; Drought; Droughts; Food production; Functional analysis; Gene expression; Gene Ontology; Gene sequencing; Genes; Genes, Plant; genetic loci; Genomes; Genomics; Metabolic Networks and Pathways - genetics; Modules; Molecular Sequence Annotation; Multivariate analysis; Network analysis; Nucleotide sequence; Oryza; Oryza sativa; Photosynthesis; Physiology; Plant pathology; Plant Proteins - genetics; Plant Proteins - metabolism; plant resistance to abiotic stress; Plant sciences; Plastic properties; Plasticity; Productivity; Promoter Regions, Genetic; Rice; Salinity; Salt-Tolerance; Stress; Stress response; Stress, Physiological; Stresses; Studies; Thermal analysis; thermal stresses; Transcription factors; Transcriptome; Triticum; Oregon; United States > US; Missouri
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0087499

Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.