Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress.
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.
Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America ; Division of Biology and Biomedical Sciences, Washington University, Saint Louis, Missouri, United States of America.
Henry D
HD
Priest
Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America.
Samuel E
SE
Fox
Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America ; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America.
Erik R
ER
Rowley
Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America.
Jessica R
JR
Murray
Waksman Institute and Department of Plant Biology and Pathology, Rutgers University, New Brunswick, New Jersey, United States of America.
Todd P
TP
Michael
Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America ; Division of Biology and Biomedical Sciences, Washington University, Saint Louis, Missouri, United States of America ; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America.
Todd C
TC
Mockler
D000064:Acclimatization; D058431:Brachypodium / Q000235:genetics* / Q000378:metabolism; D063990:Gene Ontology; D017343:Genes, Plant; D053858:Metabolic Networks and Pathways / Q000235:genetics; D058977:Molecular Sequence Annotation; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic; D055049:Salt Tolerance; D013312:Stress, Physiological; D059467:Transcriptome
D010940:Plant Proteins