title: Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions.
abstract: Plants rely on transcriptional dynamics to respond to multiple climatic fluctuations and contexts in nature. We analyzed the genome-wide gene expression patterns of rice (Oryza sativa) growing in rainfed and irrigated fields during two distinct tropical seasons and determined simple linear models that relate transcriptomic variation to climatic fluctuations. These models combine multiple environmental parameters to account for patterns of expression in the field of co-expressed gene clusters. We examined the similarities of our environmental models between tropical and temperate field conditions, using previously published data. We found that field type and macroclimate had broad impacts on transcriptional responses to environmental fluctuations, especially for genes involved in photosynthesis and development. Nevertheless, variation in solar radiation and temperature at the timescale of hours had reproducible effects across environmental contexts. These results provide a basis for broad-based predictive modeling of plant gene expression in the field.
authors.affiliation: Department of Biology, New York University, New York, United States.|Center for Genomics and Systems Biology, New York University, New York, United States.
authors.forename: Anne
authors.initials: A
authors.lastname: Plessis
authors.affiliation: Department of Biology, New York University, New York, United States.|Center for Genomics and Systems Biology, New York University, New York, United States.
authors.forename: Christoph
authors.initials: C
authors.lastname: Hafemeister
authors.affiliation: Department of Biology, New York University, New York, United States.|Center for Genomics and Systems Biology, New York University, New York, United States.
authors.forename: Olivia
authors.initials: O
authors.lastname: Wilkins
authors.affiliation: International Rice Research Institute, Metro Manila, Philippines.
authors.forename: Zennia Jean
authors.initials: ZJ
authors.lastname: Gonzaga
authors.affiliation: Department of Biology, New York University, New York, United States.|Center for Genomics and Systems Biology, New York University, New York, United States.
authors.forename: Rachel Sarah
authors.initials: RS
authors.lastname: Meyer
authors.affiliation: Department of Biology, New York University, New York, United States.|Center for Genomics and Systems Biology, New York University, New York, United States.
authors.forename: Inês
authors.initials: I
authors.lastname: Pires
authors.affiliation: Simons Center for Data Analysis, Simons Foundation, New York, United States.
authors.forename: Christian
authors.initials: C
authors.lastname: Müller
authors.affiliation: International Rice Research Institute, Metro Manila, Philippines.
authors.forename: Endang M
authors.initials: EM
authors.lastname: Septiningsih
authors.affiliation: Department of Biology, New York University, New York, United States.|Center for Genomics and Systems Biology, New York University, New York, United States.|Simons Center for Data Analysis, Simons Foundation, New York, United States.
authors.forename: Richard
authors.initials: R
authors.lastname: Bonneau
authors.affiliation: Department of Biology, New York University, New York, United States.|Center for Genomics and Systems Biology, New York University, New York, United States.
authors.forename: Michael
authors.initials: M
authors.lastname: Purugganan
mesh_terms: D002980:Climate; D004781:Environmental Exposure; D018506:Gene Expression Regulation, Plant; D012275:Oryza / Q000235:genetics* / Q000254:growth & development*; D012987:Soil / Q000737:chemistry; D013472:Sunlight; D014158:Transcription, Genetic
chemical_list: D012987:Soil
keywords: Oryza sativa; abiotic; computational biology; field; plant biology; systems biology; transcriptomics