title: Daytime soybean transcriptome fluctuations during water deficit stress.
abstract: BACKGROUND
  Since drought can seriously affect plant growth and development and little is known about how the oscillations of gene expression during the drought stress-acclimation response in soybean is affected, we applied Illumina technology to sequence 36 cDNA libraries synthesized from control and drought-stressed soybean plants to verify the dynamic changes in gene expression during a 24-h time course. Cycling variables were measured from the expression data to determine the putative circadian rhythm regulation of gene expression.
  
  
  RESULTS
  We identified 4866 genes differentially expressed in soybean plants in response to water deficit. Of these genes, 3715 were differentially expressed during the light period, from which approximately 9.55% were observed in both light and darkness. We found 887 genes that were either up- or down-regulated in different periods of the day. Of 54,175 predicted soybean genes, 35.52% exhibited expression oscillations in a 24 h period. This number increased to 39.23% when plants were submitted to water deficit. Major differences in gene expression were observed in the control plants from late day (ZT16) until predawn (ZT20) periods, indicating that gene expression oscillates during the course of 24 h in normal development. Under water deficit, dissimilarity increased in all time-periods, indicating that the applied stress influenced gene expression. Such differences in plants under stress were primarily observed in ZT0 (early morning) to ZT8 (late day) and also from ZT4 to ZT12. Stress-related pathways were triggered in response to water deficit primarily during midday, when more genes were up-regulated compared to early morning. Additionally, genes known to be involved in secondary metabolism and hormone signaling were also expressed in the dark period.
  
  
  CONCLUSIONS
  Gene expression networks can be dynamically shaped to acclimate plant metabolism under environmental stressful conditions. We have identified putative cycling genes that are expressed in soybean leaves under normal developmental conditions and genes whose expression oscillates under conditions of water deficit. These results suggest that time of day, as well as light and temperature oscillations that occur considerably affect the regulation of water deficit stress response in soybean plants.
authors.affiliation: Brazilian Agricultural Research Corporation- Embrapa Soybean, Embrapa Soybean- Rod. Carlos João Strass, s/n, Londrina, 86001-970, PR, Brazil. deganuti@gmail.com.
authors.forename: Fabiana Aparecida
authors.initials: FA
authors.lastname: Rodrigues
authors.affiliation: Brazilian Agricultural Research Corporation- Embrapa Soybean, Embrapa Soybean- Rod. Carlos João Strass, s/n, Londrina, 86001-970, PR, Brazil. renatafuganti@gmail.com.
authors.forename: Renata
authors.initials: R
authors.lastname: Fuganti-Pagliarini
authors.affiliation: Brazilian Agricultural Research Corporation- Embrapa Soybean, Embrapa Soybean- Rod. Carlos João Strass, s/n, Londrina, 86001-970, PR, Brazil. marcolino.ju@gmail.com.|Department of Biology, State University of Londrina, Londrina, PR, Brazil. marcolino.ju@gmail.com.
authors.forename: Juliana
authors.initials: J
authors.lastname: Marcolino-Gomes
authors.affiliation: Brazilian Agricultural Research Corporation- Embrapa Soybean, Embrapa Soybean- Rod. Carlos João Strass, s/n, Londrina, 86001-970, PR, Brazil. thiago84naka@gmail.com.|Department of Crop Science, Federal University of Viçosa, Viçosa, MG, Brazil. thiago84naka@gmail.com.
authors.forename: Thiago Jonas
authors.initials: TJ
authors.lastname: Nakayama
authors.affiliation: Genetics and Biotechnology Laboratory, Embrapa Agroenergy (CNPAE), Brasília, DF, Brazil. hugo.molinari@embrapa.br.|Embrapa LABEX US Plant Biotechnology at ARS/USDA Plant Gene Expression Center, Albany, CA, USA. hugo.molinari@embrapa.br.
authors.forename: Hugo Bruno Correa
authors.initials: HB
authors.lastname: Molinari
authors.affiliation: Brazilian Agricultural Research Corporation-Embrapa Agricultural Informatics, Campinas, SP, Brazil. francisco.lobo@embrapa.br.
authors.forename: Francisco Pereira
authors.initials: FP
authors.lastname: Lobo
authors.affiliation: Plant Gene Expression Center, USDA-ARS, Albany, CA, USA. fharmon@berkeley.edu.|Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA. fharmon@berkeley.edu.
authors.forename: Frank G
authors.initials: FG
authors.lastname: Harmon
authors.affiliation: Brazilian Agricultural Research Corporation- Embrapa Soybean, Embrapa Soybean- Rod. Carlos João Strass, s/n, Londrina, 86001-970, PR, Brazil. alexandre.nepomuceno@embrapa.br.|Embrapa LABEX US Plant Biotechnology at ARS/USDA Plant Gene Expression Center, Albany, CA, USA. alexandre.nepomuceno@embrapa.br.
authors.forename: Alexandre Lima
authors.initials: AL
authors.lastname: Nepomuceno
mesh_terms: D003624:Darkness; D003681:Dehydration / Q000235:genetics*; D015536:Down-Regulation / Q000235:genetics; D055864:Droughts; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D015723:Gene Library; D017343:Genes, Plant / Q000235:genetics; D008027:Light; D018515:Plant Leaves / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics; D013025:Glycine max / Q000235:genetics*; D013312:Stress, Physiological / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*; D015854:Up-Regulation / Q000235:genetics; D014867:Water
chemical_list: D010940:Plant Proteins; D014867:Water