title: Characterization of the cytokinin-responsive transcriptome in rice.
abstract: Cytokinin activates transcriptional cascades important for development and the responses to biotic and abiotic stresses. Most of what is known regarding cytokinin-regulated gene expression comes from studies of the dicotyledonous plant Arabidopsis thaliana. To expand the understanding of the cytokinin-regulated transcriptome, we employed RNA-Seq to analyze gene expression in response to cytokinin in roots and shoots of the monocotyledonous plant rice.
  
  
  
  We identified over 4,600 and approximately 2,400 genes differentially expressed in response to cytokinin in roots and shoots respectively. There were some similarities in the sets of cytokinin-regulated genes identified in rice and Arabidopsis, including an up-regulation of genes that act to reduce cytokinin function. Consistent with this, we found that the preferred DNA-binding motif of a rice type-B response regulator is similar to those from Arabidopsis. Analysis of the genes regulated by cytokinin in rice revealed a large number of transcription factors, receptor-like kinases, and genes involved in protein degradation, as well as genes involved in development and the response to biotic stress. Consistent with the over-representation of genes involved in biotic stress, there is a substantial overlap in the genes regulated by cytokinin and those differentially expressed in response to pathogen infection, suggesting that cytokinin plays an integral role in the transcriptional response to pathogens in rice, including the induction of a large number of WRKY transcription factors.
  
  
  
  These results begin to unravel the complex gene regulation after cytokinin perception in a crop of agricultural importance and provide insight into the processes and responses modulated by cytokinin in monocots.
authors.affiliation: Department of Biology, University of North Carolina, Chapel Hill, NC, 27599-3280, USA.|Present address: AgBiome, Inc., 104 TW Alexander Drive, Bldg 18, Research Triangle Park, NC, 27713, USA.
authors.forename: Tracy
authors.initials: T
authors.lastname: Raines
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, Kannapolis, NC, 28081, USA.
authors.forename: Ivory C
authors.initials: IC
authors.lastname: Blakley
authors.affiliation: Department of Biology, University of North Carolina, Chapel Hill, NC, 27599-3280, USA.|Present address: Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan.
authors.forename: Yu-Chang
authors.initials: YC
authors.lastname: Tsai
authors.affiliation: Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA.
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Worthen
authors.affiliation: Genomics Unit, Centro Nacional de Biotecnología (CNB)-Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, 28049, Madrid, Spain.
authors.forename: José Manuel
authors.initials: JM
authors.lastname: Franco-Zorrilla
authors.affiliation: Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB)-Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, 28049, Madrid, Spain.
authors.forename: Roberto
authors.initials: R
authors.lastname: Solano
authors.affiliation: Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA.
authors.forename: G Eric
authors.initials: GE
authors.lastname: Schaller
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, Kannapolis, NC, 28081, USA. aloraine@uncc.edu.
authors.forename: Ann E
authors.initials: AE
authors.lastname: Loraine
authors.affiliation: Department of Biology, University of North Carolina, Chapel Hill, NC, 27599-3280, USA. jkieber@unc.edu.
authors.forename: Joseph J
authors.initials: JJ
authors.lastname: Kieber
mesh_terms: D003583:Cytokinins / Q000494:pharmacology*; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D012275:Oryza / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism; D010937:Plant Growth Regulators / Q000494:pharmacology*; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome / Q000187:drug effects*
chemical_list: D003583:Cytokinins; D010937:Plant Growth Regulators; D010940:Plant Proteins
keywords: Arabidopsis; Cytokinin; Plant hormone; Rice; Transcriptomics