title: Signal transduction-related responses to phytohormones and environmental challenges in sugarcane.
abstract: BACKGROUND
  Sugarcane is an increasingly economically and environmentally important C4 grass, used for the production of sugar and bioethanol, a low-carbon emission fuel. Sugarcane originated from crosses of Saccharum species and is noted for its unique capacity to accumulate high amounts of sucrose in its stems. Environmental stresses limit enormously sugarcane productivity worldwide. To investigate transcriptome changes in response to environmental inputs that alter yield we used cDNA microarrays to profile expression of 1,545 genes in plants submitted to drought, phosphate starvation, herbivory and N2-fixing endophytic bacteria. We also investigated the response to phytohormones (abscisic acid and methyl jasmonate). The arrayed elements correspond mostly to genes involved in signal transduction, hormone biosynthesis, transcription factors, novel genes and genes corresponding to unknown proteins.
  
  
  RESULTS
  Adopting an outliers searching method 179 genes with strikingly different expression levels were identified as differentially expressed in at least one of the treatments analysed. Self Organizing Maps were used to cluster the expression profiles of 695 genes that showed a highly correlated expression pattern among replicates. The expression data for 22 genes was evaluated for 36 experimental data points by quantitative RT-PCR indicating a validation rate of 80.5% using three biological experimental replicates. The SUCAST Database was created that provides public access to the data described in this work, linked to tissue expression profiling and the SUCAST gene category and sequence analysis. The SUCAST database also includes a categorization of the sugarcane kinome based on a phylogenetic grouping that included 182 undefined kinases.
  
  
  CONCLUSIONS
  An extensive study on the sugarcane transcriptome was performed. Sugarcane genes responsive to phytohormones and to challenges sugarcane commonly deals with in the field were identified. Additionally, the protein kinases were annotated based on a phylogenetic approach. The experimental design and statistical analysis applied proved robust to unravel genes associated with a diverse array of conditions attributing novel functions to previously unknown or undefined genes. The data consolidated in the SUCAST database resource can guide further studies and be useful for the development of improved sugarcane varieties.
authors.affiliation: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil. flaviarr@iq.usp.br <flaviarr@iq.usp.br>
authors.forename: Flávia R
authors.initials: FR
authors.lastname: Rocha
authors.forename: Flávia S
authors.initials: FS
authors.lastname: Papini-Terzi
authors.forename: Milton Y
authors.initials: MY
authors.lastname: Nishiyama
authors.forename: Ricardo Z N
authors.initials: RZ
authors.lastname: Vêncio
authors.forename: Renato
authors.initials: R
authors.lastname: Vicentini
authors.forename: Rodrigo D C
authors.initials: RD
authors.lastname: Duarte
authors.forename: Vicente E
authors.initials: VE
authors.lastname: de Rosa
authors.forename: Fabiano
authors.initials: F
authors.lastname: Vinagre
authors.forename: Carla
authors.initials: C
authors.lastname: Barsalobres
authors.forename: Ane H
authors.initials: AH
authors.lastname: Medeiros
authors.forename: Fabiana A
authors.initials: FA
authors.lastname: Rodrigues
authors.forename: Eugênio C
authors.initials: EC
authors.lastname: Ulian
authors.forename: Sônia M
authors.initials: SM
authors.lastname: Zingaretti
authors.forename: João A
authors.initials: JA
authors.lastname: Galbiatti
authors.forename: Raul S
authors.initials: RS
authors.lastname: Almeida
authors.forename: Antonio V O
authors.initials: AV
authors.lastname: Figueira
authors.forename: Adriana S
authors.initials: AS
authors.lastname: Hemerly
authors.forename: Marcio C
authors.initials: MC
authors.lastname: Silva-Filho
authors.forename: Marcelo
authors.initials: M
authors.lastname: Menossi
authors.forename: Gláucia M
authors.initials: GM
authors.lastname: Souza
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D004190:Disasters; D015870:Gene Expression; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects* / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics*; D042803:Herbaspirillum; D009036:Moths; D020411:Oligonucleotide Array Sequence Analysis; D010710:Phosphates / Q000172:deficiency; D010937:Plant Growth Regulators / Q000494:pharmacology*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D031786:Saccharum / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism* / Q000382:microbiology; D015398:Signal Transduction / Q000187:drug effects* / Q000235:genetics
chemical_list: D010710:Phosphates; D010937:Plant Growth Regulators