Open Access Highly Accessed Research article

Signal transduction-related responses to phytohormones and environmental challenges in sugarcane

Flávia R Rocha1, Flávia S Papini-Terzi1, Milton Y Nishiyama1, Ricardo ZN Vêncio2, Renato Vicentini3, Rodrigo DC Duarte3, Vicente E de Rosa3, Fabiano Vinagre4, Carla Barsalobres5, Ane H Medeiros5, Fabiana A Rodrigues7, Eugênio C Ulian6, Sônia M Zingaretti7, João A Galbiatti7, Raul S Almeida8, Antonio VO Figueira8, Adriana S Hemerly4, Marcio C Silva-Filho5, Marcelo Menossi3 and Gláucia M Souza1*

Author Affiliations

1 Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil

2 BIOINFO-USP Núcleo de Pesquisas em Bioinformática, Universidade de São Paulo, São Paulo, SP, Brazil

3 Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil

4 Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, RJ, Brazil

5 Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, ESALQ, Universidade de São Paulo, Piracicaba, SP, Brazil

6 Centro de Tecnologia Canavieira, Piracicaba, São Paulo, SP, Brazil

7 Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, Universidade Estadual Paulista, Jaboticabal, SP, Brazil

8 Centro de Energia Nuclear na Agricultura (CENA), Universidade de São Paulo, Piracicaba, SP, Brazil

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BMC Genomics 2007, 8:71  doi:10.1186/1471-2164-8-71

Published: 13 March 2007

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.

Conclusion

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.