Location: Plant, Soil and Nutrition ResearchTitle: Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening Author
Submitted to: Biomed Central (BMC) Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/25/2010
Publication Date: 10/25/2010
Citation: Costa, F., Alba, R., Schouten, H., Sansavini, S., Fei, Z., Giovannoni, J.J. 2010. Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening. Biomed Central (BMC) Plant Biology. 10:229. Interpretive Summary: Fruit development, maturation and ripening consist of a complex series of biochemical and physiological changes that in many fruits, including apple and tomato, are coordinated by the gaseous hormone ethylene. These changes lead to final fruit quality and understanding of the functional machinery underlying these processes is of both biological and practical importance. In this study we focused our investigation on the role of ethylene during apple maturation, specifically comparing gene expression patterns during normal ripening with changes resulting from application of the widely used shelf-life extending chemical treatment and hormone receptor competitor 1-Methylcyclopropene.
Technical Abstract: To gain insight into the molecular process regulating ripening in apple, and to compare to tomato, we utilized both homologous and heterologous (tomato) microarray to profile transcriptome dynamics of genes involved in fruit development and ripening, emphasizing those which are ethylene regulated. The use of both types of microarrays facilitated transcriptome comparison between apple and highlighted genes conserved during ripening of both species, which in turn represent a foundation for further comparative genomic studies. The cross-species analysis had the secondary aim of examining the efficiency of heterologous microarray hybridization for candidate gene identification as related to the ripening process. The resulting transcriptomics data revealed coordinated gene expression during fruit ripening of a subset of ripening-related and ethylene responsive genes, further facilitating the analysis of ethylene response during fruit maturation and ripening. Our combined strategy based on microarray hybridization enabled transcriptome characterization during normal climacteric apple ripening, as well as definition of ethylene-dependent transcriptome changes. Comparison with tomato fruit maturation and ethylene responsive transcriptome activity facilitated identification of putative conserved orthologous ripening-related genes, which serve as an initial set of candidates for assessing conservation of gene activity across genomes of fruit bearing plant species.