Submitted to: GM Crops
Publication Type: Peer reviewed journal
Publication Acceptance Date: 9/23/2010
Publication Date: 10/1/2010
Citation: Srivastava, A., Aditya, G.K., Datsenka, T., Mattoo, A.K., Handa, A.K. 2010. Maturity and Ripening-Stage Specific Modulation of Tomato (Solanum lycopersicum) Fruit Transcriptome. GM Crops. 1(4):237-249. Interpretive Summary: Our model of horticultural crops for improvement of nutritional quality and long shelf-life is tomato, which is one of the highly consumed vegetables. Both the quality attributes and shelf-life are genetically programmed. Therefore, we used molecular approaches to identify genes that are specifically expressed at different stages of maturation and ripening of tomato fruit. In this manuscript we used a custom built cDNA macroarray as a platform for analyzing global gene expression at six selected developmental stages. We show that genes that are responsive to abiotic and biotic stresses and to the plant hormone ethylene are upregulated during early stages of fruit ripening. Following this genetic program, the genes involved in metabolism and nutrient accumulation are expressed at higher levels during ripening, and the post ripening phase is characterized by expression of genes that are involved in ubiquitin-mediated protein degradation. Taken together, these results show that fruit ripening is a highly regulated developmental process, and provide a window into the various cellular processes occurring at different stages of fruit maturation and ripening of tomato. A large proportion (53%) of the genes printed on the macroarray could not be assigned a clear function based on the sequences available in the public databases. These uncharacterized genes hold promise for providing additional tools to modulate process of fruit development and ripening. These data would be of interest to breeders, plant biologists, geneticists, biotechnologists and horticultural industry.
Technical Abstract: Tomato (Solanum lycopersicum) fruit is a model to study molecular basis of fleshy fruit development and ripening. We profiled gene expression in immature green and mature green fruit (fruit development program), and during advanced ripening from breaker (BR) stage onwards to obtain a global perspective of genes whose expression is modulated at each stage of fruit development and ripening . A custom made cDNA macroarray containing cDNAs representing various metabolic pathways, defense, signaling, transcription, transport, cell structure and cell wall related functions was developed to quantify changes in the abundance of different transcripts. About 34 % of 1066 unique expressed sequence tags (ESTs) printed on the macroarray were differentially expressed during tomato fruit ripening. Out of these, 25 % genes classify under metabolism and protein biosynthesis/degradation related processes, while a significant proportion represented stress-responsive genes and about 44 % represented genes with unknown functions. RNA gel blot analysis validated changes in a few represented genes. Although the results suggested transcriptionally quiescent nature of the mature green fruit, the K-means cluster analysis highlighted coordinated up or down regulation of genes during progressive ripening. Taken together, these data emphasize that ripening is a transcriptionally active process with many stress-related genes being up-regulated during this process, suggesting their role in the fruit ripening program.