Characterization of ripening-associated genes using a tomato DNA macroarray, 1-methylcyclopropene, and ripening-impaired mutants

Using a tomato (Solanum lycopersicum) DNA macroarray consisting of 11,520 genes, we identified 419 ripening-associated genes (224 upregulated, 195 downregulated). Treatment with 1-methylcyclopropene (1-MCP) at the turning stage restored expression to levels of the mature green (MG) stage in 159 upregulated and 45 downregulated genes, suggesting a strong dependence on ethylene signaling during ripening. Among 194 ethylene-upregulated genes, 143 genes in ripening inhibitor (rin) fruit and 140 genes in non-ripening (nor) fruit responded poorly to exogenous ethylene, suggesting the necessity of RIN and NOR signals for their expression. In contrast, 36 and 70 genes responded to ethylene in rin and nor fruit, respectively, to a similar extent as in wild-type fruit, suggesting a clear independence of RIN and NOR signals for their response to ethylene. Ripening-associated expression of number of genes involved in respiratory, lipid and energy metabolism, and ethylene were upregulated during ripening under strong control of an ethylene signal. Large number of photosynthesis-related genes were downregulated during ripening in an ethylene-independent manner, whereas decreased expression of a few genes such as chloroplast thiazole biosynthetic protein and phosphoenolpyruvate carboxylase, was overturned by 1-MCP treatment, suggesting ethylene dependent regulation. Ripening-associated expression of several transcription and signal transduction factors, such as TDR4, GRAS, S-adenosyl-l-homocysteine hydrolase, BNK1, bZip, and BTB showed clear ethylene dependency, suggesting their involvement in regulation of fruit ripening downstream of ethylene signaling.