Tomato is an excellent model for studying fruit development, ripening, and other secondary metabolic pathways such as carotenoid biosynthetic pathway, flavonoid pathway, and many more. Tomato fruit development and ripening occurs under tight genetic control and involves the expression of thousands of genes affecting fruit quality and accumulation of pigments and metabolites. Here, we have described the development of a microarray platform that has allowed establishment of a framework for quantification of the expression of large number of genes and transcription factors possibly regulating various secondary metabolic pathways in tomato. To unravel the molecular mechanisms of fruit development and ripening, a tomato 60-mer oligonucleotide 44 K microarray along with the custom array for many genes and transcription factors was designed and validated in the fruit and leaf tissues. Comparative profiling of gene expression studies has allowed us to identify a large number of differentially expressed genes and transcription factors. Gene ontology revealed the involvement of these genes in various biological, cellular, and molecular processes like isoprenoid, terpenoid, pigment, ethylene biosynthesis, phytohormone signaling, and fruit ripening. Further, correlation, as well as differential expression studies, has revealed that several transcription factors like RIN, AGAMOUS, TAGL1, MYB, MADS-box etc. could be the possible regulators of various secondary metabolic pathways. The present study has identified various metabolites, their biosynthetic pathways and genes which may possibly be controlled by different transcription factors. The present findings have laid a base for understanding the transcriptional and metabolic shifts which occur in parallel during programmed fruit ripening and developmental processes in tomato.

中文翻译：

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番茄 (Solanum lycopersicum L.) 中的组织特异性转录调控和代谢物积累

番茄是研究果实发育、成熟和其他次级代谢途径（如类胡萝卜素生物合成途径、黄酮途径等）的绝佳模型。番茄果实的发育和成熟发生在严格的遗传控制下，涉及影响果实质量和色素和代谢物积累的数千个基因的表达。在这里，我们描述了微阵列平台的开发，该平台允许建立量化大量基因和转录因子的表达的框架，这些基因和转录因子可能调节番茄中的各种次级代谢途径。解开果实发育和成熟的分子机制，番茄 60 聚体寡核苷酸 44 K 微阵列以及用于许多基因和转录因子的定制阵列在果实和叶组织中设计和验证。基因表达研究的比较分析使我们能够识别大量差异表达的基因和转录因子。基因本体揭示了这些基因参与各种生物、细胞和分子过程，如类异戊二烯、萜类化合物、色素、乙烯生物合成、植物激素信号传导和果实成熟。此外，相关性以及差异表达研究表明，RIN、AGAMOUS、TAGL1、MYB、MADS-box 等几种转录因子可能是各种次级代谢途径的可能调节因子。本研究鉴定了多种代谢物，它们的生物合成途径和基因可能受不同转录因子的控制。目前的研究结果为理解在番茄程序性果实成熟和发育过程中并行发生的转录和代谢变化奠定了基础。