Abstract
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.
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This work was supported by the Department of Biotechnology (DBT), Govt. of India, funded research project entitled “Towards development of Carotenoids rich Tomatoes: Structural and Functional Genomics approach” having project number BT/PR11671/PBD/16/828/2008. The authors thank the Coordinator, Bioinformatics Centre (DBT, BIF) for providing the necessary facilities. The facilities provided by School of Biotechnology under DST (PURSE) and UGC (SAP) are thankfully acknowledged. The authors unreservedly acknowledge the UDSC Microarray Center (UDSCMAC), University of Delhi, South Campus for the Microarray experimentation.
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MKD planned and designed the experiments. MKD and SK provided the necessary laboratory facilities. DS and AK conducted the experiments and analyzed the data. DS and AK wrote the initial draft of the manuscript which was suitably modified by MKD. SK performed manuscript proofreading. All the authors read and approved the final manuscript.
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Sharma, D., Koul, A., Kaul, S. et al. Tissue-specific transcriptional regulation and metabolite accumulation in tomato (Solanum lycopersicum L.). Protoplasma 257, 1093–1108 (2020). https://doi.org/10.1007/s00709-020-01492-2
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DOI: https://doi.org/10.1007/s00709-020-01492-2