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Microarray profiling of tomato provides an insight into the key transcription factors involved during fruit ripening and development

ABSTRACT: Tomato (Solanum lycopersicum) represents an established research model for studying fruit development and ripening processes which is genetically under tight control of various regulatory molecules. Elucidation of these regulatory mechanisms remains important to understand the production and accumulation of various metabolites, which ultimately determines the fruit quality. Therefore, it is essential to develop a platform that allows accurate identification and quantification of the gene transcript levels including transcription factors associated with ripening process. Microarray technology has become mainstream and preferred tool for studying the large number of targeted gene expression in a single run. In the present study, we have developed the microarray platform in the leaf and fruit tissues of four different accessions of tomato in order to check the expression levels of various genes and transcription factors involved in secondary metabolic pathways which directly or indirectly regulates the ripening process. A total of 42313 probes were used in 1 ×44k array of Agilent technology along with the custom design for many genes and transcription factors. A co-expression study revealed several transcription factors whose expression patterns strongly correlates with the genes involved in ethylene, carotenoid and flavonoid biosynthesis and accumulation. The above correlation was validated by generating expression networks using CytoScape v.3.1.1. Real time PCR was also carried out for checking the expression profiles of transcription factors known to regulate the above three pathways. This study provides an insight into multiple events associated with transcription factors involved in secondary metabolism of tomato including maturation and ripening processes

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE112777 | GEO | 2020/03/02

REPOSITORIES: GEO

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Project description:Tomato fruit ripening is under the control of ethylene as well as a group of ethylene-independent transcription factors, including NON-RIPENING (NOR) and RIPENING INHIBITOR (RIN). During ripening, the linear carotene lycopene accumulates at the expense of cyclic carotenoids. Fruit-specific overexpression of LYCOPENE β-CYCLASE (LCYb) under the control of the PHYTOENE DESATURASE (PDS) promoter resulted in increased levels of β-carotene and ABA and in decreased ethylene levels. Genes regulated by ABA, or involved in its synthesis and signaling, were overexpressed, while those associated with ethylene and cell wall remodeling were repressed. In agreement with the transcriptional data, LCYb-overexpressing fruits exhibited increased density of cell wall material containing linear, under-methylated pectins and displayed an array of additional ripening phenotypes, including delayed softening, increased turgor, enhanced shelf life and a thicker cuticle with a higher content of cutin monomers and triterpenoids. The levels of several primary metabolites and phenylpropanoids also changed in the transgenics, which could be attributed to delayed fruit ripening and to ABA respectively. Network correlation analysis suggests that ABA, acting through NOR and RIN, is responsible for many of the above phenotypes. These data reinforce suggestions that ABA plays an important role in tomato fruit ripening and provide clues that fruit b-carotene, acting as a precursor for ABA, actively participates in controlling the ripening process rather than merely being an output thereof. Overexpression of a LCYb gene from Arabidopsis under the control of the ripening-associated PDS promoter leads to ripe tomato fruits accumulating high β-carotene levels. Using several independent transgenic lines, we conducted a system-wide study of the effect of increased β-carotene levels on tomato fruit ripening and shelf life. Our data suggest that β-carotene, acting through ABA, is involved in a regulatory loop within the network controlling tomato fruit ripening.

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Microarray profiling of tomato provides an insight into the key transcription factors involved during fruit ripening and development

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