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TRANSCRIPTIONAL, TRANSLATIONAL AND EPIGENETIC DYNAMICS DURING RIPENING INITIATION IN TOMATO FRUIT

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Abstract

Ripening is a tightly regulated developmental program that renders a fruit attractive to seed dispersing organisms. The ripening process is controlled by many different genes, and studies in the experimental model tomato (Solanum lycopersicum) have shown that it is largely dependent upon key transcription factors in concert with epigenetic modifications and hormonal signaling. While a general regulatory network governing fruit ripening has been established, comparatively little is known about the events responsible for its initiation. This thesis examines transcriptional, translational and epigenetic dynamics operating across different tomato tissues during the onset of fruit ripening. First, given that the earliest ripening gene expression begins in the tissue surrounding the seeds, it is possible that seed maturity may influence ripening initiation. Parthenocarpic (i.e., seedless) fruits were utilized to identify aspects of ripening that are altered in the absence of seeds. While ripening parameters were similar between seeded and parthenocarpic fruits, this analysis revealed reduced locule liquefaction prior to ripening of seedless fruits. Interestingly, the initiation of climacteric ripening correlated with restoration of locular liquefaction to that of seeded fruit, suggesting that pre-ripening locule changes are separable from the broader ripening program and seed-dependent, while carpel ripening is seed-independent. Second, the DNA glycosylase SlDML2 has been previously shown to control ripening-associated DNA demethylation. SlDML2 expression also starts in the locule prior to ripening initiation, a pattern which mirrors that of promoter hypomethylation based on whole genome bisulfite sequencing analysis. Attempts to disrupt this pattern using sldml2 mutants revealed that the loss of SlDML2 had a surprisingly minor effect on the pre-ripening fruit transcriptome, which points to a more complex interplay between promoter methylation and gene expression patterns prior to ripening initiation. Finally, ripening research has predominantly utilized measurements of transcript abundance to assess gene function, and translational dynamics are less well understood. Ribosome profiling (Ribo-seq), was employed to compare the proportion of translated mRNAs to the bulk transcriptome before and after ripening initiation. This analysis demonstrated that the vast majority of ripening-related genes exhibit translation levels closely linked to transcript abundance, although structural genes related to plastid function may exhibit some translational regulation.

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251 pages

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2021-08

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Keywords

DNA methylation; Fruit ripening; Parthenocarpy; Ribosome profiling; RNA-seq; Tomato

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Committee Chair

Giovannoni, James J.

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Richards, Eric Jean
Rose, Jocelyn

Degree Discipline

Plant Biology

Degree Name

Ph. D., Plant Biology

Degree Level

Doctor of Philosophy

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Government Document

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dissertation or thesis

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