The Photoperiodic Transcriptome of Arabidopsis thaliana

Date of Award

Fall 1-1-2024

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Molecular, Cellular, and Developmental Biology

First Advisor

Gendron, Joshua

Abstract

Photoperiodism --- the response to day length --- is a phenomenon observed in many plants and has the function of coordinating growth, development and reproduction to favorable seasonal timings. Photoperiodism is different from a response to light, or lack thereof, in that it involves the integration of light information with the time of day. Therefore, a response to day length, i.e. photoperiod, requires the perception to both light and time-of-day signals. We performed a transcriptomics experiment on Arabidopsis plants grown in 3 different photoperiods and found that thousands of genes show photoperiodic alteration in gene expression. Gene clustering, daily expression integral calculations, and cis-element analysis then separate photoperiodic genes into co-expression subgroups that display 19 diverse seasonal expression patterns, opening the possibility that many photoperiod measurement systems work in parallel in Arabidopsis. Moreover, Paired-mRNA-miRNA analysis revealed pairs that show negative correlation across different photoperiods. Mapping of tRFs onto mature tRNA sequences revealed photoperiod-specific accumulation of specific tRF types. Lastly, using gene regulatory network methods and the non-parametric algorithm KBoost, GRNs that describe both short-day and long-day forms of MDLM were generated. These GRNs were validated through standard data sets, and the effect of computational parameters on the GRNs were assessed. Candidate MDLM transcriptional regulators were chosen through a set of conceptual principles that concern the biological nature of MDLM. The effects of incorporation of miRNA data, as well as that of a priori biological knowledge, on the search for candidate regulators were also investigated. In summary, this study used GRN methods to search for candidate transcriptional regulators that are expected to control MDLM, a form of photoperiodism in plant seedlings.

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