RUI: Genomic and integrative analysis of phytochromes E and F in tomato

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This project investigates the biology of light receptors in plants, specifically in the nightshades, a plant family which includes agriculturally important crops, such as potato, tomato, pepper, and eggplant. Plant light receptors enable a plant to assess and evaluate the conditions of its environmental surroundings and allows it to make developmental decisions that ensure reproductive success. Such decisions include, among others, the timing of germination, leaf development, flower production and fruit set. Specifically, this project aims to better understand the function of two light receptors in tomato in the context of their role in determining the plant’s architecture and overall shape. The project is conducted at a liberal arts college and emphasizes educational opportunities in research for undergraduates. One aspect of the project is to develop a research-based laboratory for first-semester Biology students investigating the genetic underpinnings of early fruit producing garden tomatoes. Through collaboration with a college in rural central Washington educational opportunities will also be made available to students in regions of the state with a traditionally less developed scientific infrastructure.This project investigates the contributions of the light receptor phytochrome, specifically phytochromes E and F in tomato, to photomorphogenesis and development. Like the model plant Arabidopsis thaliana, tomato and other nightshades have five phytochrome genes. Gene duplications of ancestral phytochrome genes occurred after the split of the Solanaceae from the Brassicaceae. This has led to differentiation between these two plant families in the functionality of each set of phytochrome genes. To this date, loss of function mutations for PHYE and PHYF have not been available in tomato. We have recently developed knock out mutants in these genes using CRISPR technology. During this granting period higher order mutants will be constructed and phenotypically evaluated. To determine the role that phytochromes E and F play in light-regulated signal transduction, RNA-seq coupled with co-expression network analysis will be conducted. Using information from these gene networks will enable us to formulate new testable hypotheses regarding the physiological functions of phytochromes in the nightshades.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.