The Virtual Berry Project: Functional Genomics of Grape Berry Development

Berries from wine and table grape (Vitis vinifera) are the most widely cultivated and economically important fruit crop worldwide. The grape berry is consumed as fresh and dried fruit, grape juice, wine and distilled liquor. In contrast to well-studied climacteric fruit models, such as tomato,relatively little is known about the molecular genetic mechanisms that govern grape berry development and ripening. Grape berries, like other berry fruits, undergo a complex series of physical and biochemical changes during development, which can be divided into three major stages. After fruit set, the initial stage of exponential berry growth (stage 1), which involves cell division and expansion accumulation of high concentrations of organic acids and chlorophyll, is followed by a lag phase (stage 2) in which the berries do not increase in size. The lag phase is followed by the onset of ripening (or véraison) that marks the third phase of berry growth (stage 3), which involves increased berry size, tissue softening, and major changes in the accumulation of sugars, amino acids, and dramatic increases in anthocyanins (in red varieties) in the berry skin. In the last several years, genomic resources in grape have increased dramatically, setting the stage for systematic functional genomic studies in grape. The long-term goal of the proposed research is to decipher the transcriptional network controlling berry development at tissue- and cell-type resolution. Towards this goal extensive transcriptome profiling was conducted throughout berry development and within seed, fleshy mesocarp, and skin tissues under well watered and water deficit stress conditions. These findings represent a unique framework upon which to build a spatio-temporal map of berry development to test hypotheses regarding the intricate regulatory controls that govern berry development.

The primary objectives of our research are to 1) conduct integrated transcriptome, proteome, and metabolome profiling on available Vitis mutants or varieties altered in seed production, flesh characteristics, and skin color in order to discern tissues-specific expression patterns associated with these phenotypes. 2) develop a robust transformation system for a dwarf, rapid flowering/fruiting Pinot Meunier grape line for use as a model system for tracking berry development in living tissues at single-cell resolution. 3) develop and test the use of a novel live-cell lineage marking system in developing flowers and berries. 4) map the spatio-temporal expression patterns of candidate tissue-specific genes and test the feasibility of establishing large-scale enhancer trapping in Vitis. 5) study the effects of gain/loss-of-function of key transcription factors on grape flower and berry development. 6) develop and present a “hands-on” educational training program on the “virtual berry”, a training workshop on grape transformation, and a  collaborative outreach workshop series on viticulture practices that influence berry development and quality.

This research is a collaborative effort among investigators at the University of Nevada, Reno, the University of California, Davis, and Oregon State University.