Newswise — A new Web-based tool at South Dakota State University called VitisNet can help plant breeders and researchers worldwide analyze large molecular data sets in ultimately practical ways to help the grape and wine industry.

Plant scientists who work with other plants besides grapevines can also benefit from the information.

VitisNet places 13,145 genes and thousands of proteins and metabolites into hundreds of molecular networks that researchers can use to rapidly visualize genes and biochemical pathways involved in grapevine growth and fruiting cycles or responses to environmental stresses.

For example, VitisNet provides plant-specific information about the molecular pathways involved in processes such as fruit ripening, grapevine dormancy or drought tolerance — knowledge that can help plant breeders breed better grapes. VitisNet can help grape breeders visualize genes and biochemical changes involved as grapevines develop flowers, carry out photosynthesis or carbon fixation, or metabolize specific sugars such as fructose and mannose, or starch and sucrose. All that information can help plant breeders build the right genetics into grapevines in order to get desired grape attributes.

“This is basic science that can be applied in practical ways, as when viticulturists look at the genes and biochemistry involved as fruit ripens, or as flavor develops. Although it’s a very important contribution to the international grape research community, it’s not limited to grapes,” said professor Anne Fennell in SDSU’s Department of Horticulture, Forestry, Landscape and Parks. “Other plant scientists can use these molecular networks as well, since the vast majority of these genes are found in most plants. The research allows plant breeders and researchers to visualize what’s going on within the plant and to see which pathways are most important in a particular process.”

VitisNet is available online at http://vitis-dormancy.sdstate.org/. The networks are also available for dynamic browsing and downloading at http://metnet3.vrac.iastate.edu/ (Vit tab). Details are available in a study published Dec. 21, 2009, in the international, peer-reviewed open-access online publication, PLoS ONE. The journal article, “VitisNet: ‘Omics’ Integration through Grapevine Molecular Networks,” is available at this link: http://dx.plos.org/10.1371/journal.pone.0008365.

The authors are former SDSU post-doctoral researcher Jérôme Grimplet (now at the Institute for Grapevine and Wine Sciences in Spain), Grant R. Cramer of the University of Nevada-Reno, Julie A. Dickerson of Iowa State University, SDSU research assistant Kathy Mathiason, John Van Hemert of Iowa State University and SDSU’s Anne Y. Fennell.

Fennell is the principal investigator in a project funded by a $3 million grant from the National Science Foundation that is now unveiling a major tool supporting grape molecular systems research. The project examines the functional genomics of bud endodormancy in grapes, or how genes, proteins and interactions with the environment determine when the grapevine becomes dormant in the fall and when it breaks dormancy in the spring. Bud dormancy is an adaptive strategy of many woody species including grapes for the survival of drought, high temperature, low temperature and freeze-dehydration stress.

To understand the coordination of environmental and genetic mechanisms regulating bud endodormancy, the project used bioinformatics tools to transform separate data sets into user-friendly information. These tools include transcriptomic, proteomic and metabolomic profiling, to track the actively expressed genes, proteins and metabolites related to endodormancy. Metabolites are chemical compounds formed as part of the natural biochemical process in the plant.

Jérôme Grimplet, an SDSU postdoctoral scholar who developed grape molecular networks, said computer modeling seemed an ideal way to work with the large data sets generated by the NSF study. It allows scientists to see how plant processes respond to a change in an environmental variable such as day length.

Fennell added that providing it in a Web-based format allows users from around the world to immediately access and use VitisNet. “This resource allows visualization of dynamic interactions of transcripts, proteins, and metabolites within known molecular networks — for example, metabolic or signaling pathways,” she said. “Integrating transcripts with protein and metabolite profiles in a comprehensive molecular map enables the researcher to explore different biochemical responses of grapevines to developmental and environmental cues.”

Fennell said Grimplet provided expert annotation of the grape genome (29,971 genes) and assigned 13,145 genes with known function to 219 molecular networks. These networks include 88 metabolic networks (those having to do with chemical reactions related to plant metabolism); 15 genetic information processing networks; 12 environmental information processing networks; 3 cellular process networks; 21 transport networks; and 80 transcription factor networks (those that have to do with proteins that help control the transfer of genetic information).

VitisNet has been built with a program called CellDesigner and can be visualized using Cytoscape. A user first identifies a set of genes, transcripts, proteins or metabolites of interest and can then overlay their expression values on the molecular networks (VitisNet) to determine biochemical events of interest. Additional plug-ins available in Cytoscape can be used to analyze the data further.

A tutorial at the VitisNet site instructs users on what software is needed, how to obtain that software, and how to upload and visualize data on the molecular networks of VitisNet. Visit the Web site or consult the PLoS ONE journal article for more details.

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CITATIONS

PLoS ONE (Dec. 21, 2009)