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Welcome to the NSF-Funded Tomato Genomics Project

NSF #0116076

Welcome to the information pages for the Tomato Genomics Project (#0116076). This project is funded by the National Science Foundation Plant Genome Research Program. The purpose of these pages is to provide information on the goals of the project, the P.I's involved in the project and public resources developed as part of this project. If you have suggestions/comments about this site or the Tomato Genomics Project please e-mail Steve Tanklsley. For more details, click on any of the topics below.


This project is the continuation and expansion of our previous tomato genome project (NSF#9872617) with an emphasis on physical, evolutionary and functional genomics of the Solanaceae. In the first part of the project a physical map, comprised of a set of overlapping BAC clones, is being constructed for the tomato genome and anchored against the genetic maps of tomato, other solanaceous species, and the arabidopsis genome. This will be accomplished by using a set of 1000 conserved ortholog (COS) markers shared between the arabidopsis and solanaceous genomes. The anchored BAC physical map will: 1) facilitate positional cloning; 2) elucidate the organization/distribution of genes with respect to centromeres, heterchromatin, euchromatin and meiotic recombination; 3) provide a new method for precise mapping; 4) provide the foundation and clone resource for eventual tomato genome sequencing; and 5) shed light on the nature of genome evolution in higher plants and help establish a syntenic network though which genomic information can be shared and compared among plants. To further investigate genome organization and to determine the level of microsynteny among the Solanaceae, a set of orthologous BAC clones from solanaceous species will be sequenced and compared with each other and to corresponding portions of the arabidopsis genome.

In the second part of the project, we apply two virus-induced gene-silencing (VIGS) approaches as a means of associating gene sequence with function. We continue to focus on defense responses and fruit development - processes for which tomato is an excellent model. In the first approach, we are developing a normalized, elicitor-induced cDNA library of Nicotiana benthamiana in a potato virus X (PVX) vector and use it for VIGS of orthologs to a set of differentially-expressed tomato genes and also a set of 5,000 random genes. The plants so derived are screened for a variety of defense responses including alterations in ethylene-regulated phenotypes. In the second approach, we will use PVX constructs to develop stable tomato transformants. These lines will contain promising defense and ethylene response genes from the transient VIGS analysis as well as genes specifically implicated in fruit development/ripening. Results from these studies will provide new information on the feasibility of large scale gene silencing for tomato functional genomics and will result in the targeted development of a comprehensive set of heritable gene repression lines focused on two biological processes for which tomato is an optimal model.

Finally, we are developing and distributing new resources for genetic/genomic research in solanaceous species, including: 1) a tomato non-redundant unigene set; 2) tomato cDNA microarrays; 3) DNA, plantlets, and associated data sets from an F2 synteny mapping population and seeds from a permanent RI mapping population; 4) 200 stable gene silenced tomato lines, 5) VIGs libraries (for transient silencing); 6) set of tiled tomato BAC clones; and 7) new solanaceous BAC libraries. To facilitate distribution of genomic information for tomato in particular and for solanaceous species in a comparative genomic context, we continue development of the Solanaceae Genome Network database - a genomics database that ties together information on sequence and genetic/physical maps among solanaceous species and anchors this information against the arabidopsis genome sequence. We will also develop a tomato gene expression profiling database to curate and deliver cDNA microarray data to the research public.

Implementation of this comprehensive tomato genomics project will result in development of additional functional and structural genomics tools built upon those developed in our previous proposal and with extended applicability from tomato to the broader Solanaceae. Functional genomics applications and the resulting public databases will allow us and others to expand knowledge in the areas of defense response, fruit development and genome evolution.


Project P.I.s Contact Organization
S. Tanksley Cornell University
J. Giovannoni Texas A&M
G. Martin Boyce Thompson Institute for Plant Research (BTI)
R. Wing Arizona Genome Initiative


Harry Klee, U. Florida, chair
Sue Rhee, Carnegie Institution of Washington
Dani Zamir, Hebrew U., Israel
Danesh Kumar, Yale U.
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