CoPIs: Carmen Catala and Zhangjun Fei (Boyce Thompson Institute for Plant Research) and James J. Giovannoni (USDA-ARS/Boyce Thompson Institute for Plant Research)

Fleshy fruit are unique plant developmental systems and provide important components of human and animal diets. Tomato (Solanum lycopersicum), an economically important crop, has emerged as the principal model for studies of fleshy fruit development, ripening, shelf life and nutritional quality. However, many fundamental questions related to key aspects of the development, physiology, quality traits and environmental responses of fleshy fruit remain unanswered. This project will decipher complex problems in plant biology that are also central to fleshy fruit development and quality: (i) the regulatory processes that influence fruit growth and ripening; (ii) the associated hormone biosynthesis and signaling pathways; and (iii) molecular events that result in cell wall formation and restructuring, and that provide protection from environmental stresses. An important element of this project is the development of a strong education and training component. This will take the form of two programs: (1) an annual Plant Genomics and Systems Biology Workshop, comprising a series of integrated 'technology modules' with both seminars and lab-based practical training in 'omics disciplines'; (2) a multi-level training course in Scientific Communication, providing guidance in both oral and written presentation skills. These will be affiliated with undergraduate students, high school students and high school teachers, with particular emphasis on the participation of under-represented groups through the support of a network of existing Cornell programs.

Studies to date have provided valuable initial insights into the identity and temporal expression patterns of some of the genes that regulate fruit development; however, they have almost exclusively used total tomato fruit pericarp ('flesh') and have largely ignored spatial variation in global gene expression in the different constituent cell types. The goal of this project is to extend these studies to characterize the responses of fruits to drought, an increasing problem in crop production, in tomato using cutting edge genomics technologies. These studies will be extended to two diverse wild relatives of tomato that show a high tolerance of water stress, and so may provide opportunities for crop improvement. The expected outcomes are: A) the Tomato Expression Atlas (TEA), a gene expression database for cultivated tomato and wild relatives, and new insights into the regulatory circuitry that controls fruit development and responses to drought, at a cell/tissue type level of resolution; B) detailed information about the tissue specificity of hormone biosynthesis and signaling pathways, and cell wall biosynthesis and remodeling during fruit development in tomato and wild relatives, and following drought treatments. Public access to all data and biological materials will be through the Tomato Expression Atlas (TEA) website and long-term public repositories. All DNA sequences will be released to the public domain immediately after generation and quality control through Genbank ( and SGN ( Raw RNA-Seq, sRNA-seq and BS-seq datasets generated under this project will be submitted to NCBI SRA ( for long term storage and public access while processed expression and methylation profiles will be archived and accessed through the TEA and through the Tomato Functional Genomics Database ( and the Tomato Epigenome database (

National Science Foundation (NSF)
Division of Integrative Organismal Systems (IOS)
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Diane Okamuro
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Cornell University
United States
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