Projects

GENOMICS APPROACHES FOR IMPROVING NUTRITIONAL QUALITY OF FOOD CROP SPECIES Appropriated (D)   Accession Number: 410826

DETERMINATION AND CHARACTERIZATION OF UNINTENDED EFFECTS IN GENETICALLY MODIFIED FOOD CROPS Appropriated (D)   Accession Number: 412821

TOMATO FRUIT EPIDERMIS AND CARPEL GENOMICS: TOOLS FOR GENE DISCOVERY, FUNCTIONAL ANALYSIS AND ENHANCEMENT OF THE SOLANACEAE TOOLKIT Grant (G)   Accession Number: 413162

CHARACTERIZATION OF THE TOMATO EXTRACELLULAR PROTEOME, OR SECRETOME, USING INTEGRATED FUNCTINAL AND COMPUTATIONAL STRATEGIES Nonfunded Cooperative Agreement (N)   Accession Number: 412736

FUNCTIONAL GENOMICS ANALYSIS OF FRUIT FLAVOR AND NUTRITION PATHWAYS Nonfunded Cooperative Agreement (N)   Accession Number: 410292

CHARACTERIZATION OF THE TOMATO EXTRACELLULAR PROTEOME, OR SECRETOME, USING INTEGRATED FUNCTIONAL AND COMPUTATIONAL STRATEGIES Nonfunded Cooperative Agreement (N)   Accession Number: 411771

GENOMICS OF TOMATO FRUIT EPIDERMIS AND CARPEL DEVELOPMENT Reimbursable (R)   Accession Number: 412490

IDENTIFICATION AND FUNCTIONAL GENOMICS OF GENES IMPACTING PHYTONUTRIENT LEVELS AND METAL TOLERANCE IN FOOD CROP SPECIES Specific Cooperative Agreement (S)   Accession Number: 409431

Publications

Genomic analysis of branched chain fatty acid and acyl sugar production in Solanum pennellii and Nicotiana benthamiana - (Peer Reviewed Journal) - (09-Apr-09)

Role of fluorescence in situ hybridization (FISH) in sequencing the tomato genome - (Peer Reviewed Journal) - (21-Mar-09)

Expression profiling of ascorbic acid-related genes during tomato fruit development and ripening and in response to stress conditions - (Peer Reviewed Journal)

Ioannidi, E., Kalamaki, M., Engineer, C., Petaraki, I., Alexandrou, D., Giovannoni, J.J., Kanellis, A. 2009. Expression profiling of ascorbic acid-related genes during tomato fruit development and ripening and in response to stress conditions. Journal of Experimental Botany. 60:663-678.

A snapshot of the emerging tomato genome sequence - (Peer Reviewed Journal)

Mueller, L., Tanksley, S., Giovannoni, J.J., Vaneck, J., Stack, S., Buels, R. 2009. A snapshot of the emerging tomato genome sequence. The Plant Genome. 2:78-92.

Differential fruit gene expression in two strawberry cultivars in response to elevated CO2 during storage revealed by a heterologous fruit microarray approach - (Peer Reviewed Journal)

Ponce-Valdez, M., Moore-Fellman, S., Giovannoni, J.J., Gan, S., Watkins, C. 2009. Differential fruit gene expression in two strawberry cultivars in response to elevated CO2 during storage revealed by a heterologous fruit microarray approach. Postharvest Biology and Technology. 51:131-140.

Tomato y-glutamilhydrolases: expression, characterization, and evidence for heterodimer formation - (Peer Reviewed Journal)

Akhtar, T., Naponelli, V., Gregory, J., Giovannoni, J.J., Hanson, A. 2008. Tomato y-glutamilhydrolases: expression, characterization, and evidence for heterodimer formation. Plant Physiology. 148:775-784.

Regulation of Fruit Ripening - (Book/Chapter) - (23-Jun-08)

Amino acid substitutions in homologs of the STAY-GREEN (SGR) protein are responsible for the green-flesh and chlorophyll retainer mutations of tomato and pepper - (Peer Reviewed Journal)

Barry, C., Mcquinn, R.P., Chung, M., Besuden, A., Giovannoni, J.J. 2008. Amino acid substitutions in homologs of the STAY-GREEN (SGR) protein are responsible for the green-flesh and chlorophyll retainer mutations of tomato and pepper. Plant Physiology. 147:179-187.

Altered Plastid Levels and Potential for Improved Fruit Nutrient Content via Down-regulation of the Tomato DDB1 Interacting Protein CUL4 - (Peer Reviewed Journal)

Wang, S., Liu, J., Feng, Y., Niu, X., Giovannoni, J.J., Liu, Y. 2008. Altered Plastid Levels and Potential for Improved Fruit Nutrient Content via Down-regulation of the Tomato DDB1 Interacting Protein CUL4. Plant Journal. 55:89-103.

The Molecular and Biochemical Basis for Varietal Variation in Sesquiterpene Content in Melon (Cucumis melo L.) Rinds - (Peer Reviewed Journal)

Portnoy, V., Benyamini, Y., Giovannoni, J.J., Schaffer, A., Tadmor, Y., Lewinshon, E., Katzir, N. 2008. The Molecular and Biochemical Basis for Varietal Variation in Sesquiterpene Content in Melon (Cucumis melo L.) Rinds. Plant Molecular Biology. 66:647-661.

Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato - (Peer Reviewed Journal)

Datema, E., Mueller, L., Buels, R., Giovannoni, J.J., Visser, R., Stiekema, W., Vanham, R. 2008. Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato. Biomed Central (BMC) Plant Biology. 8:34.

Est-Derived Expression Analysis of Watermelon Fruit Development - (Peer Reviewed Journal)

Wechter, W.P., Levi, A., Harris, K.R., Davis, A.R., Fei, Z.J., Giovannoni, J.J., Trebitsh, T., Salman, A., Hernandez, A., Thimmapuram, J., Tadmor, V., Portnoy, V., Katzir, N. 2008. Est-derived expression analysis of watermelon fruit development. Biomed Central (BMC) Genomics. 9:275-282.

Molecular Biology of ethylene during tomato fruit development and maturation - (Peer Reviewed Journal)

Beatriz, C., Giovannoni, J.J. 2008. Molecular Biology of ethylene during tomato fruit development and maturation. Plant Science. 175:106-113.

Expression and Polymorphism of Watermelon Fruit ESTs - (Proceedings/Symposium)

Levi, A., Wechter, W.P., Harris, K.R., Davis, A.R., Zhangiun, F., Giovannoni, J.J., Trebitsh, T., Salman, A., Hernandez, A., Thimmapuram, J., Tadmor, Y., Portnoy, V., Katzir, N. 2008. Expression and Polymorphism of Watermelon Fruit ESTs. Acta Horticulturae. P257-262. In: M. Pitrat (ed.). Proceddings of the IX EUCARPIA Meetings on Genetics and Breeding of Cucurbitaceae. INRA.

A new plant gene in the pathway to vitamin C - (Popular Publication)

Giovannoni, J.J. 2007. A new plant gene in the pathway to vitamin C. Proceedings of the National Academy of Sciences. 104:9109-9110.

A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation - (Peer Reviewed Journal)

Keller, C., Readman, C., Shin, H., Bosdet, I., Wilkin, J., Vrebalov, J., Giovannoni, J.J., Douglas, C. 2007. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. Plant Journal. 50:1063-1078.

Fruit ripening mutants yield insight into ripening control - (Peer Reviewed Journal)

Giovannoni, J.J. 2007. Fruit ripening mutants yield insight into ripening control. Current Opinion in Plant Biology. 10:283-284.

Ethylene and Fruit Ripening - (Peer Reviewed Journal)

Barry, C., Giovannoni, J.J. 2007. Ethylene and Fruit Ripening. Journal of Plant Growth Regulation. 26:143-159.

Microarray-Based Analysis of Gene Modulation During Watermelon Fruit Development - (Abstract)

Wechter, W.P., Levi, A., Davis, A.R., Fei, Z., Hernandez, A., Thimmapuram, J., Dang, P.M., Katzir, N., Tadmor, K., Giovannoni, J.J. 2007. Microarray-Based Analysis of Gene Modulation During Watermelon Fruit Development. HortScience. 42:447.

Fruit Ripening - (Book/Chapter)

Martel, C., Giovannoni, J.J. 2007. Fruit ripening. In: Roberts, J., Gonzalez-Carranzas, Z., editors. Plant Cell Separation and Adhesion. Oxford, UK: Blackwell Publishing Ltd. p. 164-176.

Fruit Ripening and Its Manipulation - (Book/Chapter)

Giovannoni, J.J. 2007. Fruit ripening and its manipulation. In: Gan, S., editor. Senescence Process of Plants. Oxford, UK: Blackwell Publishing Ltd. p.278-295.

A Naturally Occurring Epigenetic Mutation in An Sbp-Box Gene Inhibits Tomato Fruit Ripening - (Peer Reviewed Journal)

Manning, K., Tor, M., Poole, M., Hong, Y., Thompson, A., King, G., Giovannoni, J.J., Seymour, G. 2006. A naturally occurring epigenetic mutation in an sbp-box gene inhibits tomato fruit ripening. Nature Genetics. 38:948-952.

Ripening in the Tomato Green-Ripe Mutant Is Inhibited by Ectopic Expression of a Novel Protein That Disrupts Ethylene Signaling - (Peer Reviewed Journal)

Barry, C., Giovannoni, J.J. 2006. Ripening in the tomato green-ripe mutant is inhibited by ectopic expression of a novel protein that disrupts ethylene signaling. Proceedings of the National Academy of Sciences. 103:7923-7928.

Euchromatin and Pericentromeric Heterochromatin: Comparative Composition in the Tomato Genome - (Peer Reviewed Journal)

Wang, Y., Tang, X., Cheng, Z., Mueller, L., Giovannoni, J.J., Tanksley, S. 2006. Euchromatin and pericentromeric heterochromatin: comparative composition in the tomato genome. Genetics. 172:2529-2540.

Breeding New Life into Plant Metabolism - (Literature)

Giovannoni, J.J. 2006. Breeding new life into plant metabolism. Nature Biotechnology. 24:418-419.

Tomato Expression Database (Ted): a Suite of Data Presentation and Analysis Tools - (Peer Reviewed Journal)

Fei, Z., Tang, X., Alba, R., Giovannoni, J.J. 2006. Tomato expression database (ted): a suite of data presentation and analysis tools. Nucleic Acids Research. 34:D766-D770.

Transcriptome and Selected Metabolite Analysis Reveal Multiple Points of Ethylene Control During Tomato Fruit Development - (Peer Reviewed Journal)

Alba, R., Payton, P.R., Fei, Z., Debbie, P., Martin, G., Tanksley, S., Giovannoni, J.J. 2005. Transcriptome and selected metabolite analysis reveal multiple points of ethylene control during tomato fruit development. The Plant Cell. 17:2954-2965.

The Tomato Sequencing Project, the First Cornerstone of the International Solanaceae Project (Sol) - (Peer Reviewed Journal)

Mueller, L., Tanksley, S., Giovannoni, J.J., Van Eck, J. 2005. The tomato sequencing project, the first cornerstone of the international solanaceae project (sol). Comparative and Functional Genomics. 6:153-158.

Utilization of Tomato Microarrays for Comparative Gene Expression Analysis in the Solanceae - (Peer Reviewed Journal)

Moore, S., Payton, P.R., Wright, M., Tanksley, S., Giovannoni, J.J. 2005. Utilization of tomato microarrays for comparative gene expression analysis in the solanceae. Journal of Experimental Botany. 56:2885-2895.

Ethylene Insensitivity Conferred by the Green-Ripe (Gr) and Never-Ripe 2 (Nr-2) Ripening Mutants of Tomato - (Peer Reviewed Journal)

Barry, C., Thompson, A., Seymour, G., Grierson, D., Giovannoni, J.J. 2005. Ethylene insensitivity conferred by the green-ripe (gr) and never-ripe 2 (nr-2) ripening mutants of tomato. Plant Physiology. 138:267-275.

Genetic Regulation of Tomato Fruit Ripening and Development and Implementation of Associated Genomics Tools - (Peer Reviewed Journal)

Giovannoni, J.J., El-Rakshy, S. 2005. Genetic regulation of tomato fruit ripening and development and implementation of associated genomics tools. Acta Horticulturae. 682:63-72.

Differential Gene Expression Analysis of Strawberry Cultivar Responses to Elevated Co2 Concentrations During Storage Using a Tomato Cdna Microarray - (Peer Reviewed Journal)

Ponce-Valadez, M., Watkins, C., Moore, S., Giovannoni, J.J. 2005. Differential gene expression analysis of strawberry cultivar responses to elevated co2 concentrations during storage using a tomato cdna microarray. Acta Horticulturae. 682:255-262.

Role of - Oxidation in Jasmonate Biosynthesis and Systemic Wound Signaling in Tomato - (Peer Reviewed Journal)

Lia, C., Liua, G., Schilmillera, A., In Leea, G., Jayantya, S., Sagemana, C., Vrebalov, J., Giovannoni, J.J., Howe, G. 2005. Role of - oxidation in jasmonate biosynthesis and systemic wound signaling in tomato. The Plant Cell. 17:971-986.

Folate Synthesis in Plants: the Last Step of the P-Aminobenzoate Branch Is Catalyzed by a Plastidial Aminodeoxychorismate Lyase - (Peer Reviewed Journal)

Basset, G., Ravanel, S., Quinlivan, E., White, R.A., Giovannoni, J.J., Rebeille, F., Nichols, B., Shinozaki, K., Gregory, J., Hanson, A. 2004. Folate synthesis in plants: the last step of the p-aminobenzoate branch is catalyzed by a plastidial aminodeoxychorismate lyase. Plant Journal. 40:453-461.

Signal Transduction Systems Regulating Fruit Ripening - (Peer Reviewed Journal)

Adams-Phillips, L., Barry, C., Giovannoni, J.J. 2004. Signal transduction systems regulating fruit ripening. Trends in Plant Science. 9:331-338.

Comprehensive Est Analysis of Tomato and Comparative Genomics of Fruit Ripening - (Peer Reviewed Journal)

Fei, Z., Tang, X., Alba, R., Ronning, C., Martin, G., Tanksley, S., Giovannoni, J.J. 2004. Comprehensive EST analysis of tomato and comparative genomics of fruit ripening. Plant Journal. 40:47-59.

Tackling the Plant Proteome: Practical Approaches, Hurdles and Experimental Tools - (Peer Reviewed Journal)

Rose, J.K., Bashir, S., Giovannoni, J.J., Jahn, M.M., Saravanan, R.S. 2004. Tackling the plant proteome: practical approaches, hurdles and experimental tools. Plant Journal. 39:715-733.

Ests, Cdna Microarrays, and Gene Expression Profiling: Tools for Dissecting Plant Physiology and Development - (Peer Reviewed Journal)

Alba, R., Fei, Z., Payton, P.R., Liu, Y., Debbie, P., Rose, J., Martin, G., Tanksley, S., Jahn, M., Giovannoni, J.J. 2004. Ests, cdna microarrays, and gene expression profiling: tools for dissecting plant physiology and development. Plant Journal. 36:697-714.

Manipulation of Light Signal Transduction As a Means of Modifying Fruit Nutritional Quality in Tomato - (Peer Reviewed Journal)

Liu, Y., Roof, S., Ye, Z., Barry, C., Van Tuinen, A., Vrebalov, J., Bowler, C., Giovannoni, J.J. 2004. Manipulation of light signal transduction as a means of modifying fruit nutritional quality in tomato. Proceedings of the National Academy of Sciences. 26:9897-9902.

Genetic Control of Fruit Ripening - (Book/Chapter) - (16-Apr-04)

Genetic Regulation of Fruit Development and Ripening - (Peer Reviewed Journal)

Giovannoni, J.J. 2004. Genetic regulation of fruit development and ripening. The Plant Cell. 16:S170-180.

Monitoring Gene Expression Profiles in Response to Aluminum Stress in Maize Roots Using Cdna Microarrays - (Abstract)

Maron, L.G., Moore, S., Giovannoni, J.J., Kochian, L.V. 2004. Monitoring gene expression profiles in response to aluminum stress in maize roots using cdna microarrays. American Society of Plant Biologists Annual Meeting. p. 77.

Ctr1-Mediated Ethylene Signal Transduction in Tomato Is Encoded by a Multigene Family Whose Members Display Distinct Regulatory Features - (Peer Reviewed Journal)

Adams-Phillips, L., Barry, C., Kannan, P., Lecercq, J., Bouzayen, M., Giovannoni, J.J. 2004. Ctr1-mediated ethylene signal transduction in tomato is encoded by a multigene family whose members display distinct regulatory features. Plant Molecular Biology. 54:387-404.

Folate Synthesis in Plants: the P-Aminobenzoate Branch Is Initiated by a Bifunctional Paba-Pabb Protein That Is Targeted to Plastids - (Peer Reviewed Journal)

Basset, G., Quinlivan, E., Ravanel, S., Niochols, B., Shinozaki, K., Seki, M., Giovannoni, J.J., Adams-Phillips, L., Gregory, J., Hanson, A. 2004. Folate synthesis in plants: the p-aminobenzoate branch is initiated by a bifunctional paba-pabb protein that is targeted to plastids. Proceedings of the National Academy of Sciences. 101:1496-1501.

Plant Genetic Modification: Gene Isolation - (Book/Chapter)

Giovannoni, J.J. 2004. Plant genetic modification: Gene isolation. In: Cristou, P., Klee, H., editors. Handbook of Plant Biotechnology. Vol 1. W. Susses, UK: Wiley and Sons, Ltd. p. 66-68.

Lectr1, a Tomato Ctr1-Like Gene, Demonstrates Ethylene Signaling Ability in Arabidopsis and Novel Expression Patterns in Tomato - (Peer Reviewed Journal)

LECLERCQ, J., ADAMS-PHILLIPS, L., ZEGZOUTI, H., JONES, B., LATCHE, A., GIOVANNONI, J.J., PECHE, J., BOUZAYEN, M. LECTR1, A TOMATO CTR1-LIKE GENE, DEMONSTRATES ETHYLENE SIGNALING ABILITY IN ARABIDOPSIS AND NOVEL EXPRESSION PATTERNS IN TOMATO. PLANT PHYSIOLOGY. 2002. V. 13. P. 1132-1142.

Characterization of a Major Latex Protein (Mlp) Gene Down-Regulated by Ethylene During Peach Fruitlet Abscission - (Peer Reviewed Journal)

RUPERTI, B., BONGHI, C., ZILIOTTO, F., PAGNI, S., RASORI, A., VAROTTO, S., TUNUTTI, P., GIOVANNONI, J.J., RAMINA, A. CHARACTERIZATION OF A MAJOR LATEX PROTEIN (MLP) GENE DOWN-REGULATED BY ETHYLENE DURING PEACH FRUITLET ABSCISSION. PLANT SCIENCE. 2002. V. 163. P. 265-272.

Approaches to Clone the Aluminum Tolerance Gene in Wheat Using Segmental Deletion Lines of the Chromosome Arm 4dl - (Abstract)

MARON, L., WHITE, R.A., GIOVANNONI, J.J., SARAVANAN, R., ROSE, J., GARVIN, D.F., KOCHIAN, L.V. APPROACHES TO CLONE THE ALUMINUM TOLERANCE GENE IN WHEAT USING SEGMENTAL DELETION LINES OF THE CHROMOSOME ARM 4DL. AMERICAN SOCIETY OF PLANT BIOLOGISTS ANNUAL MEETING. 2002.

Genomics of Ethylene Signal Transduction in Tomato - (Book/Chapter)

ADAMS-PHILLIPS, L., ALBA, R., BARRY, C., GIOVANNONI, J.J. GENOMICS OF ETHYLENE SIGNAL TRANSDUCTION IN TOMATO. KLUWER ACADEMIC PUBLISHERS. BIOLOGY AND BIOTECHNOLOGY OF THE PLANT HORMONE ETHYLENE. 2003. P. 131-136.

Deductions About the Number, Organization and Evolution of Genes in the Tomato Genome Based on Analysis of Large Est Collection and Selective Genomic Sequencing - (Peer Reviewed Journal)

VAN DER HOEVEN, R., RONNING, C., GIOVANNONI, J.J., MARTIN, G., TANKSLEY, S. DEDUCTIONS ABOUT THE NUMBER, ORGANIZATION AND EVOLUTION OF GENES IN THE TOMATO GENOME BASED ON ANALYSIS OF LARGE EST COLLECTION AND SELECTIVE GENOMIC SEQUENCING. THE PLANT CELL. 2002. V. 14. P. 1441-1456.

Use of Genomics Tools to Isolate Key Ripening Genes and Analyze Fruit Maturation in Tomato - (Peer Reviewed Journal)

MOORE, S., VREBALOV, J., PAYTON, P., GIOVANNONI, J.J. USE OF GENOMICS TOOLS TO ISOLATE KEY RIPENING GENES AND ANALYZE FRUIT MATURATION IN TOMATO. JOURNAL OF EXPERIMENTAL BOTANY. 2002. V. 53. P. 2023-2030.

Use of Genomics Tools to Isolate Key Ripening Genes and Analyze Fruit Maturation in Tomato - (Peer Reviewed Journal)

MOORE, S., VREBALOV, J., PAYTON, P.R., GIOVANNONI, J.J. USE OF GENOMICS TOOLS TO ISOLATE KEY RIPENING GENES AND ANALYZE FRUIT MATURATION IN TOMATO. JOURNAL OF EXPERIMENTAL BOTANY. 2002. 53 (377) P. 2023-2030. 2002.

Characterization of Phytochrome-Regulated Tomato Ripening Utilizing Functional Genomics - (Abstract)

ALBA, R., MOORE, S., PAYTON, P.R., CORDONNIER-PRATT, M., PRATT, L., GIOVANNONI, J.J. CHARACTERIZATION OF PHYTOCHROME-REGULATED TOMATO RIPENING UTILIZING FUNCTIONAL GENOMICS. AMERICAN SOCIETY OF PLANT BIOLOGISTS ANNUAL MEETING. 2002. SUPPLEMENT 369, P. 99.