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ARS Home Northeast Area Ithaca, New York Robert W. Holley Center for Agriculture & Health Plant, Soil and Nutrition Research People & Locations







James J Giovannoni
                        Plant, Soil and Nutrition Research

                        




                        
                        Research Molecular Biologist
                        Phone: (607) 255-1414
                        
                        
                        Fax: (607) 254-2958(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)
                            ProjectsCharacterization of Fruit Ripening at the Tissue and Cellular Level
                                                    Cooperative Agreement
                                                                    (A)Accession Number: 435196Translation of Plant Pathology and Agricultural Nutritional Impact Research Outcomes to Stakeholders
                                                    Cooperative Agreement
                                                                    (A)Accession Number: 435311Computational Genomic Assessment of Gene Editing Fidelity
                                                    Cooperative Agreement
                                                                    (A)Accession Number: 438035Functional Characterization of Tomato Nutrient Genes
                                                    Cooperative Agreement
                                                                    (A)Accession Number: 442650Understanding the Genetic Basis of Fruit Development and Quality
                                                    Cooperative Agreement
                                                                    (A)Accession Number: 443147Functional Characterization of Tomato Ripening Regulators
                                                    Cooperative Agreement
                                                                    (A)Accession Number: 443930Genetic Regulation of Fruit and Vegetable Nutritional Quality and Maturation and Technology Development
                                                    In-House Appropriated
                                                                    (D)Accession Number: 444024Promoting Tomato Fruit Folate Stabilization and Storage to Enhance Plant Nutrient Bioavailability
                                                    Interagency Reimbursable Agreement
                                                                    (I)Accession Number: 444214Applying Biotechnology Techniques to Improve Disease Resistance of Tomato
                                                    Interagency Reimbursable Agreement
                                                                    (I)Accession Number: 439242Memorandum of Agreement by and Between US Dept of Agriculture and the General Services Administration, Public Buildings Service, Energy Division
                                                    Memorandum of Understanding
                                                                    (M)Accession Number: 445018Cornell University & USDA/ARS-New York Facilities: (Holley Center-Ithaca, NY; Grape Genetics & Plant Genetic Research Units-Geneva, NY)
                                                    Non-Funded Cooperative Agreement
                                                                    (N)Accession Number: 437025**Publications**
                                                (Clicking on the reprint icon
                                                    Reprint Icon
                                                    will take you to the publication reprint.)Deregulation of ¿-carotene desaturase in Arabidopsis and tomato exposes a unique carotenoid-derived redundant regulation of floral meristem identity and function
                                                        

- (Peer Reviewed Journal)Mcquinn, R., Leroux, J., Sierra, J., Escobar-Tovar, L., Frusciante, S., Finnegan, E., Diretti, G., Giuliano, G., Giovannoni, J.J., Leon, P., Pogson, B. 2023. Deregulation of ¿-carotene desaturase in Arabidopsis and tomato exposes a unique carotenoid-derived redundant regulation of floral meristem identity and function. The Plant Journal. 114(4):783-804. https://doi.org/10.1111/tpj.16168.Abscisic acid mediated strawberry receptacle ripening involves the interplay of multiple phytohormone signaling networks
                                                        

- (Peer Reviewed Journal)Li, B., Shi, Y., Jai, H., Yang, X., Lu, J., Giovannoni, J.J., Jiang, G., Rose, J., Chen, K. 2023. Abscisic acid mediated strawberry receptacle ripening involves the interplay of multiple phytohormone signaling networks. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2023.1117156.Natural overexpression of carotenoid cleavage dioxygenase 4 in tomato alters carotenoid flux
                                                        

- (Peer Reviewed Journal)Yoo, H., Chung, M., Lee, H., Lee, S., Grandillo, S., Giovannoni, J.J., Lee, J. 2023. Natural overexpression of carotenoid cleavage dioxygenase 4 in tomato alters carotenoid flux. Plant Physiology. 192(2):1289-1306. https://doi.org/10.1093/plphys/kiad049.The transcription factor VviNAC60 regulates senescence- and ripening-related processes in grapevine
                                                        

- (Peer Reviewed Journal)D'Inca, E., Foresti, C., Orduna, L., Amato, A., Vandelle, E., Santiago, A., Botton, A., Cazzaniga, S., Bertini, E., Pezzotti, M., Giovannoni, J.J., Vrebalov, J., Matus, J., Tornielli, G., Zenoni, S. 2023. The transcription factor VviNAC60 regulates senescence- and ripening-related processes in grapevine. Plant Physiology. 192(3):1928-1946. https://doi.org/10.1093/plphys/kiad050.Selection pressure on the rhizosphere microbiome can alter nitrogen use efficiency in seed yield in Brassica rapa
                                                        

- (Peer Reviewed Journal)Garcia, J., Gannett, M., Wei, L., Cheng, L., Hu, S., Sparks, J., Giovannoni, J.J., Kao-Kniffin, J. 2022. Selection pressure on the rhizosphere microbiome can alter nitrogen use efficiency in seed yield in Brassica rapa. Communications Biology. https://doi.org/10.1038/s42003-022-03860-5.Limited conservation in cross-species comparison of GLK transcription factor binding suggested wide-spread cistrome divergence
                                                        

- (Peer Reviewed Journal)Tu, X., Ren, S., Wei, S., Li, J., Li, Y., Li, C., Li, Y., Zhong, Z., Xie, W., Grierson, D., Fei, Z., Giovannoni, J.J., Li, P., Zhong, S. 2022. Limited conservation in cross-species comparison of GLK transcription factor binding suggested wide-spread cistrome divergence. Nature Communications. 13(1). Article 7632. https://doi.org/10.1038/s41467-022-35438-4.A family of methyl esterases converts methyl salicylate to salicylic acid in ripening tomato fruit
                                                        

- (Peer Reviewed Journal)Frick, E., Sapkota, M., Pereira, L., Wang, Y., Hermanns, A., Giovannoni, J.J., Van Der Knaap, E., Tieman, D., Klee, H. 2023. A family of methyl esterases converts methyl salicylate to salicylic acid in ripening tomato fruit. Plant Physiology. 191(1):110-124. https://doi.org/10.1093/plphys/kiac509.Spatiotemporal dynamics of the tomato fruit transcriptome under prolonged water stress
                                                        

- (Peer Reviewed Journal)Nicolas, P., Shinozaki, Y., Powell, A., Philippe, G., Snyder, S., Gao, K., Zheng, Y., Xu, Y., Courtney, L., Vrebalov, J., Casteel, C., Mueller, L., Fei, Z., Giovannoni, J.J., Rose, J., Catala, C. 2022. Spatiotemporal dynamics of the tomato fruit transcriptome under prolonged water stress. Plant Physiology. https://doi.org/10.1093/plphys/kiac445.Comparative transcriptomics and eQTL approach identified SlWD40 as a novel tomato fruit ripening regulator
                                                        

- (Peer Reviewed Journal)Zhu, F., Jadhav, S., Toghe, T., Salem, M., Li, J., Giovannoni, J.J., Cheng, Y., Alseekh, S., Fernie, A. 2022. Comparative transcriptomics and eQTL approach identified SlWD40 as a novel tomato fruit ripening regulator. Plant Physiology. https://doi.org/10.1093/plphys/kiac200.A solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity
                                                        

- (Peer Reviewed Journal)Powell, A., Feder, A., Li, J., Schmidt, M., Courtney, L., Alseekh, S., Jobson, E., Vogel, A., Xu, Y., Lyon, D., Dumschott, K., Mchale, M., Suplice, R., Bao, K., Lal, R., Dunhan, A., Halab, A., Denton, A., Bolger, M., Fernie, A., Hind, S., Mueller, L., Martin, G., Fei, Z., Martin, C., Giovannoni, J.J., Stickler, S., Usedal, B. 2022. A solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity. The Plant Journal. 110(6):1791-1810. https://doi.org/10.1111/tpj.15770.Laser capture of tomato pericarp tissues for microscale carotenoid analysis by supercritical fluid chromatography
                                                        

- (Peer Reviewed Journal)Ramsey, J.S., Fish, T., Thannhauser, T.W., Giovannoni, J.J. 2022. Laser capture of tomato pericarp tissues for microscale carotenoid analysis by supercritical fluid chromatography. Methods in Enzymology. 670:213-233. https://doi.org/10.1016/bs.mie.2022.01.014.SlERF.F12 modulates the transition to ripening in tomato fruit by recruiting the corepressor topless and histone deacetylases to repress key ripening genes
                                                        

- (Peer Reviewed Journal)A tomato LATERAL ORGAN BOUNDARIES transcription factor, SlLOB1, predominantly regulates cell wall and softening components of ripening
                                                        

- (Peer Reviewed Journal)Shi, Y., Vrebalov, J., Zheng, H., Xu, Y., Yin, X., Liu, W., Liu, Z., Sorensen, I., Su, G., Ma, Q., Evanich, D., Rose, J., Fei, Z., Van Eck, J., Thannhauser, T.W., Chen, K., Giovannoni, J.J. 2021. A tomato LATERAL ORGAN BOUNDARIES transcription factor, SlLOB1, predominantly regulates cell wall and softening components of ripening. Proceedings of the National Academy of Sciences (PNAS). 118(33):e2102486118. https://doi.org/10.1073/pnas.2102486118.Genome-wide association study reveals the genetic architecture of 27 agronomic traits in tomato
                                                        

- (Peer Reviewed Journal)Ye, J., Wang, X., Wang, W., Yu, H., Ai, G., Li, C., Sun, P., Wang, X., Li, H., Ouyang, B., Zhang, J., Zhang, Y., Han, H., Giovannoni, J.J., Fei, Z., Ye, Z. 2021. Genome-wide association study reveals the genetic architecture of 27 agronomic traits in tomato. Plant Physiology. 2021:00:1-15. https://doi.org/10.1093/plphys/kiab230.The NAC transcription factor FaRIF controls fruit ripening in strawberry
                                                        

- (Peer Reviewed Journal)Martin-Pizzaro, C., Villarino, J., Osorio, S., Meco, V., Urritia, M., Pillet, J., Casanal, A., Merchante, C., Amaya, I., Willmitzer, L., Fernie, A., Giovannoni, J.J., Botella, M., Valpuesta, V., Pose, D. 2021. The NAC transcription factor FaRIF controls fruit ripening in strawberry. The Plant Cell. 331574-1593. https://doi.org/10.1093/plcell/koab070.Tomato fruit as a model for tissue-specific gene silencing in crop plants
                                                        

- (Peer Reviewed Journal)Feder, A., Jensen, S., Wang, A., Courtney, L., Middleton, L., Van Eck, J., Liu, Y., Giovannoni, J.J. 2020. Tomato fruit as a model for tissue-specific gene silencing in crop plants. Horticulture Research. 7:142. https://doi.org/10.1038/s41438-020-00363-4.Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression.
                                                        

- (Peer Reviewed Journal)Yano, R., Ariizumi, T., Nonaka, S., Kawazu, Y., Zhong, S., Mueller, L., Giovannoni, J.J., Rose, J., Ezura, H. 2020. Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression. Communications Biology. 3:432. https://doi.org/10.1038/s42003-020-01172-0.Phytohormones in fruit development and maturation
                                                        

- (Literature Review)Fenn, M., Giovannoni, J.J. 2020. Phytohormones in fruit development and maturation. The Plant Journal. 105:446-458. https://doi.org/10.1111/tpj.15112.GWAS based on RNA-Seq SNPs and high-throughput phenotyping combined with climatic data highlights the reservoir of valuable genetic diversity in regional tomato landraces
                                                        

- (Peer Reviewed Journal)Rodiguez, M., Sciunti, A., Posadinu, C., Xu, Y., Nguyen, C., Sun, H., Bitocchi, E., Bellucci, E., Papa, R., Fei, Z., Giovannoni, J.J., Rau, D., Attene, G. 2020. GWAS based on RNA-Seq SNPs and high-throughput phenotyping combined with climatic data highlights the reservoir of valuable genetic diversity in regional tomato landraces. Genes. 11:1387. https://doi.org/10.3390/genes11111387.Genome of Solanum pimpinelifolium provides insights into structural variants during tomato breeding
                                                        

- (Peer Reviewed Journal)Wang, X., Gao, L., Jiao, C., Stravoravdis, S., Hosmani, P., Saha, S., Zhang, J., Mainiero, S., Strickler, S., Catala, C., Martin, G., Muller, L., Vrebalov, J., Giovannoni, J.J., Wu, S., Fei, Z. 2020. Genome of Solanum pimpinelifolium provides insights into structural variants during tomato breeding. Nature Communications. 11:5817. https://doi.org/10.1038/s41467-020-19682-0.Ectopic expression of miRNA172 in tomato (Solanum lycopersicum) reveals novel function in fruit development through regulation of an AP2 transcription factor
                                                        

- (Peer Reviewed Journal)Chung, M., Nath, U., Vrebalov, J., Gapper, N., Li, J., Kim, C., Giovannoni, J.J. 2020. Ectopic expression of miRNA172 in tomato (Solanum lycopersicum) reveals novel function in fruit development through regulation of an AP2 transcription factor. Biomed Central (BMC) Plant Biology. 20:283. doi.org/10.1186/s12870-020-02489-y.Transmission modes affect the population structure of potato virus Y in potato
                                                        

- (Peer Reviewed Journal)Da Silva, W., Kutnjak, D., Xu, Y., Xu, Y., Giovannoni, J.J., Santiago, E., Gray, S.M. 2020. Transmission modes affect the population structure of potato virus Y in potato. PLoS Pathogens. 16(6). https://doi.org/10.1371/journal.ppat.1008608.Longitudinal transcriptomic, proteomic, and metabolomic analysis of Citrus limon response to graft inoculation by ‘Candidatus Liberibacter asiaticus’
                                                        

- (Peer Reviewed Journal)Ramsey, J.S., Chin, E., Chavez, J., Saha, S., Mischuk, D., Mahoney, J., Mohr, J., Robison, F., Godfrey, K., Levesque, C., Foster, L., Xu, Y., Strickler, S., Fernandez, N., Polek, M., Giovannoni, J.J., Mueller, L., Slupsky, C., Bruce, J., Heck, M.L. 2020. Longitudinal transcriptomic, proteomic, and metabolomic analysis of Citrus limon response to graft inoculation by ‘Candidatus Liberibacter asiaticus’. Journal of Proteome Research. 19:2247-2263. https://doi.org/10.1021/acs.jproteome.9b00802.Relationships between genome methylation, levels of noncoding RNAs, mRNAs and metabolites in ripening tomato fruit
                                                        

- (Peer Reviewed Journal)Zuo, J., Grierson, D., Courtney, L., Wang, Y., Gao, L., Zhao, X., Zhu, B., Luo, Y., Wang, Q., Giovannoni, J.J. 2020. Relationships between genome methylation, levels of noncoding RNAs, mRNAs and metabolites in ripening tomato fruit. Plant Journal. https://doi.org/10.1111/tpj.14778.Manipulation of ZDS in tomato exposes carotenoid- and ABA-specific effects on fruit development and ripening
                                                        

- (Peer Reviewed Journal)Mcquinn, R., Gapper, N., Gray, A., Zhong, S., Tohge, T., Fei, Z., Fernie, A., Giovannoni, J.J. 2020. Manipulation of ZDS in tomato exposes carotenoid- and ABA-specific effects on fruit development and ripening. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.13377.Tomato

- (Book / Chapter)Heuvelin, E., Okello, R., Peet, M., Giovannoni, J.J., Dorales, M. 2020. Tomato. In: Wien, C.E., Stutzel, H., editors. The Physiology of Vegetable Crops. 2nd edition. Wallingford, United Kingdom: CAB International. p.137-171.Manipulation of ß-carotene levels in tomato fruits results in increased ABA content and extended shelf life
                                                        

- (Peer Reviewed Journal)Diretto, G., Frusciante, S., Fabbri, C., Schauer, N., Busta, L., Wang, Z., Matas, A., Fiore, A., Rose, J., Fernie, A., Jetter, R., Mattei, B., Giovannoni, J.J., Gouliano, G. 2019. Manipulation of ß-carotene levels in tomato fruits results in increased ABA content and extended shelf life. Plant Biotechnology Journal. pp. 1-15. https://doi.org/10.1111/pbi.13283.Metabolomics should be deployed in identification and characterization of gene-edited crops
                                                        

- (Peer Reviewed Journal)Fraser, P., Aharoni, A., Hall, R., Huang, S., Giovannoni, J.J., Sonnewald, U., Fernie, A. 2020. Metabolomics should be deployed in identification and characterization of gene-edited crops. Plant Journal. https://doi.org/10.1111/tpj.14679.Characterizing the involvement of FaMADS9 in the regulation of strawberry fruit receptacle development
                                                        

- (Peer Reviewed Journal)Vallarino, J., Merchante, C., Sanchez, S.J., Balaguer, M., Pott, D., Ariza, M., Casanal, A., Pose, D., Vioque, A., Amay, I., Wilmitzer, L., Solano, R., Sozzani, R., Fernie, A., Botella, M., Giovannoni, J.J., Valpuesta, V., Osorio, S. 2020. Characterizing the involvement of FaMADS9 in the regulation of strawberry fruit receptacle development. Plant Biotechnology Journal. 18:929-943. https://doi.org/10.1111/pbi.13257.Genetic and metabolic effects of ripening mutations and vine detachment on tomato fruit quality
                                                        

- (Peer Reviewed Journal)Osirio, S., Carneria, R., Lytovchenko, A., Mcquinn, R., Sorenson, I., Valarino, J., Giovannoni, J.J., Fernie, A., Rose, J. 2019. Genetic and metabolic effects of ripening mutations and vine detachment on tomato fruit quality. Plant Biotechnology Journal. 18(1). https://doi.org/10.1111/pbi.13176.Genome-wide association analysis identifies a natural variation in basic helix-loop-helix transcription factor regulating ascorbate biosynthesis via D-mannose/L-galactose
                                                        

- (Peer Reviewed Journal)Ye, J., Li, W., Ai, G., Li, C., Lu, C., Chen, W., Wang, B., Wang, W., Lu, Y., Zhang, J., Li, H., Ouyang, B., Zhang, H., Fei, Z., Giovannoni, J.J., Zhang, Y., Ye, H. 2019. Genome-wide association analysis identifies a natural variation in basic helix-loop-helix transcription factor regulating ascorbate biosynthesis via D-mannose/L-galactose. PLoS Genetics. 15(5):e1008149. https://doi.org/10.1371/journal.pgen.1008149.The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor
                                                        

- (Peer Reviewed Journal)Gao, L., Gonda, I., Sun, H., Ma, Q., Bao, K., Tieman, D., Burzynski-Chang, E., Fish, T., Stromberg, K., Sacks, G., Thannhauser, T.W., Foolad, M., Jose Diez, M., Blanca, J., Canizares, J., Xu, Y., Van Der Knaap, E., Huang, S., Klee, H., Giovannoni, J.J., Fei, Z. 2019. The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nature Genetics. 51:1044-1051. https://doi.org/10.1038/s41588-019-0410-2.The Ptr1 locus of Solanum lycopersicoides confers resistance to race 1 strains of Pseudomonas syringae pv. tomato and to Ralstonia pseudosolanacearum by recognizing the type III effectors AvrRpt2 and RipBN
                                                        

- (Peer Reviewed Journal)Mazo-Molina, C., Mainiero, S., Hind, S., Kraus, C., Vachev, M., Maviane-Macia, F., Lindeberg, M., Saha, S., Strickler, S., Feder, A., Giovannoni, J.J., Smart, C., Peeters, N., Martin, G. 2019. The Ptr1 locus of Solanum lycopersicoides confers resistance to race 1 strains of Pseudomonas syringae pv. tomato and to Ralstonia pseudosolanacearum by recognizing the type III effectors AvrRpt2 and RipBN. Molecular Plant-Microbe Interactions. 32(8):040-960. https://doi.org/10.1094/MPMI-01-19-0018-R.Plant viruses transmitted in two different modes produce differing effects on small rna-mediated processes in their aphid vector
                                                        

- (Peer Reviewed Journal)Pinheiro, P.V., Wilson, J.R., Xu, Y., Zheng, Y., Rebelo, A., Fattah-Houseini, S., Kruse, A., Santos Dos Silva, R., Xu, Y., Kramer, M.H., Giovannoni, J.J., Fei, Z., Gray, S.M., Heck, M.L. 2019. Plant viruses transmitted in two different modes produce differing effects on small rna-mediated processes in their aphid vector. Phytobiomes Journal. 3(1):71-81. https://doi.org/10.1094/PBIOMES-10-18-0045-R.MaMADS2 repression in banana fruits modifies hormone synthesis and singaling pathways prior to climacteric stage
                                                        

- (Peer Reviewed Journal)Yakir, E., Fei, Z., Sela, N., Xu, Y., Singh, V., Dagar, A., Raj Joshi, J., Muller, M., Munne-Busch, S., Giovannoni, J.J., Vrebalov, J., Freidman, H. 2018. MaMADS2 repression in banana fruits modifies hormone synthesis and singaling pathways prior to climacteric stage. Biomed Central (BMC) Plant Biology. 18(267):1-17. https://doi.org/10.1186/s12870-018-1480-5.Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops
                                                        

- (Peer Reviewed Journal)Zheng, Y., Wu, S., Bai, Y., Sun, H., Jiao, C., Guo, S., Zhao, K., Blanca, J., Zhang, Z., Huang, S., Xu, Y., Weng, Y., Mazourek, M., Reddy, U., Ando, K., McCreight, J.D., Schaffer, A.A., Burger, J., Tadmor, Y., Katzir, N., Tang, X., Liu, Y., Giovannoni, J.J., Ling, K., Wechter, W.P., Levi, A., Garcia-Mas, J., Grumet, R., Fei, Z. 2018. Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Research. 47(D1):1128-1136. https://doi.org/10.1093/nar/gky944.The tomato HIGHPIGMENT1/DAMAGED DNA BINDING PROTEIN1 gene contributes to regulation of fruit ripening
                                                        

- (Peer Reviewed Journal)Wang, A., Chen, D., Ma, Q., Rose, J., Fei, Z., Liu, Y., Giovannoni, J.J. 2018. The tomato HIGHPIGMENT1/DAMAGED DNA BINDING PROTEIN1 gene contributes to regulation of fruit ripening. Horticulture Research. 6:15. https://doi.org/10.1038/s41438-018-0093-3.HS-SPME-GC-MS analyses of volatiles in plant populations – quantitating compound x individual matrix effects
                                                        

- (Peer Reviewed Journal)Burzynski-Chang, E., Ryona, I., Reisch, B., Gonda, I., Foolad, M., Giovannoni, J.J., Sacks, G. 2018. HS-SPME-GC-MS analyses of volatiles in plant populations – quantitating compound x individual matrix effects. Molecules. 23:2436. doi.org/10.3390/molecules23102436Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitive Trait Loci Detection
                                                        

- (Peer Reviewed Journal)Gonda, I., Ashrafi, H., Lyon, S., Strickler, S., Hulse-Kemp, A.M., Thannhauser, T.W., Mueller, L., Fei, Z., Foolad, M., Giovannoni, J.J., Ma, Q., Sun, H., Stoffel, K., Powell, A., Futrell, S., Van Deynze, A. 2018. A GBS-based high-density genetic map of a tomato RIL population facilitating high resolution QTL mapping and candidate gene identification. The Plant Genome. 12:1. https://doi.org/10.3835/plantgenome2018.02.0010.Genome encode analyses reveal the basis of convergent evolution of fleshy fruit ripening
                                                        

- (Peer Reviewed Journal)Liu, P., Yu, S., Chen, Y., Zhou, B., Tzeng, D., Grierson, D., Xiang, J., Fei, Z., Giovannoni, J.J., Zhong, S. 2018. Genome encode analyses reveal the basis of convergent evolution of fleshy fruit ripening. Nature Plants. https://doi.org.10.1038/s41477-018-0249-zNatural genetic variation for expression of a SWEET transporter among wild species of Solanum lycopersicum (tomato) determines the hexose composition of ripening tomato fruit
                                                        

- (Peer Reviewed Journal)Shammai, A., Petreikov, M., Yeselson, Y., Faigenboim, A., Cohen, S., Cohen, D., White, R., Giovannoni, J.J., Levin, I., Katzir, N. 2018. Natural genetic variation for expression of a SWEET transporter among wild species of Solanum lycopersicum (tomato) determines the hexose composition of ripening tomato fruit. Plant Journal. https://doi.org/10.1111/tpj.14035.Ectopic expression of ORANGE promotes carotenoid accumulation and fruit development in tomato
                                                        

- (Peer Reviewed Journal)Yazdani, M., Sun, Z., Yuan, H., Zeng, S., Thannhauser, T.W., Vrebalov, J., Ma, Q., Xu, Y., Fei, Z., Van Eck, J., Tian, S., Tadmor, Y., Giovannoni, J.J., Li, L. 2018. Ectopic expression of ORANGE promotes carotenoid accumulation and fruit development in tomato. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.12945.Genetic mapping identifies loci that influence tomato resistance against Colorado potato beetles

- (Peer Reviewed Journal)Vargas-Ortiz, E., Gonda, I., Smeda, J., Mutschler, M., Giovannoni, J.J., Jander, G. 2018. Genetic mapping identifies loci that influence tomato resistance against Colorado potato beetles. Scientific Reports. 8:7429.Deciphering genetic factors that determine melon fruit quality traits using RNA-seq based high-resolution QTL and eQTL mapping
                                                        

- (Peer Reviewed Journal)Galpaz, N., Gonda, I., Shem-Tov, D., Barad, O., Shi, Y., Tzuri, G., Lombardi, N., Fei, Z., Giovannoni, J.J., Katzir, N. 2018. Deciphering genetic factors that determine melon fruit quality traits using RNA-seq based high-resolution QTL and eQTL mapping. Plant Journal. 94:169-191. doi.org/10.1111/tpj.13838Tomato multiomics reveals consequences of crop domestication and improvement
                                                        

- (Review Article)Giovannoni, J.J. 2018. Tomato multiomics reveals consequences of crop domestication and improvement. Review Article. 172:6-8. doi.org/10.1016/j.cell.2017.12.036High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening

- (Peer Reviewed Journal)Shinozaki, Y., Nicolas, P., Fernandez-Pozo, N., Evanich, D., Shi, Y., Thannhauser, T.W., Mueller, L., Fei, Z., Giovannoni, J.J., Rose, J. 2018. High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening. Nature Communications. 9:364.The tomato expression Atlas

- (Peer Reviewed Journal)Fernandez, P., Zheng, Y., Snyder, S., Nicolas, P., Fei, Z., Giovannoni, J.J., Rose, J., Mueller, L. 2017. The tomato expression Atlas. Bioinformatics. 33:2397-2398.Ripening activator turned repressor
                                                        

- (Review Article)Giovannoni, J.J. 2017. Ripening activator turned repressor. Nature Plants. 3:920-921. doi.org/10.1038/s41477-017-0062-0Genetic diversity within African tomato using next generation sequencing
                                                        

- (Peer Reviewed Journal)Mungai, G., Owino, W., Ambuko, J., Giovannoni, J.J., Nyende, B., Michuki, G. 2018. Genetic diversity within African tomato using next generation sequencing. Plant Genetic Resources: Characterization and Utilization. 16:296-305. https://doi.org/10.1017/S1479262117000314.Differential metabolism of 1-phenylalaninein the formation of aromatic volatiles in melon (Cumis melo) fruit
                                                        

- (Peer Reviewed Journal)Gonda, I., Davidovich-Rikanati, R., Bar, E., Lev, S., Jhirad, P., Tadmor, Y., Giovannoni, J.J., Fei, Z., Katzir, N., Lewinsohn, E. 2018. Differential metabolism of 1-phenylalaninein the formation of aromatic volatiles in melon (Cumis melo) fruit. Phytochemistry. 16:296-305. https://doi.org/10.1017/S1479262117000314.Overexpression of the class D MADS-box gene Sl-AGL11 impacts fleshy tissue differentiation and structure in tomato fruits

- (Peer Reviewed Journal)Huang, B., Routaboul, J., Liu, M., Mohamed, Z., Vrebalov, J., Giovannoni, J.J., Bouzayen, M. 2017. Overexpression of the class D MADS-box gene Sl-AGL11 impacts fleshy tissue differentiation and structure in tomato fruits. Journal of Experimental Botany. https://doi.org/10.1093/jxb/erx303.An InDel in the promoter of Al-activated malate transporter 9 selected during tomato domestication determines fruit malate content and aluminum tolerance

- (Peer Reviewed Journal)Ye, J., Wang, X., Hu, T., Zhang, F., Giovannoni, J.J., Zhang, Y., Ye, Z. 2017. An InDel in the promoter of Al-activated malate transporter 9 selected during tomato domestication determines fruit malate content and aluminum tolerance. The Plant Cell. doi:10.1105/tpc.17.00211.Transient regulation of three clustered tomato class-I small heat-shock chaperone genes by ethylene is mediated by SIMADS-RIN transcription factor
                                                        

- (Peer Reviewed Journal)Shukla, V., Upadhyay, R.K., Tucker, M.L., Giovannoni, J.J., Rudhrabhatla, S.V., Mattoo, A.K. 2017. Transient regulation of three clustered tomato class-I small heat-shock chaperone genes by ethylene is mediated by SIMADS-RIN transcription factor. Scientific Reports. 7:6474. https://doi.org/10.1038/s41598-017-06622-0.AtPDS over-expression in tomato: exposing unique patterns of carotenoid self-regulation and an alternative strategy for the enhancement of fruit carotenoid content

- (Peer Reviewed Journal)Mcquinn, R., Wong, B., Giovannoni, J.J. 2017. AtPDS over-expression in tomato: exposing unique patterns of carotenoid self-regulation and an alternative strategy for the enhancement of fruit carotenoid content. Plant Biotechnology Journal. doi:10.1111/pbi12789.Metabolomic analysis to evaluate the effects of drought stress on selected African eggplant accessions

- (Peer Reviewed Journal)Mibel, E., Owino, W., Ambolo, J., Giovannoni, J.J., Onyango, A. 2017. Metabolomic analysis to evaluate the effects of drought stress on selected African eggplant accessions. Journal of the Science of Food and Agriculture. doi:10.1002/jsfa.8458.Delayed response to cold stress is characterized by successive metabolic shifts culminating in apple fruit peel necrosis
                                                        

- (Peer Reviewed Journal)Gapper, N.E., Hertog, M., Lee, J., Buchanan, D.A., Leisso, R.S., Giovannoni, J.J., Johnston, J.W., Shaffer, R.J., Micolai, B.M., Mattheis, J.P., Watkins, C.B., Rudell Jr, D.R. 2017. Delayed response to cold stress is characterized by successive metabolic shifts culminating in apple fruit peel necrosis. Biomed Central (BMC) Plant Biology. 17:77. https://doi.org/10.1186/s12870-017-1030-6.The epigenome and transcriptional dynamics of fruit ripening

- (Review Article)Giovannoni, J.J., Nguyen, C., Ampofo, B., Zhong, S., Fei, Z. 2017. The epigenome and transcriptional dynamics of fruit ripening. Annual Reviews of Plant Biology. 68:61-85.Identification of a solanum pennellii chromosome 4 fruit flavor and nutritional quality-associated metabolite QTL

- (Peer Reviewed Journal)Liu, Z., Slseekh, S., Brotman, Y., Zheng, Y., Fei, Z., Tieman, D., Giovannoni, J.J., Fernie, A., Klee, H. 2016. Identification of a solanum pennellii chromosome 4 fruit flavor and nutritional quality-associated metabolite QTL. Frontiers in Plant Science. 7:1671.iTAK: A program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators and protein kinases

- (Peer Reviewed Journal)Zheng, Y., Jiao, C., Honghe, S., Rosli, H., Pombo, M., Martin, G., Giovannoni, J.J., Fei, Z. 2016. iTAK: A program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators and protein kinases. Molecular Plant. 9:1667-1670.Prospects: the tomato genome as a cornerstone for gene discovery
                                                        

- (Book / Chapter)Giovannoni, J.J. 2016. Prospects: the tomato genome as a cornerstone for gene discovery. In: Causse, M., Giovannoni, J., Bouzayen,M., Zouine, M., editors. Conpendium of Plant Genomes: The Tomato Genome. Berlin, Germany: Springer-Verlag Berlin Heidelberg. 257-259. https://doi.org/10.1007/978-3-662-53389-5_14.The tomato genome
                                                        

- (Book / Chapter)Causse, M., Bouzayen, M., Giovannoni, J.J. 2016. Compendium of Plant Genomes: The tomato genome. Berlin, Germany: Springer,Berlin,Heidelberg. 1-259. https://doi.org/10.1007/978-3-662-53389-5.Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation

- (Peer Reviewed Journal)Zhang, B., Tieman, D., Chen, J., Xu, Y., Chen, K., Fei, Z., Giovannoni, J.J., Klee, H. 2016. Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation. Proceedings of the National Academy of Sciences. 113:12580-12585.Involvement of an ethylene response factor in chlorophyll degradation during citrus fruit degreening

- (Peer Reviewed Journal)Yin, X., Xie, X., Xia, X., Furgeson, I., Giovannoni, J.J., Chen, K. 2016. Involvement of an ethylene response factor in chlorophyll degradation during citrus fruit degreening. Plant Journal. 86:403-412.Harnessing epigenome modifications for better crops

- (Review Article)Elitzur, T., Yakir, E., Fei, Z., Vrebalov, J., Giovannoni, J.J., Freidman, H. 2016. Harnessing epigenome modifications for better crops. Journal of Experimental Botany. 67:2535-2537.Fruit color mutants in tomato reveal a function of the plastidial isopentenyl diphosphate isomerase (IDI1) in carotenoid biosynthesis

- (Peer Reviewed Journal)Pankratov, I., Mcquinn, R., Schwartz, J., Bar, E., Fei, Z., Zamir, D., Giovannoni, J.J., Hirschberg, J. 2016. Fruit color mutants in tomato reveal a function of the plastidial isopentenyl diphosphate isomerase (IDI1) in carotenoid biosynthesis. Plant Journal. doi: 10.1111/tpj13232.Carotenoid profiling of leaves of selected eggplant accessions subjected to drought stress

- (Peer Reviewed Journal)Mibei, E., Ambuko, J., Giovannoni, J.J., Onyango, A., Owino, W. 2017. Carotenoid profiling of leaves of selected eggplant accessions subjected to drought stress. Food Science and Nutrition. 5(1):113-122.Gr and hp-1 tomato mutants unveil unprecedented interactions between arbuscular mycorrhizal symbiosis and fruit ripening

- (Peer Reviewed Journal)Chialva, M., Zouari, I., Salvioli, A., Novero, M., Cao, Z., Vrebalov, J., Giovannoni, J.J., Bonfante, P. 2016. Gr and hp-1 tomato mutants unveil unprecedented interactions between arbuscular mycorrhizal symbiosis and fruit ripening. Planta. 244(1):155-165.Banana MaMADS transcription factors are necessary for fruit ripening and molecular tools to promote shelf-life and food security

- (Peer Reviewed Journal)Elitzur, T., Yakir, E., Fei, Z., Vrebalov, J., Giovannoni, J.J., Freidman, H. 2016. Banana MaMADS transcription factors are necessary for fruit ripening and molecular tools to promote shelf-life and food security. Plant Physiology. 171:390-391.UV-damaged DNA binding protein-1 and de-etiolated-1 regulate golden 2-like transcription factor by assembling a cullin 4-based ubiquitin ligase in tomato

- (Peer Reviewed Journal)Tang, X., Miao, M., Niu, X., Zhang, D., Cao, X., Wang, A., Giovannoni, J.J., Liu, Y. 2015. UV-damaged DNA binding protein-1 and de-etiolated-1 regulate golden 2-like transcription factor by assembling a cullin 4-based ubiquitin ligase in tomato. New Phytologist. 209(3):1028-1039.A DEMETER-like DNA demethylase governs tomato fruit ripening

- (Peer Reviewed Journal)Liu, R., How-Kit, A., Stammitti, L., Teyssier, E., Rolin, D., Halle, S., Giovannoni, J.J., Gallusci, P. 2015. A DEMETER-like DNA demethylase governs tomato fruit ripening. Proceedings of the National Academy of Sciences. 112:10804-10809.More than meets the eye: from carotenoid biosynthesis to new insights into apocarotenoid signaling

- (Review Article)Mcquinn, R., Giovannoni, J.J., Pogson, B. 2015. More than meets the eye: from carotenoid biosynthesis to new insights into apocarotenoid signaling. Current Opinion in Plant Biology. 27:172-179.Ethylene suppresses tomato (solanum lycopersicum) fruit set through modification of gibberellin metabolism

- (Peer Reviewed Journal)Shinozaki, Y., Hao, S., Kojima, M., Zheng, Y., Fei, Z., Zhong, S., Giovannoni, J.J., Rose, J., Ariizumi, T. 2015. Ethylene suppresses tomato (solanum lycopersicum) fruit set through modification of gibberellin metabolism. Plant Journal. 83:237-251.Analysis of petunia hybrida in response to salt stress using high throughput RNA sequencing

- (Peer Reviewed Journal)Villarino, G., Bombarely, A., Giovannoni, J.J., Scanlon, M., Mattson, N. 2014. Analysis of petunia hybrida in response to salt stress using high throughput RNA sequencing. PLoS One. 9(4):e94651.Genome sequence of the hot pepper provides insights into the evolution of pungency in Capscicum species

- (Peer Reviewed Journal)Kim, S., Park, M., Yeom, S., Kim, Y., Lee, J., Lee, H., Giovannoni, J.J., Sorensen, I., Rose, J., Choi, D. 2014. Genome sequence of the hot pepper provides insights into the evolution of pungency in Capscicum species. Nature Genetics. 46:270-279.Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome

- (Peer Reviewed Journal)Shearer, L., Anderson, L., De Jong, H., Smit, S., Goicoechea, J., Giovannoni, J.J., Stack, S. 2014. Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome. Genes, Genomes, and Genomics. 4:1395-1405.Transcriptomic events associated with internal browning of apple during postharvest storage

- (Peer Reviewed Journal)Mellidou, I., Buts, K., Hatoum, D., Ho, Q.T., Mattheis, J.P., Johnston, J.W., Watkins, C.B., Schaffer, R.J., Gapper, N.E., Giovannoni, J.J., Rudell Jr, D.R., Hertog, M.L., Nicolai, B.M. 2014. Transcriptomic events associated with internal browning of apple during postharvest storage. Biomed Central (BMC) Plant Biology. 14:328.A brief genomic history of tomato breeding
                                                        

- (Peer Reviewed Journal)Lin, T., Zhu, G., Zhang, J., Xu, X., Yu, Q., Zheng, Z., Fei, Z., Giovannoni, J.J., Yi, Z., Huang, S. 2014. A brief genomic history of tomato breeding. Nature Genetics. 46:1220-1226.The pineapple AcMADS1 promoter confers high level expression in tomato and arabidopsis flowering and fruiting tissues, but AcMADS1 does not complement the tomato LeMADS-RIN (rin) mutant
                                                        

- (Peer Reviewed Journal)Moyle, R., Koia, J., Vrebalov, J., Giovannoni, J.J., Botella, J. 2014. The pineapple AcMADS1 promoter confers high level expression in tomato and arabidopsis flowering and fruiting tissues, but AcMADS1 does not complement the tomato LeMADS-RIN (rin) mutant. Plant Molecular Biology. 86(4-5):395-407.The genome of the stress tolerant wild tomato species solanum pennellii

- (Peer Reviewed Journal)Bolger, A., Scossa, F., Bolger, M., Fei, Z., Rose, J., Zamir, D., Cararri, F., Giovannoni, J.J., Weigel, D., Fernie, A. 2014. The genome of the stress tolerant wild tomato species solanum pennellii. Nature Genetics. 46:1034-1038.The PH gene determines fruit acidity and contributes to the evolution of sweet melons
                                                        

- (Peer Reviewed Journal)Cohen, S., Itkin, M., Yesselson, Y., Portnoi, V., Fei, Z., Xu, Y., Giovannoni, J.J., Tadmor, Y., Katzir, N., Burger, Y., Schaffer, A. 2014. The PH gene determines fruit acidity and contributes to the evolution of sweet melons. Nature Communications. 5:4026.Real time-based targeted Metabolomic approach as risk assessment tools for controlling superficial scald in ‘Granny Smith’ apples during storage

- (Abstract Only)Lee, J., Buchanan, D.A., Leisso, R.S., Mattheis, J.P., Gapper, N.E., Watkins, C.B., Giovannoni, J.J., Hertog, M.M., Nicolai, B.M., Johnston, J.W., Schaffer, R.J., Whitaker, B.D., Rudell Jr, D.R. 2014. Real time-based targeted Metabolomic approach as risk assessment tools for controlling superficial scald in ‘Granny Smith’ apples during storage. Meeting Abstract. https://ashs.confex.com/ashs/2014/webprogram/Paper18864.html.Selection of low-variance expressed Malus x domestica (apple)
genes for use as quantitative PCR reference genes (housekeepers)

- (Peer Reviewed Journal)Bowen, J., Ireland, H.S., Crowhurst, R., Luo, Z., Schaffer, R.J., Watson, A.E., Foster, T., Gapper, N., Watkins, C., Giovannoni, J.J., Mattheis, J.P., Rudell Jr, D.R., Johnston, J.W. 2014. Selection of low-variance expressed Malus x domestica (apple)genes for use as quantitative PCR reference genes (housekeepers). Tree Genetics and Genomes. 10:751-759.Conserved changes in dynamics of metabolic processes during fruit development and ripening across species
                                                        

- (Peer Reviewed Journal)Klie, S., Osorio, S., Tohge, T., Drinkovich, M., Fiat, A., Giovannoni, J.J., Fernie, A., Nikoloski, Z. 2014. Conserved changes in dynamics of metabolic processes during fruit development and ripening across species. Plant Physiology. 164(1):55-68.Tomato golden 2-like (GLK) transcription factors reveal molecular gradients that function during fruit development and ripening
                                                        

- (Peer Reviewed Journal)Nguyen, C., Vrebalov, J., Gapper, N., Zheng, Y., Zhong, S., Fei, Z., Giovannoni, J.J. 2014. Tomato golden 2-like (GLK) transcription factors reveal molecular gradients that function during fruit development and ripening. The Plant Cell. 26(2):585-601.Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factor
                                                        

- (Peer Reviewed Journal)Ricardi, M., Gonzalez, R., Zhong, S., Duffy, T., Turjanski, P., Alleva, K., Carrari, F., Giovannoni, J.J., Estevez, J., Iusem, N. 2014. Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factor. Biomed Central (BMC) Plant Biology. 14:29.The tomato UV-damaged DNA binding protein 1 (DDB1) plays a role in organ size control via an epigenetic manner

- (Peer Reviewed Journal)Liu, J., Tang, X., Gao, L., Sun, X., Miao, M., Guo, X., Niu, X., Giovannoni, J.J., Xiao, F., Liu, Y. 2012. The tomato UV-damaged DNA binding protein 1 (DDB1) plays a role in organ size control via an epigenetic manner. PLoS One. 7(8):e42621.Interactions between 1-MCP and controlled atmospheres on quality and storage disorders of fruits and vegetable

- (Proceedings)Watkins, C.B., Gapper, N.E., Nock, J.F., Rudell Jr, D.R., Leisso, R.S., Lee, J., Buchanan, D.A., Mattheis, J.P., Johnston, J., Schaffer, R., Giovannoni, J.J., Hertog, M.L., Nicolai, B.M. 2014. Interactions between 1-MCP and controlled atmospheres on quality and storage disorders of fruits and vegetable. Acta Horticulturae. doi: 10.17660/ActaHortic.2015.1071.3.Integrated metabolomic and transcriptomic profiling illustrates successive phases of increasing gene expression associated with chilling-related apple peel cell death

- (Abstract Only)Rudell Jr, D.R., Gapper, N.E., Hertog, M., Nicolai, B., Buchanan, D.A., Mattheis, J.P., Watkins, C.A., Lee, J., Leisso, R.S., Giovannoni, J.J., Johnston, J., Schaffer, R. 2013. Integrated metabolomic and transcriptomic profiling illustrates successive phases of increasing gene expression associated with chilling-related apple peel cell death. Metabolomics. 51.Assessing superficial scald risk in Granny Smith apples during controlled atmosphere storage using biomarker-based technology

- (Abstract Only)Gapper, N., Hertog, M., Nicolai, B., Watkins, C., Giovannoni, J.J., Mattheis, J.P., Lee, J., Leisso, R.S., Buchanan, D.A., Rudell Jr, D.R. 2013. Assessing superficial scald risk in Granny Smith apples during controlled atmosphere storage using biomarker-based technology. HortScience. 120.Molecular and genetic regulation of fruit ripening
                                                        

- (Review Article)Gapper, N., Mcquinn, R., Giovannoni, J.J. 2013. Molecular and genetic regulation of fruit ripening. Plant Molecular Biology. 82:575-591.Catalyzing plant science research with RNA-seq

- (Peer Reviewed Journal)Martin, L., Giovannoni, J.J., Rose, J. 2013. Catalyzing plant science research with RNA-seq. Frontiers in Plant Systems Biology. 4(66):1-10.Genetic networks influencing fruit ripening

- (Book / Chapter)Ampofo, B., Chapman, N., Seymour, G., Giovannoni, J.J. 2013. Regulatory Networks Controlling Ripening. In: Graham B. Seymour, Mervin Poole, James J. Giovannoni, Gregory A. Tucker, editors. The Molecular Biology and Biochemistry of Fruit Ripening. New Delhi, India:Wiley-Blackwell. p189-200.Biomarker development for external CO2 injury prediction in apples through exploration of both transcriptome and DNA methylation changes

- (Peer Reviewed Journal)Gapper, N., Rudell Jr, D.R., Giovannoni, J.J., Watkins, C. 2013. Biomarker development for external CO2 injury prediction in apples through exploration of both transcriptome and DNA methylation changes. AoB Plants. doi: 10.1093/aobpla/plt021.Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening

- (Peer Reviewed Journal)Zhong, S., Fei, Z., Chen, Y., Vrebalov, J., Mcquinn, R., Gapper, N., Giovannoni, J.J. 2013. Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nature Biotechnology. 31:154-159.Integrative comparative analyses of transcript and metabolite profiles from pepper and tomato ripening and development stages uncovers species-specific patterns of network regulatory behavior

- (Peer Reviewed Journal)Osorio, S., Alba, R., Nikoloski, Z., Kochevenko, A., Fernie, A., Giovannoni, J.J. 2012. Integrative comparative analyses of transcript and metabolite profiles from pepper and tomato ripening and development stages uncovers species-specific patterns of network regulatory behavior. Plant Physiology. 159:1713-1729.The tomato UV-damaged DNA-binding protein-1 (DDB1) is implicated in pathogenesis-related (PR) gene expression and resistance to Agrobacterium tumefaciens

- (Peer Reviewed Journal)Lui, J., Li, H., Miao, M., Tang, X., Giovannoni, J.J., Xiao, F., Liu, Y. 2012. The tomato UV-damaged DNA-binding protein-1 (DDB1) is implicated in pathogenesis-related (PR) gene expression and resistance to Agrobacterium tumefaciens. Molecular Plant Pathology. 13:123-134.Candidate biomarker discovery and selection for ‘Granny Smith' superficial scald risk management and diagnosis, poster board

- (Abstract Only)Gapper, N., Hertog, M., Nicolai, B., Watkins, C., Giovannoni, J.J., Mattheis, J.P., Lee, J., Leisso, R.S., Buchanan, D.A., Rudell Jr, D.R. 2012. Candidate biomarker discovery and selection for ‘Granny Smith' superficial scald risk management and diagnosis, poster board. American Society of Horticulture Science Meeting.Uniform ripening (U) encodes a Golden 2-like transcription factor regulating tomato fruit chloroplast development

- (Peer Reviewed Journal)Powell, A., Nguyen, C., Hill, T., Aktas, H., Figueroa-Balderas, R., Barry, C., Liu, Y., Chetelat, R., Granell, A., Van Deynze, A., Giovannoni, J.J., Bennett, A. 2012. Uniform ripening (U) encodes a Golden 2-like transcription factor regulating tomato fruit chloroplast development. Science. 336(6089):1711-1715. DOI: 10.1126/Science.1222218.Altered chloroplast development and delayed fruit ripening caused by mutations in a zinc metalloprotease at the lutescent 2 locus of tomato

- (Peer Reviewed Journal)Barry, C., Aldridge, G., Herzog, G., Ma, Q., Mcquinn, R., Hirschberg, J., Giovannoni, J.J. 2012. Altered chloroplast development and delayed fruit ripening caused by mutations in a zinc metalloprotease at the lutescent 2 locus of tomato. Plant Physiology. 159:1086-1098.The tomato genome sequence provides insight into fleshy fruit evolution

- (Peer Reviewed Journal)Ware, D., Thannhauser, T.W., White, R.A., Giovannoni, J.J. 2012. The tomato genome sequence provides insight into fleshy fruit evolution. Nature. 485:635-641. DOI: 10.1038/nature11119.Combined transcriptome, genetic diversity and metabolite profiling in tomato fruit reveals the ethylene response factor SlERF6 to play an important role in ripening and carotenoid accumulation

- (Peer Reviewed Journal)Lee, J., Joung, J., Mcquinn, R., Chung, M., Fei, Z., Tieman, D., Klee, H., Giovannoni, J.J. 2012. Combined transcriptome, genetic diversity and metabolite profiling in tomato fruit reveals the ethylene response factor SlERF6 to play an important role in ripening and carotenoid accumulation. Plant Journal. 70:191-204.A Diagnostic Toolbox for Integrated Management of Apple Postharvest Necrotic Disorders

- (Abstract Only)Rudell Jr, D.R., Watkins, C., Mattheis, J.P., Giovannoni, J.J., Hertog, M., Nicolai, B., Rickard, B., Johnston, J., Hanrahan, I., Reed, N., Zhu, Y. 2011. A Diagnostic Toolbox for Integrated Management of Apple Postharvest Necrotic Disorders. Meeting Abstract. N/A.Features of a unique intronless cluster of class I small heat shock protein genes in tandem with box C/D snoRNA genes on chromosome 6 in tomato (Solanum lycopersicum)

- (Peer Reviewed Journal)Goyal, R.K., Kumar, V., Shukla, V., Mattoo, R., Yongsheng, L., Chung, S.H., Giovannoni, J.J., Mattoo, A.K. 2012. Features of a unique intronless cluster of class I small heat shock protein genes in tandem with box C/D snoRNA genes on chromosome 6 in tomato (Solanum lycopersicum). Planta. 235(3):453-471.Genetics and control of tomato fruit ripening and quality attributes

- (Review Article)Klee, H., Giovannoni, J.J. 2011. Genetics and control of tomato fruit ripening and quality attributes. Annual Review of Genetics. 45:41-59. DOI: 10.1146/annurev-genet-110410-132507High-throughput illumina strand-specific RNA sequencing library preparation

- (Peer Reviewed Journal)Zhong, S., Joung, J., Zheng, Y., Liu, B., Shao, Y., Xiang, J., Zhangjun, F., Giovannoni, J.J. 2011. High-throughput illumina strand-specific RNA sequencing library preparation. Cold Spring Harbor Protocols. 8:940-949. DOI: 10.1101/pdb.prot5652.Identification of genes in the phenylalanine metabolic pathway by ectopic expression of a MYB transcription factor in tomato fruit

- (Peer Reviewed Journal)Din, V., Tieman, D.M., Tohge, T., Mcquinn, R.P., De Vos, R.C., Osorio, S., Schmelz, E.A., Taylor, M.G., Smits-Kroon, M.T., Schuurink, R.C., Haring, M.A., Giovannoni, J.J., Fernie, A.R., Klee, H.J. 2011. Identification of genes in the phenylalanine metabolic pathway by ectopic expression of a MYB transcription factor in tomato fruit. The Plant Cell. 23:2738-2753.Expression of ripening-related genes in cold stored tomato fruit

- (Peer Reviewed Journal)Rugkong, A., Mcquinn, R., Giovannoni, J.J., Rose, J., Watkins, C. 2011. Expression of ripening-related genes in cold stored tomato fruit. Postharvest Biology and Technology. 61:1-14.Regulatory control of high levels of carotenoid accumulation in potato tubers

- (Peer Reviewed Journal)Zhou, X., Mcquinn, R., Fei, Z., Wolters, A., Van Eck, J., Brown, C.R., Giovannoni, J.J., Li, L. 2011. Regulatory control of high levels of carotenoid accumulation in potato tubers. Plant, Cell & Environment. 34:1020-1030.Branched-chain and aromatic amino acid catabolism into aroma volatiles in Cucumis melo L. fruit

- (Peer Reviewed Journal)Gonda, I., Bar, E., Portnoy, V., Schaffer, A., Tadmor, Y., Gepstein, S., Giovannoni, J.J., Katzir, N., Lewinsohn, E. 2010. Branched-chain and aromatic amino acid catabolism into aroma volatiles in Cucumis melo L. fruit. Journal of Experimental Botany. 61:1111-1123.Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening

- (Peer Reviewed Journal)Costa, F., Alba, R., Schouten, H., Sansavini, S., Fei, Z., Giovannoni, J.J. 2010. Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening. Biomed Central (BMC) Plant Biology. 10:229.A SEPALLATA gene is involved in the development and ripening of strawberry (Fragaria x ananassa Duch.) fruit, a non-climacteric tissue

- (Peer Reviewed Journal)Seymour, G., Ryder, C., Cevik, V., Hammond, J., Popovich, A., King, G., Vrebalov, J., Giovannoni, J.J., Manning, K. 2011. A SEPALLATA gene is involved in the development and ripening of strawberry (Fragaria x ananassa Duch.) fruit, a non-climacteric tissue. Journal of Experimental Botany. 62:1179-1188.Tomato functional genomics database (TFGD): a comprehensive collection and analysis package for tomato functional genomics

- (Peer Reviewed Journal)Fei, Z., Joung, J., Tang, X., Zheng, Y., Huang, M., Lee, J., Mcquinn, R., Tieman, D., Klee, H., Giovannoni, J.J. 2010. Tomato functional genomics database (TFGD): a comprehensive collection and analysis package for tomato functional genomics. Nucleic Acids Research. 39:D1156-D1163.The apple genome: ripe for harvest

- (Review Article)Giovannoni, J.J. 2010. The apple genome: ripe for harvest. Nature Genetics. 42:822-823.Molecular Analysis of the Developmental and Hormonal Systems Regulating Fruit Ripening

- (Proceedings)Giovannoni, J.J., Lee, J., Chung, M., Fox, E.A. 2010. Molecular Analysis of the Developmental and Hormonal Systems Regulating Fruit Ripening. Acta Horticulture Proceedings. p. 41-50.A tomato (Solanum lycopersicum) APETALA2/ERF gene, SlAP2a, is a negative regulator of fruit ripening

- (Peer Reviewed Journal)Chung, M., Vrebalov, J., Alba, R., Lee, J., Mcquinn, R., Klein, P., Giovannoni, J.J. 2010. A tomato (Solanum lycopersicum) APETALA2/ERF gene, SlAP2a, is a negative regulator of fruit ripening. Plant Journal. 64:936-947.Functional diversification of AGAMOUS lineage genes in regulating tomato flower and fruit development

- (Peer Reviewed Journal)Pan, I., Giovannoni, J.J., Irisch, V. 2010. Functional diversification of AGAMOUS lineage genes in regulating tomato flower and fruit development. Journal of Experimental Botany. 61:1795-1806.The regulation of MADS-box gene expression during ripening of banana and their regulatory interation with ethylene

- (Peer Reviewed Journal)Elitzur, T., Vrebalov, J., Giovannoni, J.J., Ocampo, E., Goldschmidt, E., Friedman, H. 2010. The regulation of MADS-box gene expression during ripening of banana and their regulatory interation with ethylene. Journal of Experimental Botany. 61:1523-1535.Integrative transcript and metabolite analysis of DE-ETIOLATED1 down-regulated tomato fruit reveals the underlying metabolic and cellular events associated with their nutritionally enhanced chemotype

- (Peer Reviewed Journal)Enfissi, E., Barneche, F., Ahmed, I., Lichtle, C., Giovannoni, J.J., Bowler, C., Bramley, P., Fraser, P. 2010. Integrative transcript and metabolite analysis of DE-ETIOLATED1 down-regulated tomato fruit reveals the underlying metabolic and cellular events associated with their nutritionally enhanced chemotype. The Plant Cell. 22:1190-1215.A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes

- (Peer Reviewed Journal)Harel-Beja, R., Portnoy, V., Fei, Z., Giovannoni, J.J., Ori, N., Lewinsohn, E., Tadmor, Y., Schaffer, A., Katzir, N. 2010. A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes. Theoretical and Applied Genetics. 121:511-533.Genomic analysis of wild tomato introgressions determining metabolism- and yield-associated traits

- (Peer Reviewed Journal)Kamenetzky, L., Asis, R., Bassi, S., De Godoy, F., Bermudez, L., Fernie, A., Vrebalov, J., Giovannoni, J.J., Rossi, M., Carrari, F. 2010. Genomic analysis of wild tomato introgressions determining metabolism- and yield-associated traits. Plant Physiology. 152:1772-1786.Plant MetGenMAP: an integrative analysis system for plant systems biology

- (Peer Reviewed Journal)Joung, J., Corbett, A., Fellman, S., Tieman, D., Klee, H., Giovannoni, J.J., Fei, Z. 2009. Plant MetGenMAP: an integrative analysis system for plant systems biology. Plant Physiology. 151:1758-1768.Fleshy fruit expansion and ripening are regulated by the tomato SHATTERPROOF gene, TAGL1

- (Peer Reviewed Journal)Vrebalov, J., Pan, I., Arroyo, A., Chung, M., Poole, M., Rose, J., Seymour, G., Giovannoni, J.J., Irish, V. 2009. Fleshy fruit expansion and ripening are regulated by the tomato SHATTERPROOF gene, TAGL1. The Plant Cell. 21:3041:3062.Developmental and feedforward control of the expression of folate biosynthesis genes in tomato fruit

- (Peer Reviewed Journal)Waller, J., Akhtar, T., Lara-Nunez, A., Gregory, J., Giovannoni, J.J., Hanson, A. 2010. Developmental and feedforward control of the expression of folate biosynthesis genes in tomato fruit. Molecular Plant. 3:66-77.Biology and genetic engineering of fruit maturation for enhanced quality and shelf-life

- (Review Article)Matayas, A., Gapper, N., Chung, M., Giovannoni, J.J., Rose, J. 2009. Biology and genetic engineering of fruit maturation for enhanced quality and shelf-life. Current Opinion in Biotechnology. 20:197-203.Genomic analysis of branched chain fatty acid and acyl sugar production in Solanum pennellii and Nicotiana benthamiana

- (Peer Reviewed Journal)Slocombe, S., Schauvinhold, I., Azziz, N., Larson, T., Giovannoni, J.J., Dixon, R., Broun, P. 2009. Genomic analysis of branched chain fatty acid and acyl sugar production in Solanum pennellii and Nicotiana benthamiana. Plant Physiology. 148:1830-1846.Role of fluorescence in situ hybridization (FISH) in sequencing the tomato genome

- (Peer Reviewed Journal)Stack, S., Royer, S., Shearer, L., Chang, S., Giovannoni, J.J., Westfall, D., Anderson, L. 2009. Role of fluorescence in situ hybridization (FISH) in sequencing the tomato genome. Cytogenetics and Genome Research. 124:339-350.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)Giovannoni, J.J. 2009. Regulation of fruit ripening. In: Well, J., Blumel, D., Malmoll, S., Netting, J., editors. Yearbook of Science and Technology. 2009. New York, NY: McGraw Hill Publishers. p. 314-317.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.Gene expression in developing watermelon fruit

- (Peer Reviewed Journal)Wechter, W.P., Levi, A., Harris-Shultz, K.R., Davis, A.R., Fei, Z.J., Katzir, N., Giovannoni, J.J., Salman-Minkov, A., Hernandez, A., Thimmapuram, J., Tadmor, Y., Portnoy, V., Trebitsh, T. 2008. Gene expression in developing watermelon fruit. 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)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.).  Proceedings 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 Only)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 Review)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.Transcriptome and selected metabolite analyses reveal multiple points of ethylene control during tomato fruit development

- (Peer Reviewed Journal)Alba, R., Payton, P.R., Fei, Z., Mcquinn, R.P., Debbie, P., Martin, G., Tanksley, S., Giovannoni, J.J. 2005. Transcriptome and selected metabolite analyses reveal multiple points of ethylene control during tomato fruit development. The Plant Cell. 17(11):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)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 Only)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 Only)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.A MADS-BOX GENE NECESSARY FOR FRUIT RIPENING AT THE RIPENING-INHIBITOR     (RIN) LOCUS

- (Peer Reviewed Journal)VREBALOV, J., RUEZINSKY, D., PADMANABHAN, V., WHITE, R.A., MEDRANO, D., DRAKE, R., SCHUCH, W., GIOVANNONI, J.J. A MADS-BOX GENE NECESSARY FOR FRUIT RIPENING AT THE RIPENING-INHIBITOR (RIN) LOCUS. SCIENCE. 2002. V. 296. P. 343-346.CHARACTERIZATION OF PHYTOCHROME-REGULATED TOMATO RIPENING UTILIZING FUNCTIONAL GENOMICS

- (Abstract Only)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.DEVELOPMENT AND UTILIZATION OF TOMATO MICROARRAYS FOR THE SOLANACEAE

- (Abstract Only)MOORE, S.L., PAYTON, P.R., GIOVANNONI, J.J. DEVELOPMENT AND UTILIZATION OF TOMATO MICROARRAYS FOR THE SOLANACEAE. PLANT ANIMAL AND MICROBE GENOMES CONFERENCE. 2002.USE OF MOLECULAR MARKERS FOR FRUIT CROP IMPROVEMENT

- (Book / Chapter)MCCASKILL, A.R., GIOVANNONI, J.J. USE OF MOLECULAR MARKERS FOR FRUIT CROP IMPROVEMENT. KLUWER ACADEMIC PUBLISHERS. MOLECULAR TECHNIQUES IN CROP IMPROVEMENT. 2002. P. 283-297.DNA MICROARRAYS FOR GENE EXPRESSION ANALYSIS

- (Book / Chapter)MOORE, S., PAYTON, P., GIOVANNONI, J.J. DNA MICROARRAYS FOR GENE EXPRESSION ANALYSIS. OXFORD UNIVERSITY PRESS. PRACTICAL APPROACH MOLECULAR PLANT BIOLOGY. 2002. V. 2. P. 65-76.ANALYSIS OF THE ETHYLENE RESPONSE IN THE EPINASTIC (EPI) MUTANT OF TOMATO

- (Peer Reviewed Journal)BARRY, C., FOX, E., YEN, H., LEE, S., YING, T., GRIERSON, D., GIOVANNONI, J.J. ANALYSIS OF THE ETHYLENE RESPONSE IN THE EPINASTIC (EPI) MUTANT OF TOMATO. PLANT PHYSIOLOGY. 2001. V. 127. P. 58-66.MOLECULAR BIOLOGY OF FRUIT MATURATION AND RIPENING

- (Review Article)GIOVANNONI, J.J. MOLECULAR BIOLOGY OF FRUIT MATURATION AND RIPENING. ANNUAL REVIEWS OF PLANT PHYSIOLOGY AND PLANT MOLECULAR BIOLOGY. 2001. V. 52. P. 725-749.GENETIC CONTROL OF FRUIT QUALITY AND PROSPECTS FOR NUTRIENT MODIFICATION

- (Peer Reviewed Journal)GIOVANNONI, J.J. GENETIC CONTROL OF FRUIT QUALITY AND PROSPECTS FOR NUTRIENT MODIFICATION. HORTSCIENCE. 2002. V. 37. P. 453-456.
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