Faculty Home > Jim Giovannoni
Dr. Jim Giovannoni
Scientist

Office/Lab: Room 429/426
Email jjg33@cornell.edu
Office: 607-255-1414
Lab: 607-254-1259


Affiliations

Plant Molecular Biologist at the USDA-ARS Plant, Soil and Nutrition Laboratory Adjunct Professor in Cornell University’s Department of Horticulture and Department of Plant Breeding and Genetics Adjunct Assistant Professor in Department of Plant Biology

Graduate Fields

Horticulture, Plant Biology, Plant Breeding

Boyce Thompson Institute for Plant Research
Tower Road Ithaca, New York 14853-1801 U.S.A.


  1. Research Summary
  2. Selected Publications
  3. Features
  4. News
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  6. Lab Members
  7. PGRP

The focus of research in the Giovannoni laboratory is molecular and genetic analysis of fruit ripening and related signal transduction systems with emphasis on the relationship of fruit ripening to nutritional quality. We are also involved in development of tools for genomics of the Solanaceae including participation in the International Tomato Sequencing Project. We employ several experimental systems but the majority of our work involves the use of tomato. The broad objectives of the lab include deciphering the underlying molecular basis of components of ripening regulation conserved through evolution and how these regulatory networks coordinate ripening events including those related to quality and nutritional content.

Experimental approaches include: 1) positional cloning of loci known via mutation to harbor genes necessary for normal fruit development and ripening, and 2) isolation of candidate ripening regulatory genes based on expression pattern or relationship to ripening-related signal transduction systems (e.g. ethylene, light), and functional analysis in transgenic plants.

  • Clepet, C., Joobeur, T., Zheng, Y., Jublot, D., Huang, M.Y., Truniger, V., Boualem, A., Hernandez-Gonzalez, M.E., Dolcet-Sanjuan, R., Portnoy, V., Mascarell-Creus, A., Cano-Delgado, A.I., Katzir, N., Bendahmane, A., Giovannoni, J.J., Aranda, M.A., Garcia-Mas, J. and Fei, Z.J. 2011. Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon. Bmc Genomics 12: 252
  • Dai, N., Cohen, S., Portnoy, V., Tzuri, G., Harel-Beja, R., Pompan-Lotan, M., Carmi, N., Zhang, G.F., Diber, A., Pollock, S., Karchi, H., Yeselson, Y., Petreikov, M., Shen, S., Sahar, U., Hovav, R., Lewinsohn, E., Tadmor, Y., Granot, D., Ophir, R., Sherman, A., Fei, Z.J., Giovannoni, J., Burger, Y. , Katzir, N. and Schaffer, A.A. 2011. Metabolism of soluble sugars in developing melon fruit: a global transcriptional view of the metabolic transition to sucrose accumulation. Plant Mol Biol 76: 1-18
  • Fei, Z., Joung, J.G., Tang, X., Zheng, Y., Huang, M., Lee, J.M., McQuinn, R., Tieman, D.M., Alba, R., Klee, H.J. and Giovannoni, J.J. 2011. Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics. Nucleic Acids Res 39: D1156-1163
  • Klee, H.J. and Giovannoni, J.J. 2011. Genetics and control of tomato fruit ripening and quality attributes. Annu Rev Genet 45: 41-59
  • Martel, C., Vrebalov, J., Tafelmeyer , P. and Giovannoni, J.J. 2011. The tomato MADS-box transcription factor RIPENING INHIBITOR interacts with promoters involved in numerous ripening processes in a COLORLESS NONRIPENING-dependent Manner. Plant Physiol 157: 1568-1579
  • Matas, A.J., Yeats, T.H., Buda, G.J., Zheng, Y., Chatterjee, S., Tohge, T., Ponnala, L., Adato, A., Aharoni, A., Stark, R., Fernie, A.R., Fei, Z., Giovannoni, J.J. and Rose, J.K. 2011. Tissue- and cell-type specific transcriptome profiling of expanding tomato fruit provides insights into metabolic and regulatory specialization and cuticle formation. Plant Cell 23: 3893-3910
  • Osorio, S., Alba, R., Damasceno, C.M.B., Lopez-Casado, G., Lohse, M., Zanor, M.I., Tohge, T., Usadel, B., Rose, J.K.C., Fei, Z.J., Giovannoni, J.J. and Fernie, A.R. 2011. Systems biology of tomato fruit development: Combined transcript, protein, and metabolite analysis of tomato transcription factor (nor, rin) and ethylene receptor (Nr) mutants reveals novel regulatory interactions. Plant Physiol 157: 405-425
  • Rohrmann, J., Tohge, T., Alba, R., Osorio, S., Caldana, C., McQuinn, R., Arvidsson, S., van der Merwe, M.J., Riano-Pachon, D.M., Mueller-Roeber, B., Fei, Z., Nesi, A.N., Giovannoni, J.J. and Fernie, A.R. 2011. Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development. Plant J 68: 999-1013
  • Rugkong, A., McQuinn, R., Giovannoni, J.J., Rose, J.K.C. and Watkins, C.B. 2011. Expression of ripening-related genes in cold-stored tomato fruit. Postharvest Biol Tec 61: 1-14
  • Seymour, G.B., Ryder, C.D., Cevik, V., Hammond, J.P., Popovich, A., King, G.J., Vrebalov, J., Giovannoni, J.J. and Manning, K. 2011. A SEPALLATA gene is involved in the development and ripening of strawberry (FragariaXananassa Duch.) fruit, a non-climacteric tissue. J Exp Bot 62: 1179-1188
  • Zhong, S., Joung, J.G., Zheng, Y., Chen, Y.R., Liu, B., Shao, Y., Xiang, J.Z., Fei , Z. and Giovannoni, J.J. 2011. High-throughput Illumina strand-specific RNA sequencing library preparation. Cold Spring Harb Protoc 2011: 940-949
  • Zhou, X.J., Mcquinn, R., Fei, Z.J., Wolters, A.M.A., Van Eck, J., Brown, C., Giovannoni, J.J. and Li, L. 2011. Regulatory control of high levels of carotenoid accumulation in potato tubers. Environ 34: 1020-1030
  • Chung, M.Y., Han, J.S., Giovannoni, J., Liu, Y., Kim, C.K., Lim, K.B. and Chung, J.D. 2010. Modest calcium increase in tomatoes expressing a variant of Arabidopsis cation/H+ antiporter. Plant Biotechnology Reports 4: 15-21
  • Chung, M.Y., Vrebalov, J., Alba, R., Lee, J., McQuinn, R., Chung, J.D., Klein , P. and Giovannoni, J. 2010. A tomato (Solanum lycopersicum) APETALA2/ERF gene, SlAP2a, is a negative regulator of fruit ripening. Plant Journal 64: 936-947
  • Costa, F., Alba, R., Schouten, H., Soglio, V., Gianfranceschi, L., Serra, S., Musacchi, S., Sansavini, S., Costa, G., Fei, Z.J. and Giovannoni, J. 2010. Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening. BMC Plant Biology 10: 229
  • Elitzur, T., Vrebalov, J., Giovannoni, J.J., Goldschmidt, E.E. and Friedman, H. 2010. The regulation of MADS-box gene expression during ripening of banana and their regulatory interaction with ethylene. Journal of Experimental Botany 61: 1523-1535
  • Enfissi, E.M.A., Barneche, F., Ahmed, I., Lichtle, C., Gerrish, C., McQuinn, R.P., Giovannoni, J.J., Lopez-Juez, E., Bowler, C., Bramley, P.M. and Fraser, P.D. 2010. Integrative transcript and metabolite analysis of nutritionally enhanced DE-ETIOLATED1 downregulated tomato fruit. Plant Cell 22: 1190-1215
  • Giovannoni, J. 2010. Harvesting the apple genome. Nature Genetics 42: 822-823
  • Gonda, I., Bar, E., Portnoy, V., Lev, S., Burger, J., Schaffer, A.A., Tadmor, Y., Gepstein, S., Giovannoni, J.J., Katzir, N. and 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
  • Harel-Beja, R., Tzuri, G., Portnoy, V., Lotan-Pompan, M., Lev, S., Cohen, S., Dai, N., Yeselson, L., Meir, A., Libhaber, S.E., Avisar, E., Melame, T., van Koert, P., Verbakel, H., Hofstede, R., Volpin, H., Oliver, M., Fougedoire, A., Stalh, C., Fauve, J., Copes, B., Fei, Z., Giovannoni, J., Ori, N., Lewinsohn, E., Sherman, A., Burger, J., Tadmor, Y., Schaffer, A.A. and 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
  • Kamenetzky, L., Asis, R., Bassi, S., de Godoy, F., Bermudez, L., Fernie, A.R., Van Sluys, M.A., Vrebalov, J., Giovannoni, J.J., Rossi, M. and Carrari, F. 2010. Genomic analysis of wild tomato introgressions determining metabolism- and yield-associated traits. Plant Physiology 152: 1772-1786
  • Milone, D.H., Stegmayer, G.S., Kamenetzky, L., Lopez, M., Lee, J.M., Giovannoni, J.J. and Carrari, F. 2010. omeSOM: a software for clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants. BMC Bioinformatics 11: 438
  • Pan, I.L., McQuinn, R., Giovannoni, J.J. and Irish, V.F. 2010. Functional diversification of AGAMOUS lineage genes in regulating tomato flower and fruit development. Journal of Experimental Botany 61: 1795-1806
  • Rugkong, A., Rose, J.K.C., Lee, S.J., Giovannoni, J.J., O'Neill, M.A. and Watkins, C.B. 2010. Cell wall metabolism in cold-stored tomato fruit. Postharvest Biology and Technology 57: 106-113
  • Waller, J.C., Akhtar, T.A., Lara-Nunez, A., Gregory, J.F., McQuinn, R.P., Giovannoni, J.J. and Hanson, A.D. 2010. Developmental and feedforward control of the expression of folate biosynthesis genes in tomato fruit. Molecular Plant 3: 66-77
  • Joung, J.G., Corbett, A.M., Fellman, S.M., Tieman, D.M., Klee, H.J., Giovannoni , J.J. and Fei, Z. 2009. Plant MetGenMAP: an integrative analysis system for plant systems biology. Plant Physiol 151: 1758-1768
  • Matas, A.J., Gapper, N.E., Chung, M.Y., Giovannoni, J.J. and Rose, J.K.C. 2009. Biology and genetic engineering of fruit maturation for enhanced quality and shelf-life. Curr Opin Biotech 20: 197-203
  • Mueller, L.A., Lankhorst, R.K., Tanksley, S.D., Giovannoni, J.J., White, R., Vrebalov, J., Fei, Z., van Eck, J., Buels, R., Mills, A.A., Menda, N., Tecle, I.Y., Bombarely, A., Stack, S., Royer, S.M., Chang, S.-B., Shearer, L.A., Kim, B.D., Jo, S.-H., Hur, C.-G., Choi, D., Li, C.-B., Zhao, J., Jiang, H., Geng, Y., Dai, Y., Fan, H., Chen, J., Lu, F., Shi, J., Sun, S., Chen, J., Yang, X., Lu, C., Chen, M., Cheng, Z., Li, C., Ling, H., Xue, Y., Wang, Y., Seymour, G.B., Bishop, G.J., Bryan, G., Rogers, J., Sims, S., Butcher, S., Buchan, D., Abbott, J., Beasley, H., Nicholson, C., Riddle, C., Humphray, S., McLaren, K., Mathur, S., Vyas, S., Solanke, A.U., Kumar, R., Gupta, V., Sharma, A.K., Khurana, P., Khurana, J.P., Tyagi, A., Sarita, Chowdhury, P., Shridhar, S., Chattopadhyay, D., Pandit, A., Singh, P., Kumar, A., Dixit, R., Singh, A., Praveen, S., Dalal, V., Yadav, M., Ghazi, I.A., Gaikwad, K., Sharma, T.R., Mohapatra, T., Singh, N.K., Szinay, D., de Jong, H., Peters, S., van Staveren, M., Datema, E., Fiers, M.W.E.J., van Ham, R.C.H.J., Lindhout, P., Philippot, M., Frasse, P., Regad, F., Zouine, M., Bouzayen, M., Asamizu, E., Sato, S., Fukuoka, H., Tabata, S., Shibata, D., Botella, M.A., Perez-Alonso, M., Fernandez-Pedrosa, V., Osorio, S., Mico, A., Granell, A., Zhang, Z., He, J., Huang, S., Du, Y., Qu, D., Liu, L., Liu, D., Wang, J., Ye, Z., Yang, W., Wang, G., Vezzi, A., Todesco, S., Valle, G., Falcone, G., Pietrella, M., Giuliano, G., Grandillo, S., Traini, A., D'Agostino, N., Chiusano, M.L., Ercolano, M., Barone, A., Frusciante, L., Schoof, H., Jöcker, A., Bruggmann, R., Spannagl, M., Mayer, K.X.F., Guigó, R., Camara, F., Rombauts, S., Fawcett, J.A., Van de Peer, Y., Knapp, S., Zamir, D. and Stiekema, W. 2009. A snapshot of the emerging tomato genome sequence. The Plant Genome 2: 78-92
  • Ponce-Valadez, M., Fellman, S.M., Giovannoni, J., Gan, S.S. and Watkins, C.B. 2009. Differential fruit gene expression in two strawberry cultivars in response to elevated CO2 during storage revealed by a heterologous fruit microarray approach. Postharvest Biol Tec 51: 131-140
  • Stack, S.M., Royer, S.M., Shearer, L.A., Chang, S.B., Giovannoni, J.J., Westfall, D.H., White, R.A. and Anderson, L.K. 2009. Role of fluorescence in situ hybridization in sequencing the tomato genome. Cytogenet Genome Res 124: 339-350
  • Vrebalov, J., Pan, I.L., Arroyo, A.J., McQuinn, R., Chung, M., Poole, M., Rose, J., Seymour, G., Grandillo, S., Giovannoni, J. and Irish, V.F. 2009. Fleshy fruit expansion and ripening are regulated by the Tomato SHATTERPROOF gene TAGL1. Plant Cell 21: 3041-3062
  • Akhtar, T.A., McQuinn, R.P., Naponelli, V., Gregory, J.F., Giovannoni, J.J. and Hanson, A.D. 2008. Tomato gamma-glutamyl hydrolases: Expression, characterization, and evidence for heterodimer formation. Plant Physiology 148: 775-785
  • Barry, C.S., McQuinn, R.P., Chung, M.Y., Besuden, A. and Giovannoni, J.J. 2008. Amino acid substitutions in homologs of the STAY-GREEN protein are responsible for the green-flesh and chlorophyll retainer mutations of tomato and pepper. Plant Physiology 147: 179-187
  • Cara, B. and Giovannoni, J.J. 2008. Molecular biology of ethylene during tomato fruit development and maturation. Plant Sci 175: 106-113
  • Datema, E., Mueller, L.A., Buels, R., Giovannoni, J.J., Visser, R.G.F., Stiekema, W.J. and van Ham, R.C.H.J. 2008. Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato. Bmc Plant Biol 8: 34
  • Portnoy, V., Benyamini, Y., Bar, E., Harel-Beja, R., Gepstein, S., Giovannoni, J.J., Schaffer, A.A., Burger, J., Tadmor, Y., Lewinsohn, E. and 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
  • Slocombe, S.P., Schauvinhold, I., McQuinn, R.P., Besser, K., Welsby, N.A., Harper, A., Aziz, N., Li, Y., Larson, T.R., Giovannoni, J., Dixon, R.A. and Broun, P. 2008. Transcriptomic and reverse genetic analyses of branched-chain fatty acid and acyl sugar production in Solanum pennellii and Nicotiana benthamiana. Plant Physiol 148: 1830-1846
  • Wang, S.H., Liu, J.K., Feng, Y.Y., Niu, X.L., Giovannoni, J. and Liu, Y.S. 2008. Altered plastid levels and potential for improved fruit nutrient content by downregulation of the tomato DDB1-interacting protein CUL4. Plant Journal 55: 89-103
  • Wang, Y., Diehl, A., Wu, F.N., Vrebalov, J., Giovannoni, J., Siepel, A. and Tanksley, S.D. 2008. Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. Genetics 180: 391-408
  • Barry, C., J. Giovannoni. 2007. Ethylene and Fruit Ripening. J. of Plant Growth Regulation 26: 143-159
  • Giovannoni, J., . 2007. A New Plant Gene in the Pathway to Vitamin C. PNAS USA 104: 9109-9110
  • Giovannoni, J., . 2007. Fruit Ripening Mutants Yield Insights Into Ripening Control. Current Opinion in Plant Biology 10: 283-289
  • Kelleher, C., R. Chiu, H. Shin, I. Bosdet, M. Krzywinski, C. Fjell, J. Wilkin, T. Yin, S. DiFazio, J. Ali, J. Asano, S. Chan, A. Cloutier, N. Girn, S. Leach, J. Giovannoni, J. Grimwood, G. Tuskan, C. Douglas. 2007. A Physical Map of the Highly Heterozygous Populus Genome: Integration With the Genome Sequence and Genetic Map and Analysis of Haplotype Variation. The Plant Journal 50: 1063-1078
  • Barry, C. S., J. J. Giovannoni. 2006. Ripening in the Tomato Green-ripe Mutant is Inhibited by Ectopic Expression of a Protein that Disrupts Ethylene Signaling. Proc Natl Acad USA 103(20): 7923-7928
  • Fei, Z., X. Tang, R. Alba, J. Giovannoni. 2006. Tomato Expression Database (TED): A Suite of Data Presentation and Analysis Tools. Nucleic Acids Research 34: D766
  • Barry, C., R. P. McQuinn, A. J. Thompson, G. B. Seymour, D. Grierson, J. J. Giovannoni. 2005. Ethylene Insensitivity Conferred by the Green-ripe (Gr) and Never-ripe 2 (Nr-2) Ripening Mutants of Tomato. Plant Physiology 138(1): 267-275
  • Giovannoni, J. J., S. El-Rakshy. 2005. Genetic Regulation of Tomato Fruit Ripening and Development and Implementation of Associated Genomics Tools. Acta Horticulturae 682: 63-72
  • Li, C., A. L. Schilmiller, G. Liu, G. I. Lee, S. Jayanty, C. Sageman, J. Vrebalov, J. J. Giovannoni, K. Yagi, Y. Kobayashi, G. A. Howe. 2005. Role of Beta-Oxidation in Jasmonate Biosynthesis and Systemic Wound Signaling in Tomato. Plant Cell 17(3): 971-986
  • Moore, S., P. Payton, M. Wright, S. Tanksley, J. Giovannoni. 2005. Utilization of Tomato Microarrays for Comparative Gene Expression Analysis in the Solanaceae. Journal of Experimental Botany 56(421): 2885-2895
  • Mueller, L. A., S. D. Tanksley, J. J. Giovannoni, J. Van Eck, S. Stack, D. Choi, B. D. Kim, M. Chen, Z. Cheng, C. Li, H. Ling, Y. Xue, G. Seymour, G. Bishop, G. Bryan, R. Sharma, J. Khurana, A. Tyagi, D. Chattopadhyay, N. K. Singh, W. Stiekema, P. Lindhout, T. Jesse, R. K. Lankhorst, M. Bouzayen, D. Shibata, S. Tabata, A. Granell, M. A. Botella, G. Giuliano, L. Frusciante, M. Causse, D. Zamir. 2005. The Tomato Sequencing Project, the First Cornerstone of the International Solanaceae Project (SOL). Comparative and Functional Genomics 6: 153-158
  • Adams-Phillips, L., C. Barry, P. Kannan, J. Leclercq, M. Bouzayen, J. Giovannoni. 2004. Evidence that 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
  • Adams-Phillips, L., C. Barry, J. Giovannoni. 2004. Signal transduction systems regulating fruit ripening. Trends in Plant Science 9: 331-338
  • Basset, G. J. C., E. P. Quinlivan, S. Ravanel, F. Rébeillé, B. P. Nichols, K. Shinozaki, M. Seki, L. C. Adams-Phillips, J. J. Giovannoni, J. F. Gregory III, A. D. Hanson. 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, USA 101: 1496-1501
  • Giovannoni, J., . 2004. Genetic Regulation of Fruit Development and Ripening. The Plant Cell 16: S170 -180
  • Liu, Y., S. Roof, Z. Ye, C. Barry, A. van Tuinen, J. Vrebalov, C. Bowler, J. Giovannoni. 2004. Manipulation of Light Signal Transduction as a Means of Modifying Fruit Nutritional Quality in Tomato. Proceedings of the National Academy of Sciences, USA 101(26): 9897-9902
  • Vrebalov, J., D. Ruezinsky, V. Padmanabhan, R. White, D. Medrano, R. Drake, W. Schuch, J. Giovannoni. 2002. A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. Science 296: 343-346
  • Wilkinson, J., M. Lanahan, H. Yen, J. Giovannoni, H. Klee. 1995. An Ethylene-inducible Component of Signal Transduction Encoded by Never-ripe. Science 270(5243): 1807-1809
How do fruits ripen?

feature released -2008

How do fruits ripen?Learning the genetic basis of fruit ripening could significantly impact the quality and availability of certain foods. This knowledge would be particularly useful in countries where food spoilage due to over-ripening is a cause of hunger. Jim Giovannoni’s laboratory at BTI is working to understand the process by focusing on the genes and regulatory networks that control fruit ripening in tomato – knowledge that will have applications in other plants such as pepper, peach, pineapple, banana, strawberry and melon. Because many fruits ripen in response to the release of the hormone ethylene, understanding the mechanism that controls the plant’s sensitivity to ethylene can lead to basic knowledge about the ripening process. In studying mutant tomato plants that produce only unripe tomatoes,Giovannoni’s team discovered an alteration in a gene called Gr, or Greenripe, that causes overproduction of a certain protein in the fruit that decreases the fruit’s sensitivity to ethylene. So, though the plants produce ethylene in normal amounts, the fruit does not respond to it and, therefore, fails to ripen. Being able to control the production of this protein,which would make the fruit under- or over-sensitive to ethylene, could lead to the ability to speed or delay the ripening process. Giovannoni further found that overproduction of the Gr protein throughout the plant has no effect on any part of the plant except the fruit. This discovery is important because it indicates there are constituents specific to the fruit involved in its response to ethylene. The next step in the research is to develop transgenic tomato plants in which the Gr gene has been“knocked out,” or disabled, so that the plants are no longer able to produce the Gr protein. This work will demonstrate whether or not normal Gr expression plays a significant role in ripening. Giovannoni predicts that these plants will be highly sensitive to ethylene and will, therefore, ripen early. The ability to control the ripening process by controlling the ethylene response could lead to fruit, such as strawberry, papaya and even tomato, that have a longer shelf life. Because ripening is directly related to fruit flavor, texture and nutrient content, these discoveries could lead to higher quality food as well.


Exploring the Genome.

feature released -2007

Exploring the Genome.Most scientific exploration is much less telegenic than planting a flag on the moon or tracking whales on the high seas. Molecular biology is no exception: its giant leaps usually appear as lines on gels or colored dots on microarrays. But when Jim Giovannoni, Joyce Van Eck, and their collaborators proposed an international endeavor to sequence the tomato genome, they drummed up support by promising countries a prize befitting the occasion: the chance to put their flag on one of tomato's 12 chromosomes.. This will be the first fruit or vegetable genome sequenced. The sequence will yield information not only about tomato and other members of the Solanaceae (nightshade) family, including potato, pepper, eggplant, but also other related species such as coffee and sunflower. But the potential agricultural benefits weren't enough to entice some nations to participate, so the U.S. team structured their proposal so that each country would be in charge of sequencing a discrete piece of the genome. “If these countries had each given a little money to the project, they wouldn't have gotten much credit,” Giovannoni explained. “This way, each of them can point to a chromosome and say, ‘we did that.’'” The U.S. team—made up of Giovannoni and Van Eck at BTI, two labs at Cornell, and one at Colorado State University—got funding late in 2004 to lay the foundation for the project. Soon afterward, labs and funding agencies in nine other countries each agreed to take on a chromosome. Tackling the project this way ruled out shotgun sequencing, in which the genome is cut into small pieces and sequenced, with the sequence information then pieced together into the complete genetic code. Instead, the U.S. team would have to cut the genome into larger DNA segments and find out which chromosomes those segments belonged to before they were sequenced. Fortunately, previous studies had shown that most tomato genes are clustered near the ends of chromosomes in areas called euchromatin islands. So the team made the project more manageable by concentrating on these islands, leaving out vast stretches of DNA with little useful genetic information. Giovannoni believes the information contained in the euchromatin will help his lab learn more about fruit ripening and nutritional quality in tomato. His lab's role in the sequencing is to isolate the DNA and break it up into large chunks. They then paste the chunks into vectors for US collaborators and labs overseas to use. Van Eck manages the project, communicating with researchers around the world, coordinating shipments of DNA, and writing reports. She also edits the SOL Newsletter, which keeps interested researchers apprised of sequencing progress and other information of interest to the Solanaceae community. And she runs the outreach component of the sequencing project, including a summer bioinformatics internship that blends biology and computer science. She hopes the completed sequence will yield information helpful to her work on antioxidant accumulation in potatoes. Giovannoni and Van Eck’s U.S. collaborators determine where and on which chromosome each section of DNA belongs, and later process the sequence information from abroad and make it available on a Web site. The team recently submitted a proposal to the National Science Foundation to sequence the three remaining tomato chromosomes, and if all goes well, the tomato genome should be unlocked sometime in 2008. In addition to helping scientists understand economically important nightshades, the sequence should yield clues to the puzzle of how such genetically similar plants evolved very diverse traits.


Toward a Better Tomato.

feature released -2007

Toward a Better Tomato.Most shoppers in America have access to a wide selection of fresh fruits and vegetables year-round, but these rarely measure up to home grown varieties. “In general, things are harvested very prematurely so that they have the shelf life and the firmness to survive shipping,” Giovannoni explains. “What's always lost in that tradeoff is taste, appearance, aroma—things that are associated with quality.” To make store-bought fruit more palatable, agricultural scientists need a better understanding of how fruits “decide” when and how much to ripen. Giovannoni’s lab studies tomatoes and other plants to find the genes responsible for that decision. In 2004 they discovered several such genes, including two that may play a role in a broad range of species. The lab is now working to find similar genes that cooperate with these genes to regulate ripening and associated quality characteristics. Giovannoni’s group also participates in a broader effort, with others at BTI and in nine foreign countries, to map and sequence the tomato genome. The completed genome will represent a giant step toward unlocking tomato's inner workings, just as the Human Genome Project did for people. In a related project, the lab uses microarrays and computer analysis to learn how groups of genes switch on and off at the right time at each stage of ripening. This eagle's eye view of the dynamics of development enables them to compare the process across different species, and to pick out genes that may control the timing of ripening.