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United States Department of Agriculture

Agricultural Research Service

Research Project: GENOMICS APPROACHES FOR IMPROVING NUTRITIONAL QUALITY OF FOOD CROP SPECIES Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

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.
The purple cauliflower arises from activation of a MYB transcription factor - (Peer Reviewed Journal)
Chiu, L., Zhou, X., Burke, S., Wu, X., Prior, R.L., Li, L. 2010. The purple cauliflower arises from activation of a MYB transcription factor. Plant Physiology. 154:1470-1480.
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.
Genomics of fruit ripening and related nutritional metabolites - (Proceedings)
Giovannoni, J.J., Chung, M., Fox, E.A. 2012. Genomics of fruit ripening and related nutritional metabolites. Acta Horticulture Proceedings. 884:41-50.
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.
Think outside of the box: selenium volatilization altered by a broccoli gene in the ubiquinone biosynthetic pathway - (Peer Reviewed Journal)
Zhou, X., Li, L. 2010. Think outside of the box: selenium volatilization altered by a broccoli gene in the ubiquinone biosynthetic pathway. Plant Signaling and Behavior. 5:74-75.
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.
Eukaryotic release factor 1-2 affects Arabidopsis responses to glucose and phytohormones during germination and early seedling development - (Peer Reviewed Journal)
Xiangjun, Z., Cooke, P.H., Li, L. 2009. Eukaryotic release factor 1-2 affects Arabidopsis responses to glucose and phytohormones during germination and early seedling development. Journal of Experimental Botany. 61:357-367.
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.
Transcriptional regulation of anthocyanin biosynthesis in red cabbage - (Peer Reviewed Journal)
Yuan, Y., Chiu, L., Li, L. 2009. Transcriptional regulation of anthocyanin biosynthesis in red cabbage. Planta. 230:1141-1153.
Involvement of a broccoli COQ5 methyltransferase in the production of volatile selenium compounds - (Peer Reviewed Journal)
Li, L., Zhou, X., Yuan, Y., Yang, Y., Rutzke, M., Thannhauser, T.W., Kochian, L.V. 2009. Involvement of a broccoli COQ5 methyltransferase in the production of volatile selenium compounds. Plant Physiology. 151:528-540.
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.
A broccoli COQ5 methyltransferase involved in ubiquinone biosynthesis mediates selenium volatilization - (Abstract Only)
Li, L., Zhou, X., Yang, Y., Thannhauser, T.W., Kochian, L.V. 2009. A broccoli COQ5 methyltransferase involved in ubiquinone biosynthesis mediates selenium volatilization. Meeting Abstract.
Modulation of carotenoid accumulation in transgenic potato by inducing chromoplast formation with enhanced sink strength - (Book / Chapter)
Van Eck, J., Zhou, X., Lu, S., Li, L. 2010. Modulation of carotenoid accumulation in transgenic potato by inducing chromoplast formation with enhanced sink strength. In: Fett-Neto, A., editor. Metabolic Engineering of Plant Secondary Pathways with Methods in Molecular Biology Book Series. Chapter 6. New York, NY: Springer. p. 77-93.
Eukaryotic release factor 1-2 is involved in GA signaling pathway and regulates cell elongation in petioles - (Abstract Only)
Zhou, X., Cooke, P.H., Li, L. 2009. Eukaryotic release factor 1-2 is involved in GA signaling pathway and regulates cell elongation in petioles. Meeting Abstract.
Regulation of anthocyanin biosynthesis in red cabbages - (Abstract Only)
Yuan, Y., Chiu, L., Li, L. 2009. Regulation of anthocyanin biosynthesis in red cabbages [abstract]. Plant Biology 2009 Meeting.
Transcriptional activation of a MYB gene controls the tissue-specific anthocyanin accumulation in a purple cauliflower mutant - (Abstract Only)
Chiu, L., Burke, S., Li, L. 2009. Transcriptional activation of a MYB gene controls the tissue-specific anthocyanin accumulation in a purple cauliflower mutant [abstract]. Plant Biology 2009 Meeting.
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.
Salt Induced and Salt Suppressed Proteins in Tomato Leaves - (Peer Reviewed Journal)
Suping, Z., Zhou, S., Fish, T., Thannhauser, T.W. 2009. Salt Induced and Salt Suppressed Proteins in Tomato Leaves. Journal of the American Society for Horticultural Science. 134(2):289-294.
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.
An evaluation of the basis and consequences of a stay-green mutation in the navel negra (nan) citrus mutant using transcriptomic and proteomic profiling and metabolite analysis - (Peer Reviewed Journal)
Alos, E., Roca, M., Iglesias, D., Minguez-Mosquera, M., Borges-Damasceno, C., Thannhauser, T.W., Campbell-Rose, J., Talon, M., Cercos, M. 2008. An evaluation of the basis and consequences of a stay-green mutation in the navel negra (nan) citrus mutant using transcriptomic and proteomic profiling and metabolite analysis. Journal of Plant Physiology. 147:1300-1315.
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.
Carotenoid Metabolism: the Biosynthesis, Regulation, and Beyond - (Review Article)
Li, L., Lu, S. 2008. Carotenoid Metabolism: the Biosynthesis, Regulation, and Beyond. Journal of Integrative Plant Biology. 50:778-785.
Use of the cauliflower OR gene for improving crop nutritional quality - (Book / Chapter)
Zhou, X., Van Eck, J., Li, L. 2008. Use of the cauliflower OR gene for improving crop nutritional quality. Biotechnology Annual Review. 14(6):171-190.
Characterization of Extracellular Proteins in Tomato Fruit using Lectin Affinity Chromatography and LC-MALDI-MS/MS analysis - (Abstract Only)
Hucko, S., Catala, C., Howe, K.J., Rose, J., Thannhauser, T.W. 2008. Characterization of Extracellular Proteins in Tomato Fruit using Lectin Affinity Chromatography and LC-MALDI-MS/MS analysis. Journal of Biomolecular Techniques. Vol. 19:57
Quantitative trait loci analysis of endosperm color and carotenoid content in sorghum grain - (Peer Reviewed Journal)
Salas Fernandez, M.G., Hamblin, M., Li, L., Rooney, W.L., Tuinstra, M.R., Kresovich, S. 2008. Quantitative trait loci analysis of endosperm color and carotenoid content in sorghum grain. Crop Science. 48:1732-1743.
Enhancing Plant Carotenoids via Manipulation of Sink Strength - (Popular Publication)
Zhou, X., Li, L. 2008. Enhancing Plant Carotenoids via Manipulation of Sink Strength. Information Systems for Biotechnology News Report. February 2008:5-7
Phytoene desaturase is present in a large protein complex in the plastid membrane - (Peer Reviewed Journal)
Lopez, A., Yang, Y., Thannhauser, T.W., Li, L. 2008. Phytoene desaturase is present in a large protein complex in the plastid membrane. Physiologia Plantarum. 133:190-198.
Effect of the cauliflower Or transgene on carotenoid accumulation and chromoplast formation in transgenic potato tubers - (Peer Reviewed Journal)
Lopez, A., Van Eck, J., Conlin, B., Paolillo, D., O'Neill, J., Li, L. 2008. Effect of the cauliflower Or transgene on carotenoid accumulation and chromoplast formation in transgenic potato tubers. Journal of Experimental Botany. 59:213-223.
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.
Enhanced carotenoid accumulation as a result of alteration of metabolic sinks in transgenic plants - (Abstract Only)
Lopez, A.B., Van Eck, J., Conlin, B.J., Paolillo, D., Li, L. Enchanced carotenoid accumulation as a result of alteration of metabolic sinks in transgenic plants. American Society of Plant Biologists Annual Meeting. 2007. M23004, p127.
Metabolic engineering of carotenoid accumulation by creating a metabolic sink - (Peer Reviewed Journal)
Li, L., Van Eck, J. 2007. Metabolic engineering of carotenoid accumulation by creating a metabolic sink. Transgenic Research 16:581-585.
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.
On slide chemical modification as a means to improve confidence in protein identifications made by peptide mass finger prints - (Abstract Only)
Yang, X., Thannhauser, T.W. 2007. On slide chemical modification as a means to improve confidence in protein identifications made by peptide mass finger prints [abstract]. Journal of Biomolecular Techniques. 18:67.
Biochemical and Molecular Characterization of the Homocysteine S-Methyltransferase from Broccoli (Brassica Oleracea Var. Italica) - (Peer Reviewed Journal)
Li, L., Lyi, S.M., Zhou, X., Kochian, L.V. 2007. Biochemical and molecular characterization of the homocysteine s-methyltransferase from broccoli (brassica oleracea var. italica). Phytochemistry. 68:1112-1119.
Development of an integrated approach for evaluation of 2-D gel image analysis: Impact of multiple proteins in single spots on comparative proteomics in conventional 2-D gel/MALDI workflow - (Peer Reviewed Journal)
Yang, Y., Thannhauser, T.W., Li, L., Zhang, S. 2007. Development of an integrated approach for evaluation of 2-D gel image analysis: Impact of multiple proteins in single spots on comparative proteomics in conventional 2-D gel/MALDI workflow. Electrophoresis. 28:2080-2094.
The Cauliflower Or Gene Encodes a Dnaj Cysteine-Rich Domain-Containing Protein That Mediates High-Levels of B-Carotene Accumulation - (Peer Reviewed Journal)
Li, L., Lu, S., Van Eck, J., O'Halloran, D., Zhou, X., Lopez, A.B., Cosman, K., Conlin, B., Paolillo, D., Garvin, D.F., Vrebalov, J., Kochian, L.V., Kupper, H., Earle, E., Cao, J. 2006. The cauliflower or gene encodes a cysteine-rich zinc finger domain-containing protein that induces high-level of B-carotene accumulation. The Plant Cell. 18:3594-3605.
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.
B-Carotene Accumulation Induced by the Cauliflower Or Gene Is Not Due to An Increased Capacity of Biosynthesis - (Peer Reviewed Journal)
Li, L., Lu, S., Cosman, K., Earle, E., Garvin, D.F., O'Neill, J. 2006. B-carotene accumulation induced by the cauliflower or gene is not due to an increased capacity of biosynthesis. Phytochemistry. 67:1177-1184.
Last Modified: 10/21/2014
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