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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic and Genomic Basis of Vegetable and Fruit Biology, Quality and Nutrient Content

Location: Plant, Soil and Nutrition Research

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

The tomato genome as a cornerstone for gene discovery - (Book / chapter)

The tomato genome - (Book / chapter)

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.

Selenium promotes sulfur accumulation and plant growth in wheat (Triticum aestivum) - (Peer reviewed journal)
Boldrin, P.F., Figueiredo, M., Yang, Y., Luo, H., Giri, S., Hart, J.J., Faquin, V., Guilherme, L., Thannhauser, T.W., Li, L. 2016. Selenium promotes sulfur accumulation and plant growth in wheat (Triticum aestivum). Physiologia Plantarum. 158:80-91.

Plastids and carotenoid accumulation - (Book / chapter)
Li, L., Yuan, H., Zeng, Y., Xu, O. 2016. Plastids and carotenoid accumulation. In: Carotenoids in Nature - Biosynthesis, Regulation and function" (edited by Claudia Stange), Subcellular Biochemistry. 79(10):273-293.

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.

Characterization of a citrus R2R3-MYB transcription factor that regulates the flavonol and hydroxycinnamic acid biosynthesis - (Peer reviewed journal)
Liu, C., Long, J., Zhu, K., Liu, L., Yang, W., Zhang, H., Li, L., Xu, Q., Deng, X. 2016. Characterization of a citrus R2R3-MYB transcription factor that regulates the flavonol and hydroxycinnamic acid biosynthesis. Scientific Reports. 6:25352.

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.

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.

Plastid ribosomal protein S5 plays a critical role in photosynthesis, plant development, and cold stress tolerance in arabidopsis - (Peer reviewed journal)
Zhang, J., Yuan, H., Yang, Y., Fish, T., Lyi, S., Thannhauser, T.W., Zhang, L., Li, L. 2016. Plastid ribosomal protein S5 plays a critical role in photosynthesis, plant development, and cold stress tolerance in arabidopsis. Journal of Experimental Botany. doi: 10.1093/jxb/erw106.

A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with melon orange allelic variation and fruit B-carotene accumulation - (Peer reviewed journal)
Chayut, N., Yuan, H., Ohali, S., Meir, A., Yeselson, Y., Portnoy, V., Fei, Z., Lewinsohn, E., Katzir, N., Schaffer, A., Gepstein, S., Burger, J., Li, L., Tadmor, Y. 2015. A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with melon orange allelic variation and fruit B-carotene accumulation. Biomed Central (BMC) Plant Biology. 15:274.

Improving selenium nutritional value of major crops - (Proceedings)
Li, L., Avila, F., Souza, G., Boldrin, P., Figueiredo, M., Faquin, V., Andrade, M., Guilherme, L., Ramos, S. 2015. Improving selenium nutritional value of major crops. In: 4th International Conference on Selenium in the Environment and Human Health, October 18-21, 2015, Sao Paulo, Brazil. p. 23-24.

Effect of selenium treatment on biomass production and mineral content in common bean varieties - (Proceedings)
Figueiredo, M., Oliveira, D., Andrade, M., Guilherme, L., Li, L. 2015. Effect of selenium treatment on biomass production and mineral content in common bean varieties. In: 4th International Conference on Selenium in the Environment and Human Health, October 18-21, 2015, Sao Paulo, Brazil. p.23-24.

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.

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 single amino acid substitution in an ORANGE protein promotes carotenoid overaccumulation in arabidopsis - (Peer reviewed journal)
Yuan, H., Owsiang, K., Sheeja, T., Zhou, X., Rodriguez, C., Li, Y., Welsch, R., Chayut, N., Yang, Y., Thannhauser, T.W., Pathasarathy, M.V., Xu, Q., Deng, X., Fei, Z., Schaffer, A., Katzir, N., Burger, J., Tadmor, Y., Li, L. 2014. A single amino acid substitution in an ORANGE protein promotes carotenoid overaccumulation in arabidopsis. Plant Physiology. 169(1):421-431.

Carotenoid metabolism and regulation in horticultural crops - (Review article)
Yuan, H., Zhang, J., Nageswaran, D., Li, L. 2015. Carotenoid metabolism and regulation in horticultural crops. Horticulture Research. 8:68-82.

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.

A golden SNP in CmOr governs fruit flesh color of melon (cucumis melo) - (Peer reviewed journal)
Tzuri, G., Zhou, X., Chayut, N., Yuan, H., Portnoy, V., Meir, A., Saar, U., Baumkoler, F., Mazoureck, M., Lewinsohn, E., Fei, Z., Schaffer, A., Li, L., Burger, J., Katzir, N., Tadmor, Y. 2015. A golden SNP in CmOr governs fruit flesh color of melon (cucumis melo). Plant Journal. 82:267-279.

Molecular characterization and transcriptome analysis of orange head Chinese cabbage (brassica rapa L. ssp.pekinensis) - (Peer reviewed journal)
Zhang, J., Yuan, H., Fei, Z., Pogson, B.J., Li, L. 2015. Molecular characterization and transcriptome analysis of orange head Chinese cabbage (brassica rapa L. ssp.pekinensis). Planta. 241:1381-1394.

Arabidopsis OR proteins are the major post-transcriptional regulators of phytoene synthase in mediating carotenoid biosynthesis - (Peer reviewed journal)
Zhou, X., Welsch, R., Yang, Y., Riediger, M., Alvarez, D., Yuan, H., Fish, T., Liu, J., Thannhauser, T.W., Li, L. 2015. Arabidopsis OR proteins are the major post-transcriptional regulators of phytoene synthase in mediating carotenoid biosynthesis. Proceedings of the National Academy of Sciences. 112:3558-3563.

Development of carotenoid-enriched vegetables with increased nutritional quality and visual appearance - (Proceedings)
Li, L. 2015. Development of carotenoid-enriched vegetables with increased nutritional quality and visual appearance. p. 23-24.

Carotenoid metabolism in plants - (Review article)
Nazia, N., Li, L., Lu, S., Khin, N., Pogson, B.J. 2015. Carotenoid metabolism in plants. Molecular Plant. 6:68-82.

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.

A brief genomic history of tomato breeding Reprint Icon - (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 Reprint Icon - (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.

Regulatory control of carotenoid accumulation in winter squash during storage - (Peer reviewed journal)
Zhang, M., Zhang, M., Mazourek, M., Tadmor, Y., Li, L. 2014. Regulatory control of carotenoid accumulation in winter squash during storage. Planta. 240:1063-1074.

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.

Impact of selenium supply on se-methylselenocysteine and glucosinolates accumulation in selenium-biofortified brassica sprouts - (Peer reviewed journal)
Avila, F., Yang, Y., Faquin, V., Ramos, S., Guilherme, L., Thannhauser, T.W., Li, L. 2014. Impact of selenium supply on se-methylselenocysteine and glucosinolates accumulation in selenium-biofortified brassica sprouts. Food Chemistry. 165:578-586.

Approaches for vegetable and fruit quality trait improvement Reprint Icon - (Book / chapter)
Li, L., Tadmor, Y., Qiang, X. 2014. Approaches for vegetable and fruit quality trait improvement. In: Ricroch, A., Chopra, S., Fleischer, S., editors. Plant Biotechnology - Experience and Future Prospects. Switzerland: Springer International Publishing. 18:227-243.

The PH gene determines fruit acidity and contributes to the evolution of sweet melons Reprint Icon - (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.

Genotypic variation of zinc and selenium content in grains of Brazilian wheat lines - (Peer reviewed journal)
Souza, G., Hart, J., Carvalho, J., Rutzke, M., Albrecht, J., Guilherme, L., Kochian, L.V., Li, L. 2014. Genotypic variation of zinc and selenium content in grains of Brazilian wheat lines. Plant Science. 224:27-35.

Conserved changes in dynamics of metabolic processes during fruit development and ripening across species Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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.

A comparative study of lectin affinity based plant n-glycoproteome profiling using tomato fruit as a model - (Peer reviewed journal)
Ruiz-May, E., Hucko, S., Howe, K.J., Zhang, S., Sherwood, R.W., Thannhauser, T.W., Rose, J.K. 2014. A comparative study of lectin affinity based plant n-glycoproteome profiling using tomato fruit as a model. Proteomes. 13:566-579.

Chromoplast biogenesis and carotenoid accumulation - (Review article)
Li, L., Yuan, H. 2013. Chromoplast biogenesis and carotenoid accumulation. Archives Of Biochemistry and Biophysics. 539:102-109.

Fine mapping and identification of candidate Bo-or gene controlling orange head of Chinese cabbage (Brassica rapa L. ssp. Pekinensis) - (Peer reviewed journal)
Zhang, J., Li, H., Zhang, M., Hui, M., Wang, Q., Li, L., Zhang, L. 2013. Fine mapping and identification of candidate Bo-or gene controlling orange head of Chinese cabbage (Brassica rapa L. ssp. Pekinensis). Molecular Breeding. 32:799-805.

Molecular and genetic regulation of fruit ripening Reprint Icon - (Review article)
Gapper, N., Mcquinn, R., Giovannoni, J.J. 2013. Molecular and genetic regulation of fruit ripening. Plant Molecular Biology. 82:575-591.

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.

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.

A workflow for large-scale empirical identification of cell wall N-linked glycoproteins of tomato (Solanum lycopersicum) fruit by tandem mass spectrometry - (Peer reviewed journal)
Thannhauser, T.W., Shen, M., Sherwood, R., Howe, K.J., Fish, T., Yang, Y., Chen, W., Zhang, S. 2013. A workflow for large-scale empirical identification of cell wall N-linked glycoproteins of tomato (Solanum lycopersicum) fruit by tandem mass spectrometry. Electrophoresis. DOI: 10.1002/elps.201200656.

Last Modified: 2/23/2016
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