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United States Department of Agriculture

Agricultural Research Service

Research Project: GENOMICS APPROACHES FOR IMPROVING NUTRITIONAL QUALITY OF FOOD CROP SPECIES

Location: Plant, Soil and Nutrition Research

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

The tomato UV-damaged DNA binding protein 1 (DDB1) plays a role in organ size control via an epigenetic manner     Reprint Icon - (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.
Assessing the anticancer compounds Se-methylselenocysteine and glucosinolates in Se-biofortified broccoli (brassica oleracea L. var. italica) sprouts and florets - (Peer Reviewed Journal)
Avila, F., Faquin, V., Yang, Y., Ramos, S., Guilherme, L., Thannhauser, T.W., Li, L. 2013. Assessing the anticancer compounds Se-methylselenocysteine and glucosinolates in Se-biofortified broccoli (brassica oleracea L. var. italica) sprouts and florets. Journal of Agricultural and Food Chemistry. 61:6216-6223.
Evaluation of germplasm effect on Fe, Zn and Se content in wheat seedlings - (Peer Reviewed Journal)
Souza, G., Carvalho, J., Rutzke, M., Albrecht, J., Guilherme, L., Li, L. 2013. Evaluation of germplasm effect on Fe, Zn and Se content in wheat seedlings. Plant Science. 210:206-213.
Proteomic analysis of chromoplasts from six crop species reveals insights into chromoplast function and development     Reprint Icon - (Peer Reviewed Journal)
Wang, Y., Yang, Y., Fei, Z., Yuan, H., Fish, T., Thannhauser, T.W., Mazourek, M., Kochian, L.V., Wang, X., Li, L. 2013. Proteomic analysis of chromoplasts from six crop species reveals insights into chromoplast function and development. Journal of Experimental Botany. 64(4):949-961.
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.
Genomics and breeding in food crops     Reprint Icon - (Book / Chapter)
Brown, A., Paterson, A., Li, L. 2012. Genomics and breeding in food crops. In: Benkeblia, N., editor. OMICs technologies: tools for food science. Boca Raton, FL: CRC Press. p. 141-162.
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.
Characterization of the regulatory network of BoMYB2 in controlling anthocyanin biosynthesis in purple cauliflower - (Peer Reviewed Journal)
Chiu, L., Li, L. 2012. Characterization of the regulatory network of BoMYB2 in controlling anthocyanin biosynthesis in purple cauliflower. Planta. 236:1153-1164.
Altered chloroplast development and delayed fruit ripening caused by mutations in a zinc metalloprotease at the lutescent 2 locus of tomato     Reprint Icon - (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.
Transcriptome analysis of ectopic chloroplast development in green curd cauliflower (Brassica oleracea L. var. botrytis) - (Peer Reviewed Journal)
Zhou, X., Fei, Z., Thannhauser, T.W., Li, L. 2012. Transcriptome analysis of ectopic chloroplast development in green curd cauliflower (Brassica oleracea L. var. botrytis). Biomed Central (BMC) Plant Biology. 11:169.
The Or gene enhances carotenoid accumulation and stability during post-harvest storage of potato tubers - (Peer Reviewed Journal)
Li, L., Yang, Y., Xu, Q., Owsiany, K., Welsch, R., Chitchumroonchokchai, C., Lu, S., Van Eck, J., Deng, X., Failla, M., Thannhauser, T.W. 2012. The Or gene enhances carotenoid accumulation and stability during post-harvest storage of potato tubers. Molecular Plant. 5:339-352.
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.
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-110410-132507
High-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.
Evaluation of genotypic variation of broccoli (brassica oleracea var. italic) in response to selenium treatment - (Peer Reviewed Journal)
Ramos, S., Yuan, Y., Faquin, V., Guilherme, L., Li, L. 2011. Evaluation of genotypic variation of broccoli (brassica oleracea var. italic) in response to selenium treatment. Journal of Agricultural and Food Chemistry. 59(8):3657-65.
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.
Selenium accumulation in lettuce germplasm - (Peer Reviewed Journal)
Ramos, S., Rutzke, M., Hayes, R.J., Faquin, V., Guilherme, L.R., Li, L. 2010. Selenium accumulation in lettuce germplasm. Planta. 233:649-660.
The cauliflower Orange gene enhances petiole elongation by suppressing expression of eukaryotic release factor 1 - (Peer Reviewed Journal)
Zhou, X., Lu, S., Ling, H., Li, L. 2011. The cauliflower Orange gene enhances petiole elongation by suppressing expression of eukaryotic release factor 1. New Phytologist. 190:89-100.
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.
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.
Last Modified: 8/22/2014
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