Skip to main content
ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Research Project #434706

Research Project: Genetics, Epigenetics, Genomics, and Biotechnology for Fruit and Vegetable Quality

Location: Plant, Soil and Nutrition Research

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

Biochemical basis of differential selenium tolerance in arugula (Eruca sativa Mill.) and lettuce (Lactuca sativa L.) Reprint Icon - (Peer Reviewed Journal)
Santiago, F., Silva, M., Cardoso, A., Duan, Y., Guilherme, L., Liu, J., Li, L. 2020. Biochemical basis of differential selenium tolerance in arugula (Eruca sativa Mill.) and lettuce (Lactuca sativa L.). Plant Physiology and Biochemistry. 157:328-338. https://doi.org/10.1016/j.plaphy.2020.11.001.

Ectopic expression of miRNA172 in tomato (Solanum lycopersicum) reveals novel function in fruit development through regulation of an AP2 transcription factor Reprint Icon - (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.

Relationships between genome methylation, levels of noncoding RNAs, mRNAs and metabolites in ripening tomato fruit Reprint Icon - (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.

ORHis, a natural variant of OR, specifically interacts with plastid division factor ARC3 to regulate chromoplast number and carotenoid accumulation Reprint Icon - (Peer Reviewed Journal)
Sun, T., Yuan, H., Chen, C., Kadirjan-Kalbach, D., Mazourek, M., Osteryoung, K., Li, L. 2020. ORHis, a natural variant of OR, specifically interacts with plastid division factor ARC3 to regulate chromoplast number and carotenoid accumulation. Molecular Plant. https://doi.org/10.1016/j.molp.2020.03.007.

Editorial: Illuminating carotenoid synthesis and plastid transition in plants Reprint Icon - (Research Notes)
Stange, C., Rodriguez-Concepcion, M., Li, L. 2020. Editorial: Illuminating carotenoid synthesis and plastid transition in plants. Frontiers in Plant Science. 11:301. https://doi.org/10.3389/fpls.2020.00301.

Comparative proteomic and ultrastructural analysis shed light on fruit pigmentation distinct in two Lycium species Reprint Icon - (Peer Reviewed Journal)
Zeng, S., Huang, S., Yang, T., Ai, P., Li, L., Wang, Y. 2020. Comparative proteomic and ultrastructural analysis shed light on fruit pigmentation distinct in two Lycium species. Industrial Crops and Products. 147. https://doi.org/10.1016/j.indcrop.2020.112267.

Manipulation of ZDS in tomato exposes carotenoid- and ABA-specific effects on fruit development and ripening Reprint Icon - (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 KingdomNew York, NY: University Press. p.137-171.

Manipulation of ß-carotene levels in tomato fruits results in increased ABA content and extended shelf life Reprint Icon - (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.

Plant synthetic metabolic engineering for enhancing crop nutritional quality Reprint Icon - (Review Article)
Zhu, Q., Wang, B., Tan, J., Liu, T., Li, L., Liu, Y. 2020. Plant synthetic metabolic engineering for enhancing crop nutritional quality. Plant Communications. 1:100017. https://doi.org/10.1016/j.xplc.2019.100017.

Metabolomics should be deployed in identification and characterization of gene-edited crops Reprint Icon - (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.

Characterization of cauliflower OR mutant variants Reprint Icon - (Peer Reviewed Journal)
Welsch, R., Zhou, X., Koschmieder, J., Yuan, H., Riedinger, M., Sun, T., Li, L. 2020. Characterization of cauliflower OR mutant variants. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2019.01716.

Characterizing the involvement of FaMADS9 in the regulation of strawberry fruit receptacle development Reprint Icon - (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.

Pathways for carotenoid biosynthesis, degradation, and storage Reprint Icon - (Book / Chapter)
Sun, T., Tadmor, Y., Li, L. 2019. Pathways for carotenoid biosynthesis, degradation, and storage. In: Rodriguez-Concepcion M., Welsch, R. (eds). Plant and Food Carotenoids. Methods in Molecular Biology. Vol 2083. New York, NY:Humana. p. 3-23. https://doi.org/10.1007/978-1-4939-9952-1_1.

Toward the 'golden' era: the status in uncovering the regulatory control of carotenoid accumulation in plants Reprint Icon - (Review Article)
Sun, T., Li, L. 2019. Toward the 'golden' era: the status in uncovering the regulatory control of carotenoid accumulation in plants. Plant Science. 290:110343. https://doi.org/10.1016/j.plantsci.2019.110331.

Genetic mapping of green curd gene Gr in cauliflower Reprint Icon - (Peer Reviewed Journal)
Tan, H., Wang, X., Chayut, N., Li, H., Tadmor, Y., Mazourek, M., Li, L. 2019. Genetic mapping of green curd gene Gr in cauliflower. Journal of Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-019-03466-2.

Effects of selenium treatment on sulfur nutrition and metabolism - (Book / Chapter)
Santiago, F., Tian, M., Boldrin, P., Li, L. 2019. Effects of selenium treatment on sulfur nutrition and metabolism. In: Selenium research for environment and human health: Perspectives, Technologies, and Advancements. 1st Edition. CRC Press. p. 47-48.

The role of the carotenogenic metabolic flux in carotenoid accumulation and chromoplast differentiation: lessons from the melon fruit Reprint Icon - (Review Article)
Feder, A., Chayut, N., Freiman, Z., Tzuri, G., Meir, A., Gal-On, A., Shnaider, Y., Wolf, D., Katzir, N., Schaffer, A., Burger, J., Li, L., Tadmor, Y. 2020. The role of the carotenogenic metabolic flux in carotenoid accumulation and chromoplast differentiation: lessons from the melon fruit. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2019.01250.

ORANGE represses chloroplast biogenesis in etiolated Arabidopsis Cotyledons via interacting with TCP14 - (Peer Reviewed Journal)
Sun, T., Zhou, F., Huang, X., Chen, W., Kong, M., Zhou, C., Zhuang, Z., Li, L., Lu, S. 2019. ORANGE represses chloroplast biogenesis in etiolated Arabidopsis Cotyledons via interacting with TCP14. The Plant Cell. 31:2996-3014.

A neighboring aromatic-aromatic amino acid combination governs activity divergence of tomato PSY1 and PSY2 Reprint Icon - (Peer Reviewed Journal)
Cao, H., Luo, H., Yuan, H., Eissa, M.A., Thannhauser, T.W., Welsch, R., Hao, Y., Cheng, L., Li, L. 2020. A neighboring aromatic-aromatic amino acid combination governs activity divergence of tomato PSY1 and PSY2. Plant Physiology. 180(4):1988-2003. https://doi.org/10.1104/pp.19.00384.

Genetic and metabolic effects of ripening mutations and vine detachment on tomato fruit quality Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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.

MaMADS2 repression in banana fruits modifies hormone synthesis and singaling pathways prior to climacteric stage Reprint Icon - (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.

The tomato HIGHPIGMENT1/DAMAGED DNA BINDING PROTEIN1 gene contributes to regulation of fruit ripening Reprint Icon - (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 Reprint Icon - (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/molecules23102436

Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitive Trait Loci Detection Reprint Icon - (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 Reprint Icon - (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-z

Effects of selenium supplementation on glucosinolate biosynthesis in broccoli - (Peer Reviewed Journal)
Tian, M., Yang, Y., Avila, F., Fish, T., Yuan, H., Hui, M., Pan, S., Thannhauser, T.W., Li, L. 2018. Effects of selenium supplementation on glucosinolate biosynthesis in broccoli. Journal of Agricultural and Food Chemistry. 66:8036-8044.

Natural genetic variation for expression of a SWEET transporter among wild species of Solanum lycopersicum (tomato) determines the hexose composition of ripening tomato fruit Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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.13838

Tomato multiomics reveals consequences of crop domestication and improvement Reprint Icon - (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.2017.12.036

High-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.

Interference with Clp protease impairs carotenoid accumulation during tomato fruit ripening - (Peer Reviewed Journal)
D'Andrea, L., Simon-Moya, M., Liorente, B., Llamas, E., Marro, M., Loza-Alvarez, P., Li, L., Rodriguez-Concepcion, M. 2018. Interference with Clp protease impairs carotenoid accumulation during tomato fruit ripening. Journal of Experimental Botany. 69:1557-1568.

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 Reprint Icon - (Review Article)
Giovannoni, J.J. 2017. Ripening activator turned repressor. Nature Plants. 3:920-921. doi.org/10.1038/s41477-017-0062-0

Differential metabolism of 1-phenylalaninein the formation of aromatic volatiles in melon (Cumis melo) fruit Reprint Icon - (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.

Genetic diversity within African tomato using next generation sequencing Reprint Icon - (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.