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

Location: Plant, Soil and Nutrition Research

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

Glutathione is involved in selenium detoxification and suppresses the selenate-induced SULTR1:1 gene expression in plants - (Peer Reviewed Journal)
Cardoso, A., Namaorato, F., Guilherme, L., Silva, M., Liu, J., Li, L. 2023. Glutathione is involved in selenium detoxification and suppresses the selenate-induced SULTR1:1 gene expression in plants. Environmental and Experimental Botany. http://dx.doi.org/10.2139/ssrn.4427870.

Carotenoid sequestration protein fibrillin participates in CmOr-regulated B-carotene accumulation in melon - (Peer Reviewed Journal)
Zhou, X., Sun, T., Owens, L., Yang, Y., Fish, T., Liu, A., Wrightstone, E., Yuan, H., Chayut, N., Burger, J., Tadmor, Y., Thannhauser, T.W., Guo, W., Cheng, L., Li, L. 2023. Carotenoid sequestration protein fibrillin participates in CmOr-regulated B-carotene accumulation in melon. Plant Physiology. 193:643-660. https://doi.org/10.1093/plphys/kiad312.

A chromosome-scale genome assembly of Artemisia argyi reveals unbiased subgenome evolution and key contributions of gene duplication to volatile terpenoid diversity - (Peer Reviewed Journal)

Iron counteracts zinc-induced toxicity in soybeans - (Peer Reviewed Journal)
Oliveira, N., Namorato, F., Rao, S., Cardoso, A., Renendeluiz, P., Guiherme, L., Liu, J., Li, L. 2023. Iron counteracts zinc-induced toxicity in soybeans. Plant Physiology and Biochemistry. 194:335-344. https://doi.org/10.1016/j.plaphy.2022.11.024.

Spatiotemporal dynamics of the tomato fruit transcriptome under prolonged water stress - (Peer Reviewed Journal)
Nicolas, P., Shinozaki, Y., Powell, A., Philippe, G., Snyder, S., Gao, K., Zheng, Y., Xu, Y., Courtney, L., Vrebalov, J., Casteel, C., Mueller, L., Fei, Z., Giovannoni, J.J., Rose, J., Catala, C. 2022. Spatiotemporal dynamics of the tomato fruit transcriptome under prolonged water stress. Plant Physiology. https://doi.org/10.1093/plphys/kiac445.

Sulfate availability and soil selenate adsorption alleviate selenium toxicity in rice plants - (Peer Reviewed Journal)
Cardoso, A., Gomes, F., Antonio, J., Guilherme, L., Liu, J., Li, L., Silva, M. 2022. Sulfate availability and soil selenate adsorption alleviate selenium toxicity in rice plants. Environmental and Experimental Botany. 201: Article e104971. https://doi.org/10.1016/j.envexpbot.2022.104971.

Comparative transcriptomics and eQTL approach identified SlWD40 as a novel tomato fruit ripening regulator - (Peer Reviewed Journal)
Zhu, F., Jadhav, S., Toghe, T., Salem, M., Li, J., Giovannoni, J.J., Cheng, Y., Alseekh, S., Fernie, A. 2022. Comparative transcriptomics and eQTL approach identified SlWD40 as a novel tomato fruit ripening regulator. Plant Physiology. https://doi.org/10.1093/plphys/kiac200.

A solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity - (Peer Reviewed Journal)
Powell, A., Feder, A., Li, J., Schmidt, M., Courtney, L., Alseekh, S., Jobson, E., Vogel, A., Xu, Y., Lyon, D., Dumschott, K., Mchale, M., Suplice, R., Bao, K., Lal, R., Dunhan, A., Halab, A., Denton, A., Bolger, M., Fernie, A., Hind, S., Mueller, L., Martin, G., Fei, Z., Martin, C., Giovannoni, J.J., Stickler, S., Usedal, B. 2022. A solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity. The Plant Journal. 110(6):1791-1810. https://doi.org/10.1111/tpj.15770.

Phytoene synthase: the key rate-limiting enzyme of carotenoid biosynthesis in plants - (Review Article)
Zhou, X., Rao, S., Wrightstone, E., Lui, A., Welsch, R., Li, L. 2022. Phytoene synthase: the key rate-limiting enzyme of carotenoid biosynthesis in plants. Frontiers in Plant Science. 13:884720. https://doi.org/10.3389/fpls.2022.884720.

Golden rice—lessons learned for inspiring future metabolic engineering strategies and synthetic biology solutions - (Book / Chapter)
Welsch, R., Li, L. 2022. Golden rice—lessons learned for inspiring future metabolic engineering strategies and synthetic biology solutions. In: Wurtzel, E., editor. Methods in Enzymology. Frontiers in Plant Science. Amsterdam, Netherlands: Elsevier, Inc. (671):1-29. https://doi.org/10.1016/bs.mie.2022.03.014.

Laser capture of tomato pericarp tissues for microscale carotenoid analysis by supercritical fluid chromatography - (Peer Reviewed Journal)
Ramsey, J.S., Fish, T., Thannhauser, T.W., Giovannoni, J.J. 2022. Laser capture of tomato pericarp tissues for microscale carotenoid analysis by supercritical fluid chromatography. Methods in Enzymology. 670:213-233. https://doi.org/10.1016/bs.mie.2022.01.014.

Triptychon-like regulates aspects of both fruit flavor and color in citrus - (Peer Reviewed Journal)
He, J., Xu, Y., Huang, D., Fu, J., Liu, Z., Wang, L., Zhang, Y., Xu, R., Li, L., Deng, X., Xu, Q. 2022. Triptychon-like regulates aspects of both fruit flavor and color in citrus. Journal of Experimental Botany. 73(11):3610-3624. https://doi.org/10.1093/jxb/erac069.

Orchestration of chlorophyll and carotenoid biosynthesis by orange family proteins in plant - (Pre-print Publication)
Sun, T., Wang, P., Lu, S., Yuan, H., Yang, Y., Fish, T., Thannhauser, T.W., Liu, J., Mazourek, M., Grimm, B., Li, L. 2022. Orchestration of chlorophyll and carotenoid biosynthesis by orange family proteins in plant. bioRxiv. https://doi.org/10.1101/2022.02.08.479616.

Protein–protein interaction techniques to investigate post-translational regulation of carotenogenesis - (Book / Chapter)
Sun, T., Zhou, X., Rao, S., Liu, J., Li, L. 2022. Protein–protein interaction techniques to investigate post-translational regulation of carotenogenesis. In: Wurtzel, E., editor. Methods in Enzymology. Amsterdam, Netherlands: Elsevier, Inc. 167:301-325. https://doi.org/10.1016/bs.mie.2022.02.001.

Plant carotenoids: recent advances and future perspectives - (Review Article)
Sun, T., Rao, S., Zhou, X., Li, L. 2022. Plant carotenoids: recent advances and future perspectives. Molecular Horticulture. https://doi.org/10.1186/s43897-022-00023-2.

Characterization of cassava orange proteins and their capability to increase provitamin A carotenoids accumulation - (Peer Reviewed Journal)
Jaramillo, A., Sierra, S., Chavarriaga-Aguirre, P., Castillo, D., Gkanogiannis, A., Lopez-Lavalle, L., Acriniegas, J., Sun, T., Li, L., Welsch, R., Boy, E., Alvarez, D. 2022. Characterization of cassava orange proteins and their capability to increase provitamin A carotenoids accumulation. PLoS ONE. 17(1):Article e0262412. https://doi.org/10.1371/journal.pone.0262412.

SlERF.F12 modulates the transition to ripening in tomato fruit by recruiting the corepressor topless and histone deacetylases to repress key ripening genes - (Peer Reviewed Journal)

A tomato LATERAL ORGAN BOUNDARIES transcription factor, SlLOB1, predominantly regulates cell wall and softening components of ripening - (Peer Reviewed Journal)
Shi, Y., Vrebalov, J., Zheng, H., Xu, Y., Yin, X., Liu, W., Liu, Z., Sorensen, I., Su, G., Ma, Q., Evanich, D., Rose, J., Fei, Z., Van Eck, J., Thannhauser, T.W., Chen, K., Giovannoni, J.J. 2021. A tomato LATERAL ORGAN BOUNDARIES transcription factor, SlLOB1, predominantly regulates cell wall and softening components of ripening. Proceedings of the National Academy of Sciences (PNAS). 118(33):e2102486118. https://doi.org/10.1073/pnas.2102486118.

Multi-strategy engineering greatly enhances provitamin A carotenoid accumulation and stability in Arabidopsis seeds - (Peer Reviewed Journal)
Sun, T., Zhu, Q., Wei, Z., Owens, L.A., Fish, T., Kim, H., Thannhauser, T.W., Cahoon, E.B., Li, L. 2021. Multi-strategy engineering greatly enhances provitamin A carotenoid accumulation and stability in Arabidopsis seeds. aBIOTECH. https://doi.org/10.1007/s42994-021-00046-1.

Comparative transcriptome analyses shed light on carotenoid production and plastid development in melon fruit - (Peer Reviewed Journal)
Chayut, N., Yuan, H., Saar, Y., Zheng, Y., Sun, T., Zhou, X., Hermanns, A., Oren, E., Faigenboim, A., Hui, M., Fei, Z., Mazourek, M., Burger, J., Tadmor, Y., Li, L. 2021. Comparative transcriptome analyses shed light on carotenoid production and plastid development in melon fruit. Horticulture Research. 8:112. https://doi.org/10.1038/s41438-021-00547-6.

Effect of continuous white light illumination on glucosinolate metabolism during postharvest storage of broccoli - (Peer Reviewed Journal)
Casajus, V., Civello, P., Martinez, G., Howe, K.J., Fish, T., Yang, Y., Thannhauser, T.W., Li, L., Lobato, M.G. 2021. Effect of continuous white light illumination on glucosinolate metabolism during postharvest storage of broccoli. LWT - Food Science and Technology. 145:111302. https://doi.org/10.1016/j.lwt.2021.111302.

Genome-wide association study reveals the genetic architecture of 27 agronomic traits in tomato - (Peer Reviewed Journal)
Ye, J., Wang, X., Wang, W., Yu, H., Ai, G., Li, C., Sun, P., Wang, X., Li, H., Ouyang, B., Zhang, J., Zhang, Y., Han, H., Giovannoni, J.J., Fei, Z., Ye, Z. 2021. Genome-wide association study reveals the genetic architecture of 27 agronomic traits in tomato. Plant Physiology. 2021:00:1-15. https://doi.org/10.1093/plphys/kiab230.

The NAC transcription factor FaRIF controls fruit ripening in strawberry - (Peer Reviewed Journal)
Martin-Pizzaro, C., Villarino, J., Osorio, S., Meco, V., Urritia, M., Pillet, J., Casanal, A., Merchante, C., Amaya, I., Willmitzer, L., Fernie, A., Giovannoni, J.J., Botella, M., Valpuesta, V., Pose, D. 2021. The NAC transcription factor FaRIF controls fruit ripening in strawberry. The Plant Cell. 331574-1593. https://doi.org/10.1093/plcell/koab070.

Tomato fruit as a model for tissue-specific gene silencing in crop plants - (Peer Reviewed Journal)
Feder, A., Jensen, S., Wang, A., Courtney, L., Middleton, L., Van Eck, J., Liu, Y., Giovannoni, J.J. 2020. Tomato fruit as a model for tissue-specific gene silencing in crop plants. Horticulture Research. 7:142. https://doi.org/10.1038/s41438-020-00363-4.

Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression. - (Peer Reviewed Journal)
Yano, R., Ariizumi, T., Nonaka, S., Kawazu, Y., Zhong, S., Mueller, L., Giovannoni, J.J., Rose, J., Ezura, H. 2020. Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression. Communications Biology. 3:432. https://doi.org/10.1038/s42003-020-01172-0.

Phytohormones in fruit development and maturation - (Literature Review)
Fenn, M., Giovannoni, J.J. 2020. Phytohormones in fruit development and maturation. The Plant Journal. 105:446-458. https://doi.org/10.1111/tpj.15112.

GWAS based on RNA-Seq SNPs and high-throughput phenotyping combined with climatic data highlights the reservoir of valuable genetic diversity in regional tomato landraces - (Peer Reviewed Journal)
Rodiguez, M., Sciunti, A., Posadinu, C., Xu, Y., Nguyen, C., Sun, H., Bitocchi, E., Bellucci, E., Papa, R., Fei, Z., Giovannoni, J.J., Rau, D., Attene, G. 2020. GWAS based on RNA-Seq SNPs and high-throughput phenotyping combined with climatic data highlights the reservoir of valuable genetic diversity in regional tomato landraces. Genes. 11:1387. https://doi.org/10.3390/genes11111387.

Biochemical basis of differential selenium tolerance in arugula (Eruca sativa Mill.) and lettuce (Lactuca sativa L.) - (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.

Arabidopsis OR protein regulates plastid preprotein import through interacting with Tic proteins - (Peer Reviewed Journal)
Yuan, H., Pawlowski, E., Yang, Y., Sun, T., Thannhauser, T.W., Mazourek, M., Schnell, D., Li, L. 2020. Arabidopsis OR protein regulates plastid preprotein import through interacting with Tic proteins. Journal of Experimental Botany. 2(4):1059-1072. https://doi.org/10.1093/jxb/eraa528.

Genome of Solanum pimpinelifolium provides insights into structural variants during tomato breeding - (Peer Reviewed Journal)
Wang, X., Gao, L., Jiao, C., Stravoravdis, S., Hosmani, P., Saha, S., Zhang, J., Mainiero, S., Strickler, S., Catala, C., Martin, G., Muller, L., Vrebalov, J., Giovannoni, J.J., Wu, S., Fei, Z. 2020. Genome of Solanum pimpinelifolium provides insights into structural variants during tomato breeding. Nature Communications. 11:5817. https://doi.org/10.1038/s41467-020-19682-0.

Carotenoid pigment accumulation in horticultural plants - (Review Article)
Hermanns, A., Zhou, X., Xu, Q., Tadmor, Y., Li, L. 2020. Carotenoid pigment accumulation in horticultural plants. Horticultural Plant Journal. 6(6):343-360. https://doi.org/10.1016/j.hpj.2020.10.002.

Genotypic variation of flavonols and antioxidant capacity in broccoli - (Peer Reviewed Journal)
Duan, Y., Santiago, F., Reis, A., Figueiredo, M., Zhou, S., Thannhauser, T.W., Li, L. 2021. Genotypic variation of flavonols and antioxidant capacity in broccoli. Food Chemistry. 338:127997. https://doi.org/10.1016/j.foodchem.2020.127997.

Ectopic expression of miRNA172 in tomato (Solanum lycopersicum) reveals novel function in fruit development through regulation of an AP2 transcription factor - (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 - (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 - (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 - (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 - (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 - (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 Kingdom: CAB International. p.137-171.

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