| [1] |
Sun T, Tadmor Y, Li L. 2019. Pathways for carotenoid biosynthesis, degradation, and storage. In Plant and Food Carotenoids: Methods and Protocols, eds. Rodríguez-Concepción M, Welsch R. New York, NY: Humana. pp. 3–23 doi: 10.1007/978-1-4939-9952-1_1 |
| [2] |
Gupta P, Rodriguez-Franco M, Bodanapu R, Sreelakshmi Y, Sharma R. 2022. Phytoene synthase 2 in tomato fruits remains functional and contributes to abscisic acid formation. |
| [3] |
Zhou XS, Rao SM, Wrightstone E, Sun TH, Lui ACW, et al. 2022. Phytoene synthase: the key rate-limiting enzyme of carotenoid biosynthesis in plants. |
| [4] |
Barja MV, Ezquerro M, Beretta S, Diretto G, Florez-Sarasa I, et al. 2021. Several geranylgeranyl diphosphate synthase isoforms supply metabolic substrates for carotenoid biosynthesis in tomato. |
| [5] |
Ezquerro M, Burbano-Erazo E, Rodriguez-Concepcion M. 2023. Overlapping and specialized roles of tomato phytoene synthases in carotenoid and abscisic acid production. |
| [6] |
Burbano-Erazo E, Ezquerro M, Sanchez-Bel P, Rodriguez-Concepcion M. 2025. Specific sets of geranylgeranyl diphosphate synthases and phytoene synthases control the production of carotenoids and ABA in different tomato tissues. |
| [7] |
Bartley GE, Scolnik PA. 1989. Carotenoid biosynthesis in photosynthetic bacteria. Genetic characterization of the Rhodobacter capsulatus CrtI protein. The Journal of Biological Chemistry 264:13109−13113 |
| [8] |
Römer S, Fraser P, Kiano J, Shipton C, Misawa N, et al. 2000. Elevation of the provitamin A content of transgenic tomato plants. |
| [9] |
Fray RG, Grierson D. 1993. Identification and genetic analysis of normal and mutant phytoene synthase genes of tomato by sequencing, complementation and co-suppression. |
| [10] |
Fray RG, Wallace A, Fraser PD, Valero D, Hedden P, et al. 1995. Constitutive expression of a fruit phytoene synthase gene in transgenic tomatoes causes dwarfism by redirecting metabolites from the gibberellin pathway. |
| [11] |
Fraser PD, Romer S, Shipton CA, Mills PB, Kiano JW, et al. 2002. Evaluation of transgenic tomato plants expressing an additional phytoene synthase in a fruit-specific manner. |
| [12] |
Ye XD, Al-Babili S, Kloti A, Zhang J, Lucca P, et al. 2000. Engineering the provitamin A (β-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm. |
| [13] |
Paine JA, Shipton CA, Chaggar S, Howells RM, Kennedy MJ, et al. 2005. Improving the nutritional value of Golden Rice through increased pro-vitamin A content. |
| [14] |
Cong L, Wang C, Chen L, Liu H, Yang G, et al. 2009. Expression of phytoene synthase1 and carotene desaturase crtI genes result in an increase in the total carotenoids content in transgenic elite wheat (Triticum aestivum L.). |
| [15] |
Bai C., Capell T., Berman J., Medina V., Sandmann G., et al. 2016. Bottlenecks in carotenoid biosynthesis and accumulation in rice endosperm are influenced by the precursor-product balance. |
| [16] |
Lu S, Van Eck J, Zhou X, Lopez AB, O’Halloran DM, et al. 2006. The cauliflower Or gene encodes a DnaJ cysteine-rich domain-containing protein that mediates high levels of β-carotene accumulation. |
| [17] |
Sirohi P, Vishnoi R, Baliyan S, Gupta BB, Demiwal P, et al. 2026. Boosting β-carotene in rice and wheat grains through seed-specific expression of a modified wheat or gene. |
| [18] |
Fraser PD, Enfissi EM, Halket JM, Truesdale MR, Yu D, et al. 2007. Manipulation of phytoene levels in tomato fruit: effects on isoprenoids, plastids, and intermediary metabolism. |
| [19] |
Xiao Y, Kang BS, Li M, Xiao LJ, Xiao H, et al. 2020. Transcription of lncRNA ACoS-AS1 is essential to trans-splicing between SlPsy1 and ACoS-AS1 that causes yellow fruit in tomato. |
| [20] |
Sun L, Rodriguez GR, Clevenger JP, Illa-Berenguer E, Lin JS, et al. 2015. Candidate gene selection and detailed morphological evaluations of fs8.1, a quantitative trait locus controlling tomato fruit shape. |
| [21] |
Yang YF, Zhu GN, Li R, Yan SJ, Fu DQ, et al. 2017. The RNA editing factor SlORRM4 is required for normal fruit ripening in tomato. |
| [22] |
Li HS, 2000. The experiment principle and technique on plant physiology and biochemistry. Beijing: Higher Education Press. 278 pp |
| [23] |
Chen ML, Fu XM, Liu JQ, Ye TT, Hou SY, et al. 2012. Highly sensitive and quantitative profiling of acidic phytohormones using derivatization approach coupled with nano-LC–ESI-Q-TOF-MS analysis. |
| [24] |
Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. |
| [25] |
Varet H, Brillet-Guéguen L, Coppée JY, Dillies MA. 2016. SARTools: a DESeq2-and EdgeR-based R pipeline for comprehensive differential analysis of RNA-seq data. |
| [26] |
Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. |
| [27] |
Chen CJ, Chen H, Zhang Y, Thomas HR, Frank MH, et al. 2020. TBtools: an integrative toolkit developed for interactive analyses of big biological data. |
| [28] |
Hugueney P, Bouvier F, Badillo A, d’Harlingue A, Kuntz M, et al. 1995. Identification of a plastid protein involved in vesicle fusion and/or membrane-protein translocation. |
| [29] |
Shaul O. 2017. How introns enhance gene expression. |
| [30] |
Cazzonelli CI, Pogson BJ. 2010. Source to sink: regulation of carotenoid biosynthesis in plants. |
| [31] |
Hedden P, Thomas SG. 2012. Gibberellin biosynthesis and its regulation. |
| [32] |
Liu LH, Shao ZY, Zhang M, Wang QM. 2015. Regulation of carotenoid metabolism in tomato. |
| [33] |
Moreno JC, Cerda A, Simpson K, Lopez-Diaz I, Carrera E, et al. 2016. Increased Nicotiana tabacum fitness through positive regulation of carotenoid, gibberellin and chlorophyll pathways promoted by Daucus carota lycopene β-cyclase (Dclcyb1) expression. |
| [34] |
Zhou F, Wang CY, Gutensohn M, Jiang L, Zhang P, et al. 2017. A recruiting protein of geranylgeranyl diphosphate synthase controls metabolic flux toward chlorophyll biosynthesis in rice. |
| [35] |
Ezquerro M, Li C, Pérez-Pérez J, Burbano-Erazo E, Barja MV, et al. 2023. Tomato geranylgeranyl diphosphate synthase isoform 1 is involved in the stress-triggered production of diterpenes in leaves and strigolactones in roots. |
| [36] |
Barja MV, Rodriguez-Concepcion M. 2021. Plant geranylgeranyl diphosphate synthases: every (gene) family has a story. |
| [37] |
Falcioni R, Moriwaki T, Bonato CM, de Souza LA, Nanni MR, et al. 2017. Distinct growth light and gibberellin regimes alter leaf anatomy and reveal their influence on leaf optical properties. |
| [38] |
Qin GJ, Gu HY, Ma LG, Peng YB, Deng XW, et al. 2007. Disruption of phytoene desaturase gene results in albino and dwarf phenotypes in Arabidopsis by impairing chlorophyll, carotenoid, and gibberellin biosynthesis. |
| [39] |
Wang P, Zhao X, Liu L, Gao C, Zhu K, et al. 2026. Carotenoid aggregates negatively impact chlorophyll levels and disrupt chloroplast development in peaches. |
| [40] |
Ali M, Shi L, Khan MA, Ali A, Hu S, et al. 2025. Auxin biodynamics and its integral role in enhancing plant resilience to environmental cues. |
| [41] |
Yu MY, Xie YG, Qian ZL, Zhong Y, Shen HL, et al. 2025. A single nucleotide substitution in the SlMCT gene contributes to great morphological alternations in tomato. |
| [42] |
Shumskaya M, Bradbury LM, Monaco RR, Wurtzel ET. 2012. Plastid localization of the key carotenoid enzyme phytoene synthase is altered by isozyme, allelic variation, and activity. |
| [43] |
Liu YS, Roof S, Ye ZB, Barry C, van Tuinen A, et al. 2004. Manipulation of light signal transduction as a means of modifying fruit nutritional quality in tomato. |
| [44] |
Mustilli AC, Fenzi F, Ciliento R, Alfano F, Bowler C. 1999. Phenotype of the tomato high pigment-2 mutant is caused by a mutation in the tomato homolog of DEETIOLATED1. |
| [45] |
Kolotilin I, Koltai H, Tadmor Y, Bar-Or C, Reuveni M, et al. 2007. Transcriptional profiling of high pigment-2dg tomato mutant links early fruit plastid biogenesis with its overproduction of phytonutrients. |
| [46] |
Galpaz N, Wang Q, Menda N, Zamir D, Hirschberg J. 2008. Abscisic acid deficiency in the tomato mutant high-pigment 3 leading to increased plastid number and higher fruit lycopene content. |
| [47] |
Inaba T, Ito-Inaba Y. 2010. Versatile roles of plastids in plant growth and development. |
| [48] |
Solymosi K, Lethin J, Aronsson H. 2018. Diversity and plasticity of plastids in land plants. In Plastids: Methods and Protocols, ed. Maréchal E. New York, NY: Humana. pp. 55–72 doi: 10.1007/978-1-4939-8654-5_4 |
| [49] |
Llorente B, D’andrea L, Ruiz-Sola MA, Botterweg E, Pulido P, et al. 2016. Tomato fruit carotenoid biosynthesis is adjusted to actual ripening progression by a light-dependent mechanism. |
| [50] |
Ali M, Wang Z, Guo Q, Wang Y, Cai Y, et al. 2026. Mapping plant cell-type-specific responses to environmental stresses. |
| [51] |
Cao X, Du R, Xu Y, Wu Y, Ye K, et al. 2024. Phytoene synthases 1 modulates tomato fruit quality through influencing the metabolic flux between carotenoid and flavonoid pathways. |
| [52] |
Giovannoni JJ, Noensie EN, Ruezinsky DM, Lu XH, Tracy SL, et al. 1995. Molecular genetic analysis of the ripening-inhibitor and non-ripening loci of tomato: a first step in genetic map-based cloning of fruit ripening genes. |
| [53] |
Clarke AK. 2012. The chloroplast ATP-dependent Clp protease in vascular plants–new dimensions and future challenges. |
| [54] |
Luo ZD, Zhang JH, Li JH, Yang CX, Wang TT, et al. 2013. A STAY-GREEN protein SlSGR1 regulates lycopene and β-carotene accumulation by interacting directly with SlPSY1 during ripening processes in tomato. |
| [55] |
Toledo-Ortiz G, Johansson H, Lee KP, Bou-Torrent J, Stewart K, et al. 2014. The HY5-PIF regulatory module coordinates light and temperature control of photosynthetic gene transcription. |
| [56] |
Nishimura K, van Wijk KJ. 2015. Organization, function and substrates of the essential Clp protease system in plastids. |
| [57] |
Ito Y, Nishizawa-Yokoi A, Endo M, Mikami M, Shima Y, et al. 2017. Re-evaluation of the rin mutation and the role of RIN in the induction of tomato ripening. |
| [58] |
Welsch R, Zhou XJ, Yuan H, Álvarez D, Sun TH, et al. 2018. Clp protease and OR directly control the proteostasis of phytoene synthase, the crucial enzyme for carotenoid biosynthesis in Arabidopsis. |
| [59] |
Xiong C, Luo D, Lin AH, Zhang CL, Shan LB, et al. 2019. A tomato B-box protein SlBBX20 modulates carotenoid biosynthesis by directly activating PHYTOENE SYNTHASE 1, and is targeted for 26S proteasome-mediated degradation. |
| [60] |
Lin YY, He MX, Wang JL, Huang JC. 2021. Fruit-specific expression of crtB, HpBHY, CrBKT and SlLCYB in a special tomato Landrace triggers hyper production of carotenoids in the fruit. |
| [61] |
Li Y, Meng F, You H, Shao Z, Xu C, et al. 2025. SlWRKY14 integrates carotenoid and flavonoid biosynthetic pathways to regulate coloration and quality of tomato fruits. |
| [62] |
Davuluri GR, van Tuinen A, Fraser PD, Manfredonia A, Newman R, et al. 2005. Fruit-specific RNAi-mediated suppression of DET1 enhances carotenoid and flavonoid content in tomatoes. |