| [1] |
Buitink J, Leprince O. 2008. Intracellular glasses and seed survival in the dry state. |
| [2] |
Holdsworth MJ, Finch-Savage WE, Grappin P, Job D. 2008. Post-genomics dissection of seed dormancy and germination. |
| [3] |
Rajjou L, Duval M, Gallardo K, Catusse J, Bally J, et al. 2012. Seed germination and vigor. |
| [4] |
Nonogaki H, Bassel GW, Bewley JD. 2010. Germination—still a mystery. |
| [5] |
Ali F, Qanmber G, Li F, Wang Z. 2022. Updated role of ABA in seed maturation, dormancy, and germination. |
| [6] |
Dong NQ, Lin HX. 2021. Contribution of phenylpropanoid metabolism to plant development and plant–environment interactions. |
| [7] |
Wang Y, Sun X, Peng J, Li F, Ali F, et al. 2025. Regulation of seed germination: ROS, epigenetic, and hormonal aspects. |
| [8] |
Vogt T. 2010. Phenylpropanoid biosynthesis. |
| [9] |
Jun SY, Sattler SA, Cortez GS, Vermerris W, Sattler SE, et al. 2018. Biochemical and structural analysis of substrate specificity of a phenylalanine ammonia-lyase. |
| [10] |
Ehlting J, Hamberger B, Million-Rousseau R, Werck-Reichhart D. 2006. Cytochromes P450 in phenolic metabolism. |
| [11] |
Alariqi M, Ramadan M, Wang Q, Yang Z, Hui X, et al. 2023. Cotton 4-coumarate-CoA ligase 3 enhanced plant resistance to Verticillium dahliae by promoting jasmonic acid signaling-mediated vascular lignification and metabolic flux. |
| [12] |
Besseau S, Hoffmann L, Geoffroy P, Lapierre C, Pollet B, et al. 2007. Flavonoid accumulation in Arabidopsis repressed in lignin synthesis affects auxin transport and plant growth. |
| [13] |
Gallego-Giraldo L, Escamilla-Trevino L, Jackson LA, Dixon RA. 2011. Salicylic acid mediates the reduced growth of lignin down-regulated plants. |
| [14] |
Serrani-Yarce JC, Escamilla-Trevino L, Barros J, Gallego-Giraldo L, Pu Y, et al. 2021. Targeting hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase for lignin modification in Brachypodium distachyon. |
| [15] |
Xiao R, Zhang C, Guo X, Li H, Lu H. 2021. MYB transcription factors and its regulation in secondary cell wall formation and lignin biosynthesis during xylem development. |
| [16] |
Zhao M, Li J, Zhu L, Chang P, Li L, et al. 2019. Identification and characterization of MYB-bHLH-WD40 regulatory complex members controlling anthocyanidin biosynthesis in blueberry fruits development. |
| [17] |
Dao TTH, Linthorst HJM, Verpoorte R. 2011. Chalcone synthase and its functions in plant resistance. |
| [18] |
Feng Q, Lv B, Wang S, Gao Y, Wang M, et al. 2026. SmCAD4-mediated lignin biosynthesis and improved root architecture are crucial for drought tolerance in Salvia miltiorrhiza. |
| [19] |
Chen L, Guo H, Lin Y, Wu Y, Cheng H. 2014. Molecular cloning and characterization of the cinnamate 4-hydroxylase gene from Eupatorium adenophorum. |
| [20] |
Stocker CW, Wong VNL, Patti AF, Garnier G. 2024. Effect of lignin in cellulose nanofibers on biodegradation and seed germination. |
| [21] |
Rao MJ, Zheng B. 2025. The role of polyphenols in abiotic stress tolerance and their antioxidant properties to scavenge reactive oxygen species and free radicals. |
| [22] |
Yadav V, Wang Z, Wei C, Amo A, Ahmed B, et al. 2020. Phenylpropanoid pathway engineering: an emerging approach towards plant defense. |
| [23] |
Noel JP, Austin MB, Bomati EK. 2005. Structure-function relationships in plant phenylpropanoid biosynthesis. |
| [24] |
Emiliani G, Fondi M, Fani R, Gribaldo S. 2009. A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land. |
| [25] |
Ehlting J, Büttner D, Wang Q, Douglas CJ, Somssich IE, et al. 1999. Three 4-coumarate: coenzyme A ligases in Arabidopsis thaliana represent two evolutionarily divergent classes in angiosperms. |
| [26] |
MacGregor DR, Kendall SL, Florance H, Fedi F, Moore K, et al. 2015. Seed production temperature regulation of primary dormancy occurs through control of seed coat phenylpropanoid metabolism. |
| [27] |
Chen F, Tobimatsu Y, Jackson L, Nakashima J, Ralph J, et al. 2013. Novel seed coat lignins in the Cactaceae: structure, distribution and implications for the evolution of lignin diversity. |
| [28] |
Zhuo C, Wang X, Docampo-Palacios M, Sanders BC, Engle NL, et al. 2022. Developmental changes in lignin composition are driven by both monolignol supply and laccase specificity. |
| [29] |
Zhuang Y, Zhao J, Xiao L, Liu X, Li L. 2025. The LACCASE3/5/12/13 clade mediates seed coat lignin deposition and regulates imbibition and germination. |
| [30] |
Blaschek L, Murozuka E, Serk H, Ménard D, Pesquet E. 2023. Different combinations of laccase paralogs nonredundantly control the amount and composition of lignin in specific cell types and cell wall layers in Arabidopsis. |
| [31] |
Wu J, Lv S, Zhao L, Gao T, Yu C, et al. 2023. Advances in the study of the function and mechanism of the action of flavonoids in plants under environmental stresses. |
| [32] |
Shomali A, Das S, Arif N, Sarraf M, Zahra N, et al. 2022. Diverse physiological roles of flavonoids in plant environmental stress responses and tolerance. |
| [33] |
Bailly C. 2019. The signalling role of ROS in the regulation of seed germination and dormancy. |
| [34] |
Sharma A, Shahzad B, Rehman A, Bhardwaj R, Landi M, et al. 2019. Response of phenylpropanoid pathway and the role of polyphenols in plants under abiotic stress. |
| [35] |
Chapman JM, Muhlemann JK, Gayomba SR, Muday GK. 2019. RBOH-dependent ROS synthesis and ROS scavenging by plant specialized metabolites to modulate plant development and stress responses. |
| [36] |
Rao MJ, Duan M, Ikram M, Zheng B. 2025. ROS regulation and antioxidant responses in plants under air pollution: molecular signaling, metabolic adaptation, and biotechnological solutions. |
| [37] |
Santelia D, Henrichs S, Vincenzetti V, Sauer M, Bigler L, et al. 2008. Flavonoids redirect PIN-mediated polar auxin fluxes during root gravitropic responses. |
| [38] |
Chapman JM, Muday GK. 2021. Flavonols modulate lateral root emergence by scavenging reactive oxygen species in Arabidopsis thaliana. |
| [39] |
Gayomba SR, Muday GK. 2020. Flavonols regulate root hair development by modulating accumulation of reactive oxygen species in the root epidermis. |
| [40] |
Teale WD, Pasternak T, Dal Bosco C, Dovzhenko A, Kratzat K, et al. 2021. Flavonol‐mediated stabilization of PIN efflux complexes regulates polar auxin transport. |
| [41] |
Zhang Y, Xia Y. 2026. Quercetin enhances tomato seed germination via phenylpropanoid-dependent regulation of ROS, hormone signaling, and starch hydrolysis. |
| [42] |
Huang Y, Wang H, Zhang Y, Zhang P, Xiang Y, et al. 2024. SCPL acyltransferases catalyze the metabolism of chlorogenic acid during purple coneflower seed germination. |
| [43] |
Yang J, Zhang Y, Jia J, Wang C, Fu Y. 2025. Flavonoid-lignin crosstalk: engineering metabolic flux for optimised plant growth and stress resilience. |
| [44] |
Zhao X, Niu Y, Bai X, Mao T. 2022. Transcriptomic and metabolic profiling reveals a lignin metabolism network involved in mesocotyl elongation during maize seed germination. |
| [45] |
Balcerzak M, Harris LJ, Subramaniam R, Ouellet T. 2012. The feruloyl esterase gene family of Fusarium graminearum is differentially regulated by aromatic compounds and hosts. |
| [46] |
Martínez-Fraca J, de la Torre-Hernández ME, Meshoulam-Alamilla M, Plasencia J. 2022. In search of resistance against Fusarium ear rot: ferulic acid contents in maize pericarp are associated with antifungal activity and inhibition of fumonisin production. |
| [47] |
Šoln K, Klemenčič M, Koce JD. 2022. Plant cell responses to allelopathy: from oxidative stress to programmed cell death. |
| [48] |
Rasmussen HN, Dixon KW, Jersáková J, Těšitelová T. 2015. Germination and seedling establishment in orchids: a complex of requirements. |
| [49] |
Steinbrecher T, Leubner-Metzger G. 2017. The biomechanics of seed germination. |
| [50] |
Gianinetti A, Finocchiaro F, Bagnaresi P, Zechini A, Faccioli P, et al. 2018. Seed dormancy involves a transcriptional program that supports early plastid functionality during imbibition. |
| [51] |
Zhang X, Gou M, Liu CJ. 2014. Arabidopsis kelch repeat f-box proteins regulate phenylpropanoid biosynthesis via controlling the turnover of phenylalanine ammonia-lyase. |
| [52] |
Zhang X, Gou M, Guo C, Yang H, Liu CJ. 2015. Down-regulation of Kelch domain-containing F-box protein in Arabidopsis enhances the production of (poly)phenols and tolerance to ultraviolet radiation. |
| [53] |
Shin D, Cho KH, Tucker E, Yoo CY, Kim J. 2024. Identification of tomato F-box proteins functioning in phenylpropanoid metabolism. |
| [54] |
Wolny E, Betekhtin A, Rojek M, Braszewska-Zalewska A, Lusinska J, et al. 2018. Germination and the early stages of seedling development in Brachypodium distachyon. |
| [55] |
Crosby KC, Pietraszewska-Bogiel A, Gadella TWJ, Winkel BSJ. 2011. Förster resonance energy transfer demonstrates a flavonoid metabolon in living plant cells that displays competitive interactions between enzymes. |
| [56] |
Jørgensen K, Rasmussen AV, Morant M, Nielsen AH, Bjarnholt N, et al. 2005. Metabolon formation and metabolic channeling in the biosynthesis of plant natural products. |
| [57] |
Winkel BSJ. 2004. Metabolic channeling in plants. |
| [58] |
Aravena-Calvo J, Busck-Mellor S, Laursen T. 2024. Global organization of phenylpropanoid and anthocyanin pathways revealed by proximity labeling of trans-cinnamic acid 4-hydroxylase in Petunia inflata petal protoplasts. |
| [59] |
Yang X, Huang Y, Xia P. 2024. The property and function of proteins undergoing liquid-liquid phase separation in plants. |
| [60] |
Dorone Y, Boeynaems S, Flores E, Jin B, Hateley S, et al. 2021. A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation. |
| [61] |
Ro DK, Douglas CJ. 2004. Reconstitution of the entry point of plant phenylpropanoid metabolism in yeast (Saccharomyces cerevisiae): implications for control of metabolic flux into the phenylpropanoid pathway. |
| [62] |
Pierce S, Spada A, Caporali E, Ceriani RM, Buffa G. 2019. Enzymatic scarification of Anacamptis morio (Orchidaceae) seed facilitates lignin degradation, water uptake and germination. |
| [63] |
Hameed A, Rasheed A, Gul B, Khan MA. 2014. Salinity inhibits seed germination of perennial halophytes Limonium stocksii and Suaeda fruticosa by reducing water uptake and ascorbate dependent antioxidant system. |
| [64] |
Ranade SS, García-Gil MR. 2024. Lignin biosynthesis pathway repressors in gymnosperms: differential repressor domains as compared to angiosperms. |
| [65] |
Li W, Niu Y, Zheng Y, Wang Z. 2022. Advances in the understanding of reactive oxygen species-dependent regulation on seed dormancy, germination, and deterioration in crops. |
| [66] |
Liszkay A, van der Zalm E, Schopfer P. 2004. Production of reactive oxygen intermediates (O2·−, H2O2, and ·OH) by maize roots and their role in wall loosening and elongation growth. |
| [67] |
Tenhaken R. 2015. Cell wall remodeling under abiotic stress. |
| [68] |
Chen L, Guo H, Lin Y, Cheng H. 2015. Chalcone synthase EaCHS1 from Eupatorium adenophorum functions in salt stress tolerance in tobacco. |
| [69] |
Jiang J, Huang H, Gao Q, Li Y, Xiang H, et al. 2023. Effects of editing DFR genes on flowers, leaves, and roots of tobacco. |
| [70] |
Luo S, Wang S, Yang L, Luo K, Cheng J, et al. 2025. A comprehensive evolutionary analysis of the dihydroflavonol 4-reductase (DFR) gene family in plants: insights from 237 species. |
| [71] |
Zhou XE, Soon FF, Ng LM, Kovach A, Suino-Powell KM, et al. 2012. Catalytic mechanism and kinase interactions of ABA-signaling PP2C phosphatases. |
| [72] |
Chevriau J, Zerbetto De Palma G, Alleva K, Zeida A. 2025. Hydrogen peroxide transport by aquaporins: insights from molecular modeling and simulations. |
| [73] |
Wen Y, Zhou Y, Ding M, Luo Z, Wang C, et al. 2025. OsGSTT3 regulates seed germination by modulating reactive oxygen species homeostasis in rice. |
| [74] |
Sachdev S, Ansari SA, Ansari MI, Fujita M, Hasanuzzaman M. 2021. Abiotic stress and reactive oxygen species: generation, signaling, and defense mechanisms. |
| [75] |
Peng L, Lang S, Wang Y, Pritchard HW, Wang X. 2017. Modulating role of ROS in re-establishing desiccation tolerance in germinating seeds of Caragana korshinskii Kom. |
| [76] |
Grabsztunowicz M, Koskela MM, Mulo P. 2017. Post-translational modifications in regulation of chloroplast function: recent advances. |
| [77] |
Li X, Bonawitz ND, Weng JK, Chapple C. 2010. The growth reduction associated with repressed lignin biosynthesis in Arabidopsis thaliana is independent of flavonoids. |
| [78] |
Lin JS, Huang XX, Li Q, Cao Y, Bao Y, et al. 2016. UDP-glycosyltransferase 72B1 catalyzes the glucose conjugation of monolignols and is essential for the normal cell wall lignification in Arabidopsis thaliana. |
| [79] |
Ohtani M, Demura T. 2019. The quest for transcriptional hubs of lignin biosynthesis: beyond the NAC-MYB-gene regulatory network model. |
| [80] |
Liu C, Yu H, Rao X, Li L, Dixon RA. 2021. Abscisic acid regulates secondary cell-wall formation and lignin deposition in Arabidopsis thaliana through phosphorylation of NST1. |
| [81] |
Zhong R, Lee C, McCarthy RL, Reeves CK, Jones EG, et al. 2011. Transcriptional activation of secondary wall biosynthesis by rice and maize NAC and MYB transcription factors. |
| [82] |
Bomal C, Bedon F, Caron S, Mansfield SD, Levasseur C, et al. 2008. Involvement of Pinus taeda MYB1 and MYB8 in phenylpropanoid metabolism and secondary cell wall biogenesis: a comparative in planta analysis. |
| [83] |
Geng P, Zhang S, Liu J, Zhao C, Wu J, et al. 2020. MYB20, MYB42, MYB43, and MYB85 regulate phenylalanine and lignin biosynthesis during secondary cell wall formation. |
| [84] |
Zhou J, Lee C, Zhong R, Ye ZH. 2009. MYB58 and MYB63 are transcriptional activators of the lignin biosynthetic pathway during secondary cell wall formation in Arabidopsis. |
| [85] |
Xing M, Xin P, Wang Y, Han C, Lei C, et al. 2024. A negative feedback regulatory module comprising R3-MYB repressor MYBL2 and R2R3-MYB activator PAP1 fine-tunes high light-induced anthocyanin biosynthesis in Arabidopsis. |
| [86] |
Xu W, Grain D, Le Gourrierec J, Harscoët E, Berger A, et al. 2013. Regulation of flavonoid biosynthesis involves an unexpected complex transcriptional regulation of TT8 expression, in Arabidopsis. |
| [87] |
Feyissa DN, Løvdal T, Olsen KM, Slimestad R, Lillo C. 2009. The endogenous GL3, but not EGL3, gene is necessary for anthocyanin accumulation as induced by nitrogen depletion in Arabidopsis rosette stage leaves. |
| [88] |
Wang XC, Wu J, Guan ML, Zhao CH, Geng P, et al. 2020. Arabidopsis MYB4 plays dual roles in flavonoid biosynthesis. |
| [89] |
Fornalé S, Shi X, Chai C, Encina A, Irar S, et al. 2010. ZmMYB31 directly represses maize lignin genes and redirects the phenylpropanoid metabolic flux. |
| [90] |
Wind JJ, Peviani A, Snel B, Hanson J, Smeekens SC. 2013. ABI4: versatile activator and repressor. |
| [91] |
Boonyaves K, Wu TY, Dong Y, Urano D. 2022. Interplay between Arabidopsis Gβ and WRKY transcription factors differentiates environmental stress responses. |
| [92] |
Liu X, Hou X. 2018. Antagonistic regulation of ABA and GA in metabolism and signaling pathways. |
| [93] |
Jie Y, Wang W, Wu Z, Ren Z, Li L, et al. 2024. Deciphering physiological and transcriptional mechanisms of maize seed germination. |
| [94] |
Zdzieszynska J, Stawska M, Oracz K. 2016. Role of cell wall remodeling proteins in the regulation of seed germination. Postepy Biologii Komorki 43:503−523 |
| [95] |
Richards SL, Wilkins KA, Swarbreck SM, Anderson AA, Habib N, et al. 2015. The hydroxyl radical in plants: from seed to seed. |
| [96] |
Schopfer P, Liszkay A. 2006. Plasma membrane-generated reactive oxygen intermediates and their role in cell growth of plants. |
| [97] |
Alabadí D, Sun TP. 2025. Green revolution DELLA proteins: functional analysis and regulatory mechanisms. |
| [98] |
Cappellini F, Marinelli A, Toccaceli M, Tonelli C, Petroni K. 2021. Anthocyanins: from mechanisms of regulation in plants to health benefits in foods. |
| [99] |
Gonzalez-Guzman M, Pizzio GA, Antoni R, Vera-Sirera F, Merilo E, et al. 2012. Arabidopsis PYR/PYL/RCAR receptors play a major role in quantitative regulation of stomatal aperture and transcriptional response to abscisic acid. |
| [100] |
Shu K, Liu XD, Xie Q, He ZH. 2016. Two faces of one seed: hormonal regulation of dormancy and germination. |
| [101] |
Yan H, Pei X, Zhang H, Li X, Zhang X, et al. 2021. MYB-mediated regulation of anthocyanin biosynthesis. |
| [102] |
Lismer A, Siklenka K, Lafleur C, Dumeaux V, Kimmins S. 2020. Sperm histone H3 lysine 4 trimethylation is altered in a genetic mouse model of transgenerational epigenetic inheritance. |
| [103] |
Ali S, Huang S, Zhou J, Bai Y, Liu Y, et al. 2023. miR397-LACs mediated cadmium stress tolerance in Arabidopsis thaliana. |
| [104] |
Sharma D, Tiwari M, Pandey A, Bhatia C, Sharma A, et al. 2016. MicroRNA858 is a potential regulator of phenylpropanoid pathway and plant development. |
| [105] |
Chen H, Tong J, Fu W, Liang Z, Ruan J, et al. 2020. The H3K27me3 demethylase RELATIVE OF EARLY FLOWERING6 suppresses seed dormancy by inducing abscisic acid catabolism. |
| [106] |
Jeong CY, Lee WJ, Truong HA, Trịnh CS, Jin JY, et al. 2018. Dual role of SND1 facilitates efficient communication between abiotic stress signalling and normal growth in Arabidopsis. |
| [107] |
de Freitas GM, Thomas J, Liyanage R, Lay JO, Basu S, et al. 2019. Cold tolerance response mechanisms revealed through comparative analysis of gene and protein expression in multiple rice genotypes. |
| [108] |
Qiao L, Sun Y, Cao S, Zhao X, Qi X, et al. 2026. SNAC4/9 negatively regulate the resistance of tomatoes to B. cinerea by suppressing phenylpropanoid metabolic pathway. |
| [109] |
Li J, Yu Q, Liu C, Zhang N, Xu W. 2025. Flavonoids as key players in cold tolerance: molecular insights and applications in horticultural crops. |
| [110] |
Wang Y, Jin G, Song S, Jin Y, Wang X, et al. 2024. A peroxisomal cinnamate: CoA ligase-dependent phytohormone metabolic cascade in submerged rice germination. |
| [111] |
Qian W, Zhu Y, Chen Q, Wang S, Chen L, et al. 2023. Comprehensive metabolomic and lipidomic alterations in response to heat stress during seed germination and seedling growth of Arabidopsis. |
| [112] |
Cai Z, He F, Feng X, Liang T, Wang H, et al. 2020. Transcriptomic analysis reveals important roles of lignin and flavonoid biosynthetic pathways in rice thermotolerance during reproductive stage. |
| [113] |
Liu S, Zenda T, Tian Z, Huang Z. 2023. Metabolic pathways engineering for drought or/and heat tolerance in cereals. |
| [114] |
Bouzroud S, Henkrar F, Fahr M, Smouni A. 2023. Salt stress responses and alleviation strategies in legumes: a review of the current knowledge. |
| [115] |
Zhang Q, Zheng G, Wang Q, Zhu J, Zhou Z, et al. 2022. Molecular mechanisms of flavonoid accumulation in germinating common bean (Phaseolus vulgaris) under salt stress. |
| [116] |
Al-Khayri JM, Rashmi R, Toppo V, Chole PB, Banadka A, et al. 2023. Plant secondary metabolites: the weapons for biotic stress management. |
| [117] |
Ma QH. 2024. Lignin biosynthesis and its diversified roles in disease resistance. |
| [118] |
Ramaroson ML, Koutouan C, Helesbeux JJ, Le Clerc V, Hamama L, et al. 2022. Role of phenylpropanoids and flavonoids in plant resistance to pests and diseases. |
| [119] |
Rubby S, Nunna S, Raval K, Sunidhi T, Tushadri S, et al. 2025. Dynamic interactions between biotic and abiotic stressors in plants: mechanisms, crosstalk and sustainable mitigation strategies. |
| [120] |
Severino LS. 2021. Plants make smart decisions in complex environments. |
| [121] |
Maymon T, Eisner N, Bar-Zvi D. 2022. The ABCISIC ACID INSENSITIVE (ABI) 4 Transcription Factor Is Stabilized by Stress, ABA and Phosphorylation. |
| [122] |
Gao F, Qi X, Guo H, Wang W, Liu F, et al. 2026. MPK3 as a signalling hub in plants: integrating plant growth, development and stress response. |
| [123] |
Lassowskat I, Böttcher C, Eschen-Lippold L, Scheel D, Lee J. 2014. Sustained mitogen-activated protein kinase activation reprograms defense metabolism and phosphoprotein profile in Arabidopsis thaliana. |
| [124] |
Haller E, Iven T, Feussner I, Stahl M, Fröhlich K, et al. 2020. ABA-dependent salt stress tolerance attenuates Botrytis immunity in Arabidopsis. |
| [125] |
Ramos-Muñoz M, Blanco-Sánchez M, Pías B, Ramírez-Valiente JA, Benavides R, et al. 2025. Interactive effects of warming and competition do not limit the adaptive plastic response to drought in populations of a Mediterranean plant. |
| [126] |
Abley K, Goswami R, Locke JCW. 2024. Bet-hedging and variability in plant development: seed germination and beyond. |