Guozheng Qin

WRKY transcription factors and jasmonic acid (JA) signaling are essential for plant responses to stress, but their roles in strawberry resistance to Botrytis cinerea remain unclear. Here, we investigated the function of FaWRKY7 in strawberry fruit and transgenic Arabidopsis thaliana. FaWRKY7 expression was significantly induced at 72 h after B. cinerea inoculation. Transient overexpression of FaWRKY7 enhanced strawberry fruit resistance to B. cinerea, whereas silencing increased susceptibility. Similarly, FaWRKY7-overexpressing Arabidopsis plants showed enhanced resistance to B. cinerea and greater responsiveness to exogenous methyl jasmonate (MeJA), although basal levels of free JA, JA-Ile, and OPDA were not detectably altered in non-inoculated samples. Pharmacological assays further showed that FaWRKY7-mediated resistance was maintained under MeJA treatment and only partially reduced by Jarin-1, an inhibitor of JA-Ile formation, indicating that this effect is only partially dependent on JA-Ile formation. Mechanistically, DAP-seq, yeast one-hybrid, EMSA, and dual-luciferase assays showed that FaWRKY7 directly binds to the promoters of FaJAZ4 and FaJAZ8 and represses their transcription. These findings indicate that FaWRKY7 enhances resistance to B. cinerea, at least in part by directly repressing FaJAZ4 and FaJAZ8 and thereby modulating jasmonate signaling responses.

Fruit quality is a complex trait shaped by developmental programs, metabolic networks, and environmental responses; yet, the RNA‐level regulatory processes that determine functional outputs remain insufficiently integrated and underexplored. In this review, we provide an integrated overview of RNA‐mediated regulatory mechanisms underlying fleshy fruit quality formation, focusing on five major layers, including RNA modification, organellar RNA editing, alternative splicing, long non‐coding RNAs, microRNAs, and their crosstalk. We summarize their molecular modes of action and discuss how these regulatory mechanisms shape diverse quality traits, including fruit morphology, pigmentation, flavor, texture remodeling, ripening progression, and postharvest performance. Furthermore, we highlight emerging strategies for harnessing RNA‐mediated regulation to improve and maintain fruit quality, including RNA‐centered multi‐omics integration, AI‐driven design of RNA regulatory elements, and precision of RNA‐level manipulation. We propose that deciphering and manipulating post‐transcriptional regulatory codes will provide a conceptual and technological framework for shifting fruit improvement from empirical selection toward rational RNA‐guided quality design, with broad implications for crop improvement, nutritional enhancement, and sustainable postharvest management.

Ripening inducing factor (RIF) is a key NAC transcription factor (TF) regulating strawberry fruit ripening. Previous studies using RIF-RNAi and overexpression lines in Fragaria × ananassa and CRISPR knock-out lines in F. vesca have established the role of RIF in controlling ABA biosynthesis and signaling, cell wall remodeling, and secondary metabolism. In this study, we deciphered FaRIF’s transcriptional regulatory network by combining ChIP-seq-based identification of its direct targets with an analysis of FaRIF-RNAi transcriptome data. These analyses revealed FaRIF’s direct role in multiple aspects of strawberry fruit ripening, including the regulation of ripening-related TFs, phytohormone content and signaling, primary and secondary metabolism, and cell wall degradation. Additionally, using the TurboID-based proximity labeling approach, we have identified FaRIF interactors, including proteins involved in mRNA and protein homeostasis, as well as several NAC TFs. Among these, FaNAC021 and FaNAC034 were found to potentially cooperate with FaRIF to enhance the transcription of shared target genes. This integrative analysis, combining transcriptome analysis, in vivo ChIP-seq, and proximity labeling, broadens our understanding of FaRIF-mediated transcriptional networks and interaction partners, providing valuable insights into the molecular regulation of strawberry fruit ripening by this TF.

Cultivated strawberry (Fragaria × ananassa) is a kind of Rosaceae fruit crops grown worldwide. It is popularly consumed for its attractive color, juicy flesh, and nutrient content. The rich anthocyanin in strawberry fruits is responsible for its coloration. Anthocyanins are polyphenolic compounds, belonging to the four types of natural plant pigments. As important antioxidant secondary metabolites, anthocyanins substantially affect the internal quality and nutritional value of strawberry fruits. Here, we summarize the molecular mechanism underlying anthocyanin accumulation in strawberry fruits and discuss the ways to increase the content of anthocyanins in order to provide theoretical support for improving the color of strawberry fruits and enhance its commercial value by molecular biology methods.

Cutin serves as the foundational structure of the plant cuticle and plays a crucial role in determining fruit development and quality. However, the transcriptional regulation of cutin deposition by fruit-specific transcription factors remains largely unknown. This study delves into the regulatory role of the tomato (Solanum lycopersicum) SBP-box protein Colorless Non-ripening (SlCNR), primarily expressed in fruits, in cutin formation. We found that CRISPR/Cas9-induced slcnr mutants exhibited thicker cuticles and elevated contents in total cutin and cutin monomers compared to wild-type fruits, whereas SlCNR overexpression lines displayed the opposite tendency. Transcriptome-wide RNA sequencing identified differentially expressed genes in SlCNR overexpression fruits. Further validation by gene expression, DNA binding, and transcriptional activity assays revealed that SlCNR directly binds to and represses the transcription of thirteen genes associated with cutin synthesis, export, and assembly, including glycerol-3-phosphate acyltransferase 4/6 (SlGPAT4/6), ATP-binding cassette transporter subfamily G protein 36/42 (SlABCG36/42), and cutin synthase (SlCUS1). In addition, SlCNR directly bound to and repressed the transcription activities of the promoter of NON-RIPENING like-1 (SlNOR-like1), which encodes a positive regulator of cutin deposition. Thus, SlCNR emerged as a negative transcription regulator of cutin content and cuticle thickness, ultimately affecting fruit firmness and cuticle permeability. This study sheds light on the molecular mechanisms governing cutin deposition through transcriptional regulatory networks, highlighting the role of SlCNR as an important player in fruit cuticle development.

Ripening Inducing Factor (RIF) is a key NAC transcription factor regulating strawberry fruit ripening. Previous studies using RIF- RNAi and overexpression lines in Fragaria × ananassa and CRISPR knock-out lines in F. vesca have established the role of RIF in controlling ABA biosynthesis and signaling, cell wall remodeling, and secondary metabolism. In this study, we deciphered FaRIF’s transcriptional regulatory network by combining ChIP-seq-based identification of its direct targets with an analysis of FaRIF -RNAi transcriptome data. These analyses revealed FaRIF’s direct role in multiple aspects of strawberry fruit ripening, including the regulation of ripening-related transcription factors, phytohormone content and signaling, primary and secondary metabolism, and cell wall degradation. Additionally, using the TurboID-based proximity labeling approach, we have identified FaRIF interactors, including proteins involved in mRNA and protein homeostasis, as well as several NAC transcription factors. Among these, FaNAC034 was found to synergistically enhance FaRIF’s transcriptional activity. This integrative analysis, combining transcriptome analysis, in vivo ChIP-seq, and proximity labeling, broadens our knowledge of FaRIF-mediated transcriptional networks and interaction partners, providing valuable insights into the molecular mechanisms underlying strawberry fruit ripening regulation by this transcription factor.

Hydrogen peroxide (H₂O₂) functions as a critical signalling molecule in controlling multiple biological processes. How H₂O₂ signalling integrates with other regulatory pathways such as epigenetic modification to coordinately regulate plant development remains elusive. Here we report that SlALKBH2, an m⁶A demethylase required for normal ripening of tomato fruit, is sensitive to oxidative modification by H₂O₂, which leads to the formation of homodimers mediated by intermolecular disulfide bonds, and Cys39 serves as a key site in this process. The oxidation of SlALKBH2 promotes protein stability and facilitates its function towards the target transcripts including the pivotal ripening gene SlDML2 encoding a DNA demethylase. Furthermore, we demonstrate that the thioredoxin reductase SlNTRC interacts with SlALKBH2 and catalyses its reduction, thereby modulating m⁶A levels and fruit ripening. Our study establishes a molecular link between H₂O₂ and m⁶A methylation and highlights the importance of redox regulation of m⁶A modifiers in controlling fruit ripening.

Fruit ripening is a highly-orchestrated process that requires the fine-tuning and precise control of gene expression, which is mainly governed by phytohormones, epigenetic modifiers, and transcription factors. How these intrinsic regulators coordinately modulate the ripening remains elusive. Here we report the identification and characterization of FvALKBH10B as an N⁶-methyladenosine (m⁶A) RNA demethylase necessary for the normal ripening of strawberry (Fragaria vesca) fruit. FvALKBH10B is induced by phytohormone abscisic acid (ABA), and ABA-Responsive Element Binding Factor 3 (FvABF3), a master regulator in ABA signaling, is responsible for this activation. FvALKBH10B mutation leads to a delay in fruit ripening and causes global m⁶A hypermethylation of 1859 genes. Further analyses show that FvALKBH10B positively modulates the mRNA stability of SEPALLATA3 (FvSEP3) encoding a transcription factor via m⁶A demethylation. In turn, FvSEP3 targets numerous ripening-related genes including those associated with biosynthesis of ABA and anthocyanin and regulates their expression. Our findings uncover an FvABF3-FvALKBH10B-FvSEP3 cascade in controlling fruit ripening in strawberry and provide insights into the complex regulatory networks involved in this process.

CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), a pivotal repressor in plant photomorphogenesis, has been extensively studied in various plant processes. However, the specific roles of COP1 in fruit remain poorly understood. Here, we functionally characterized SlCOP1-1 (also known as LeCOP1), an Arabidopsis (Arabidopsis thaliana) COP1 ortholog, in tomato (Solanum lycopersicum) fruit ripening and disease resistance. Despite the clear upregulation of SlCOP1-1 during fruit ripening, knockout or overexpression of SlCOP1-1 in tomatoes only minimally affected ripening. Intriguingly, these genetic manipulations substantially altered fruit resistance to the fungal pathogen Botrytis cinerea. Proteomic analysis revealed differential accumulation of proteins associated with fruit disease resistance upon SlCOP1-1 knockout or overexpression. To unravel the mechanism of SlCOP1-1 in disease resistance, we conducted a screen for SlCOP1-1-interacting proteins and identified the stress-related bZIP transcription factor SlOpaque2. We provide evidence that SlOpaque2 functions in tomato resistance to B. cinerea, and SlCOP1-1-mediated mono-ubiquitination and stabilization of SlOpaque2 contributes to fruit resistance against B. cinerea. Our findings uncover a regulatory role of COP1 in controlling fruit disease resistance, enriching our understanding of the regulatory network orchestrating fruit responses to disease.