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Article

Transcriptomics and Metabolomics Reveal the Dwarfing Mechanism of Pepper Plants Under Ultraviolet Radiation

by
Zejin Zhang
1,†,
Zhengnan Yan
2,†,
Xiangyu Ding
2,
Haoxu Shen
2,
Qi Liu
2,
Jinxiu Song
3,
Ying Liang
1,
Na Lu
4 and
Li Tang
1,*
1
Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
2
College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
3
College of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, China
4
Center for Environment, Health and Field Sciences, Chiba University, 6-2-1 Kashiwanoha, Kashiwa 277-0882, Chiba, Japan
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to the work.
Agriculture 2025, 15(14), 1535; https://doi.org/10.3390/agriculture15141535 (registering DOI)
Submission received: 1 May 2025 / Revised: 9 July 2025 / Accepted: 10 July 2025 / Published: 16 July 2025
(This article belongs to the Special Issue The Effects of LED Lighting on Crop Growth, Quality, and Yield)
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Versions Notes

Abstract

As a globally significant economic crop, pepper (Capsicum annuum L.) plants display excessive plant height (etiolation) in greenhouse production under an undesirable environment, leading to lodging-prone plants with reduced stress resistance. In the present study, we provided supplementary ultraviolet-B (UV-B, 280–315 nm) light to pepper plants grown in a greenhouse to assess the influences of UV-B on pepper growth, with an emphasis on the molecular mechanisms mediated through the gibberellin (GA) signaling pathway. The results indicated that UV-B significantly decreased the plant height and the fresh weight of pepper plants. However, no significant differences were observed in the chlorophyll content of pepper plants grown under natural light and supplementary UV-B radiation. The results of the transcriptomic and metabolomic analyses indicated that differentially expressed genes (DEGs) were significantly enriched in plant hormone signal transduction and that UV radiation altered the gibberellin synthesis pathway of pepper plants. Specifically, the GA3 content of the pepper plants grown with UV-B radiation decreased by 39.1% compared with those grown without supplementary UV-B radiation; however, the opposite trend was observed in GA34, GA7, and GA51 contents. In conclusion, UV-B exposure significantly reduced plant height, a phenotypic response mechanistically linked to an alteration in GA homeostasis, which may be caused by a decrease in GA3 content. Our study elucidated the interplay between UV-B and gibberellin biosynthesis in pepper morphogenesis, offering a theoretical rationale for developing UV-B photoregulation technologies as alternatives to chemical growth inhibitors.

1. Introduction

Pepper (Capsicum annuum L.), as a globally important vegetable crop, has witnessed a steady increase in its planting area and production around the world. In addition, pepper production in China accounted for approximately 44.7% of global output in 2023, followed by India, Bangladesh, and Thailand [1,2].
Greenhouse production has revolutionized modern agriculture by providing a controlled environment to cultivate crops year-round, ensuring food security and economic stability, particularly for high-value vegetables [3,4]. Compared with traditional production, greenhouse-based production offers advantages such as attaining high and stable yields, off-season production capabilities, and resistance to natural disasters [5,6]. However, achieving optimal conditions for plant growth in greenhouses is challenging due to the complex interplay between environmental factors, among which light, air temperature, and nutrition play pivotal roles.
As one of the most important environmental factors, light drives photosynthesis and acts as a critical regulatory signal for plant growth, shaping photomorphogenic processes such as stem elongation and leaf expansion, and affecting plant yield [7,8]. However, light availability is often constrained by structural components (e.g., frames, glazing materials) and environmental conditions (e.g., cloud cover, seasonal variations) in greenhouse production, leading to suboptimal light quantity and quality [8,9,10]. Insufficient or undesired light can disrupt plant photomorphogenesis, resulting in elongated, weak seedlings with reduced vigor—a phenomenon commonly known as “etiolation”. Vegetable plants grown under these conditions are more susceptible to pathogens, exhibit delayed transplant adaptation, and ultimately display compromised crop productivity [11,12,13]. Moreover, the spectral composition of light in greenhouses, dominated by certain wavelengths due to artificial lighting or shading, can alter plant hormone signaling and metabolic pathways, further impacting growth trajectories.
For most horticultural plants, red plus blue light is commonly applied in the controlled environment [14]. Previous studies have demonstrated that red light promotes stem elongation and leaf expansion [15,16,17,18]. However, excessive red-light exposure leads to excessive vegetative growth, resulting in plants with reduced stress resistance and heightened susceptibility to lodging [19,20]. In contrast, blue light inhibits leaf expansion and stem growth, shortens the internodes, and reduces plant height [21]. In addition to red and blue light, ultraviolet (UV) radiation, particularly UV-B (280–315 nm), plays a significant role in shaping plant growth and development [22]. Plants have evolved sophisticated mechanisms to perceive and respond to UV-B radiation, which can influence various physiological processes, including photomorphogenesis, secondary metabolite biosynthesis, and stress adaptation [23]. Among these responses, alterations in plant architecture, such as reduced plant height, are commonly observed under UV-B exposure in tomato plants [24], chili pepper plants [25], and rice seedlings [26]. Phenylpropanoids, a class of specialized secondary metabolites, play pivotal roles in plant development and adaptive responses to environmental stresses, including drought and UV radiation [27]. In addition, UV-B radiation is influenced by factors such as latitude, altitude, and weather conditions. Previous studies have indicated that organisms inhabiting low-latitude regions receive more UV-B radiation compared to those growing in high-latitude areas and that UV-B radiation increases with an increase in altitude [28,29].
Plant height is a critical agronomic trait that affects crop yield, resource allocation, and resistance to environmental stress [30,31]. Excessive or insufficient plant height is detrimental to plant growth and subsequently reduces crop yield [32,33]. Horticultural plants with a greater height, due to their relatively narrow base and potentially weaker stem structure, are more vulnerable to external forces and thus more prone to lodging [34]. For instance, reducing plant height reduced lodging in maize by reducing the magnitude of bending moments imparted on the plant by the wind [35,36]. Therefore, plant height and stem strength are often modulated by chemical regulation (e.g., plant growth regulators), which serves as an effective approach commonly applied by growers [37]. However, this approach of using chemical agents to regulate plant height is associated with issues such as environmental pollution, potential harm to non-target organisms, and the risk of chemical residue [38]. Therefore, it is imperative to develop an efficient, environmentally benign, and straightforward approach for the regulation of plant morphology.
Gibberellins (GAs), a class of diterpenoid hormones, are central regulators of plant height through their promotion of stem elongation [39,40]. The biosynthesis and catabolism of GAs are tightly controlled by a network of enzymes, including GA 3-oxidases (GA3oxs) and GA 2-oxidases (GA2oxs) [41]. Previous studies have shown that environmental factors, such as light quality and quantity, can modulate GA metabolism to influence plant height [42]. For instance, UV-B radiation has been reported to alter GA levels in Arabidopsis and other plant species, suggesting a potential link between UV-B signaling and GA-mediated growth regulation [43]. However, the metabolic process and molecular mechanisms underlying the UV-B-mediated regulation of plant height, particularly in crops such as pepper, remain incompletely understood.
At present, the effects of UV-B radiation on plant architecture and the underlying molecular mechanisms remain elusive. Specifically, whether UV-B regulates pepper plant height through GA metabolism and the relative genes and pathways involved, is still unclear. Addressing these gaps could provide valuable insights into optimizing pepper cultivation under UV-B-enriched environments, such as in high-altitude regions or under specific agricultural practices.
In this study, we aim to characterize the transcriptional and biochemical responses of GA-related genes and metabolites in pepper plants exposed to UV-B treatment. By integrating physiological measurements, gene expression analysis, and hormonal profiling, we seek to explore the molecular mechanisms through which UV-B influences GA metabolism and, consequently, plant height in pepper plants. Our research will enhance the comprehension of UV-B–GA interactions in crop plants and establish a fundamental basis for the cultivation of UV-B-tolerant pepper varieties with an optimized plant architecture.

2. Materials and Methods

2.1. Plant Materials and Light Treatment Design

Pepper (Capsicum annuum L. cv. Zhenlazaoyou) plants at the six-true-leaf stage were transplanted in plastic pots (2 L) filled with cocopeat in a plastic greenhouse of the Horticultural Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu City, Sichuan Province from September 12th to October 28th, 2024, which was considered as the control. An additional UV-B was included (TL20W/01, PHILIPS Co., Ltd., Eindhoven, The Netherlands), which was marked as UV. The light intensity and supplementary light duration were 15 μmol m−2 s−1 and 12 h d−1, respectively. In this study, each treatment was replicated in three blocks (20 plants per block).

2.2. Growth Measurement

2.2.1. Plant Morphology and Growth Characteristics

Three uniform plants were randomly chosen from each block for measurement. The plant height and dry/fresh weight of pepper plants were measured using rulers and electronic analytical balances (DXL-JCS3100A, DELIXI Co., Ltd., Leqing, China), respectively. The stem diameter was measured in the middle part between the cotyledon and hypocotyl using a vernier caliper (Yantai Greenery Tools Co., Ltd., Yantai, China).

2.2.2. Photosynthetic Pigment Content

The chlorophyll contents of the pepper leaves were measured using spectrophotometry by a spectrophotometer (T600, PERSEE Co., Ltd., Beijing, China), following the method described by Lichtenthaler and Wellburn [44]. Briefly, leaf samples of pepper plant (0.1 g) were cut into small pieces and then extracted in 80% acetone (v/v) for 72 h in the dark. The absorbance of the extracts was measured at 663 nm and 645 nm using the aforementioned spectrophotometer.

2.2.3. RNA-Seq and Data Processing

There were three biological replicate samples for transcriptomic and hormone metabolomic measurements. Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and its quality was evaluated by NanoDrop spectrophotometry (NC2000, Thermo Scientific, Waltham, MA, USA). Using 3 μg of total RNA as input, mRNA was purified with poly-T oligo-conjugated magnetic beads, fragmented with divalent cations in an Illumina buffer (Illumina, Inc., San Diego, CA, USA), and reverse-transcribed to cDNA. Double-stranded cDNA was synthesized, blunted, adenylated at the 3′ end, and ligated with Illumina PE adapters. Library fragments (400–500 bp) were purified by the AMPure XP system (Beckman Coulter, Beverly, MA, USA), enriched by 15-cycle PCR with Illumina primers, and repurified. Library quality was assessed by Agilent High Sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent Technologies, Inc., Santa Clara, CA, USA), with total and effective concentrations determined by PicoGreen and qPCR, respectively. Primers for RNA amplification are provided in the Supplementary Table S1. Sequencing was performed on a NovaSeq 6000 platform (Illumina, Inc., San Diego, CA, USA) at Shanghai Personal Biotechnology Co., Ltd, Shanghai, China. High-quality clean reads were aligned to the reference genome of Capsicum annuum (https://solgenomics.net/ftp//genomes/Capsicum_annuum/C.annuum_cvCM334/, accessed on 10 March 2025). The summary of quality control of mRNA-seq data and the gene expression profile of the pepper plants are shown in the Supplementary Tables S1 and S2.

2.2.4. qRT-PCR Analysis

Total RNA samples were extracted with TriZOL reagent (InvitrogenTM, Carlsbad, CA, USA). The Advantage® RT-for-PCR Kit (Clontech, Mountain View, CA, USA) was used to generate the first strand cDNA according to the manufacturer’s instructions. The reaction mixtures used for qPCR consist of 10 μL of 2 × SYBR real-time PCR premixture, 0.4 μL (each) of primers F and R, 1 μL of template cDNA, and 8.2 μL RNase-free ddH2O. The primers for qRT-PCR are listed in Supplementary Table S3. Gene expression was analyzed by qRT-PCR using a LightCycler 480 II (Roche, Basel, Switzerland), according to the manufacturer’s instructions. The PCR conditions were as follows: denaturation at 95 °C for 5 min; 40 cycles of 95 °C for 15 s, and 60 °C for 30s. The mRNA levels of the pepper reference gene were used to normalize the data for each qRT-PCR run. Relative gene expression was calculated based on the 2−ΔΔCt method [45].

2.2.5. Metabolomics Analysis of Gibberellins

The sample pretreatment of fresh pepper samples referred to previous studies [46,47,48]. Gibberellins were precisely quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Subsequently, clustering analysis was carried out on the determined contents of gibberellins, and functional annotation and enrichment analysis of KEGG pathways were conducted for the differential metabolites.

2.3. Statistical Analysis

Statistical differences were determined by a Student’s t-test using SPSS 26.0 software (IBM, Inc., Chicago, IL, USA) (p < 0.05). Data are presented as mean ± SD. Differentially expressed genes (DEGs) identified between the two samples were filtered for |log2FoldChange| > 1 and significance p-value < 0.05 using DESeq2 (v1.38.3) [49]. Functional-enrichment analyses including Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) were performed to identify the DEGs significantly enriched in metabolic pathways and GO terms based on Li et al. [50]. GO annotations were leveraged to characterize gene functions from cell components (CC), molecular functions (MF), and biological processes (BP). Heatmap showed the expression levels [log2(FPKM+1)] of genes related to gibberellin biosynthesis.

3. Results

3.1. Plant Morphology, Photosynthetic Pigment Content, and Biomass Accumulation of Pepper Plants as Affected by UV-B Radiation

Significant differences were observed in plant height, shoot fresh weight, and root fresh weight of pepper plants between the control and UV treatments (Figure 1 and Figure 2); however, no remarkable differences were found in stem diameter, chlorophyll a content, chlorophyll b content, and total chlorophyll content of pepper plants (Figure 2 and Figure 3). Plant height, shoot fresh weight, and root fresh weight of pepper plants exposed to UV radiation decreased by 32.5%, 23.3%, and 42.3% compared with those grown under the control treatment.

3.2. Transcriptome Sequencing, Clustering, and Function Enrichment

To elucidate the molecular mechanisms underlying the responses of pepper plants to control and UV-B radiation conditions, three biological replicate samples of pepper leaves were collected for transcriptome sequencing analysis (Figure 4). Our results demonstrated that UV radiation induced 1977 upregulated genes and 804 downregulated genes in pepper plants. (Figure 4A,B). To comprehensively dissect the intricate molecular functions of the DEGs identified in control and UV treatments, GO and KEGG enrichment analyses were performed (Figure 5). Biological pathways were assigned to the DEGs from the KEGG database after screening for pathways and the results showed that the DEGs in the ‘UV and Control’ comparison were significantly enriched in plant hormone signal transduction, phenylpropanoid biosynthesis, and diterpenoid biosynthesis (Figure 5A). It was found that the enrichment score (ES value) of the plant hormone signal transduction pathway in the KEGG was 0.55 by gene set enrichment analysis (GSEA) (Figure 5B). A GO enrichment analysis indicated that the genes affected by UV treatments were significantly enriched in the cell components, molecular functions, and biological processes (Figure 5C). These genes were enriched in GO terms mainly in response to regulation of nucleic acid-templated transcription, regulation of RNA biosynthetic process, DNA-binding transcription factor activity, and transcription regulation activity.

3.3. Analysis of the Gibberellin Metabolic Pathway of Pepper Plants Exposed to UV Radiation

Our results exhibited the diterpenoid biosynthesis pathway, gibberellin content, and relative expression of associated genes under control and UV-treated conditions in pepper plants (Figure 6, Figure 7 and Figure S1). The content of GA19, GA20, and GA3 of pepper plants exposed to UV-B radiation decreased significantly; however, the content of GA34, GA7, and GA51 of pepper plants exposed to UV-B radiation increased significantly compared with those grown without UV-B radiation. Specifically, the GA19, GA20, and GA3 contents of pepper plants grown under UV treatment decreased by 49.9%, 42.5%, and 39.1% compared with those grown under the control treatment. On the contrary, GA51, GA7, and GA34 contents of pepper plants grown under UV treatment increased by 45.7%, 50.0%, and 49.3% compared with those grown under the control treatment (Figure 7). Gibberellin 20-oxidase (GA20ox), Gibberellin 2-oxidase (GA2ox), and Gibberellin 3-oxidase (GA3ox) content of pepper plants exposed to UV-B radiation were increased significantly. The transcriptome results obtained by RNA-seq indicated that the expression levels of CA01g10440, CA06g16820, CA07g16060, CA02g10780, CA01g22480, and CA05g06370 in pepper plants exposed to UV-B radiation was 29.1-, 3.3-, 1.4-, 13.3-, 4.9-, and 6.0-folds that of peppers treated without UV-B radiation (Figure 6). In addition, the relative expression levels of CA01g10440, CA06g16820, CA07g16060, CA02g10780, CA01g22480, and CA05g06370 in pepper plants exposed to UV-B radiation analyzed by qRT-PCR was 99.4-, 9.4-, 4.7-, 16.2-, 11.5-, and 4.5-fold that of peppers treated without UV-B radiation (Figure 8). The relative expressions analyzed by qRT-PCR were consistent with the transcriptomic data, indicating their reliability and accuracy.

4. Discussion

4.1. Effects of UV-B Radiation on the Leaf Morphology, Pigment Content, and Biomass of Pepper Plants

Understanding how light modulates plant physiology and development is essential for optimizing greenhouse systems [51,52]. Previous research has highlighted the profound effects of light spectral distribution on the key processes of horticultural plants under a controlled environment, such as photosynthetic efficiency [53], secondary metabolite biosynthesis [54], and stress tolerance [55]. However, the integrated effects of supplementary UV-B light with dynamic light environments as the background on pepper plants, particularly in commercial greenhouse operations, remain underexplored. Addressing this knowledge gap is critical for developing precision lighting strategies that enhance plant quality, reduce production costs, and improve crop performance.
Plant height serves as a particularly crucial parameter of plant architecture, acting as a key determinant of a plant’s capacity to access essential resources [56]. Growers typically prefer plants with a compact architecture, aiming for high-yield and high-quality products in the future [57]. Taller plants often have a competitive edge in capturing sunlight, as they can position their leaves above those of neighboring plants, maximizing photosynthetic efficiency [58]. However, if plants grow overly tall or experience excessive vegetative growth (etiolation), their stems may become thin and weak, which makes the plants highly susceptible to lodging, and in turn reduces the yield and quality in the subsequent growth stages [59]. Some previous studies have focused on the influences of UV-A radiation on leaf morphology and plant growth, such as tomato plants [60,61] and bell pepper plants [62]; however, there has been relatively little research on the effects of UV-B radiation on horticultural plants. Our results indicated that the plant height of pepper plants grown under UV-B radiation decreased significantly (Figure 1 and Figure 2). Similar trends were observed in chili pepper [25], rice seedlings [26], and barley plants [63], indicating that UV-B lowers the plant height and alters the plant morphology.
Plant biomass accumulation, which reflects the growth and productivity of plants, represents the results of various physiological processes such as photosynthesis, respiration, and nutrient uptake [64,65]. UV-B was once considered a harmful radiation, which could cause damage to the leaf surface, inhibit the biomass production of fruits, and lead to a reduction in the weight of products [66,67]. However, studies have found that the low-intensity of UV-B can regulate the secondary metabolism of plants and promote the accumulation of secondary compounds [68]. A decreased trend was observed in fresh weight of pepper plants exposed to UV-B radiation in our study (Figure 2). Similarly, decreased plant height associated with decreased dry shoot weight was observed in barley plants exposed to UV-B radiation [63]. However, increased biomass with UV-B radiation was observed in some previous studies [69] but no significant differences were found in chili pepper [25]. The reason for these different results may be caused by the experimental design (e.g., light intensity or supplementary light duration of UV-B treatment), or the differences in other environmental conditions. For instance, there was no significant difference in leaf dry weight between UV-treated and non-UV-treated plants, regardless of whether the plants were under drought or well-watered conditions. However, under well-watered conditions, the stem dry weight of chili pepper plants decreased when exposed to UV-B radiation [25]. UVR8 is a plant-specific UV-B photoreceptor. Previous studies indicated that uvr8 mutants exhibited longer hypocotyls, reduced flavonoid accumulation, and more severe damage under UV-B radiation compared to wild-type plants, and UVR8 has been recognized as a crucial positive regulator in UV-B-induced photomorphogenic development and stress acclimation [67,70].
Chlorophyll content in plants drives photosynthesis and impacts plant competition [71,72]. Previous studies indicated that no significant differences were observed in total chlorophyll content of bell pepper plants exposed to UV-B radiation compared with the control [73], similar results were also found in barley plants [63]. The stable chlorophyll content in plants under UV-B may result from efficient photoprotection (including UV-absorber synthesis and antioxidant enzyme boost) maintaining synthesis–degradation equilibrium, plant acclimation, and possibly low UV-B intensity or brief exposure.

4.2. Transcriptomics and Metabolomics Reveal the Changes in the Plant Height of Pepper Plants Under UV Radiation

Plant height, as one of the key agronomic traits, is an ideal target for breeding elite crop varieties with optimized plant architectures, influencing yield performance and lodging resistance. Previous studies indicated that several phytohormones are involved in the regulation of plant height, including gibberellin [74,75], auxins [76], and ethylene [77]. Gibberellic acid, a crucial plant growth regulator, plays an active role in cell elongation and is intricately engaged in other vital physiological processes during plant growth, development, and the flowering phase [78]. Gibberellins are recognized as phytohormones and constitute a large family of diterpenoids. Correspondingly, KEGG enrichment analysis identified significant enrichment in plant hormone signal transduction pathways and diterpenoid biosynthesis processes in our study (Figure 5A). Although gibberellins regulate a diverse range of developmental processes in plants, their most prominent role is the regulation of plant height [74]. Previous studies have investigated the effects of exogenous gibberellin application on plants [79,80]. For instance, a previous study indicated that foliar application of GA3 at the four-leaf stage increased the plant height of globe artichoke across growing seasons [79], while similar trends were also observed in sugar beet [81]; however, this phenomenon may be related to the gibberellin concentration. For example, the shoot length of calla lily (Zantedeschia aethiopica) increased as the concentration of exogenous applications of gibberellic acid increased from 25 to 100 mg L−1, while an excess gibberellic acid concentration (200 mg L−1) led to a decreased shoot length in the plants [80]; similar trends were also reported by Muniandi et al. [78]. Additionally, the endogenous gibberellin content in the plants was affected by water deficiency [82], light intensity [83], and temperature [84]. For instance, the plant height of soybean plants decreased with additional UV-B irradiation [85]. Similar results were also observed in pepper plants in our study; additionally, whether and how the plant height of pepper plants is modulated by UV-B-mediated changes in GA metabolism are also revealed in the present study. It is worth noting that the synergistic and antagonistic interactions between GAs and other phytohormones, including auxins and ethylene, play critical roles in the regulation of plant height [86,87]. For instance, Huang et al. [86] indicated that tomato SlGRAS24 is a key transcription factor for the coordinated regulation of GA and auxin signaling pathways, which provides critical insight into the molecular mechanisms underlying the enhanced plant height observed in mutant plants. In addition, GA and brassinosteroids (BR) exhibit distinct and overlapping regulatory roles in organ elongation and the determination of final plant height [87]. Notably, the intricate crosstalk between gibberellins and other phytohormones, along with their combined regulatory effects on the molecular and physiological mechanisms underlying plant dwarfism, remains incompletely elucidated and thus necessitates in-depth investigation in future study.
The phenylpropanoid pathway persists as a pivotal target in the development of climate-resilient crops, encompassing core metabolites such as flavonoids and lignin. These compounds play pivotal roles in mediating biotic and abiotic interactions, with their functional relevance extending to critical adaptive traits including tolerance to drought, temperature fluctuations, and UV radiation stress [88]. For instance, flavonoids—a major class of secondary metabolites biosynthesized via the phenylpropanoid pathway—were significantly upregulated in Ginkgo biloba [89], lettuce [90], and blueberry [91] under UV-B radiation exposure. Our transcriptomic analyses revealed that DEGs identified in the ‘UV vs. Control’ comparison were significantly enriched in pathways related to plant hormone signal transduction, phenylpropanoid biosynthesis, and diterpenoid biosynthesis (Figure 5A). Similarly, DEGs were mainly enriched in the pathways of plant hormone signal transduction and terpenoid biosynthesis in Dryopteris fragrans upon exposure to UV-B radiation [92]. Additionally, Zhan et al. [93] observed that UV-B-induced CbMYB108 exhibits a dual function, simultaneously enhancing diterpene biosynthesis and glandular trichome development in Conyza blinii. Integrated transcriptomics and metabolomics uncover a complex molecular interplay, revealing regulatory mechanisms at the gene and metabolite levels [94]. The differences in the gibberellin content and related enzyme genes between plants subjected to the UV-B and control treatments in our results reveal the mechanism underlying the reduction in the plant height of pepper plants (Figure 6, Figure 7 and Figure 8). Transcriptomic profiling in our study demonstrated that DEGs identified from the ‘UV vs. Control’ comparison was significantly enriched in pathways associated with plant hormone signal transduction and diterpenoid biosynthesis (Figure 5A). As a key subclass of diterpenoids, gibberellins, a class of plant growth hormones with complex synthesis pathways in horticultural plants, play a pivotal role in regulating plant height [39,95]. There are a wide variety of gibberellins (such as GA3, GA8, GA34, and GA51), which differ in stability and activity [96,97]. Our results indicate that the contents of GA7, GA34, and GA51 increased significantly with the UV-B treatment; conversely, the contents of GA19, GA20, and GA3 decreased significantly (Figure 7). GA19 and GA20 are precursors for the synthesis of GA3, and GA3 promotes the activity of the apical meristem in plants [98]. The variations in plant height may primarily stem from the GA3 content, with the activity and effectiveness of GA3 serving as the underlying determinants. GA3 can promote cell elongation, induce flowering, and enhance seed germination [99], which could potentially lead to the observed discrepancies in our results. Our study also indicated that the GA51 and GA34 contents (the inactive 2b-hydroxylated product of GA4) increased in pepper plants exposed to UV-B radiation. In addition, a previous study indicated that the 2β-hydroxylated compound GA51 was virtually inactive [100]. It is thus speculated that UV conditions alter the production of substances in the synthesis pathway, reducing the production of highly active gibberellins, which in turn affects plant height and alleviates the excessive growth of pepper plants.
The gene expression levels of related enzymes in the pepper plants in the two experimental groups were measured, and our results showed an increase in the expression levels of GA20ox, GA2ox, and GA3ox under UV-B exposure. The contents of the corresponding enzymes in pepper plants changed accordingly (Figure 6). This metabolic cascade elucidates the dynamic regulatory mechanisms of key rate-limiting enzymes in controlling bioactive GA isoforms during gibberellin biosynthesis. Previous studies indicated that the mutations that cause loss of function in GA biosynthetic genes, including GA20ox and GA3ox, result in dwarf phenotypes in plants [101]. In contrast, GA2ox enzymes are responsible for GA catabolism, inactivating the phytohormone and imposing negative regulation on plant growth. The overexpression of genes encoding GA2ox enzymes inhibits stem elongation [102]. However, based on the gibberellin synthesis pathway and the final product contents of the gibberellins of pepper plants grown under the two treatments, we infer that the gibberellin pathway is inhibited under UV conditions, resulting in a decrease in the content of GA20 and a reduction in the content of GA3, leading to the decreased plant height of pepper plants. These results indicate that UV-B radiation disrupts the established hormone distribution pattern by regulating the processes of hormone synthesis, transport, and biological activation, thereby suppressing the apical meristem and inhibiting the lateral meristem (Figure 6 and Figure 9). The gibberellin signaling pathway in plants is governed by a homeostatic balance: repressing the expression of genes involved in GA biosynthesis while enhancing the production of GA receptors and catabolic enzymes for bioactive GAs. Current mechanistic models of GA action demonstrate that DELLA family regulatory proteins suppress plant growth, whereas GA activation promotes growth by alleviating DELLA-mediated growth inhibition [103]. Our study offers insights into the link between altered GA metabolism and plant dwarfing; however, the absence of functional assays, such as exogenous GA3 rescue experiments and mutant/overexpression line analyses, means that the mechanisms behind this link remain unsubstantiated. Future research should integrate gene expression analysis with functional validation to accurately elucidate the underlying mechanisms.

5. Conclusions

Our study provides a comprehensive elucidation of UV-B radiation’s effects on pepper growth dynamics by integrating morphological, transcriptomic, and metabolomic analyses. UV-B exposure significantly reduced plant height, a phenotypic response mechanistically linked to alteration in gibberellin homeostasis. Targeted metabolomic profiling revealed a marked decrease in bioactive GA3 levels, concomitant with the transcriptional reprogramming of GA metabolic pathways. Specifically, UV-B irradiation simultaneously upregulated key biosynthetic enzymes (GA20ox and GA3ox) and catabolic regulators (GA2ox), establishing a dynamic equilibrium that redirects GA metabolic flux toward deactivation. This coordinated regulation of GA20ox, GA3ox, and GA2ox effectively constrains stem elongation while maintaining metabolic flexibility. These findings elevate our sophisticated understanding of the molecular mechanisms underlying the responses of pepper plants to UV-B radiation and provide valuable insights for manipulating plant architecture and optimizing growth regulation in horticultural species.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/agriculture15141535/s1.

Author Contributions

Methodology: Z.Z., Z.Y., Y.L., N.L. and L.T.; data curation: Z.Z., Z.Y., X.D., H.S. and Q.L.; software: Z.Z., X.D. and H.S.; investigation: Z.Z., Y.L. and L.T.; conceptualization: Z.Z., X.D., H.S., Q.L., J.S., N.L., Y.L. and L.T.; writing–original draft: Z.Z., Z.Y., X.D. and H.S.; writing–review and editing: Z.Z., Z.Y., L.T., X.D. and H.S.; supervision: X.D., H.S., Q.L., J.S., N.L. and Y.L.; funding acquisition: Z.Z.,Y.L. and L.T.; resources and project administration: Z.Z. and L.T. All authors have read and agreed to the published version of the manuscript.

Funding

This work was completed with financial support from the Sichuan innovation team (SCCXTD-2024-5).

Data Availability Statement

The original contributions presented in the study are included in the article and Supplementary Materials, further inquiries can be directed to the corresponding author.

Conflicts of Interest

The authors declare no conflicts of interest.

References

  1. Zhang, D.; Sun, X.; Battino, M.; Wei, X.; Shi, J.; Zhao, L.; Liu, S.; Xiao, J.; Shi, B.; Zou, X. A comparative overview on chili pepper (capsicum genus) and sichuan pepper (zanthoxylum genus): From pungent spices to pharma-foods. Trends Food Sci. Technol. 2021, 117, 148–162. [Google Scholar] [CrossRef]
  2. FAOSTAT. Available online: www.fao.org/faostat/zh/#data/QCL (accessed on 20 March 2025).
  3. Lemarie, S.; Guérin, V.; Jouault, A.; Proost, K.; Cordier, S.; Guignard, G.; Demotes-Mainard, S.; Bertheloot, J.; Sakr, S.; Peilleron, F. Melon and potato crops productivity under a new generation of optically active greenhouse films. Acta Hortic. 2019, 1296, 517–526. [Google Scholar] [CrossRef]
  4. Kim, M.; Lee, Y.-B.; Choi, K.-Y. Effects of greenhouse temperatures and solar irradiance levels on the monthly production of summer-cultivated Paprika. Hortic. Sci. Technol. 2024, 42, 339–349. [Google Scholar] [CrossRef]
  5. Šalagovič, J.; Vanhees, D.; Verboven, P.; Holsteens, K.; Verlinden, B.; Huysmans, M.; Van de Poel, B.; Nicolaï, B. Microclimate monitoring in commercial tomato (Solanum lycopersicum L.) greenhouse production and its effect on plant growth, yield and fruit quality. Front. Hortic. 2024, 3, 1425285. [Google Scholar] [CrossRef]
  6. Weiss, J.; Gruda, N.S. Novel breeding techniques and strategies for enhancing greenhouse vegetable product quality. Agronomy 2025, 15, 207. [Google Scholar] [CrossRef]
  7. Kharshiing, E.V.; Lyngdoh, M.O.I.; Vardhana, L.; Ramyani, B.; Sahoo, L. Manipulation of light environment for optimising photoreceptor activity towards enhancing plant traits of agronomic and horticultural importance in crops. J. Hortic. Sci. Biotechnol. 2022, 97, 535–551. [Google Scholar] [CrossRef]
  8. Lemarié, S.; Proost, K.; Quellec, A.-S.; Cordier, S.; Guignard, G.; Guérin, V.; Sakr, S.; Peilleron, F. The innovative ‘LIGHT CASCADE®’ sunlight photoconversion greenhouse films enhance horticultural crops production in Europe. Acta Hortic. 2023, 1377, 275–282. [Google Scholar] [CrossRef]
  9. Lin, T.; Maier, C.R.; Liang, W.; Klause, N.; He, J.; Tissue, D.T.; Lan, Y.-C.; Sethuvenkatraman, S.; Goldsworthy, M.; Chen, Z.-H. A light-blocking greenhouse film differentially impacts climate control energy use and capsicum production. Front. Energy Res. 2024, 12, 1360536. [Google Scholar] [CrossRef]
  10. Mu, Z.; Bo, Y.; Xu, J.; Song, K.; Dong, B.; Wang, J.; Shu, S.; Wang, Y.; Guo, S. Development and application of greenhouse light environment simulation technology based on light path tracing. Comput. Electron. Agric. 2024, 218, 108652. [Google Scholar] [CrossRef]
  11. Chen, Z.; Liu, Y.; Zeng, B.; Jiang, Q.; Wang, S.; Li, X. Growth and transcriptomics analysis of Michelia macclurei Dandy plantlets with different LED quality treatments. Phyton-Int. J. Exp. Bot. 2023, 92, 2891–2906. [Google Scholar] [CrossRef]
  12. Wei, Y.; Wang, S.; Yu, D. The role of light quality in regulating early seedling development. Plants 2023, 12, 2746. [Google Scholar] [CrossRef] [PubMed]
  13. Zhou, M.; Sun, H.; Xu, X.; Yang, J.; Wang, G.; Wei, Z.; Xu, T.; Yin, J. Study on the method and mechanism of seedling picking for pepper (Capsicum annuum L.) plug seedlings. Agriculture 2024, 14, 11. [Google Scholar] [CrossRef]
  14. 14Si, C.; Lin, Y.; Luo, S.; Yu, Y.; Liu, R.; Naz, M.; Dai, Z. Effects of LED light quality combinations on growth and leaf colour of tissue culture-generated plantlets in Sedum rubrotinctum. Hortic. Sci. Technol. 2024, 42, 53–67. [Google Scholar]
  15. Bi, X.; Xu, H.; Yang, C.; Zhang, H.; Li, W.; Su, W.; Zheng, M.; Lei, B. Investigating the influence of varied ratios of red and far-red light on lettuce (Lactuca sativa): Effects on growth, photosynthetic characteristics and chlorophyll fluorescence. Front. Plant Sci. 2024, 15, 1430241. [Google Scholar] [CrossRef] [PubMed]
  16. Wang, T.; Sun, Q.; Zheng, Y.; Xu, Y.; Liu, B.; Li, Q. Effects of red and blue light on the growth, photosynthesis, and subsequent growth under fluctuating light of cucumber seedlings. Plants 2024, 13, 1668. [Google Scholar] [CrossRef] [PubMed]
  17. Mahajan, S.; Chowdhury, M.K.; Mazumder, S.R.; Solaiman, A.H.M.; Tasnim, Z.; Arefin, S.M.A.; Uddain, J. Evaluation of growth and nutritional profile of microgreens of different crops under various LEDs light spectrums. J. Appl. Hortic. 2024, 26, 231–236. [Google Scholar] [CrossRef]
  18. Shen, Y.; Han, X.; Wang, H.; Shen, J.; Sun, L.; Fan, K.; Wang, Y.; Ding, S.; Song, D.; Ding, Z. Full-length transcriptome sheds light into the molecular mechanism of tea leaf yellowing induced by red light. Sci. Rep. 2024, 14, 29901. [Google Scholar] [CrossRef] [PubMed]
  19. Mickens, M.A.; Skoog, E.J.; Reese, L.E.; Barnwell, P.L.; Spencer, L.E.; Massa, G.D.; Wheeler, R.M. A strategic approach for investigating light recipes for ‘Outredgeous’ red romaine lettuce using white and monochromatic LEDs. Life Sci. Space Res. 2018, 19, 53–62. [Google Scholar] [CrossRef] [PubMed]
  20. Agrawal, A.A.; Kearney, E.E.; Hastings, A.P.; Ramsey, T.E. Attenuation of the jasmonate burst, plant defensive traits, and resistance to specialist monarch caterpillars on shaded common milkweed (Asclepias syriaca). J. Chem. Ecol. 2012, 38, 893–901. [Google Scholar] [CrossRef] [PubMed]
  21. Ke, X.; Yoshida, H.; Hikosaka, S.; Goto, E. Effect of red and blue light versus white light on fruit biomass radiation-use efficiency in dwarf tomatoes. Front. Plant Sci. 2024, 15, 1393918. [Google Scholar] [CrossRef] [PubMed]
  22. Heijde, M.; Ulm, R. UV-B photoreceptor-mediated signalling in plants. Trends Plant Sci. 2012, 17, 230–237. [Google Scholar] [CrossRef] [PubMed]
  23. Liu, M.; Sun, W.; Ma, Z.; Guo, C.; Chen, J.; Wu, Q.; Wang, X.; Chen, H. Integrated network analyses identify MYB4R1 neofunctionalization in the UV-B adaptation of Tartary buckwheat. Plant Commun. 2022, 3, 100414. [Google Scholar] [CrossRef] [PubMed]
  24. Lima, I.H.A.; Rodrigues, A.A.; Resende, E.C.; da Silva, F.B.; Farnese, F.D.S.; Silva, L.J.; Rosa, M.; Reis, M.N.O.; Bessa, L.A.; de Oliveira, T.C.; et al. Light means power: Harnessing light spectrum and UV-B to enhance photosynthesis and rutin levels in microtomato plants. Front. Plant Sci. 2023, 14, 1261174. [Google Scholar] [CrossRef] [PubMed]
  25. Rodríguez-Calzada, T.; Qian, M.; Strid, Å.; Neugart, S.; Schreiner, M.; Torres-Pacheco, I.; Guevara-González, R.G. Effect of UV-B radiation on morphology, phenolic compound production, gene expression, and subsequent drought stress responses in chili pepper (Capsicum annuum L.). Plant Physiol. Biochem. 2019, 134, 94–102. [Google Scholar] [CrossRef] [PubMed]
  26. Hu, S.; Chen, Y.; Qian, C.; Ren, H.; Liang, X.; Tao, W.; Chen, Y.; Wang, J.; Dong, Y.; Han, J. Nuclear accumulation of rice UV-B photoreceptors is UV-B-and OsCOP1-independent for UV-B responses. Nat. Commun. 2024, 15, 6396. [Google Scholar] [CrossRef] [PubMed]
  27. Li, C.; Jiang, Y.; Xu, C.; Mei, X. Editorial: Contribution of phenylpropanoid metabolism to plant development and stress responses. Front. Plant Sci. 2024, 15, 1456913. [Google Scholar] [CrossRef] [PubMed]
  28. Caldwell, M.M.; Robberecht, R.; Billings, W. A steep latitudinal gradient of solar ultraviolet-B radiation in the arctic-alpine life zone. Ecology 1980, 61, 600–611. [Google Scholar] [CrossRef]
  29. Qian, G.; Ran, X.; Zhou, C.; Deng, D.; Zhang, P.; Guo, Y.; Luo, J.; Zhou, X.; Xie, H.; Cai, M. Systemic lupus erythematosus patients in the low-latitude plateau of China: Altitudinal influences. Lupus 2014, 23, 1537–1545. [Google Scholar] [CrossRef] [PubMed]
  30. Lee, M.B.; Shekasteband, R.; Hutton, S.F.; Lee, T.G. A mutant allele of the flowering promoting factor 1 gene at the tomato BRACHYTIC locus reduces plant height with high quality fruit. Plant Direct. 2022, 6, e422. [Google Scholar] [CrossRef] [PubMed]
  31. Park, J.R.; Jang, Y.H.; Kim, E.G.; Hur, S.S.; Kim, K.M. Quantitative Trait Loci Mapping Identified Candidate Genes Involved in Plant Height Regulation in Rice. Int. J. Mol. Sci. 2023, 24, 16895. [Google Scholar] [CrossRef] [PubMed]
  32. Bhat, J.A.; Karikari, B.; Adeboye, K.A.; Ganie, S.A.; Barmukh, R.; Hu, D.; Varshney, R.K.; Yu, D. Identification of superior haplotypes in a diverse natural population for breeding desirable plant height in soybean. Theor. Appl. Genet. 2022, 135, 2407–2422. [Google Scholar] [CrossRef] [PubMed]
  33. Bhujbal, S.K.; Rai, A.N.; Joshi-Saha, A. Dwarfs standing tall: Breeding towards the ‘Yellow revolution’ through insights into plant height regulation. Plant Mol. Biol. 2025, 115, 34. [Google Scholar] [CrossRef] [PubMed]
  34. Han, L.; Mo, M.; Gao, Y.; Ma, H.; Xiang, D.; Ma, G.; Mao, H. Effects of new compounds into substrates on seedling qualities for efficient transplanting. Agronomy 2022, 12, 983. [Google Scholar] [CrossRef]
  35. Stubbs, C.J.; Kunduru, B.; Bokros, N.; Verges, V.; Porter, J.; Cook, D.D.; DeBolt, S.; McMahan, C.; Sekhon, R.S.; Robertson, D.J. Moving toward short stature maize: The effect of plant height on maize stalk lodging resistance. Field Crops Res. 2023, 300, 109008. [Google Scholar] [CrossRef]
  36. Niu, Y.; Han, W.; Zhang, H.; Zhang, L.; Chen, H. Estimating maize plant height using a crop surface model constructed from UAV RGB images. Biosyst. Eng. 2024, 241, 56–67. [Google Scholar] [CrossRef]
  37. Zhang, J.; Zhang, Y.; Xing, J.; Yu, H.; Zhang, R.; Chen, Y.; Zhang, D.; Yin, P.; Tian, X.; Wang, Q.; et al. Introducing selective agrochemical manipulation of gibberellin metabolism into a cereal crop. Nat. Plants 2020, 6, 67–72. [Google Scholar] [CrossRef] [PubMed]
  38. Rostami, S.; Azhdarpoor, A. The application of plant growth regulators to improve phytoremediation of contaminated soils: A review. Chemosphere 2019, 220, 818–827. [Google Scholar] [CrossRef] [PubMed]
  39. Urbanova, T.; Tarkowská, D.; Strnad, M.; Hedden, P. Gibberellins-Terpenoid plant hormones: Biological importance and chemical analysis. Collect. Czech. Chem. Commun. 2012, 76, 1669–1686. [Google Scholar] [CrossRef]
  40. Sarwar, R.; Zhu, K.M.; Jiang, T.; Ding, P.; Gao, Y.; Tan, X.L. DELLAs directed gibberellins responses orchestrate crop development: A brief review. Crop Sci. 2023, 63, 1–28. [Google Scholar] [CrossRef]
  41. Yamaguchi, S. Gibberellin metabolism and its regulation. Annu. Rev. Plant Biol. 2008, 59, 225–251. [Google Scholar] [CrossRef] [PubMed]
  42. Li, K.; Yu, R.; Fan, L.-M.; Wei, N.; Chen, H.; Deng, X.W. DELLA-mediated PIF degradation contributes to coordination of light and gibberellin signalling in Arabidopsis. Nat. Commun. 2016, 7, 11868. [Google Scholar] [CrossRef] [PubMed]
  43. Qian, C.; Chen, Z.; Liu, Q.; Mao, W.; Chen, Y.; Tian, W.; Liu, Y.; Han, J.; Ouyang, X.; Huang, X. Coordinated Transcriptional regulation by the UV-B photoreceptor and multiple transcription factors for plant UV-B responses. Mol. Plant 2020, 13, 777–792. [Google Scholar] [CrossRef] [PubMed]
  44. Lichtenthaler, H.; Wellburn, A.R. Determination of total carotenoids and chlorophylls a and b of leaf in different solvents. Biochem. Soc. Trans. 1985, 11, 591–592. [Google Scholar] [CrossRef]
  45. Livak, K.J.; Schmittgen, T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 2001, 25, 402–408. [Google Scholar] [CrossRef] [PubMed]
  46. Deng, T.; Wu, D.; Duan, C.; Yan, X.; Du, Y.; Zou, J.; Guan, Y. Spatial profiling of gibberellins in a single leaf based on microscale matrix solid-phase dispersion and precolumn derivatization coupled with ultraperformance liquid chromatography-tandem mass spectrometry. Anal. Chem. 2017, 89, 9537–9543. [Google Scholar] [CrossRef] [PubMed]
  47. Zhang, Z.; Hao, Y.-H.; Ding, J.; Xu, S.-N.; Yuan, B.-F.; Feng, Y.-Q. One-pot preparation of a mixed-mode organic-silica hybrid monolithic capillary column and its application in determination of endogenous gibberellins in plant tissues. J. Chromatogr. A. 2015, 1416, 64–73. [Google Scholar] [CrossRef] [PubMed]
  48. Li, D.; Guo, Z.; Liu, C.; Li, J.; Xu, W.; Chen, Y. Quantification of near-attomole gibberellins in floral organs dissected from a single Arabidopsis thaliana flower. Plant J. 2017, 91, 547–557. [Google Scholar] [CrossRef] [PubMed]
  49. Love, M.I.; Huber, W.; Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014, 15, 550. [Google Scholar] [CrossRef] [PubMed]
  50. Li, Y.; Tian, Q.; Wang, Z.; Li, J.; Liu, S.; Chang, R.; Chen, H.; Liu, G. Integrated analysis of transcriptomics and metabolomics of peach under cold stress. Front. Plant Sci. 2023, 14, 1153902. [Google Scholar] [CrossRef] [PubMed]
  51. Hang, T.; Lu, N.; Takagaki, M.; Mao, H. Leaf area model based on thermal effectiveness and photosynthetically active radiation in lettuce grown in mini-plant factories under different light cycles. Sci. Hortic. 2019, 252, 113–120. [Google Scholar] [CrossRef]
  52. Lazzarin, M.; Meisenburg, M.; Meijer, D.; van Ieperen, W.; Marcelis, L.F.M.; Kappers, I.F.; van der Krol, A.R.; van Loon, J.J.A.; Dicke, M. LEDs make it resilient: Effects on plant growth and defense. Trends Plant Sci. 2021, 26, 496–508. [Google Scholar] [CrossRef] [PubMed]
  53. Leschevin, M.; Ksas, B.; Baltenweck, R.; Hugueney, P.; Caffarri, S.; Havaux, M. Photosystem rearrangements, photosynthetic efficiency, and plant growth in far red-enriched light. Plant J. 2024, 120, 2536–2552. [Google Scholar] [CrossRef] [PubMed]
  54. Xiao, L.; Shibuya, T.; Watanabe, T.; Kato, K.; Kanayama, Y. Effect of light quality on metabolomic, ionomic, and transcriptomic profiles in tomato fruit. Int. J. Mol. Sci. 2022, 23, 13288. [Google Scholar] [CrossRef] [PubMed]
  55. Roeber, V.M.; Bajaj, I.; Rohde, M.; Schmülling, T.; Cortleven, A. Light acts as a stressor and influences abiotic and biotic stress responses in plants. Plant Cell Environ. 2021, 44, 645–664. [Google Scholar] [CrossRef] [PubMed]
  56. Liu, H.; Gleason, S.M.; Hao, G.; Hua, L.; He, P.; Goldstein, G.; Ye, Q. Hydraulic traits are coordinated with maximum plant height at the global scale. Sci. Adv. 2019, 5, eaav1332. [Google Scholar] [CrossRef] [PubMed]
  57. Sheng, H.; Zhang, H.; Deng, H.; Zhang, Z.; Qiu, F.; Yang, F. Maize COMPACT PLANT 3 regulates plant architecture and facilitates high-density planting. Plant Cell. 2025, 37, koaf029. [Google Scholar] [CrossRef] [PubMed]
  58. Cui, M.; Wang, J.; Zhang, X.; Wang, C.; Li, G.; Wan, J.S.H.; Du, D. Warming significantly inhibited the competitive advantage of native plants in interspecific competition under phosphorus deposition. Plant Soil. 2023, 486, 503–518. [Google Scholar] [CrossRef]
  59. Guo, F.; Hou, L.; Ma, C.; Li, G.; Lin, R.; Zhao, Y.; Wang, X. Comparative transcriptome analysis of the peanut semi-dwarf mutant 1 reveals regulatory mechanism involved in plant height. Gene 2021, 791, 145722. [Google Scholar] [CrossRef] [PubMed]
  60. Zhang, Y.; Kaiser, E.; Zhang, Y.; Zou, J.; Bian, Z.; Yang, Q.; Li, T. UVA radiation promotes tomato growth through morphological adaptation leading to increased light interception. Environ. Exp. Bot. 2020, 176, 104073. [Google Scholar] [CrossRef]
  61. Zhang, Y.; Sun, X.; Aphalo, P.J.; Zhang, Y.; Cheng, R.; Li, T. Ultraviolet-A1 radiation induced a more favorable light-intercepting leaf-area display than blue light and promoted plant growth. Plant Cell Environ. 2024, 47, 197–212. [Google Scholar] [CrossRef] [PubMed]
  62. Escobar-Hernández, D.I.; González-García, Y.; Olivares-Sáenz, E.; Juárez-Maldonado, A. Seedling priming with UV-A radiation induces positive responses in tomato and bell pepper plants under water stress. Sci. Hortic. 2024, 332, 113235. [Google Scholar] [CrossRef]
  63. Zhang, C.; Gao, N.; Na, X.; Li, K.; Pu, M.; Sun, H.; Song, Y.; Peng, T.; Fei, P.; Li, J.; et al. UV-B stress reshapes root-associated microbial communities and networks, driven by host plant resistance. Soil Biol. Biochem. 2025, 205, 109767. [Google Scholar] [CrossRef]
  64. Li, W.; Zhang, C.; Ma, T.; Li, W. Estimation of summer maize biomass based on a crop growth model. Emir. J. Food Agric. 2021, 33, 742–750. [Google Scholar] [CrossRef]
  65. Song, J.; Zhang, R.; Yang, F.; Wang, J.; Cai, W.; Zhang, Y. Nocturnal LED supplemental lighting improves quality of tomato seedlings by increasing biomass accumulation in a controlled environment. Agronomy 2024, 14, 1888. [Google Scholar] [CrossRef]
  66. Xiong, F.S.; Day, T.A. Effect of solar ultraviolet-B radiation during springtime ozone depletion on photosynthesis and biomass production of Antarctic vascular plants. Plant Physiol. 2001, 125, 738–751. [Google Scholar] [CrossRef] [PubMed]
  67. Chen, Z.; Dong, Y.; Huang, X. Plant responses to UV-B radiation: Signaling, acclimation and stress tolerance. Stress Biol. 2022, 2, 51. [Google Scholar] [CrossRef] [PubMed]
  68. Jaiswal, D.; Pandey, A.; Agrawal, M.; Agrawal, S.B. Photosynthetic, biochemical and secondary metabolite changes in a medicinal plant Chlorophytum borivillianum (Safed musli) against low and high doses of UV-B radiation. Photochem. Photobiol. 2023, 99, 45–56. [Google Scholar] [CrossRef] [PubMed]
  69. Skowron, E.; Trojak, M.; Pacak, I.; Wezigowska, P.; Szymkiewicz, J. Enhancing the quality of indoor-grown basil microgreens with low-dose UV-B or UV-C light supplementation. Int. J. Mol. Sci. 2025, 26, 2352. [Google Scholar] [CrossRef] [PubMed]
  70. Tilbrook, K.; Arongaus, A.B.; Binkert, M.; Heijde, M.; Yin, R.; Ulm, R. The UVR8 UV-B photoreceptor: Perception, signaling and response. Arab. Book Am. Soc. Plant Biol. 2013, 11, e0164. [Google Scholar] [CrossRef] [PubMed]
  71. Rasool, G.; Guo, X.; Wang, Z.; Hassan, M.; Aleem, M.; Javed, Q.; Chen, S. Effect of buried straw layer coupled with fertigation on florescence and yield parameters of Chinese cabbage under greenhouse environment. J. Soil Sci. Plant Nutr. 2020, 20, 598–609. [Google Scholar] [CrossRef]
  72. Elsayed, S.; El-Hendawy, S.; Elsherbiny, O.; Okasha, A.M.; Elmetwalli, A.H.; Elwakeel, A.E.; Memon, M.S.; Ibrahim, M.E.M.; Ibrahim, H.H. Estimating chlorophyll content, production, and quality of sugar beet under various nitrogen levels using machine learning models and novel spectral indices. Agronomy 2023, 13, 2743. [Google Scholar] [CrossRef]
  73. León-Chan, R.G.; López-Meyer, M.; Osuna-Enciso, T.; Sañudo-Barajas, J.A.; Heredia, J.B.; León-Félix, J. Low temperature and ultraviolet-B radiation affect chlorophyll content and induce the accumulation of UV-B-absorbing and antioxidant compounds in bell pepper (Capsicum annuum) plants. Environ. Exp. Bot. 2017, 139, 143–151. [Google Scholar] [CrossRef]
  74. Yue, J.; Zhang, D.; Chen, G.; Shen, X. ApGA20ox1, a key gibberellin biosynthesis gene, regulates somatic embryogenesis and plant height in Agapanthus praecox. Sci. Hortic. 2023, 312, 111846. [Google Scholar] [CrossRef]
  75. Zhang, H.; Li, J.; Liu, W.; Mu, X.; Xu, Y.; Gu, Z.; Hong, B.; Zhao, X. Diversity of gibberellins contributes to different flowering ecotypes in chrysanthemum. Sci. Hortic. 2024, 338, 113702. [Google Scholar] [CrossRef]
  76. Hao, P.; Jian, C.; Hao, C.; Liu, S.; Hou, J.; Liu, H.; Liu, H.; Zhang, X.; Zhao, H.; Li, T. Coordination of miR319–TaPCF8 with TaSPL14 orchestrates auxin signaling and biosynthesis to regulate plant height in common wheat. J. Integr. Plant Biol. 2024, 66, 2362–2378. [Google Scholar] [CrossRef] [PubMed]
  77. Lopez, D.J.C.; Arruda, R.S.; Pimenta, T.M.; Souza, G.A.; Teixeira, L.S.; Araújo, W.L.; Zsogon, A.; Ribeiro, D.M. Ethylene modulates peanut (Arachis hypogaea L.) growth and yield in response to planting depth. Field Crops Res. 2025, 322, 109751. [Google Scholar] [CrossRef]
  78. Muniandi, S.K.M.; Hossain, M.A.; Abdullah, M.P.; Ab Shukor, N.A. Gibberellic acid (GA3) affects growth and development of some selected kenaf (Hibiscus cannabinus L.) cultivars. Ind. Crops Prod. 2018, 118, 180–187. [Google Scholar] [CrossRef]
  79. Othman, Y.A.; Leskovar, D.I. Foliar application of gibberellic acid improves yield and head phenolic compounds in globe artichoke. Sci. Hortic. 2022, 301, 111115. [Google Scholar] [CrossRef]
  80. Chandel, A.; Thakur, M.; Rakwal, A.; Chauhan, S.; Bhargava, B. Exogenous applications of gibberellic acid modulate the growth, flowering and longevity of calla lily. Heliyon 2023, 9, e16319. [Google Scholar] [CrossRef] [PubMed]
  81. Wei, Z.; Shu, A.; Wang, Y.; Geng, G. Effects of foliar spraying gibberellin and brassicin physiological characteristics of sugar beet. J. Eng. Heilongjiang Univ. 2022, 13, 91–96. [Google Scholar]
  82. Shohat, H.; Cheriker, H.; Kilambi, H.V.; Illouz Eliaz, N.; Blum, S.; Amsellem, Z.; Tarkowská, D.; Aharoni, A.; Eshed, Y.; Weiss, D. Inhibition of gibberellin accumulation by water deficiency promotes fast and long-term ‘drought avoidance’ responses in tomato. New Phytol. 2021, 232, 1985–1998. [Google Scholar] [CrossRef] [PubMed]
  83. Xu, P.; Hu, J.; Chen, H.; Cai, W. SMAX1 interacts with DELLA protein to inhibit seed germination under weak light conditions via gibberellin biosynthesis in Arabidopsis. Cell Rep. 2023, 42, 112740. [Google Scholar] [CrossRef] [PubMed]
  84. Yamauchi, Y.; Ogawa, M.; Kuwahara, A.; Hanada, A.; Kamiya, Y.; Yamaguchi, S. Activation of gibberellin biosynthesis and response pathways by low temperature during imbibition of Arabidopsis thaliana seeds. Plant Cell. 2004, 16, 367–378. [Google Scholar] [CrossRef] [PubMed]
  85. Sun, J.; Huang, S.; Lu, Q.; Li, S.; Zhao, S.; Zheng, X.; Zhou, Q.; Zhang, W.; Li, J.; Wang, L.; et al. UV-B irradiation-activated E3 ligase GmILPA1 modulates gibberellin catabolism to increase plant height in soybean. Nat. Commun. 2023, 14, 6262. [Google Scholar] [CrossRef] [PubMed]
  86. Huang, W.; Peng, S.; Xian, Z.; Lin, D.; Hu, G.; Yang, L.; Ren, M.; Li, Z. Overexpression of a tomato miR171 target gene SlGRAS24 impacts multiple agronomical traits via regulating gibberellin and auxin homeostasis. Plant Biotechnol. J. 2017, 15, 472–488. [Google Scholar] [CrossRef] [PubMed]
  87. Wang, Y.; Zhao, J.; Lu, W.; Deng, D. Gibberellin in plant height control: Old player, new story. Plant Cell Rep. 2017, 36, 391–398. [Google Scholar] [CrossRef] [PubMed]
  88. Ninkuu, V.; Aluko, O.O.; Yan, J.; Zeng, H.; Liu, G.; Zhao, J.; Li, H.; Chen, S.; Dakora, F.D. Phenylpropanoids metabolism: Recent insight into stress tolerance and plant development cues. Front. Plant Sci. 2025, 16, 1571825. [Google Scholar] [CrossRef] [PubMed]
  89. Liu, S.; Gu, X.; Jiang, Y.; Wang, L.; Xiao, N.; Chen, Y.; Jin, B.; Wang, L.; Li, W. UV-B promotes flavonoid biosynthesis in Ginkgo biloba by inducing the GbHY5-GbMYB1-GbFLS module. Hortic. Res. 2023, 10, uhad118. [Google Scholar] [CrossRef] [PubMed]
  90. Zhang, H.; He, H.; Song, W.; Zheng, L. Pre-harvest UVB irradiation enhances the phenolic and flavonoid content, and antioxidant activity of green- and red-leaf lettuce cultivars. Horticulturae 2023, 9, 695. [Google Scholar] [CrossRef]
  91. Song, Y.; Ma, B.; Guo, Q.; Zhou, L.; Lv, C.; Liu, X.; Wang, J.; Zhou, X.; Zhang, C. UV-B induces the expression of flavonoid biosynthetic pathways in blueberry (Vaccinium corymbosum) calli. Front. Plant Sci. 2022, 13, 1079087. [Google Scholar] [CrossRef] [PubMed]
  92. Song, C.; Guan, Y.; Zhang, D.; Tang, X.; Chang, Y. Integrated mRNA and miRNA transcriptome analysis suggests a regulatory network for UV–B-controlled terpenoid synthesis in fragrant woodfern (Dryopteris fragrans). Int. J. Mol. Sci. 2022, 23, 5708. [Google Scholar] [CrossRef] [PubMed]
  93. Zhan, J.; Di, T.; Chen, X.; Zheng, T.; Sun, W.; Yang, M.; Zhou, M.; Shen, Z.; Chen, H.; Su, N. CbMYB108 Integrates the Regulation of Diterpene Biosynthesis and Trichome Development in Conyza blini against UV-B. Plant Cell Environ. 2024, 47, 1300–1318. [Google Scholar] [CrossRef] [PubMed]
  94. Wu, T.; Feng, S.Y.; Yang, Q.H.; Bhetariya, P.J.; Gong, K.; Cui, C.L.; Song, J.; Ping, X.R.; Pei, Q.Y.; Yu, T.; et al. Integration of the metabolome and transcriptome reveals the metabolites and genes related to nutritional and medicinal value in Coriandrum sativum. J. Integr. Agric. 2021, 20, 1807–1818. [Google Scholar] [CrossRef]
  95. He, J.; Xin, P.; Ma, X.; Chu, J.; Wang, G. Gibberellin metabolism in flowering plants: An update and perspectives. Front. Plant Sci. 2020, 11, 532. [Google Scholar] [CrossRef] [PubMed]
  96. Wang, Y.; Sun, J.; Ali, S.S.; Gao, L.; Ni, X.; Li, X.; Wu, Y.; Jiang, J. Identification and expression analysis of Sorghum bicolor gibberellin oxidase genes with varied gibberellin levels involved in regulation of stem biomass. Ind. Crops Prod. 2020, 145, 111951. [Google Scholar] [CrossRef]
  97. Camut, L.; Gallova, B.; Jilli, L.; Sirlin-Josserand, M.; Carrera, E.; Sakvarelidze-Achard, L.; Ruffel, S.; Krouk, G.; Thomas, S.G.; Hedden, P.; et al. Nitrate signaling promotes plant growth by upregulating gibberellin biosynthesis and destabilization of DELLA proteins. Curr. Biol. 2021, 31, 4971–4982.e4. [Google Scholar] [CrossRef] [PubMed]
  98. Zhang, J.; Zhou, T.; Zhang, C.; Zheng, W.; Li, J.; Jiang, W.; Xiao, C.; Wei, D.; Yang, C.; Xu, R.; et al. Gibberellin disturbs the balance of endogenesis hormones and inhibits adventitious root development of Pseudostellaria heterophylla through regulating gene expression related to hormone synthesis. Saudi J. Biol. Sci. 2021, 28, 135–147. [Google Scholar] [CrossRef] [PubMed]
  99. Cheng, W.; Yin, S.; Tu, Y.; Mei, H.; Wang, Y.; Yang, Y. SlCAND1, encoding cullin-associated Nedd8-dissociated protein 1, regulates plant height, flowering time, seed germination, and root architecture in tomato. Plant Mol. Biol. 2020, 102, 537–551. [Google Scholar] [CrossRef] [PubMed]
  100. Sponsel, V.M.; Hoad, G.; Beeley, L. The biological activities of some new gibberellins (GAs) in six plant bioassays. Planta 1977, 135, 143–147. [Google Scholar] [CrossRef] [PubMed]
  101. Chen, Y.; Hou, M.; Liu, L.; Wu, S.; Shen, Y.; Ishiyama, K.; Kobayashi, M.; McCarty, D.R.; Tan, B.-C. The maize DWARF1 encodes a gibberellin 3-oxidase and is dual localized to the nucleus and cytosol. Plant Physiol. 2014, 166, 2028–2039. [Google Scholar] [CrossRef] [PubMed]
  102. Sun, X.; Kaiser, E.; Aphalo, P.J.; Marcelis, L.F.M.; Li, T. Plant responses to UV-A1 radiation are genotype and background irradiance dependent. Environ. Exp. Bot. 2024, 219, 105621. [Google Scholar] [CrossRef]
  103. Salazar-Cerezoa, S.; Martínez-Montiel, N.; García-Sáncheza, J.; Pérez-y-Terrón, R.; Martínez-Contreras, R.D. Gibberellin biosynthesis and metabolism: A convergent route for plants, fungi and bacteria. Microbiol. Res. 2018, 208, 85–98. [Google Scholar] [CrossRef] [PubMed]
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Figure 1. The phenotype of pepper plants grown under natural light (control) and supplementary ultraviolet (UV) radiation.
Figure 1. The phenotype of pepper plants grown under natural light (control) and supplementary ultraviolet (UV) radiation.
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Figure 2. Plant morphology and biomass of pepper plants grown under natural light (control) and supplementary ultraviolet (UV) radiation. (A) plant height, (B) stem diameter, (C) shoot fresh weight, and (D) root fresh weight. * and *** indicate the significant difference between control and UV treatments by the Student’s t-test at p < 0.05 and p < 0.001, respectively. Data represents the mean ± standard deviation (SD).
Figure 2. Plant morphology and biomass of pepper plants grown under natural light (control) and supplementary ultraviolet (UV) radiation. (A) plant height, (B) stem diameter, (C) shoot fresh weight, and (D) root fresh weight. * and *** indicate the significant difference between control and UV treatments by the Student’s t-test at p < 0.05 and p < 0.001, respectively. Data represents the mean ± standard deviation (SD).
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Figure 3. (A) chlorophyll a content, (B) chlorophyll b content, and (C) total chlorophyll content of pepper plants grown under natural light (control) and supplementary ultraviolet (UV) radiation in the greenhouse. Data represents the mean ± standard deviation (SD).
Figure 3. (A) chlorophyll a content, (B) chlorophyll b content, and (C) total chlorophyll content of pepper plants grown under natural light (control) and supplementary ultraviolet (UV) radiation in the greenhouse. Data represents the mean ± standard deviation (SD).
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Figure 4. Transcriptome profiles of leaves in pepper plants under natural light (control) and supplementary ultraviolet (UV) radiation. (A) Heat map of different expression genes (DEGs) in control and UV treatments. (B) Volcano plot of DEGs between UV and Control.
Figure 4. Transcriptome profiles of leaves in pepper plants under natural light (control) and supplementary ultraviolet (UV) radiation. (A) Heat map of different expression genes (DEGs) in control and UV treatments. (B) Volcano plot of DEGs between UV and Control.
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Figure 5. Transcriptome profiles of leaves in celery under natural light (control) and supplementary ultraviolet (UV) treatments. (A) pathway enrichment analysis of different expression genes (DEGs) for control and UV treatments. The color of the point represents p, and the size of the point represents the number of enriched DEGs. (B) Gene set enrichment analysis (GSEA) for control and UV treatments. (C) Go analysis of DEGs for control and UV treatments. BP, CC, and MF represent biological processes, cell components, and molecular functions, respectively.
Figure 5. Transcriptome profiles of leaves in celery under natural light (control) and supplementary ultraviolet (UV) treatments. (A) pathway enrichment analysis of different expression genes (DEGs) for control and UV treatments. The color of the point represents p, and the size of the point represents the number of enriched DEGs. (B) Gene set enrichment analysis (GSEA) for control and UV treatments. (C) Go analysis of DEGs for control and UV treatments. BP, CC, and MF represent biological processes, cell components, and molecular functions, respectively.
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Figure 6. Metabolome and expression levels of key genes in gibberellin (GA) synthesis pathways in pepper plants grown under natural light (control) and supplementary ultraviolet (UV) radiation.
Figure 6. Metabolome and expression levels of key genes in gibberellin (GA) synthesis pathways in pepper plants grown under natural light (control) and supplementary ultraviolet (UV) radiation.
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Figure 7. Gibberellin (GA) content of pepper plants grown under natural light (control) and supplementary ultraviolet (UV) radiation. (A) GA19 content, (B) GA20 content, (C) GA3 content, (D) GA51 content, (E) GA7 content, and (F) GA34 content. * and ** indicate the significant difference between control and UV treatments by the Student’s t-test at p < 0.05 and p < 0.01, respectively.
Figure 7. Gibberellin (GA) content of pepper plants grown under natural light (control) and supplementary ultraviolet (UV) radiation. (A) GA19 content, (B) GA20 content, (C) GA3 content, (D) GA51 content, (E) GA7 content, and (F) GA34 content. * and ** indicate the significant difference between control and UV treatments by the Student’s t-test at p < 0.05 and p < 0.01, respectively.
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Figure 8. RT-qPCR validation of the transcriptome data results for 6 selected genes in gibberellin synthesis pathways. (A) relative expression of CA01g10440, (B) relative expression of CA06g16820, (C) relative expression of CA07g16060, (D) relative expression of CA02g10780, (E) relative expression of CA01g22480, and (F) relative expression of CA05g06370. *** indicates the significant difference between control and UV treatments by the Student’s t-test at p < 0.001.
Figure 8. RT-qPCR validation of the transcriptome data results for 6 selected genes in gibberellin synthesis pathways. (A) relative expression of CA01g10440, (B) relative expression of CA06g16820, (C) relative expression of CA07g16060, (D) relative expression of CA02g10780, (E) relative expression of CA01g22480, and (F) relative expression of CA05g06370. *** indicates the significant difference between control and UV treatments by the Student’s t-test at p < 0.001.
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Figure 9. Proposed model of how ultraviolet (UV) radiation affects the growth of pepper plants grown in the greenhouse. UVR8 serves as the primary UV-B photoreceptor in plants, where exposure to UV-B radiation triggers UVR8 activation. This activation elicits a robust accumulation of HY5 and HYH transcripts and proteins. These transcription factors play a regulatory role in gibberellin (GA) catabolic processes. Concurrently, the phytohormone GA, its receptor, and the DELLA repressor constitute a GA–GID1–DELLA regulatory module within the GA signaling cascade.
Figure 9. Proposed model of how ultraviolet (UV) radiation affects the growth of pepper plants grown in the greenhouse. UVR8 serves as the primary UV-B photoreceptor in plants, where exposure to UV-B radiation triggers UVR8 activation. This activation elicits a robust accumulation of HY5 and HYH transcripts and proteins. These transcription factors play a regulatory role in gibberellin (GA) catabolic processes. Concurrently, the phytohormone GA, its receptor, and the DELLA repressor constitute a GA–GID1–DELLA regulatory module within the GA signaling cascade.
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MDPI and ACS Style

Zhang, Z.; Yan, Z.; Ding, X.; Shen, H.; Liu, Q.; Song, J.; Liang, Y.; Lu, N.; Tang, L. Transcriptomics and Metabolomics Reveal the Dwarfing Mechanism of Pepper Plants Under Ultraviolet Radiation. Agriculture 2025, 15, 1535. https://doi.org/10.3390/agriculture15141535

AMA Style

Zhang Z, Yan Z, Ding X, Shen H, Liu Q, Song J, Liang Y, Lu N, Tang L. Transcriptomics and Metabolomics Reveal the Dwarfing Mechanism of Pepper Plants Under Ultraviolet Radiation. Agriculture. 2025; 15(14):1535. https://doi.org/10.3390/agriculture15141535

Chicago/Turabian Style

Zhang, Zejin, Zhengnan Yan, Xiangyu Ding, Haoxu Shen, Qi Liu, Jinxiu Song, Ying Liang, Na Lu, and Li Tang. 2025. "Transcriptomics and Metabolomics Reveal the Dwarfing Mechanism of Pepper Plants Under Ultraviolet Radiation" Agriculture 15, no. 14: 1535. https://doi.org/10.3390/agriculture15141535

APA Style

Zhang, Z., Yan, Z., Ding, X., Shen, H., Liu, Q., Song, J., Liang, Y., Lu, N., & Tang, L. (2025). Transcriptomics and Metabolomics Reveal the Dwarfing Mechanism of Pepper Plants Under Ultraviolet Radiation. Agriculture, 15(14), 1535. https://doi.org/10.3390/agriculture15141535

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