Red and far-red light contrastingly influence storage root development and gene expression profile in radish (Raphanus sativus L.)

Red and far-red light contrastingly influence storage root development and gene expression profile in radish (Raphanus sativus L.) | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Red and far-red light contrastingly influence storage root development and gene expression profile in radish (Raphanus sativus L.) Irina E. Dodueva, Xenia A. Kuznetsova, Ivan G. Tarakanov, Daria S. Gorshkova, and 7 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7318257/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 9 You are reading this latest preprint version Abstract The storage root is a specialized underground organ of biennial and perennial plants. In most root crops, the modification of roots for nutrient storage has a strictly defined seasonality and is regulated by environmental cues such as photoperiod and light quality. Here, we have shown that red light (660 nm, R 660 ) and far-red light (730 nm, FR 730 ) have opposite effects on storage root formation and flowering in radish ( Raphanus sativus L.). The R 660 caused taproot thickening and the formation of a storage root, attenuating the flowering, while FR 730 negatively affected the development of the storage root, stimulating flowering. Taproots of radish plants grown under R 660 demonstrated extensive proliferation in the cambium and xylem parenchyma cells, while in the taproots of plants grown on FR 730 xylem parenchyma was largely transformed into sclerenchyma. In the taproots of plants grown under R 660 , in contrast to FR 730 , an increase in the content of water-soluble sugars and starch was detected. Transcriptome analysis revealed that RL 660 caused downregulation of key 'flowering genes' such as CONSTANS-LIKE, FT, SOC1 , etc. in both leaves and roots of radish. At the same time, several key regulators of root development, such as WOX11, WOX5, LBD3 and SCR , were specifically upregulated in the taproots of radish plants on R 660 . Moreover, numerous genes involved in sucrose metabolism and phytohormonal balance also demonstrated contrasting expression patterns on R 660 and FR 730 . Our results suggest a potential molecular basis for the red-light-dependent stimulation of storage root formation. radish storage root red light far-red light transcriptome analysis Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 1. Introduction Plant life cycle is strongly influenced by the ever-changing light environment, including photoperiod and such light quality characteristics as spectrum, intensity, and direction. By sensing light cues, plants can optimize their development in response to environmental fluctuations including the regulation of seasonal processes such as flowering and storage organ formation. Photosynthetically active red light (RL, wavelength 600–700 nm) and photosynthetically inactive far-red light (FRL, wavelength 700–760 nm) are among the most important regulators of plant physiological processes, with the RL/FRL balance “informing” the plant about the time of day, seasonality and the presence/absence of shade. The perception of RL and FRL is mediated by phytochromes, of which phytochrome B (PHYB) senses RL and mediates responses to it, while PHYA has a broader absorption spectrum and plays a primary role in the transduction of FRL signals (Burgie and Vierstra 2014 ; Lei et al. 2024 ). Through interactions with different classes of proteins, phytochromes regulate the expression of numerous genes, and interact with other protein regulators of morphogenesis, in particular, components of the circadian clock (Cheng et al. 2021 ). The transition from the vegetative to the reproductive phase is the best known light-regulated developmental program in higher plants. All plant photoreceptors have been shown to contribute to this complex regulatory network by either directly or indirectly affecting the expression and stability of key regulator of the floral transition, the B-box TF CONSTANS (CO) (Takagi et al. 2023 ). The CO in turn directly regulates the FLOWERING LOCUS T (FT) gene, which encodes a small protein of the PHOSPHATIDYL ETHANOLAMINE BINDING PROTEIN (PEBP) family. The FT protein, also known as florigen, is transported through the phloem to the shoot apex where it interacts as a co-activator with the bZIP FT FD whose targets include key flowering regulatory genes such as SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1), APETALA1 (AP1), LEAFY (LFY) and FRUITFULL (FUL) (Lebedeva et al. 2020 ; Tsuji et al. 2011 ). The RL and FRL sensed by PHYB and PHYA have been shown to oppositely regulate the stability of the CO protein, mediating its daily dynamics: in the morning, PHYB promotes the degradation of the CO protein, whereas in the evening, PHYA stabilizes CO by attenuating the activity of the E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), whose target is CO (Hajdu et al. 2015 ; Sarid-Krebs et al. 2015 ). Photoperiod and light spectrum are also known to regulate the development of underground storage organs, such as tubers and bulbs (Yan et al. 2022 ; Zhou et al. 2019 ). In potato ( Solanum tuberosum ), tuber development is mediated by mechanisms similar to those used in the photoperiodic control of flowering. Under long day, the CO-like TF StCOL1 represses both flowering and tuberization in potato by directly activating the expression of the PEPB family gene StSP5G . The StSP5G in turn represses other PEPB genes: the potato florigen StSP3D , and StSP6A , which encodes the mobile signal for tuberization called tuberigen (Abelenda et al. 2016 ; Navarro et al. 2011 ). The similar light-dependent regulators, including CO-like TFs and PEPBs, have been shown to be involved in the bulb development in Liliaceae species (Khosa et al. 2021 ). The mechanisms of influence of RL and FRL on tuber and bulbs development have not been studied, but it is known that FRL has a stimulating effect on potato tuber production, reversing the negative effect of RL on this process (Batutis and Ewing 1982 ; Rahman et al. 2021 ). The storage root is another specialized underground organ of biennial and perennial plants that undergoes modifications to store nutrients. Like tubers and bulbs, it facilitates vegetative propagation and enables plants to survive unfavourable conditions. The development of storage roots depends on the activity of the cambium, a lateral meristem that gives rise to the xylem and phloem tissues with a high proportion of storage parenchyma cells (Hoang et al. 2020b ; Kuznetsova et al. 2020 ). In most root crops, the formation of storage roots has a defined seasonality and is regulated by the environmental cues, including photoperiod and light quality (Hoang et al. 2020b ). Thus, it is discussed that key regulators of photoperiodic development such as COL and PEBP proteins may also be involved in the storage root development (Natarajan et al. 2019 ). Radish ( Raphanus sativus L. var. radicula Pers.) is a root crop plant with short life cycle closely related to Arabidopsis . It has been shown that radish forms large storage roots under long day (Guo et al. 2019 ) and high levels of RL (Zha, Liu, 2018 ), but the exact mechanisms underliyng this have not been studied. Here we have shown that RL (660 nm, R 660 ) and FRL (730 nm, FR 730 ) have opposite effects on storage root formation and flowering in radish. RL was shown to stimulate the growth of storage roots and suppress flowering, whereas FRL promoted flowering and suppressed storage root formation. In the taproots of radish plants RL stimulated the proliferation of cambium and xylem parenchyma, while under FRL xylem parenchyma transformed to sclerenchyma. RL and FRL also had contrasting effects on the content of water-soluble sugars and starch in radish roots and leaves. Transcriptome analysis revealed that more than fifty radish genes encoding key players of photoperiodic flowering control were downregulated in both radish leaves and taproots under RL, while several key genes involved in the root growth were specifically upregulated under RL in the taproot. There were also numerous DEGs involved in sucrose metabolism and phytohormonal balance. Change in the expression of these genes may play a key role in switching between two opposing developmental programs, flowering and storage root formation, depending on the RL:FRL balance. 2. Materials and Methods 2.1. Plant material Radish inbred line 19 from the genetic collection of Saint Petersburg State University (Buzovkina and Lutova 2007 ) was used in this work. This line is approximately the 50th inbred generation originated from the Saxa cultivar, which belongs to the European group of radish cultivars and forms a round-shape storage root. 2.2. Plant growing and sampling Plants were grown in growth chambers (Urbangrower 150, PR China) with various light treatments according to the experimental layout. Seeds were sown in the in 2 L vegetation vessels with commercial neutralised peat-based substrate ‘Agrobalt-C’ (Russia) with pH 6.0-6.5 and complete macro- and micronutrient supply including 150 mg L − 1 [NH 4 + and NO 3 − ], 270 mg L − 1 P 2 O 5 , and 300 mg L − 1 K 2 O. The substrate humidity was maintained at 70% of the full water capacity, watering on the scales. Plant chambers were illuminated with lamps consisting of different light-emitting diode (LED) bars, specifically designed to provide a custom spectrum in each chamber. Fixtures consisted of light modules with tunable LEDs that varied in the wavelength and spectral composition of the emitted light. Four types of high-performance narrow-band 3 w LEDs (Estar, Cidly, PR China) were used: short-wave red ( ∆ λ 0,5 = 623 ÷ 641 nm, λ max = 632 nm), long-wave red (∆λ 0,5 = 646 ÷ 674 nm, λ max = 660 nm), far-red (∆λ 0,5 = 727 ÷ 751 nm, λ max = 739 nm), and blue (∆λ 0,5 = 452 ÷ 477 nm, λ max = 465 nm). The same daily light integral was maintained in all treatments. In all light treatments, photosynthetic photon flux density (PPFD) was maintained at 75 µmol m − 2 s − 1 , with a photoperiod of 18 h. The spectra of the resulting lamp systems were measured with a spectrometer UPRtek PG100N (Taiwan). A LI-191R quantum sensor with an LI-250A data logger (Li-Cor, NE, USA) was used to measure the PPFD in the PAR region. Taking into account the differences in the spectral absorbance of phytochrome P r and P fr (Sager et al. 1988 ), two different spectral treatments were set to vary the PFD of narrow-band LEDs with peak irradiance at 730 and 660 nm. One treatment named ‘FRL’ included 0% R 660 and 100% FR 730 , another named ‘RL’ – 100% R 660 + 0% FR 730 . In addition, LEDs with λ max = 632 nm were applied to compensate for a possible decrease in PPFD in the red region according to the experimental set-up; the combined R 632 + R 660 PPFD had been adjusted to the same level in all treatments. Blue light PPFD was at the same level in all the spectral treatments ( Fig. S1 ). Plant leaf photosynthetic rate and respiration rate analyses were carried out using a LI-6400XT Portable Photosynthesis System (Li-Cor, NE, USA). During the measurements CO 2 concentration was maintained at 400 ± 12.0 µmol mol − 1 , air temperature 21–23°C, air humidity 60 ± 4.0%. 3. Light microscopy The whole taproot and lower part of the stem of radish plants were fixed in FAA on 14, 28, 42 days after germination with post-fixation in 70% ethanol according to the standard protocol (Stasolla and Yeung 2015 ). Samples were dehydrated in an alcohol series of increasing concentrations (80%, 85%, 90%, two times 96%, two times 100%) and then in a series of xylene mixed with 100% isopropyl alcohol (25%, 50%, 75%) followed by infiltration with 100% xylene for 1–3 hours according to the size. The samples were then embedded in paraffin. Transverse sections (10 µm thick) were obtained with a rotary microtome Microm HM355S (Thermo Fisher Scientific). Deparaffinised and hydrated sections were stained with a combination of 1% aqueous Safranin O and 0.1% Alcian Blue solutions in 3% acetic acid in accordance with a standard procedure (Barykina et al. 2004 ) on an automated slide stainer Varistain Gemini ES (Thermo Fisher Scientific). Slides were examined using a VS120-S6 (Olympus) slide scanner. Part of the fixed material was hand sectioned, stained with a solution of 0.5% phloroglucinol (in an equal mixture of water and ethanol) with the addition of 20% hydrochloric acid (Barykina et al. 2004 ) and observed under an AxioPlan light microscope (Carl Zeiss) for the analysis of the lignified cell distribution. Images were adjusted for colour and contrast using Adobe Photoshop (Adobe, USA) or ImageJ (Schindelin et al. 2012 ). 4. Measurement of soluble sugars and starch content Sugar and starch determinations were carried out in the samples of radish taproot and leaves of plants grown for 14 days and 28 days under RL or FRL in four replicates with material of five plants in each. 200 mg of plant material was grinded in the liquid nitrogen. Before carbohydrate extraction the samples were depigmented with 100% acetone (Marshall, 1986 ) and transferred to clean tubes. The soluble sugars were extracted twice with 80% ethanol at 50°C. The remaining sediments were used for starch extraction with 1.1% hydrochloric acid at 100°C for 30 min (Oren et al., 1988 ). Soluble sugars and starch were determined spectrophotometrically at 620 nm by the anthrone reaction (Hansen and Moller 1975). Calibration curves were built with glucose and potato starch. 5. RNA isolation, library preparation and sequencing For RNA-seq, total RNA was extracted from leaves and taproots of radish plants on 14 and 28 days after germination, which were grown under RL or FRL. Plants were sampled 4 h after the onset of daylight. Three biological replicates were used for each light treatment. RNA isolation was performed as follows: plant material grinded in the liquid nitrogen was treated with 500 µl of Trizol reagent (Invitrogen, USA) for 5 min at 25ºC, followed by chloroform purification and RNA precipitation with isopropanol. The precipitate was washed three times with 80% ethanol, air dried and dissolved in sterile deionized water. RNA was purified from genomic DNA contamination using a DNA-free DNA Removal Kit (Thermo Fisher Scientific, USA). Library preparation and sequencing were performed by CeGaT GmbH company (Tuebingen, Germany). Illumina libraries were prepared from the polyA RNA with the NEBNext® Ultra™ DNA Library Prep Kit (New England Biolabs, Hitchin, UK) according to the manufacturer’s instructions. Dual barcoding was performed using the NEBNext® Ultra™ DNA Index Prep Kit for Illumina and the NEBNext® Multiplex Oligos® Illumina® (Dual Index Primers Set 1). Sequencing of libraries was performed on an Illumina HiSeq2500 sequencer with 50 bp read length. 6. Bioinformatic processing of sequencing results Purification of fastq raw reads from radish mitochondrial, plastid and ribosomal DNA was performed using the bbduk tool from the bbtools package (v. 38.96) ( https://jgi.doe.gov/data-and-tools/bbtools/ , accessed on 9 January 2025). Quality filtered and decontaminated reads were trimmed with Trimmomatic (v. 0.40) with the ‘HEADCROP:15 CROP:95’ options. Reads quality control was performed with MultiQC (v.1.12) (Ewels et al. 2016 ). Filtered reads were aligned on sequences of GCA_000801105.3 R.sativus reference genome with HISAT2 v. 2.01.2 (Kim et al. 2015 ) and then counted with Stringtie (Pertea et al. 2015 ) tool. Differential expression between experimental and control samples was analysed with the DESeq2 package (v. 1.28.1) for R (v. 3.6.2) (Love et al. 2014 ). Genes with p-value adjusted 1 were considered to be differentially expressed. The GSEABase v. 1.50 (“GSEABase,” n.d.) R package was used for GO gene enrichment analysis. 3. Results 3.1. Phenotypes and root anatomy of radish plants grown under different light conditions Radish plants for the analysis of root anatomy, gene transcription and sugar content were grown under two light spectra contrastingly differed in the proportion of R 660 and FR 730 : 0% R 660 and 100% FR 730 (‘FRL’) and 100% R 660 and 0% FR 730 (‘RL’). When growing radish on RL and FRL, we observed two opposite strategies for plant development (Fig. 1 ). The shade avoidance response (SAR) was observed in FRL-treated plants at the early stages as hypocotyl elongation and later leaf blade elongation ( Fig. S2 ). By 28 days after germination (DAG), plants subjected to FRL began to form inflorescence meristems, and by 42 DAG all FRL-grown plants were actively flowering. At the same time, in the absence of FRL plants did not form inflorescence meristems even after 42 DAG. Plants grown under FRL showed no transition to taproot thickening, whereas plants grown under RL were characterized by an intense increase in taproot diameter and formed a large storage root (Fig. 1 , Fig. S3 ). The addition of FRL and the subsequent transition of the plants to flowering resulted in an increase in the net photosynthetic rate in the leaves, while the respiration rate was reduced ( Fig. S4 ). The scale indicates the plant height in cm. Despite the name ‘storage root’, in radish and other plants with storage taproots this is a composite structure consisting of the primary root and the hypocotyl. Thickening occurs in both morphological parts of the storage root and is associated with the storage parenchyma development in the secondary xylem (Meng et al. 2024 ; Zaki et al. 2012 ). By the 14 DAG, the transition to secondary growth occurred in radish plants grown both under FR and FRL (Fig. 2 a, b), and no significant differences were observed at the anatomical level. A well-developed cambium was present in all plants regardless of light conditions, with approximately the same number of cell layers in the cambial zone. Anatomical differences between plants grown under RL or FRL started at the 28 DAG. Although the formation of secondary xylem with a relatively large number of parenchyma cells occurred regardless of the light conditions, the number of cell layers formed and deposited by the cambium inside, was significantly lower when plant was grown under FRL (Fig. 2 c, d). The number of vessels did not vary significantly, and the differences in xylem volume were associated with changes in the number of cell layers of the storage xylem parenchyma. At 42 DAG, the secondary xylem parenchyma in plants grown at FRL was largely transformed into sclerenchyma with thickened and lignified cell walls. At the same time, parenchymal lignification did not occur in plants grown under RL (Fig. 2 e, f). Plants grown at FRL also lack any proliferating parenchyma both in the central part of the stele and in the secondary xylem (Fig. 2 d, f, Fig. S5 ). In plants grown under RL, at 28 and 42 DAG, proliferation of vasicentric parenchyma (associated with vessels) was observed around all vessels in both primary and secondary xylem, forming the characteristic ‘halo’ of parenchymal cells. Proliferation of the apotracheal parenchyma (not associated with vessels) was detected both in the central part of the stele and in the secondary xylem. Proliferation of the vasicentric and apotracheal parenchyma is an essential process in radish and some other Brassicaceae and contributes significantly to the root thickening (Hearn et al. 2018 ; Magendans 1991 ). Thus, the observed proliferation of xylem parenchyma in the plants grown under RL can be the main cause of the thickening of the storage root. At the same time, plants grown on FRL lack storage xylem parenchyma and instead differentiate mechanical tissue. 3.2. Content of starch and soluble sugars in radish leaves and taproots During plant growth, carbohydrates are produced as photosynthates in the source organs (mainly leaves) and are translocated in the form of sucrose through the phloem to the sinks. Among sink organs and tissues can be the sites of active growth (e.g., meristems) and storage organs. During its growth, the storage root is the main sink organ which is competing with other sinks, e.g. with floral meristem (Hoang et al. 2020b ). In storage root, sucrose is metabolized to provide tissue growth and also can be deposited, mainly in the form of starch, in the parenchyma. Thus, in the mature xylem-type storage roots of Brassicaceae, xylem is almost exclusively composed of parenchyma cells filled with starch granules (Kuznetsova et al. 2020 ). At stage 14 DAG, RL-grown and FRL-grown radish plants showed almost no difference in the content of water-soluble sugars in the taproot and leaves (Fig. 3 a, c). At the same time, the starch content in RL-grown plants at 14 DAG was about 30% higher in the leaves, probably reflecting more efficient photosynthesis, and 50% lower in the taproot as compared with FRL-grown plants (Fig. 3 b, d). At stage 28 DAG, differences in the distribution of both starch and water-soluble sugars were observed between plants grown on RL and FRL. In the leaves of RL-grown radish plants, the content of water-soluble sugars was slightly increased at 28 DAG as compared to 14 DAG, while in their taproot, the content of water-soluble sugars was increased by about 30% (Fig. 3 a, c). The starch content in 28 DAG RL-grown plants was sharply decreased (by 30%) in the leaves and almost by 40% increased in the taproot as compared to plants at 14 DAG (Fig. 3 b, d). These trends can reflect the delivery of photosynthates to the main sink - the actively growing storage root. In plants grown under FRL, the level of soluble sugars by 28 DAG was significantly decreased in the leaves (by 12%) and taproot (almost twice) as compared to 14 DAG, and the starch content in both leaves and taproot tended to slightly increase and remained higher than in RL-grown plants. Thus, radish plants grown under RL and FRL were contrasted in the dynamics of sugar accumulation. In FRL-grown plants, amounts of water-soluble sugars in the leaves and especially in the taproot were decreased while the starch content did not change significantly. At the same time, when plants were grown on RL, the amount of soluble sugars and starch increased significantly in the root and did not change or decreased in the leaves. It is remarkable that these changes in sugar content precede anatomical changes in the radish roots associated with an increase in the amount of storage parenchyma: differences in this parameter in plants grown on RL and FRL were observed later than 28 DAG. It can be assumed that an increase in carbohydrate content can trigger proliferation of cambium and/or xylem parenchyma, thus creating tissue for their deposition. This is well consistent with data on sucrose-mediated inhibition of the differentiation of phloem and xylem conductive elements in Arabidopsis (Narutaki et al. 2023 ). 3.3. Transcriptome analysis of gene expression in roots and leaves of radish plants grown under RL and FRL To understand the molecular mechanism underlying the contrasting variants of radish development under different red spectrum compositions, we performed the transcriptome analysis of leaves and taproots of 14 DAG and 28 DAG plants grown under RL and FRL. We analyzed the changes in the gene expression under RL compared to FRL because RL was inductive for the development of the radish storage root. As a result, we have identified a number of genes that were differentially expressed in the leaves and taproots (Table 1 ). Table 1 Number of differentially expressed genes (DEGs) identified in the roots and leaves of radish plants grown under the red light (RL) in comparison with far-red light (FRL) Stage Comparison DEG downregulated DEG upregulated Total DEG 14 DAG Leaf RL vs Leaf FRL 373 187 560 Root RL vs Root FRL 2363 1859 4222 28 DAG Leaf RL vs Leaf FRL 1335 1961 3296 Root RL vs Root FRL 2398 897 3295 Since the leaves are the main organs of light perception, whereas the taproots grew in the soil, we can assume that the formation of the storage root under the influence of RL may depend on signals coming from the aboveground part of the plant. These observations led us to speculate that flowering and storage root formation, which seemed to be two opposing light-dependent processes, are controlled by different sets of regulators, which are induced by RL or FRL. Therefore, we compared the number of differentially expressed genes (DEGs) characterized by similar or opposite patterns of expression changes in radish leaves and roots under RL (Fig. 4 a). As a result, there were many more genes with a similar pattern of expression in both leaf and taproot than genes with the opposite pattern of expression. Thus, the supposed ‘sink competition’ between the storage root and inflorescence is unlikely to depend on opposite patterns of gene expression in the underground and aboveground parts of the plant. Several DEGs were identified that showed a common pattern of expression changes in both radish leaves and taproots at 14 DAG and 28 DAG (Fig. 4 b, Table S1 ). It is interesting to note that among these ‘common’ downregulated DEGs, genes involved in the control of flowering, such as radish homologs of SOC1 and CONSTANS-LIKE 5 , predominated (5 out of 8 genes with known functions). A list of ‘common’ upregulated DEGs included one gene for the cytokinin response regulator ARR4 , which also acts as a modulator of RL signaling (Sweere et al. 2001 ), and several genes encoding myrosinases, enzymes that catalyze the biosynthesis of glucosinolates, defense metabolites of Brassicaceae (Halkier and Gershenzon 2006 ). At the same time, there were ‘root-specific’ and ‘leaf-specific’ DEGs, the expression of which were changed under RL only in the underground or above-ground part of the plant. Interestingly, there were many more root-specific DEGs among the than leaf-specific (Fig. 4 b): 400 versus 31 among downregulated ones and 210 versus 24 among upregulated. Generally, a significant proportion of the identified DEGs were key regulators of photomorphogenesis. There were also numerous DEGs involved in the sugar metabolism and in the biosynthesis and signaling of phytohormones. Among root-specific DEGs, there were several radish homologs of Arabidopsis genes which are known as key regulators of root development. Genes involved in the light signaling and photomorphogenesis Radish genes, whose homologues in Arabidopsis act at different stages of light signaling and photomorphogenesis, were the most represented functional group of DEGs identified in this work (Fig. 5 , Tables S2-S5 ). Firstly, there were DEGs involved in the sensing and primary transmission of RL/FRL signals. Among genes encoding photoreceptors, one of the three radish PHYB and one of two PHYA genes were downregulated under RL in leaves. The best known direct targets of phytochromes are the bHLH TFs named PHYTOCROME INTERACTING FACTORs (PIFs) (Cordeiro et al. 2022 ). Several radish PIF genes were downregulated under RL in the leaves and/or taproots. Among them there were homologs of the closely related Arabidopsis PIF4 and PIF5 , which are integrators of light signaling with other stimuli, including hormonal responses (Pham et al. 2018 ). The PIF3-LIKE 1 ( PIL1 ), key regulator of the response to FRL and shade (Li et al. 2014 ), and PIF6 , which is close to PIL1 , were also specifically downregulated in the leaves. Among the strongly downregulated genes there also was the LONG HYPOCOTYL IN FAR-RED1 ( HFR1 ), whose product, an atypical bHLH, interacts with PIFs and antagonizes them in the regulation of gene expression (Li et al. 2014 ; Shi et al. 2013 ). In Arabidopsis , the PIL1 and HFR1 are direct positively regulated targets of the PIF4 and PIF5 (Hornitschek et al. 2012 ), and the HFR1 protein interacts with at least PIF4 and PIL1 to modulate their functions (Li et al. 2014 ; Shi et al. 2013 ; Sng et al. 2023 ), suggesting that all these radish DEGs may operate in the same pathway. Secondly, radish genes encoding components of the circadian clock were also found to be downregulated under RL mainly in the taproots. Radish homologs of LATE ELONGATED HYPOCOTYL (LHY) and ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 1 / TIMING OF CAB EXPRESSION 1 (APRR1/ TOC1 ), which are component of core oscillator in plant circadian clock (Oakenfull and Davis 2017 ), were specifically downregulated in the taproots. The same was found for four homologs of APRR5 which act downstream of APRR1 in Arabidopsis , while other probable targets of APRR1 (Huang et al. 2012 ; Nakamichi et al. 2010 ), three radish APRR9 genes and one APRR7 were downregulated in the taproots and leaves. Moreover, REVEILLE (RVE) genes related to LHY (Gray et al. 2017 ), were also among the downregulated: the expression of REV1, REV3 and REV4 were decreased under RL in the taproot, while both two radish RVE7 genes were downregulated at 14 DAG in both leaves and roots but upregulated at 28 DAG. Among downregulated also were components of the ‘evening loop’ in the circadian clock, genes encoding TFs EARLY FLOWERING 4 (ELF4), ELF3 and LUX ARRHYTHMO (LUX) (Zhao et al. 2021 ): two radish ELF4 , one ELF3 and one LUX gene were specifically downregulated in the taproot. Two radish homologs of ELONGATED HYPOCOTYL5 ( HY5 ), a master positive regulator of many key genes involved in light response, circadian clock and flowering (Gangappa and Botto 2016 ), were also strongly downregulated in the taproots of RL-grown plants. In turn, a single radish homolog of GIGANTEA (GI) , which is a central player in the circadian clock-controlled flowering pathway (Mishra and Panigrahi 2015 ), was downregulated in the leaves, suggesting its suppression as a mechanism for delaying radish flowering on the RL. At the same time, downregulation of circadian clock genes in the taproot of RL-grown radish plants allows us to suggest their functions in storage root development. Thirdly, the large group of radish genes which were downregulated under RL are homologs of known key players of light-dependent transition to flowering and/or tuberization. The most important of them is CONSTANS ( CO ), encoding B-box-type zinc finger (BBX) TF. Several CO-LIKE (COL) proteins act redundantly and interact with CO (Zhang et al. 2023 ). In radish plants grown under RL, both homologs of COL5 were strongly downregulated in the leaves and taproots of 14 DAG and 28 DAG plants. At the same time, other radish COLs , including COL2 , COL8 , two COL4 , three COL10 and four BBX24 , were differentially expressed only in radish roots: all of them were downregulated under RL, but COL10 homologs were upregulated. In Arabidopsis , COL2 , 4, 5 and 8 are known as regulators of flowering (Zhang et al. 2023 ), BBX24 mainly participates in stress tolerance (Chiriotto et al. 2023 ), and the functions of COL10 are unknown. Major direct targets of CO and COLs are FT gene encoding major mobile flower-promoting signal (Takagi et al. 2023 ), and also FT-like genes which are positive and negative regulators of tuberization in potato and Liliaceae (Khosa et al. 2021 ). In radish, expression of one of two FT genes is severely downregulated under RL in both leaves and taproots. The same was observed for one of two radish homologs of BROTHER OF FT AND TFL1 ( BFT1 ) and for single radish MOTHER OF FT AND TFL1 ( MFT ) gene. At the same time, another radish BFT1 was downregulated under RL in the leaves but upregulated in taproots. Although the functions of COL and FT family genes in root development are unknown, they could have functions beyond flowering. In Arabidopsis, COL3 regulates root elongation (Datta et al. 2006 ), and MFT suppresses seed germination under FRL (Vaistij et al. 2018 ). In potato, StCOL1 together with several more StCOLs function as negative regulators of tuberization (González-Schain et al. 2012 ; Yin et al. 2024 ). Their targets are FT -like SP6A and SP5G which encode stimulator and repressor of tuber induction (Abelenda et al. 2016 ). According to expression data, we can suppose that several radish COL and FT-like genes can be negative regulators of storage root growth. The exception is one of radish BFT1- like genes which was strongly upregulated in the taproot under RL. In Arabidopsis , BFT1 functions as a flowering suppressor under high salinity (Ryu et al. 2011 ), but in radish, it could acquire an additional function. Finally, among DEGs there were probable targets of FT-like proteins. In Arabidopsis and other plants, FT is a mobile coactivator of FLOWERING LOCUS D (FD) TF which induces transcription of key floral meristem identity genes such as SOC1, LFY and AP1 (Zhu et al. 2020 ). Several MADS family TFs, such as AGAMOUS-LIKE24 (AGL24) and AGL42 act in the same pathway, positively regulating SOC1 gene expression and/or forming a transcriptional activator complex with SOC1 (Liu et al. 2008 ; Dorca-Fornell et al. 2011 ). In radish, all four homologs of SOC1 and both homologs of AGL24 were strongly downregulated under RL in the taproot and leaves, indicating the repressive role of RL in flowering initiation. A strong downregulation of two radish LFY genes was only detected in the taproot, and the same was revealed for some other genes known as flowering regulators, such as AGL3/ SEPALLATA4 (Jetha et al. 2014 ), AGL8/ FRUITFULL (van Mourik et al. 2023 ) and AGL16 (Dong et al. 2023 ). At the same time, radish homologs of AGL18 , known as a repressor of flowering and stimulator of regeneration (Paul et al. 2022 ), and AGL42 , which is a stimulator of flowering but also a positive regulator of root meristem (Dorca-Fornell et al. 2011 ; Nawy et al. 2005 ), were upregulated in both radish roots and leaves under RL. Thus, we can speculate that in radish many ‘flowering genes’ may have dual functions in flowering and storage root development. Genes involved in the control of phytohormonal balance The light response is known to affect the phytohormonal balance (Hornitschek et al. 2012 ; Li et al. 2012 ; Sng et al. 2023 ). In radish, we identified a large number of genes involved in auxin, cytokinin, gibberellin and ethylene homeostasis, that were differentially expressed between RL- and FRL-grown plants (Fig. 6 , Tables S2-S5 ). In general, under RL we observed a downregulation of genes involved in gibberellin biosynthesis and signaling, as well as in cytokinin and ethylene biosynthesis, whereas certain genes of auxin biosynthesis and also cytokinin- and ethylene-responsive genes were predominantly upregulated in the taproot. Most of the ‘phytohormone-related’ genes demonstrated similar expression patterns in radish leaves and taproots under RL. At the same time, there were several 'exceptional' genes with opposite expression dynamics in leaves and roots. These genes may be necessary for RL-mediated developmental shift towards delayed flowering and storage root formation. Firstly, there were DEGs involved in the control of free auxin level. Auxin is central regulator of cambium position and also plays an important role in the storage root formation and starch deposition in cassava (Rüscher et al. 2021 ). Among radish DEGs, the TAA-related 2 (TAR2) was upregulated in both leaves and taproots while two YUCCA8 ( YUC8) genes, whose products act downstream TAR2 in the auxin biosynthesis via indole-2-pyruvic acid (Cao et al. 2019 ), were strongly downregulated in leaves and taproots. At the same time, two YUCCA6 ( YUC6) genes were upregulated in the root at 14 DAG and downregulated at 28 DAG. Four radish genes encoding GRETCHEN HAGEN 3 (GH3) enzymes, which catalyze the formation of inactive auxin conjugates with amino acids (Luo et al. 2023 ), were downregulated in the leaves and roots under RL, except of one which was downregulated in the leaves and strongly upregulated in the roots. Among auxin-responsive genes, several radish Aux/IAA s, which work in the negative feedback in the auxin response and coordinate it with other signaling pathways (Luo et al. 2018 ), were strongly downregulated under RL in both leaves and taproots. Remarkably, some of these ‘auxin-related’ radish DEGs can act in the regulation of photomorphogenesis. Indeed, in Arabidopsis , the TAA1 , several YUCCAs (including YUC6 and YUC8 ), certain GH3s and IAA29 are direct targets of PIF4, PIF5, and HFR1 (Franklin et al. 2011 ; Hornitschek et al. 2012 ; Li et al. 2012 ; Shi et al. 2013 ; Sun et al. 2013 ; Sng et al. 2023 ). Plant photomorphogenesis also is based on regulation of level of the gibberellins, hormones that control growth processes throughout the plant life cycle, including formation of storage organs. In potato, decrease in gibberellin content under inductive short day facilitate tuberization (Roumeliotis et al. 2012 ), and in the radish gibberellin suppresses cambium activity and storage root thickening (Meng et al., 2024 ). In Arabidopsis , genes encoding 2-oxoglutarate-dependent dioxygenases which regulate the level of free gibberellins in plant tissues, are under direct transcriptional control of ELF3, PIF4 and PIF5 (Filo et al. 2015 ). In RL-grown radish plants, genes of GA 20 OX, which catalyze formation of the bioactive gibberellins from the GA 12 precursor (Yang et al. 2020 ), were strongly downregulated mainly in the leaves. An exception is GA 20 OX 3 gene, which was strongly upregulated in the taproot. In addition, the KAO gene encoding ent -kaurenoic acid oxidase, which catalyzes the early steps of the gibberellin biosynthetic pathway, was downregulated under RL in radish leaves and taproots. At the same time, genes of GA 2 OX enzymes which modify the bioactive gibberellins rendering them incapable of binding to the receptor (Hedden 2020 ), were severely downregulated only in the taproot. This suggests that RL mainly reduces gibberellin level in radish leaves but can increase it in the taproot. In the regulation of plant body architecture, including photomorphogenesis (Yang and Li 2017 ) and root secondary growth (Fischer et al. 2019 ), cytokinins mainly act as antagonists of auxin and gibberellins. The stimulating role of cytokinins in the control of cambium cell division and storage root growth was previously demonstrated in radish (Jang et al. 2015 ). In this work, we have identified numerous DEGs that are probably involved in cytokinin biosynthesis, degradation and response. Radish LONELY GUY 1 (LOG1), LOG2, LOG3, LOG5 and LOG7 genes, whose products catalyze the synthesis of bioactive cytokinin (Kuroha et al. 2009 ), were among the most strongly downregulated under RL. The same was true for cytokinin oxidase/dehydrogenase genes CKX1, 2, 3, 5 and 7 , whose products trigger irreversible degradation of cytokinins (Kowalska et al. 2010 ). At the same time, we revealed upregulation of seven radish genes encoding A-type Arabidopsis response regulators (ARRs), primary cytokinin-responsive genes encoding repressors of signaling (Kieber and Schaller 2014 ), and most of them had common expression dynamics in roots and leaves. Among them is the radish homolog of ARR4 , major integrator of RL/FRL signaling and cytokinin response, whose protein directly interacts with PHYB increasing its activity (Mira-Rodado et al. 2007 ). At the same time, since the upregulation of A-type ARR genes is usually used as a marker of increased cytokinin level and/or response, the effect of RL on cytokinin homeostasis in radish plants has been ambiguous. Ethylene, a gaseous phytohormone, plays an important role in various aspects of plant development including photomorphogenesis (Ahammed et al. 2020 ) and cambium stem cell activity (Yu et al. 2023 ). Ethylene biosynthesis and signaling are regulated by multiple stimuli, including RL and FRL: in particular, genes encoding the ethylene biosynthesis enzymes ACC synthases (ACS) are positively regulated by PIFs and HFR1 (Khanna et al. 2007 ; Shi et al. 2013 ). In addition, RL-activated PHYB can directly bind to the primary ethylene-responsive TFs ETYLENE-INSENSITIVE 3 (EIN3) triggering its ubiquitin-dependent proteasome degradation (Shi et al. 2016 ). Among the ethylene-related DEGs in radish under RL, there were numerous ACS genes. Most of them were strongly downregulated in radish leaves and taproots under RL, indicating a negative effect of RL irradiance on ethylene levels, with the exception of ACS4 and ACS11 , which were upregulated in radish taproot at 28 DAG. At the same time, several genes encoding ACC oxidases (ACO) which act after ACS in ethylene biosynthesis were upregulated in both leaves and taproots under RL. The list of radish ethylene-responsive DEGs includes numerous genes encoding TFs of ETHYLENE-RESPONSE FACTOR (ERF) family. There were up- and downregulated radish ERFs , but the exact functions of most of their Arabidopsis homologs are unknown. Among the most strongly upregulated in the taproots of RL-grown plants was multifunctional ERF115 , which is known to be a major regulator of cell divisions in the quiescent centre of the root apical meristem (Heyman et al. 2013 ), a cytokinin-activated repressor of adventitious root development (Lakehal et al. 2020 ), and a stimulator of plant regeneration (Heyman et al. 2016 ). Based on these data, we can propose the function of ethylene and ERF115 as activators of the radish storage root growth under RL. Genes encoding transcription factors involved in the root development A significant proportion of genes which were strongly up- or downregulated in the taproots of RL-grown radish plants encode TFs of different families. Among them there were radish genes, whose homologs play important roles in Arabidopsis root development (Fig. 7 ). These list of root-specific upregulated DEGs included all four radish homologs of WUSCHEL RELATED HOMEOBOX11 (WOX11) and both homologs of WOX5 , whose products, homeodomain TFs, work together in root meristem initiation (Aliaga Fandino et al. 2019 ; Hu and Xu 2016 ) and also adventitious root formation and callus induction in Arabidopsis (Baesso et al. 2018 ) and radish (Aliaga Fandino et al. 2019 ). Both WOX5 and WOX11 are targets of auxin action, furthermore, WOX11 directly activates WOX5 transcription in promoting root regeneration (Aliaga Fandino et al. 2019 ; Hu and Xu 2016 ). Among genes that were specifically upregulated in radish roots under RL also were PLETHORA 1 ( PLT1 ) and PLT2 , and two homologs of the SCARECROW ( SCR ). In Arabidopsis , PLT and SCR are essential for auxin-mediated root stem cell niche specification (Gao et al. 2004 hönen et al. 2014), WOX5 transcription (Shimotohno et al. 2018 ), and interaction of WOX5 TF with its target genes (Burkart et al. 2022 ; Shimotohno et al. 2018 ). Thus, upregulation of all these genes, working in the same pathway under inductive RL, can be involved in the storage root development. Another TF-encoding radish gene upregulated under RL was LATERAL ORGAN BOUNDARIES DOMAIN 3 (LBD3) , an important cytokinin-responsive regulator of cambium activity and secondary growth of root (Ye et al. 2021 ). Finally, among the upregulated under RL there were two radish homologs of the UPBEAT 1 (UPB1) gene, which encodes a bHLH TF involved in the regulation of D-class cyclin genes expression in the Arabidopsis root meristem (Li et al. 2019 ). The radish homolog of MYB61 , which was, in turn, downregulated in roots under RL, is a positive regulator of xylem formation, lateral root development and plant resource allocation (Romano et al. 2012 ). In addition, among root-specific TF-encoding DEGs were those known to be involved in photomorphogenesis and light response ( LBD25, NAC2, GRF5 ) (Mangeon et al. 2011 ; Morishita et al. 2009 ; Vercruyssen et al. 2015 ), shoot apical meristem maintenance ( ATH1 ) (Gómez-Mena and Sablowski 2008 ), specification of epiderm and its derivatives ( ATML1, PDF1, GTL ) (Abe et al. 2001 ; Shibata et al. 2018 ), stress response ( MYB14, MYB34 ) (Chen et al. 2013 ; Frerigmann and Gigolashvili 2014 ) and leaf and floral organ development ( TCP5, WOX1, YABBY5, MYB108, GRF5, LBD10 ) (Nakata et al. 2012 ; Shen et al. 2019 ; Stahle et al. 2009 ; Yu et al. 2021 ; Kim et al. 2015 ). We can propose that some of the TF-encoding DEGs may also be involved in root development or have dual functions. In particular, the Arabidopsis homolog of PETAL LOSS ( PTL ), which was upregulated in radish taproot and downregulated in the leaves under RL, is involved in the control of floral organs development (Kaplan-Levy et al. 2014 ) but also functions as an important regulator of cambium activity (Zhang et al. 2019 ). Genes involved in the metabolism of sugars The distribution of sugars plays a key role in the choice of plant development strategy. Sucrose, the end product of photosynthesis and key carbon source for plant growth, is produced in source leaves and translocated to various sinks through the sieve element/ companion cell complex of the phloem (van Bel 2021 ). Metabolism of sucrose yields hexoses which are necessary to generate energy and produce cellulose and starch. Moreover, hexoses and sucrose itself provides sugar signaling directly regulating plant development (Yoon et al., 2021 ) including cambium activity (Narutaki et al. 2023 ). In the developing storage root, sucrose is usually deposited in the form of starch forming a reservoir of easy-to-remobilize energy (Hoang et al., 2020b ). The first step of sucrose biosynthesis in the leaf mesophyll, which is catalyzed by sucrose phosphate synthase, includes the formation of sucrose-6-phosphate from fructose-6-phosphate and UDP-glucose. Subsequently, sucrose-6-phosphate is hydrolyzed by sucrose-phosphate phosphatase, releasing sucrose (Huber, Huber, 1996 ). Another enzyme, sucrose synthase, catalyzes reversible reaction of sucrose biosynthesis from UDP-glucose and fructose (Bieniawska et al., 2007 ). After its synthesis, sucrose can be loaded into the phloem, either symplastically or apoplastically, for delivery to sinks, e.g. to storage root. The active transport of sucrose from apoplast is mediated by the several families of sucrose transporters, in particular SWEET (Sugars Will Eventually be Exported Transporters) family of bidirectional sugar uniporters (Chen et al., 2012 ), and sucrose/H+-symporters SUT/SUC (Kühn, Grof, 2010 ). In the phloem companion cells, sucrose could convert into raffinose-type trisaccharides, which increases the intensity of transport. Two steps of raffinose biosynthesis, the formation of galactinol from UDP-galactose and the addition of galactose moieties donated by galactinol to sucrose, are catalyzed by galactinol synthase and raffinose synthase (Taji et al., 2002 ). In its turn, UDP-galactose can be formed from UDP-glucose by means of UDP-glucose-4-epimerase which catalyzes the interconversion of UDP-glucose and UDP-galactose. UDP-glucose can also convert to UDP-glucuronic acid, which is used for the synthesis of major plant cell wall polysaccharides such as xylan. The NAD+-dependent oxidation of UDP-glucose to UDP-glucuronic acid is catalyzed by UDP-glucose-6-dehydrogenase (Reboul et al., 2011 ). Upon translocation through the phloem to sinks, sucrose is degraded by either sucrose synthase (into UDP-glucose and fructose) or invertase (into glucose and fructose). The invertase enzymes are classified into three groups: cell wall invertases, vacuolar and cytoplasmic invertases (Ruan, 2014 ). The vacuolar invertases work together with Early Response to Dehydration 6-Like (ERD6-like, ESL) hexose transporters which unload glucose from vacuole (Slawinski et al., 2021 ). The activities of invertases are under control of specific proteinaceous inhibitors which are also responsible for regulating activities of pectin methylesterases - enzymes necessary to cell wall elasticity and cell adhesion. This large protein family is named INVIs/PMEIs (Plant Invertase/ Pectin Methylesterase Inhibitor Superfamily (Coculo, Lionetti, 2022 ). In the root, unloading of sucrose from phloem to parenchyma cells is provided symplastically via plasmodesmata or by active transport via the same transporter proteins (SWEET, SUC/SUT) (Rüscher et al., 2024 ). Here, sucrose can be stored temporarily in vacuoles, or mainly catabolized by sucrose synthase into fructose and UDP-glucose, which enter starch synthesis. At the same time, invertases do not play a role in the catabolism of sucrose in the root (Li, Zhang, 2003 ). The substrate for starch biosynthesis is provided by ADP-glucose pyrophosphorylase which produces ADP-glucose from glucose-1-phosphate and ATP. Then starch synthase (glycosyltransferase family 5) catalyzes the transfer of the glucosyl moiety of ADP-glucose to the non-reducing end of an existing glucosyl chain. The granule-bound starch synthase is responsible for amylose synthesis, while amylopectin is synthesized by starch-branching and debranching enzymes, members of alpha-amylase superfamily (Pfister, Zeeman, 2016 ). In the taproot and leaves of RL-grown radish plants, we observed a change in the expression of a large number of genes involved in the regulation of metabolism and transport of sugars (Fig. 8 ). Among DEGs there were four radish sucrose synthase genes homologous to Arabidopsis SUS1 and SUS3 , and one gene encoding sucrose phosphate synthase. All these genes were upregulated in the leaves of RL-grown plants and downregulated in the taproot, which suggests an increase in the level of sucrose biosynthesis under the influence of RL. There were also numerous DEGs encoding enzymes of UDP-glucose metabolism, such as UDP-glucose 4-epimerases and UDP-glucose 6-dehydrogenases. Radish genes for these enzymes were downregulated under RL in both taproot and leaves. At the same time, numerous radish genes encoding UDP-glycosyltransferases, enzymes responsible for synthesis of galactolipids for photosynthetic membranes (Lin et al., 2016 ), were upregulated in the leaves and predominantly downregulated in the taproot of RL-grown plants reflecting the necessity of photosynthetic membranes composition in the leaves grown under high level of photosynthetically active RL. The same trend was observed for radish genes encoding nucleotide-sugar transporters which are involved in supplying UDP-glucose into the ER and Golgi lumen (Reyes et al., 2010 ). Among DEGs encoding sucrose transporters, three radish homologs of SUC1 and one homolog of SUC2 were downregulated in the taproot. At the same time, numerous radish SWEET genes were upregulated or downregulated in the taproot and leaves of RL-grown plants. Among upregulated in the taproot and leaves there was homolog of SWEET12 , which was shown to be involved in vascular development (Le et al., 2015), and thus can participate in the formation of xylem-type radish storage root. However, the other two SWEET12 genes were specifically downregulated in the taproot of RL-grown plants. Two homologs of SWEET14 , which mediate not only sugar transport but also cellular gibberellin uptake (Kanno et al., 2016 ), were severely upregulated in the radish taproot under RL, probably reflecting high levels of sucrose and gibberellin transport in the growing storage root. In the RL-grown radish plants, gene of cytoplasmic invertase homologous to Arabidopsis CINV1 was one of major upregulated genes in the leaves, while other invertase genes expressed similarly under RL and FRL. At the same time, among DEGs there were numerous ESL genes, some of which were among major upregulated and downregulated in the leaves and taproot of RL-grown radish plants. Similarly, among very numerous INVIs/PMEIs-encoding DEGs there were both upregulated and downregulated under RL. Among DEGs, involved in starch composition and mobilization, there were radish homologs of alpha-amilase gene AMY1 and four beta-amylase genes: homolog of Arabidopsis BAM5 and three genes encoding inactive beta-amylases. All these genes were specifically downregulated in the taproot of RL-grown radish plants with the exception of BAM5 , which was upregulated. The functions of Arabidopsis BAM5 may be somehow related to the utilization or storage of sucrose because its expression is inducible by sugar (Mita et al., 1995 ). Thus, we can assume that in radish BAM5 can be involved in starch deposition during the formation of the storage root. Moreover, there were DEGs involved in the sugar metabolism and cell wall integrity. Among them there was homolog of Arabidopsis IRREGULAR XYLEM 7 ( IRX7 ), which encodes glycosyltransferase family protein necessary for secondary cell wall formation, cambium functioning and xylem differentiation (Persson et al., 2007 ). In radish, IRX7 was strongly upregulated in the taproots of RL-grown plants and probably can play a role in the growth of xylem-type storage root. 4. Discussion The formation of storage root is an excellent evolutionary adaptation which was designed to create a reservoir of easily mobilized energy in the form of carbohydrates. Further, this reserve can be used for resource-intensive developmental processes such as growth after unfavourable conditions, flowering and fruiting. In this context, the formation of storage roots should have a strictly defined developmental seasonality and can be regulated by both developmental signals and environmental cues including photoperiod and light spectrum. Although the role of light conditions in the initiation of another type of underground storage organ - potato tuber - has been well studied, there is not much data on the molecular mechanisms underlying storage root development, and nothing is known about the light-dependent regulation of this process. Radish is a perspective model object for study mechanisms of storage root development due to its short life cycle (it is the only annual plant with a storage root), diploidy, small genome, and close relationship with Arabidopsis thaliana . Numerous transcriptomic studies on radish have identified candidate genes that play a role in the transition to flowering (Nie et al. 2016 ; Li et al. 2023 ) and various aspects of storage root development, including biosynthesis of anthocyanins (Gao et al. 2019 ), glucosinolates (Wang et al. 2013 ), and lignin (Feng et al. 2017 ). The analysis of radish root transcriptome allowed to identify TF-encoding genes which are presumably involved in the storage root formation. Among them were genes of the WOX and ERF families as well as LHY gene (Hoang et al. 2020a ). The correlation between expression level of sucrose synthase gene SUS1 and radish taproot thickening suggested an important role of sucrose signaling in the development of storage root (Mitsui et al. 2015 ). The dynamics of occurrence of different small RNAs during radish taproot thickening allowed to assume the role their presumable targets, including TF-encoding genes, in the development of the storage root (Yu et al., 2015 ). Due to the high conservatism underlying the main programs of plant development (Kuznetsova et al. 2023 ), a number of data obtained on radish can be extrapolated to other root crops. Moreover, based on this logic, the similarity of light-mediated mechanisms in the development of storage roots and potato tuber is discussed (Natarajan et al. 2019 ; Hoang et al. 2020b ). These mechanisms include CONSTANS-LIKE TFs, as well as mobile signals from the phloem, e.g. PEPB proteins, and their targets. In our experiment, flowering and storage root development behaved as oppositely regulated programs in the radish plants grown under RL and FRL. The antagonism of these developmental strategies can be explained by the fact that plant can usually either flower or form a storage root at the same time because the storage root serves as a major sink of photoassimilates during its formation (Hoang et al. 2020b ). In this context, the FRL-induced shade avoidance response with switch to bolting and flowering could reorganize photoassimilate flux to this new sink instead of storage root growth, while RL in radish retained flowering stimulating taproot thickening. The choice of one of these development strategies was accompanied by anatomical changes in the radish root, including differentiation of sclerenchyma in FRL-grown plants, and proliferation of cambium and xylem parenchyma under RL. In the same developmental stages, a contrasting pattern of water-soluble sugars and starch redistribution was revealed in RL-grown and FRL-grown radish plants, - in particular, a significant increase of their content in the taproots under RL. Finally, growing of radish under RL or FRL was accompanied by changes in the expression of a large number of genes in the leaves and especially in the taproot. The large part of DEGs in our transcriptome analysis included genes whose products are involved in light perception and signaling. In particular, among them were several genes encoding PEPB proteins which can be consider as radish florigens or “root tuberigens”. The only PEPB-encoding gene which was specifically upregulated in the radish taproot under RL, one of two BFT1-like genes, could be a light-dependent stimulator for the storage root development. There were also numerous DEGs involved in the homeostasis of phytohormones, including cytokinin which is necessary for cambium proliferation (Ye et al. 2021 ) and radish taproot thickening (Jang et al. 2015 ). Finally, among root-specific DEGs there were TF-encoding genes whose homologs in Arabidopsis are involved in the control of cambium activity (Zhang et al. 2019 ). Thus, in this work, we revealed a probable molecular basis that may underlie the opposite developmental programs - flowering and formation of a storage root - in response to RL and FRL. Abbreviations DAG: Day(s) after germination; DEG: differentially expressed gene; FRL, FR 730 : Far-red light, 730 nm; LED: Light-emitting diode; PEBP: Phosphatidyl Ethanolamine-Binding Protein; PPF: Photosynthetic photon flux; PPFD: Photosynthetic photon flux density; RL, R 660 : Red light, 660 nm; TF: Transcription factor. Declarations Author Contributions Conceptualization: ID, IT and LL; Methodology: XK, IT, MG, VT, AF; Software: XK, MG; Validation XK, MG; Formal analysis: XK, MG; Investigation: XK, DG; Resources: XK; Data curation: XK; Writing - original draft preparation: ID; Writing - review and editing: ID, IT, ZK and XK; Visualization: MG, AF, DG and ID; Supervision: ID; Project administration: LL; Funding acquisition: LL. Acknowledgments We thank CeGAT company (Tübingen, Germany) for cDNA sequencing. Funding This work was supported by Saint Petersburg State University research project 124032000041-1. 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Int J Mol Sci 23:8341. https://doi.org/10.3390/ijms23158341 Yang C, Li L (2017) Hormonal Regulation in Shade Avoidance. Front Plant Sci 8:1527. https://doi.org/10.3389/fpls.2017.01527 Yang L, Jiang Z, Jing Y, Lin R (2020) PIF1 and RVE1 form a transcriptional feedback loop to control light-mediated seed germination in Arabidopsis . J Integr Plant Biol 62:1372–1384. https://doi.org/10.1111/jipb.12938 Ye L, Wang X, Lyu M et al (2021) Cytokinins initiate secondary growth in the Arabidopsis root through a set of LBD genes. Curr Biol 31:3365–3373e7. https://doi.org/10.1016/j.cub.2021.05.036 Yin W, Wang L, Shu Q et al (2024) Genome-wide identification and expression analysis of the CONSTANS-like family in potato ( Solanum tuberosum L.). Front Genet. 2024 15:1390411. https://doi.org/10.3389/fgene.2024.1390411 Yoon J, Cho LH, Tun W et al (2021) Sucrose signaling in higher plants. 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Hortic Environ Biotechnol 59:511–518. https://doi.org/10.1007/s13580-018-0048-5 Zaki HEM, Takahata Y, Yokoi S (2012) Analysis of the morphological and anatomical characteristics of roots in three radish (Raphanus sativus) cultivars that differ in root shape. J Hortic Sci Biotechnol 87:172–178. https://doi.org/10.1080/14620316.2012.11512849 Zhang B, Feng M, Zhang J, Song Z (2023) Involvement of CONSTANS-like Proteins in Plant Flowering and Abiotic Stress Response. Int J Mol Sci 24:16585. https://doi.org/10.3390/ijms242316585 Zhang J, Eswaran G, Alonso-Serra J et al (2019) Transcriptional regulatory framework for vascular cambium development in Arabidopsis roots. Nat Plants 5:1033–1042. https://doi.org/10.1038/s41477-019-0522-9 Zhao H, Xu D, Tian T et al (2021) Molecular and functional dissection of EARLY-FLOWERING 3 (ELF3) and ELF4 in Arabidopsis. Plant Sci 303:110786. https://doi.org/10.1016/j.plantsci.2020.110786 Zhou T, Song B, Liu T et al (2019) Phytochrome F plays critical roles in potato photoperiodic tuberization. Plant J 98:42–54. https://doi.org/10.1111/tpj.14198 Zhu Y, Klasfeld S, Jeong CW et al (2020) TERMINAL FLOWER 1-FD Complex Target Genes and Competition with FLOWERING LOCUS T. Nat Commun 11:5118. https://doi.org/10.1038/s41467-020-18782-1 Additional Declarations No competing interests reported. Supplementary Files supplementary.docx Cite Share Download PDF Status: Under Review Version 1 posted Editorial decision: Revision requested 22 Oct, 2025 Reviews received at journal 22 Oct, 2025 Reviews received at journal 10 Sep, 2025 Reviewers agreed at journal 25 Aug, 2025 Reviewers agreed at journal 11 Aug, 2025 Reviewers invited by journal 10 Aug, 2025 Editor assigned by journal 09 Aug, 2025 Submission checks completed at journal 09 Aug, 2025 First submitted to journal 07 Aug, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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Dodueva","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA00lEQVRIiWNgGAWjYDACZuYGCRDNDyJ4iNPC2CBxAEhLNhCthQGqxeAAsVoMjjM23v7YdkfO+EbyswdvKg4zmM9IIKDlMGOzxcG2Z8ZmN9LMDeecSWOQuUFAi9lhxjaJg22HE7fdSDCT5m2zYZCQIFJL/eYZ6d+kef9JEK8lwUAiB2hLAxG22IP8cubcM8MZZ96USc45lsYjwfMAvxbJ/sMHb1SU3ZHnb0/fJvGm5rCcBDsBW8CAke0AA4MARCWRscnwB6iF/wCRikfBKBgFo2DEAQCDq0d4wQc3iQAAAABJRU5ErkJggg==","orcid":"","institution":"Saint Petersburg State University","correspondingAuthor":true,"prefix":"","firstName":"Irina","middleName":"E.","lastName":"Dodueva","suffix":""},{"id":498744144,"identity":"b68ce8f1-65e7-42e3-bfb7-d33d8c959695","order_by":1,"name":"Xenia A. Kuznetsova","email":"","orcid":"","institution":"Saint Petersburg State University","correspondingAuthor":false,"prefix":"","firstName":"Xenia","middleName":"A.","lastName":"Kuznetsova","suffix":""},{"id":498744145,"identity":"e24e2be9-4062-4b3f-8681-3a4aa38eb15b","order_by":2,"name":"Ivan G. Tarakanov","email":"","orcid":"","institution":"Russian State Agrarian University Moscow Timiryazev Agricultural Academy","correspondingAuthor":false,"prefix":"","firstName":"Ivan","middleName":"G.","lastName":"Tarakanov","suffix":""},{"id":498744146,"identity":"184a7a24-3857-4fc9-8999-c77b7925c404","order_by":3,"name":"Daria S. Gorshkova","email":"","orcid":"","institution":"Russian State Agrarian University Moscow Timiryazev Agricultural Academy","correspondingAuthor":false,"prefix":"","firstName":"Daria","middleName":"S.","lastName":"Gorshkova","suffix":""},{"id":498744147,"identity":"0db76b8f-5672-4900-ab20-356f9dcad845","order_by":4,"name":"Alexey P. Fedotov","email":"","orcid":"","institution":"Lomonosov Moscow State University","correspondingAuthor":false,"prefix":"","firstName":"Alexey","middleName":"P.","lastName":"Fedotov","suffix":""},{"id":498744148,"identity":"2e6cc870-5a60-4848-8cc8-e15f0febb316","order_by":5,"name":"Vladislav V. Yemelyanov","email":"","orcid":"","institution":"Saint Petersburg State University","correspondingAuthor":false,"prefix":"","firstName":"Vladislav","middleName":"V.","lastName":"Yemelyanov","suffix":""},{"id":498744149,"identity":"14d501cc-d67f-44d7-83aa-dcb90c7ea78b","order_by":6,"name":"Polina K. Gurianova","email":"","orcid":"","institution":"Sirius University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Polina","middleName":"K.","lastName":"Gurianova","suffix":""},{"id":498744150,"identity":"c84f8e35-2161-47b9-9465-779c3a2cbf51","order_by":7,"name":"Zakhar S. Konstantinov","email":"","orcid":"","institution":"Saint Petersburg State University","correspondingAuthor":false,"prefix":"","firstName":"Zakhar","middleName":"S.","lastName":"Konstantinov","suffix":""},{"id":498744151,"identity":"3b44a41f-35d6-4d0a-904a-2717af98a82f","order_by":8,"name":"Maria S. Gancheva","email":"","orcid":"","institution":"Saint Petersburg State University","correspondingAuthor":false,"prefix":"","firstName":"Maria","middleName":"S.","lastName":"Gancheva","suffix":""},{"id":498744152,"identity":"2a284586-d261-41ee-b7bc-bc4b2a897ca8","order_by":9,"name":"Varvara E. Tvorogova","email":"","orcid":"","institution":"Saint Petersburg State University","correspondingAuthor":false,"prefix":"","firstName":"Varvara","middleName":"E.","lastName":"Tvorogova","suffix":""},{"id":498744154,"identity":"5f491647-378e-482b-bc39-855e3221575c","order_by":10,"name":"Lyudmila A. Lutova","email":"","orcid":"","institution":"Saint Petersburg State University","correspondingAuthor":false,"prefix":"","firstName":"Lyudmila","middleName":"A.","lastName":"Lutova","suffix":""}],"badges":[],"createdAt":"2025-08-07 11:23:45","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-7318257/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7318257/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":89097543,"identity":"78889caa-85e3-4266-9c89-67c323dcbe32","added_by":"auto","created_at":"2025-08-14 15:44:15","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":257021,"visible":true,"origin":"","legend":"\u003cp\u003eRadish plants grown under red light (RL, 660 nm) and far-red light (FRL, 730 nm) 28 and 42 days after germination (DAG). Short-wave length red light (λ\u003csub\u003emax\u003c/sub\u003e= 632 nm) was used to compensate for a possible decrease in PPFD in the red region according to the experimental set-up; the combined R\u003csub\u003e632 \u003c/sub\u003e+ R\u003csub\u003e660 \u003c/sub\u003ePPFD had been adjusted to the same level in all treatments. Blue light PPFD was at the same level in all the spectral treatments.\u0026nbsp;\u003c/p\u003e","description":"","filename":"FIG1.png","url":"https://assets-eu.researchsquare.com/files/rs-7318257/v1/be36c5d3d1c690e70b6cabe5.png"},{"id":89098326,"identity":"2b242605-779d-48d7-8a6a-b2c7df19e37d","added_by":"auto","created_at":"2025-08-14 15:52:15","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":765475,"visible":true,"origin":"","legend":"\u003cp\u003eStorage root formation zone transverse sections of \u003cem\u003eRaphanus sativus\u003c/em\u003e plants grown on FRL (a, c, e) and RL (b, d, f). Plants in different light conditions lack any significant anatomical differences by the 14 DAG (a, b), and a well-established cambial zone (cz) was clearly observed. At the 28 DAG, the storage root of plants grown on FRL (c) consists of a significantly lower number of the secondary xylem parenchyma cells compared to plants grown on RL (d). The latter were also characterised by both vasicentric (vpp) and apotracheal (app) xylem parenchyma proliferation (d), which was not evident in plants grown on FRL (c). The following development of the storage root formation zone led to the lignification of parenchyma cell walls and sclerenchyma (sc) differentiation in plants grown on FRL (e) by the 42 DAG while parenchyma in storage roots of plants grown on RL showed no evidence of any lignification (f). Only cells with lignified secondary cell walls are stained in figures E and F showing the results of the qualitative reaction for lignin with phloroglucinol. app, apotracheal proliferating parenchyma; cor, cortex; cz, cambial zone; phl, phloem; pxv, protoxylem vessel; sc, sclerenchyma; sxv, secondary xylem vessel, vpp, vasicentric proliferating parenchyma. Scale bars, a, b - 20 µm, c-f - 100 µm.\u003c/p\u003e","description":"","filename":"FIG2.png","url":"https://assets-eu.researchsquare.com/files/rs-7318257/v1/963cdf983e50c4f5f1e79574.png"},{"id":89098324,"identity":"64fdacb1-eb07-4bf5-8109-5d4640b4f956","added_by":"auto","created_at":"2025-08-14 15:52:15","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":22566,"visible":true,"origin":"","legend":"\u003cp\u003eContent of water-soluble sugars and starch in the radish plants grown under red light (RL, 660 nm) and far-red light (FRL, 730 nm) 28 and 42 days after germination (DAG).\u003c/p\u003e\n\u003cp\u003eWater-soluble sugars (a, c) and starch (b, d) were determined spectrophotometrically in the leaves (a, b) and taproots (c, d).\u003c/p\u003e","description":"","filename":"FIG3.png","url":"https://assets-eu.researchsquare.com/files/rs-7318257/v1/4814e00b91281d12e1663714.png"},{"id":89097548,"identity":"61f9f48d-ec92-49fa-831a-6a6c59977482","added_by":"auto","created_at":"2025-08-14 15:44:15","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":179763,"visible":true,"origin":"","legend":"\u003cp\u003eNumber of differentially expressed genes (DEGs) in radish plants grown under red light (RL) as compared to plants grown under red light + far red light (FRL).\u003c/p\u003e\n\u003cp\u003e(a) – Number of DEGs with similar and opposite expression patterns in the radish leaves and roots at 14 and 28 days after germination (DAG); (b) – Number of DEGs which were downregulated and upregulated both at 14 DAG and 28 DAG in the radish leaves, roots and both leaves and roots; (c) – Venn diagrams showing downregulated and upregulated DEGs in the radish leaves and roots at 14 DAG and 28 DAG (adjusted p-value \u0026lt; 0.05 for each group of DEGs).\u003c/p\u003e","description":"","filename":"FIG4.png","url":"https://assets-eu.researchsquare.com/files/rs-7318257/v1/18bd7cc1502afaaddef20781.png"},{"id":89098327,"identity":"7e16db07-6471-42a4-966f-11bb2dfd32a9","added_by":"auto","created_at":"2025-08-14 15:52:15","extension":"jpg","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":942958,"visible":true,"origin":"","legend":"\u003cp\u003eHeatmap diagram illustrating the transcript levels of radish genes involved in the control of light response and photomorphogenesis in the leaves and roots of plants grown under red light (RL) and red light + far red light (FRL). Scale: transcripts per million, DAG – day after germination. The heatmap was generated using Morpheus software (https://software.broadinstitute.org/morpheus) based on DESeq normalized values. The minimum and maximum values were taken independently for each row.\u003c/p\u003e","description":"","filename":"FIG5.jpg","url":"https://assets-eu.researchsquare.com/files/rs-7318257/v1/137707973499f9d4f5add85a.jpg"},{"id":89098328,"identity":"020f3a27-5e73-4559-a0f8-88e6c0cd50a7","added_by":"auto","created_at":"2025-08-14 15:52:15","extension":"jpg","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":1472423,"visible":true,"origin":"","legend":"\u003cp\u003eHeatmap diagram illustrating the transcript levels of radish genes involved in the control of phytohormone homeostasis in the leaves and roots of radish plants grown under red light (RL) and red light + far red light (FRL). Scale: transcripts per million, DAG – day after germination. The heatmap was generated using Morpheus software (\u003ca href=\"https://software.broadinstitute.org/morpheus\"\u003ehttps://software.broadinstitute.org/morpheus\u003c/a\u003e) based on DESeq normalized values. The minimum and maximum values were taken independently for each row.\u003c/p\u003e","description":"","filename":"FIG6.jpg","url":"https://assets-eu.researchsquare.com/files/rs-7318257/v1/3e5527672535f81dc4b8c67e.jpg"},{"id":89097554,"identity":"c56b022f-97a6-48b5-8a8c-9c21224f4c29","added_by":"auto","created_at":"2025-08-14 15:44:15","extension":"jpg","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":965205,"visible":true,"origin":"","legend":"\u003cp\u003eHeatmap diagram illustrating the transcript levels of radish genes encoding transcription factors that were highly up- and downregulated in roots of plants grown under red light (RL) and red light + far red light (FRL) Scale: transcripts per million, DAG – day after germination.\u003c/p\u003e\n\u003cp\u003eThe heatmap was generated using Morpheus software (\u003ca href=\"https://software.broadinstitute.org/morpheus\"\u003ehttps://software.broadinstitute.org/morpheus\u003c/a\u003e) based on DESeq normalized values. The minimum and maximum values were taken independently for each row.\u003c/p\u003e","description":"","filename":"FIG7.jpg","url":"https://assets-eu.researchsquare.com/files/rs-7318257/v1/67b6dac6ef18f68953b8e577.jpg"},{"id":89097552,"identity":"1b6ca225-d5d4-45b8-aac6-8d31f45de4d4","added_by":"auto","created_at":"2025-08-14 15:44:15","extension":"jpg","order_by":8,"title":"Figure 8","display":"","copyAsset":false,"role":"figure","size":1024858,"visible":true,"origin":"","legend":"\u003cp\u003eHeatmap diagram illustrating the transcript levels of radish genes involved in the regulation of sugar metabolism and transport that were highly up- and downregulated in the leaves and taproots of plants grown under red light (RL) and red light + far red light (FRL) Scale: transcripts per million, DAG – day after germination.\u003c/p\u003e\n\u003cp\u003eThe heatmap was generated using Morpheus software (\u003ca href=\"https://software.broadinstitute.org/morpheus\"\u003ehttps://software.broadinstitute.org/morpheus\u003c/a\u003e) based on DESeq normalized values. The minimum and maximum values were taken independently for each row.\u003c/p\u003e","description":"","filename":"FIG8.jpg","url":"https://assets-eu.researchsquare.com/files/rs-7318257/v1/c5a67ec29e0f52368d671021.jpg"},{"id":89101160,"identity":"e20434e6-f188-4b24-bc89-2f1caddc5018","added_by":"auto","created_at":"2025-08-14 16:16:22","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":6880734,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7318257/v1/027cbcb4-551a-43dc-b889-e460bc760455.pdf"},{"id":89097547,"identity":"d8ca34e5-ac55-4581-9846-3a6720adddce","added_by":"auto","created_at":"2025-08-14 15:44:15","extension":"docx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":1672028,"visible":true,"origin":"","legend":"","description":"","filename":"supplementary.docx","url":"https://assets-eu.researchsquare.com/files/rs-7318257/v1/9f8a1f08c8954257d5e018e7.docx"}],"financialInterests":"No competing interests reported.","formattedTitle":"Red and far-red light contrastingly influence storage root development and gene expression profile in radish (Raphanus sativus L.)","fulltext":[{"header":"1. Introduction","content":"\u003cp\u003ePlant life cycle is strongly influenced by the ever-changing light environment, including photoperiod and such light quality characteristics as spectrum, intensity, and direction. By sensing light cues, plants can optimize their development in response to environmental fluctuations including the regulation of seasonal processes such as flowering and storage organ formation. Photosynthetically active red light (RL, wavelength 600\u0026ndash;700 nm) and photosynthetically inactive far-red light (FRL, wavelength 700\u0026ndash;760 nm) are among the most important regulators of plant physiological processes, with the RL/FRL balance \u0026ldquo;informing\u0026rdquo; the plant about the time of day, seasonality and the presence/absence of shade. The perception of RL and FRL is mediated by phytochromes, of which phytochrome B (PHYB) senses RL and mediates responses to it, while PHYA has a broader absorption spectrum and plays a primary role in the transduction of FRL signals (Burgie and Vierstra \u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e2014\u003c/span\u003e; Lei et al. \u003cspan citationid=\"CR69\" class=\"CitationRef\"\u003e2024\u003c/span\u003e). Through interactions with different classes of proteins, phytochromes regulate the expression of numerous genes, and interact with other protein regulators of morphogenesis, in particular, components of the circadian clock (Cheng et al. \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e2021\u003c/span\u003e).\u003c/p\u003e\u003cp\u003eThe transition from the vegetative to the reproductive phase is the best known light-regulated developmental program in higher plants. All plant photoreceptors have been shown to contribute to this complex regulatory network by either directly or indirectly affecting the expression and stability of key regulator of the floral transition, the B-box TF CONSTANS (CO) (Takagi et al. \u003cspan citationid=\"CR128\" class=\"CitationRef\"\u003e2023\u003c/span\u003e). The CO in turn directly regulates the \u003cem\u003eFLOWERING LOCUS T (FT)\u003c/em\u003e gene, which encodes a small protein of the PHOSPHATIDYL ETHANOLAMINE BINDING PROTEIN (PEBP) family. The FT protein, also known as florigen, is transported through the phloem to the shoot apex where it interacts as a co-activator with the bZIP FT FD whose targets include key flowering regulatory genes such as \u003cem\u003eSUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1), APETALA1 (AP1), LEAFY (LFY)\u003c/em\u003e and \u003cem\u003eFRUITFULL (FUL)\u003c/em\u003e (Lebedeva et al. \u003cspan citationid=\"CR68\" class=\"CitationRef\"\u003e2020\u003c/span\u003e; Tsuji et al. \u003cspan citationid=\"CR129\" class=\"CitationRef\"\u003e2011\u003c/span\u003e). The RL and FRL sensed by PHYB and PHYA have been shown to oppositely regulate the stability of the CO protein, mediating its daily dynamics: in the morning, PHYB promotes the degradation of the CO protein, whereas in the evening, PHYA stabilizes CO by attenuating the activity of the E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), whose target is CO (Hajdu et al. \u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e2015\u003c/span\u003e; Sarid-Krebs et al. \u003cspan citationid=\"CR114\" class=\"CitationRef\"\u003e2015\u003c/span\u003e).\u003c/p\u003e\u003cp\u003ePhotoperiod and light spectrum are also known to regulate the development of underground storage organs, such as tubers and bulbs (Yan et al. \u003cspan citationid=\"CR136\" class=\"CitationRef\"\u003e2022\u003c/span\u003e; Zhou et al. \u003cspan citationid=\"CR150\" class=\"CitationRef\"\u003e2019\u003c/span\u003e). In potato (\u003cem\u003eSolanum tuberosum\u003c/em\u003e), tuber development is mediated by mechanisms similar to those used in the photoperiodic control of flowering. Under long day, the CO-like TF StCOL1 represses both flowering and tuberization in potato by directly activating the expression of the \u003cem\u003ePEPB\u003c/em\u003e family gene \u003cem\u003eStSP5G\u003c/em\u003e. The StSP5G in turn represses other \u003cem\u003ePEPB\u003c/em\u003e genes: the potato florigen \u003cem\u003eStSP3D\u003c/em\u003e, and \u003cem\u003eStSP6A\u003c/em\u003e, which encodes the mobile signal for tuberization called tuberigen (Abelenda et al. \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2016\u003c/span\u003e; Navarro et al. \u003cspan citationid=\"CR94\" class=\"CitationRef\"\u003e2011\u003c/span\u003e). The similar light-dependent regulators, including CO-like TFs and PEPBs, have been shown to be involved in the bulb development in \u003cem\u003eLiliaceae\u003c/em\u003e species (Khosa et al. \u003cspan citationid=\"CR56\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). The mechanisms of influence of RL and FRL on tuber and bulbs development have not been studied, but it is known that FRL has a stimulating effect on potato tuber production, reversing the negative effect of RL on this process (Batutis and Ewing \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e1982\u003c/span\u003e; Rahman et al. \u003cspan citationid=\"CR104\" class=\"CitationRef\"\u003e2021\u003c/span\u003e).\u003c/p\u003e\u003cp\u003eThe storage root is another specialized underground organ of biennial and perennial plants that undergoes modifications to store nutrients. Like tubers and bulbs, it facilitates vegetative propagation and enables plants to survive unfavourable conditions. The development of storage roots depends on the activity of the cambium, a lateral meristem that gives rise to the xylem and phloem tissues with a high proportion of storage parenchyma cells (Hoang et al. \u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e2020b\u003c/span\u003e; Kuznetsova et al. \u003cspan citationid=\"CR64\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). In most root crops, the formation of storage roots has a defined seasonality and is regulated by the environmental cues, including photoperiod and light quality (Hoang et al. \u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e2020b\u003c/span\u003e). Thus, it is discussed that key regulators of photoperiodic development such as COL and PEBP proteins may also be involved in the storage root development (Natarajan et al. \u003cspan citationid=\"CR93\" class=\"CitationRef\"\u003e2019\u003c/span\u003e).\u003c/p\u003e\u003cp\u003eRadish (\u003cem\u003eRaphanus sativus\u003c/em\u003e L. var. radicula Pers.) is a root crop plant with short life cycle closely related to \u003cem\u003eArabidopsis\u003c/em\u003e. It has been shown that radish forms large storage roots under long day (Guo et al. \u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e2019\u003c/span\u003e) and high levels of RL (Zha, Liu, \u003cspan citationid=\"CR145\" class=\"CitationRef\"\u003e2018\u003c/span\u003e), but the exact mechanisms underliyng this have not been studied. Here we have shown that RL (660 nm, R\u003csub\u003e660\u003c/sub\u003e) and FRL (730 nm, FR\u003csub\u003e730\u003c/sub\u003e) have opposite effects on storage root formation and flowering in radish. RL was shown to stimulate the growth of storage roots and suppress flowering, whereas FRL promoted flowering and suppressed storage root formation. In the taproots of radish plants RL stimulated the proliferation of cambium and xylem parenchyma, while under FRL xylem parenchyma transformed to sclerenchyma. RL and FRL also had contrasting effects on the content of water-soluble sugars and starch in radish roots and leaves. Transcriptome analysis revealed that more than fifty radish genes encoding key players of photoperiodic flowering control were downregulated in both radish leaves and taproots under RL, while several key genes involved in the root growth were specifically upregulated under RL in the taproot. There were also numerous DEGs involved in sucrose metabolism and phytohormonal balance. Change in the expression of these genes may play a key role in switching between two opposing developmental programs, flowering and storage root formation, depending on the RL:FRL balance.\u003c/p\u003e"},{"header":"2. Materials and Methods","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e\u003ch2\u003e2.1. Plant material\u003c/h2\u003e\u003cp\u003eRadish inbred line 19 from the genetic collection of Saint Petersburg State University (Buzovkina and Lutova \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e2007\u003c/span\u003e) was used in this work. This line is approximately the 50th inbred generation originated from the Saxa cultivar, which belongs to the European group of radish cultivars and forms a round-shape storage root.\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec4\" class=\"Section2\"\u003e\u003ch2\u003e2.2. Plant growing and sampling\u003c/h2\u003e\u003cp\u003e Plants were grown in growth chambers (Urbangrower 150, PR China) with various light treatments according to the experimental layout.\u003c/p\u003e\u003cp\u003eSeeds were sown in the in 2 L vegetation vessels with commercial neutralised peat-based substrate \u0026lsquo;Agrobalt-C\u0026rsquo; (Russia) with pH 6.0-6.5 and complete macro- and micronutrient supply including 150 mg L\u003csup\u003e\u0026minus;\u0026thinsp;1\u003c/sup\u003e [NH\u003csub\u003e4\u003c/sub\u003e\u003csup\u003e+\u003c/sup\u003e and NO\u003csub\u003e3\u003c/sub\u003e\u003csup\u003e\u0026minus;\u003c/sup\u003e], 270 mg L\u003csup\u003e\u0026minus;\u0026thinsp;1\u003c/sup\u003e P\u003csub\u003e2\u003c/sub\u003eO\u003csub\u003e5\u003c/sub\u003e, and 300 mg L\u003csup\u003e\u0026minus;\u0026thinsp;1\u003c/sup\u003e K\u003csub\u003e2\u003c/sub\u003eO. The substrate humidity was maintained at 70% of the full water capacity, watering on the scales.\u003c/p\u003e\u003cp\u003ePlant chambers were illuminated with lamps consisting of different light-emitting diode (LED) bars, specifically designed to provide a custom spectrum in each chamber. Fixtures consisted of light modules with tunable LEDs that varied in the wavelength and spectral composition of the emitted light. Four types of high-performance narrow-band 3 w LEDs (Estar, Cidly, PR China) were used: short-wave red (\u003cb\u003e∆\u003c/b\u003eλ\u003csub\u003e0,5\u003c/sub\u003e\u0026thinsp;=\u0026thinsp;623\u0026thinsp;\u0026divide;\u0026thinsp;641 nm, λ\u003csub\u003emax\u003c/sub\u003e\u0026thinsp;=\u0026thinsp;632 nm), long-wave red (∆λ\u003csub\u003e0,5\u003c/sub\u003e\u0026thinsp;=\u0026thinsp;646\u0026thinsp;\u0026divide;\u0026thinsp;674 nm, λ\u003csub\u003emax\u003c/sub\u003e\u0026thinsp;=\u0026thinsp;660 nm), far-red (∆λ\u003csub\u003e0,5\u003c/sub\u003e\u0026thinsp;=\u0026thinsp;727\u0026thinsp;\u0026divide;\u0026thinsp;751 nm, λ\u003csub\u003emax\u003c/sub\u003e\u0026thinsp;=\u0026thinsp;739 nm), and blue (∆λ\u003csub\u003e0,5\u003c/sub\u003e\u0026thinsp;=\u0026thinsp;452\u0026thinsp;\u0026divide;\u0026thinsp;477 nm, λ\u003csub\u003emax\u003c/sub\u003e\u0026thinsp;=\u0026thinsp;465 nm). The same daily light integral was maintained in all treatments. In all light treatments, photosynthetic photon flux density (PPFD) was maintained at 75 \u0026micro;mol m\u003csup\u003e\u0026minus;\u0026thinsp;2\u003c/sup\u003e s\u003csup\u003e\u0026minus;\u0026thinsp;1\u003c/sup\u003e, with a photoperiod of 18 h. The spectra of the resulting lamp systems were measured with a spectrometer UPRtek PG100N (Taiwan).\u003c/p\u003e\u003cp\u003eA LI-191R quantum sensor with an LI-250A data logger (Li-Cor, NE, USA) was used to measure the PPFD in the PAR region. Taking into account the differences in the spectral absorbance of phytochrome \u003cem\u003eP\u003c/em\u003e\u003csub\u003e\u003cem\u003er\u003c/em\u003e\u003c/sub\u003e and \u003cem\u003eP\u003c/em\u003e\u003csub\u003e\u003cem\u003efr\u003c/em\u003e\u003c/sub\u003e (Sager et al. \u003cspan citationid=\"CR113\" class=\"CitationRef\"\u003e1988\u003c/span\u003e), two different spectral treatments were set to vary the PFD of narrow-band LEDs with peak irradiance at 730 and 660 nm. One treatment named \u0026lsquo;FRL\u0026rsquo; included 0% R\u003csub\u003e660\u003c/sub\u003e and 100% FR\u003csub\u003e730\u003c/sub\u003e, another named \u0026lsquo;RL\u0026rsquo; \u0026ndash; 100% R\u003csub\u003e660\u003c/sub\u003e\u0026thinsp;+\u0026thinsp;0% FR\u003csub\u003e730\u003c/sub\u003e. In addition, LEDs with λ\u003csub\u003emax\u003c/sub\u003e\u0026thinsp;=\u0026thinsp;632 nm were applied to compensate for a possible decrease in PPFD in the red region according to the experimental set-up; the combined R\u003csub\u003e632\u003c/sub\u003e\u0026thinsp;+\u0026thinsp;R\u003csub\u003e660\u003c/sub\u003e PPFD had been adjusted to the same level in all treatments. Blue light PPFD was at the same level in all the spectral treatments (\u003cb\u003eFig. \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e\u003c/b\u003e).\u003c/p\u003e\u003cp\u003ePlant leaf photosynthetic rate and respiration rate analyses were carried out using a LI-6400XT Portable Photosynthesis System (Li-Cor, NE, USA). During the measurements CO\u003csub\u003e2\u003c/sub\u003e concentration was maintained at 400\u0026thinsp;\u0026plusmn;\u0026thinsp;12.0 \u0026micro;mol mol\u003csup\u003e\u0026minus;\u0026thinsp;1\u003c/sup\u003e, air temperature 21\u0026ndash;23\u0026deg;C, air humidity 60\u0026thinsp;\u0026plusmn;\u0026thinsp;4.0%.\u003c/p\u003e\u003c/div\u003e\n\u003ch3\u003e3. Light microscopy\u003c/h3\u003e\n\u003cp\u003eThe whole taproot and lower part of the stem of radish plants were fixed in FAA on 14, 28, 42 days after germination with post-fixation in 70% ethanol according to the standard protocol (Stasolla and Yeung \u003cspan citationid=\"CR124\" class=\"CitationRef\"\u003e2015\u003c/span\u003e). Samples were dehydrated in an alcohol series of increasing concentrations (80%, 85%, 90%, two times 96%, two times 100%) and then in a series of xylene mixed with 100% isopropyl alcohol (25%, 50%, 75%) followed by infiltration with 100% xylene for 1\u0026ndash;3 hours according to the size. The samples were then embedded in paraffin.\u003c/p\u003e\u003cp\u003eTransverse sections (10 \u0026micro;m thick) were obtained with a rotary microtome Microm HM355S (Thermo Fisher Scientific). Deparaffinised and hydrated sections were stained with a combination of 1% aqueous Safranin O and 0.1% Alcian Blue solutions in 3% acetic acid in accordance with a standard procedure (Barykina et al. \u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e2004\u003c/span\u003e) on an automated slide stainer Varistain Gemini ES (Thermo Fisher Scientific). Slides were examined using a VS120-S6 (Olympus) slide scanner. Part of the fixed material was hand sectioned, stained with a solution of 0.5% phloroglucinol (in an equal mixture of water and ethanol) with the addition of 20% hydrochloric acid (Barykina et al. \u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e2004\u003c/span\u003e) and observed under an AxioPlan light microscope (Carl Zeiss) for the analysis of the lignified cell distribution. Images were adjusted for colour and contrast using Adobe Photoshop (Adobe, USA) or ImageJ (Schindelin et al. \u003cspan citationid=\"CR115\" class=\"CitationRef\"\u003e2012\u003c/span\u003e).\u003c/p\u003e\n\u003ch3\u003e4. Measurement of soluble sugars and starch content\u003c/h3\u003e\n\u003cp\u003eSugar and starch determinations were carried out in the samples of radish taproot and leaves of plants grown for 14 days and 28 days under RL or FRL in four replicates with material of five plants in each. 200 mg of plant material was grinded in the liquid nitrogen. Before carbohydrate extraction the samples were depigmented with 100% acetone (Marshall, \u003cspan citationid=\"CR83\" class=\"CitationRef\"\u003e1986\u003c/span\u003e) and transferred to clean tubes. The soluble sugars were extracted twice with 80% ethanol at 50\u0026deg;C. The remaining sediments were used for starch extraction with 1.1% hydrochloric acid at 100\u0026deg;C for 30 min (Oren et al., \u003cspan citationid=\"CR98\" class=\"CitationRef\"\u003e1988\u003c/span\u003e). Soluble sugars and starch were determined spectrophotometrically at 620 nm by the anthrone reaction (Hansen and Moller 1975). Calibration curves were built with glucose and potato starch.\u003c/p\u003e\n\u003ch3\u003e5. RNA isolation, library preparation and sequencing\u003c/h3\u003e\n\u003cp\u003eFor RNA-seq, total RNA was extracted from leaves and taproots of radish plants on 14 and 28 days after germination, which were grown under RL or FRL. Plants were sampled 4 h after the onset of daylight. Three biological replicates were used for each light treatment.\u003c/p\u003e\u003cp\u003eRNA isolation was performed as follows: plant material grinded in the liquid nitrogen was treated with 500 \u0026micro;l of Trizol reagent (Invitrogen, USA) for 5 min at 25\u0026ordm;C, followed by chloroform purification and RNA precipitation with isopropanol. The precipitate was washed three times with 80% ethanol, air dried and dissolved in sterile deionized water. RNA was purified from genomic DNA contamination using a DNA-free DNA Removal Kit (Thermo Fisher Scientific, USA).\u003c/p\u003e\u003cp\u003eLibrary preparation and sequencing were performed by CeGaT GmbH company (Tuebingen, Germany). Illumina libraries were prepared from the polyA RNA with the NEBNext\u0026reg; Ultra\u0026trade; DNA Library Prep Kit (New England Biolabs, Hitchin, UK) according to the manufacturer\u0026rsquo;s instructions. Dual barcoding was performed using the NEBNext\u0026reg; Ultra\u0026trade; DNA Index Prep Kit for Illumina and the NEBNext\u0026reg; Multiplex Oligos\u0026reg; Illumina\u0026reg; (Dual Index Primers Set 1). Sequencing of libraries was performed on an Illumina HiSeq2500 sequencer with 50 bp read length.\u003c/p\u003e\n\u003ch3\u003e6. Bioinformatic processing of sequencing results\u003c/h3\u003e\n\u003cp\u003ePurification of fastq raw reads from radish mitochondrial, plastid and ribosomal DNA was performed using the bbduk tool from the bbtools package (v. 38.96) (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://jgi.doe.gov/data-and-tools/bbtools/\u003c/span\u003e\u003cspan address=\"https://jgi.doe.gov/data-and-tools/bbtools/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e, accessed on 9 January 2025). Quality filtered and decontaminated reads were trimmed with Trimmomatic (v. 0.40) with the \u0026lsquo;HEADCROP:15 CROP:95\u0026rsquo; options. Reads quality control was performed with MultiQC (v.1.12) (Ewels et al. \u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e2016\u003c/span\u003e). Filtered reads were aligned on sequences of GCA_000801105.3 \u003cem\u003eR.sativus\u003c/em\u003e reference genome with HISAT2 v. 2.01.2 (Kim et al. \u003cspan citationid=\"CR58\" class=\"CitationRef\"\u003e2015\u003c/span\u003e) and then counted with Stringtie (Pertea et al. \u003cspan citationid=\"CR101\" class=\"CitationRef\"\u003e2015\u003c/span\u003e) tool. Differential expression between experimental and control samples was analysed with the DESeq2 package (v. 1.28.1) for R (v. 3.6.2) (Love et al. \u003cspan citationid=\"CR77\" class=\"CitationRef\"\u003e2014\u003c/span\u003e). Genes with p-value adjusted\u0026thinsp;\u0026lt;\u0026thinsp;0.01 and logFoldChange\u0026thinsp;\u0026gt;\u0026thinsp;1 were considered to be differentially expressed. The GSEABase v. 1.50 (\u0026ldquo;GSEABase,\u0026rdquo; n.d.) R package was used for GO gene enrichment analysis.\u003c/p\u003e"},{"header":"3. Results","content":"\u003cdiv id=\"Sec10\" class=\"Section2\"\u003e\n \u003ch2\u003e3.1. Phenotypes and root anatomy of radish plants grown under different light conditions\u003c/h2\u003e\n \u003cp\u003eRadish plants for the analysis of root anatomy, gene transcription and sugar content were grown under two light spectra contrastingly differed in the proportion of R\u003csub\u003e660\u003c/sub\u003e and FR\u003csub\u003e730\u003c/sub\u003e: 0% R\u003csub\u003e660\u003c/sub\u003e and 100% FR\u003csub\u003e730\u003c/sub\u003e (\u0026lsquo;FRL\u0026rsquo;) and 100% R\u003csub\u003e660\u003c/sub\u003e and 0% FR\u003csub\u003e730\u003c/sub\u003e (\u0026lsquo;RL\u0026rsquo;).\u003c/p\u003e\n \u003cp\u003eWhen growing radish on RL and FRL, we observed two opposite strategies for plant development (Fig. \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003e). The shade avoidance response (SAR) was observed in FRL-treated plants at the early stages as hypocotyl elongation and later leaf blade elongation (\u003cstrong\u003eFig. S2\u003c/strong\u003e). By 28 days after germination (DAG), plants subjected to FRL began to form inflorescence meristems, and by 42 DAG all FRL-grown plants were actively flowering. At the same time, in the absence of FRL plants did not form inflorescence meristems even after 42 DAG.\u003c/p\u003e\n \u003cp\u003ePlants grown under FRL showed no transition to taproot thickening, whereas plants grown under RL were characterized by an intense increase in taproot diameter and formed a large storage root (Fig. \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003e, \u003cstrong\u003eFig. S3\u003c/strong\u003e). The addition of FRL and the subsequent transition of the plants to flowering resulted in an increase in the net photosynthetic rate in the leaves, while the respiration rate was reduced (\u003cstrong\u003eFig. S4\u003c/strong\u003e).\u003c/p\u003e\n \u003cp\u003eThe scale indicates the plant height in cm.\u003c/p\u003e\n \u003cp\u003eDespite the name \u0026lsquo;storage root\u0026rsquo;, in radish and other plants with storage taproots this is a composite structure consisting of the primary root and the hypocotyl. Thickening occurs in both morphological parts of the storage root and is associated with the storage parenchyma development in the secondary xylem (Meng et al. \u003cspan class=\"CitationRef\"\u003e2024\u003c/span\u003e; Zaki et al. \u003cspan class=\"CitationRef\"\u003e2012\u003c/span\u003e).\u003c/p\u003e\n \u003cp\u003eBy the 14 DAG, the transition to secondary growth occurred in radish plants grown both under FR and FRL (Fig. \u003cspan class=\"InternalRef\"\u003e2\u003c/span\u003ea, b), and no significant differences were observed at the anatomical level. A well-developed cambium was present in all plants regardless of light conditions, with approximately the same number of cell layers in the cambial zone.\u003c/p\u003e\n \u003cp\u003eAnatomical differences between plants grown under RL or FRL started at the 28 DAG. Although the formation of secondary xylem with a relatively large number of parenchyma cells occurred regardless of the light conditions, the number of cell layers formed and deposited by the cambium inside, was significantly lower when plant was grown under FRL (Fig. \u003cspan class=\"InternalRef\"\u003e2\u003c/span\u003ec, d). The number of vessels did not vary significantly, and the differences in xylem volume were associated with changes in the number of cell layers of the storage xylem parenchyma.\u003c/p\u003e\n \u003cp\u003eAt 42 DAG, the secondary xylem parenchyma in plants grown at FRL was largely transformed into sclerenchyma with thickened and lignified cell walls. At the same time, parenchymal lignification did not occur in plants grown under RL (Fig. \u003cspan class=\"InternalRef\"\u003e2\u003c/span\u003ee, f).\u003c/p\u003e\n \u003cp\u003ePlants grown at FRL also lack any proliferating parenchyma both in the central part of the stele and in the secondary xylem (Fig. \u003cspan class=\"InternalRef\"\u003e2\u003c/span\u003ed, f, \u003cstrong\u003eFig. S5\u003c/strong\u003e). In plants grown under RL, at 28 and 42 DAG, proliferation of vasicentric parenchyma (associated with vessels) was observed around all vessels in both primary and secondary xylem, forming the characteristic \u0026lsquo;halo\u0026rsquo; of parenchymal cells. Proliferation of the apotracheal parenchyma (not associated with vessels) was detected both in the central part of the stele and in the secondary xylem.\u003c/p\u003e\n \u003cp\u003eProliferation of the vasicentric and apotracheal parenchyma is an essential process in radish and some other \u003cem\u003eBrassicaceae\u003c/em\u003e and contributes significantly to the root thickening (Hearn et al. \u003cspan class=\"CitationRef\"\u003e2018\u003c/span\u003e; Magendans \u003cspan class=\"CitationRef\"\u003e1991\u003c/span\u003e). Thus, the observed proliferation of xylem parenchyma in the plants grown under RL can be the main cause of the thickening of the storage root. At the same time, plants grown on FRL lack storage xylem parenchyma and instead differentiate mechanical tissue.\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec11\" class=\"Section2\"\u003e\n \u003ch2\u003e3.2. Content of starch and soluble sugars in radish leaves and taproots\u003c/h2\u003e\n \u003cp\u003eDuring plant growth, carbohydrates are produced as photosynthates in the source organs (mainly leaves) and are translocated in the form of sucrose through the phloem to the sinks. Among sink organs and tissues can be the sites of active growth (e.g., meristems) and storage organs. During its growth, the storage root is the main sink organ which is competing with other sinks, e.g. with floral meristem (Hoang et al. \u003cspan class=\"CitationRef\"\u003e2020b\u003c/span\u003e). In storage root, sucrose is metabolized to provide tissue growth and also can be deposited, mainly in the form of starch, in the parenchyma. Thus, in the mature xylem-type storage roots of Brassicaceae, xylem is almost exclusively composed of parenchyma cells filled with starch granules (Kuznetsova et al. \u003cspan class=\"CitationRef\"\u003e2020\u003c/span\u003e).\u003c/p\u003e\n \u003cp\u003eAt stage 14 DAG, RL-grown and FRL-grown radish plants showed almost no difference in the content of water-soluble sugars in the taproot and leaves (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003ea, c). At the same time, the starch content in RL-grown plants at 14 DAG was about 30% higher in the leaves, probably reflecting more efficient photosynthesis, and 50% lower in the taproot as compared with FRL-grown plants (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003eb, d). At stage 28 DAG, differences in the distribution of both starch and water-soluble sugars were observed between plants grown on RL and FRL.\u003c/p\u003e\n \u003cp\u003eIn the leaves of RL-grown radish plants, the content of water-soluble sugars was slightly increased at 28 DAG as compared to 14 DAG, while in their taproot, the content of water-soluble sugars was increased by about 30% (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003ea, c). The starch content in 28 DAG RL-grown plants was sharply decreased (by 30%) in the leaves and almost by 40% increased in the taproot as compared to plants at 14 DAG (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003eb, d). These trends can reflect the delivery of photosynthates to the main sink - the actively growing storage root. In plants grown under FRL, the level of soluble sugars by 28 DAG was significantly decreased in the leaves (by 12%) and taproot (almost twice) as compared to 14 DAG, and the starch content in both leaves and taproot tended to slightly increase and remained higher than in RL-grown plants.\u003c/p\u003e\n \u003cp\u003eThus, radish plants grown under RL and FRL were contrasted in the dynamics of sugar accumulation. In FRL-grown plants, amounts of water-soluble sugars in the leaves and especially in the taproot were decreased while the starch content did not change significantly. At the same time, when plants were grown on RL, the amount of soluble sugars and starch increased significantly in the root and did not change or decreased in the leaves. It is remarkable that these changes in sugar content precede anatomical changes in the radish roots associated with an increase in the amount of storage parenchyma: differences in this parameter in plants grown on RL and FRL were observed later than 28 DAG. It can be assumed that an increase in carbohydrate content can trigger proliferation of cambium and/or xylem parenchyma, thus creating tissue for their deposition. This is well consistent with data on sucrose-mediated inhibition of the differentiation of phloem and xylem conductive elements in \u003cem\u003eArabidopsis\u003c/em\u003e (Narutaki et al. \u003cspan class=\"CitationRef\"\u003e2023\u003c/span\u003e).\u003c/p\u003e\n \u003cdiv class=\"BlockQuote\"\u003e\n \u003cp\u003e\u003cstrong\u003e3.3. Transcriptome analysis of gene expression in roots and leaves of radish plants grown under RL and FRL\u003c/strong\u003e\u003c/p\u003e\n \u003c/div\u003e\n \u003cp\u003eTo understand the molecular mechanism underlying the contrasting variants of radish development under different red spectrum compositions, we performed the transcriptome analysis of leaves and taproots of 14 DAG and 28 DAG plants grown under RL and FRL. We analyzed the changes in the gene expression under RL compared to FRL because RL was inductive for the development of the radish storage root. As a result, we have identified a number of genes that were differentially expressed in the leaves and taproots (Table\u0026nbsp;\u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e\n \u003cdiv class=\"gridtable\"\u003e\n \u003ctable id=\"Tab1\" border=\"1\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eNumber of differentially expressed genes (DEGs) identified in the roots and leaves of radish plants grown under the red light (RL) in comparison with far-red light (FRL)\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eStage\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eComparison\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eDEG downregulated\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eDEG upregulated\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eTotal DEG\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\" rowspan=\"2\"\u003e\n \u003cp\u003e14 DAG\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLeaf RL \u0026nbsp;vs \u0026nbsp;Leaf FRL\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e373\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e187\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e560\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eRoot RL \u0026nbsp;vs \u0026nbsp;Root FRL\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e2363\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1859\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e4222\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\" rowspan=\"2\"\u003e\n \u003cp\u003e28 DAG\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLeaf RL \u0026nbsp;vs \u0026nbsp;Leaf FRL\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1335\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1961\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3296\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eRoot RL \u0026nbsp;vs \u0026nbsp;Root FRL\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e2398\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e897\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3295\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n \u003c/div\u003e\n \u003cp\u003eSince the leaves are the main organs of light perception, whereas the taproots grew in the soil, we can assume that the formation of the storage root under the influence of RL may depend on signals coming from the aboveground part of the plant. These observations led us to speculate that flowering and storage root formation, which seemed to be two opposing light-dependent processes, are controlled by different sets of regulators, which are induced by RL or FRL.\u003c/p\u003e\n \u003cp\u003eTherefore, we compared the number of differentially expressed genes (DEGs) characterized by similar or opposite patterns of expression changes in radish leaves and roots under RL (Fig. \u003cspan class=\"InternalRef\"\u003e4\u003c/span\u003ea). As a result, there were many more genes with a similar pattern of expression in both leaf and taproot than genes with the opposite pattern of expression. Thus, the supposed \u0026lsquo;sink competition\u0026rsquo; between the storage root and inflorescence is unlikely to depend on opposite patterns of gene expression in the underground and aboveground parts of the plant.\u003c/p\u003e\n \u003cp\u003eSeveral DEGs were identified that showed a common pattern of expression changes in both radish leaves and taproots at 14 DAG and 28 DAG (Fig. \u003cspan class=\"InternalRef\"\u003e4\u003c/span\u003eb, \u003cstrong\u003eTable \u003cspan class=\"InternalRef\"\u003eS1\u003c/span\u003e\u003c/strong\u003e). It is interesting to note that among these \u0026lsquo;common\u0026rsquo; downregulated DEGs, genes involved in the control of flowering, such as radish homologs of \u003cem\u003eSOC1\u003c/em\u003e and \u003cem\u003eCONSTANS-LIKE 5\u003c/em\u003e, predominated (5 out of 8 genes with known functions). A list of \u0026lsquo;common\u0026rsquo; upregulated DEGs included one gene for the cytokinin response regulator \u003cem\u003eARR4\u003c/em\u003e, which also acts as a modulator of RL signaling (Sweere et al. \u003cspan class=\"CitationRef\"\u003e2001\u003c/span\u003e), and several genes encoding myrosinases, enzymes that catalyze the biosynthesis of glucosinolates, defense metabolites of \u003cem\u003eBrassicaceae\u003c/em\u003e (Halkier and Gershenzon \u003cspan class=\"CitationRef\"\u003e2006\u003c/span\u003e). At the same time, there were \u0026lsquo;root-specific\u0026rsquo; and \u0026lsquo;leaf-specific\u0026rsquo; DEGs, the expression of which were changed under RL only in the underground or above-ground part of the plant. Interestingly, there were many more root-specific DEGs among the than leaf-specific (Fig. \u003cspan class=\"InternalRef\"\u003e4\u003c/span\u003eb): 400 versus 31 among downregulated ones and 210 versus 24 among upregulated.\u003c/p\u003e\n \u003cp\u003eGenerally, a significant proportion of the identified DEGs were key regulators of photomorphogenesis. There were also numerous DEGs involved in the sugar metabolism and in the biosynthesis and signaling of phytohormones. Among root-specific DEGs, there were several radish homologs of \u003cem\u003eArabidopsis\u003c/em\u003e genes which are known as key regulators of root development.\u003c/p\u003e\n \u003cp\u003e\u003cstrong\u003eGenes involved in the light signaling and photomorphogenesis\u003c/strong\u003e\u003c/p\u003e\n \u003cp\u003eRadish genes, whose homologues in \u003cem\u003eArabidopsis\u003c/em\u003e act at different stages of light signaling and photomorphogenesis, were the most represented functional group of DEGs identified in this work (Fig. \u003cspan class=\"InternalRef\"\u003e5\u003c/span\u003e, \u003cstrong\u003eTables S2-S5\u003c/strong\u003e).\u003c/p\u003e\n \u003cp\u003eFirstly, there were DEGs involved in the sensing and primary transmission of RL/FRL signals. Among genes encoding photoreceptors, one of the three radish \u003cem\u003ePHYB\u003c/em\u003e and one of two \u003cem\u003ePHYA\u003c/em\u003e genes were downregulated under RL in leaves. The best known direct targets of phytochromes are the bHLH TFs named PHYTOCROME INTERACTING FACTORs (PIFs) (Cordeiro et al. \u003cspan class=\"CitationRef\"\u003e2022\u003c/span\u003e). Several radish \u003cem\u003ePIF\u003c/em\u003e genes were downregulated under RL in the leaves and/or taproots. Among them there were homologs of the closely related \u003cem\u003eArabidopsis PIF4\u003c/em\u003e and \u003cem\u003ePIF5\u003c/em\u003e, which are integrators of light signaling with other stimuli, including hormonal responses (Pham et al. \u003cspan class=\"CitationRef\"\u003e2018\u003c/span\u003e). The \u003cem\u003ePIF3-LIKE 1\u003c/em\u003e (\u003cem\u003ePIL1\u003c/em\u003e), key regulator of the response to FRL and shade (Li et al. \u003cspan class=\"CitationRef\"\u003e2014\u003c/span\u003e), and \u003cem\u003ePIF6\u003c/em\u003e, which is close to \u003cem\u003ePIL1\u003c/em\u003e, were also specifically downregulated in the leaves. Among the strongly downregulated genes there also was the \u003cem\u003eLONG HYPOCOTYL IN FAR-RED1\u003c/em\u003e (\u003cem\u003eHFR1\u003c/em\u003e), whose product, an atypical bHLH, interacts with PIFs and antagonizes them in the regulation of gene expression (Li et al. \u003cspan class=\"CitationRef\"\u003e2014\u003c/span\u003e; Shi et al. \u003cspan class=\"CitationRef\"\u003e2013\u003c/span\u003e). In \u003cem\u003eArabidopsis\u003c/em\u003e, the \u003cem\u003ePIL1\u003c/em\u003e and \u003cem\u003eHFR1\u003c/em\u003e are direct positively regulated targets of the PIF4 and PIF5 (Hornitschek et al. \u003cspan class=\"CitationRef\"\u003e2012\u003c/span\u003e), and the HFR1 protein interacts with at least PIF4 and PIL1 to modulate their functions (Li et al. \u003cspan class=\"CitationRef\"\u003e2014\u003c/span\u003e; Shi et al. \u003cspan class=\"CitationRef\"\u003e2013\u003c/span\u003e; Sng et al. \u003cspan class=\"CitationRef\"\u003e2023\u003c/span\u003e), suggesting that all these radish DEGs may operate in the same pathway.\u003c/p\u003e\n \u003cp\u003eSecondly, radish genes encoding components of the circadian clock were also found to be downregulated under RL mainly in the taproots. Radish homologs of \u003cem\u003eLATE ELONGATED HYPOCOTYL (LHY)\u003c/em\u003e and \u003cem\u003eARABIDOPSIS PSEUDO-RESPONSE REGULATOR 1 / TIMING OF CAB EXPRESSION 1 (APRR1/ TOC1\u003c/em\u003e), which are component of core oscillator in plant circadian clock (Oakenfull and Davis \u003cspan class=\"CitationRef\"\u003e2017\u003c/span\u003e), were specifically downregulated in the taproots. The same was found for four homologs of \u003cem\u003eAPRR5\u003c/em\u003e which act downstream of \u003cem\u003eAPRR1\u003c/em\u003e in \u003cem\u003eArabidopsis\u003c/em\u003e, while other probable targets of APRR1 (Huang et al. \u003cspan class=\"CitationRef\"\u003e2012\u003c/span\u003e; Nakamichi et al. \u003cspan class=\"CitationRef\"\u003e2010\u003c/span\u003e), three radish \u003cem\u003eAPRR9\u003c/em\u003e genes and one \u003cem\u003eAPRR7\u003c/em\u003e were downregulated in the taproots and leaves. Moreover, \u003cem\u003eREVEILLE (RVE)\u003c/em\u003e genes related to \u003cem\u003eLHY\u003c/em\u003e (Gray et al. \u003cspan class=\"CitationRef\"\u003e2017\u003c/span\u003e), were also among the downregulated: the expression of \u003cem\u003eREV1, REV3\u003c/em\u003e and \u003cem\u003eREV4\u003c/em\u003e were decreased under RL in the taproot, while both two radish \u003cem\u003eRVE7\u003c/em\u003e genes were downregulated at 14 DAG in both leaves and roots but upregulated at 28 DAG. Among downregulated also were components of the \u0026lsquo;evening loop\u0026rsquo; in the circadian clock, genes encoding TFs EARLY FLOWERING 4 (ELF4), ELF3 and LUX ARRHYTHMO (LUX) (Zhao et al. \u003cspan class=\"CitationRef\"\u003e2021\u003c/span\u003e): two radish \u003cem\u003eELF4\u003c/em\u003e, one \u003cem\u003eELF3\u003c/em\u003e and one \u003cem\u003eLUX\u003c/em\u003e gene were specifically downregulated in the taproot. Two radish homologs of \u003cem\u003eELONGATED HYPOCOTYL5\u003c/em\u003e (\u003cem\u003eHY5\u003c/em\u003e), a master positive regulator of many key genes involved in light response, circadian clock and flowering (Gangappa and Botto \u003cspan class=\"CitationRef\"\u003e2016\u003c/span\u003e), were also strongly downregulated in the taproots of RL-grown plants. In turn, a single radish homolog of \u003cem\u003eGIGANTEA (GI)\u003c/em\u003e, which is a central player in the circadian clock-controlled flowering pathway (Mishra and Panigrahi \u003cspan class=\"CitationRef\"\u003e2015\u003c/span\u003e), was downregulated in the leaves, suggesting its suppression as a mechanism for delaying radish flowering on the RL. At the same time, downregulation of circadian clock genes in the taproot of RL-grown radish plants allows us to suggest their functions in storage root development.\u003c/p\u003e\n \u003cp\u003eThirdly, the large group of radish genes which were downregulated under RL are homologs of known key players of light-dependent transition to flowering and/or tuberization. The most important of them is \u003cem\u003eCONSTANS\u003c/em\u003e (\u003cem\u003eCO\u003c/em\u003e), encoding B-box-type zinc finger (BBX) TF. Several CO-LIKE (COL) proteins act redundantly and interact with CO (Zhang et al. \u003cspan class=\"CitationRef\"\u003e2023\u003c/span\u003e). In radish plants grown under RL, both homologs of \u003cem\u003eCOL5\u003c/em\u003e were strongly downregulated in the leaves and taproots of 14 DAG and 28 DAG plants. At the same time, other radish \u003cem\u003eCOLs\u003c/em\u003e, including \u003cem\u003eCOL2\u003c/em\u003e, \u003cem\u003eCOL8\u003c/em\u003e, two \u003cem\u003eCOL4\u003c/em\u003e, three \u003cem\u003eCOL10\u003c/em\u003e and four \u003cem\u003eBBX24\u003c/em\u003e, were differentially expressed only in radish roots: all of them were downregulated under RL, but \u003cem\u003eCOL10\u003c/em\u003e homologs were upregulated. In \u003cem\u003eArabidopsis\u003c/em\u003e, \u003cem\u003eCOL2\u003c/em\u003e, \u003cem\u003e4, 5\u003c/em\u003e and \u003cem\u003e8\u003c/em\u003e are known as regulators of flowering (Zhang et al. \u003cspan class=\"CitationRef\"\u003e2023\u003c/span\u003e), \u003cem\u003eBBX24\u003c/em\u003e mainly participates in stress tolerance (Chiriotto et al. \u003cspan class=\"CitationRef\"\u003e2023\u003c/span\u003e), and the functions of \u003cem\u003eCOL10\u003c/em\u003e are unknown.\u003c/p\u003e\n \u003cp\u003eMajor direct targets of CO and COLs are \u003cem\u003eFT\u003c/em\u003e gene encoding major mobile flower-promoting signal (Takagi et al. \u003cspan class=\"CitationRef\"\u003e2023\u003c/span\u003e), and also \u003cem\u003eFT-like\u003c/em\u003e genes which are positive and negative regulators of tuberization in potato and Liliaceae (Khosa et al. \u003cspan class=\"CitationRef\"\u003e2021\u003c/span\u003e). In radish, expression of one of two \u003cem\u003eFT\u003c/em\u003e genes is severely downregulated under RL in both leaves and taproots. The same was observed for one of two radish homologs of \u003cem\u003eBROTHER OF FT AND TFL1\u003c/em\u003e (\u003cem\u003eBFT1\u003c/em\u003e) and for single radish \u003cem\u003eMOTHER OF FT AND TFL1\u003c/em\u003e (\u003cem\u003eMFT\u003c/em\u003e) gene. At the same time, another radish \u003cem\u003eBFT1\u003c/em\u003e was downregulated under RL in the leaves but upregulated in taproots.\u003c/p\u003e\n \u003cp\u003eAlthough the functions of \u003cem\u003eCOL\u003c/em\u003e and \u003cem\u003eFT\u003c/em\u003e family genes in root development are unknown, they could have functions beyond flowering. In \u003cem\u003eArabidopsis, COL3\u003c/em\u003e regulates root elongation (Datta et al. \u003cspan class=\"CitationRef\"\u003e2006\u003c/span\u003e), and \u003cem\u003eMFT\u003c/em\u003e suppresses seed germination under FRL (Vaistij et al. \u003cspan class=\"CitationRef\"\u003e2018\u003c/span\u003e). In potato, \u003cem\u003eStCOL1\u003c/em\u003e together with several more \u003cem\u003eStCOLs\u003c/em\u003e function as negative regulators of tuberization (Gonz\u0026aacute;lez-Schain et al. \u003cspan class=\"CitationRef\"\u003e2012\u003c/span\u003e; Yin et al. \u003cspan class=\"CitationRef\"\u003e2024\u003c/span\u003e). Their targets are \u003cem\u003eFT\u003c/em\u003e-like \u003cem\u003eSP6A\u003c/em\u003e and \u003cem\u003eSP5G\u003c/em\u003e which encode stimulator and repressor of tuber induction (Abelenda et al. \u003cspan class=\"CitationRef\"\u003e2016\u003c/span\u003e). According to expression data, we can suppose that several radish \u003cem\u003eCOL\u003c/em\u003e and \u003cem\u003eFT-like\u003c/em\u003e genes can be negative regulators of storage root growth. The exception is one of radish \u003cem\u003eBFT1-\u003c/em\u003elike genes which was strongly upregulated in the taproot under RL. In \u003cem\u003eArabidopsis\u003c/em\u003e, \u003cem\u003eBFT1\u003c/em\u003e functions as a flowering suppressor under high salinity (Ryu et al. \u003cspan class=\"CitationRef\"\u003e2011\u003c/span\u003e), but in radish, it could acquire an additional function.\u003c/p\u003e\n \u003cp\u003eFinally, among DEGs there were probable targets of FT-like proteins. In \u003cem\u003eArabidopsis\u003c/em\u003e and other plants, FT is a mobile coactivator of FLOWERING LOCUS D (FD) TF which induces transcription of key floral meristem identity genes such as \u003cem\u003eSOC1, LFY\u003c/em\u003e and \u003cem\u003eAP1\u003c/em\u003e (Zhu et al. \u003cspan class=\"CitationRef\"\u003e2020\u003c/span\u003e). Several MADS family TFs, such as AGAMOUS-LIKE24 (AGL24) and AGL42 act in the same pathway, positively regulating \u003cem\u003eSOC1\u003c/em\u003e gene expression and/or forming a transcriptional activator complex with SOC1 (Liu et al. \u003cspan class=\"CitationRef\"\u003e2008\u003c/span\u003e; Dorca-Fornell et al. \u003cspan class=\"CitationRef\"\u003e2011\u003c/span\u003e). In radish, all four homologs of \u003cem\u003eSOC1\u003c/em\u003e and both homologs of \u003cem\u003eAGL24\u003c/em\u003e were strongly downregulated under RL in the taproot and leaves, indicating the repressive role of RL in flowering initiation. A strong downregulation of two radish \u003cem\u003eLFY\u003c/em\u003e genes was only detected in the taproot, and the same was revealed for some other genes known as flowering regulators, such as \u003cem\u003eAGL3/ SEPALLATA4\u003c/em\u003e (Jetha et al. \u003cspan class=\"CitationRef\"\u003e2014\u003c/span\u003e), \u003cem\u003eAGL8/ FRUITFULL\u003c/em\u003e (van Mourik et al. \u003cspan class=\"CitationRef\"\u003e2023\u003c/span\u003e) and \u003cem\u003eAGL16\u003c/em\u003e (Dong et al. \u003cspan class=\"CitationRef\"\u003e2023\u003c/span\u003e). At the same time, radish homologs of \u003cem\u003eAGL18\u003c/em\u003e, known as a repressor of flowering and stimulator of regeneration (Paul et al. \u003cspan class=\"CitationRef\"\u003e2022\u003c/span\u003e), and \u003cem\u003eAGL42\u003c/em\u003e, which is a stimulator of flowering but also a positive regulator of root meristem (Dorca-Fornell et al. \u003cspan class=\"CitationRef\"\u003e2011\u003c/span\u003e; Nawy et al. \u003cspan class=\"CitationRef\"\u003e2005\u003c/span\u003e), were upregulated in both radish roots and leaves under RL. Thus, we can speculate that in radish many \u0026lsquo;flowering genes\u0026rsquo; may have dual functions in flowering and storage root development.\u003c/p\u003e\n \u003cp\u003e\u003cstrong\u003eGenes involved in the control of phytohormonal balance\u003c/strong\u003e\u003c/p\u003e\n \u003cp\u003eThe light response is known to affect the phytohormonal balance (Hornitschek et al. \u003cspan class=\"CitationRef\"\u003e2012\u003c/span\u003e; Li et al. \u003cspan class=\"CitationRef\"\u003e2012\u003c/span\u003e; Sng et al. \u003cspan class=\"CitationRef\"\u003e2023\u003c/span\u003e). In radish, we identified a large number of genes involved in auxin, cytokinin, gibberellin and ethylene homeostasis, that were differentially expressed between RL- and FRL-grown plants (Fig. \u003cspan class=\"InternalRef\"\u003e6\u003c/span\u003e, \u003cstrong\u003eTables S2-S5\u003c/strong\u003e). In general, under RL we observed a downregulation of genes involved in gibberellin biosynthesis and signaling, as well as in cytokinin and ethylene biosynthesis, whereas certain genes of auxin biosynthesis and also cytokinin- and ethylene-responsive genes were predominantly upregulated in the taproot. Most of the \u0026lsquo;phytohormone-related\u0026rsquo; genes demonstrated similar expression patterns in radish leaves and taproots under RL. At the same time, there were several \u0026apos;exceptional\u0026apos; genes with opposite expression dynamics in leaves and roots. These genes may be necessary for RL-mediated developmental shift towards delayed flowering and storage root formation.\u003c/p\u003e\n \u003cp\u003eFirstly, there were DEGs involved in the control of free auxin level. Auxin is central regulator of cambium position and also plays an important role in the storage root formation and starch deposition in cassava (R\u0026uuml;scher et al. \u003cspan class=\"CitationRef\"\u003e2021\u003c/span\u003e). Among radish DEGs, the \u003cem\u003eTAA-related 2 (TAR2)\u003c/em\u003e was upregulated in both leaves and taproots while two \u003cem\u003eYUCCA8\u003c/em\u003e (\u003cem\u003eYUC8)\u003c/em\u003e genes, whose products act downstream TAR2 in the auxin biosynthesis via indole-2-pyruvic acid (Cao et al. \u003cspan class=\"CitationRef\"\u003e2019\u003c/span\u003e), were strongly downregulated in leaves and taproots. At the same time, two \u003cem\u003eYUCCA6\u003c/em\u003e (\u003cem\u003eYUC6)\u003c/em\u003e genes were upregulated in the root at 14 DAG and downregulated at 28 DAG. Four radish genes encoding GRETCHEN HAGEN 3 (GH3) enzymes, which catalyze the formation of inactive auxin conjugates with amino acids (Luo et al. \u003cspan class=\"CitationRef\"\u003e2023\u003c/span\u003e), were downregulated in the leaves and roots under RL, except of one which was downregulated in the leaves and strongly upregulated in the roots. Among auxin-responsive genes, several radish \u003cem\u003eAux/IAA\u003c/em\u003es, which work in the negative feedback in the auxin response and coordinate it with other signaling pathways (Luo et al. \u003cspan class=\"CitationRef\"\u003e2018\u003c/span\u003e), were strongly downregulated under RL in both leaves and taproots. Remarkably, some of these \u0026lsquo;auxin-related\u0026rsquo; radish DEGs can act in the regulation of photomorphogenesis. Indeed, in \u003cem\u003eArabidopsis\u003c/em\u003e, the \u003cem\u003eTAA1\u003c/em\u003e, several \u003cem\u003eYUCCAs\u003c/em\u003e (including \u003cem\u003eYUC6\u003c/em\u003e and \u003cem\u003eYUC8\u003c/em\u003e), certain \u003cem\u003eGH3s\u003c/em\u003e and \u003cem\u003eIAA29\u003c/em\u003e are direct targets of PIF4, PIF5, and HFR1 (Franklin et al. \u003cspan class=\"CitationRef\"\u003e2011\u003c/span\u003e; Hornitschek et al. \u003cspan class=\"CitationRef\"\u003e2012\u003c/span\u003e; Li et al. \u003cspan class=\"CitationRef\"\u003e2012\u003c/span\u003e; Shi et al. \u003cspan class=\"CitationRef\"\u003e2013\u003c/span\u003e; Sun et al. \u003cspan class=\"CitationRef\"\u003e2013\u003c/span\u003e; Sng et al. \u003cspan class=\"CitationRef\"\u003e2023\u003c/span\u003e).\u003c/p\u003e\n \u003cp\u003ePlant photomorphogenesis also is based on regulation of level of the gibberellins, hormones that control growth processes throughout the plant life cycle, including formation of storage organs. In potato, decrease in gibberellin content under inductive short day facilitate tuberization (Roumeliotis et al. \u003cspan class=\"CitationRef\"\u003e2012\u003c/span\u003e), and in the radish gibberellin suppresses cambium activity and storage root thickening (Meng et al., \u003cspan class=\"CitationRef\"\u003e2024\u003c/span\u003e). In \u003cem\u003eArabidopsis\u003c/em\u003e, genes encoding 2-oxoglutarate-dependent dioxygenases which regulate the level of free gibberellins in plant tissues, are under direct transcriptional control of ELF3, PIF4 and PIF5 (Filo et al. \u003cspan class=\"CitationRef\"\u003e2015\u003c/span\u003e). In RL-grown radish plants, genes of GA\u003csub\u003e20\u003c/sub\u003eOX, which catalyze formation of the bioactive gibberellins from the GA\u003csub\u003e12\u003c/sub\u003e precursor (Yang et al. \u003cspan class=\"CitationRef\"\u003e2020\u003c/span\u003e), were strongly downregulated mainly in the leaves. An exception is \u003cem\u003eGA\u003c/em\u003e\u003csub\u003e\u003cem\u003e20\u003c/em\u003e\u003c/sub\u003e\u003cem\u003eOX\u003c/em\u003e\u003csub\u003e\u003cem\u003e3\u003c/em\u003e\u003c/sub\u003e gene, which was strongly upregulated in the taproot. In addition, the \u003cem\u003eKAO\u003c/em\u003e gene encoding \u003cem\u003eent\u003c/em\u003e-kaurenoic acid oxidase, which catalyzes the early steps of the gibberellin biosynthetic pathway, was downregulated under RL in radish leaves and taproots. At the same time, genes of GA\u003csub\u003e2\u003c/sub\u003eOX enzymes which modify the bioactive gibberellins rendering them incapable of binding to the receptor (Hedden \u003cspan class=\"CitationRef\"\u003e2020\u003c/span\u003e), were severely downregulated only in the taproot. This suggests that RL mainly reduces gibberellin level in radish leaves but can increase it in the taproot.\u003c/p\u003e\n \u003cp\u003eIn the regulation of plant body architecture, including photomorphogenesis (Yang and Li \u003cspan class=\"CitationRef\"\u003e2017\u003c/span\u003e) and root secondary growth (Fischer et al. \u003cspan class=\"CitationRef\"\u003e2019\u003c/span\u003e), cytokinins mainly act as antagonists of auxin and gibberellins. The stimulating role of cytokinins in the control of cambium cell division and storage root growth was previously demonstrated in radish (Jang et al. \u003cspan class=\"CitationRef\"\u003e2015\u003c/span\u003e). In this work, we have identified numerous DEGs that are probably involved in cytokinin biosynthesis, degradation and response. Radish \u003cem\u003eLONELY GUY 1 (LOG1), LOG2, LOG3, LOG5\u003c/em\u003e and \u003cem\u003eLOG7\u003c/em\u003e genes, whose products catalyze the synthesis of bioactive cytokinin (Kuroha et al. \u003cspan class=\"CitationRef\"\u003e2009\u003c/span\u003e), were among the most strongly downregulated under RL. The same was true for cytokinin oxidase/dehydrogenase genes \u003cem\u003eCKX1, 2, 3, 5\u003c/em\u003e and \u003cem\u003e7\u003c/em\u003e, whose products trigger irreversible degradation of cytokinins (Kowalska et al. \u003cspan class=\"CitationRef\"\u003e2010\u003c/span\u003e). At the same time, we revealed upregulation of seven radish genes encoding A-type Arabidopsis response regulators (ARRs), primary cytokinin-responsive genes encoding repressors of signaling (Kieber and Schaller \u003cspan class=\"CitationRef\"\u003e2014\u003c/span\u003e), and most of them had common expression dynamics in roots and leaves. Among them is the radish homolog of \u003cem\u003eARR4\u003c/em\u003e, major integrator of RL/FRL signaling and cytokinin response, whose protein directly interacts with PHYB increasing its activity (Mira-Rodado et al. \u003cspan class=\"CitationRef\"\u003e2007\u003c/span\u003e). At the same time, since the upregulation of A-type \u003cem\u003eARR\u003c/em\u003e genes is usually used as a marker of increased cytokinin level and/or response, the effect of RL on cytokinin homeostasis in radish plants has been ambiguous.\u003c/p\u003e\n \u003cp\u003eEthylene, a gaseous phytohormone, plays an important role in various aspects of plant development including photomorphogenesis (Ahammed et al. \u003cspan class=\"CitationRef\"\u003e2020\u003c/span\u003e) and cambium stem cell activity (Yu et al. \u003cspan class=\"CitationRef\"\u003e2023\u003c/span\u003e). Ethylene biosynthesis and signaling are regulated by multiple stimuli, including RL and FRL: in particular, genes encoding the ethylene biosynthesis enzymes ACC synthases (ACS) are positively regulated by PIFs and HFR1 (Khanna et al. \u003cspan class=\"CitationRef\"\u003e2007\u003c/span\u003e; Shi et al. \u003cspan class=\"CitationRef\"\u003e2013\u003c/span\u003e). In addition, RL-activated PHYB can directly bind to the primary ethylene-responsive TFs ETYLENE-INSENSITIVE 3 (EIN3) triggering its ubiquitin-dependent proteasome degradation (Shi et al. \u003cspan class=\"CitationRef\"\u003e2016\u003c/span\u003e). Among the ethylene-related DEGs in radish under RL, there were numerous \u003cem\u003eACS\u003c/em\u003e genes. Most of them were strongly downregulated in radish leaves and taproots under RL, indicating a negative effect of RL irradiance on ethylene levels, with the exception of \u003cem\u003eACS4\u003c/em\u003e and \u003cem\u003eACS11\u003c/em\u003e, which were upregulated in radish taproot at 28 DAG. At the same time, several genes encoding ACC oxidases (ACO) which act after ACS in ethylene biosynthesis were upregulated in both leaves and taproots under RL. The list of radish ethylene-responsive DEGs includes numerous genes encoding TFs of ETHYLENE-RESPONSE FACTOR (ERF) family. There were up- and downregulated radish \u003cem\u003eERFs\u003c/em\u003e, but the exact functions of most of their \u003cem\u003eArabidopsis\u003c/em\u003e homologs are unknown. Among the most strongly upregulated in the taproots of RL-grown plants was multifunctional \u003cem\u003eERF115\u003c/em\u003e, which is known to be a major regulator of cell divisions in the quiescent centre of the root apical meristem (Heyman et al. \u003cspan class=\"CitationRef\"\u003e2013\u003c/span\u003e), a cytokinin-activated repressor of adventitious root development (Lakehal et al. \u003cspan class=\"CitationRef\"\u003e2020\u003c/span\u003e), and a stimulator of plant regeneration (Heyman et al. \u003cspan class=\"CitationRef\"\u003e2016\u003c/span\u003e). Based on these data, we can propose the function of ethylene and \u003cem\u003eERF115\u003c/em\u003e as activators of the radish storage root growth under RL.\u003c/p\u003e\n \u003cp\u003e\u003cstrong\u003eGenes encoding transcription factors involved in the root development\u003c/strong\u003e\u003c/p\u003e\n \u003cp\u003eA significant proportion of genes which were strongly up- or downregulated in the taproots of RL-grown radish plants encode TFs of different families. Among them there were radish genes, whose homologs play important roles in \u003cem\u003eArabidopsis\u003c/em\u003e root development (Fig. \u003cspan class=\"InternalRef\"\u003e7\u003c/span\u003e).\u003c/p\u003e\n \u003cp\u003eThese list of root-specific upregulated DEGs included all four radish homologs of \u003cem\u003eWUSCHEL RELATED HOMEOBOX11 (WOX11)\u003c/em\u003e and both homologs of \u003cem\u003eWOX5\u003c/em\u003e, whose products, homeodomain TFs, work together in root meristem initiation (Aliaga Fandino et al. \u003cspan class=\"CitationRef\"\u003e2019\u003c/span\u003e; Hu and Xu \u003cspan class=\"CitationRef\"\u003e2016\u003c/span\u003e) and also adventitious root formation and callus induction in \u003cem\u003eArabidopsis\u003c/em\u003e (Baesso et al. \u003cspan class=\"CitationRef\"\u003e2018\u003c/span\u003e) and radish (Aliaga Fandino et al. \u003cspan class=\"CitationRef\"\u003e2019\u003c/span\u003e). Both \u003cem\u003eWOX5\u003c/em\u003e and \u003cem\u003eWOX11\u003c/em\u003e are targets of auxin action, furthermore, WOX11 directly activates \u003cem\u003eWOX5\u003c/em\u003e transcription in promoting root regeneration (Aliaga Fandino et al. \u003cspan class=\"CitationRef\"\u003e2019\u003c/span\u003e; Hu and Xu \u003cspan class=\"CitationRef\"\u003e2016\u003c/span\u003e). Among genes that were specifically upregulated in radish roots under RL also were \u003cem\u003ePLETHORA 1\u003c/em\u003e (\u003cem\u003ePLT1\u003c/em\u003e) and \u003cem\u003ePLT2\u003c/em\u003e, and two homologs of the \u003cem\u003eSCARECROW\u003c/em\u003e (\u003cem\u003eSCR\u003c/em\u003e). In \u003cem\u003eArabidopsis\u003c/em\u003e, PLT and SCR are essential for auxin-mediated root stem cell niche specification (Gao et al. \u003cspan class=\"CitationRef\"\u003e2004\u003c/span\u003eh\u0026ouml;nen et al. 2014), \u003cem\u003eWOX5\u003c/em\u003e transcription (Shimotohno et al. \u003cspan class=\"CitationRef\"\u003e2018\u003c/span\u003e), and interaction of WOX5 TF with its target genes (Burkart et al. \u003cspan class=\"CitationRef\"\u003e2022\u003c/span\u003e; Shimotohno et al. \u003cspan class=\"CitationRef\"\u003e2018\u003c/span\u003e). Thus, upregulation of all these genes, working in the same pathway under inductive RL, can be involved in the storage root development. Another TF-encoding radish gene upregulated under RL was \u003cem\u003eLATERAL ORGAN BOUNDARIES DOMAIN 3 (LBD3)\u003c/em\u003e, an important cytokinin-responsive regulator of cambium activity and secondary growth of root (Ye et al. \u003cspan class=\"CitationRef\"\u003e2021\u003c/span\u003e). Finally, among the upregulated under RL there were two radish homologs of the \u003cem\u003eUPBEAT 1 (UPB1)\u003c/em\u003e gene, which encodes a bHLH TF involved in the regulation of D-class cyclin genes expression in the \u003cem\u003eArabidopsis\u003c/em\u003e root meristem (Li et al. \u003cspan class=\"CitationRef\"\u003e2019\u003c/span\u003e). The radish homolog of \u003cem\u003eMYB61\u003c/em\u003e, which was, in turn, downregulated in roots under RL, is a positive regulator of xylem formation, lateral root development and plant resource allocation (Romano et al. \u003cspan class=\"CitationRef\"\u003e2012\u003c/span\u003e).\u003c/p\u003e\n \u003cp\u003eIn addition, among root-specific TF-encoding DEGs were those known to be involved in photomorphogenesis and light response (\u003cem\u003eLBD25, NAC2, GRF5\u003c/em\u003e) (Mangeon et al. \u003cspan class=\"CitationRef\"\u003e2011\u003c/span\u003e; Morishita et al. \u003cspan class=\"CitationRef\"\u003e2009\u003c/span\u003e; Vercruyssen et al. \u003cspan class=\"CitationRef\"\u003e2015\u003c/span\u003e), shoot apical meristem maintenance (\u003cem\u003eATH1\u003c/em\u003e) (G\u0026oacute;mez-Mena and Sablowski \u003cspan class=\"CitationRef\"\u003e2008\u003c/span\u003e), specification of epiderm and its derivatives (\u003cem\u003eATML1, PDF1, GTL\u003c/em\u003e) (Abe et al. \u003cspan class=\"CitationRef\"\u003e2001\u003c/span\u003e; Shibata et al. \u003cspan class=\"CitationRef\"\u003e2018\u003c/span\u003e), stress response (\u003cem\u003eMYB14, MYB34\u003c/em\u003e) (Chen et al. \u003cspan class=\"CitationRef\"\u003e2013\u003c/span\u003e; Frerigmann and Gigolashvili \u003cspan class=\"CitationRef\"\u003e2014\u003c/span\u003e) and leaf and floral organ development (\u003cem\u003eTCP5, WOX1, YABBY5, MYB108, GRF5, LBD10\u003c/em\u003e) (Nakata et al. \u003cspan class=\"CitationRef\"\u003e2012\u003c/span\u003e; Shen et al. \u003cspan class=\"CitationRef\"\u003e2019\u003c/span\u003e; Stahle et al. \u003cspan class=\"CitationRef\"\u003e2009\u003c/span\u003e; Yu et al. \u003cspan class=\"CitationRef\"\u003e2021\u003c/span\u003e; Kim et al. \u003cspan class=\"CitationRef\"\u003e2015\u003c/span\u003e). We can propose that some of the TF-encoding DEGs may also be involved in root development or have dual functions. In particular, the \u003cem\u003eArabidopsis\u003c/em\u003e homolog of \u003cem\u003ePETAL LOSS\u003c/em\u003e (\u003cem\u003ePTL\u003c/em\u003e), which was upregulated in radish taproot and downregulated in the leaves under RL, is involved in the control of floral organs development (Kaplan-Levy et al. \u003cspan class=\"CitationRef\"\u003e2014\u003c/span\u003e) but also functions as an important regulator of cambium activity (Zhang et al. \u003cspan class=\"CitationRef\"\u003e2019\u003c/span\u003e).\u003c/p\u003e\n \u003cp\u003e\u003cstrong\u003eGenes involved in the metabolism of sugars\u003c/strong\u003e\u003c/p\u003e\n \u003cp\u003eThe distribution of sugars plays a key role in the choice of plant development strategy. Sucrose, the end product of photosynthesis and key carbon source for plant growth, is produced in source leaves and translocated to various sinks through the sieve element/ companion cell complex of the phloem (van Bel \u003cspan class=\"CitationRef\"\u003e2021\u003c/span\u003e). Metabolism of sucrose yields hexoses which are necessary to generate energy and produce cellulose and starch. Moreover, hexoses and sucrose itself provides sugar signaling directly regulating plant development (Yoon et al., \u003cspan class=\"CitationRef\"\u003e2021\u003c/span\u003e) including cambium activity (Narutaki et al. \u003cspan class=\"CitationRef\"\u003e2023\u003c/span\u003e). In the developing storage root, sucrose is usually deposited in the form of starch forming a reservoir of easy-to-remobilize energy (Hoang et al., \u003cspan class=\"CitationRef\"\u003e2020b\u003c/span\u003e).\u003c/p\u003e\n \u003cp\u003eThe first step of sucrose biosynthesis in the leaf mesophyll, which is catalyzed by sucrose phosphate synthase, includes the formation of sucrose-6-phosphate from fructose-6-phosphate and UDP-glucose. Subsequently, sucrose-6-phosphate is hydrolyzed by sucrose-phosphate phosphatase, releasing sucrose (Huber, Huber, \u003cspan class=\"CitationRef\"\u003e1996\u003c/span\u003e). Another enzyme, sucrose synthase, catalyzes reversible reaction of sucrose biosynthesis from UDP-glucose and fructose (Bieniawska et al., \u003cspan class=\"CitationRef\"\u003e2007\u003c/span\u003e). After its synthesis, sucrose can be loaded into the phloem, either symplastically or apoplastically, for delivery to sinks, e.g. to storage root. The active transport of sucrose from apoplast is mediated by the several families of sucrose transporters, in particular SWEET (Sugars Will Eventually be Exported Transporters) family of bidirectional sugar uniporters (Chen et al., \u003cspan class=\"CitationRef\"\u003e2012\u003c/span\u003e), and sucrose/H+-symporters SUT/SUC (K\u0026uuml;hn, Grof, \u003cspan class=\"CitationRef\"\u003e2010\u003c/span\u003e). In the phloem companion cells, sucrose could convert into raffinose-type trisaccharides, which increases the intensity of transport. Two steps of raffinose biosynthesis, the formation of galactinol from UDP-galactose and the addition of galactose moieties donated by galactinol to sucrose, are catalyzed by galactinol synthase and raffinose synthase (Taji et al., \u003cspan class=\"CitationRef\"\u003e2002\u003c/span\u003e). In its turn, UDP-galactose can be formed from UDP-glucose by means of UDP-glucose-4-epimerase which catalyzes the interconversion of UDP-glucose and UDP-galactose. UDP-glucose can also convert to UDP-glucuronic acid, which is used for the synthesis of major plant cell wall polysaccharides such as xylan. The NAD+-dependent oxidation of UDP-glucose to UDP-glucuronic acid is catalyzed by UDP-glucose-6-dehydrogenase (Reboul et al., \u003cspan class=\"CitationRef\"\u003e2011\u003c/span\u003e). Upon translocation through the phloem to sinks, sucrose is degraded by either sucrose synthase (into UDP-glucose and fructose) or invertase (into glucose and fructose). The invertase enzymes are classified into three groups: cell wall invertases, vacuolar and cytoplasmic invertases (Ruan, \u003cspan class=\"CitationRef\"\u003e2014\u003c/span\u003e). The vacuolar invertases work together with Early Response to Dehydration 6-Like (ERD6-like, ESL) hexose transporters which unload glucose from vacuole (Slawinski et al., \u003cspan class=\"CitationRef\"\u003e2021\u003c/span\u003e). The activities of invertases are under control of specific proteinaceous inhibitors which are also responsible for regulating activities of pectin methylesterases - enzymes necessary to cell wall elasticity and cell adhesion. This large protein family is named INVIs/PMEIs (Plant Invertase/ Pectin Methylesterase Inhibitor Superfamily (Coculo, Lionetti, \u003cspan class=\"CitationRef\"\u003e2022\u003c/span\u003e). In the root, unloading of sucrose from phloem to parenchyma cells is provided symplastically via plasmodesmata or by active transport via the same transporter proteins (SWEET, SUC/SUT) (R\u0026uuml;scher et al., \u003cspan class=\"CitationRef\"\u003e2024\u003c/span\u003e). Here, sucrose can be stored temporarily in vacuoles, or mainly catabolized by sucrose synthase into fructose and UDP-glucose, which enter starch synthesis. At the same time, invertases do not play a role in the catabolism of sucrose in the root (Li, Zhang, \u003cspan class=\"CitationRef\"\u003e2003\u003c/span\u003e). The substrate for starch biosynthesis is provided by ADP-glucose pyrophosphorylase which produces ADP-glucose from glucose-1-phosphate and ATP. Then starch synthase (glycosyltransferase family 5) catalyzes the transfer of the glucosyl moiety of ADP-glucose to the non-reducing end of an existing glucosyl chain. The granule-bound starch synthase is responsible for amylose synthesis, while amylopectin is synthesized by starch-branching and debranching enzymes, members of alpha-amylase superfamily (Pfister, Zeeman, \u003cspan class=\"CitationRef\"\u003e2016\u003c/span\u003e).\u003c/p\u003e\n \u003cp\u003eIn the taproot and leaves of RL-grown radish plants, we observed a change in the expression of a large number of genes involved in the regulation of metabolism and transport of sugars (Fig. \u003cspan class=\"InternalRef\"\u003e8\u003c/span\u003e). Among DEGs there were four radish sucrose synthase genes homologous to \u003cem\u003eArabidopsis SUS1\u003c/em\u003e and \u003cem\u003eSUS3\u003c/em\u003e, and one gene encoding sucrose phosphate synthase. All these genes were upregulated in the leaves of RL-grown plants and downregulated in the taproot, which suggests an increase in the level of sucrose biosynthesis under the influence of RL.\u003c/p\u003e\n \u003cp\u003eThere were also numerous DEGs encoding enzymes of UDP-glucose metabolism, such as UDP-glucose 4-epimerases and UDP-glucose 6-dehydrogenases. Radish genes for these enzymes were downregulated under RL in both taproot and leaves. At the same time, numerous radish genes encoding UDP-glycosyltransferases, enzymes responsible for synthesis of galactolipids for photosynthetic membranes (Lin et al., \u003cspan class=\"CitationRef\"\u003e2016\u003c/span\u003e), were upregulated in the leaves and predominantly downregulated in the taproot of RL-grown plants reflecting the necessity of photosynthetic membranes composition in the leaves grown under high level of photosynthetically active RL. The same trend was observed for radish genes encoding nucleotide-sugar transporters which are involved in supplying UDP-glucose into the ER and Golgi lumen (Reyes et al., \u003cspan class=\"CitationRef\"\u003e2010\u003c/span\u003e).\u003c/p\u003e\n \u003cp\u003eAmong DEGs encoding sucrose transporters, three radish homologs of \u003cem\u003eSUC1\u003c/em\u003e and one homolog of \u003cem\u003eSUC2\u003c/em\u003e were downregulated in the taproot. At the same time, numerous radish \u003cem\u003eSWEET\u003c/em\u003e genes were upregulated or downregulated in the taproot and leaves of RL-grown plants. Among upregulated in the taproot and leaves there was homolog of \u003cem\u003eSWEET12\u003c/em\u003e, which was shown to be involved in vascular development (Le et al., 2015), and thus can participate in the formation of xylem-type radish storage root. However, the other two \u003cem\u003eSWEET12\u003c/em\u003e genes were specifically downregulated in the taproot of RL-grown plants. Two homologs of \u003cem\u003eSWEET14\u003c/em\u003e, which mediate not only sugar transport but also cellular gibberellin uptake (Kanno et al., \u003cspan class=\"CitationRef\"\u003e2016\u003c/span\u003e), were severely upregulated in the radish taproot under RL, probably reflecting high levels of sucrose and gibberellin transport in the growing storage root.\u003c/p\u003e\n \u003cp\u003eIn the RL-grown radish plants, gene of cytoplasmic invertase homologous to \u003cem\u003eArabidopsis CINV1\u003c/em\u003e was one of major upregulated genes in the leaves, while other invertase genes expressed similarly under RL and FRL. At the same time, among DEGs there were numerous \u003cem\u003eESL\u003c/em\u003e genes, some of which were among major upregulated and downregulated in the leaves and taproot of RL-grown radish plants. Similarly, among very numerous INVIs/PMEIs-encoding DEGs there were both upregulated and downregulated under RL.\u003c/p\u003e\n \u003cp\u003eAmong DEGs, involved in starch composition and mobilization, there were radish homologs of alpha-amilase gene \u003cem\u003eAMY1\u003c/em\u003e and four beta-amylase genes: homolog of \u003cem\u003eArabidopsis BAM5\u003c/em\u003e and three genes encoding inactive beta-amylases. All these genes were specifically downregulated in the taproot of RL-grown radish plants with the exception of \u003cem\u003eBAM5\u003c/em\u003e, which was upregulated. The functions of \u003cem\u003eArabidopsis BAM5\u003c/em\u003e may be somehow related to the utilization or storage of sucrose because its expression is inducible by sugar (Mita et al., \u003cspan class=\"CitationRef\"\u003e1995\u003c/span\u003e). Thus, we can assume that in radish \u003cem\u003eBAM5\u003c/em\u003e can be involved in starch deposition during the formation of the storage root.\u003c/p\u003e\n \u003cp\u003eMoreover, there were DEGs involved in the sugar metabolism and cell wall integrity. Among them there was homolog of \u003cem\u003eArabidopsis IRREGULAR XYLEM 7\u003c/em\u003e (\u003cem\u003eIRX7\u003c/em\u003e), which encodes glycosyltransferase family protein necessary for secondary cell wall formation, cambium functioning and xylem differentiation (Persson et al., \u003cspan class=\"CitationRef\"\u003e2007\u003c/span\u003e). In radish, \u003cem\u003eIRX7\u003c/em\u003e was strongly upregulated in the taproots of RL-grown plants and probably can play a role in the growth of xylem-type storage root.\u003c/p\u003e\n\u003c/div\u003e"},{"header":"4. Discussion","content":"\u003cp\u003eThe formation of storage root is an excellent evolutionary adaptation which was designed to create a reservoir of easily mobilized energy in the form of carbohydrates. Further, this reserve can be used for resource-intensive developmental processes such as growth after unfavourable conditions, flowering and fruiting. In this context, the formation of storage roots should have a strictly defined developmental seasonality and can be regulated by both developmental signals and environmental cues including photoperiod and light spectrum. Although the role of light conditions in the initiation of another type of underground storage organ - potato tuber - has been well studied, there is not much data on the molecular mechanisms underlying storage root development, and nothing is known about the light-dependent regulation of this process.\u003c/p\u003e\u003cp\u003eRadish is a perspective model object for study mechanisms of storage root development due to its short life cycle (it is the only annual plant with a storage root), diploidy, small genome, and close relationship with \u003cem\u003eArabidopsis thaliana\u003c/em\u003e. Numerous transcriptomic studies on radish have identified candidate genes that play a role in the transition to flowering (Nie et al. \u003cspan citationid=\"CR96\" class=\"CitationRef\"\u003e2016\u003c/span\u003e; Li et al. \u003cspan citationid=\"CR73\" class=\"CitationRef\"\u003e2023\u003c/span\u003e) and various aspects of storage root development, including biosynthesis of anthocyanins (Gao et al. \u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e2019\u003c/span\u003e), glucosinolates (Wang et al. \u003cspan citationid=\"CR135\" class=\"CitationRef\"\u003e2013\u003c/span\u003e), and lignin (Feng et al. \u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e2017\u003c/span\u003e). The analysis of radish root transcriptome allowed to identify TF-encoding genes which are presumably involved in the storage root formation. Among them were genes of the \u003cem\u003eWOX\u003c/em\u003e and \u003cem\u003eERF\u003c/em\u003e families as well as \u003cem\u003eLHY\u003c/em\u003e gene (Hoang et al. \u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e2020a\u003c/span\u003e). The correlation between expression level of sucrose synthase gene \u003cem\u003eSUS1\u003c/em\u003e and radish taproot thickening suggested an important role of sucrose signaling in the development of storage root (Mitsui et al. \u003cspan citationid=\"CR88\" class=\"CitationRef\"\u003e2015\u003c/span\u003e). The dynamics of occurrence of different small RNAs during radish taproot thickening allowed to assume the role their presumable targets, including TF-encoding genes, in the development of the storage root (Yu et al., \u003cspan citationid=\"CR143\" class=\"CitationRef\"\u003e2015\u003c/span\u003e).\u003c/p\u003e\u003cp\u003eDue to the high conservatism underlying the main programs of plant development (Kuznetsova et al. \u003cspan citationid=\"CR65\" class=\"CitationRef\"\u003e2023\u003c/span\u003e), a number of data obtained on radish can be extrapolated to other root crops. Moreover, based on this logic, the similarity of light-mediated mechanisms in the development of storage roots and potato tuber is discussed (Natarajan et al. \u003cspan citationid=\"CR93\" class=\"CitationRef\"\u003e2019\u003c/span\u003e; Hoang et al. \u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e2020b\u003c/span\u003e). These mechanisms include CONSTANS-LIKE TFs, as well as mobile signals from the phloem, e.g. PEPB proteins, and their targets.\u003c/p\u003e\u003cp\u003eIn our experiment, flowering and storage root development behaved as oppositely regulated programs in the radish plants grown under RL and FRL. The antagonism of these developmental strategies can be explained by the fact that plant can usually either flower or form a storage root at the same time because the storage root serves as a major sink of photoassimilates during its formation (Hoang et al. \u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e2020b\u003c/span\u003e). In this context, the FRL-induced shade avoidance response with switch to bolting and flowering could reorganize photoassimilate flux to this new sink instead of storage root growth, while RL in radish retained flowering stimulating taproot thickening. The choice of one of these development strategies was accompanied by anatomical changes in the radish root, including differentiation of sclerenchyma in FRL-grown plants, and proliferation of cambium and xylem parenchyma under RL. In the same developmental stages, a contrasting pattern of water-soluble sugars and starch redistribution was revealed in RL-grown and FRL-grown radish plants, - in particular, a significant increase of their content in the taproots under RL.\u003c/p\u003e\u003cp\u003eFinally, growing of radish under RL or FRL was accompanied by changes in the expression of a large number of genes in the leaves and especially in the taproot. The large part of DEGs in our transcriptome analysis included genes whose products are involved in light perception and signaling. In particular, among them were several genes encoding PEPB proteins which can be consider as radish florigens or \u0026ldquo;root tuberigens\u0026rdquo;. The only PEPB-encoding gene which was specifically upregulated in the radish taproot under RL, one of two \u003cem\u003eBFT1-like\u003c/em\u003e genes, could be a light-dependent stimulator for the storage root development. There were also numerous DEGs involved in the homeostasis of phytohormones, including cytokinin which is necessary for cambium proliferation (Ye et al. \u003cspan citationid=\"CR139\" class=\"CitationRef\"\u003e2021\u003c/span\u003e) and radish taproot thickening (Jang et al. \u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e2015\u003c/span\u003e). Finally, among root-specific DEGs there were TF-encoding genes whose homologs in \u003cem\u003eArabidopsis\u003c/em\u003e are involved in the control of cambium activity (Zhang et al. \u003cspan citationid=\"CR148\" class=\"CitationRef\"\u003e2019\u003c/span\u003e). Thus, in this work, we revealed a probable molecular basis that may underlie the opposite developmental programs - flowering and formation of a storage root - in response to RL and FRL.\u003c/p\u003e"},{"header":"Abbreviations","content":"\u003cp\u003eDAG: Day(s) after germination; DEG: differentially expressed gene; FRL, FR\u003csub\u003e730\u003c/sub\u003e: Far-red light, 730 nm; LED: Light-emitting diode; PEBP: Phosphatidyl Ethanolamine-Binding Protein; PPF: Photosynthetic photon flux; PPFD: Photosynthetic photon flux density; RL, R\u003csub\u003e660\u003c/sub\u003e: Red light, 660 nm; TF: Transcription factor.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAuthor Contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eConceptualization: ID, IT and LL; Methodology: XK, IT, MG, VT, AF; Software: XK, MG; Validation XK, MG; Formal analysis: XK, MG; Investigation: XK, DG; Resources: XK; Data curation: XK; Writing - original draft preparation: ID; Writing - review and editing: ID, IT, ZK and XK; Visualization: MG, AF, DG and ID; Supervision: ID; Project administration: LL; Funding acquisition: LL.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAcknowledgments\u003c/strong\u003e We thank CeGAT company (T\u0026uuml;bingen, Germany) for cDNA sequencing.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u0026nbsp;\u003c/strong\u003eThis work was supported by Saint Petersburg State University research project 124032000041-1.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConflicts of Interest\u003c/strong\u003e The authors declare that the research was conducted in the absence of any commercial relationships, and there was no potential conflict of interest.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eAbe M, Takahashi T, Komeda Y (2001) Identification of a cis-regulatory element for L1 layer-specific gene expression, which is targeted by an L1-specific homeodomain protein. 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Nat Commun 11:5118. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1038/s41467-020-18782-1\u003c/span\u003e\u003cspan address=\"10.1038/s41467-020-18782-1\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"plant-growth-regulation","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"grow","sideBox":"Learn more about [Plant Growth Regulation](https://www.springer.com/journal/10725)","snPcode":"10725","submissionUrl":"https://submission.nature.com/new-submission/10725/3","title":"Plant Growth Regulation","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"radish, storage root, red light, far-red light, transcriptome analysis","lastPublishedDoi":"10.21203/rs.3.rs-7318257/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7318257/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eThe storage root is a specialized underground organ of biennial and perennial plants. In most root crops, the modification of roots for nutrient storage has a strictly defined seasonality and is regulated by environmental cues such as photoperiod and light quality. Here, we have shown that red light (660 nm, R\u003csub\u003e660\u003c/sub\u003e) and far-red light (730 nm, FR\u003csub\u003e730\u003c/sub\u003e) have opposite effects on storage root formation and flowering in radish (\u003cem\u003eRaphanus sativus\u003c/em\u003e L.). The R\u003csub\u003e660\u003c/sub\u003e caused taproot thickening and the formation of a storage root, attenuating the flowering, while FR\u003csub\u003e730\u003c/sub\u003e negatively affected the development of the storage root, stimulating flowering. Taproots of radish plants grown under R\u003csub\u003e660\u003c/sub\u003e demonstrated extensive proliferation in the cambium and xylem parenchyma cells, while in the taproots of plants grown on FR\u003csub\u003e730\u003c/sub\u003e xylem parenchyma was largely transformed into sclerenchyma. In the taproots of plants grown under R\u003csub\u003e660\u003c/sub\u003e, in contrast to FR\u003csub\u003e730\u003c/sub\u003e, an increase in the content of water-soluble sugars and starch was detected. Transcriptome analysis revealed that RL\u003csub\u003e660\u003c/sub\u003e caused downregulation of key 'flowering genes' such as \u003cem\u003eCONSTANS-LIKE, FT, SOC1\u003c/em\u003e, etc. in both leaves and roots of radish. At the same time, several key regulators of root development, such as \u003cem\u003eWOX11, WOX5, LBD3\u003c/em\u003e and \u003cem\u003eSCR\u003c/em\u003e, were specifically upregulated in the taproots of radish plants on R\u003csub\u003e660\u003c/sub\u003e. Moreover, numerous genes involved in sucrose metabolism and phytohormonal balance also demonstrated contrasting expression patterns on R\u003csub\u003e660\u003c/sub\u003e and FR\u003csub\u003e730\u003c/sub\u003e. Our results suggest a potential molecular basis for the red-light-dependent stimulation of storage root formation.\u003c/p\u003e","manuscriptTitle":"Red and far-red light contrastingly influence storage root development and gene expression profile in radish (Raphanus sativus L.)","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-08-14 15:44:10","doi":"10.21203/rs.3.rs-7318257/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-10-22T10:26:38+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-10-22T09:51:44+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-09-10T13:51:01+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"32602101103422945668396411994463643130","date":"2025-08-25T10:08:51+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"29119415557344126345445754881483205016","date":"2025-08-11T11:36:56+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-08-10T10:11:48+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-08-09T10:06:52+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-08-09T10:06:12+00:00","index":"","fulltext":""},{"type":"submitted","content":"Plant Growth Regulation","date":"2025-08-07T11:12:55+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"plant-growth-regulation","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"grow","sideBox":"Learn more about [Plant Growth Regulation](https://www.springer.com/journal/10725)","snPcode":"10725","submissionUrl":"https://submission.nature.com/new-submission/10725/3","title":"Plant Growth Regulation","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"0e22778f-1ab5-4255-a892-ed128b67c61d","owner":[],"postedDate":"August 14th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2025-12-17T03:53:44+00:00","versionOfRecord":[],"versionCreatedAt":"2025-08-14 15:44:10","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7318257","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7318257","identity":"rs-7318257","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}