Transcriptome analysis of radish sprouts hypocotyls reveals the regulatory role of hydrogen-rich water in anthocyanin biosynthesis under UV-A

Hydrogen-rich water enhances vegetable growth and fruit quality by regulating ascorbate biosynthesis

Under aerobic conditions, the growth and fruit quality of vegetable crops are significantly influenced by reactive oxygen species (ROS) metabolism. Hydrogen-rich water (HRW) has emerged as a promising tool for enhancing resistance to abiotic stresses and delaying postharvest ripening and senescence. However, the physiological response and adaptation mechanisms of vegetable crops to HRW remain rarely understood. This study explores the effects of low concentrations of HRW on the growth and physiological processes of lettuce, tomato, and cucumber. The results indicate that HRW enhances seedling vigor, boosts photosynthetic efficiency, and promotes biomass accumulation. Additionally, HRW-irrigated cucumber fruit showed a 15-20 % increase in vitamin C (ascorbic acid) content, a 10-15 % rise in soluble sucrose levels, and an increase in fruit weight and diameter by 25-35 % and 8-12 %, respectively. Transcriptomic analyses revealed variations in genes associated with carbon fixation in photosynthesis, glyoxylate and dicarboxylate metabolism, hormonal regulation, and phenylalanine metabolism. These findings illuminate the mechanisms behind improved antioxidant production and L-ascorbate biosynthesis. Notably, this marks the documented case of HRW irrigation enhancing natural antioxidants in fruits. Given the unique properties of hydrogen and the potential of HRW technology in horticultural industry, the findings of this study provide valuable insights into hydrogen's role in biological processes and its impact on vegetable crops production and fruit quality.

Evolution of phenylalanine ammonia-lyase protein family from algae to angiosperm

Phenylpropanes, the precursors of various phenolic compounds in plants, are widely distributed. Phenylalanine ammonia-lyase (PAL) is the main enzyme that catalyzes the early step of the phenylpropanoid pathway to generate trans-cinnamic acid, which is the common precursor for the lignin and flavonoid biosynthetic pathways. Therefore, in this study, we focused on PAL evolution. A total of 584 PAL-like protein sequences were obtained, and only two PAL-like genes were found in algae, primary. Three main groups are separated by their different evolutionary stages. Group I mainly cluster ancient plants, and groups II and III are formed by angiosperms, which separate monocots (group II) and eudicots (group III). According to the sequence alignment, five main differences in amino acids may correlate with this separation, which involve the change of amino acid phosphorylation. The prediction analysis of GO and KEGG annotation information of each PAL protein showed that the proteins were clustered in cytoplasm and correlated with phenylalanine ammonia-lyase activity. Our results suggested that the PAL enzyme family expanded alongside the development of vascular tissues and underwent duplication events that facilitated gene cluster expansion and phenotypic diversity. Analysis of a reassembled and publicly available gene database confirmed that only two PAL genes were present in algae, whereas land plants possess a significantly greater number of PAL-like genes. This expansion is closely of PAL genes in land plants is closely associated with gene duplication events occurring at various evolutionary stages after algae plants. Futhermore, investigation into miRNAs revealed limited specificity across the plant evolution spectrum, with their primary role being the regulation and modulation of gene function. Additionally, analysis of PAL proteins across the plant kingdom ultimately elucidates that the evolution of their functions is intricately linked to the widespread distribution of cis-acting elements. This evolutionary trajectory reflected the natural selection processes that plants had undergone over time to enhance their eadaptability to diverse environments. These findings provide a valuable reference for future research into the functional evolution of PAL genes and their role in .plant adaptation and phenotypic diversity.

Integrated metabolomics and transcriptomics analysis provides insights into biosynthesis and accumulation of flavonoids and glucosinolates in different radish varieties

Radish is an important vegetable worldwide, with wide medicinal functions and health benefits. The quality of radish, strongly affected by phytochemicals like flavonoids and glucosinolates, are quite different depending on the radish varieties. However, the comprehensive accumulation profiles of secondary metabolites and their molecular regulatory mechanisms in different radish cultivars remain unclear thus far. Herein, we comprehensively analyzed the secondary metabolite and gene expression profiles of the flesh and skin of four popular radish varieties with different flesh and/or skin colors, using UPLC-MS/MS-based metabolomics and transcriptomics approach combined with RT-qPCR. The results showed that altogether 352 secondary metabolites were identified in radish, of which flavonoids and phenolic acids accounted for 60.51% of the total. The flesh and skin of each variety exhibited distinct metabolic profiles, making them unique in coloration, flavor, taste, and nutritional quality. The differential metabolites were mostly enriched in flavonoid biosynthesis, flavone and flavonol biosynthesis, phenylpropanoid biosynthesis, and glucosinolate biosynthesis pathway. Further, 19 key genes regulating the differential accumulation of flavonoids among different radish varieties were identified, such as RsCHS, RsCCOAMT, RsF3H, RsFLS, RsCYP75B1, RsDFR, and RsANS that were significantly upregulated in red-colored radish tissue. Also, 10 key genes affecting the differential accumulation of glucosinolates among different varieties were identified, such as RsCYP83B1, RsSUR1, and RsST5a that were significantly increased in the skin of green radish. Moreover, systematical biosynthetic pathways of flavonoids and glucosinolates and co-expression networks between genes and metabolites were constructed based on integrative analysis between metabolomics and transcriptomics. Our findings provide a novel insight into the mechanisms of radish quality formation, thereby providing a molecular basis for breeding and cultivation of radish with excellent nutritional quality.

Jasmonate enhances cold acclimation in jojoba by promoting flavonol synthesis

Jojoba is an industrial oil crop planted in tropical arid areas, and its low-temperature sensitivity prevents its introduction into temperate areas. Studying the molecular mechanisms associated with cold acclimation in jojoba is advantageous for developing breeds with enhanced cold tolerance. In this study, metabolomic analysis revealed that various flavonols accumulate in jojoba during cold acclimation. Time-course transcriptomic analysis and weighted correlation network analysis (WGCNA) demonstrated that flavonol biosynthesis and jasmonates (JAs) signaling pathways played crucial roles in cold acclimation. Combining the biochemical and genetic analyses showed that ScMYB12 directly activated flavonol synthase gene (ScFLS). The interaction between ScMYB12 and transparent testa 8 (ScTT8) promoted the expression of ScFLS, but the negative regulator ScJAZ13 in the JA signaling pathway interacted with ScTT8 to attenuate the transcriptional activity of the ScTT8 and ScMYB12 complex, leading to the downregulation of ScFLS. Cold acclimation stimulated the production of JA in jojoba leaves, promoted the degradation of ScJAZ13, and activated the transcriptional activity of ScTT8 and ScMYB12 complexes, leading to the accumulation of flavonols. Our findings reveal the molecular mechanism of JA-mediated flavonol biosynthesis during cold acclimation in jojoba and highlight the JA pathway as a promising means for enhancing cold tolerance in breeding efforts.

Comparative transcriptome analysis reveals transcriptional regulation of anthocyanin biosynthesis in purple radish (Raphanus sativus L.)

Radish exhibits significant variation in color, particularly in sprouts, leaves, petals, fleshy roots, and other tissues, displaying a range of hues such as green, white, red, purple, and black. Although extensive research has been conducted on the color variation of radish, the underlying mechanism behind the variation in radish flower color remains unclear. To date, there is a lack of comprehensive research investigating the variation mechanism of radish sprouts, leaves, fleshy roots, and flower organs. This study aims to address this gap by utilizing transcriptome sequencing to acquire transcriptome data for white and purple radish flowers. Additionally, the published transcriptome data of sprouts, leaves, and fleshy roots were incorporated to conduct a systematic analysis of the regulatory mechanisms underlying anthocyanin biosynthesis in these four radish tissues. The comparative transcriptome analysis revealed differential expression of the anthocyanin biosynthetic pathway genes DFR, UGT78D2, TT12 and CPC in the four radish tissues. Additionally, the WGCNA results identified RsDFR.9c and RsUGT78D2.2c as hub genes responsible for regulating anthocyanin biosynthesis. By integrating the findings from the comparative transcriptome analysis, WGCNA, and anthocyanin biosynthetic pathway-related gene expression patterns, it is hypothesized that genes RsDFR.9c and RsUGT78D2.2c may serve as pivotal regulators of anthocyanins in the four radish tissues. Furthermore, the tissue-specific expression of the four copies of RsPAP1 is deemed crucial in governing anthocyanin synthesis and accumulation. Our results provide new insights into the molecular mechanism of anthocyanin biosynthesis and accumulation in different tissues of radish.

Effect of UV-A Irradiation on Bioactive Compounds Accumulation and Hypoglycemia-Related Enzymes Activities of Broccoli and Radish Sprouts

In the present study, different intensities of UV-A were applied to compare their effects on growth, bioactive compounds and hypoglycemia-related enzyme activities in broccoli and radish sprouts. The growth of sprouts was decreased after UV-A irradiation. A total of 12 W of UV-A irradiation resulted in the highest content of anthocyanin, chlorophyll, polyphenol and ascorbic acid in broccoli and radish sprouts. The highest soluble sugar content was recorded in sprouts under 8 W of UV-A irradiation, while no significant difference was obtained in soluble protein content among different UV-A intensities. Furthermore, 12 W of UV-A irradiation induced the highest glucosinolate accumulation, especially glucoraphanin and glucoraphenin in broccoli and radish sprouts, respectively; thus, it enhanced sulforaphane and sulforaphene formation. The α-amylase, α-glucosidase and pancrelipase inhibitory rates of two kinds of sprouts were enhanced significantly after UV-A irradiation, indicating UV-A-irradiation-treated broccoli and radish sprouts have new prospects as hypoglycemic functional foods.

Radish microgreens produced without substrate in a vertical multi-layered growing unit are rich in nutritional metabolites

Growing microgreens on trays without substrate in a vertical multilayered growing unit offers several advantages over traditional agriculture methods. This study investigated the yield performance and nutritional quality of five selections of radish microgreens grown in sprouting trays, without a substrate using only water, in an indoor multilayer cultivation system using artificial light. Various parameters were measured, including fresh weight, dry matter, chlorophyll, minerals, amino acids, phenolics, flavonoids, anthocyanins, vitamin C, glucosinolates, and antioxidant activity with four different in vitro assays. After ten days, the biomass had increased by 6-10 times, and the dry matter varied from 4.75-7.65%. The highest yield was obtained from 'Asia red', while the lowest was from 'Koregon red'. However, 'Koregon red' and 'Asia red' had the highest dry matter. 'Asia red' was found to have the highest levels of both Chls and vitamin C compared to the other cultivars, while 'Koregon red' exhibited the highest levels of total phenolics and flavonoids. Although variations in the levels of individual glucosinolates were observed, there were no significant differences in the total content of glucosinolates among the five cultivars. 'Asia purple' had the highest anthocyanin content, while 'Asia green 2' had the lowest. The K, Mg, and Na concentrations were significantly highest in 'Asia green 2', and the highest Ca was recorded in 'Asia purple'. Overall, 'Asia purple' and 'Koregon red' were the best cultivars in terms of nutritional quality among the tested radish microgreens. These cultivars exhibited high levels of dry weight, total phenolics, flavonoids, anthocyanins, essential and total amino acids, and antioxidant activities. Moreover, the implementation of this vertical cultivation method for microgreens, which relies solely on water and seeds known for their tall shoots during the sprouting could hold promise as a sustainable approach. This method can effectively be utilized for cultivar screening and fulfilling the nutritional and functional needs of the population while minimizing the environmental impacts associated with traditional agriculture practices.

Transcriptome Analysis Revealed the Potential Molecular Mechanism of Anthocyanidins' Improved Salt Tolerance in Maize Seedlings

Anthocyanin, a kind of flavonoid, plays a crucial role in plant resistance to abiotic stress. Salt stress is a kind of abiotic stress that can damage the growth and development of plant seedlings. However, limited research has been conducted on the involvement of maize seedlings in salt stress resistance via anthocyanin accumulation, and its potential molecular mechanism is still unclear. Therefore, it is of great significance for the normal growth and development of maize seedlings to explore the potential molecular mechanism of anthocyanin improving salt tolerance of seedlings via transcriptome analysis. In this study, we identified two W22 inbred lines (tolerant line pur-W22 and sensitive line bro-W22) exhibiting differential tolerance to salt stress during seedling growth and development but showing no significant differences in seedling characteristics under non-treatment conditions. In order to identify the specific genes involved in seedlings' salt stress response, we generated two recombinant inbred lines (RILpur-W22 and RILbro-W22) by crossing pur-W22 and bro-W22, and then performed transcriptome analysis on seedlings grown under both non-treatment and salt treatment conditions. A total of 6100 and 5710 differentially expressed genes (DEGs) were identified in RILpur-W22 and RILbro-W22 seedlings, respectively, under salt-stressed conditions when compared to the non-treated groups. Among these DEGs, 3160 were identified as being present in both RILpur-W22 and RILbro-W22, and these served as commonly stressed EDGs that were mainly enriched in the redox process, the monomer metabolic process, catalytic activity, the plasma membrane, and metabolic process regulation. Furthermore, we detected 1728 specific DEGs in the salt-tolerant RILpur-W22 line that were not detected in the salt-sensitive RILbro-W22 line, of which 887 were upregulated and 841 were downregulated. These DEGs are primarily associated with redox processes, biological regulation, and the plasma membrane. Notably, the anthocyanin synthesis related genes in RILpur-W22 were strongly induced under salt treatment conditions, which was consistented with the salt tolerance phenotype of its seedlings. In summary, the results of the transcriptome analysis not only expanded our understanding of the complex molecular mechanism of anthocyanin in improving the salt tolerance of maize seedlings, but also, the DEGs specifically expressed in the salt-tolerant line (RILpur-W22) provided candidate genes for further genetic analysis.

Important Roles of Key Genes and Transcription Factors in Flower Color Differences of Nicotianaalata

Nicotiana alata is an ornamental horticultural plant with a variety of flower colors and a long flowering period. The genes in four different colored N. alata (white, purple, red, and lemon green) were analyzed to explain the differences in flower color using transcriptomes. A total of 32 differential expression genes in the chlorophyll biosynthesis pathway and 41 in the anthocyanin biosynthesis pathway were identified. The enrichment analysis showed that the chlorophyll biosynthesis pathway and anthocyanin biosynthesis pathway play critical roles in the color differences of N. alata. The HEMA of the chlorophyll biosynthesis pathway was up-regulated in lemon green flowers. Compared with white flowers, in the red and purple flowers, F3H, F3'5'H and DFR were significantly up-regulated, while FLS was significantly down-regulated. Seventeen differential expression genes homologous to transcription factor coding genes were obtained, and the homologues of HY5, MYB12, AN1 and AN4 were also involved in flower color differences. The discovery of these candidate genes related to flower color differences is significant for further research on the flower colors formation mechanism and color improvements of N. alata.

The Applications of Molecular Hydrogen in Horticulture

Improvements in the growth, yield, and quality of horticultural crops require the development of simply integrated, cost-efficient, and eco-friendly solutions. Hydrogen gas (H2) has been observed to have fertilization effects on soils by influencing rhizospheric microorganisms, resulting in improvements in crop yield and quality. Ample studies have shown that H2 has positive effects on horticultural crops, such as promoting root development, enhancing tolerance against abiotic and biotic stress, prolonging storage life, and improving postharvest quality of fruits, vegetables and cut flowers. In this review, we aim to evaluate the feasibility of molecular hydrogen application in horticulture and the strategies for its application, including H2 delivery methods, treatment timing, and the concentration of H2 applied. The discussion will be accompanied by outlining the effects of H2 and the likely mechanisms of its efficacy. In short, the application of H2 may provide novel opportunities for simple and cost efficient improvements of horticultural production in terms of increased yield and product quality but with low carbon dioxide emissions.

Morphophysiological and Proteomic Responses on Plants of Irradiation with Electromagnetic Waves

Electromagnetic energy is the backbone of wireless communication systems, and its progressive use has resulted in impacts on a wide range of biological systems. The consequences of electromagnetic energy absorption on plants are insufficiently addressed. In the agricultural area, electromagnetic-wave irradiation has been used to develop crop varieties, manage insect pests, monitor fertilizer efficiency, and preserve agricultural produce. According to different frequencies and wavelengths, electromagnetic waves are typically divided into eight spectral bands, including audio waves, radio waves, microwaves, infrared, visible light, ultraviolet, X-rays, and gamma rays. In this review, among these electromagnetic waves, effects of millimeter waves, ultraviolet, and gamma rays on plants are outlined, and their response mechanisms in plants through proteomic approaches are summarized. Furthermore, remarkable advancements of irradiating plants with electromagnetic waves, especially ultraviolet, are addressed, which shed light on future research in the electromagnetic field.

Hydrogen-rich water promotes the formation of bulblets in Lilium davidii var. unicolor through regulating sucrose and starch metabolism

HRW increased the content of starch and sucrose via regulating a series of sucrose and starch synthesis genes, which induced the formation of bulblets and adventitious roots of Lilium davidii var. unicolor. Hydrogen gas (H₂), as a signaling molecule, has been reported to be involved in plant growth and development. Here, the effect of hydrogen-rich water (HRW) on the formation of bulblets and adventitious roots in the scale cuttings of Lilium davidii var. unicolor and its mechanisms at the molecular levels were investigated. The results revealed that compared with distilled water treatment (Con), the number of bulblets and adventitious roots were significantly promoted by different concentrations of HRW treatment. Treatment with 100% HRW obtained the most positive effects. RNA sequencing (RNA-seq) analysis found that compared with Con, a total of 1702 differentially expressed genes (DEGs, upregulated 552 DEGs, downregulated 1150 DEGs) were obtained under HRW treatment. The sucrose and starch metabolism, cysteine and methionine metabolism and phenylalanine metabolism were significantly enriched in the analysis of the Kyoto encyclopedia of genes and genomes (KEGG). In addition, the genes involved in carbohydrate metabolism were significantly upregulated or downregulated (upregulated 22 DEGs, downregulated 15 DEGs), indicating that starch and sucrose metabolism held a central position. The expressions of 12 DEGs were identified as coding for key enzymes in metabolism of carbohydrates was validated by qPCR during bulblet formation progress. RNA-seq analysis and expression profiles indicated that the unigene levels such as glgc, Susy, otsA and glgP, BMY and TPS were well correlated with sucrose and starch metabolism during HRW-induced bulblet formation. The change of key enzyme content in starch and sucrose metabolism pathway was explored during bulblet formation in Lilium under HRW treatment. Meanwhile, compared with Con, 100% HRW treatment increased the levels of sucrose and starch, and decreased the trehalose content, which were agreed with the expression pattern of DEGs related to the biosynthesis pathway of sucrose, starch and trehalose. Therefore, this study suggested that HRW could promote the accumulation of sucrose and starch contents in mother scales, and decreased the trehalose content, this might provide more energy for bulblet formation.

Transcriptome and metabolome analysis of stress tolerance to aluminium in Vitis quinquangularis

Transcriptional and metabolic regulation of aluminium tolerance of Chinese wild Vitis quinquangularis after Al treatment for 12 h: genes and pathways related to stress resistance are activated to cope with Al stress. The phytotoxicity of aluminium (Al) has become a major issue in inhibiting plant growth in acidic soils. Chinese wild Vitis species have excellent stress resistance. In this study, to explore the mechanism underlying Al tolerance in Chinese wild Vitis quinquangularis, we conducted a transcriptome analysis to understand the changes in gene expression and pathways in V. quinquangularis leaves after Al treatment for 12 h (Al_12 h). Compared with the control (CK) treatment, 2266 upregulated differentially expressed genes (DEGs) and 2943 downregulated DEGs were identified after Al treatment. We analysed the top 60 upregulated DEGs and found that these genes were related mostly to cell wall organization or biogenesis, transition metal ion binding, etc. Another analysis of all the upregulated DEGs showed that genes related to the ABC transport pathway, salicylic acid (SA), jasmonic acid (JA) and abscisic acid (ABA) hormone signalling pathway were expressed. Transcriptome and metabolome analysis revealed that genes and metabolites (phenylalanine, cinnamate and quercetin) related to the phenylalanine metabolic pathway were expressed. In summary, the results provide a new contribution to a better understanding of the metabolic changes that occur in grapes after Al stress as well as to research on improving the resistance of grape cultivars.

Molecular Hydrogen: Is This a Viable New Treatment for Plants in the UK?

Despite being trialed in other regions of the world, the use of molecular hydrogen (H₂) for enhanced plant growth and the postharvest storage of crops has yet to be widely accepted in the UK. The evidence that the treatment of plants and plant products with H₂ alleviates plant stress and slows crop senescence continues to grow. Many of these effects appear to be mediated by the alteration of the antioxidant capacity of plant cells. Some effects seem to involve heme oxygenase, whilst the reduction in the prosthetic group Fe³⁺ is also suggested as a mechanism. Although it is difficult to use as a gaseous treatment in a field setting, the use of hydrogen-rich water (HRW) has the potential to be of significant benefit to agricultural practices. However, the use of H₂ in agriculture will only be adopted if the benefits outweigh the production and application costs. HRW is safe and relatively easy to use. If H₂ gas or HRW are utilized in other countries for agricultural purposes, it is tempting to suggest that they could also be widely used in the UK in the future, particularly for postharvest storage, thus reducing food waste.

Hydrogen Nanobubble Water Delays Petal Senescence and Prolongs the Vase Life of Cut Carnation (Dianthus caryophyllus L.) Flowers

The short vase life of cut flowers limits their commercial value. To ameliorate this practical problem, this study investigated the effect of hydrogen nanobubble water (HNW) on delaying senescence of cut carnation flowers (Dianthuscaryophyllus L.). It was observed that HNW had properties of higher concentration and residence time for the dissolved hydrogen gas in comparison with conventional hydrogen-rich water (HRW). Meanwhile, application of 5% HNW significantly prolonged the vase life of cut carnation flowers compared with distilled water, other doses of HNW (including 1%, 10%, and 50%), and 10% HRW, which corresponded with the alleviation of fresh weight and water content loss, increased electrolyte leakage, oxidative damage, and cell death in petals. Further study showed that the increasing trend with respect to the activities of nucleases (including DNase and RNase) and protease during vase life period was inhibited by 5% HNW. The results indicated that HNW delayed petal senescence of cut carnation flowers through reducing reactive oxygen species accumulation and initial activities of senescence-associated enzymes. These findings may provide a basic framework for the application of HNW for postharvest preservation of agricultural products.

Development of Molecular Markers for Predicting Radish (Raphanus sativus) Flesh Color Based on Polymorphisms in the RsTT8 Gene

Red radish (Raphanus sativus L.) cultivars are a rich source of health-promoting anthocyanins and are considered a potential source of natural colorants used in the cosmetic industry. However, the development of red radish cultivars via conventional breeding is very difficult, given the unusual inheritance of the anthocyanin accumulation trait in radishes. Therefore, molecular markers linked with radish color are needed to facilitate radish breeding. Here, we characterized the RsTT8 gene isolated from four radish genotypes with different skin and flesh colors. Sequence analysis of RsTT8 revealed a large number of polymorphisms, including insertion/deletions (InDels), single nucleotide polymorphisms (SNPs), and simple sequence repeats (SSRs), between the red-fleshed and white-fleshed radish cultivars. To develop molecular markers on the basis of these polymorphisms for discriminating between radish genotypes with different colored flesh tissues, we designed four primer sets specific to the RsTT8 promoter, InDel, SSR, and WD40/acidic domain (WD/AD), and tested these primers on a diverse collection of radish lines. Except for the SSR-specific primer set, all primer sets successfully discriminated between red-fleshed and white-fleshed radish lines. Thus, we developed three molecular markers that can be efficiently used for breeding red-fleshed radish cultivars.

Genome-wide transcriptome analysis of microspore abortion initiation in radish (Raphanus sativus L.)

The use of male sterile lines is one of the ideal means in hybrid seed production. Despite the widespread application of Ogura cytoplasmic male sterile (CMS) lines, the molecular mechanisms remain largely unknown. In this study, histological analyses of floral buds from a CMS line 40MA and its corresponding maintainer line 40MB were conducted, which indicate that microspore abortion was initiated shortly after the tetrad stage. RNA sequencing was performed to analyze the transcriptomes of floral buds from the tetrad stage and the early microspore stages of these two lines. More than 39 million clean reads were generated for each library, and the portions mapped to the reference genome were all above 70.60%. To further analyze the differentially expressed genes (DEGs), the samples were grouped into four pairs, of which the pair of 40MA and 40MB at the early microspore stage showed the most DEGs (5100 members). According to the abnormal appearance of the tapetum cells in 40MA, a series of tapetum development related genes were screened and analyzed. In addition, a total of 623 genes with differential expressions in the tetrad stage, but not in the early microspore stage between the two lines were filtered as the microspore abortion initiation related candidates. Twelve genes were selected to validate the sequencing result by quantitative RT-PCR. In this study, we identified a number of candidate genes involved in the initiation of microspore degeneration, which may provide a new perspective to unravel the molecular mechanism of Ogura CMS.

Hydrogen Commonly Applicable from Medicine to Agriculture: From Molecular Mechanisms to the Field

The emerging field of hydrogen biology has to date mainly been applied in medicine. However, hydrogen biology can also enable positive outcomes in agriculture. Agriculture faces significant challenges resulting from a growing population, climate change, natural disasters, environmental pollution, and food safety issues. In fact, hydrogen agriculture is a practical application of hydrogen biology, which may assist in addressing many of these challenges. It has been demonstrated that hydrogen gas (H₂) may enhance plant tolerance towards abiotic and biotic stresses, regulate plant growth and development, increase nutritional values, prolong the shelf life, and decrease the nitrite accumulation during the storage of vegetables, as well as increase the resilience of livestock to pathogens. Our field trials show that H₂ may have a promising potential to increase yield and improve the quality of agricultural products. This review aims to elucidate mechanisms for a novel agricultural application of H₂ in China. Future development of hydrogen agriculture is proposed as well. Obviously, hydrogen agriculture belongs to a low carbon economy, and has great potential to provide "safe, tasty, healthy, and high-yield" agricultural products so that it may improve the sustainability of agriculture.

Single-Molecule Long-Read Sequencing of Purslane (Portulaca oleracea) and Differential Gene Expression Related with Biosynthesis of Unsaturated Fatty Acids

This study aimed to obtain the full-length transcriptome of purslane (Portulaca oleracea); assorted plant samples were used for single-molecule real-time (SMRT) sequencing. Based on SMRT, functional annotation of transcripts, transcript factors (TFs) analysis, simple sequence repeat analysis and long non-coding RNAs (LncRNAs) prediction were accomplished. Total 15.33-GB reads were produced; with 9,350,222 subreads and the average length of subreads, 1640 bp was counted. With 99.99% accuracy, after clustering, 132,536 transcripts and 78,559 genes were detected. All unique SMART transcripts were annotated in seven functional databases. 4180 TFs (including transcript regulators) and 7289 LncRNAs were predicted. The results of RNA-seq were confirmed with qRT–PCR analysis. Illumina sequencing of leaves and roots of two purslane genotypes was carried out. Amounts of differential expression genes and related KEGG pathways were found. The expression profiles of related genes in the biosynthesis of unsaturated fatty acids pathway in leaves and roots of two genotypes of purslane were analyzed. Differential expression of genes in this pathway built the foundation of ω-3 fatty acid accumulation in different organs and genotypes of purslane. The aforementioned results provide sequence information and may be a valuable resource for whole-genome sequencing of purslane in the future.

Enhanced antioxidant capacity and upregulated transporter genes contribute to the UV-B-induced increase in blinin in Conyza blinii

Conyza blinii (C. blinii) is a traditional Chinese medicinal plant mainly grown in Sichuan, China. C. blinii is suitable for studying the mechanism of plant tolerance to UV-B due to its living conditions, characterized by a high altitude and exposure to strong ultraviolet radiation. Our results showed that the growth and photosynthetic activity of C. blinii were improved under a specific intensity of UV-B, rather than being significantly inhibited. Although UV-B increased the content of reactive oxygen species (ROS) in C. blinii, the activities of antioxidative enzymes were elevated, including superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX), which contributed to the elimination of ROS. Additionally, the content of blinin, the characteristic diterpene in C. blinii, was markedly increased by UV-B. Furthermore, RNA sequencing analyses were used to explore the molecular mechanism of UV-B tolerance in C. blinii. According to the results, most of the key enzyme genes in the blinin synthesis pathway were upregulated by UV-B. In addition, 23 upregulated terpene transporter genes were identified, and these genes might participate in blinin transport during the response to UV-B. Taken together, these results implied that enhanced antioxidant capacity and upregulated transporter genes contributed to increased synthesis of blinin in response to UV-B in C. blinii.

Transcriptome analyses revealed the ultraviolet B irradiation and phytohormone gibberellins coordinately promoted the accumulation of artemisinin in Artemisia annua L

Background

Artemisinin-based combination therapy has become the preferred approach for treating malaria and has successfully reduced malaria-related mortality. Currently, the main source of artemisinin is Artemisia annua L., and thus, it is of strategic importance to enhance artemisinin contents in A. annua plants. Phytohormones and illumination are known to be important external environmental factor that can have notable effects on the production of secondary metabolite. The activities of different hormones can be influenced to varying degrees by light, and thus light and hormones may jointly regulate various processes in plants. Here, we performed transcriptome and metabolome analyses revealed that ultraviolet B irradiation and phytohormone gibberellins coordinately promoted the accumulation of artemisinin in Artemisia annua.

Methods

Artemisinin analysis was performed by ultra-high performance liquid chromatography-tandem quadrupole mass spectrometry (UPLC-ESI-QqQ-MS/MS). RNA sequencing, GO and KEGG enrichment analysis were applied to analyzing the differentially expressed genes (DEGs) under ultraviolet B irradiation and gibberellins treatments. Weighted gene co-expression network (WGCNA) analyzed the genes in artemisinin‑related modules and identified candidate hub genes in these modules.

Results

In this study, we found that cross-talk between UV-B and GA induced processes leading to modifications in artemisinin accumulation. A total of 14,762 genes differentially expressed (DEGs) among different treatments were identified by transcriptome analysis. UV-B and GA treatments enhanced the accumulation of artemisinin by up-regulating the expression of the key artemisinin biosynthesis genes ADS and CYP71AV1. According to the high degree value and high expression level, a total of 84 co-expressed transcription factors were identified. Among them, MYB and NAC TFs mainly involved in regulating the biosynthesis of artemisinin. Weighted gene co-expression network analysis revealed that GA + UV in blue modules was positively correlated with artemisinin synthesis, suggesting that the candidate hub genes in these modules should be up-regulated to enhance artemisinin synthesis in response to GA + UV treatment.

Conclusion

Our study demonstrated the co-regulation of artemisinin biosynthetic pathway genes under ultraviolet B irradiation and phytohormone gibberellins treatment. The co-expression was analysis revealed that the selected MYB and NAC TFs might have regulated the artemisinin biosynthesis gene expression with ADS and CYP71AV1 genes. Weighted gene co-expression network analysis revealed that GA + UV treatment in blue modules was positively correlated with artemisinin synthesis. We established the network to distinguish candidate hub genes in blue modules might be up-regulated to enhance artemisinin synthesis in response to GA + UV treatment.

Transcriptome analysis reveals insight into molecular hydrogen-induced cadmium tolerance in alfalfa: the prominent role of sulfur and (homo)glutathione metabolism

BACKGROUND

Hydrogen gas (H2) is hypothesised to play a role in plants that are coping with stresses by regulating signal transduction and gene expression. Although the beneficial role of H2 in plant tolerance to cadmium (Cd) has been investigated previously, the corresponding mechanism has not been elucidated. In this report, the transcriptomes of alfalfa seedling roots under Cd and/or hydrogen-rich water (HRW) treatment were first analysed. Then, the sulfur metabolism pathways were focused on and further investigated by pharmacological and genetic approaches.

RESULTS

A total of 1968 differentially expressed genes (DEGs) in alfalfa seedling roots under Cd and/or HRW treatment were identified by RNA-Seq. The DEGs were classified into many clusters, including glutathione (GSH) metabolism, oxidative stress, and ATP-binding cassette (ABC) transporters. The results validated by RT-qPCR showed that the levels of relevant genes involved in sulfur metabolism were enhanced by HRW under Cd treatment, especially the genes involved in (homo)glutathione metabolism. Additional experiments carried out with a glutathione synthesis inhibitor and Arabidopsis thaliana cad2-1 mutant plants suggested the prominent role of glutathione in HRW-induced Cd tolerance. These results were in accordance with the effects of HRW on the contents of (homo)glutathione and (homo)phytochelatins and in alleviating oxidative stress under Cd stress. In addition, the HRW-induced alleviation of Cd toxicity might also be caused by a decrease in available Cd in seedling roots, achieved through ABC transporter-mediated secretion.

CONCLUSIONS

Taken together, the results of our study indicate that H2 regulated the expression of genes relevant to sulfur and glutathione metabolism and enhanced glutathione metabolism which resulted in Cd tolerance by activating antioxidation and Cd chelation. These results may help to elucidate the mechanism governing H2-induced Cd tolerance in alfalfa.

Effects of hydrogen-rich water on the nutrient composition and antioxidative characteristics of sprouted black barley

Hydrogen gas (H₂), a multifunctional signaling molecule, has received increasing attention in recent years. In the present study, hydrogen-rich water (HRW) (2 ppm) was used for the processing of sprouted black barley (Hordeum distichum L.), and the results showed that the HRW treatment could significantly increase the germination rate and growth rate of black barley (P < 0.05). A chemical component analysis showed that in sprouted black barley, the HRW treatment could change the distribution of phytochemicals (e.g., the ionic strength of guanosine), increase the concentrations of free vanillic acid, coumaric acid, sinapic acid, conjugated sinapic acid, Ca and Fe and the hydroxyl radical scavenging rate, and decrease the protein, fat, starch and dietary fibre contents compared with the results obtained after treatment with ultra-pure water (P < 0.05). HRW can be used for the processing of sprouted grains to effectively increase their germination efficiency and concentrations of bioactive phytochemicals.

Transcriptome Analysis Reveals the Accumulation Mechanism of Anthocyanins in Buckwheat (Fagopyrum esculentum Moench) Cotyledons and Flowers

Buckwheat (Fagopyrum esculentum) is a valuable crop which can produce multiple human beneficial secondary metabolites, for example, the anthocyanins in sprouts and flowers. However, as the predominant group of visible polyphenols in pigmentation, little is known about the molecular mechanisms underlying the anthocyanin biosynthesis within buckwheat. In this study, a comparative transcriptome analysis of green and red common buckwheat cultivars was carried out through RNA sequencing. Overall, 3727 and 5323 differently expressed genes (DEGs) were identified in flowers and cotyledons, respectively. Through GO and KEGG analysis, we revealed that DEGs in flowers and cotyledons are predominately involved in biosynthesis of anthocyanin. A total of 42 unigenes encoding 11 structural enzymes of the anthocyanin biosynthesis were identified as DEGs. We also identified some transcription factor families involved in the regulation of anthocyanin biosynthesis. Real-time qPCR validation of candidate genes was performed in flowers and cotyledons, and the results suggested that the high expression level of structural genes involved in anthocyanin biosynthetic pathway promotes anthocyanin accumulation. Our results provide the insight understanding for coloration of red common buckwheat.