Heterosis in the freezing tolerance, and sugar and flavonoid contents of crosses between Arabidopsis thaliana accessions of widely varying freezing tolerance

Mechanism of flavonols on detoxification, migration and transformation of indium in rhizosphere system

Soil contamination by toxic heavy metal induces serious environmental hazards. In recent years, the use of indium (In) in semiconductor products has increased considerably and the release of In is inevitable, which will pose great risk to the ecosystem. The interaction between metal and plants which are the fundamental components of all ecosystems are an indispensable aspect of indium assessment and remediation. The role of flavonols, which is essential to plant resistance to In stress, remains largely unknown. FLS1 related lines of A. thaliana (Col, fls1-3 and OE) were exposed to In stress in soil and flavonols as root exudates were analyzed in exogenous application test. The accumulation and release of flavonols could be induced by In stress. However, flavonols exhibited different function in vivo and in vitro of plant. The basic function of flavonols was to affect root morphology via regulating auxin, but being intervened by In stress. The synthesis and accumulation of flavonols in vivo could activate the antioxidant system and the metal detoxification system to alleviate the toxic effects of In on plant. In addition, plants could make phone calls to rhizosphere microbes for help when exposed to In. Flavonols in vitro might act as the information transmission. Combination of endogenous and exogenous flavonols could affect the migration and transformation of In in soil-plant system via metal complexation and transportation pathway.

Integrated transcriptomic and metabolomic data reveal the cold stress responses molecular mechanisms of two coconut varieties

Among tropical fruit trees, coconut holds significant edible and economic importance. The natural growth of coconuts faces a challenge in the form of low temperatures, which is a crucial factor among adverse environmental stresses impacting their geographical distribution. Hence, it is essential to enhance our comprehension of the molecular mechanisms through which cold stress influences various coconut varieties. We employed analyses of leaf growth morphology and physiological traits to examine how coconuts respond to low temperatures over 2-hour, 8-hour, 2-day, and 7-day intervals. Additionally, we performed transcriptome and metabolome analyses to identify the molecular and physiological shifts in two coconut varieties displaying distinct sensitivities to the cold stress. As the length of cold stress extended, there was a prominent escalation within the soluble protein (SP), proline (Pro) concentrations, the activity of peroxidase (POD) and superoxide dismutase (SOD) in the leaves. Contrariwise, the activity of glutathione peroxidase (GSH) underwent a substantial reduction during this period. The widespread analysis of metabolome and transcriptome disclosed a nexus of genes and metabolites intricately cold stress were chiefly involved in pathways centered around amino acid, flavonoid, carbohydrate and lipid metabolism. We perceived several stress-responsive metabolites, such as flavonoids, carbohydrates, lipids, and amino acids, which unveiled considerably, lower in the genotype subtle to cold stress. Furthermore, we uncovered pivotal genes in the amino acid biosynthesis, antioxidant system and flavonoid biosynthesis pathway that presented down-regulation in coconut varieties sensitive to cold stress. This study broadly enriches our contemporary perception of the molecular machinery that contributes to altering levels of cold stress tolerance amid coconut genotypes. It also unlocks several unique prospects for exploration in the areas of breeding or engineering, aiming to identifying tolerant and/or sensitive coconut varieties encompassing multi-omics layers in response to cold stress conditions.

Comparisons in phytochemical components and in vitro digestion properties of corresponding peels, flesh and seeds separated from two blueberry cultivars

Highbush blueberries (HB) and rabbiteye blueberries (RB) were separated into peels, flesh, and seeds to assess the compositions of nutriment, anthocyanins, soluble sugars and fatty acids, and the in vitro digesting abilities. Total phenolics contents (TPC) of 51-56 mg GAE/g DW were found in blueberry peels. Compared with HB peels, RB peels showed much higher TPC, but only contained 35 phenolics and lacked peonidin-3-O-rutinoside. Glucose, fructose, and sucrose were all present in HB and RB, but RB flesh had a higher acid-sugar ratio. Unsaturated fatty acid concentrations in HB and RB seeds were comparable (26.65 and 26.43 mg/g, respectively). However, HB seeds have 35 fatty acids, but RB seeds lacked cis-4,7,10,13,16,19-docosahexaenoic acid and cis-10-pentadecenoic acid. The in vitro digestion test showed that the whole fruit/peels/flesh of RB had a higher recovery and bioavailability index of phenolics and anthocyanins. Therefore, the reuse of blueberry pomace needs to be emphasized.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-023-01326-w.

Metabolomic Analysis of the Effect of Freezing on Leaves of Malus sieversii (Ledeb.) M.Roem. Histoculture Seedlings

Malus sieversii (Ledeb.) M.Roem. is the ancestor of cultivated apples, and is an excellent germplasm resource with high resistance to cold. Artificial refrigerators were used to simulate the low temperature of -3 °C to treat Malus sieversii (Ledeb.) M.Roem. histoculture seedlings. Observations were performed to find the effects of freezing stress on the status of open or closed stomata, photosystems, and detection of metabolomic products in leaves of Malus sieversii (Ledeb.) M.Roem. histoculture seedlings. The percentage of closed stomata in the Malus sieversii (Ledeb.) M.Roem. histoculture seedlings increased, the maximum fluorescence (Fm') excited by a strong light (saturating pulse) was weakened relative to the real-time fluorescence in its vicinity, and the quantum yield of unregulated energy dissipation was increased in PSII under freezing stress. The metabolites in the leaves of the Malus sieversii (Ledeb. M.Roem.) histoculture seedlings were analyzed by ultra-performance liquid chromatography-tandem mass spectrometry using CK, T12h, T36 h, and HF24h. Results demonstrated that cold stress in the Malus sieversii (Ledeb.) M.Roem. histoculture seedlings led to wilting, leaf stomatal closure, and photosystem damage. There were 1020 metabolites identified as lipids (10.2%), nucleotides and their derivatives (5.2%), phenolic acids (19.12%), flavonoids (24.51%), amino acids and their derivatives (7.75%), alkaloids (5.39%), terpenoids (8.24%), lignans (3.04%), organic acids (5.88%), and tannins (0.88%). There were 110 differential metabolites at CKvsT12h, 113 differential metabolites at CKvsT36h, 87 differential metabolites at T12hvsT36h, 128 differential metabolites at CKvsHF24h, 121 differential metabolites at T12hvsHF24h, and 152 differential metabolites at T36hvsHF24h. The differential metabolites in the leaves of the Malus sieversii (Ledeb.) M.Roem. seedlings grown under low-temperature stress mainly involved glycolysis, amino acid metabolism, lipid metabolism, pyrimidine metabolism, purine metabolism, and secondary metabolite metabolism. The Malus sieversii (Ledeb.) M.Roem. seedlings responded to the freezing stress by coordinating with each other through these metabolic pathways. The metabolic network of the leaves of the Malus sieversii (Ledeb.) M.Roem. histoculture seedlings under low temperature stress was also proposed based on the above pathways to deepen understanding of the response of metabolites of Malus sieversii (Ledeb.) M.Roem. to low-temperature stress and to lay a theoretical foundation for the development and utilization of Malus sieversii (Ledeb.) M.Roem. cultivation resources.

Over-activation of cold tolerance in arabidopsis causes carbohydrate shortage compared with Chorispora bungeana

Many plants cope with cold stress by developing acquired freezing tolerance (AFT) through cold acclimation (CA), and some species have strong basal freezing tolerance (BFT) independent of CA. Although CA has been extensively studied, its potential in agricultural applications is still unclear. Here, carbohydrate metabolism and transcriptome in AFT plant Arabidopsis and BFT plant Chorispora bungeana were compared with each other. The results showed that, although both species were able to accumulate soluble sugars during CA, leaf starch accumulation in the daytime was almost blocked in Arabidopsis while it was greatly enhanced in C. bungeana, revealing that Arabidopsis experienced carbohydrate shortage during CA. Transcriptome and pathway enrichment analysis found that genes for photosynthesis antenna proteins were generally repressed by cold stress in both species. However, cold-up-regulated genes were enriched in protein translation in Arabidopsis, whilst they were enriched in carotenoid biosynthesis, flavonoid biosynthesis, and beta-amylases in C. bungeana. Furthermore, weighted gene co-expression network analysis (WGCNA) showed that the inhibition of starch accumulation was associated with down-regulation of genes for photosynthesis antenna proteins and up-regulation of genes for protein translation, DNA repair, and proteasome in Arabidopsis but not in C. bungeana. Taken together, our results revealed that over-activation of common tolerant mechanisms resulted in insufficient carbohydrate supplies in Arabidopsis during CA, and photoprotective mechanisms played important roles in cold adaptation of C. bungeana. These findings uncovered the drawback of CA in improving freezing tolerance and highlighted photoprotection as a possible solution for agricultural applications.

Feeding on rapid cold hardening Ambrosia artemisiifolia enhances cold tolerance of Ophraella communa

Low temperatures greatly influence newly introduced species, and increased cold tolerance can facilitate their establishment in new environments. The invasive alien species Ambrosia artemisiifolia is distributed at high latitudes and altitudes, where it suffers more from cold stress than it would at low latitudes or altitudes. Whether cold stress influences the accumulation of cryoprotectants and cold tolerance in A. artemisiifolia, and further influences the cold tolerance of its biological control agent, Ophraella communa, through feeding remain unknown. We investigated the levels of cryoprotectants and metabolic changes in A. artemisiifolia. We found that the level of total sugar, trehalose, proline, and other cold responsible metabolites increased in A. artemisiifolia after rapid cold-hardening (RCH) treatment, when compared to normal plants. These indicated that RCH treatment could improve the cold-hardiness of A. artemisiifolia. We then investigated the levels of cryoprotectants and metabolic changes in O. communa. We found that O. communa fed on RCH-treated A. artemisiifolia had higher levels of total sugar, trehalose, proline, glycerol, lipid, lower water content, lower super-cooling point, and increased cold tolerance compared to O. communa fed on normal A. artemisiifolia. This suggested that O. communa fed on cold-hardened A. artemisiifolia could increase its cold tolerance. Results showed a trophic transmission in insect cold tolerance. Our study enriches the theoretical basis for the co-evolution of cold tolerance in invasive and herbivorous insects.

BcMYB111 Responds to BcCBF2 and Induces Flavonol Biosynthesis to Enhance Tolerance under Cold Stress in Non-Heading Chinese Cabbage

Flavonols have been shown to respond to a variety of abiotic stresses in plants, including cold stress. Higher total flavonoid content was found in non-heading Chinese cabbage (NHCC, Brassica campestris (syn. Brassica rapa) ssp. chinensis) after cold stress. A non-targeted metabolome analysis showed a significant increase in flavonol content, including that of quercetin and kaempferol. Here, we found that an R2R3-MYB transcription factor, BcMYB111, may play a role in this process. BcMYB111 was up-regulated in response to cold treatment, with an accompanying accumulation of flavonols. Then, it was found that BcMYB111 could regulate the synthesis of flavonols by directly binding to the promoters of BcF3H and BcFLS1. In the transgenic hairy roots of NHCC or stable transgenic Arabidopsis, overexpression of BcMYB111 increased flavonol synthesis and accumulation, while these were reduced in virus-induced gene silencing lines in NHCC. After cold stress, the higher proline content and lower malondialdehyde (MDA) content showed that there was less damage in transgenic Arabidopsis than in the wild-type (WT). The BcMYB111 transgenic lines performed better in terms of antioxidant capacity because of their lower H₂O₂ content and higher superoxide dismutase (SOD) and peroxidase (POD) enzyme activities. In addition, a key cold signaling gene, BcCBF2, could specifically bind to the DRE element and activate the expression of BcMYB111 in vitro and in vivo. The results suggested that BcMYB111 played a positive role in enhancing the flavonol synthesis and cold tolerance of NHCC. Taken together, these findings reveal that cold stress induces the accumulation of flavonols to increase tolerance via the pathway of BcCBF2-BcMYB111-BcF3H/BcFLS1 in NHCC.

Transcriptomics Reveals the Effect of Short-Term Freezing on the Signal Transduction and Metabolism of Grapevine

Low temperature is an important factor limiting plant growth. Most cultivars of Vitis vinifera L. are sensitive to low temperatures and are at risk of freezing injury or even plant death during winter. In this study, we analyzed the transcriptome of branches of dormant cv. Cabernet Sauvignon exposed to several low-temperature conditions to identify differentially expressed genes and determine their function based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG)enrichment analyses. Our results indicated that exposure to subzero low temperatures resulted in damage to plant cell membranes and extravasation of intracellular electrolytes, and that this damage increased with decreasing temperature or increasing duration. The number of differential genes increased as the duration of stress increased, but most of the common differentially expressed genes reached their highest expression at 6 h of stress, indicating that 6 h may be a turning point for vines to tolerate extreme low temperatures. Several pathways play key roles in the response of Cabernet Sauvignon to low-temperature injury, namely: (1) the role of calcium/calmodulin-mediated signaling; (2) carbohydrate metabolism, including the hydrolysis of cell wall pectin and cellulose, decomposition of sucrose, synthesis of raffinose, and inhibition of glycolytic processes; (3) the synthesis of unsaturated fatty acids and metabolism of linolenic acid; and (4) the synthesis of secondary metabolites, especially flavonoids. In addition, pathogenesis-related protein may also play a role in plant cold resistance, but the mechanism is not yet clear. This study reveals possible pathways for the freezing response and leads to new insights into the molecular basis of the tolerance to low temperature in grapevine.

Limitation of sucrose biosynthesis shapes carbon partitioning during plant cold acclimation

Cold acclimation is a multigenic process by which many plant species increase their freezing tolerance. Stabilization of photosynthesis and carbohydrate metabolism plays a crucial role in cold acclimation. To study regulation of primary and secondary metabolism during cold acclimation of Arabidopsis thaliana, metabolic mutants with deficiencies in either starch or flavonoid metabolism were exposed to 4°C. Photosynthesis was determined together with amounts of carbohydrates, anthocyanins, organic acids and enzyme activities of the central carbohydrate metabolism. Starch deficiency was found to significantly delay soluble sugar accumulation during cold acclimation, while starch overaccumulation did not affect accumulation dynamics but resulted in lower total amounts of \sucrose and glucose. Anthocyanin amounts were lowered in both starch deficient and overaccumulating mutants. Vice versa, flavonoid deficiency did not result in a changed starch amount, which suggested a unidirectional signalling link between starch and flavonoid metabolism. Mathematical modelling of carbon metabolism indicated kinetics of sucrose biosynthesis to be limiting for carbon partitioning in leaf tissue during cold exposure. Together with cold-induced dynamics of citrate, fumarate and malate amounts, this provided evidence for a central role of sucrose phosphate synthase activity in carbon partitioning between biosynthetic and dissimilatory pathways which stabilizes photosynthesis and metabolism at low temperature.

Does phenotyping of Hypericum secondary metabolism reveal a tolerance to biotic/abiotic stressors?

In this review we summarize the current knowledge about the changes in Hypericum secondary metabolism induced by biotic/abiotic stressors. It is known that the extreme environmental conditions activate signaling pathways leading to triggering of enzymatic and non-enzymatic defense systems, which stimulate production of secondary metabolites with antioxidant and protective effects. Due to several groups of bioactive compounds including naphthodianthrones, acylphloroglucinols, flavonoids, and phenylpropanes, the world-wide Hypericum perforatum represents a high-value medicinal crop of Hypericum genus, which belongs to the most diverse genera within flowering plants. The summary of the up-to-date knowledge reveals a relationship between the level of defense-related phenolic compounds and interspecific differences in the stress tolerance. The chlorogenic acid, and flavonoids, namely the amentoflavone, quercetin or kaempferol glycosides have been reported as the most defense-related metabolites associated with plant tolerance against stressful environment including temperature, light, and drought, in association with the biotic stimuli resulting from plant-microbe interactions. As an example, the species-specific cold-induced phenolics profiles of 10 Hypericum representatives of different provenances cultured in vitro are illustrated in the case-study. Principal component analysis revealed a relationship between the level of defense-related phenolic compounds and interspecific differences in the stress tolerance indicating a link between the provenance of Hypericum species and inherent mechanisms of cold tolerance. The underlying metabolome alterations along with the changes in the activities of ROS-scavenging enzymes, and non-enzymatic physiological markers are discussed. Given these data it can be anticipated that some Hypericum species native to divergent habitats, with interesting high-value secondary metabolite composition and predicted high tolerance to biotic/abiotic stresses would attract the attention as valuable sources of bioactive compounds for many medicinal purposes.

What can cold-induced transcriptomes of Arctic Brassicaceae tell us about the evolution of cold tolerance?

Little is known about the evolution of cold tolerance in polar plant species and how they differ from temperate relatives. To gain insight into their biology and the evolution of cold tolerance, we compared the molecular basis of cold response in three Arctic Brassicaceae species. We conducted a comparative time series experiment to examine transcriptional responses to low temperature. RNA was sampled at 22°C, and after 3, 6, and 24 at 2°C. We then identified sets of genes that were differentially expressed in response to cold and compared them between species, as well as to published data from the temperate Arabidopsis thaliana. Most differentially expressed genes were species‐specific, but a significant portion of the cold response was also shared among species. Among thousands of differentially expressed genes, ~200 were shared among the three Arctic species and A. thaliana, while ~100 were exclusively shared among the three Arctic species. Our results show that cold response differs markedly between Arctic Brassicaceae species, but probably builds on a conserved basis found across the family. They also confirm that highly polygenic traits such as cold tolerance may show little repeatability in their patterns of adaptation.

Genome-Wide Identification and Expression Profiles of 13 Key Structural Gene Families Involved in the Biosynthesis of Rice Flavonoid Scaffolds

Flavonoids are a class of key polyphenolic secondary metabolites with broad functions in plants, including stress defense, growth, development and reproduction. Oryza sativa L. (rice) is a well-known model plant for monocots, with a wide range of flavonoids, but the key flavonoid biosynthesis-related genes and their molecular features in rice have not been comprehensively and systematically characterized. Here, we identified 85 key structural gene candidates associated with flavonoid biosynthesis in the rice genome. They belong to 13 families potentially encoding chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavonol synthase (FLS), leucoanthocyanidin dioxygenase (LDOX), anthocyanidin synthase (ANS), flavone synthase II (FNSII), flavanone 2-hydroxylase (F2H), flavonoid 3′-hydroxylase (F3′H), flavonoid 3′,5′-hydroxylase (F3′5′H), dihydroflavonol 4-reductase (DFR), anthocyanidin reductase (ANR) and leucoanthocyanidin reductase (LAR). Through structural features, motif analyses and phylogenetic relationships, these gene families were further grouped into five distinct lineages and were examined for conservation and divergence. Subsequently, 22 duplication events were identified out of a total of 85 genes, among which seven pairs were derived from segmental duplication events and 15 pairs were from tandem duplications, demonstrating that segmental and tandem duplication events play important roles in the expansion of key flavonoid biosynthesis-related genes in rice. Furthermore, these 85 genes showed spatial and temporal regulation in a tissue-specific manner and differentially responded to abiotic stress (including six hormones and cold and salt treatments). RNA-Seq, microarray analysis and qRT-PCR indicated that these genes might be involved in abiotic stress response, plant growth and development. Our results provide a valuable basis for further functional analysis of the genes involved in the flavonoid biosynthesis pathway in rice.

Genetic basis and dual adaptive role of floral pigmentation in sunflowers

Variation in floral displays, both between and within species, has been long known to be shaped by the mutualistic interactions that plants establish with their pollinators. However, increasing evidence suggests that abiotic selection pressures influence floral diversity as well. Here, we analyse the genetic and environmental factors that underlie patterns of floral pigmentation in wild sunflowers. While sunflower inflorescences appear invariably yellow to the human eye, they display extreme diversity for patterns of ultraviolet pigmentation, which are visible to most pollinators. We show that this diversity is largely controlled by cis-regulatory variation affecting a single MYB transcription factor, HaMYB111, through accumulation of ultraviolet (UV)-absorbing flavonol glycosides in ligules (the ‘petals’ of sunflower inflorescences). Different patterns of ultraviolet pigments in flowers are strongly correlated with pollinator preferences. Furthermore, variation for floral ultraviolet patterns is associated with environmental variables, especially relative humidity, across populations of wild sunflowers. Ligules with larger ultraviolet patterns, which are found in drier environments, show increased resistance to desiccation, suggesting a role in reducing water loss. The dual role of floral UV patterns in pollinator attraction and abiotic response reveals the complex adaptive balance underlying the evolution of floral traits.

Flowers are an important part of how many plants reproduce. Their distinctive colours, shapes and patterns attract specific pollinators, but they can also help to protect the plant from predators and environmental stresses.

Many flowers contain pigments that absorb ultraviolet (UV) light to display distinct UV patterns – although invisible to the human eye, most pollinators are able to see them. For example, when seen in UV, sunflowers feature a ‘bullseye’ with a dark centre surrounded by a reflective outer ring. The sizes and thicknesses of these rings vary a lot within and between flower species, and so far, it has been unclear what causes this variation and how it affects the plants.

To find out more, Todesco et al. studied the UV patterns in various wild sunflowers across North America by considering the ecology and molecular biology of different plants. This revealed great variation between the UV patterns of the different sunflower populations. Moreover, Todesco et al. found that a gene called HaMYB111 is responsible for the diverse UV patterns in the sunflowers. This gene controls how plants make chemicals called flavonols that absorb UV light.

Flavonols also help to protect plants from damage caused by droughts and extreme temperatures. Todesco et al. showed that plants with larger bullseyes had more flavonols, attracted more pollinators, and were better at conserving water. Accordingly, these plants were found in drier locations.

This study suggests that, at least in sunflowers, UV patterns help both to attract pollinators and to control water loss. These insights could help to improve pollination – and consequently yield – in cultivated plants, and to develop plants with better resistance to extreme weather. This work also highlights the importance of combining biology on small and large scales to understand complex processes, such as adaptation and evolution.

Temperature-induced dynamics of plant carbohydrate metabolism

Carbohydrates are direct products of photosynthetic CO₂ assimilation. Within a changing temperature regime, both photosynthesis and carbohydrate metabolism need tight regulation to prevent irreversible damage of plant tissue and to sustain energy metabolism, growth and development. Due to climate change, plants are and will be exposed to both long-term and short-term temperature changes with increasing amplitude. Particularly sudden fluctuations, which might comprise a large temperature amplitude from low to high temperature, pose a challenge for plants from the cellular to the ecosystem level. A detailed understanding of fundamental regulatory processes, which link photosynthesis and carbohydrate metabolism under such fluctuating environmental conditions, is essential for an estimate of climate change consequences. Further, understanding these processes is important for biotechnological application, breeding and engineering. Environmental light and temperature regimes are sensed by a molecular network that comprises photoreceptors and molecular components of the circadian clock. Photosynthetic efficiency and plant productivity then critically depend on enzymatic regulation and regulatory circuits connecting plant cells with their environment and re-stabilising photosynthetic efficiency and carbohydrate metabolism after temperature-induced deflection. This review summarises and integrates current knowledge about re-stabilisation of photosynthesis and carbohydrate metabolism after perturbation by changing temperature (heat and cold).

Comparison of chrysanthemum flowers grown under hydroponic and soil-based systems: yield and transcriptome analysis

BACKGROUND

Flowers of Chrysanthemum × morifolium Ramat. are used as tea in traditional Chinese cuisine. However, with increasing population and urbanization, water and land availability have become limiting for chrysanthemum tea production. Hydroponic culture enables effective, rapid nutrient exchange, while requiring no soil and less water than soil cultivation. Hydroponic culture can reduce pesticide residues in food and improve the quantity or size of fruits, flowers, and leaves, and the levels of active compounds important for nutrition and health. To date, studies to improve the yield and active compounds of chrysanthemum have focused on soil culture. Moreover, the molecular effects of hydroponic and soil culture on chrysanthemum tea development remain understudied.

RESULTS

Here, we studied the effects of soil and hydroponic culture on yield and total flavonoid and chlorogenic acid contents in chrysanthemum flowers (C. morifolium 'wuyuanhuang'). Yield and the total flavonoids and chlorogenic acid contents of chrysanthemum flowers were higher in the hydroponic culture system than in the soil system. Transcriptome profiling using RNA-seq revealed 3858 differentially expressed genes (DEGs) between chrysanthemum flowers grown in soil and hydroponic conditions. Gene Ontology (GO) enrichment annotation revealed that these differentially transcribed genes are mainly involved in "cytoplasmic part", "biosynthetic process", "organic substance biosynthetic process", "cell wall organization or biogenesis" and other processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed enrichment in "metabolic pathways", "biosynthesis of secondary metabolites", "ribosome", "carbon metabolism", "plant hormone signal transduction" and other metabolic processes. In functional annotations, pathways related to yield and formation of the main active compounds included phytohormone signaling, secondary metabolism, and cell wall metabolism. Enrichment analysis of transcription factors also showed that under the hydroponic system, bHLH, MYB, NAC, and ERF protein families were involved in metabolic pathways, biosynthesis of secondary metabolites, and plant hormone signal transduction.

CONCLUSIONS

Hydroponic culture is a simple and effective way to cultivate chrysanthemum for tea production. A transcriptome analysis of chrysanthemum flowers grown in soil and hydroponic conditions. The large number of DEGs identified confirmed the difference of the regulatory machinery under two culture system.

McMYB4 improves temperature adaptation by regulating phenylpropanoid metabolism and hormone signaling in apple

Temperature changes affect apple development and production. Phenylpropanoid metabolism and hormone signaling play a crucial role in regulating apple growth and development in response to temperature changes. Here, we found that McMYB4 is induced by treatment at 28 °C and 18 °C, and McMYB4 overexpression results in flavonol and lignin accumulation in apple leaves. Yeast one-hybrid (Y1H) assays and electrophoretic mobility shift assays (EMSAs) further revealed that McMYB4 targets the promoters of the flavonol biosynthesis genes CHS and FLS and the lignin biosynthesis genes CAD and F5H. McMYB4 expression resulted in higher levels of flavonol and lignin biosynthesis in apple during growth at 28 °C and 18 °C than during growth at 23 °C. At 28 °C and 18 °C, McMYB4 also binds to the AUX/ARF and BRI/BIN promoters to activate gene expression, resulting in acceleration of the auxin and brassinolide signaling pathways. Taken together, our results demonstrate that McMYB4 promotes flavonol biosynthesis and brassinolide signaling, which decreases ROS contents to improve plant resistance and promotes lignin biosynthesis and auxin signaling to regulate plant growth. This study suggests that McMYB4 participates in the abiotic resistance and growth of apple in response to temperature changes by regulating phenylpropanoid metabolism and hormone signaling.

Natural Variation among Arabidopsis Accessions in the Regulation of Flavonoid Metabolism and Stress Gene Expression by Combined UV Radiation and Cold

Plants are constantly exposed to stressful environmental conditions. Plant stress reactions were mainly investigated for single stress factors. However, under natural conditions plants may be simultaneously exposed to different stresses. Responses to combined stresses cannot be predicted from the reactions to the single stresses. Flavonoids accumulate in Arabidopsis thaliana during exposure to UV-A, UV-B or cold, but the interactions of these factors on flavonoid biosynthesis were unknown. We therefore investigated the interaction of UV radiation and cold in regulating the expression of well-characterized stress-regulated genes, and on transcripts and metabolites of the flavonoid biosynthetic pathway in 52 natural Arabidopsis accessions that differ widely in their freezing tolerance. The data revealed interactions of cold and UV on the regulation of stress-related and flavonoid biosynthesis genes, and on flavonoid composition. In many cases, plant reactions to a combination of cold and UV were unique under combined stress and not predictable from the responses to the single stresses. Strikingly, all correlations between expression levels of flavonoid biosynthesis genes and flavonol levels were abolished by UV-B exposure. Similarly, correlations between transcript levels of flavonoid biosynthesis genes or flavonoid contents, and freezing tolerance were lost in the presence of UV radiation, while correlations with the expression levels of cold-regulated genes largely persisted. This may indicate different molecular cold acclimation responses in the presence or absence of UV radiation.

An enhanced photosynthesis and carbohydrate metabolic capability contributes to heterosis of the cotton (Gossypium hirsutum) hybrid 'Huaza Mian H318', as revealed by genome-wide gene expression analysis

Background

Heterosis has been exploited for decades in different crops due to resulting in dramatic increases in yield, but relatively little molecular evidence on this topic was reported in cotton.

Results

The elite cotton hybrid variety ‘Huaza Mian H318’ (H318) and its parental lines were used to explore the source of its yield heterosis. A four-year investigation of yield-related traits showed that the boll number of H318 showed higher stability than that of its two parents, both in suitable and unsuitable climate years. In addition, the hybrid H318 grew faster and showed higher fresh and dry weights than its parental lines at the seedling stage. Transcriptome analysis of seedlings identified 17,308 differentially expressed genes (DEGs) between H318 and its parental lines, and 3490 extremely changed DEGs were screened out for later analysis. Most DEGs (3472/3490) were gathered between H318 and its paternal line (4–5), and only 64 DEGs were found between H318 and its maternal line (B0011), which implied that H318 displays more similar transcriptional patterns to its maternal parent at the seedling stage. GO and KEGG analyses showed that these DEGs were highly enriched in photosynthesis, lipid metabolic, carbohydrate metabolic and oxidation-reduction processes, and the expression level of these DEGs was significantly higher in H318 relative to its parental lines, which implied that photosynthesis, metabolism and stress resistances were enhanced in H318.

Conclusion

The enhanced photosynthesis, lipid and carbohydrate metabolic capabilities contribute to the heterosis of H318 at the seedling stage, and establishes a material foundation for subsequent higher boll-setting rates in complex field environments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07580-8.

Allotetraploidization in Brachypodium May Have Led to the Dominance of One Parent's Metabolome in Germinating Seeds

Seed germination is a complex process during which a mature seed resumes metabolic activity to prepare for seedling growth. In this study, we performed a comparative metabolomic analysis of the embryo and endosperm using the community standard lines of three annual Brachypodium species, i.e., B. distachyon (Bd) and B. stacei (Bs) and their natural allotetraploid B. hybridum (BdBs) that has wider ecological range than the other two species. We explored how far the metabolomic impact of allotetraploidization would be observable as over-lapping changes at 4, 12, and 24 h after imbibition (HAI) with water when germination was initiated. Metabolic changes during germination were more prominent in Brachypodium embryos than in the endosperm. The embryo and endosperm metabolomes of Bs and BdBs were similar, and those of Bd were distinctive. The Bs and BdBs embryos showed increased levels of sugars and the tricarboxylic acid cycle compared to Bd, which could have been indicative of better nutrient mobilization from the endosperm. Bs and BdBs also showed higher oxalate levels that could aid nutrient transfer through altered cellular events. In Brachypodium endosperm, the thick cell wall, in addition to starch, has been suggested to be a source of nutrients to the embryo. Metabolites indicative of sugar metabolism in the endosperm of all three species were not prominent, suggesting that mobilization mostly occurred prior to 4 HAI. Hydroxycinnamic and monolignol changes in Bs and BdBs were consistent with cell wall remodeling that arose following the release of nutrients to the respective embryos. Amino acid changes in both the embryo and endosperm were broadly consistent across the species. Taking our data together, the formation of BdBs may have maintained much of the Bs metabolome in both the embryo and endosperm during the early stages of germination. In the embryo, this conserved Bs metabolome appeared to include an elevated sugar metabolism that played a vital role in germination. If these observations are confirmed in the future with more Brachypodium accessions, it would substantiate the dominance of the Bs metabolome in BdBs allotetraploidization and the use of metabolomics to suggest important adaptive changes.

Measuring Freezing Tolerance of Leaves and Rosettes: Electrolyte Leakage and Chlorophyll Fluorescence Assays

Quantitative assessment of freezing tolerance is essential to unravel plant adaptations to cold temperatures. Not only the survival of whole plants, but also impairment of detached leaves or small rosettes after a freeze-thaw cycle can be used to accurately quantify plant freezing tolerance in terms of LT₅₀ values. Here we describe two methods to determine the freezing tolerance of detached leaves or rosettes using a full or selected set of freezing temperatures and an additional method using chlorophyll fluorescence as a different physiological parameter. Firstly, we illustrate how to assess the integrity of (predominantly) the plasma membrane during freezing using an electrolyte leakage assay. Secondly, we provide a chlorophyll fluorescence imaging protocol to determine the freezing tolerance of the photosynthetic apparatus.

HEAT SHOCK FACTOR A8a Modulates Flavonoid Synthesis and Drought Tolerance

Drought is an important environmental factor affecting the growth and production of agricultural crops and fruits worldwide, including apple (Malus domestica). Heat shock factors (HSFs) have well-documented functions in stress responses, but their roles in flavonoid synthesis and the flavonoid-mediated drought response mechanism remain elusive. In this study, we demonstrated that a drought-responsive HSF, designated MdHSFA8a, promotes the accumulation of flavonoids, scavenging of reactive oxygen species, and plant survival under drought conditions. A chaperone, HEAT SHOCK PROTEIN90 (HSP90), interacted with MdHSFA8a to inhibit its binding activity and transcriptional activation. However, under drought stress, the MdHSP90-MdHSFA8a complex dissociated and the released MdHSFA8a further interacted with the APETALA2/ETHYLENE RESPONSIVE FACTOR family transcription factor RELATED TO AP2.12 to activate downstream gene activity. In addition, we demonstrated that MdHSFA8a participates in abscisic acid-induced stomatal closure and promotes the expression of abscisic acid signaling-related genes. Collectively, these findings provide insight into the mechanism by which stress-inducible MdHSFA8a modulates flavonoid synthesis to regulate drought tolerance.

In-depth analysis of the Quercus suber metabolome under drought stress and recovery reveals potential key metabolic players

Cork oak (Quercus suber L.) is a species of ecological, social and economic importance in the Mediterranean region. Given its xerophytic adaptability, the study of cork oak's response to drought stress conditions may provide important data in the global scenario of climate change. The mechanisms behind cork oak's adaptation to drought conditions can inform the design and development of tools to better manage this species under the changing climate patterns. Metabolomics is one of the most promising omics layers to capture a snapshot of a particular physiological state and to identify putative biomarkers of stress tolerance. Drastic changes were observed in the leaf metabolome of Q. suber between the different experimental conditions, namely at the beginning of the drought stress treatment, after one month under drought and post rehydration. All experimental treatments were analyzed through sPLS to inspect for global changes and stress and rehydration responses were analyzed independently for specific alterations. This allowed a more in-depth study and a search for biomarkers specific to a given hydric treatment. The metabolome analyses showed changes in both primary and secondary metabolism, but highlighted the role of secondary metabolism. In addition, a compound-specific response was observed in stress and rehydration. Key compounds such as L-phenylalanine and epigallocatechin 3-gallate were identified in relation to early drought response, terpenoid leonuridine and the flavonoid glycoside (-)-epicatechin-3'-O-glucuronide in long-term drought response, and flavone isoscoparine was identified in relation to the recovery process. The results here obtained provide novel insights into the biology of cork oak, highlighting pathways and metabolites potentially involved in the response of this species during drought and recovery that may be essential for its adaptation to long periods of drought. It is expected that this knowledge can encourage further functional studies in order to validate potential biomarkers of drought and recovery that maybe used to support decision-making in cork oak breeding programs.

Effects of low temperature on photoinhibition and singlet oxygen production in four natural accessions of Arabidopsis

Low temperature decreases PSII damage in vivo, confirming earlier in vitro results. Susceptibility to photoinhibition differs among Arabidopsis accessions and moderately decreases after 2-week cold-treatment. Flavonols may alleviate photoinhibition. The rate of light-induced inactivation of photosystem II (PSII) at 22 and 4 °C was measured from natural accessions of Arabidopsis thaliana (Rschew, Tenela, Columbia-0, Coimbra) grown under optimal conditions (21 °C), and at 4 °C from plants shifted to 4 °C for 2 weeks. Measurements were done in the absence and presence of lincomycin (to block repair). PSII activity was assayed with the chlorophyll a fluorescence parameter F_v/F_m and with light-saturated rate of oxygen evolution using a quinone acceptor. When grown at 21 °C, Rschew was the most tolerant to photoinhibition and Coimbra the least. Damage to PSII, judged from fitting the decrease in oxygen evolution or F_v/F_m to a first-order equation, proceeded more slowly or equally at 4 than at 22 °C. The 2-week cold-treatment decreased photoinhibition at 4 °C consistently in Columbia-0 and Coimbra, whereas in Rschew and Tenela the results depended on the method used to assay photoinhibition. The rate of singlet oxygen production by isolated thylakoid membranes, measured with histidine, stayed the same or slightly decreased with decreasing temperature. On the other hand, measurements of singlet oxygen from leaves with Singlet Oxygen Sensor Green suggest that in vivo more singlet oxygen is produced at 4 °C. Under high light, the PSII electron acceptor Q_A was more reduced at 4 than at 22 °C. Singlet oxygen production, in vitro or in vivo, did not decrease due to the cold-treatment. Epidermal flavonols increased during the cold-treatment and, in Columbia-0 and Coimbra, the amount correlated with photoinhibition tolerance.

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.

Revealing biomass heterosis in the allodiploid xBrassicoraphanus, a hybrid between Brassica rapa and Raphanus sativus, through integrated transcriptome and metabolites analysis

BACKGROUND

Heterosis is biologically important but the molecular basis of the phenomenon is poorly understood. We characterized intergeneric hybrids between B. rapa cv. Chiifu and R. sativus cv. WK10039 as an extreme example of heterosis. Taking advantage of clear heterosis phenotypes and the genetic distance between parents, we performed transcriptome and metabolite analysis to decipher the molecular basis of heterosis.

RESULTS

The heterosis was expressed as fresh weight in the field and as inflorescence stem length in the glass house. Flowering time, distributed as a normal segregating population, ranged from the early flowering of one parent to the late flowering of the other, in contrast to the homogeneous flowering time in a typical F1 population, indicating unstable allelic interactions. The transcriptome and metabolome both indicated that sugar metabolism was altered, suggesting that the change in metabolism was linked to the heterosis. Because alleles were not shared between the hybridized genomes, classic models only partly explain this heterosis, indicating that other mechanisms are involved.

CONCLUSION

The differential expression of genes for primary and secondary metabolism, along with the altered metabolite profiles, suggests that heterosis could involve a change in balance between primary and secondary metabolism.

Comparative metabolomics analysis of the response to cold stress of resistant and susceptible Tibetan hulless barley (Hordeum distichon)

Plants cultivated on the Qinghai-Tibetan Plateau grow in an extremely cold environment and thus are exposed to cold stress. To assess the metabolic processes during cold exposure of Tibetan hulless barley (Hordeum distichon L.), metabolic analyses were conducted on one tolerant (XiLa) and one sensitive (ZangQing) cultivar exposed to six temperatures (24 °C, 12 °C, 5 °C, 0 °C, -5 °C, -8 °C) for 24 h. In total, 770 metabolites were identified, including amino acids and derivatives, carbohydrates, flavonoids, lipids, nucleotides and derivatives, and phenolamides. In principal component analysis, the samples were clearly grouped according to the cultivar, suggesting that the two cultivars have differential responses to cold stress. In cold-grown plants, eight metabolites, including monoacylglycerol (MAG, 18:2), MAG (18:3), deoxyadenosine, 6-methylmercaptopurine, and coniferin, were significantly altered in XiLa, but not in ZangQing when compared to the levels in control plants, and thus, these compounds can be considered as potential biomarkers of exposure to cold stress in hulless barley. Furthermore, differentially altered metabolites between seedlings exposed to -8 °C and those maintained at 24 °C were significantly enriched in glutathione metabolism. The findings of this study will be useful for the development of cultivars with cold stress tolerance.

Introduction: Plant Cold Acclimation and Winter Survival

This introductory chapter provides a brief overview of plant freezing tolerance, cold acclimation, including subzero acclimation, and the subsequent deacclimation when plants return to warm conditions favoring growth and development. We describe the basic concepts and approaches that are currently followed to investigate these phenomena. We highlight the multidisciplinary nature of these investigations and the necessity to use methodologies from different branches of science, such as ecology, genetics, physiology, cell biology, biochemistry, and biophysics to gain a complete understanding of the complex adaptive mechanisms ultimately underlying plant winter survival.

Nitric oxide deficiency decreases C-repeat binding factor-dependent and -independent induction of cold acclimation

Plant tolerance to freezing temperatures is governed by endogenous components and environmental factors. Exposure to low non-freezing temperatures is a key factor in the induction of freezing tolerance in the process called cold acclimation. The role of nitric oxide (NO) in cold acclimation was explored in Arabidopsis using triple nia1nia2noa1-2 mutants that are impaired in the nitrate-dependent and nitrate-independent pathways of NO production, and are thus NO deficient. Here, we demonstrate that cold-induced NO accumulation is required to promote the full cold acclimation response through C-repeat Binding Factor (CBF)-dependent gene expression, as well as the CBF-independent expression of other cold-responsive genes such as Oxidation-Related Zinc Finger 2 (ZF/OZF2). NO deficiency also altered abscisic acid perception and signaling and the cold-induced production of anthocyanins, which are additional factors involved in cold acclimation.

Evolutionary response to coexistence with close relatives: increased resistance against specialist herbivores without cost for climatic-stress resistance

Why can hosts coexist with conspecifics or phylogenetically proximate neighbours despite sharing specialist enemies? Do the hosts evolve increased enemy resistance? If so, does this have costs in terms of climatic-stress resistance, or in such neighbourhoods, does climatic-stress select for resistances that are multifunctional against climate and enemies? We studied oak (Quercus petraea) descendants from provenances of contrasting phylogenetic neighbourhoods and climates in a 25-year-old common garden. We found that descendants from conspecific or phylogenetically proximate neighbourhoods had the toughest leaves and fewest leaf miners, but no reduction in climatic-stress resistance. Descendants from such neighbourhoods under cold or dry climates had the highest flavonol and anthocyanin levels and the thickest leaves. Overall, populations facing phylogenetically proximate neighbours can rapidly evolve herbivore resistance, without cost to climatic-stress resistance, but possibly facilitating resistance against cold and drought via multifunctional traits. Microevolution might hence facilitate ecological coexistence of close relatives and thereby macroevolutionary conservatism of niches.

The light-induced transcription factor FtMYB116 promotes accumulation of rutin in Fagopyrum tataricum

Tartary buckwheat (Fagopyrum tataricum) not only provides a supplement to primary grain crops in China but also has high medicinal value, by virtue of its rich content of flavonoids possessing antioxidant, anti-inflammatory, and anticancer properties. Light is an important environmental factor that can regulate the synthesis of plant secondary metabolites. In this study, we treated tartary buckwheat seedlings with different wavelengths of light and found that red and blue light could increase the content of flavonoids and the expression of genes involved in flavonoid synthesis pathways. Through coexpression analysis, we identified a new MYB transcription factor (FtMYB116) that can be induced by red and blue light. Yeast one-hybrid assays and an electrophoretic mobility shift assay showed that FtMYB116 binds directly to the promoter region of flavonoid-3'-hydroxylase (F3'H), and a transient luciferase activity assay indicated that FtMYB116 can induce F3'H expression. After transforming FtMYB116 into the hairy roots of tartary buckwheat, we observed significant increases in the content of rutin and quercetin. Collectively, our results indicate that red and blue light promote an increase in flavonoid content in tartary buckwheat seedlings; we also identified a new MYB transcription factor, FtMYB116, that promotes the accumulation of rutin via direct activation of F3'H expression.

Identification of new regulators through transcriptome analysis that regulate anthocyanin biosynthesis in apple leaves at low temperatures

Anthocyanin pigments play many roles in plants, including providing protection against biotic and abiotic stresses. To identify new regulatory genes in apple (Malus domestica) that may be involved in regulating low temperature induced anthocyanin biosynthesis, we performed RNA-seq analysis of leaves from the ‘Gala’ apple cultivar following exposure to a low temperature (16 °C). A visible red color appeared on the upper leaves and the anthocyanin content increased significantly after the low temperature treatment. Genes from the flavonoid biosynthesis pathway were significantly enriched among the differentially expressed genes, and the expression of several transcription factors was shown by WGCNA (weighted gene co-expression network analysis) to correlate with anthocyanin accumulation, including members of the MYB, MADS, WRKY, WD40, Zinc Finger and HB-ZIP families. Three MYB transcription factors (MdMYB12, MdMYB22 and MdMYB114), which had several CBF/DREB response elements in their promoters, were significantly induced by low temperature exposure and their expression also correlated highly with anthocyanin accumulation. We hypothesize that they may act as regulators of anthocyanin biosynthesis and be regulated by CBF/DREB transcription factors in apple leaves under low temperature conditions. The analyses presented here provide insights into the molecular mechanisms underlying anthocyanin accumulation during low temperature exposure.

Flavonoid Glycosides and Hydroxycinnamic Acid Derivatives in Baby Leaf Rapeseed From White and Yellow Flowering Cultivars With Repeated Harvest in a 2-Years Field Study

Recently, new annual and biennial cultivars of rapeseed with white flowers have been introduced to the baby leaf market. The white flower trait has been bred into modern cultivars of yellow flowering rapeseed. In baby leaf production, it is common practice to perform several cuts of the same plants, thereby harvesting regrown material. Seven white and yellow flowering annual and biennial rapeseed cultivars were harvested as baby leaves, baby leaf re-growths, and intact plants in order to investigate the content of flavonoid glycosides and hydroxycinnamic acid derivatives. The field experiment was conducted over two consecutive years to obtain seasonal differences. The yields and levels of flavonoid glycosides and hydroxycinnamic acids were higher in 2016 than 2017, due to higher temperatures and radiation. Within the growing stage, the effects of flower color, cultivar, and life cycle on flavonoid glycosides and hydroxycinnamic acids varied; however, in general, life cycle was the main influence that resulted in elevated levels of flavonoid glycosides and hydroxycinnamic acids in biennial cultivars, compared to annual cultivars. The effects of the growing stage differed between years, and were influenced by climatic conditions. In conclusion, the choice of life cycle (annual or biennial cultivars) and seasonal effects was of major influence, overruling the effect of developmental stage on the content of flavonoid glycosides and hydroxycinnamic acids.

Assessment of heterosis in two Arabidopsis thaliana common-reference mapping populations

Hybrid vigour, or heterosis, has been of tremendous importance in agriculture for the improvement of both crops and livestock. Notwithstanding large efforts to study the phenomenon of heterosis in the last decades, the identification of common molecular mechanisms underlying hybrid vigour remain rare. Here, we conducted a systematic survey of the degree of heterosis in Arabidopsis thaliana hybrids. For this purpose, two overlapping Arabidopsis hybrid populations were generated by crossing a large collection of naturally occurring accessions to two common reference lines. In these Arabidopsis hybrid populations the range of heterosis for several developmental and yield related traits was examined, and the relationship between them was studied. The traits under study were projected leaf area at 17 days after sowing, flowering time, height of the main inflorescence, number of side branches from the main stem or from the rosette base, total seed yield, seed weight, seed size and the estimated number of seeds per plant. Predominantly positive heterosis was observed for leaf area and height of the main inflorescence, whereas mainly negative heterosis was observed for rosette branching. For the other traits both positive and negative heterosis was observed in roughly equal amounts. For flowering time and seed size only low levels of heterosis were detected. In general the observed heterosis levels were highly trait specific. Furthermore, no correlation was observed between heterosis levels and the genetic distance between the parental lines. Since all selected lines were a part of the Arabidopsis genome wide association (GWA) mapping panel, a genetic mapping approach was applied to identify possible regions harbouring genetic factors causal for heterosis, with separate calculations for additive and dominance effects. Our study showed that the genetic mechanisms underlying heterosis were highly trait specific in our hybrid populations and greatly depended on the genetic background, confirming the elusive character of heterosis.

Comprehensive analysis of wintersweet flower reveals key structural genes involved in flavonoid biosynthetic pathway

Wintersweet (Chimonanthus praecox (L.)), with an over-one-thousand-years long history in cultivation, is still a popular ornamental woody plant in China. The tepals of wintersweet flower are waxy in nature and the overall color of the flower is yellow, while the inner tepals range from yellow to red, which makes it an ideal plant to study floral color formation in ornamental shrubs. In our current work, HPLC analysis revealed that the principal pigments in tepals were the metabolite of flavonoids. All the tepals were containing quercetin, kaempferol 3‑O‑rutinoside and rutin while cyanidin‑3‑O‑glucoside and cyanidin‑3‑O‑rutinoside were only found in the in the red tepals. Moreover, we found the rutin as the principal component of all the pigments revealed. As well as in this study, a reference transcriptome library constructed from two varieties H29 and H64 flower. Further, 30 proteins of flavonoid biosynthesis pathway were identified in H29 flower using proteome analysis. Based on these dataset, the flavonoid biosynthesis pathway was also speculated. After quantitative analysis of gene expression, we found that ANS act as an on-off switch for the accumulation of red pigments and had positive correlations with various steps genes of the flavonoid pathway. This expression profiling demonstrates that no gene products compete for common substrates to redirect the metabolic flux in wintersweet. It is also demonstrated that high expression of F3'H would provide sufficient content of the precursor, dihydroquercetin, for both flavonol and anthocyanin biosynthesis. The results help us to deepen and enrich the gene resource of color formation in wintersweet flower, and provide specific breeding strategies for increasing diversity of flower color.

Nitric Oxide Controls Constitutive Freezing Tolerance in Arabidopsis by Attenuating the Levels of Osmoprotectants, Stress-Related Hormones and Anthocyanins

Plant tolerance to freezing temperatures is governed by endogenous constitutive components and environmental inducing factors. Nitric oxide (NO) is one of the endogenous components that participate in freezing tolerance regulation. A combined metabolomic and transcriptomic characterization of NO-deficient nia1,2noa1-2 mutant plants suggests that NO acts attenuating the production and accumulation of osmoprotective and regulatory metabolites, such as sugars and polyamines, stress-related hormones, such as ABA and jasmonates, and antioxidants, such as anthocyanins and flavonoids. Accordingly, NO-deficient plants are constitutively more freezing tolerant than wild type plants.

Degradation of chlorophyll and synthesis of flavonols during autumn senescence-the story told by individual leaves

Autumn senescence of deciduous trees is characterized by chlorophyll degradation and flavonoid synthesis. In the present study, chlorophyll and flavonol contents were measured every morning and evening during the whole autumn with a non-destructive method from individual leaves of Sorbus aucuparia, Acer platanoides, Betula pendula and Prunus padus. In most of the studied trees, the chlorophyll content of each individual leaf remained constant until a phase of rapid degradation commenced. The fast phase lasted only ~1 week and ended with abscission. In S. aucuparia, contrary to the other species, the chlorophyll content of leaflets slowly but steadily decreased during the whole autumn, but rapid chlorophyll degradation commenced only prior to leaflet abscission also in this species. An increase in flavonols commonly accompanied the rapid degradation of chlorophyll. The results may suggest that each individual tree leaf retains its photosynthetic activity, reflected by a high chlorophyll content, until a rapid phase of chlorophyll degradation and flavonoid synthesis begins. Therefore, in studies of autumn senescence, leaves whose chlorophyll content is decreasing and leaves with summertime chlorophyll content (i.e. the leaves that have not yet started to degrade chlorophyll) should be treated separately.

Red and Blue Light Promote the Accumulation of Artemisinin in Artemisia Annua L

Artemisinin, which has been isolated from Artemisia annua L., is the most effective antimalarial drug and has saved millions of lives. In addition, artemisinin and its derivatives have anti-tumor, anti-parasitic, anti-fibrosis, and anti-arrhythmic properties, which enhances the demand for these compounds. Improving the content of artemisinin in A. annua is therefore becoming an increasing research interest, as the chemical synthesis of this metabolite is not viable. Ultraviolet B and C irradiation have been reported to improve the artemisinin content in A. annua, but they are harmful to plant growth and development. Therefore, we screened other light sources to examine if they could promote artemisinin content without affecting plant growth and development. We found that red and blue light could enhance artemisinin accumulation by promoting the expression of the genes that were involved in artemisinin biosynthesis, such as amorpha-4,11-diene synthase (ADS) and cytochrome P450 monooxygenase (CYP71AV1) genes. Thus, in addition to being the main light sources for photosynthesis, red and blue light play a key role in plant secondary metabolism, and optimizing the combination of these light might allow for the productionof artemisinin-rich A. annua.

Transcriptomic studies reveal a key metabolic pathway contributing to a well-maintained photosynthetic system under drought stress in foxtail millet (Setaria italica L.)

Drought stress is one of the most important abiotic factors limiting crop productivity. A better understanding of the effects of drought on millet (Setaria italica L.) production, a model crop for studying drought tolerance, and the underlying molecular mechanisms responsible for drought stress responses is vital to improvement of agricultural production. In this study, we exposed the drought resistant F1 hybrid, M79, and its parental lines E1 and H1 to drought stress. Subsequent physiological analysis demonstrated that M79 showed higher photosynthetic energy conversion efficiency and drought tolerance than its parents. A transcriptomic study using leaves collected six days after drought treatment, when the soil water content was about ∼20%, identified 3066, 1895, and 2148 differentially expressed genes (DEGs) in M79, E1 and H1 compared to the respective untreated controls, respectively. Further analysis revealed 17 Gene Ontology (GO) enrichments and 14 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in M79, including photosystem II (PSII) oxygen-evolving complex, peroxidase (POD) activity, plant hormone signal transduction, and chlorophyll biosynthesis. Co-regulation analysis suggested that these DEGs in M79 contributed to the formation of a regulatory network involving multiple biological processes and pathways including photosynthesis, signal transduction, transcriptional regulation, redox regulation, hormonal signaling, and osmotic regulation. RNA-seq analysis also showed that some photosynthesis-related DEGs were highly expressed in M79 compared to its parental lines under drought stress. These results indicate that various molecular pathways, including photosynthesis, respond to drought stress in M79, and provide abundant molecular information for further analysis of the underlying mechanism responding to this stress.

Recent research on the mechanism of heterosis is important for crop and vegetable breeding systems

Heterosis or hybrid vigor is a phenomenon where hybrid progeny have superior performance compared to their parental inbred lines. This is important in the use of F₁ hybrid cultivars in many crops and vegetables. However, the molecular mechanism of heterosis is not clearly understood. Gene interactions between the two genomes such as dominance, overdominance, and epistasis have been suggested to explain the increased biomass and yield. Genetic analyses of F₁ hybrids in maize, rice, and canola have defined a large number of quantitative trait loci, which may contribute to heterosis. Recent molecular analyses of transcriptomes together with reference to the epigenome of the parents and hybrids have begun to uncover new facts about the generation of heterosis. These include the identification of gene expression changes in hybrids, which may be important for heterosis, the role of epigenetic processes in heterosis, and the development of stable high yielding lines.

Accumulation of the coumarin scopolin under abiotic stress conditions is mediated by the Arabidopsis thaliana THO/TREX complex

Secondary metabolites are involved in the plant stress response. Among these are scopolin and its active form scopoletin, which are coumarin derivatives associated with reactive oxygen species scavenging and pathogen defence. Here we show that scopolin accumulation can be induced in the root by osmotic stress and in the leaf by low-temperature stress in Arabidopsis thaliana. A genetic screen for altered scopolin levels in A. thaliana revealed a mutant compromised in scopolin accumulation in response to stress; the lesion was present in a homologue of THO1 coding for a subunit of the THO/TREX complex. The THO/TREX complex contributes to RNA silencing, supposedly by trafficking precursors of small RNAs. Mutants defective in THO, AGO1, SDS3 and RDR6 were impaired with respect to scopolin accumulation in response to stress, suggesting a mechanism based on RNA silencing such as the trans-acting small interfering RNA pathway, which requires THO/TREX function.

Supercooling-Promoting (Anti-ice Nucleation) Substances

Studies on supercooling-promoting substances (SCPSs) are reviewed introducing name of chemicals, experimental conditions and the supercooling capability (SCC) in all, so far recognized, reported SCPSs and results of our original study are presented in order to totally show the functional properties of SCPSs which are known in the present state. Many kinds of substances have been identified as SCPSs that promote supercooling of aqueous solutions in a non-colligative manner by reducing the ice nucleation capability (INC) of ice nucleators (INs). The SCC as revealed by reduction of freezing temperature (°C) by SCPSs differs greatly depending on the INs. While no single SCPS that affects homogeneous ice nucleation to reduce ice nucleation point has been found, many SCPSs have been found to reduce freezing temperatures by heterogeneous ice nucleation with a large fluctuation of SCC depending on the kind of heterogeneous IN. Not only SCPSs increase the degree of SCC (°C), but also some SCPSs have additional SCC to stabilize a supercooling state for a long term to stabilize supercooling against strong mechanical disturbance and to reduce sublimation of ice crystals. The mechanisms underlying the diverse functions of SCPSs remain to be determined in future studies.

Transcriptomic studies reveal a key metabolic pathway contributing to a well-maintained photosynthetic system under drought stress in foxtail millet (Setaria italica L.)

Drought stress is one of the most important abiotic factors limiting crop productivity. A better understanding of the effects of drought on millet (Setaria italica L.) production, a model crop for studying drought tolerance, and the underlying molecular mechanisms responsible for drought stress responses is vital to improvement of agricultural production. In this study, we exposed the drought resistant F₁ hybrid, M79, and its parental lines E1 and H1 to drought stress. Subsequent physiological analysis demonstrated that M79 showed higher photosynthetic energy conversion efficiency and drought tolerance than its parents. A transcriptomic study using leaves collected six days after drought treatment, when the soil water content was about ∼20%, identified 3066, 1895, and 2148 differentially expressed genes (DEGs) in M79, E1 and H1 compared to the respective untreated controls, respectively. Further analysis revealed 17 Gene Ontology (GO) enrichments and 14 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in M79, including photosystem II (PSII) oxygen-evolving complex, peroxidase (POD) activity, plant hormone signal transduction, and chlorophyll biosynthesis. Co-regulation analysis suggested that these DEGs in M79 contributed to the formation of a regulatory network involving multiple biological processes and pathways including photosynthesis, signal transduction, transcriptional regulation, redox regulation, hormonal signaling, and osmotic regulation. RNA-seq analysis also showed that some photosynthesis-related DEGs were highly expressed in M79 compared to its parental lines under drought stress. These results indicate that various molecular pathways, including photosynthesis, respond to drought stress in M79, and provide abundant molecular information for further analysis of the underlying mechanism responding to this stress.

Rapid transcriptional and metabolic regulation of the deacclimation process in cold acclimated Arabidopsis thaliana

Background

During low temperature exposure, temperate plant species increase their freezing tolerance in a process termed cold acclimation. This is accompanied by dampened oscillations of circadian clock genes and disrupted oscillations of output genes and metabolites. During deacclimation in response to warm temperatures, cold acclimated plants lose freezing tolerance and resume growth and development. While considerable effort has been directed toward understanding the molecular and metabolic basis of cold acclimation, much less information is available about the regulation of deacclimation.

Results

We report metabolic (gas chromatography-mass spectrometry) and transcriptional (microarrays, quantitative RT-PCR) responses underlying deacclimation during the first 24 h after a shift of Arabidopsis thaliana (Columbia-0) plants cold acclimated at 4 °C back to warm temperature (20 °C). The data reveal a faster response of the transcriptome than of the metabolome and provide evidence for tightly regulated temporal responses at both levels. Metabolically, deacclimation is associated with decreasing contents of sugars, amino acids, glycolytic and TCA cycle intermediates, indicating an increased need for carbon sources and respiratory energy production for the activation of growth. The early phase of deacclimation also involves extensive down-regulation of protein synthesis and changes in the metabolism of lipids and cell wall components. Hormonal regulation appears particularly important during deacclimation, with extensive changes in the expression of genes related to auxin, gibberellin, brassinosteroid, jasmonate and ethylene metabolism. Members of several transcription factor families that control fundamental aspects of morphogenesis and development are significantly regulated during deacclimation, emphasizing that loss of freezing tolerance and growth resumption are transcriptionally highly interrelated processes. Expression patterns of some clock oscillator components resembled those under warm conditions, indicating at least partial re-activation of the circadian clock during deacclimation.

Conclusions

This study provides the first combined metabolomic and transcriptomic analysis of the regulation of deacclimation in cold acclimated plants. The data indicate cascades of rapidly regulated genes and metabolites that underlie the developmental switch resulting in reduced freezing tolerance and the resumption of growth. They constitute a large-scale dataset of genes, metabolites and pathways that are crucial during the initial phase of deacclimation. The data will be an important reference for further analyses of this and other important but under-researched stress deacclimation processes.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4126-3) contains supplementary material, which is available to authorized users.

Genetic mapping with testcrossing associations and F2:3 populations reveals the importance of heterosis in chilling tolerance at maize seedling stage

Maize seedlings are sensitive to low temperatures, and genetic mapping for chilling tolerance at the seedling stage with genetically diverse populations would facilitate the genetic improvement of this important trait. In this study, quantitative trait loci (QTL) mapping for four chilling tolerance-related traits at the seedling stage was conducted via a genome-wide association study (GWAS) with 338 testcrosses. A total of 32 significant loci and 36 stress tolerance-related candidate genes were identified, though none of them have been revealed by QTL mapping using maize inbred lines in previous reports. Moreover, expression of ten of the candidate genes was induced by chilling stress in a maize hybrid, though only a few of these genes were upregulated in its tolerant parent. These implied that heterosis might be involved in maize chilling tolerance. To further evaluate the importance of heterosis in chilling tolerance at the seedling stage, genetic mapping for chilling tolerance was conducted using an F_2:3 population derived from the two inbred lines used for the gene expression assay. Of the seven QTL revealed, six loci showed partial dominance or over-dominance effects. Results from this study demonstrate that heterosis plays an important role in chilling tolerance in maize seedlings.

Genome-wide association analysis of seedling traits in diverse Sorghum germplasm under thermal stress

BACKGROUND

Climate variability due to fluctuation in temperature is a worldwide concern that imperils crop production. The need to understand how the germplasm variation in major crops can be utilized to aid in discovering and developing breeding lines that can withstand and adapt to temperature fluctuations is more necessary than ever. Here, we analyzed the genetic variation associated with responses to thermal stresses in a sorghum association panel (SAP) representing major races and working groups to identify single nucleotide polymorphisms (SNPs) that are associated with resilience to temperature stress in a major cereal crop.

RESULTS

The SAP exhibited extensive variation for seedling traits under cold and heat stress. Genome-wide analyses identified 30 SNPs that were strongly associated with traits measured at seedling stage under cold stress and tagged genes that act as regulators of anthocyanin expression and soluble carbohydrate metabolism. Meanwhile, 12 SNPs were significantly associated with seedling traits under heat stress and these SNPs tagged genes that function in sugar metabolism, and ion transport pathways. Evaluation of co-expression networks for genes near the significantly associated SNPs indicated complex gene interactions for cold and heat stresses in sorghum. We focused and validated the expression of four genes in the network of Sb06g025040, a basic-helix-loop-helix (bHLH) transcription factor that was proposed to be involved in purple color pigmentation of leaf, and observed that genes in this network were upregulated during cold stress in a moderately tolerant line as compared to the more sensitive line.

CONCLUSION

This study facilitated the tagging of genome regions associated with variation in seedling traits of sorghum under cold and heat stress. These findings show the potential of genotype information for development of temperature resilient sorghum cultivars and further characterization of genes and their networks responsible for adaptation to thermal stresses. Knowledge on the gene networks from this research can be extended to the other cereal crops to better understand the genetic basis of resilience to temperature fluctuations during plant developmental stages.

Effects of flavonol glycosides on liposome stability during freezing and drying

Flavonoids are a large and diverse group of plant secondary metabolites that are mainly present as glycosides. They are often accumulated in response to abiotic stresses such as UV radiation, drought, cold and freezing. The most extensively studied function of flavonoids is their antioxidant activity although their importance as antioxidants in plants has been questioned. We therefore aim to study effects of flavonols on cellular stress tolerance that are independent of their antioxidant function. Here we investigate the effects of the glycosylated flavonols kaempferol-3-O-glucoside, kaempferol-7-O-glucoside, quercetin-3-O-glucoside and quercetin-3-O-rhamnoside on liposome stability after freezing and drying. Insertion of flavonols in lipid bilayers destabilized egg phosphatidylcholine (EPC) liposomes and to a lesser extent vesicles made from equal proportions of EPC and egg phosphatidylethanolamine (EPE) during a freeze-thaw cycle, while liposomes containing the unsaturated non-bilayer lipid 18:2 PE were either unaffected or slightly stabilized. In general, the kaempferol derivatives were more destabilizing for liposomes during freezing than the quercetin derivatives. Fourier-transform infrared spectroscopy revealed that all flavonols were localized in the interfacial region of the lipid bilayers, forming H-bonds with the lipid phosphate and carbonyl groups. The phase transition temperature of dry 16:0/18:1 PC (POPC) and POPC/EPE liposomes was decreased by 75°C and 55°C, respectively. Changes in the vibration bands attributed to the phenolic ring structures of the flavonols in the presence of liposomes provided further evidence of interactions of these molecules in particular with the interfacial region of the bilayers.

Flavonoids are determinants of freezing tolerance and cold acclimation in Arabidopsis thaliana

In plants from temperate climates such as Arabidopsis thaliana low, non-freezing temperatures lead to increased freezing tolerance in a process termed cold acclimation. This process is accompanied by massive changes in gene expression and in the content of primary metabolites and lipids. In addition, most flavonols and anthocyanins accumulate upon cold exposure, along with most transcripts encoding transcription factors and enzymes of the flavonoid biosynthetic pathway. However, no evidence for a functional role of flavonoids in plant freezing tolerance has been shown. Here, we present a comprehensive analysis using qRT-PCR for transcript, LC-MS for flavonoid and GC-MS for primary metabolite measurements, and an electrolyte leakage assay to determine freezing tolerance of 20 mutant lines in two Arabidopsis accessions that are affected in different steps of the flavonoid biosynthetic pathway. This analysis provides evidence for a functional role of flavonoids in plant cold acclimation. The accumulation of flavonoids in the activation tagging mutant line pap1-D improved, while reduced flavonoid content in different knock-out mutants impaired leaf freezing tolerance. Analysis of the different knock-out mutants suggests redundancy of flavonoid structures, as the lack of flavonols or anthocyanins could be compensated by other compound classes.

Fortune telling: metabolic markers of plant performance

BACKGROUND

In the last decade, metabolomics has emerged as a powerful diagnostic and predictive tool in many branches of science. Researchers in microbes, animal, food, medical and plant science have generated a large number of targeted or non-targeted metabolic profiles by using a vast array of analytical methods (GC-MS, LC-MS, 1H-NMR….). Comprehensive analysis of such profiles using adapted statistical methods and modeling has opened up the possibility of using single or combinations of metabolites as markers. Metabolic markers have been proposed as proxy, diagnostic or predictors of key traits in a range of model species and accurate predictions of disease outbreak frequency, developmental stages, food sensory evaluation and crop yield have been obtained.

AIM OF REVIEW

(i) To provide a definition of plant performance and metabolic markers, (ii) to highlight recent key applications involving metabolic markers as tools for monitoring or predicting plant performance, and (iii) to propose a workable and cost-efficient pipeline to generate and use metabolic markers with a special focus on plant breeding.

KEY MESSAGE

Using examples in other models and domains, the review proposes that metabolic markers are tending to complement and possibly replace traditional molecular markers in plant science as efficient estimators of performance.

Arabidopsis thaliana G2-LIKE FLAVONOID REGULATOR and BRASSINOSTEROID ENHANCED EXPRESSION1 are low-temperature regulators of flavonoid accumulation

Flavonoid synthesis is predominantly regulated at the transcriptional level through the MYB-basic helix-loop-helix (bHLH)-WD40 (MBW) (MYB: transcription factor of the myeloblastosis protein family, WD40: tanscription factor with a short structural motif of 40 amino acids which terminates in an aspartic acid-tryptophan dipeptide) complex, and responds to both environmental and developmental stimuli. Although the developmental regulation of flavonoid accumulation in Arabidopsis thaliana has been examined in great detail, the response of the flavonoid synthesis pathway to abiotic stress (particularly low temperature) remains unclear. A screen of a Dissociation element (Ds) transposon-induced mutation collection identified two lines which exhibited an altered profile of phenylpropanoid accumulation following exposure to low-temperature stress. One of the mutated genes (BRASSINOSTEROID ENHANCED EXPRESSION1 (BEE1)) encoded a brassinosteroid enhanced expression transcription factor, while the other (G2-LIKE FLAVONOID REGULATOR (GFR)) encoded a G2-like flavonoid regulator. Phenylpropanoid-targeted analysis was performed using high-performance LC-MS, and gene expression analysis using quantitative reverse transcription-PCR. In both mutants, the accumulation of quercetins and scopolin was reduced under low-temperature growing conditions, whereas that of anthocyanin was increased. BEE1 and GFR were both shown to negatively regulate anthocyanin accumulation by inhibiting anthocyanin synthesis genes via the suppression of the bHLH (TRANSPARENT TESTA8 (TT8) and GLABROUS3 (GL3)) and/or the MYB (PRODUCTION OF ANTHOCYANIN PIGMENTS2 (PAP2)) components of the MBW complex. Our results provide new insight into the regulatory control of phenylpropanoid metabolism at low temperatures, and reveal that BEE1 and GFR act as important components of the signal transduction chain.