Flavonoids modify root growth and modulate expression of SHORT-ROOT and HD-ZIP III

Transcription factor NtMYB59 targets NtMYB12 to negatively regulate the biosynthesis of polyphenols in Nicotiana tabacum

MYB12 is a key regulator that has been shown to promote the accumulation of various phenylpropanoid compounds in plants. However, the regulation of MYB12 gene is largely unknown. In this study, we found that overexpression of the NtMYB59 gene significantly inhibited the accumulation of chlorogenic acid (CGA), flavonols, and anthocyanins in tobacco, while knock-down and knock-out of NtMYB59 significantly increased the contents of these polyphenol compounds. Transcriptome analysis between WT and NtMYB59-OE plants revealed several differentially expressed genes (DEGs) encoding crucial enzymes in the phenylpropanoid pathway and the transcription factor NtMYB12. ChIP-seq assay further indicated that NtMYB12 might be a direct target of NtMYB59. Subsequent yeast one-hybrid, electrophoretic mobility shift assay, and Dual-Luciferase assays confirmed that NtMYB59 directly binds to the promoter of NtMYB12 to inhibit its expression. Moreover, loss-function of NtMYB59 significantly promoted the accumulation of flavonols and anthocyanins in ntmyb59, but their contents in ntmyb59/ntmyb12 double mutants were significantly lower than that of WT and ntmyb59 plants, indicating that the regulation of NtMYB59 on flavonoids biosynthesis depends on the activity of NtMYB12. Our study revealed that NtMYB59 regulates the expression of NtMYB12, and provided new potential strategies for modulating phenylpropanoids biosynthesis in tobacco.

Integrative proteome and metabolome unveil the central role of IAA alteration in axillary bud development following topping in tobacco

Axillary bud is an important aspect of plant morphology, contributing to the final tobacco yield. However, the mechanisms of axillary bud development in tobacco remain largely unknown. To investigate this aspect of tobacco biology, the metabolome and proteome of the axillary buds before and after topping were compared. A total of 569 metabolites were differentially abundant before and 1, 3, and 5 days after topping. KEGG analyses further revealed that the axillary bud was characterized by a striking enrichment of metabolites involved in flavonoid metabolism, suggesting a strong flavonoid biosynthesis activity in the tobacco axillary bud after topping. Additionally, 9035 differentially expressed proteins (DEPs) were identified before and 1, 3, and 5 days after topping. Subsequent GO and KEGG analyses revealed that the DEPs in the axillary bud were enriched in oxidative stress, hormone signal transduction, MAPK signaling pathway, and starch and sucrose metabolism. The integrated proteome and metabolome analysis revealed that the indole-3-acetic acid (IAA) alteration in buds control dormancy release and sustained growth of axillary bud by regulating proteins involved in carbohydrate metabolism, amino acid metabolism, and lipid metabolism. Notably, the proteins related to reactive oxygen species (ROS) scavenging and flavonoid biosynthesis were strongly negatively correlated with IAA content. These findings shed light on a critical role of IAA alteration in regulating axillary bud outgrowth, and implied a potential crosstalk among IAA alteration, ROS homeostasis, and flavonoid biosynthesis in tobacco axillary bud under topping stress, which could improve our understanding of the IAA alteration in axillary bud as an important regulator of axillary bud development.

Allelochemicals: A source for developing economically and environmentally friendly plant growth regulators

Allelochemicals are specific secondary metabolites that can exhibit autotoxicity by inhibiting the growth of the same plant species that produced them. These metabolites have been found to affect various physical processes during plant growth and development, including inhibition of seed germination, photosynthesis, respiration, root growth, and nutrient uptake, with diverse mechanisms involving cell destruction, oxidative homeostasis and photoinhibition. In some cases, allelochemicals can also have positive effects on plant growth and development. In addition to their ecological significance, allelochemicals also possess potential as plant growth regulators (PGRs) due to their extensive physiological effects. However, a comprehensive summary of the development and applications of allelochemicals as PGRs is currently lacking. In this review, we present an overview of the sources and categories of allelochemicals, discuss their effects and the underlying mechanisms on plant growth and development. We showcase numerous instances of key phytohormonal allelochemicals and non-phytohormonal allelochemicals, highlighting their potential as candidates for the development of PGRs. This review aims to provide a theoretical basis for the development of economical, safe and effective PGRs utilizing allelochemicals, and emphasizes the need for further research in this area.

Flavonols affect the interrelated glucosinolate and camalexin biosynthetic pathways in Arabidopsis thaliana

Flavonols are structurally and functionally diverse biomolecules involved in plant biotic and abiotic stress tolerance, pollen development, and inhibition of auxin transport. However, their effects on global gene expression and signaling pathways are unclear. To explore the roles of flavonol metabolites in signaling, we performed comparative transcriptome and targeted metabolite profiling of seedlings from the flavonol-deficient Arabidopsis loss-of-function mutant flavonol synthase1 (fls1) with and without exogenous supplementation of flavonol derivatives (kaempferol, quercetin, and rutin). RNA-seq results indicated that flavonols modulate various biological and metabolic pathways, with significant alterations in camalexin and aliphatic glucosinolate synthesis. Flavonols negatively regulated camalexin biosynthesis but appeared to promote the accumulation of aliphatic glucosinolates via transcription factor-mediated up-regulation of biosynthesis genes. Interestingly, upstream amino acid biosynthesis genes involved in methionine and tryptophan synthesis were altered under flavonol deficiency and exogenous supplementation. Quercetin treatment significantly up-regulated aliphatic glucosinolate biosynthesis genes compared with kaempferol and rutin. In addition, expression and metabolite analysis of the transparent testa7 mutant, which lacks hydroxylated flavonol derivatives, clarified the role of quercetin in the glucosinolate biosynthesis pathway. This study elucidates the molecular mechanisms by which flavonols interfere with signaling pathways, their molecular targets, and the multiple biological activities of flavonols in plants.

Water extract of Fagopyrum dibotrys (D. Don) Hara straw increases selenium accumulation in peach seedlings under selenium-contaminated soil

To promote the selenium (Se) uptakes in fruit trees under Se-contaminated soil, the effects of water extract of Fagopyrum dibotrys (D. Don) Hara straw on the Se accumulation in peach seedlings under selenium-contaminated soil were studied. The results showed that the root biomass, chlorophyll content, activities of antioxidant enzymes, and soluble protein content of peach seedlings were increased by the F. dibotrys straw extract. The different forms of Se (total Se, inorganic Se, and organic Se) were also increased in peach seedlings following treatment with the F. dibotrys straw extract. The highest total shoot Se content was treated by the 300-fold dilution of F. dibotrys straw, which was 30.87% higher than the control. The F. dibotrys straw extract also increased the activities of adenosine triphosphate sulfurase (ATPS), and adenosine 5'-phosphosulfate reductase (APR) in peach seedlings, but decreased the activity of serine acetyltransferase (SAT). Additionally, correlation and grey relational analyses revealed that chlorophyll a content, APR activity, and root biomass were closely associated with the total shoot Se content. Overall, this study shows that the water extract of F. dibotrys straw can promote Se uptake in peach seedlings, and 300-fold dilution is the most suitable concentration.

Aztreonam is a novel chemical inducer that promotes Agrobacteium transformation and lateral root development in soybean

Agrobacterium-mediated soybean transformation is the simplest method of gene transfer. However, the low transformation due to the intractable nature of soybean genotypes hinders this process. The use of biochemicals (acetosyringone, cinnamic acid, flavonoids, etc.) plays an important role in increasing soybean transformation. These biochemicals induce chemotaxis and virulence gene activation during the infection process. Here we identified a biochemical, aztreonam (a monobactam), for high agrobacterium-mediated transformation in soybean. The soybean explants from three genotypes were inoculated with A. tumefaciens (GV3101) harboring the pMDC32 vector containing hpt or the GmUbi-35S-GUS vector containing the GUS gene during two separate events. High transient GUS expression was obtained during cotyledon explant culture on MS media supplemented with 2.5 mg/L aztreonam. The aztreonam-treated explants showed high efficiency in transient and stable transformation as compared to the untreated control. The transformation of aztreonam-treated explants during seed imbibition resulted in an average of 21.1% as compared to 13.2% in control by using the pMDC32 vector and 28.5 and 20.7% while using the GUS gene cassette, respectively. Based on these findings, the metabolic analysis of the explant after aztreonam treatment was assessed. The high accumulation of flavonoids was identified during an untargeted metabolic analysis. The quantification results showed a significantly high accumulation of the four compounds, i.e., genistein, apigenin, naringenin, and genistin, in cotyledon explants after 18 hours of aztreonam treatment. Alongside this, aztreonam also had some surprising effects on root elongation and lateral root formation when compared to indole-3-butyric acid (IBA). Our findings were limited to soybeans. However, the discovery of aztreonam and its effect on triggering flavonoids could lead to the potential role of aztreonam in the agrobacterium-mediated transformation of different crops.

Advances in the study of the function and mechanism of the action of flavonoids in plants under environmental stresses

MAIN CONCLUSION

This review summarizes the anti-stress effects of flavonoids in plants and highlights its role in the regulation of polar auxin transport and free radical scavenging mechanism. As secondary metabolites widely present in plants, flavonoids play a vital function in plant growth, but also in resistance to stresses. This review introduces the classification, structure and synthetic pathways of flavonoids. The effects of flavonoids in plant stress resistance were enumerated, and the mechanism of flavonoids in plant stress resistance was discussed in detail. It is clarified that plants under stress accumulate flavonoids by regulating the expression of flavonoid synthase genes. It was also determined that the synthesized flavonoids are transported in plants through three pathways: membrane transport proteins, vesicles, and bound to glutathione S-transferase (GST). At the same time, the paper explores that flavonoids regulate polar auxin transport (PAT) by acting on the auxin export carrier PIN-FORMED (PIN) in the form of ATP-binding cassette subfamily B/P-glycoprotein (ABCB/PGP) transporter, which can help plants to respond in a more dominant form to stress. We have demonstrated that the number and location of hydroxyl groups in the structure of flavonoids can determine their free radical scavenging ability and also elucidated the mechanism by which flavonoids exert free radical removal in cells. We also identified flavonoids as signaling molecules to promote rhizobial nodulation and colonization of arbuscular mycorrhizal fungi (AMF) to enhance plant-microbial symbiosis in defense to stresses. Given all this knowledge, we can foresee that the in-depth study of flavonoids will be an essential way to reveal plant tolerance and enhance plant stress resistance.

Evaluation of allelopathic effects of Parthenium hysterophorus L. methanolic extracts on some selected plants and weeds

Herbicides made from natural molecules are cost-effective and environmentally friendly alternatives to synthetic chemical herbicides for controlling weeds in the crop field. In this context, an investigation was carried out to ascertain the allelopathic potential of Parthenium hysterophorus L. as well as to identify its phenolic components which are responsible for the allelopathic effect. During the observation, the rate of germination and seedlings' growth of Vigna subterranea (L.) Verdc, Raphanus sativus (L.) Domin, Cucurbita maxima Duchesne., Cucumis sativus L., Solanum lycopersicum L., Capsicum frutescens L., Zea mays L., Abelmoschus esculentus (L.) Moench, Daucus carota L., Digitaria sanguinalis (L.) Scop and Eleusine indica (L.) Gaertn were investigated by using methanol extracts, isolated from leaf, stem and flower of P. hysterophorus. Six concentrations (i.e., 25, 50, 75, 100, and 150 g L-1) of methanol extracts were isolated from P. hysterophorus leaf, stem and flower were compared to the control (distilled water). It was also observed that the concentration of methanol extracts (isolated from P. hysterophorus leaf, stem, and flower) while increased, the rate of seed germination and seedling growth of both selected crops and weeds decreased drastically, indicating that these methanol extracts have allelopathic potential. The allelopathic potential of P. hysterophorus leaf extraction (811) was found higher than the extraction of the stem (1554) and flower (1109), which is confirmed by EC50 values. The principal component analysis (PCA) was also used to re-validate the allelopathic potentiality of these methanol extracts and confirmed that Raphanus sativus, Solanum lycopersicum, Capsicum frutescens, Abelmoschus esculentus, Daucus carota, Digitaria sanguinalis, and Eleusine indica were highly susceptible to allelochemicals of P. hysterophorus. Besides these, the LC-MS analysis also revealed that the P. hysterophorus leaf extract contained 7 phenolic compounds which were responsible for the inhibition of tested crops and weeds through allelopathic effect. The results of the current study revealed that the leaf of P. hysterophorus is a major source of allelopathic potential on crops and weeds and which could be used as a valuable natural herbicide in the future for the sustainability of crop production through controlling weeds.

Phytotoxicity and allelopathic potential of Juglans regia L. leaf extract

Implementation of plant extracts that are rich in phytochemicals and have the allelopathic potential for weed management could help reduce the use of chemical herbicides. The present study investigated the herbicidal potential of walnut (Juglans regia L.) leaf extract (WLE) against two weeds, Amaranthus retroflexus L. and Chenopodium album L., by testing in vitro their seed germination and seedling growth, and then evaluated in vivo the oxidative stress of potted plants. The effects of the walnut leaf extract were also tested on maize (Zea mays L.) to eliminate possible negative impacts on a cultivated plant. Total phenolic acids and total flavonoid content in the extract were determined in prior bioassays, followed by separation and analysis of flavonoids and phenolic acids by high-performance liquid chromatography (HPLC). Phytochemical analysis revealed that the obtained extract was notably rich in phenolic compounds, while HPLC analysis confirmed the presence of (+)-catechin, luteolin, myricetin, rutin, (-)-epicatechin, genistin, protocatechuic acid, and caffeic acid as major extract components. The results obtained in bioassays revealed a significant negative impact of the walnut leaf extract on germination and seedling growth of the tested weeds, as well as significant oxidative stress in weeds grown in pots. Although it affected the maize seedling growth in vitro similar to the tested weeds, maize germination was less sensitive to treatment, and the extract did not have a significant negative impact in terms of oxidative stress in maize plants grown in pots. The findings show that walnut leaf extract may have a promising role in replacing chemical herbicides in maize.

Improved seed germination and plant growth mediated by compounds synthesized by endophytic Aspergillus niger (isolate 29) isolated from Albizia lebbeck (L.) Benth

Plant-microbe interactions are remarkably diverse and dynamic. These interactions can be in the form of endophytic association. Colonization of endophytic microflora in crop plants improves crop health leading to crop enhancement. They stimulate the overall growth of plants by facilitating nutrient uptake and regulating various hormones. This eventually improves the plant biomass and grain yield. Owing to the assistance of the endophytes to the host plants, augmentation of crop plants with potential fungal endophytes or their extracted bioactive compound can upsurge the overall crop production and provide promising solutions for environmentally sustainable agriculture. In this light, the present study deals with the prospects of bioactive metabolites produced by endophytic fungi in Albizia lebbeck (L.) Benth, a medicinal native plant of Rajasthan. The metabolomic analysis of a partially purified extract of Aspergillus niger (isolate 29) showed the presence of a total of 919 compounds using UHPLC-MS/MS. The metabolic pathway analysis revealed that these compounds were influencing super pathway of gibberellin and isoflavonoid biosynthesis. Significant increase in seed germination percentage (73-93%), seed vigour index (834.44-1498.21) and germination index (2.54-3.67 seeds/day) was found in treated seeds compared to untreated. There was a significant improvement in root (45-185%) and shoot length (215-295%) of wheat, barley and millet and a significant increase in root number (38-97%) in wheat and barley. Positive correlation was observed in the growth parameters of all the crops upon treatment. Overall, the results indicated that the partially purified fraction of A. niger (isolate 29) improved seed germination and promoted plant growth in cash crops. The results emphasize towards the importance of secondary metabolites in seed germination and enhancement of plant growth. These results also suggest a probable mutualistic role of endophyte with the host plant.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03332-x.

Mapping and functional characterization of the tomato spotted wilt virus resistance gene SlCHS3 in Solanum lycopersicum

Tomato spotted wilt virus (TSWV) poses a serious threat to tomato (Solanum lycopersicum) production. In this study, tomato inbred line YNAU335 was developed without the Sw-5 locus, which confers resistance or immunity to TSWV (absence of infection). Genetic analysis demonstrated that immunity to TSWV was controlled by a dominant nuclear gene. The candidate genes were mapped into a 20-kb region in the terminal of the long arm of chromosome 9 using bulk segregant analysis and linkage analysis. In this candidate region, a chalcone synthase-encoding gene (SlCHS3) was identified as a strong candidate gene for TSWV resistance. Silencing SlCHS3 reduced flavonoid synthesis, and SlCHS3 overexpression increased flavonoid content. The increase in flavonoids improved TSWV resistance in tomato. These findings indicate that SlCHS3 is indeed involved in the regulation of flavonoid synthesis and plays a significant role in TSWV resistance of YNAU335. This could provide new insights and lay the foundation for analyzing TSWV resistance mechanisms.

Supplementary information

The online version contains supplementary material available at 10.1007/s11032-022-01325-5.

Reduction of Weed Growth under the Influence of Extracts and Metabolites Isolated from Miconia spp

Weeds pose a problem, infesting areas and imposing competition and harvesting difficulties in agricultural systems. Studies that provide the use of alternative methods for weed control, in order to minimize negative impacts on the environment, have intensified. Native flora represents a source of unexplored metabolites with multiple applications, such as bioherbicides. Therefore, we aimed to carry out a preliminary phytochemical analysis of crude extracts and fractions of Miconia auricoma and M. ligustroides and to evaluate these and the isolated metabolites phytotoxicity on the growth of the target species. The growth bioassays were conducted with Petri dishes with lettuce, morning glory, and sourgrass seeds incubated in germination chambers. Phytochemical analysis revealed the presence of flavonoids, isolated myricetin, and a mixture of quercetin and myricetin. The results showed that seedling growth was affected in a dose-dependent manner, with the root most affected and the seedlings of the lettuce, morning glory, and sourgrass as the most sensitive species, respectively. Chloroform fractions and myricetin were the most inhibitory bioassays evaluated. The seedlings showed structural changes, such as yellowing, nonexpanded cotyledons, and less branched roots. These results indicate the phytotoxic potential of Miconia allelochemicals, since there was the appearance of abnormal seedlings and growth reduction.

ADH2/GSNOR1 is a key player in limiting genotoxic damage mediated by formaldehyde and UV-B in Arabidopsis

Maintenance of genome stability is an essential requirement for all living organisms. Formaldehyde and UV-B irradiation cause DNA damage and affect genome stability, growth and development, but the interplay between these two genotoxic factors is poorly understood in plants. We show that Arabidopsis adh2/gsnor1 mutant, which lacks alcohol dehydrogenase 2/S-nitrosoglutathione reductase 1 (ADH2/GSNOR1), are hypersensitive to low fluence UV-B irradiation or UV-B irradiation-mimetic chemicals. Although the ADH2/GSNOR1 enzyme can act on different substrates, notably on S-hydroxymethylglutathione (HMG) and S-nitrosoglutathione (GSNO), our study provides several lines of evidence that the sensitivity of gsnor1 to UV-B is caused mainly by UV-B-induced formaldehyde accumulation rather than other factors such as alteration of the GSNO concentration. Our results demonstrate an interplay between formaldehyde and UV-B that exacerbates genome instability, leading to severe DNA damage and impaired growth and development in Arabidopsis, and show that ADH2/GSNOR1 is a key player in combating these effects.

Three Active Phytotoxic Compounds from the Leaves of Albizia richardiana (Voigt.) King and Prain for the Development of Bioherbicides to Control Weeds

The global population is increasing day by day. To meet the food demand for such a huge number of people, crop production must increase without damaging the environment, and to prevent synthetic chemical herbicides from polluting the environment, controlling weeds using bioherbicides is essential. Accordingly, using phytotoxic substances obtained from plants for biological weed management has attracted attention. The plant Albizia richardiana possesses phytotoxic compounds that have been previously recorded. Hence, we have conducted this research to characterize more phytotoxic compounds in Albizia richardiana. Aqueous methanolic extracts of Albizia richardiana plant significantly restricted the growth of the examined plants lettuce and Italian ryegrass in a species- and concentration-dependent manner. Three active phytotoxic compounds were isolated through various chromatographic methods and identified as compound 1, 2, and 3. Compound 3 exhibited stronger phytotoxic potentials than the other two compounds and significantly suppressed the growth of Lepidium sativum (cress). The concentration of the compounds required for 50% growth reduction (I₅₀ value) of the Lepidium sativum seedlings ranged between 0.0827 to 0.4133 mg/mL. The results suggest that these three phytotoxic compounds might contribute to the allelopathic potential of Albizia richardiana.

The role of quercetin in plants

Flavonoids are a special category of hydroxylated phenolic compounds having an aromatic ring structure. Quercetin is aspecial subclass of flavonoid. It is a bioactive natural compound built upon the flavon structure nC6(ring A)-C3(ring C)-C6(ring B). Quercetin facilitates several plant physiological processes, such as seed germination, pollen growth, antioxidant machinery, and photosynthesis, as well as induces proper plant growth and development. Quercetin is a powerful antioxidant, so it potently provides plant tolerance against several biotic and abiotic stresses. This review highlights quercetin's role in increasing several physiological and biochemical processes under stress and non-stress environments. Additionally, this review briefly assesses quercetin's role in mitigating biotic and abiotic stresses (e.g., salt, heavy metal, and UV stress). The biosynthesis of flavonoids, their signaling pathways, and quercetin's role in plant signaling are also discussed.

HD-ZIP Gene Family: Potential Roles in Improving Plant Growth and Regulating Stress-Responsive Mechanisms in Plants

Exploring the molecular foundation of the gene-regulatory systems underlying agronomic parameters or/and plant responses to both abiotic and biotic stresses is crucial for crop improvement. Thus, transcription factors, which alone or in combination directly regulated the targeted gene expression levels, are appropriate players for enlightening agronomic parameters through genetic engineering. In this regard, homeodomain leucine zipper (HD-ZIP) genes family concerned with enlightening plant growth and tolerance to environmental stresses are considered key players for crop improvement. This gene family containing HD and LZ domain belongs to the homeobox superfamily. It is further classified into four subfamilies, namely HD-ZIP I, HD-ZIP II, HD-ZIP III, and HD-ZIP IV. The first HD domain-containing gene was discovered in maize cells almost three decades ago. Since then, with advanced technologies, these genes were functionally characterized for their distinct roles in overall plant growth and development under adverse environmental conditions. This review summarized the different functions of HD-ZIP genes in plant growth and physiological-related activities from germination to fruit development. Additionally, the HD-ZIP genes also respond to various abiotic and biotic environmental stimuli by regulating defense response of plants. This review, therefore, highlighted the various significant aspects of this important gene family based on the recent findings. The practical application of HD-ZIP biomolecules in developing bioengineered plants will not only mitigate the negative effects of environmental stresses but also increase the overall production of crop plants.

Phytochemical Constituents and Allelopathic Potential of Parthenium hysterophorus L. in Comparison to Commercial Herbicides to Control Weeds

The allelopathic effect of various concentrations (0, 6.25, 12.5, 50 and 100 g L^-1) of Parthenium hysterophorus methanol extract on Cyperus iria was investigated under laboratory and glasshouse conditions. No seed germination was recorded in the laboratory when P. hysterophorus extract was applied at 50 g L^-1. In the glasshouse, C. iria was mostly injured by P. hysterophorus extract at 100 g L^-1. The phytochemical constituents of the methanol extract of P. hysterophorus were analyzed by LC-ESI-QTOF-MS=MS. The results indicated the presence of phenolic compounds, terpenoids, alkaloids, amino acids, fatty acids, piperazines, benzofuran, indole, amines, azoles, sulfonic acid and other unknown compounds in P. hysterophorus methanol extract. A comparative study was also conducted between P. hysterophorus extract (20, 40 and 80 g L^-1) with a synthetic herbicide (glyphosate and glufosinate ammonium at 2 L ha^-1) as a positive control and no treatment (negative control) on Ageratumconyzoides, Oryzasativa and C. iria. The growth and biomass of test weeds were remarkably inhibited by P. hysterophorus extract. Nevertheless, no significant difference was obtained when P. hysterophorus extract (80 g L^-1) and synthetic herbicides (glyphosate and glufosinate ammonium) were applied on A.conyzoides.

Integrating transcriptome, co-expression and QTL-seq analysis reveals that primary root growth in maize is regulated via flavonoid biosynthesis and auxin signal transduction

The primary root is critical for early seedling growth and survival. To understand the molecular mechanisms governing primary root development, we performed a dynamic transcriptome analysis of two maize (Zea mays) inbred lines with contrasting primary root length at nine time points over a 12-day period. A total of 18 702 genes were differentially expressed between two lines or different time points. Gene enrichment, phytohormone content determination, and metabolomics analysis showed that auxin biosynthesis and signal transduction, as well as the phenylpropanoid and flavonoid biosynthesis pathways, were associated with root development. Co-expression network analysis revealed that eight modules were associated with lines/stages, as well as primary or lateral root length. In root-related modules, flavonoid metabolism accompanied by auxin biosynthesis and signal transduction constituted a complex gene regulatory network during primary root development. Two candidate genes (rootless concerning crown and seminal roots, rtcs and Zm00001d012781) involved in auxin signaling and flavonoid biosynthesis were identified by co-expression network analysis, QTL-seq and functional annotation. These results increase our understanding of the regulatory network controlling the development of primary and lateral root length, and provide a valuable genetic resource for improvement of root performance in maize.

Asteraceae family: a review of its allelopathic potential and the case of Acmella oleracea and Sphagneticola trilobata

Abstract Asteraceae family is as an interesting target for researching natural alternatives for crop protection. Many species from this family grow as weeds, and some of them can influence the development of other species by the allelopathy phenomenon. This paper aimed to review the literature for the main genera and species of the Asteraceae family with allelopathic or phytotoxic potential, as well as the classes of secondary metabolites present in this family and responsible for such activity. Artemisia, Ambrosia, Bellis, Bidens, Helianthus and Tagetes were identified as the main genera with phytotoxic or allelopathic activity. Among the secondary metabolites from this family, terpenes, polyacetylenes, saponins, sesquiterpene lactones, phenolic acids and flavonoids were described as responsible for inhibiting the development of other species. In addition, the phytotoxic potential of Acmella oleracea and Sphagneticola trilobata against the weeds Calopogonium mucunoides. and Ipomoea purpurea was described for the first time. At 0.2 mg/mL, crude extract and fractions of A. oleracea inhibited above 60% of C. mucunoides root growth. Hydroalcoholic extract and fractions of S. trilobata, except hexane, significantly affected I. purpurea root growth, ranging from 38 ± 14% to 59 ± 8% of inhibitory effect at different concentrations (0.19 mg/mL to 1.13 mg/mL).

Metabolome and Transcriptome Association Analysis Reveals Regulation of Flavonoid Biosynthesis by Overexpression of LaMIR166a in Larix kaempferi (Lamb.) Carr

Somatic embryogenesis is an ideal model process for studying early plant development. Embryonic cell lines of Larix kaempferi (Lamb.) Carr overexpressing LaMIR166a were obtained in our previous study. Here, a combination of de novo transcriptomics and extensively targeted metabolomics was used to study the transcriptional profiles and metabolic changes in wild-type and LaMIR166a-overexpressed embryonic cell lines. A total of 459 metabolites were found in the wild-type and transgenic cell lines. Compared to those in the wild-type cell lines, transcripts and metabolites were significantly altered in the LaMIR166a-overexpressed cell lines. Among differentially expressed genes (DEGs), phenylalanine and flavonoid synthesis genes were significantly enriched, and among differentially accumulated metabolites (DAMs), phenolic acids and flavonoids accumulated in particularly high amounts. Thus, the flavonoid biosynthetic pathway seems to be the most abundant pathway in response to LaMIR166a overexpression. Based on the Kyoto Encyclopedia of Genes and Genomes database, the association analysis of metabolome and transcriptome data showed that flavonoid biosynthesis and plant hormone signal transduction processes were significantly changed in miR166a-overexpression lines, suggesting that miR166 might be involved in these processes. The present study identified a number of potential metabolites associated with LaMIR166a overexpression, providing a significant foundation for a better understanding of the regulatory mechanisms underlying miR166.

Canavanine Increases the Content of Phenolic Compounds in Tomato (Solanum lycopersicum L.) Roots

Canavanine (CAN) is a nonproteinogenic amino acid, and its toxicity comes from its utilization instead of arginine in many cellular processes. As presented in previous experiments, supplementation of tomato (Solanum lycopersicum L.) with CAN led to decreased nitric oxide (NO) level and induced secondary oxidative stress. CAN improved total antioxidant capacity in roots, with parallel inhibition of enzymatic antioxidants. The aim of this work was to determine how CAN-dependent limitation of NO emission and reactive oxygen species overproduction impact content, localization, and metabolism of phenolic compounds (PCs) in tomato roots. Tomato seedlings were fed with CAN (10 and 50 µM) for 24 or 72 h. Inhibition of root growth due to CAN supplementation correlated with increased concentration of total PCs; CAN (50 µM) led to the homogeneous accumulation of PCs all over the roots. CAN increased also flavonoids content in root tips. The activity of polyphenol oxidases and phenylalanine ammonia-lyase increased only after prolonged treatment with 50 µM CAN, while expressions of genes encoding these enzymes were modified variously, irrespectively of CAN dosage and duration of the culture. PCs act as the important elements of the cellular antioxidant system under oxidative stress induced by CAN.

Four HD-ZIPs are involved in banana fruit ripening by activating the transcription of ethylene biosynthetic and cell wall-modifying genes

Four MaHDZs are possibly involved in banana fruit ripening by activating the transcription of genes related to ethylene biosynthesis and cell wall degradation, such as MaACO5, MaEXP2, MaEXPA10, MaPG4 and MaPL4. The homeodomain-leucine zipper (HD-ZIP) proteins represent plant-specific transcription factors, which contribute to various plant physiological processes. However, little information is available regarding the association of HD-ZIPs with banana fruit ripening. In this study, we identified a total of 96 HD-ZIP genes in banana genome, which were divided into four different groups consisting of 35, 31, 9 and 21 members in the I, II, III and IV subfamilies, respectively. The expression patterns of MaHDZ genes during fruit ripening showed that MaHDZI.19, MaHDZI.26, MaHDZII.4 and MaHDZII.7 were significantly up-regulated in the ripening stage and thus suggested to be potential regulators of banana fruit ripening. Furthermore, MaHDZI.19, MaHDZI.26, MaHDZII.4 and MaHDZII.7 were found to localize exclusively in the nucleus and exhibit transcriptional activation capacities. Importantly, MaHDZI.19, MaHDZI.26, MaHDZII.4 and MaHDZII.7 stimulated the transcription of several ripening-related genes including MaACO5 related to ethylene biosynthesis, MaEXP2, MaEXPA10, MaPG4 and MaPL4 were associated with cell wall degradation, through directly binding to their promoters. Taken together, our findings expand the functions of HD-ZIP transcription factors and identify four MaHDZs likely involved in regulating banana fruit ripening by activating the expression of genes related to ethylene biosynthesis and cell wall modification, which may have potential application in banana molecular breeding.

Gene Expression Profiles and microRNA Regulation Networks in Tiller Primordia, Stem Tips, and Young Spikes of Wheat Guomai 301

Tillering and spike differentiation are two key events for wheat (Triticum aestivum L.). A study on the transcriptomes and microRNA group profiles of wheat at the two key developmental stages will bring insight into the molecular regulation mechanisms. Guomai 301 is a representative excellent new high yield wheat cultivar in the Henan province in China. The transcriptomes and microRNA (miRNA) groups of tiller primordia (TPs), stem tips (STs), and young spikes (YSs) in Guomai 301 were compared to each other. A total of 1741 tillering specifically expressed and 281 early spikes differentiating specifically expressed differentially expressed genes (DEGs) were identified. Six major expression profile clusters of tissue-specific DEGs for the three tissues were classified by gene co-expression analysis using K-means cluster. The ribosome (ko03010), photosynthesis-antenna proteins (ko00196), and plant hormone signal transduction (ko04075) were the main metabolic pathways in TPs, STs, and YSs, respectively. Similarly, 67 TP specifically expressed and 19 YS specifically expressed differentially expressed miRNAs were identified, 65 of them were novel. The roles of 3 well known miRNAs, tae-miR156, tae-miR164, and tae-miR167a, in post-transcriptional regulation were similar to that of other researches. There were 651 significant negative miRNA-mRNA interaction pairs in TPs and YSs, involving 63 differentially expressed miRNAs (fold change > 4) and 416 differentially expressed mRNAs. Among them 12 key known miRNAs and 16 novel miRNAs were further analyzed, and miRNA-mRNA regulatory networks during tillering and early spike differentiating were established.

Salinity-associated microRNAs and their potential roles in mediating salt tolerance in rice colonized by the endophytic root fungus Piriformospora indica

Piriformospora indica (P. indica), an endophytic root fungus, supports the growth and enhanced tolerance of plants to biotic and abiotic stresses. Several recent studies showed the significant role of small RNA (sRNA) molecules including microRNAs (miRNAs) in plant adaption to environmental stress, but little is known concerning the symbiosis-mediated salt stress tolerance regulated at miRNAs level. The overarching goal of this research is to elucidate the impact of miRNAs in regulating the P. indica-mediated salt tolerance in rice. Applying sRNA-seq analysis led to identify a set of 547 differentially abundant miRNAs in response to P. indica inoculation and salt stress. These included 206 rice-specific and 341 previously known miRNAs from other plant species. In silico analysis of miRNAs predictions of the differentially abundant miRNAs led to identifying of 193 putatively target genes, most of which were encoded either genes or transcription factors involved in nutrient uptake, sodium ion transporters, growth regulators, and auxin- responsive proteins. The rice-specific miRNAs targeted the transcription factors involved in the import of potassium ions into the root cells, the export of sodium ions, and plant growth and development. Interestingly, P. indica affected the differential abundance of miRNAs regulated genes and transcription factors linked to salt stress tolerance. Our data helps to understand the molecular basis of salt stress tolerance mediated by symbionts in plant and the potential impact of miRNAs for genetic improvement of rice varieties for tolerance to salt stress.

RNA-Seq Transcriptome Analysis of Rice Primary Roots Reveals the Role of Flavonoids in Regulating the Rice Primary Root Growth

Flavonoids play important roles in root development and in its tropic responses, whereas the flavonoids-mediated changes of the global transcription levels during root growth remain unclear. Here, the global transcription changes in quercetin-treated rice primary roots were analyzed. Quercetin treatment significantly induced the inhibition of root growth and the reduction of H₂O₂ and O₂⁻ levels. In addition, the RNA-seq analysis revealed that there are 1243 differentially expressed genes (DEGs) identified in quercetin-treated roots, including 1032 up-regulated and 211 down-regulated genes. A gene ontology (GO) enrichment analysis showed that the enriched GO terms are mainly associated with the cell wall organization, response to oxidative stress, and response to hormone stimulus. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment pathway analysis showed that the enriched DEGs are involved in phenylpropanoid biosynthesis, glutathione metabolism, and plant hormone signal transduction. Moreover, the quercetin treatment led to an increase of the antioxidant enzyme activities of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) in rice roots. Also, the quercetin treatment altered the DR5:GUS expression pattern in the root tips. All of these data indicated that the flavonoids-mediated transcription changes of genes are related to the genes involved in cell wall remodeling, redox homeostasis, and auxin signaling, leading to a reduced cell division in the meristem zone and cell elongation in the elongation zone of roots.

Genome-Wide Identification and Expression Analysis of the HD-Zip Gene Family in Wheat (Triticum aestivum L.)

The homeodomain-leucine zipper (HD-Zip) gene family, as plant-specific transcription factors, plays an important role in plant development and growth as well as in the response to diverse stresses. Although HD-Zip genes have been extensively studied in many plants, they had not yet been studied in wheat, especially those involved in response to abiotic stresses. In this study, 46 wheat HD-Zip genes were identified using a genome-wide search method. Phylogenetic analysis classified these genes into four groups, numbered 4, 5, 17 and 20 respectively. In total, only three genes with A, B and D homoeologous copies were identified. Furthermore, the gene interaction networks found that the TaHDZ genes played a critical role in the regulatory pathway of organ development and osmotic stress. Finally, the expression profiles of the wheat HD-Zips in different tissues and under various abiotic stresses were investigated using the available RNA sequencing (RNA-Seq) data and then validated by quantitative real-time polymerase chain reaction (qRT-PCR) to obtain the tissue-specific and stress-responsive candidates. This study systematically identifies the HD-Zip gene family in wheat at the genome-wide level, providing important candidates for further functional analysis and contributing to the better understanding of the molecular basis of development and stress tolerance in wheat.

Characterisation of a flavonoid ligand of the fungal protein Alt a 1

Spores of pathogenic fungi are virtually ubiquitous and cause human disease and severe losses in crops. The endophytic fungi Alternaria species produce host-selective phytotoxins. Alt a 1 is a strongly allergenic protein found in A. alternata that causes severe asthma. Despite the well-established pathogenicity of Alt a 1, the molecular mechanisms underlying its action and physiological function remain largely unknown. To gain insight into the role played by this protein in the pathogenicity of the fungus, we studied production of Alt a 1 and its activity in spores. We found that Alt a 1 accumulates inside spores and that its release with a ligand is pH-dependent, with optimum production in the 5.0-6.5 interval. The Alt a 1 ligand was identified as a methylated flavonoid that inhibits plant root growth and detoxifies reactive oxygen species. We also found that Alt a 1 changes its oligomerization state depending on the pH of the surrounding medium and that these changes facilitate the release of the ligand. Based on these results, we propose that release of Alt a 1 should be a pathogenic target in approaches used to block plant defenses and consequently to favor fungal entry into the plant.