MYB transcription factors-master regulators of phenylpropanoid biosynthesis and diverse developmental and stress responses

Heterologous expression of physic nut JcHDZ25 confers tolerance to drought stress in transgenic rice

BACKGROUND

The HD-Zip family of plant-specific transcription factors coordinates developmental processes and abiotic stress adaptation, including drought tolerance in bioenergy crops such as physic nut. Although HD-Zip proteins are known regulators of stress responses, the functional roles of physic nut HD-Zip genes in drought adaptation remain uncharacterized.

RESULTS

In this study, we functionally characterized JcHDZ25, a drought-inducible HD-Zip I gene from physic nut, which is predominantly expressed in roots and upregulated by ABA and drought. Subcellular localization and transcriptional activity assays confirmed that JcHDZ25 localized to the nucleus and exhibited intrinsic transcriptional activation. Transgenic rice overexpressing JcHDZ25 displayed enhanced drought tolerance and ABA sensitivity compared to wild-type plants. Under drought stress, JcHDZ25-overexpressing lines showed significantly higher proline content, elevated SOD and CAT activities, and reduced electrolyte leakage and MDA accumulation relative to wild-type controls. Furthermore, transgenic plants showed higher expression of abiotic stress-responsive genes (OsAPX2, OsCATA, OsLEA3, OsP5 CS, OsDREB2 A, OsADC1) and ABA pathway-related genes (OsNCED3, OsRD29 A) under drought stress compared to wild-type plants.

CONCLUSIONS

JcHDZ25 positively regulates drought tolerance in rice possibly through an ABA-dependent transcriptional regulation, providing mechanistic insights into physic nut's drought adaptation and highlighting its potential as a genetic resource for engineering stress-resilient crops.

Integrated genomic and transcriptomic analyses reveal the genetic and molecular mechanisms underlying hawthorn peel color and seed hardness diversity

Hawthorn (Crataegus pinnatifida) fruit peel color and seed hardness are key traits that significantly impact economic value. We present here the high-quality chromosome-scale genomes of two cultivars, including the hard-seed, yellow-peel C. pinnatifida "Jinruyi" (JRY) and the soft-seed, red-peel C. pinnatifida "Ruanzi" (RZ). The assembled genomes comprising 17 chromosomes are 809.1 Mb and 760.5 Mb in size, achieving scaffold N50 values of 48.5 Mb and 46.8 Mb for JRY and RZ, respectively. Comparative genomic analysis identifies 3.6-3.8 million single nucleotide polymorphisms, 8.5-9.3 million insertions/deletions, and approximately 30 Mb of presence/absence variations across different hawthorn genomes. Through integrating differentially expressed genes and accumulated metabolites, we filter candidate genes CpMYB114 and CpMYB44 associated with differences in hawthorn fruit peel color and seed hardness, respectively. Functional validation confirms that the CpMYB114-CpANS regulates anthocyanin biosynthesis in hawthorn peels, contributing to the observed variation in peel color. CpMYB44-CpCOMT is significantly upregulated in JRY and is verified to promote lignin biosynthesis, resulting in the distinction in seed hardness. Overall, this study reveals the new insights into understanding of distinct peel pigmentation and seed hardness in hawthorn and provides an abundant resource for molecular breeding.

Phytohormone and Amino Acid Changes in Cherry Radish as Metabolic Adaptive Response to Arsenic Single and Multi-Contamination

This study investigated the metabolic adaptive responses to As contamination and As co-contamination with cadmium, lead, and zinc in the leaves and tubers of cherry radish (Raphanus sativus var. sativus Pers.). The response was assessed by measuring malondialdehyde levels, total phenolic content (TPC), total anthocyanin pigment (TAC), growth and stress phytohormone concentration, and free amino acid content. The characteristic As accumulation of single contamination resulted in a decrease in tuber growth. However, in the case of co-contamination, As uptake was influenced by the presence of other potentially toxic elements (PTEs), mainly zinc, with no significant effect on growth. Both contaminated treatments exhibited significant differences in metabolite levels among the organs, along with notable changes in their contents. Increases in malondialdehyde, TPC, and TAC indicated induced oxidative stress and an antioxidant response that was more pronounced by As co-contamination. Also, the results for phytohormones, which showed both increases and decreases, along with selected free amino acids (which showed increases), demonstrated a more significant influence of As co-contamination. Based on these findings, it can be concluded that the response of cherry radish to contaminated treatments exhibited significant differences in the studied parameters, along with variability in the results, reflecting the extent of the effects of PTEs that induce oxidative stress.

Diverse roles of MYB transcription factors in plants

MYB transcription factors (TFs), one of the largest TF families in plants, are involved in various plant-specific processes as the central regulators, such as in phenylpropanoid metabolism, cell cycle, formation of root hair and trichome, phytohormones responses, reproductive growth and abiotic or biotic stress responses. Here we summarized multiple roles and explained the molecular mechanisms of MYB TFs in plant development and stress adaptation. The exploration of MYB TFs contributes to a better comprehension of molecular regulation in plant development and environmental adaptability.

SlMYB72 and SlMYB75 antagonistically regulate trichome formation via the MYB-bHLH-WD40 complex in tomato

Trichomes are specialized epidermal outgrowths serving as protective barriers for plants against various stresses such as herbivore attacks. MYB-bHLH-WD40 complex is of great significance for unicellular trichome formation in Arabidopsis, whereas its role in the formation of multicellular trichomes in tomatoes remains largely unknown. In the present study, we identified that the R2R3-type MYB transcription factor SlMYB72 promotes the formation of type II, V, and VI trichomes by inhibiting the expression of SlCycB2, a repressor of trichome initiation. SlMYB75 is a negative regulator of trichome formation and positively regulates SlCycB2 expression. Interaction analyses showed that SlMYB72 and SlMYB75 can form MYB-bHLH-WD40 complexes with SlbHLH150 and SlTTG1, respectively, through mutual interactions. The dual-luciferase assay demonstrated that the regulatory functions of SlMYB72 and SlMYB75 in SlCycB2 expression can be enhanced by their corresponding MYB-bHLH-WD40 complexes. Interestingly, yeast-three-hybrid assay indicated that SlMYB75 competes with SlMYB72 for SlbHLH150 and SlTTG1, and counterbalances the down-regulation of SlCycB2 expression controlled by SlMYB72 alone, which is further confirmed by genetic hybrid experiments. These results reveal that SlMYB72 and SlMYB75 antagonistically regulate trichome formation and SlCycB2 expression through MYB-bHLH-WD40 complexes. These findings provide a novel perspective and theoretical basis for the formation of multicellular trichomes in tomatoes and the development of highly resistant plants.

CRISPR-Cas9-mediated deletions of FvMYB46 in Fragaria vesca reveal its role in regulation of fruit set and phenylpropanoid biosynthesis

The phenylpropanoid pathway, regulated by transcription factors of the MYB family, produces secondary metabolites that play important roles in fertilization and early phase of fruit development. The MYB46 transcription factor is a key regulator of secondary cell wall structure, lignin and flavonoid biosynthesis in many plants, but little is known about its activity in flowers and berries in F. vesca. For functional analysis of FvMYB46, we designed a CRISPR-Cas9 construct with an endogenous F. vesca-specific U6 promoter for efficient and specific expression of two gRNAs targeting the first exon of FvMYB46. This generated mutants with an in-frame 81-bp deletion of the first conserved MYB domain or an out-of-frame 82-bp deletion potentially knocking out gene function. In both types of mutant plants, pollen germination and fruit set were significantly reduced compared to wild type. Transcriptomic analysis of flowers revealed that FvMYB46 positively regulates the expression of genes involved in processes like xylan biosynthesis and metabolism, homeostasis of reactive oxygen species (ROS) and the phenylpropanoid pathway, including secondary cell wall biosynthesis and flavonoid biosynthesis. Genes regulating carbohydrate metabolism and signalling were also deregulated, suggesting that FvMYB46 might regulate the crosstalk between carbohydrate metabolism and phenylpropanoid biosynthesis. In the FvMYB46-mutant flowers, the flavanol and flavan-3-ol contents, especially epicatechin, quercetin-glucoside and kaempferol-3-coumaroylhexoside, were reduced, and we observed a local reduction in the lignin content in the anthers. Together, these results suggest that FvMYB46 controls fertility and efficient fruit set by regulating the cell wall structure, flavonoid biosynthesis, carbohydrate metabolism, and sugar and ROS signalling in flowers and early fruit development in F. vesca.

Identification and characteristics of differentially expressed genes under UV-B stress in Gossypium hirsutum

Objective

This study aimed to screen the differentially expressed genes (DEGs) of Gossypium hirsutum under UV-B stress and identify the significant pathways based on gene enrichment analysis results.

Methods

In this study, the allotetraploid crop G. hirsutum was used to examine changes in various physiological indexes under UV-B stress, and screened out all DEGs under UV-B stress (16 kJ m-2 d-1) based on six leaf transcriptomes. The main enrichment pathways of DEGs were analyzed according to gene annotation. Finally, we predicted the regulatory genes of phenylpropanoid pathway under UV-B stress by co-expression network analysis, and selected GhMYB4 for verification.

Results

Gene annotation analysis revealed that DEGs were predominantly enriched in pathways related to photosynthesis and secondary metabolism. Further analysis revealed that UV-B stress impaired photosynthesis mainly by damaging photosystem II (PSII) and inhibiting electron transport, whereas G. hirsutum responded to UV-B stress by synthesizing secondary metabolites such as anthocyanins and lignin. We selected the regulatory genes GhMYB4 for verification. It was found to be an anthocyanin negative regulator in response to UV-B stress.

Conclusions

UV-B stress impaired photosynthesis mainly by damaging photosystem II (PSII) and inhibiting electron transport, whereas G. hirsutum responded to UV-B stress by synthesizing secondary metabolites such as anthocyanins and lignin.

Exploring the differences in traits and genes between brown cotton and white cotton hybrid offspring (Gossypium hirsutum L.)

Brown cotton and white cotton are two important raw materials used in the cotton fiber industry. Clarifying the differences in morphology, agronomic traits, and fiber pigments between these varieties can facilitate the implementation of corresponding cultivation and breeding techniques. Therefore, we obtained F2 generation brown cotton plants through hybridization and compared them with their parents. In terms of agronomic traits, plant morphology and leaf shape were similar, but brown cotton presented more villi on the main stem. The first fruiting branch node was within the range of 4-6 cm, and the first fruiting branch node height was greater than that of TM-1, i.e., between 13.25 cm and 22.79 cm, with no difference compared with that of P26. The plant height was greater than that of the parents, and the number of bolls was essentially the same as that in TM-1 and greater than that in P26. The lint percentage and average fiber length were lower in TM-1 than in P26, and the seed index was greater than that in TM-1 and P26. Pigment measurements revealed that the chlorophyll a content in brown cotton during the boll stage was lower than that in white cotton, and the content of proanthocyanidin in the cotton fibers was greater in brown cotton than in white cotton. At 15 days after pollination, the highest content was 159.8 mg/g. To determine the differences in gene expression levels, we conducted transcriptome sequencing. Gene Ontology (GO) analysis revealed that the differentially expressed genes (DEGs) were enriched in pathways related to the cell wall and enzyme activity, whereas Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the DEGs were enriched in flavonoid synthesis pathways. Transcription factor analysis revealed that the expression of the MYB3 transcription factor (Ghir_D07G002110) was higher in brown cotton, and bioinformatics analysis revealed that this gene has regulatory effects on the CHS, CHI1, and F3H genes.

Combined metabolomic and transcriptomic analysis to reveal the response of rice to Mn toxicity stress

Excessive manganese (Mn) concentrations affect plant gene expression, alter metabolite content, and impede plant growth. Rice plants are particularly susceptible to Mn toxicity stress in acidic soil; however, the underlying molecular mechanisms are so far unclear. This study used transcriptomic and metabolomic sequencing to examine roots and leaves of rice plants subjected to Mn toxicity stress. The findings showed that high Mn stress increased the content of malondialdehyde, proline, and soluble sugar in rice roots by 262.28 %, 803.37 %, and 167.25 %, respectively. In rice roots, the enzymatic activities of peroxidase (POD), superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX) elevated by 119.69 %, 408.44 %, 151.97 %, and 27.19 %, respectively. In rice leaves, the proline content increased by 632.45 %, whereas the enzymatic activities of POD, SOD, CAT, and APX were elevated by 167.17 %, 14.08 %, 103.60 %, and 146.74 %, respectively. Mn toxicity stress decreased soluble protein content in rice roots, and in the leaves, it reduced the soluble protein, soluble sugar, and chlorophyll contents. In addition, Mn toxicity led to reduced biomass accumulation, plant height, stem diameter, and root growth. The contents of salicylic acid (increased by 118.40 % in roots and 66.38 % in leaves) and jasmonic acid (decreased by 50.18 % in roots and increased by 143.97 % in leaves) were also affected. Transcriptome analysis identified differentially expressed genes associated with transcription factors, antioxidant enzymes, and metal transporters. Metabolomics revealed 176 and 214 different metabolites in the roots and leaves, respectively, that under Mn toxicity stress affected major metabolic pathways associated with fatty and amino acids. The phenylalanine metabolism pathway was significantly enriched in both the roots and leaves. Combined transcriptomic and metabolomic analyses revealed three key pathways: lysine degradation and phenylpropanoid biosynthesis in roots and alpha-linolenic acid metabolism in leaves. Metabolic substances and genes associated with metabolic enzymes were identified. These results enhance our understanding of the molecular processes underlying the responses of rice to Mn toxicity stress and provide a basis for breeding Mn-tolerant rice varieties.

A glutathione S-transferase regulates lignin biosynthesis and enhances salt tolerance in tomato

Salt stress adversely affects the growth and yield of crops. Glutathione S-transferases (GSTs) are involved in plant growth and responses to biotic and abiotic stresses. In this study, 400 mm NaCl stress significantly induced the expression of Glutathione S-transferase U43 (SlGSTU43) in the roots of the wild-type tomato (Solanum lycopersicum L.) plants. Overexpressing SlGSTU43 enhanced the ability of scavenging reactive oxygen species in tomato leaves and roots under NaCl stress, while SlGSTU43 knock-out mutants showed the opposite performance. RNA sequencing analysis revealed that overexpressing SlGSTU43 affected the expression of genes related to lignin biosynthesis. We demonstrated that SlGSTU43 can regulate the lignin content in tomato through its interaction with SlCOMT2, a key enzyme involved in lignin biosynthesis, and promote the growth of tomato plants under NaCl stress. In addition, SlMYB71 and SlWRKY8 interact each other, and can directly bind to the promoter of SlGSTU43 to transcriptionally activate its expression separately or in combination. When SlMYB71 and SlWRKY8 were silenced in tomato plants individually or collectively, the plants were sensitive to NaCl stress, and their GST activities and lignin contents decreased. Our research indicates that SlGSTU43 can enhance salt stress tolerance in tomato by regulating lignin biosynthesis, which is regulated by interacting with SlCOMT2, as well as SlMYB71 and SlWRKY8. This finding broadens our understanding of GST functions.

Combined transcriptomic, metabolomic and physiological analysis reveals the key role of nitrogen, but not phosphate and potassium in regulating anthocyanin biosynthesis induced by nutrient deficiency in Eucalyptus

Anthocyanin biosynthesis in Eucalyptus plants can be flexibly and rapidly modulated in response to hormones or environmental stimuli, including nutrient deprivation (ND). However, the underlying mechanism of ND in inducing anthocyanin biosynthesis in plants remains largely elusive. In this study, we discovered that anthocyanin levels in leaves and stems could well reflect nitrogen availability in Eucalyptus. Supplementation with nitrogen, but not with phosphate or potassium, effectively inhibited ND-induced anthocyanin biosynthesis. To further investigate how nitrogen regulates this process, comprehensive time-resolved transcriptomic and targeted metabolomic analyses were conducted. The results revealed that 3405, 2706, and 3153 genes were differentially regulated by nitrogen treatment at 1, 2, and 3 d, respectively. Pathway analysis indicated the majority of the enriched KEGG pathways were associated with cellular metabolism, such as amino acid and flavonoid biosynthesis. Moreover, metabolomic analysis showed that the most abundantly accumulated anthocyanins, cyanidin-3-O-galactoside and cyanidin-3-O-glucoside, along with key intermediates in the flavonoid pathway, were downregulated by nitrogen treatment. Furthermore, nitrogen-responsive MYB-bHLH-WDR complex genes were identified, including six EgrMYB113 family members. Overexpression of one of the EgrMYB113-like genes induced anthocyanin biosynthesis in the transgenic hairy roots of Eucalyptus. Interestingly, mutation of AtMYB113 inhibited nitrogen deficiency-induced anthocyanin biosynthesis in Arabidopsis, suggesting that MYB113 is a novel N-responsive MYB transcriptional regulator of anthocyanin biosynthesis. Additionally, nitrogen treatment upregulated a few GA biosynthesis genes while simultaneously downregulated the expression of several GA2ox genes. Exogenous application of GA3 decreased ND-induced anthocyanin biosynthesis. Conclusively, this study provides novel insights into the molecular mechanism of nitrogen in the regulation of anthocyanin biosynthesis in Eucalyptus.

A transposon DNA/hAT-Ac insertion promotes the formation of yellow tepals in lotus (Nelumbo)

Yellow tepal is a unique trait of the American lotus (Nelumbo lutea), and all yellow lotus cultivars in the market possess genetic material from the American lotus. However, the formation of yellow tepals in lotus and the genetic mechanism of their formation remain unclear. In this study, we identified a transposon DNA/hAT-Ac, located within the promoter region of an R2R3-MYB transcription factor, MYB12, by comparing the insertion patterns of transposons in the genomes of American and Asian lotus (Nelumbo nucifera). The transposon was found exclusively in yellow lotus cultivars and not in red or white lotus. The insertion of DNA/hAT-Ac facilitated the specific expression of MYB12 in the yellow lotus tepals. Transient expression in lotus tepals, dual-luciferase, and yeast one-hybrid assays demonstrated that MYB12 promotes the accumulation of carotenoids and flavonols by activating the expression of genes involved in carotenoid and flavonols biosynthesis, and it directly binds to the promoters of PSY and FLS. Our results indicated that the transposon DNA/hAT-Ac-mediated specific expression of MYB12 is crucial for the formation of yellow tepals in lotus, and the findings provide a theoretical basis for the breeding of yellow lotus cultivars.

Functional impacts of PtrMYB203 on phenylpropanoid pathway regulation and wood properties in hybrid poplar

The phenylpropanoid pathway is vital for plant growth and development, producing lignin and flavonoids. This study investigates PtrMYB203, a homolog of MYB repressors of proanthocyanidin (PA) biosynthesis in Populus trichocarpa, as a transcriptional repressor in the phenylpropanoid pathway of hybrid poplar (Populus alba x P. glandulosa). Overexpression of PtrMYB203 (35S::PtrMYB203) in hybrid poplar detrimentally impacted plant growth and development. Histological analysis revealed irregular xylem vessel formation and decreased lignin content, corroborated by Klason lignin assays. Moreover, 35S::PtrMYB203 transgenic poplars exhibited significant decreases in anthocyanin and PA accumulations in callus tissues, even under high light conditions. Quantitative RT-PCR analysis and protoplast-based transcriptional activation assay confirmed the downregulation of lignin and flavonoid biosynthesis genes. This genetic modification also alters the expression of several MYB transcription factors, essential for phenylpropanoid pathway regulation. Remarkably, saccharification efficiency in the 35S::PtrMYB203 poplar was improved by over 34% following hot water treatment alone. These findings suggest PtrMYB203 as a potential genetic target for enhancing wood properties for bioenergy production, providing valuable insights into the manipulation of metabolite pathways in woody perennials to advance wood biotechnology.

Sweetpotato sucrose transporter IbSUT1 alters storage roots formation by regulating sucrose transport and lignin biosynthesis

The formation and development of storage roots is the most important physiological process in sweetpotato production. Sucrose transporters (SUTs) regulate sucrose transport from source to sink organs and play important roles in growth and development of plants. However, whether SUTs involved in sweetpotato storage roots formation is so far unknown. In this study, we show that IbSUT1, a SUT, is localized to the plasma membrane. Overexpression of IbSUT1 in sweetpotato promotes the sucrose efflux rate from leaves, leading to increased sucrose levels in roots, thus induces lignin deposition in the stele, which inhibits the storage roots formation and compromises the yield. Heterologous expression of IbSUT1 in Arabidopsis significantly increases the sucrose accumulation and promotes lignification in the inflorescence stems. RNA-seq and biochemical analysis further demonstrated that IbMYB1 negatively regulates the expression of IbSUT1. Overexpression of IbMYB1 in Arabidopsis reduces the sucrose accumulation and lignification degree in the inflorescence stems. Moreover, co-overexpression of IbMYB1 and IbSUT1 restores the phenotype of lignin over-deposition in Arabidopsis. Collectively, our results reveal that IbSUT1 regulates source-sink sucrose transport and participates in the formation of sweetpotato storage roots and highlight the potential application of IbSUT1 in improving sweetpotato yield in the future.

OsJRL negatively regulates rice cold tolerance via interfering phenylalanine metabolism and flavonoid biosynthesis

The identification of new genes involved in regulating cold tolerance in rice is urgent because low temperatures repress plant growth and reduce yields. Cold tolerance is controlled by multiple loci and involves a complex regulatory network. Here, we show that rice jacalin-related lectin (OsJRL) modulates cold tolerance in rice. The loss of OsJRL gene functions increased phenylalanine metabolism and flavonoid biosynthesis under cold stress. The OsJRL knock-out (KO) lines had higher phenylalanine ammonia-lyase (PAL) activity and greater flavonoid accumulation than the wild-type rice, Nipponbare (NIP), under cold stress. The leaves had lower levels of reactive oxygen species (ROS) and showed significantly enhanced cold tolerance compared to NIP. In contrast, the OsJRL overexpression (OE) lines had higher levels of ROS accumulation and showed lower cold tolerance than NIP. Additionally, the OsJRL KO lines accumulated more abscisic acid (ABA) and jasmonic acid (JA) under cold stress than NIP. The OsJRL OE lines showed increased sensitivity to ABA compared to NIP. We conclude that OsJRL negatively regulates the cold tolerance of rice via modulation of phenylalanine metabolism and flavonoid biosynthesis.

A GhLac1-centered transcriptional regulatory cascade mediates cotton resistance to Verticillium dahliae through the lignin biosynthesis pathway

The lignin biosynthesis pathway plays a crucial role in the defense response against V. dahliae in cotton, and it is essential to identify the key regulators in this pathway for disease-resistant breeding. In a previous study, the cotton laccase gene GhLac1 was identified as mediating plant broad-spectrum biotic stress tolerance by manipulating phenylpropanoid metabolism. However, the upstream master regulators and regulatory mechanism of lignin are still largely unknown. This study aims to identify the upstream regulators of GhLac1 and explore the molecular mechanism underlying cotton's disease resistance response to V. dahliae. Through the study, three WRKY, three MYB, and one APETALA2/ETHYLENE RESPONSIVE FACTOR (ERF) TFs were identified as differentially responding to V. dahliae infection in cotton. Among these TFs, GhWRKY30, GhWRKY41, GhMYB42, and GhTINY2 were found to directly bind to the GhLac1 promoter and activate its expression. Transient overexpression of these four TFs in cotton led to increased expression of GhLac1 and other the laccase family members, while knockdown of these TFs resulted in reduced lignin accumulation and increased susceptibility to V. dahliae. Additionally, GhWRKY30 and GhWRKY41 were observed to interact with themselves and with each other, synergistically transactivating the GhLac1 promoter. This study reveals a GhLac1-centered transcriptional regulatory cascade of lignin synthesis that contributes to cotton's defense response by modulating lignin metabolism.

Transcriptomic and metabolomic reveal OsCOI2 as the jasmonate-receptor master switch in rice root

Jasmonate is an essential phytohormone involved in plant development and stress responses. Its perception occurs through the CORONATINE INSENSITIVE (COI) nuclear receptor allowing to target the Jasmonate-ZIM domain (JAZ) repressors for degradation by the 26S proteasome. Consequently, repressed transcription factors are released and expression of jasmonate responsive genes is induced. In rice, three OsCOI genes have been identified, OsCOI1a and the closely related OsCOI1b homolog, and OsCOI2. While the roles of OsCOI1a and OsCOI1b in plant defense and leaf senescence are well-established, the significance of OsCOI2 in plant development and jasmonate signaling has only emerged recently. To unravel the role of OsCOI2 in regulating jasmonate signaling, we examined the transcriptomic and metabolomic responses of jasmonate-treated rice lines mutated in both the OsCOI1a and OsCOI1b genes or OsCOI2. RNA-seq data highlight OsCOI2 as the primary driver of the extensive transcriptional reprogramming observed after a jasmonate challenge in rice roots. A series of transcription factors exhibiting an OsCOI2-dependent expression were identified, including those involved in root development or stress responses. OsCOI2-dependent expression was also observed for genes involved in specific processes or pathways such as cell-growth and secondary metabolite biosynthesis (phenylpropanoids and diterpene phytoalexins). Although functional redundancy exists between OsCOI1a/b and OsCOI2 in regulating some genes, oscoi2 plants generally exhibit a weaker response compared to oscoi1ab plants. Metabolic data revealed a shift from the primary metabolism to the secondary metabolism primarily governed by OsCOI2. Additionally, differential accumulation of oryzalexins was also observed in oscoi1ab and oscoi2 lines. These findings underscore the pivotal role of OsCOI2 in jasmonate signaling and suggest its involvement in the control of the growth-defense trade-off in rice.

Transcriptome profiling of two rice varieties reveals their molecular responses under high night-time temperature

High night-time temperatures (HNT) pose a threat to the sustainability of crop production, including rice. HNT can affect crop productivity and quality by influencing plant physiology, morphology, and phenology. The ethylene perception inhibitor, 1-methylcyclopropene (1-MCP), can minimize HNT-induced damage to plant membranes, thereby preventing decrease in rice yield. In this study, we employed a transcriptome approach to investigate the effects of HNT, 1-MCP, and their interaction on two Texas rice varieties, Antonio and Colorado. The plants were exposed to temperatures of 25°C (ambient night-time temperature, ANT) and 30°C (HNT) using an infrared heating system from the booting stage until harvest, while 1-MCP was applied at the booting stage of rice development. Several physiological and agronomical traits were evaluated under each condition to assess plant responses. Leaf tissues were collected from the plants grown in the ANT and HNT conditions after the heat stress and 1-MCP treatments. Based on agronomic performance, Colorado was less negatively affected than Antonio under HNT, showing a slight reduction in spikelet fertility and leaf photosynthetic rate but no significant reduction in yield. The application of 1-MCP significantly mitigated the adverse effects of HNT in Antonio. However, no significant differences were observed in yield and leaf photosynthetic rate in Colorado. Furthermore, transcriptomic data revealed distinct responsive mechanisms in Antonio and Colorado in response to both HNT and 1-MCP. Several ethylene and senescence-related transcription factors (TFs) were identified only in Antonio, suggesting that 1-MCP affected the ethylene signaling pathway in Antonio but not in Colorado. These findings contribute to our understanding of the physiological differences between varieties exhibiting susceptible and tolerant responses to high night-time temperatures, as well as their response to 1-MCP and ethylene regulation under 1-MCP.

A Novel MsEOBI-MsPAL1 Module Enhances Salinity Stress Tolerance, Floral Scent Emission and Seed Yield in Alfalfa

Alfalfa (Medicago sativa L.) is an important and widely cultivated forage legume, yet its yield is constrained by salinity stress. In this study, we characterized an R2R3-MYB transcription factor MsEOBI in alfalfa. Its salt tolerance function and regulatory pathways were investigated. The nuclear-localized MsEOBI functions as a transcriptional activator, enhancing salinity tolerance by promoting the biosynthesis of flavonoids and lignin, as well as facilitating the scavenging of reactive oxygen species (ROS). Additionally, MsEOBI promotes pollinator attraction and increases seed yield by activating the biosynthesis of volatile phenylpropanoids. Yeast one-hybrid (Y1H), dual-luciferase reporter and chromatin immunoprecipitation coupled with quantitative PCR (ChIP-qPCR) assays demonstrated that MsEOBI directly binds to the promoter regions of MsPAL1, a key gene in the phenylpropanoid pathway, thereby activating its expression. Overexpression of MsPAL1 enhances salinity tolerance in alfalfa. These findings elucidate the role of the MsEOBI-MsPAL1 regulatory module and provide valuable genetic resources for the future breeding of salt-tolerant alfalfa varieties.

Multi-omics analysis reveals the effects of three application modes of plant growth promoting microbes biofertilizer on potato (Solanum tuberosum L.) growth under alkaline loess conditions

Potato is an important crop due to its high contents of starch, protein, and various vitamins and minerals. Biofertilizers are composed of plant growth promoting microbes (PGPMs) which are essential for improving the growth and resistance of potato. However, little information has focused on the modes of inoculation of biofertilizers on plant growth and microecology. This study aims to reveal the response mechanism of the potato to three modes of inoculation of biofertilizers all containing PGPM Bacillus amyloliquefaciens EZ99, i.e. scattered mode of 5 kg/ha biofertilizer (M5), soaking seed tubers with dissolved 5 kg/ha biofertilizer (MZG), and scattered mode of 3 kg/ha biofertilizer + 2 kg/ha sucrose (MY34) in alkaline loess field through multi-omics analysis of transcriptome, metabolome and microbiome. The physiological result revealed that two application modes of equal amount of biofertilizer M5 and MZG significantly improved the growth and yield of potatoes. Furthermore, the transcriptome of potato exhibited sets of differentially expressed genes enriched in photosynthesis, sugar metabolism, and phenylpropanoid biosynthesis among the three modes, with the M5 mode exhibiting overall up-regulation of 828 genes. Based on the untargeted metabolomic analysis of potato tuber, M5 mode significantly accumulated sucrose, while MZG and MY34 mode significantly accumulated the stress metabolites euchrenone b6 and mannobiose, respectively. Besides, the microbial structure of potato rhizosphere showed that the diversity of bacteria and fungi was similar in all soils, but their abundances varied significantly. Specifically, beneficial Penicillium was enriched in M5 and MZG soils, whereas MY34 soil accumulated potential pathogens Plectosphaerella and saccharophilic Mortierella. Collectively, these e findings highlight that MZG is the most effective mode to promote potato growth and stimulate rhizosphere effect. The present study not only encourages sustainable agriculture through agroecological practices, but also provides broad prospects for the application of PGPM biofertilizer in staple foods.

Lignin biosynthesis pathway repressors in gymnosperms: differential repressor domains as compared to angiosperms

Lignin is a polyphenolic polymer present in the cell walls of specialized plant cell types in vascular plants that provides structural support and plays a major role in plant protection. The lignin biosynthesis pathway is regulated by transcription factors from the MYB (myeloblastosis) family. While several MYB members positively regulate lignin synthesis, only a few negatively regulate lignin synthesis. These lignin suppressors are well characterized in model plant species; however, their role has not been fully explored in gymnosperms. Lignin forms one of the major hurdles for the forest-based industry e.g. paper, pulp, and biofuel production. Therefore, the detailed mechanisms involved in the regulation of lignin synthesis are valuable, especially in conifers that form the major source of softwood for timber and paper production. In this review, the potential and differential domains present in the MYB suppressors in gymnosperms are discussed, along with their phylogenetic analysis. Sequence analysis revealed that the N-terminal regions of the MYB suppressor members were found to be conserved among the gymnosperms and angiosperms containing the R2, R3, and bHLH domains, while the C-terminal regions were found to be highly variable. The typical repressor motifs like the LxLxL-type EAR motif and the TLLLFR motif were absent from the C-terminal regions of MYB suppressors from most gymnosperms. However, although the gymnosperms lacked the characteristic repressor domains, a R2R3-type MYB member from Ginkgo was reported to repress the lignin biosynthetic pathway. It is proposed that gymnosperms possess unique kinds of repressors that need further functional validation.

RNA-Seq and WGCNA Analyses Reveal Key Regulatory Modules and Genes for Salt Tolerance in Cotton

The problem of soil salinization has seriously hindered agricultural development. Cotton is a pioneering salinity-tolerant crop, so harvesting its key salinity-tolerant genes is important for improving crop salt tolerance. In this study, we analyzed changes in the transcriptome expression profiles of the salt-tolerant cultivar Lu Mian 28 (LM) and the salt-sensitive cultivar Zhong Mian Suo 12 (ZMS) after applying salt stress, and we constructed weighted gene co-expression networks (WGCNA). The results indicated that photosynthesis, amino acid biosynthesis, membrane lipid remodeling, autophagy, and ROS scavenging are key pathways in the salt stress response. Plant-pathogen interactions, plant hormone signal transduction, the mitogen-activated protein kinase (MAPK) signaling pathway, and carotenoid biosynthesis are the regulatory networks associated with these metabolic pathways that confer cotton salt tolerance. The gene-weighted co-expression network was used to screen four modules closely related to traits, identifying 114 transcription factors, including WRKYs, ERFs, NACs, bHLHs, bZIPs, and MYBs, and 11 hub genes. This study provides a reference for acquiring salt-tolerant cotton and abundant genetic resources for molecular breeding.

Unveiling Iso- and Aniso-Hydric Disparities in Grapevine-A Reanalysis by Transcriptome Portrayal Machine Learning

Mechanisms underlying grapevine responses to water(-deficient) stress (WS) are crucial for viticulture amid escalating climate change challenges. Reanalysis of previous transcriptome data uncovered disparities among isohydric and anisohydric grapevine cultivars in managing water scarcity. By using a self-organizing map (SOM) transcriptome portrayal, we elucidate specific gene expression trajectories, shedding light on the dynamic interplay of transcriptional programs as stress duration progresses. Functional annotation reveals key pathways involved in drought response, pinpointing potential targets for enhancing drought resilience in grapevine cultivation. Our results indicate distinct gene expression responses, with the isohydric cultivar favoring plant growth and possibly stilbenoid synthesis, while the anisohydric cultivar engages more in stress response and water management mechanisms. Notably, prolonged WS leads to converging stress responses in both cultivars, particularly through the activation of chaperones for stress mitigation. These findings underscore the importance of understanding cultivar-specific WS responses to develop sustainable viticultural strategies in the face of changing climate.

Phosphorylated transcription factor PuHB40 mediates ROS-dependent anthocyanin biosynthesis in pear exposed to high light

Plants are increasingly vulnerable to environmental stresses because of global warming and climate change. Stress-induced reactive oxygen species (ROS) accumulation results in plant cell damage, even cell death. Anthocyanins are important antioxidants that scavenge ROS to maintain ROS homeostasis. However, the mechanism underlying ROS-induced anthocyanin accumulation is unclear. In this study, we determined that the HD-Zip I family member transcription factor PuHB40 mediates ROS-dependent anthocyanin biosynthesis under high-light stress in pear (Pyrus ussuriensis). Specifically, PuHB40 induces the PuMYB123-like-PubHLH3 transcription factor complex for anthocyanin biosynthesis. The PuHB40-mediated transcriptional activation depends on its phosphorylation level, which is regulated by protein phosphatase PP2A. Elevated ROS content maintains high PuHB40 phosphorylation levels while also enhancing the PuHB40-induced PuMYB123-like transcription by decreasing the PuPP2AA2 expression, ultimately leading to increased anthocyanin biosynthesis. Our study reveals a pathway regulating the ROS-induced anthocyanin biosynthesis in pears, further clarifying the mechanism underlying the abiotic stress-induced anthocyanin biosynthesis, which may have implications for improving plant stress tolerance.

Sphingolipid inhibitor response gene GhMYB86 controls fiber elongation by regulating microtubule arrangement

Although the cell membrane and cytoskeleton play essential roles in cellular morphogenesis, the interaction between the membrane and cytoskeleton is poorly understood. Cotton fibers are extremely elongated single cells, which makes them an ideal model for studying cell development. Here, we used the sphingolipid biosynthesis inhibitor, fumonisin B1 (FB1), and found that it effectively suppressed the myeloblastosis (MYB) transcription factor GhMYB86, thereby negatively affecting fiber elongation. A direct target of GhMYB86 is GhTUB7, which encodes the tubulin protein, the major component of the microtubule cytoskeleton. Interestingly, both the overexpression of GhMYB86 and GhTUB7 caused an ectopic microtubule arrangement at the fiber tips, and then leading to shortened fibers. Moreover, we found that GhMBE2 interacted with GhMYB86 and that FB1 and reactive oxygen species induced its transport into the nucleus, thereby enhancing the promotion of GhTUB7 by GhMYB86. Overall, we established a GhMBE2-GhMYB86-GhTUB7 regulation module for fiber elongation and revealed that membrane sphingolipids affect fiber elongation by altering microtubule arrangement.

Unveiling the power of MYB transcription factors: Master regulators of multi-stress responses and development in cotton

Plants, being immobile, are subject to environmental stresses more than other creatures, necessitating highly effective stress tolerance systems. Transcription factors (TFs) play a crucial role in the adaptation mechanism as they can be activated by diverse signals and ultimately control the expression of stress-responsive genes. One of the most prominent plant TFs family is MYB (myeloblastosis), which is involved in secondary metabolites, developmental mechanisms, biological processes, cellular architecture, metabolic pathways, and stress responses. Extensive research has been conducted on the involvement of MYB TFs in crops, while their role in cotton remains largely unexplored. We also utilized genome-wide data to discover potential 440 MYB genes and investigated their plausible roles in abiotic and biotic stress conditions, as well as in different tissues across diverse transcriptome databases. This review primarily summarized the structure and classification of MYB TFs biotic and abiotic stress tolerance and their role in secondary metabolism in different crops, especially in cotton. However, it intends to identify gaps in current knowledge and emphasize the need for further research to enhance our understanding of MYB roles in plants.

NtMYB27 acts downstream of NtBES1 to modulate flavonoids accumulation in response to UV-B radiation in tobacco

UV-B radiation can induce the accumulation of many secondary metabolites, including flavonoids, in plants to protect them from oxidative damage. BRI1-EMS-SUPPRESSOR1 (BES1) has been shown to mediate the biosynthesis of flavonoids in response to UV-B. However, the detailed mechanism by which it acts still needs to be further elucidated. Here, we revealed that UV-B significantly inhibited the transcription of multiple transcription factor genes in tobacco, including NtMYB27, which was subsequently shown to be a repressor of flavonoids synthesis in tobacco. We further demonstrated that NtBES1 directly binds to the E-box motifs present in the promoter of NtMYB27 to mediate its transcriptional repression upon UV-B exposure. The UV-B-repressed NtMYB27 could bind to the ACCT-containing element (ACE) in the promoters of Nt4CL and NtCHS and served as a modulator that promoted the biosynthesis of lignin and chlorogenic acid (CGA) but inhibited the accumulation of flavonoids in tobacco. The expression of NtMYB27 was also significantly repressed by heat stress, suggesting its putative roles in regulating heat-induced flavonoids accumulation. Taken together, our results revealed the role of NtBES1 and NtMYB27 in regulating the synthesis of flavonoids during the plant response to UV-B radiation in tobacco.

Integrated metabolomic and transcriptomic analysis reveals biosynthesis mechanism of flavone and caffeoylquinic acid in chrysanthemum

BACKGROUND

Chrysanthemum morifolium 'HangBaiJu', a popular medicinal and edible plant, exerts its biological activities primarily through the presence of flavones and caffeoylquinic acids (CQAs). However, the regulatory mechanism of flavone and CQA biosynthesis in the chrysanthemum capitulum remains unclear.

RESULTS

In this study, the content of flavones and CQAs during the development of chrysanthemum capitulum was determined by HPLC, revealing an accumulation pattern with higher levels at S1 and S2 and a gradual decrease at S3 to S5. Transcriptomic analysis revealed that CmPAL1/2, CmCHS1/2, CmFNS, CmHQT, and CmHCT were key structural genes in flavones and CQAs biosynthesis. Furthermore, weighted gene co-expression correlation network analysis (WGCNA), k-means clustering, correlation analysis and protein interaction prediction were carried out in this study to identify transcription factors (TFs) associated with flavone and CQA biosynthesis, including MYB, bHLH, AP2/ERF, and MADS-box families. The TFs CmERF/PTI6 and CmCMD77 were proposed to act as upstream regulators of CmMYB3 and CmbHLH143, while CmMYB3 and CmbHLH143 might form a complex to directly regulate the structural genes CmPAL1/2, CmCHS1/2, CmFNS, CmHQT, and CmHCT, thereby controlling flavone and CQA biosynthesis.

CONCLUSIONS

Overall, these findings provide initial insights into the TF regulatory network underlying flavones and CQAs accumulation in the chrysanthemum capitulum, which laid a theoretical foundation for the quality improvement of C. morifolium 'HangBaiJu' and the high-quality development of the industry.

Aloe vera and tea polyphenols composite coating delays passion fruit senescence by promoting phenolic and flavonoid accumulation

Passion fruits are highly perishable during postharvest storage and transportation, prompting the exploration of natural preservatives. This study investigates the synergistic effects of Aloe vera (ALV) and tea polyphenols (TP) coatings on quality retention, ripening modulation, and associated regulatory mechanisms in stored "golden" passion fruit (Passiflora spp.) at 10 °C. The application of a composite coating comprising 40 % ALV and 0.1 g/L TP led to notable improvements in fruit preservation over a 28-day storage period. At the day of 28, quantitatively, the ALV + TP treatment reduced weight loss by 41.60 %, shrinkage index by 28.13 %, and decay index by 50 %, significantly outperforming the control and individual treatments; the treated fruits exhibited enhanced firmness, reduced ethylene production, and the respiration peak was delayed about 6 days. Metabolomic analysis revealed pronounced alterations in key metabolic pathways, notably phenylpropanoid and flavonoid biosynthesis. Specifically, significant increases in metabolites such as phenolic acids (Feruloylmalic acid and Acropyrone) and flavonoids (Okanin-4'-O-glucoside, Apigenin-8-C-Arabinoside, Quercetin-3-O- (2'-O-galloyl) galactoside, and Catechin callate) were observed. Concurrently, transcript levels of key biosynthetic genes including cinnamate 4-hydroxylase (PeC4H), 4-coumarate-coenzyme a ligase (PeC4L), hydroxycinnamoyl transferase (PeHCT) and flavonol synthase (PeFLS) were significantly up-regulated by ALV + TP coating, indicating a robust activation of these pathways. The findings underscore the effectiveness of the ALV + TP composite coating as an environmentally friendly strategy for enhancing postharvest quality by promoting the accumulation of beneficial phenolic acids and flavonoids in passion fruits.

Identification of MYB Transcription Factor, a Regulator Related to Hydrolysable Tannin Synthesis in Canarium album L., and Functional Analysis of CaMYBR04

Hydrolysed tannins (HTs) are polyphenols, which are related to the astringency, flavour, colour, stability, medicinal value and other characteristics of many fruits and vegetables. The biosynthetic mechanism of the majority of HTs remains unknown, and many biosynthetic pathways of HTs are speculative conclusions that have not been confirmed. The fruit of Canarium album L. (Chinese olive), which is notable for its pharmacological and edible properties, is rich in HTs. The fruit has a distinctive bitter and astringent taste when initially consumed, which mellows to a sweet sensation upon chewing. HTs serve as the primary material basis for the formation of the Chinese olive fruit's astringent quality and pharmacological effects. In this study, the fruit of C. album Changying was utilised as the research material. The objective of this study was to provide a theoretical basis for the quality control of Chinese olive fruit and the application and development of its medicinal value. In addition, the study aimed to identify and screen related MYB transcription factors involved in the synthesis of HTs in the fruit and to clarify the mechanism of MYBs in the process of synthesis and regulation of HTs in Chinese olive fruit. The principal findings were as follows. A total of 83 differentially expressed Chinese olive MYB transcription factors (CaMYBs) were identified, including 54 1R-MYBs (MYB-related), 25 2R-MYBs (R2R3-MYBs), 3 3R-MYBs, and 1 4R-MYB. Through trend analysis and correlation analysis, it was found that CaMYBR04 (Isoform0032534) exhibited a significantly higher expression (FPKM) than the other CaMYBs. The full-length cDNA sequence of CaMYBR04 was cloned and transformed into strawberry. The results demonstrated that CaMYBR04 significantly enhanced the fruit's hydrolysable tannin content. Consequently, this study elucidated the function of CaMYBR04, a regulator of the Chinese olive fruit hydrolysable tannin synthesis pathway, and established a theoretical foundation for the synthesis and regulation of fruit HTs.

Flavonoids: Potential therapeutic agents for cardiovascular disease

Flavonoids are found in the roots, stems, leaves, and fruits of many plant taxa. They are related to plant growth and development, pigment formation, and protection against environmental stress. Flavonoids function as antioxidants and exert anti-inflammatory effects in the cardiovascular system by modulating classical inflammatory response pathways, such as the TLR4-NF-ĸB, PI3K-AKT, and Nrf2/HO-1 signalling pathways. There is increasing evidence for the therapeutic effects of flavonoids on hypertension, atherosclerosis, and other diseases. The potential clinical value of flavonoids for diseases of the cardiovascular system has been widely explored. For example, studies have evaluated the roles of flavonoids in the regulation of blood pressure via endothelium-dependent and non-endothelium-dependent pathways and in the regulation of myocardial systolic and diastolic functions by influencing calcium homeostasis and smooth muscle-related protein expression. Flavonoids also have hypoglycaemic, hypolipidemic, anti-platelet, autophagy, and antibacterial effects. In this paper, the role and mechanism of flavonoids in cardiovascular diseases were reviewed in order to provide reference for the clinical application of flavonoids in the future.

Metabolic engineering of Oryza sativa for lignin augmentation and structural simplification

The sustainable production and utilization of lignocellulose biomass are indispensable for establishing sustainable societies. Trees and large-sized grasses are the major sources of lignocellulose biomass, while large-sized grasses greatly surpass trees in terms of lignocellulose biomass productivity. With an overall aim to improve lignocellulose usability, it is important to increase the lignin content and simplify lignin structures in biomass plants via lignin metabolic engineering. Rice (Oryza sativa) is not only a representative and important grass crop, but also is a model for large-sized grasses in biotechnology. This review outlines progress in lignin metabolic engineering in grasses, mainly rice, including characterization of the lignocellulose properties, the augmentation of lignin content and the simplification of lignin structures. These findings have broad applicability for the metabolic engineering of lignin in large-sized grass biomass plants.

Unveiling phenylpropanoid regulation: the role of DzMYB activator and repressor in durian (Durio zibethinus) fruit

KEY MESSAGE

DzMYB2 functions as an MYB activator, while DzMYB3 acts as an MYB repressor. They bind to promoters, interact with DzbHLH1, and influence phenolic contents, revealing their roles in phenylpropanoid regulation in durian pulps. Durian fruit has a high nutritional value attributed to its enriched bioactive compounds, including phenolics, carotenoids, and vitamins. While various transcription factors (TFs) regulate phenylpropanoid biosynthesis, MYB (v-myb avian myeloblastosis viral oncogene homolog) TFs have emerged as pivotal players in regulating key genes within this pathway. This study aimed to identify additional candidate MYB TFs from the transcriptome database of the Monthong cultivar at five developmental/postharvest ripening stages. Candidate transcriptional activators were discerned among MYBs upregulated during the ripe stage based on the positive correlation observed between flavonoid biosynthetic genes and flavonoid contents in ripe durian pulps. Conversely, MYBs downregulated during the ripe stage were considered candidate repressors. This study focused on a candidate MYB activator (DzMYB2) and a candidate MYB repressor (DzMYB3) for functional characterization. LC-MS/MS analysis using Nicotiana benthamiana leaves transiently expressing DzMYB2 revealed increased phenolic compound contents compared with those in leaves expressing green fluorescence protein controls, while those transiently expressing DzMYB3 showed decreased phenolic compound contents. Furthermore, it was demonstrated that DzMYB2 controls phenylpropanoid biosynthesis in durian by regulating the promoters of various biosynthetic genes, including phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), chalcone isomerase (CHI), and dihydroflavonol reductase (DFR). Meanwhile, DzMYB3 regulates the promoters of PAL, 4-coumaroyl-CoA ligase (4CL), CHS, and CHI, resulting in the activation and repression of gene expression. Moreover, it was discovered that DzMYB2 and DzMYB3 could bind to another TF, DzbHLH1, in the regulation of flavonoid biosynthesis. These findings enhance our understanding of the pivotal role of MYB proteins in regulating the phenylpropanoid pathway in durian pulps.

Genome-Wide Identification and Characterization of Lignin Synthesis Genes in Maize

Lignin is a crucial substance in the formation of the secondary cell wall in plants. It is widely distributed in various plant tissues and plays a significant role in various biological processes. However, the number of copies, characteristics, and expression patterns of genes involved in lignin biosynthesis in maize are not fully understood. In this study, bioinformatic analysis and gene expression analysis were used to discover the lignin synthetic genes, and two representative maize inbred lines were used for stem strength phenotypic analysis and gene identification. Finally, 10 gene families harboring 117 related genes involved in the lignin synthesis pathway were retrieved in the maize genome. These genes have a high number of copies and are typically clustered on chromosomes. By examining the lignin content of stems and the expression patterns of stem-specific genes in two representative maize inbred lines, we identified three potential stem lodging resistance genes and their interactions with transcription factors. This study provides a foundation for further research on the regulation of lignin biosynthesis and maize lodging resistance genes.

Transcriptome sequencing of medical herb Salvia Rosmarinus (Rosemary) revealed the phenylpropanoid biosynthesis pathway genes and their phylogenetic relationships

BACKGROUND

The Salvia rosmarinus spenn. (rosemary) is considered an economically important ornamental and medicinal plant and is widely utilized in culinary and for treating several diseases. However, the procedure behind synthesizing secondary metabolites-based bioactive compounds at the molecular level in S. rosmarinus is not explored completely.

METHODS AND RESULTS

We performed transcriptomic sequencing of the pooled sample from leaf and stem tissues on the Illumina HiSeqTM X10 platform. The transcriptomics analysis led to the generation of 29,523,608 raw reads, followed by data pre-processing which generated 23,208,592 clean reads, and de novo assembly of S. rosmarinus obtained 166,849 unigenes. Among them, nearly 75.1% of unigenes i.e., 28,757 were interpreted against a non-redundant protein database. The gene ontology-based annotation classified them into 3 main categories and 55 sub-categories, and clusters of orthologous genes annotation categorized them into 23 functional categories. The Kyoto Encyclopedia of Genes and Genomes database-based pathway analysis confirmed the involvement of 13,402 unigenes in 183 biochemical pathways, among these unigenes, 1,186 are involved in the 17 secondary metabolite production pathways. Several key enzymes involved in producing aromatic amino acids and phenylpropanoids were identified from the transcriptome database. Among the identified 48 families of transcription factors from coding unigenes, bHLH, MYB, WRKYs, NAC, C2H2, C3H, and ERF are involved in flavonoids and other secondary metabolites biosynthesis.

CONCLUSION

The phylogenetic analysis revealed the evolutionary relationship between the phenylpropanoid pathway genes of rosemary with other members of Lamiaceae. Our work reveals a new molecular mechanism behind the biosynthesis of phenylpropanoids and their regulation in rosemary plants.

Biochemical and Molecular Insights into Variation in Sesame Seed Antioxidant Capability as Revealed by Metabolomics and Transcriptomics Analysis

Sesame seeds are important resources for relieving oxidation stress-related diseases. Although a significant variation in seeds' antioxidant capability is observed, the underlying biochemical and molecular basis remains elusive. Thus, this study aimed to reveal major seed components and key molecular mechanisms that drive the variability of seeds' antioxidant activity (AOA) using a panel of 400 sesame accessions. The seeds' AOA, total flavonoid, and phenolic contents varied from 2.03 to 78.5%, 0.072 to 3.104 mg CAE/g, and 2.717 to 21.98 mg GAE/g, respectively. Analyses revealed that flavonoids and phenolic acids are the main contributors to seeds' AOA variation, irrespective of seed coat color. LC-MS-based polyphenol profiling of high (HA) and low (LA) antioxidant seeds uncovered 320 differentially accumulated phenolic compounds (DAPs), including 311 up-regulated in HA seeds. Tricin, persicoside, 5,7,4',5'-tetrahydro-3',6-dimethoxyflavone, 8-methoxyapigenin, and 6,7,8-tetrahydroxy-5-methoxyflavone were the top five up-regulated in HA. Comparative transcriptome analysis at three seed developmental stages identified 627~2357 DEGs and unveiled that differential regulation of flavonoid biosynthesis, phenylpropanoid biosynthesis, and stilbene biosynthesis were the key underlying mechanisms of seed antioxidant capacity variation. Major differentially regulated phenylpropanoid structural genes and transcription factors were identified. SINPZ0000571 (MYB), SINPZ0401118 (NAC), and SINPZ0500871 (C3H) were the most highly induced TFs in HA. Our findings may enhance quality breeding.

Soybean RVE8a confers salt and drought tolerance in Arabidopsis

Soybean is an economically important crop, which often suffers various abiotic stresses. REVEILLE (RVE) genes have been generally considered as circadian oscillators to mediate diverse developmental processes and plant response to environmental stresses. Addressing their roles is of significance for utilizing them to enhance agronomic traits in crops. However, our understanding of soybean RVEs is extremely limited. In the study, we investigated the expression patterns of soybean CCA1-like genes under salt stress using our RNA-Seq data. Subsequently, a salt stress-inducible gene, GmRVE8a, was chosen for further study. Phylogenetic analysis indicated that GmRVE8a is most closely related to Arabidopsis RVE4 and RVE8. Also, GmRVE8a showed circadian expression pattern with 24 h rhythmic period, suggesting that it might be a clock-regulated gene. Moreover, transgenic Arabidopsis lines over-expressing GmRVE8a were generated. It was observed that ectopic over-expression of GmRVE8a caused a significant delay in flowering. Further observation indicated that under salt and drought stress, transgenic seedlings were stronger than wild type. Consistently, three-week-old transgenic plants grew better than wild type under salt and drought conditions, and the MDA content in transgenic lines was significantly lower than wild type, suggesting that GmRVE8a might be a positive regulator in response to salt and drought stress. Intriguingly, Y2H assay indicated that GmRVE8a physically interacted with a drought-tolerant protein, GmNAC17. Overall, our findings provided preliminary information regarding the functional roles of GmRVE8a in response to salt and drought stress.

Metabolome and transcriptome analyses reveal changes of rapeseed in response to ABA signal during early seedling development

Seed germination is an important development process in plant growth. The phytohormone abscisic acid (ABA) plays a critical role during seed germination. However, the mechanism of rapeseed in response to ABA is still elusive. In order to understand changes of rapeseed under exogenous ABA treatment, we explored differentially expressed metabolites (DEMs) and the differentially expressed genes (DEGs) between mock- and ABA-treated seedlings. A widely targeted LC-MS/MS based metabolomics were used to identify and quantify metabolic changes in response to ABA during seed germination, and a total of 186 significantly DEMs were identified. There are many compounds which are involved in ABA stimuli, especially some specific ABA transportation-related metabolites such as starches and lipids were screened out. Meanwhile, a total of 4440 significantly DEGs were identified by transcriptomic analyses. There was a significant enrichment of DEGs related to phenylpropanoid and cell wall organization. It suggests that exogenous ABA mainly affects seed germination by regulating cell wall loosening. Finally, the correlation analysis of the key DEMs and DEGs indicates that many DEGs play a direct or indirect regulatory role in DEMs metabolism. The integrative analysis between DEGs and DEMs suggests that the starch and sucrose pathways were the key pathway in ABA responses. The two metabolites from starch and sucrose pathways, levan and cellobiose, both were found significantly down-regulated in ABA-treated seedlings. These comprehensive metabolic and transcript analyses provide useful information for the subsequent post-transcriptional modification and post germination growth of rapeseed in response to ABA signals and stresses.

Identification and Expression Analysis of R2R3-MYB Transcription Factors Associated with Flavonoid Biosynthesis in Panax quinquefolius

Panax quinquefolius L. is an important medicinal plant, and flavonoids are among its main secondary metabolites. The R2R3-MYB transcription factor plays an irreplaceable role in plant growth, development, and secondary metabolism. In our study, we identified 159 R2R3-MYBs and analyzed their physical and chemical properties in P. quinquefolius. The protein length of 159 PqMYBs varied from 107 to 1050 amino acids. The molecular weight ranged from 12.21 to 116.44 kDa. The isoelectric point was between 4.57 and 10.34. We constructed a phylogenetic tree of P. quinquefolius and Arabidopsis thaliana R2R3-MYB family members, and PqMYB members were divided into 33 subgroups. Transcriptome data analysis showed that the expression patterns of PqMYBs in root, leaf, and flower were significantly different. Following the MeJA treatment of seedlings, five candidate PqMYB genes demonstrated a response. A correlation analysis of PqMYBs and candidate flavonoid pathway genes showed that PqMYB2, PqMYB46, and PqMYB72 had correlation coefficients that were higher than 0.8 with PqCHS, PqANS4, and PqCCoAMT10, respectively. Furthermore, a transient expression assay confirmed that the three PqMYBs were localized in the nucleus. We speculated that these three PqMYBs were related to flavonoid biosynthesis in P. quinquefolius. These results provided a theoretical basis and a new perspective for further understanding the R2R3-MYB gene family and the biosynthesis mechanism of secondary metabolites in P. quinquefolius.

Full-Length Transcriptome Sequencing and Comparative Transcriptomic Analyses Provide Comprehensive Insight into Molecular Mechanisms of Flavonoid Metabolites Biosynthesis in Styphnolobium japonicum

Styphnolobium japonicum L. is a commonly consumed plant in China, known for its medicinal and nutritional benefits. This study focuses on the medicinal properties influenced by flavonoid metabolites, which vary during flower development. Utilizing full-length transcriptome sequencing on S. japonicum flowers, we observed changes in gene expression levels as the flowers progressed through growth stages. During stages S1 and S2, key genes related to flavonoid synthesis (PAL, 4CL, CHS, F3H, etc.) exhibited heightened expression. A weighted gene co-expression network analysis (WGCNA) identified regulatory genes (MYB, bHLH, WRKY) potentially involved in the regulatory network with flavonoid biosynthesis-related genes. Our findings propose a regulatory mechanism for flavonoid synthesis in S. japonicum flowers, elucidating the genetic underpinnings of this process. The identified candidate genes present opportunities for genetic enhancements in S. japonicum, offering insights into potential applications for improving its medicinal attributes.

NO enhances the adaptability to high-salt environments by regulating osmotic balance, antioxidant defense, and ion homeostasis in eelgrass based on transcriptome and metabolome analysis

Introduction

Eelgrass is a typical marine angiosperm that exhibits strong adaptability to high-salt environments. Previous studies have shown that various growth and physiological indicators were significantly affected after the nitrate reductase (NR) pathway for nitric oxide (NO) synthesis in eelgrass was blocked.

Methods

To analyze the molecular mechanism of NO on the adaptability to high-salt environment in eelgrass, we treated eelgrass with artificial seawater (control group) and artificial seawater with 1 mM/L Na2WO4 (experimental group). Based on transcriptomics and metabolomics, we explored the molecular mechanism of NO affecting the salt tolerance of eelgrass.

Results

We obtained 326, 368, and 859 differentially expressed genes (DEGs) by transcriptome sequencing in eelgrass roots, stems, and leaves, respectively. Meanwhile, we obtained 63, 52, and 36 differentially accumulated metabolites (DAMs) by metabolomics in roots, stems, and leaves, respectively. Finally, through the combined analysis of transcriptome and metabolome, we found that the NO regulatory mechanism of roots and leaves of eelgrass is similar to that of terrestrial plants, while the regulatory mechanism of stems has similar and unique features.

Discussion

NO in eelgrass roots regulates osmotic balance and antioxidant defense by affecting genes in transmembrane transport and jasmonic acid-related pathways to improve the adaptability of eelgrass to high-salt environments. NO in eelgrass leaves regulates the downstream antioxidant defense system by affecting the signal transduction of plant hormones. NO in the stems of eelgrass regulates ion homeostasis by affecting genes related to ion homeostasis to enhance the adaptability of eelgrass to high-salt environments. Differently, after the NO synthesis was inhibited, the glyoxylate and dicarboxylate metabolism, as well as the tricarboxylic acid (TCA) cycle, was regulated by glucose metabolism as a complementary effect to cope with the high-salt environment in the stems of eelgrass. These are studies on the regulatory mechanism of NO in eelgrass, providing a theoretical basis for the study of the salt tolerance mechanism of marine plants and the improvement of terrestrial crop traits. The key genes discovered in this study can be applied to increase salt tolerance in terrestrial crops through cloning and molecular breeding methods in the future.

The functional decline of tomato plants infected by Candidatus Liberbacter solanacearum: an RNA-seq transcriptomic analysis

Introduction

Candidatus Liberibacter solanacearum (CLso) is a regulated plant pathogen in European and some Asian countries, associated with severe diseases in economically important Apiaceous and Solanaceous crops, including potato, tomato, and carrot. Eleven haplotypes of CLso have been identified based on the difference in rRNA and conserved genes and host and pathogenicity. Although it is pathogenic to a wide range of plants, the mechanisms of plant response and functional decline of host plants are not well defined. This study aims to describe the underlying mechanism of the functional decline of tomato plants infected by CLso by analyzing the transcriptomic response of tomato plants to CLso haplotypes A and B.

Methods

Next-generation sequencing (NGS) data were generated from total RNA of tomato plants infected by CLso haplotypes A and B, and uninfected tomato plants, while qPCR analysis was used to validate the in-silico expression analysis. Gene Ontology and KEGG pathways were enriched using differentially expressed genes.

Results

Plants infected with CLso haplotype B saw 229 genes upregulated when compared to uninfected plants, while 1,135 were downregulated. Healthy tomato plants and plants infected by haplotype A had similar expression levels, which is consistent with the fact that CLso haplotype A does not show apparent symptoms in tomato plants. Photosynthesis and starch biosynthesis were impaired while starch amylolysis was promoted in plants infected by CLso haplotype B compared with uninfected plants. The changes in pathway gene expression suggest that carbohydrate consumption in infected plants was more extensive than accumulation. In addition, cell-wall-related genes, including steroid biosynthesis pathways, were downregulated in plants infected with CLso haplotype B suggesting a reduction in membrane fluidity, cell signaling, and defense against bacteria. In addition, genes in phenylpropanoid metabolism and DNA replication were generally suppressed by CLso infection, affecting plant growth and defense.

Discussion

This study provides insights into plants' defense and functional decline due to pathogenic CLso using whole transcriptome sequencing and qPCR validation. Our results show how tomato plants react in metabolic pathways during the deterioration caused by pathogenic CLso. Understanding the underlying mechanisms can enhance disease control and create opportunities for breeding resistant or tolerant varieties.

Comparative transcriptome and metabolome analyses revealed quality difference between beauty tea processed through indoor withering and outdoor solar withering

BACKGROUND

Withering is the first processing procedure of beauty tea, and there are few reports on the impact of withering methods on the quality of beauty tea and its regulatory mechanisms.

RESULTS

Through comparison of fresh tea leaves (FT) with the leaves after indoor natural withering for 18 h (IWT-18) and outdoor solar withering for 6 h (OWT-6), which were collected at the end of the two withering processes, 17 282 and 13 984 differentially expressed genes (DEGs) were respectively screened and 267 and 154 differential metabolites (DMs) were respectively identified. The coexpression network revealed that a large number of DEGs and DMs were enriched in phenylpropanoid, flavonoid, and adenosine triphosphate binding cassette (ABC) transporter pathways, and the number of DMs and DEGs in IWT-18 versus FT exceeded that in OWT-6 versus FT. Both withering methods promoted a significant increase in content of phenylalanine and upregulation of β-glucoside expression in the phenylpropanoid metabolism pathway. Five theaflavin-type proanthocyanidins in the flavonoid synthesis pathway were more significantly accumulated in FT versus IWT-18 than in FT versus OWT-6. Meanwhile, both withering methods can affect the ABC transporter pathway to promote the accumulation of amino acids and their derivatives, but different withering methods affect different ABC transporter families. Outdoor withering with more severe abiotic stress has a greater impact on the ABCG family, whereas indoor withering has a more significant effect on the ABCC family. Sensory evaluation results showed that the dry tea of IWT-18 was slightly better than that of OWT-6 because of the longer withering time and more thorough substance transformation.

CONCLUSION

In conclusion, the formation of honey flavor in beauty tea may be closely related to the DEGs and DMs in these three pathways. Our research provides theoretical data support for further revealing the mechanism of quality formation during the withering process of beauty tea. © 2023 Society of Chemical Industry.

Transcriptomic-Proteomic Analysis Revealed the Regulatory Mechanism of Peanut in Response to Fusarium oxysporum

Peanut Fusarium rot, which is widely observed in the main peanut-producing areas in China, has become a significant factor that has limited the yield and quality in recent years. It is highly urgent and significant to clarify the regulatory mechanism of peanuts in response to Fusarium oxysporum. In this study, transcriptome and proteome profiling were combined to provide new insights into the molecular mechanisms of peanut stems after F. oxysporums infection. A total of 3746 differentially expressed genes (DEGs) and 305 differentially expressed proteins (DEPs) were screened. The upregulated DEGs and DEPs were primarily enriched in flavonoid biosynthesis, circadian rhythm-plant, and plant-pathogen interaction pathways. Then, qRT-PCR analysis revealed that the expression levels of phenylalanine ammonia-lyase (PAL), chalcone isomerase (CHI), and cinnamic acid-4-hydroxylase (C4H) genes increased after F. oxysporums infection. Moreover, the expressions of these genes varied in different peanut tissues. All the results revealed that many metabolic pathways in peanut were activated by improving key gene expressions and the contents of key enzymes, which play critical roles in preventing fungi infection. Importantly, this research provides the foundation of biological and chemical analysis for peanut disease resistance mechanisms.

SmWRKY11 acts as a positive regulator in eggplant response to salt stress

Salt stress is one of the most threatening abiotic stresses to plants, which can seriously affect plant growth, development, reproduction, and yield. However, the mechanisms of plant against salt stress largely remain unclear. Herein, SmWRKY11, an assumed WRKY transcription factor, was functionally characterized in eggplant against salt stress. SmWRKY11 was significantly up-regulated by salt, dehydration stress, and ABA treatment. SmWRKY11 located in the nucleus, and the Plant_zn_clust conserved domain exhibited transcriptional activation activity. Silencing of SmWRKY11 enhanced the susceptibility of eggplant to salt stress, accompanied by significantly down-regulation of transcript expression levels of salt stress defense-related genes SmNCED1, SmGSTU10, and positive regulator of salt stress response SmERF1 as well as increase of hydrogen peroxide (H2O2) content and decrease of the enzyme activities of catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX). In addition, silencing of SmERF1 also could significantly down-regulate SmWRKY11 expression in eggplant response to salt stress. By luciferase reporter assay and chromatin immunoprecipitation PCR assay, SmERF1 expression was found to be indirectly activated by SmWRKY11. These data indicate that SmWRKY11 acts as a positive regulator by forming positive feedback loop with SmERF1 via an indirect regulatory manner in eggplant response to salt stress.

Characterization and nutritional valorization of agricultural waste corncobs from Italian maize landraces through the growth of medicinal mushrooms

The research investigates the potential use of maize cobs (or corncobs) from five genotypes, including the B73 inbred line and four locally cultivated landraces from Northern Italy, as substrate for implementing Solid State fermentation processes with four Medicinal Mushrooms (MMs). The corncobs were characterized based on their proximate composition, lignin, phenolics content (both free and bound), and total antioxidant capacity. Among the MMs tested, Pleurotus ostreatus and Ganoderma annularis demonstrated the most robust performance. Their growth was parametrized using Image Analysis technique, and chemical composition of culture samples was characterized compared to that of corncobs alone. In all culture samples, the growth of MMs led to a significant reduction (averaging 40%) in the total phenolics contents compared to that measured in corncobs alone. However, the high content of free phenolics in the cobs negatively impacted the growth of P. ostreatus. The final MM-corncob matrix exhibited reduced levels of free sugars and starch (≤ 2.2% DW, as a sum) and increased levels of proteins (up to 5.9% DW) and soluble dietary fiber (up to 5.0% DW), with a notable trend toward higher levels of β-glucan compared to corncobs alone. This research paves the way for the use of this matrix as an active ingredient to enhance the nutritional value of food preparations.

The Characterization of R2R3-MYB Genes in Ammopiptanthus nanus Uncovers That the miR858-AnaMYB87 Module Mediates the Accumulation of Anthocyanin under Osmotic Stress

R2R3-MYB transcription factors (TFs) participate in the modulation of plant development, secondary metabolism, and responses to environmental stresses. Ammopiptanthus nanus, a leguminous dryland shrub, tolerates a high degree of environmental stress, including drought and low-temperature stress. The systematic identification, structural analysis, evolutionary analysis, and gene profiling of R2R3-MYB TFs under cold and osmotic stress in A. nanus were performed. Up to 137 R2R3-MYB TFs were identified and clustered into nine clades, with most A. nanus R2R3-MYB members belonging to clade VIII. Tandem and segmental duplication events drove the expansion of the A. nanus R2R3-MYB family. Expression profiling revealed that multiple R2R3-MYB genes significantly changed under osmotic and cold stress conditions. MiR858 and miR159 targeted 88 R2R3-MYB genes. AnaMYB87, an miR858-targeted clade VIII R2R3-MYB TF, was up-regulated under both osmotic and cold stress. A transient expression assay in apples showed that the overexpression of AnaMYB87 promoted anthocyanin accumulation. A luciferase reporter assay in tobacco demonstrated that AnaMYB87 positively affected the transactivation of the dihydroflavonol reductase gene, indicating that the miR858-MYB87 module mediates anthocyanin accumulation under osmotic stress by regulating the dihydroflavonol reductase gene in A. nanus. This study provides new data to understand the roles of R2R3-MYB in plant stress responses.

Comparative transcriptome analysis of major lodging resistant factors in hulless barley

Hulless barley (Hordeum vulgare L. var. nudum Hook. f.), belonging to the genus Gramineae, has high and steady output and thus considered as a principal food crop by Tibetan people. Hulless barley grain can be used for food, brewing, and functional health product development, while its straw serves as an essential supplementary forage and is a crucial cereal crop. Lodging can reduce the yield and quality of barley grain and straw, and it hinders mechanical harvesting. It is a significant factor affecting high and stable yields of barley. Unlike other Poaceae plants (such as rice, wheat), hulless barley is mainly grown in high-altitude regions, where it is susceptible to low temperatures, strong winds, and heavy rainfall. As a result, its stem lodging resistance is relatively weak, making it prone to lodging during the growth period. In this study, we observed that the lignin concentration and the contents of lignin monomers (H, S, and G), and neutral detergent fibre of the lodging-resistant variety Kunlun14 were substantially greater than those of the lodging-sensitive variety Menyuanlianglan. We performed the weighted gene co-expression network analysis (WGCNA) and Short Time-series Expression Miner (STEM) analysis of both the lodging-resistant and lodging-sensitive varieties. Through transcriptome sequencing analysis at different developmental stages, combined with the previously annotated genes related to lodging resistance, a total of 72 DEGs were identified. Among these DEGs, 17 genes were related to lignin, cellulose, and hemicellulose synthesis or regulation, including five transcription factors about NAC, MYB and WRKY. Our results provide a basis for further exploring the molecular mechanism of stem lodging resistance in hulless barley and provide valuable gene resources for stem lodging resistance molecular breeding.