Transcriptomic Analysis Reveals Possible Influences of ABA on Secondary Metabolism of Pigments, Flavonoids and Antioxidants in Tomato Fruit during Ripening

Enhancing abscisic acid production in Botrytis cinerea through metabolic engineering based on a constitutive promoter library

Abscisic acid (ABA) is an important plant growth regulator with broad applications in agriculture, forestry, and other fields. Currently, the industrial production of ABA primarily relies on microbial fermentation using Botrytis cinerea, but its genetic toolbox is limited. To address this, we first screened 10 strong constitutive promoters from the genome of B. cinerea through transcriptomic analysis. The expression levels of the promoters covered a range of 3-4 orders of magnitude according to the measured β-glucuronidase activity. Subsequently, four promoters of different strength were used to balance the cofactor supply in B. cinerea. Overexpression of NADH kinase using the medium-strength promoter Pef1a significantly enhanced ABA production, resulting in a 32.26 % increase compared to the control. Finally, by combining promoter engineering with a push-pull strategy, we optimized the biosynthesis of ABA. The recombinant strain Pthi4:hmgr-Pef1a:a4, overexpressing HMGR under the Pthi4 promoter and Bcaba4 under the Pef1a promoter, achieved an ABA titer of 1.18 g/L, a 58.92 % increase. To our best knowledge, this is the first constitutive promoter library suitable for B. cinerea, providing important tools for the industrial production of ABA.

Genome-wide screening of mitogen-activated protein kinase (MAPK) gene family and expression profile under heavy metal stress in Solanum lycopersicum

MAPKs are one of the essential signal transduction complexes which are responsible for the perception of abiotic stress and for the producing of related transcripts for responding to abiotic stress. For systematical analyzes of the mitogen-activated protein (MAP) kinase gene families and their expression profiles in Solanum lycopersicum L. exposed to diverse heavy metal stresses, 17 SlMAPK genes were studied in comparison with their 159 orthologs from various plant species. The result of phylogenetic analysis revealed that SlMAPKs were divided into four different subgroups (A, B, C, and D) based on their nucleic acid and protein sequence alignments. SlMAPKs including A, B and C group had lower molecular weights and more hydrophobic structures than D group SlMAPKs, while possible extra phosphorylation sites predicted in D-group SLMAPKs. 24 cis regulating elements such as Box 4, TATA-box, ABRE and CAAT-box were detected in their upstream parts of DNA sequences. Also, it was determined that SlMAPKs show interactions with important proteins such as Guanine nucleotide-binding protein beta subunit, heterotrimeric G-protein, protein phosphatase 2C and HY5. The results from our gene expression analyzes, significant increases were found in the expressions of the selected SLMAPK gene with applications of a range of increasing heavy metal concentrations (e.g., by the application of the 400 mM Ni + Pb exposure, a 16-fold increase in the expression of SlMAPK gene was noted). Overall, SlMAPK genes and proteins known were re-evaluated, and the SlMAPKs interactions with some other important proteins were observed. Also, some predictions about the extra phosphorylation sites of SlMAPKs having effects on their functions were done. In addition, the expression levels of SlMAPK genes were monitored under different levels of heavy metal stress exposures.

Determining the function of ripening associated genes and biochemical changes during tomato (Solanum lycopersicum L.) fruit maturation

This article examines biochemical alterations and gene expression changes during tomato fruit physiology. The chroma index increases from mature green (41.27) to red ripe (48.36) stages, and the texture softens from mature green (43.56 N) to red ripe (24.75 N). Reducing sugar and total carotenoid levels rise at the red ripe stage. Free radical content was elevated in the early stages (7 nM) of ripening and declined at the later stages (4 nM). The specific activity of α-mannosidase and β-N-acetyl hexosaminidase was high at the breaker (0.077 & 0.075 U/mg, respectively) stages, while polygalacturonase activity was high at red ripe (1.173 U/mg) stage. qPCR experiments revealed that the α-mannosidase was upregulated during the breaker (1.2 fold) stages of tomato ripening, the β-N-acetyl Hexosaminidase was upregulated throughout the breaker (2 fold), and pink (1.2 fold) stages of tomato ripening, and the β-xylosidase was upregulated significantly during the breaker stage (3.9 fold) of tomato ripening. The current findings revealed that the α-Mannosidase (0.77), β-N-acetylhexosaminidase (0.99), xylosidase (0.85), ethylene-responsive factors (0.86), aminocylco propane carboxylic oxidase (0.90), and pectin methylesterase (0.83), were significantly associated with textural softening. Polygalacturonase (0.75) positively correlated to reducing sugar formation, aminocylco propane carboxylic synthase 4 (0.96) expression correlates with chroma changes during tomato fruit ripening. These correlations illustrate the complex interplay between gene expression and the physical and biochemical changes occurring during tomato fruit ripening.

Metabolome and transcriptome analysis reveal the pigments biosynthesis pathways in different color fruit peels of Clausena lansium L. Skeels

Introduction

The color of Clausena lansium L. Skeels cv. Jixin fruit peel is brown (BP), while the mutant cv. Zijin had purple fruit peels (PP). The coloration of the peels was attributed to significant differences in chlorophyll, carotenoid, and anthocyanin content between BP and PP.

Methods

This study investigates the biosynthetic metabolic activities in the brown and purple peels of Clausena lansium L. Skeels using metabolomics and transcriptomics. It aims to identify metabolic pathways and differentially expressed genes related to flavonoids and anthocyanins biosynthesis.

Results

The PP (purple peel) has higher levels of a-carotene and b-carotene but lower levels of chlorophyll a, chlorophyll b, and lutein compared to BP. Zeaxanthin was absent from both peels, suggesting that the b-carotene hydroxylase enzyme is not active. Both peels contain delphinidin-based (Dp) and cyanidin-based (Cy) anthocyanins, but not pelargonidin-based (Pg). The total anthocyanin content and the Dp/Cy ratio are higher in PP than in BP. The delphinidin, cyanidin, and mallow derivatives in the PP were significantly higher than in the BP. The increase of total anthocyanin content and Dp/Cy ratio may be the main reason for the peel color changing from brown to purple. The significant increase of F3H expression in purple peels suggested a higher efficiency of catalyzing the conversion of naringenin into dihydroflavonols in the PP, leading to the higher content of total anthocyanin. Despite the significant increase of FLS expression in PP, the contents of kaempferol, quercetin, and myricetin significantly decreased, suggesting that the increase of FLS expression did not lead to an increase in flavonol biosynthesis.

Discussion

The competition between F3'H and F3'5'H may determine the ratio of Dp/Cy, the higher levels of F3'H, F3'5'H, and UFGT expression, lead to the increase accumulation of total anthocyanin and Dp/Cy in PP. The deficiency of Pg in both peels resulted from the substrate specificity of the DFR enzyme. The research also describes the transition in color from BP to PP and details of the biosynthetic pathways for carotenoids and anthocyanins, elucidating the molecular processes underlying anthocyanin production.

Comparative Transcriptome Analysis Revealing the Potential Salt Tolerance Mechanism of Exogenous Abscisic Acid Application in Melilotus albus

Melilotus albus, which contains abundant pharmacologically active coumarins, is usually used as a rotation crop and green manure worldwide. Abscisic acid (ABA) is a crucial plant hormone that plays an important role in plant stress responses. There is a paucity of information about the ABA signaling pathway and its regulatory network in M. albus. Here, we performed a comparative physiological and transcriptomic analysis to assess the response of M. albus to exogenous ABA. Physiological analysis revealed that proline (Pro), soluble protein and H2O2 content after ABA treatment 3 h significantly increased by 14.0%, 12.0% and 32.4% compared with 0 h in M. albus. A total of 19,855 differentially expressed genes (DEGs) were identified under ABA treatment, including 13,392 in shoots and 15,471 in roots. We obtained two modules that were significantly correlated with the ABA treatment (the darkorange module was positively correlated at 24 h in the shoot, brown2 module positively correlated at 3 h in the root) by weighted correlation network analysis (WGCNA). KEGG enrichment analysis showed that genes within two modules were primarily enriched in protein synthesis and metabolism, secondary metabolites, purine and pyrimidine metabolism, and phenylalanine, tyrosine and tryptophan biosynthesis. GO enrichment analysis indicated that genes within two modules were primarily enriched in energy substance metabolism. These pathways were mainly associated with abiothic stress, which indicated that exogenous application of ABA activated the stress resistance system of M. albus. The hub gene 4CL1 (4-Coumarate: CoA ligase 1) was translated and expressed in yeast, resulting in enhanced salt and ABA tolerance in the transgenic yeast. Overexpression of Ma4CL1 in M. albus improved the salt resistance of the transgenic plants. Profiling ABA-responsive genes offers valuable insights into the molecular functions of regulatory genes and will facilitate future molecular breeding efforts in M. albus.

Transcriptional and genetic characteristic of chimera pea generation via double ethyl methanesulfonate-induced mutation revealed by transcription analysis

Ethyl methanesulfonate (EMS)-induced mutagenesis is a prominent method for generating plant mutants, often resulting in chimera plants; however, their transcriptional and genetic characteristic remain elusive. In this investigation, chimera pea (Pisum sativum L.) specimens, labeled GY1 and GY2, exhibiting a distinctive phenotype with yellow and green leaves were meticulously cultivated via sequential double EMS mutagenesis. The observed color disparity between the yellow and green leaves was attributed to a significant reduction in chlorophyll content coupled with heightened lutein levels in both chimeric variants. Transcriptome profiling revealed the enrichment of differentially expressed genes in both GY1 and GY2, specifically implicating Kyoto Encyclopedia of Genes and Genomes pathways linked to amino acid biosynthesis and ribosome development, alongside Gene Ontology (GO) biological processes linked with stress response mechanisms. Few structural genes associated with chlorophyll and lutein biosynthesis exhibited discernible differential expression. Despite these functional similarities, distinctive nuances were evident between specimens, with GY1 exhibiting enrichment in GO pathways related to chloroplast development and GY2 showing enrichment for ribosome development pathways. Single-nucleotide polymorphism (SNP) analysis uncovered a shared pool of 599 and 598 polymorphisms in the yellow and green leaves of GY1 and GY2, respectively, likely stemming from the initial EMS mutagenesis step. Further investigation revealed an increased number of unique SNPs in the yellow leaves following the second EMS application, whereas the green leaves exhibited sparse and unique SNP occurrences, suggestive of potential evasion from secondary mutagenesis. This inherent genetic variability underpins the mechanism underlying the formation of chimera plants. Predominant base mutations induced by EMS were characterized by G/A and C/T transitions, constituting 74.1% of the total mutations, aligning with established EMS mutation induction paradigms. Notably, genes encoding the eukaryotic translation initiation factor eIIso4G and the ubiquitin ligase RKP, known to modulate leaf color in model plants, harbored two SNPs in the yellow leaves of both GY1 and GY2, implicating their putative role in the yellow leaf phenotype. Collectively, this study provides novel insights into the transcriptional and genetic characteristics of chimera plants via EMS-induced mutagenesis.

Drought Protective Effects of Exogenous ABA and Kinetin on Lettuce: Sugar Content, Antioxidant Enzyme Activity, and Productivity

Drought is an environmental stressor that significantly impacts plant growth and development. Comprehending the complexity of drought stress and water utilization in the context of plant growth and development holds significant importance for sustainable agriculture. The aim of this study was to evaluate the effect of exogenously applied phytohormones on lettuce (Lactuca sativa L.) sugar content profiles and antioxidant enzyme activity and productivity. Lettuce plants were grown under normal and drought conditions in a growth chamber with a photoperiod of 14/10 h (day/night). Kinetin and abscisic acid were applied separately and in combinations when the second leaf was fully expanded. The results showed that sugar accumulation and productivity of the pretreated plants under drought were significantly higher than the controls. The perspective offered by this work showed that growth-related and stress-related phytohormones significantly influenced plant sugar metabolism, metabolic profiles, and productivity, thus enabling the control of yield and quality.

Quantitative proteomic analysis of tomato fruit ripening behavior in response to exogenous abscisic acid

BACKGROUND

To determine how abscisic acid (ABA) affects tomato fruit ripening at the protein level, mature green cherry tomato fruit were treated with ABA, nordihydroguaiaretic acid (NDGA) or sterile water (control, CK). The proteomes of treated fruit were analyzed and quantified using tandem mass tags (TMTs) at 7 days after treatment, and the gene transcription abundances of differently expressed proteins (DEPs) were validated with quantitative real-time polymerase chain reaction.

RESULTS

Postharvest tomato fruit underwent faster color transformation and ripening than the CK when treated with ABA. In total, 6310 proteins were identified among the CK and treatment groups, of which 5359 were quantified. Using a change threshold of 1.2 or 0.83 times, 1081 DEPs were identified. Among them, 127 were upregulated and 127 were downregulated in the ABA versus CK comparison group. According to KEGG and protein-protein interaction network analyses, the ABA-regulated DEPs were primarily concentrated in the photosynthesis system and sugar metabolism pathways, and 102 DEPs associated with phytohormones biosynthesis and signal transduction, pigment synthesis and metabolism, cell wall metabolism, photosynthesis, redox reactions, allergens and defense responses were identified in the ABA versus CK and NDGA versus CK comparison groups.

CONCLUSION

ABA affects tomato fruit ripening at the protein level to some extent. The results of this study provided comprehensive insights and data for further research on the regulatory mechanism of ABA in tomato fruit ripening. © 2023 Society of Chemical Industry.

Uncovering the Role of Hormones in Enhancing Antioxidant Defense Systems in Stressed Tomato (Solanum lycopersicum) Plants

Tomato is one of the most important fruits worldwide. It is widely consumed due to its sensory and nutritional attributes. However, like many other industrial crops, it is affected by biotic and abiotic stress factors, reducing its metabolic and physiological processes. Tomato plants possess different mechanisms of stress responses in which hormones have a pivotal role. They are responsible for a complex signaling network, where the antioxidant system (enzymatic and non-enzymatic antioxidants) is crucial for avoiding the excessive damage caused by stress factors. In this sense, it seems that hormones such as ethylene, auxins, brassinosteroids, and salicylic, jasmonic, abscisic, and gibberellic acids, play important roles in increasing antioxidant system and reducing oxidative damage caused by different stressors. Although several studies have been conducted on the stress factors, hormones, and primary metabolites of tomato plants, the effect of endogenous and/or exogenous hormones on the secondary metabolism is still poorly studied, which is paramount for tomato growing management and secondary metabolites production. Thus, this review offers an updated overview of both endogenous biosynthesis and exogenous hormone application in the antioxidant system of tomato plants as a response to biotic and abiotic stress factors.

A metabolome and transcriptome survey to tap the dynamics of fruit prolonged shelf-life and improved quality within Greek tomato germplasm

Introduction

Tomato is a high economic value crop worldwide with recognized nutritional properties and diverse postharvest potential. Nowadays, there is an emerging awareness about the exploitation and utilization of underutilized traditional germplasm in modern breeding programs. In this context, the existing diversity among Greek accessions in terms of their postharvest life and nutritional value remains largely unexplored.

Methods

Herein, a detailed evaluation of 130 tomato Greek accessions for postharvest and nutritional characteristics was performed, using metabolomics and transcriptomics, leading to the selection of accessions with these interesting traits.

Results

The results showed remarkable differences among tomato Greek accessions for overall ripening parameters (color, firmness) and weight loss. On the basis of their postharvest performance, a balance between short shelf life (SSL) and long shelf life (LSL) accessions was revealed. Metabolome analysis performed on 14 selected accessions with contrasting shelf-life potential identified a total of 206 phytonutrients and volatile compounds. In turn, transcriptome analysis in fruits from the best SSL and the best LSL accessions revealed remarkable differences in the expression profiles of transcripts involved in key metabolic pathways related to fruit quality and postharvest potential.

Discussion

The pathways towards cell wall synthesis, polyamine synthesis, ABA catabolism, and steroidal alkaloids synthesis were mostly induced in the LSL accession, whereas those related to ethylene biosynthesis, cell wall degradation, isoprenoids, phenylpropanoids, ascorbic acid and aroma (TomloxC) were stimulated in the SSL accession. Overall, these data would provide valuable insights into the molecular mechanism towards enhancing shelf-life and improving flavor and aroma of modern tomato cultivars.

Comparative Analysis of the PYL Gene Family in Three Ipomoea Species and the Expression Profiling of IbPYL Genes during Abiotic Stress Response in Sweetpotato

Abscisic acid (ABA), a critical phytohormone that regulates plant development and stress response, is sensed by the ABA receptors PYR/PYL/RCAR (PYLs). The PYL genes have been widely studied in multiple plant species, while a systematic analysis of PYL genes in the genus Ipomoea remains unperformed. Here, a total of 13, 14, and 14 PYLs were identified in Ipomoea batatas, Ipomoea trifida, and Ipomoea triloba, respectively. Fragment duplication was speculated to play prominent roles in Ipomoea PYL gene expansions. These Ipomoea PYLs were classified into three subfamilies via phylogenetic analysis, which was supported by exon-intron structures and conserved motif analyses. Additionally, the interspecies collinearity analysis further depicted a potential evolutionary relationship between them. Moreover, qRT-PCR analysis showed that multiple IbPYLs are highly and differentially responsive to abiotic stress treatments, suggesting their potential roles in sweetpotato stress responses. Taken together, these data provide valuable insights into the PYLs in the genus Ipomoea, which may be useful for their further functional analysis of their defense against environmental changes.

ChIP-Seq Analysis of SlAREB1 Downstream Regulatory Network during Tomato Ripening

SlAREB1, a member of the abscisic acid (ABA) response element-binding factors (AREB/ABFs) family, was reported to play a crucial role in the expression of ABA-regulated downstream genes and affect the ripening of tomato fruit. However, the downstream genes of SlAREB1 are still unclear. Chromatin immunoprecipitation (ChIP) is a powerful tool and a standard method for studying the interactions between DNA and proteins at the genome-wide level. In the present study, SlAREB1 was proved to continually increase until the mature green stage and then decrease during the ripening period, and a total of 972 gene peaks were identified downstream of SlAREB1 by ChIP-seq analysis, mainly located in the intergenic and promoter regions. Further gene ontology (GO) annotation analysis revealed that the target sequence of SlAREB1 was the most involved in biological function. Kyoto Encylopaedia of Genes and Genomes (KEGG) pathway analysis showed that the identified genes were mainly involved in the oxidative phosphorylation and photosynthesis pathways, and some of them were associated with tomato phytohormone synthesis, the cell wall, pigment, and the antioxidant characteristic of the fruit as well. Based on these results, an initial model of SlAREB1 regulation on tomato fruit ripening was constructed, which provided a theoretical basis for further exploring the effects of the regulation mechanism of SlAREB1 and ABA on tomato fruit ripening.

Transcriptomic analysis reveals that Bacillomycin D-C16 induces multiple pathways of disease resistance in cherry tomato

BACKGROUND

Bacillomycin D-C16 can induce resistance in cherry tomato against pathogens; however, the underlying molecular mechanism is poorly understood. Here, the effect of Bacillomycin D-C16 on induction of disease resistance in cherry tomato was investigated using a transcriptomic analysis.

RESULTS

Transcriptomic analysis revealed a series of obvious enrichment pathways. Bacillomycin D-C16 induced phenylpropanoid biosynthesis pathways and activated the synthesis of defense-related metabolites including phenolic acids and lignin. Moreover, Bacillomycin D-C16 triggered a defense response through both hormone signal transduction and plant-pathogen interactions pathways, and increased the transcription of several transcription factors (e.g., AP2/ERF, WRKY and MYB). These transcription factors might contribute to the further activated the expression of defense-related genes (PR1, PR10 and CHI) and stimulated the accumulation of H2O2.

CONCLUSION

Bacillomycin D-C16 can induce resistance in cherry tomato by activating the phenylpropanoid biosynthesis pathway, hormone signal transduction pathway and plant-pathogen interactions pathway, thus activating comprehensive defense reaction against pathogen invasion. These results provided a new insight into the bio-preservation of cherry tomato by the Bacillomycin D-C16.

Transcriptomic insights into the effects of abscisic acid on the germination of Magnolia sieboldii K. Koch seed

Magnolia sieboldii K. Koch is a deciduous tree species. However, the wild resource of M. sieboldii has been declining due to excessive utilization and seed dormancy. In our previous research, M. sieboldii seeds have morphophysiological dormancy and low germination rates under natural conditions. The aim of the present study was to identify the genes involved in dormancy maintenance. In this study, the germination percentage of M. sieboldii seeds negatively correlated with the content of endogenous abscisic acid (ABA). The hydration of seeds for germination showed three distinct phases. Five key time points were identified: 0 h imbibition (dry seed, GZ), 0 day after imbibition (DAI), 16 DAI, 40 DAI, and 56 DAI. The comprehensive transcript profiles of M. sieboldii seeds treated with ABA and water at the five key germinating stages were obtained. A total of 9641 differentially expressed genes (DEGs) were identified, and 208 and 197 common DEGs were found throughout the ABA and water treatments, respectively. Compared with that in the GZ, 518, 696, 2133, and 1535 DEGs were identified in the SH group at 0, 16, 40 and 56 DAI, respectively. 666, 1725, 1560 and 1415 DEGs were identified in the ABA group at 0, 16, 40, and 56 DAI, respectively. Among the identified DEGs, 12 722 were annotated with GO terms, the top three enriched GO terms were different among the DEGs at 56 DAI in the ABA vs. SH treatments. KEGG pathway enrichment analysis for DEGs indicated that oxidative phosphorylation, protein processing in endoplasmic reticulum, starch and sucrose metabolism play an important role in seed response to ABA. 1926 TFs are obtained and classified into 72 families from the M. sieboldii transcriptome. Results of differential gene expression analysis together with qRT-PCR indicated that phase II is crucial for rapid and successful seed germination. This study is the first to present the global expression patterns of ABA-regulated transcripts in M. sieboldii seeds at different germinating phases.

Dynamics of the sucrose metabolism and related gene expression in tomato fruits under water deficit

The impact of water deficit on sucrose metabolism in sink organs like the fruit remains poorly known despite the need to improve fruit crops resilience to drought in the face of climate change. The present study investigated the effects of water deficit on sucrose metabolism and related gene expression in tomato fruits, aiming to identify candidate genes for improving fruit quality upon low water availability. Tomato plants were subjected to irrigated control and water deficit (-60% water supply compared to control) treatments, which were applied from the first fruit set to first fruit maturity stages. The results have shown that water deficit significantly reduced fruit dry biomass and number, among other plant physiological and growth variables, but substantially increased the total soluble solids content. The determination of soluble sugars on the basis of fruit dry weight revealed an active accumulation of sucrose and concomitant reduction in glucose and fructose levels in response to water deficit. The complete repertoire of genes encoding sucrose synthase (SUSY1-7), sucrose-phosphate synthase (SPS1-4), and cytosolic (CIN1-8), vacuolar (VIN1-2) and cell wall invertases (WIN1-4) was identified and characterized, of which SlSUSY4, SlSPS1, SlCIN3, SlVIN2, and SlCWIN2 were shown to be positively regulated by water deficit. Collectively, these results show that water deficit regulates positively the expression of certain genes from different gene families related to sucrose metabolism in fruits, favoring the active accumulation of sucrose in this organ under water-limiting conditions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01288-7.

AabHLH113 integrates jasmonic acid and abscisic acid signaling to positively regulate artemisinin biosynthesis in Artemisia annua

Artemisinin, a sesquiterpene lactone isolated from Artemisia annua, is in huge market demand due to its efficient antimalarial action, especially after the COVID-19 pandemic. Many researchers have elucidated that phytohormones jasmonic acid (JA) and abscisic acid (ABA) positively regulate artemisinin biosynthesis via types of transcription factors (TFs). However, the crosstalk between JA and ABA in regulating artemisinin biosynthesis remains unclear. Here, we identified a novel ABA- and JA-induced bHLH TF, AabHLH113, which positively regulated artemisinin biosynthesis by directly binding to the promoters of artemisinin biosynthetic genes, DBR2 and ALDH1. The contents of artemisinin and dihydroartemisinic acid increased by 1.71- to 2.06-fold and 1.47- to 2.23-fold, respectively, in AabHLH1113 overexpressed A. annua, whereas they decreased by 14-36% and 26-53%, respectively, in RNAi-AabHLH113 plants. Furthermore, we demonstrated that AabZIP1 and AabHLH112, which, respectively, participate in ABA and JA signaling pathway to regulate artemisinin biosynthesis, directly bind to and activate the promoter of AabHLH113. Collectively, we revealed a complex network in which AabHLH113 plays a key interrelational role to integrate ABA- and JA-mediated regulation of artemisinin biosynthesis.

Crosstalk between melatonin and reactive oxygen species in fruits and vegetables post-harvest preservation: An update

Fruits and vegetables contain numerous nutrients, such as vitamins, minerals, phenolic compounds, and dietary fibers. They reduce the incidence of cardiovascular diseases and the risk of certain chronic diseases, and improve the antioxidant and anti-inflammatory capacity. Moreover, melatonin was found in various fruits and vegetables species. Melatonin acts as a multifunctional compound to participate in various physiological processes. In recent years, many advances have been found that melatonin is also appraised as a key modulator on the fruits and vegetables post-harvest preservation. Fruits and vegetables post-harvest usually elicit reactive oxygen species (ROS) generation and accumulation. Excess ROS stimulate cell damage, protein structure destruction, and tissue aging, and thereby reducing their quality. Numerous studies find that exogenous application of melatonin modulates ROS homeostasis by regulating the antioxidant enzymes and non-enzymatic antioxidants systems. Further evidences reveal that melatonin often interacts with hormones and other signaling molecules, such as ROS, nitric oxide (NO), hydrogen sulfide (H₂S), and etc. Among these 'new' molecules, crosstalks of melatonin and ROS, especially the H₂O₂ produced by RBOHs, are provided in fruits and vegetables post-harvest preservation in this review. It will provide reference for complicated integration of both melatonin and ROS as signal molecules in future study.

Multifaceted effects of difenoconazole in tomato fruit ripening: Physiology, flavour and nutritional quality

Difenoconazole is widely used in crop growth, however, its effects on the quality of agricultural products are poorly studied. In this study, the application of difenoconazole on tomato plants could increase soluble sugar content, reduce organic acid and raise accumulation of nutrient-related metabolites during late fruit ripening. Consumer surveys in our study showed that the treatment of difenoconazole tomatoes group had higher sweetness and lower acidity, and those tomatoes were preferred by consumers. Alterations in fruit flavor-related attributes were at least in part corroborated by the abundance of transcripts related to sucrose (SlLin5, SlLin7, SlSuS2, SlSuS6, SlSPS1, SlSPS3) and organic acids (CS, ICDH, cMDH) anabolism. Furthermore, the difenoconazole also significantly promoted the expression of phytohormones synthesis genes, and consequently increased abscisic acid and ethylene levels. Our study not only provides theoretical support for the use of difenoconazole on tomatoes at the level of flavor quality and nutritional health, but also provides valuable information on the mechanism of triazole fungicides in the flavor quality of tomato fruits.

BcGRP23: A novel gene involved in the chlorophyll metabolic pathway that is activated by BES1 in flowering Chinese cabbage

Glycine-rich proteins (GRPs) are a large family of proteins that play vital roles in cell wall remodeling, metabolism and development, and abiotic stress response. Although the functions of GRPs in cell wall remodeling have been extensively characterized, only a few studies have explored their effects on chlorophyll metabolism and hormone response. Accordingly, we aimed to determine the molecular mechanism of BcGRP23 and its role in chlorophyll metabolism and the BRI1-EMS-SUPPRESSOR 1 (BES1) signaling pathway in flowering Chinese cabbage. The expression levels of BcGRP23 in the leaves and stems gradually decreased with increasing growth and development of flowering Chinese cabbage, while BcGRP23 was barely expressed after flowering. As plant growth continued, the GUS (β-glucuronidase) stain gradually became lighter in hypocotyls and was largely free of growth points. The petioles and stems of BcGRP23-silenced plants lost their green color, and the contents of chlorophyll a (Chl a) and Chl b were significantly reduced. Further research revealed that the expression levels of chlorophyll degradation-related genes were significantly increased in silenced plants compared with the control; however, the opposite was noted for the BcGRP23-overexpressing lines. The BcGRP23 promoter sequence contains numerous hormone-responsive elements. In fact, the expression of BcGRP23 was upregulated in flowering Chinese cabbage following treatment with the hormones indole-3-acetic acid (IAA), gibberellin (GA), 6-benzylaminopurine (6-BA), methyl jasmonate (MeJA), and brassinosteroid (BR). Treatment with BR led to the most significant upregulation. BES1, in response to BRs, directly activated the BcGRP23 promoter. Overall, BcGRP23 regulated the expression of chlorophyll degradation-related genes, thereby affecting the chlorophyll content. Furthermore, the expression of BcGRP23 was significantly regulated by exogenous BR application and was directly activated by BES1. These findings preliminarily suggest the molecular mechanism and regulatory pathway of BcGRP23 in the growth and development of flowering Chinese cabbage plants and their response to environmental stress.

Environmentally driven transcriptomic and metabolic changes leading to color differences in "Golden Reinders" apples

Apple is characterized by its high adaptation to diverse growing environments. However, little is still known about how different environments can regulate at the metabolic or molecular level specific apple quality traits such as the yellow fruit peel color. In this study, changes in carotenoids and chlorophylls, antioxidants as well as differences in the transcriptome were investigated by comparing the peel of "Golden Reinders" apples grown at different valley and mountain orchards. Mountain environment favored the development of yellow color, which was not caused by an enhanced accumulation of carotenoids but rather by a decrease in the chlorophyll content. The yellow phenotype was also associated to higher expression of genes related to chloroplast functions and oxidative stress. Time-course analysis over the last stages of apple development and ripening, in fruit from both locations, further revealed that the environment differentially modulated isoprenoids and phenylpropanoid metabolism and pointed out a key role for H₂O₂ in triggering apple peel degreening. Overall, the results presented herein provide new insights into how different environmental conditions regulate pigment and antioxidant metabolism in apple leading to noticeable differences in the apple peel color.

SlDREB3, a negative regulator of ABA responses, controls seed germination, fruit size and the onset of ripening in tomato

SlDREB3 was identified as a ripening up-regulated gene of the AP2/ERF-domain family of transcription factors. Its manipulation affects processes primarily governed by ABA. It negatively regulates ABA responses in tomato by altering ABA levels/signaling and is, in turn, negatively regulated by ABA. SlDREB3 over-expression lines show higher transcript levels of the ABA metabolism genes CYP707A3 and UGT75C1 and an 85% reduction in ABA levels leading to early seed germination. In contrast, suppression lines show decreased CYP707A3/UGT75C1 expression, 3-fold higher ABA levels and delayed germination. The expression of other ABA signaling and response genes is also affected. Suppression of SlDREB3 accelerates the onset of ripening by 4-5 days while its over-expression delays it and also reduces final fruit size. SlDREB3 manipulation effects large scale changes in the fruit transcriptome with suppression lines showing early increase in ABA levels and activation of most ripening pathway genes that govern ethylene, carotenoids and softening. Strikingly, key transcription factors like CNR, NOR, RIN, FUL1, governing ethylene-dependent and ethylene-independent aspects of ripening, are activated early upon SlDREB3 suppression suggesting their control by ABA. The studies identify SlDREB3 as a negative regulator of ABA responses across tissues and a key ripening regulator controlling ethylene-dependent and ethylene-independent aspects.

Comparative transcriptomic and physiological analyses of weedy rice and cultivated rice to identify vital differentially expressed genes and pathways regulating the ABA response

Weedy rice is a valuable germplasm resource characterized by its high tolerance to both abiotic and biotic stresses. Abscisic acid (ABA) serves as a regulatory signal in plant cells as part of their adaptive response to stress. However, a global understanding of the response of weedy rice to ABA remains to be elucidated. In the present study, the sensitivity to ABA of weedy rice (WR04-6) was compared with that of temperate japonica Shennong9816 (SN9816) in terms of seed germination and post-germination growth via the application of exogenous ABA and diniconazole, an inhibitor of ABA catabolism. Physiological analysis and a transcriptomic comparison allowed elucidation of the molecular and physiological mechanisms associated with continuous ABA and diniconazole treatment. WR04-6 was found to display higher ABA sensitivity than SN9816, resulting in the rapid promotion of antioxidant enzyme activity. Comparative transcriptomic analyses indicated that the number of differentially expressed genes (DEGs) in WR04-6 seedlings treated with 2 μM ABA or 10 μM diniconazole was greater than that in SN9816 seedlings. Genes involved in stress defense, hormone signal transduction, and glycolytic and citrate cycle pathways were highly expressed in WR04-6 in response to ABA and diniconazole. These findings provide new insight into key processes mediating the ABA response between weedy and cultivated rice.

Effects of selenate on Se, flavonoid, and glucosinolate in broccoli florets by combined transcriptome and metabolome analyses

Broccoli is a nutritious vegetable popular all over the world. This study investigated the effects of different concentrations of selenate (0, 0.1, 0.2, 0.4, 0.8, and 1.6 mmol/L) on the selenium (Se), glucosinolate, and flavonoid contents of broccoli florets. Results showed that the total Se, selenomethionine, and methyl selenocysteine contents increased following selenate dosage. Interestingly, selenate treatment of 0.4 mmol/L decreased the flavonoid but increased the glucosinolate content. Metabolome analysis revealed changes in the individual contents of glucosinolates and flavonoids. Conjoint analysis of transcriptome and metabolome showed that the glucosinolate and flavonoid compounds were potentially regulated by two sulfate transporter genes (Sultr3;1 and Sultr4;2) and several cytochrome P450 genes (e.g., CYP71B21, CYP72C1, and CYP81F1). These new findings indicated that Se treatment may influence glucosinolate and flavonoid accumulation by regulating the expression of these genes. The results of this study provide some novel insights into the effects of Se on glucosinolates and flavonoids in broccoli florets and deepen our understanding of the regulatory network between some specific genes and these compounds.

Metabolomics and transcriptome analysis of the biosynthesis mechanism of flavonoids in the seeds of Euryale ferox Salisb at different developmental stages

Flavonoids belong to polyphenolic compounds, which are widely distributed in plants and have rich functions. Euryale ferox Salisb is an important medicinal and edible homologous plant, and flavonoids are its main functional substances. However, the biosynthesis mechanism of flavonoids in E. ferox is still poorly understood. To explore the dynamic changes of flavonoid biosynthesis during the development of E. ferox seeds, the targeted flavonoid metabolome was determined. A total of 129 kinds of flavonoid metabolites were characterized in the seeds of E. ferox, including 11 flavanones, 8 dihydroflavanols, 16 flavanols, 29 flavones, 3 isoflavones, 12 anthocyanins, 29 flavonols, 6 flavonoid carbonosides, 3 chalcones and 13 proanthocyanidins. The relative content of flavonoid metabolites accumulated continuously during the development of E. ferox seeds, and reached the highest at T30. In transcriptome, the expression of key genes in the flavonoid pathway, such as PAL, CHS, F3H, FLS, ANS, was highest in T30, which was consistent with the trend of metabolites. Six candidate transcription factors (R2R3MYBs and bHLHs) may affect the biosynthesis of flavonoids by regulating the expression of structural genes. Furthermore, transcriptome analysis and exogenous ABA and SA treatment demonstrated that ABA (PYR1, PP2Cs, SnRK2s) and SA (NPR1) are involved in the positive regulation of flavonoid biosynthesis. This study clarified the differential changes of flavonoid metabolites during the development of E. ferox seeds, confirmed that ABA and SA promote the synthesis of flavonoids, and found key candidate genes that are involved in the regulation of ABA and SA in the positive regulation of flavonoid biosynthesis.

Transcriptional and metabolite analysis reveal a shift in fruit quality in response to calcium chloride treatment on "Kyoho" grapevine

'Kyoho' grapevine (Vitis vinifera) treated by calcium ions solution has been proved as an effective treatment to extend grape quality during storage to reduce disease, but its molecular mechanism was not clear yet. In the current work, grape berries were treated with different concentration of Calcium chloride (CaCl₂) solution, and their effects on antioxidant enzyme activity and transcriptome and metabolome in fruit were investigated. CaCl₂ treatments reduced weight loss and inhibited the decrement of flesh firmness. 80 mM CaCl₂ significantly increased the activity of antioxidant enzymes POD, SOD and CAT, which was the optimum experimental concentration. The study showed that the expression level of heat shock transcription factor and UBX which involved in endoplasmic reticulum stress and degradation pathway increased significantly. Moreover, the corresponding metabolites, such as heat shock protein and organic acid, also increased significantly. The misfolded proteins are transported to the cytosol for degradation, so that the preservation ability of grape is improved.

Seasonal Variation in Transcriptomic Profiling of Tetrastigma hemsleyanum Fully Developed Tuberous Roots Enriches Candidate Genes in Essential Metabolic Pathways and Phytohormone Signaling

Tetrastigma hemsleyanum Diels et Gilg (Sanyeqing, SYQ) is a perennial climbing liana and an endemic plant to southern China. Its tuberous roots (TRs) are used in traditional Chinese medicine for treating some diseases such as high fever, pneumonia, asthma, hepatitis, and cancers. However, the mechanisms underlying the development of TR and the content of flavonoids and phenylpropanoids (FPs) are not well-understood. In this study, we performed a transcriptomic analysis of 12 fully developed TR (FD-TR) samples harvested in four seasons [spring (Sp), summer (Su), autumn (Au), and winter (Wi)] using the RNA-Sequencing (RNA-Seq). We obtained a total of 78.54 Gb raw data and 65,578 unigenes. Then, the unigenes were annotated by using six databases such as non-redundant protein database (NR), Pfam, eggNOG, SWISSProt, Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene ontology (GO). The transcriptomic profiling showed closer relationships between the samples obtained in Su and Au than those obtained in Sp and Wi based on the results of both total unigenes and differentially expressed genes (DEGs). Three pathways, including the biosynthesis of FPs, metabolism of starch and sucrose, and signaling of phytohormones, were highly enriched, suggesting a gene-level seasonal variation. Based on the numbers of DEGs, brassinosteroid (BR) signal transduction factors appeared to play a key role in modulating the development of TRs while most of the auxin signaling genes were mainly activated in Wi and Sp FD-TRs. Most genes in the biosynthesis and biodegradation of starch and biodegradation of cellulose were activated in Wi FD-TRs. As determined by the high performance liquid chromatography (HPLC) and aluminum nitrate colorimetric method, the contents of total flavonoids and most detected FP components increased from Sp to Au but decreased in Wi. Enhanced expression levels of some genes in the biosynthetic pathways of FPs were detected in Su and Au samples, which corroborated well with metabolite content. Our findings provide the first transcriptomic and biochemical data on a seasonal variation in the composition of medically important metabolites in SYQ FD-TRs.

Identification, structure analysis, and transcript profiling of purple acid phosphatases under Pi deficiency in tomato (Solanum lycopersicum L.) and its wild relatives

Purple acid phosphatases (PAPs), a family of metallo-phosphoesterase enzymes, are involved in phosphorus nutrition in plants. In this study, we report that the tomato genome encodes 25 PAP members. Physio-biochemical analyses revealed relatively lower total root-associated acid phosphatase activity in the seedlings of Solanum pimpinellifolium than their cultivated tomato seedlings under Pi deficiency. Scrutiny of their transcript abundance shows that most of PAPs are activated, although to varying levels, under Pi deficiency in tomato. Further investigation demonstrates that the magnitude of induction of phosphate starvation inducible root-associated PAP homologs remains lower in the Pi-starved S. pimpinellifolium seedlings, hence, accounting for the lower acid phosphatase activity in this wild relative. Examination of their amino acid sequences revealed significant variation in their substrate-specificity defining residues. Among all members, only SlPAP15 possesses the critical lysine residue (R337) and atypical REKA motif in its C-terminal region. Homology modeling and docking studies revealed that ADP and ATP are preferred substrates of SlPAP15. We also identified other amino acid residues present in the vicinity of the active site, possibly facilitating such physical interactions. Altogether, the results presented here will help in the functional characterization of these genes in the tomato in the future.

SlEAD1, an EAR motif-containing ABA down-regulated novel transcription repressor regulates ABA response in tomato

EAR motif-containing proteins are able to repress gene expression, therefore play important roles in regulating plants growth and development, plant response to environmental stimuli, as well as plant hormone signal transduction. ABA is a plant hormone that regulates abiotic stress tolerance in plants via signal transduction. ABA signaling via the PYR1/PYLs/RCARs receptors, the PP2Cs phosphatases, and SnRK2s protein kinases activates the ABF/AREB/ABI5-type bZIP transcription factors, resulting in the activation/repression of ABA response genes. However, functions of many ABA response genes remained largely unknown. We report here the identification of the ABA-responsive gene SlEAD1 (Solanum lycopersicum EAR motif-containing ABA down-regulated 1) as a novel EAR motif-containing transcription repressor gene in tomato. We found that the expression of SlEAD1 was down-regulated by ABA treatment, and SlEAD1 repressed reporter gene expression in transfected protoplasts. By using CRISPR gene editing, we generated transgene-free slead1 mutants and found that the mutants produced short roots. By using seed germination and root elongation assays, we examined ABA response of the slead1 mutants and found that ABA sensitivity in the mutants was increased. By using qRT-PCR, we further show that the expression of some of the ABA biosynthesis and signaling component genes were increased in the slead1 mutants. Taken together, our results suggest that SlEAD1 is an ABA response gene, that SlEAD1 is a novel EAR motif-containing transcription repressor, and that SlEAD1 negatively regulates ABA responses in tomato possibly by repressing the expression of some ABA biosynthesis and signaling genes.

Abscisic Acid Biosynthesis and Signaling in Plants: Key Targets to Improve Water Use Efficiency and Drought Tolerance

The observation of a much-improved fitness of wild-type plants over abscisic acid (ABA)-deficient mutants during drought has led researchers from all over to world to perform experiments aiming at a better understanding of how this hormone modulates the physiology of plants under water-limited conditions. More recently, several promising approaches manipulating ABA biosynthesis and signaling have been explored to improve water use efficiency and confer drought tolerance to major crop species. Here, we review recent progress made in the last decade on (i) ABA biosynthesis, (ii) the roles of ABA on plant-water relations and on primary and secondary metabolisms during drought, and (iii) the regulation of ABA levels and perception to improve water use efficiency and drought tolerance in crop species.

Melatonin promotes carotenoid biosynthesis in an ethylene-dependent manner in tomato fruits

In tomato, red color is a key commercial trait and arises from the accumulation of carotenoids. Previous studies have revealed that melatonin promotes lycopene accumulation and ethylene production. However, it is unclear if melatonin similarly increases other carotenoids, and whether any increase of carotenoids in tomato fruit is directly related to ethylene production. In this study, changes in carotenoid profiles during fruit ripening were investigated in control (CK) and in fruits treated with melatonin (M50). The α, β-carotene, and lycopene levels were significantly increased in M50, and there was increased carotenoid biosynthetic gene expression. We also observed up-regulated transcript levels of SlRIN, SlCNR, and SlNOR in M50 compared to CK. To better understand the regulation of carotenoid biosynthesis by melatonin and its potential response to endogenous ethylene, we tested an ethylene-insensitive mutant, Never ripe (Nr). Melatonin-treated Nr failed to accumulate more carotenoids compared to CK, although there was significantly changed ethylene production. Additionally, there was no general upregulation of expression of ripening-related genes in this mutant under melatonin treatment. These results suggest melatonin function might require ethylene to promote carotenoid synthesis in tomato.

Anthocyanin accumulation is initiated by abscisic acid to enhance fruit color during fig (Ficus carica L.) ripening

Fig fruit is well-known for its attractive flavor, color, and nutritional and medicinal value. Anthocyanin contributes to the fruit's color and constitutes a high percentage of the total antioxidant content of the fig fruit. We quantified the major anthocyanins and characterized the expression levels of anthocyanin-biosynthesis and transcription factor genes in fruit treated on-tree with exogenous abscisic acid (ABA) or ethephon, or the ABA inhibitors nordihydroguaiaretic acid (NDGA) or fluridone. The major anthocyanins cyanidin 3-O-glucoside and cyanidin 3-O-rutinoside were found in significantly higher quantities in exogenous ABA- and ethephon-treated fruit, with early dark purple color compared to the controls. On the other hand, NDGA- and fluridone-treated fruit had significantly lower amounts of anthocyanins, with less purple color coverage than controls. Expression levels of the anthocyanin-biosynthesis genes FcPAL, FcCHS2, FcCHI, FcF3H, FcDFR, FcANS, FcUFGT and Fc3RT were upregulated by exogenous ABA and ethephon treatment, and downregulated by NDGA and fluridone treatment. The MYB-bHLH-WD40 complex-related genes of ripe fig fruit were identified. In particular, FcMYB113 was strongly upregulated by exogenous ABA and ethephon, and strongly downregulated by NDGA and fluridone. In addition, moderate upregulation of FcGL3 and FcWD40 was observed with exogenous ABA and ethephon treatment, and moderate downregulation in NDGA- and fluridone-treated fruit. These results indicate that ABA can initiate anthocyanin biosynthesis, which ultimately improves the color and nutritional value of fig fruit, enhancing their attractiveness to consumers.

Based on RNA-Seq analysis identification and expression analysis of Trans-scripusinA synthesize-related genes of UV-treatment in postharvest grape fruit

Stilbenes, an active substances closely related to resistance and quality of grapes, are rarely found in natural resources. However its cumulative amount is affected by ultraviolet radiation (UV). The purpose of this study is to screen key genes in biosynthesis of stilbenes Trans-scripusin A and explore its synthetic pathway. We tested content of stilbenes with UHPLC-QQQ-MS², results revealed that stilbenes accumulation is positively correlated with UV-B exposure time. Then, we performed transcriptome high-throughput sequencing of grapes under treatments. Results shown that 13,906 differentially expressed genes were obtained, which were mainly enriched in three major regions (ribosome, plant-pathogen interaction and biosynthesis of flavonoid). Three genes of trans-scripusin A synthesis pathway key got by combining KEGG annotation and reference gene HsCYP1B1. Phylogenetic analysis showed that SAH genes had high homology with other hydroxylase genes, and distributed in two subgroups. Gene structure analysis showed that SAH genes contained four exons, indicating that gene has low genetic diversity. Chromosome localization revealed that SAH genes were distributed on different chromosomes, in addition, the number of gene pairs between Vitis vinifera and other species was not related to genome size of other species. The expression profiles of SAH genes in different parts of Vitis vinifera L. were analyzed using qRT-PCR analysis, results indicated that expression of SAH genes be specific to fruit part. These paper provide theoretical basis for further study of polyphenols biosynthesis pathway in grape fruits. The study provides novel insights for further understanding quality of grapes response to UV radiation.

Manipulation of β-carotene levels in tomato fruits results in increased ABA content and extended shelf life

Tomato fruit ripening is controlled by the hormone ethylene and by a group of transcription factors, acting upstream of ethylene. During ripening, the linear carotene lycopene accumulates at the expense of cyclic carotenoids. Fruit-specific overexpression of LYCOPENE β-CYCLASE (LCYb) resulted in increased β-carotene (provitamin A) content. Unexpectedly, LCYb-overexpressing fruits also exhibited a diverse array of ripening phenotypes, including delayed softening and extended shelf life. These phenotypes were accompanied, at the biochemical level, by an increase in abscisic acid (ABA) content, decreased ethylene production, increased density of cell wall material containing linear pectins with a low degree of methylation, and a thicker cuticle with a higher content of cutin monomers and triterpenoids. The levels of several primary metabolites and phenylpropanoid compounds were also altered in the transgenic fruits, which could be attributed to delayed fruit ripening and/or to ABA. Network correlation analysis and pharmacological experiments with the ABA biosynthesis inhibitor, abamine, indicated that altered ABA levels were a direct effect of the increased β-carotene content and were in turn responsible for the extended shelf life phenotype. Thus, manipulation of β-carotene levels results in an improvement not only of the nutritional value of tomato fruits, but also of their shelf life.

Effects of Exogenous Abscisic Acid on Bioactive Components and Antioxidant Capacity of Postharvest Tomato during Ripening

Abscisic acid (ABA) is a phytohormone which is involved in the regulation of tomato ripening. In this research, the effects of exogenous ABA on the bioactive components and antioxidant capacity of the tomato during postharvest ripening were evaluated. Mature green cherry tomatoes were infiltrated with either ABA (1.0 mM) or deionized water (control) and stored in the dark for 15 days at 20 °C with 90% relative humidity. Fruit colour, firmness, total phenolic and flavonoid contents, phenolic compounds, lycopene, ascorbic acid, enzymatic activities, and antioxidant capacity, as well as the expression of major genes related to phenolic compounds, were periodically monitored. The results revealed that exogenous ABA accelerated the accumulations of total phenolic and flavonoid contents; mostly increased the contents of detected phenolic compounds; enhanced FRAP and DPPH activity; and promoted the activities of PAL, POD, PPO, CAT, and APX during tomato ripening. Meanwhile, the expressions of the major genes (PAL1, C4H, 4CL2, CHS2, F3H, and FLS) involved in the phenylpropanoid pathway were up-regulated (1.13- to 26.95-fold) in the tomato during the first seven days after treatment. These findings indicated that ABA promoted the accumulation of bioactive components and the antioxidant capacity via the regulation of gene expression during tomato ripening.

Metabolome and Transcriptome Analysis of Hexaploid Solidago canadensis Roots Reveals its Invasive Capacity Related to Polyploidy

Polyploid plants are more often invasive species than their diploid counterparts. As the invasiveness of a species is often linked to its production of allelopathic compounds, we hypothesize that differences in invasive ability between cytotypes may be due to their different ability to synthesize allelopathic metabolites. We test this using two cytotypes of Solidago canadensis as the model and use integrated metabolome and transcriptome data to resolve the question. Metabolome analysis identified 122 metabolites about flavonoids, phenylpropanoids and terpenoids, of which 57 were differentially accumulated between the two cytotypes. Transcriptome analysis showed that many differentially expressed genes (DEGs) were enriched in ‘biosynthesis of secondary metabolites’, ‘plant hormone signal transduction’, and ‘MAPK signaling’, covering most steps of plant allelopathic metabolite synthesis. Importantly, the differentially accumulated flavonoids, phenylpropanoids and terpenoids were closely correlated with related DEGs. Furthermore, 30 miRNAs were found to be negatively associated with putative targets, and they were thought to be involved in target gene expression regulation. These miRNAs probably play a vital role in the regulation of metabolite synthesis in hexaploid S. canadensis. The two cytotypes of S. canadensis differ in the allelopathic metabolite synthesis and this difference is associated with regulation of expression of a range of genes. These results suggest that changes in gene expression may underlying the increased invasive potential of the polyploidy.

Exogenous Melatonin and Abscisic Acid Expedite the Flavonoids Biosynthesis in Grape Berry of Vitis vinifera cv. Kyoho

Grape polyphenols contributing to more than half of the global polyphenol market were well studied; however, how melatonin (MLT), a potential plant hormone, and abscisic acid (ABA) affects polyphenols profile is still poorly understood. To explore whether these hormones are involved in polyphenolic biosynthesis, grape (Vitis vinifera cv. Kyoho) was exposed to MLT, ABA, and NDGA (nordihydroguaiaretic acid, an ABA biosynthesis inhibitor) treatments, and 16 polyphenols were identified from grape extracts by high performance liquid chromatography quadrupole time of flight mass spectrometry (HPLC-Q-TOF-MS). Both exogenous MLT and ABA significantly enhanced the biosynthesis of each flavonol and flavanol component, especially catechin, which was almost increased double by 200 µM of MLT treatment. Furthermore, the expression of genes involved in flavonoid biosynthesis, including 4-coumaroyl-CoA synthase, chalcone synthase, flavonoid 3′-hydroxylase, anthocyanin 3′-methyltransferase, flavonol synthase, flavonoid-3-O-glucosyltransferase, and flavonoid 3′,5′-methyltransferase were highly up-regulated as well but were down-regulated by NDGA. The present study provided new insights for improving flavonoids accumulation in agricultural production and its underlying mechanism.

Genome-wide identification and characterization of ABA receptor PYL/RCAR gene family reveals evolution and roles in drought stress in Nicotiana tabacum

BACKGROUND

Abscisic acid (ABA) is an important phytohormone for plant growth, development and responding to stresses such as drought, salinity, and pathogen infection. Pyrabactin Resistance 1 (PYR1)/PYR1-Like (PYL)/Regulatory Component of ABA Receptor (RCAR) (hereafter referred to as PYLs) has been identified as the ABA receptors. The PYL family members have been well studied in many plants. However, the members of PYL family have not been systematically identified at genome level in cultivated tobacco (Nicotiana tabacum) and its two ancestors. In this study, the phylogenic relationships, chromosomal distribution, gene structures, conserved motifs/regions, and expression profiles of NtPYLs were analyzed.

RESULTS

We identified 29, 11, 16 PYLs in the genomes of allotetraploid N. tabacum, and its two diploid ancestors N. tomentosiformis and N. sylvestris, respectively. The phylogenetic analysis revealed that NtPYLs can be divided into three subfamilies, and each NtPYL has one counterpart in N. sylvestris or N. tomentosiformis. Based on microarray analysis of NtPYL transcripts, four NtPYLs (from subfamily II, III), and five NtPYLs (from subfamily I) are highlighted as potential candidates for further functional characterization in N. tabacum seed development, response to ABA, and germination, and resistance to abiotic stresses, respectively. Interestingly, the expression profiles of members in the same NtPYL subfamily showed somehow similar patterns in tissues at different developmental stages and in leaves of seedlings under drought stress, suggesting particular NtPYLs might have multiple functions in both plant development and drought stress response.

CONCLUSIONS

NtPYLs are highlighted for important functions in seed development, germination and response to ABA, and particular in drought tolerance. This work will not only shed light on the PYL family in tobacco, but also provides some valuable information for functional characterization of ABA receptors in N. tabacum.

Comparative proteomic analysis provides novel insights into the regulation mechanism underlying papaya (Carica papaya L.) exocarp during fruit ripening process

BACKGROUND

Papaya (Carica papaya L.) is a popular climacteric fruit, undergoing various physico-chemical changes during ripening. Although papaya is widely cultivated and consumed, few studies on the changes in metabolism during its ripening process at the proteasome level have been performed. Using a newly developed TMT-LCMS analysis, proteomes of papaya fruit at different ripening stages were investigated.

RESULTS

In total, 3220 proteins were identified, of which 2818 proteins were quantified. The differential accumulated proteins (DAPs) exhibited various biological functions and diverse subcellular localizations. The KEGG enrichment analysis showed that various metabolic pathways were significantly altered, particularly in flavonoid and fatty acid metabolisms. The up-regulation of several flavonoid biosynthesis-related proteins may provide more raw materials for pigment biosynthesis, accelerating the color variation of papaya fruit. Variations in the fatty acid metabolism- and cell wall degradation-related proteins were investigated during the ripening process. Furthermore, the contents of several important fatty acids were determined, and increased unsaturated fatty acids may be associated with papaya fruit volatile formation.

CONCLUSIONS

Our data may give an intrinsic explanation of the variations in metabolism during the ripening process of papaya fruit.

Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube

BACKGROUND

Chinese jujube (Ziziphus jujuba Mill.) is a non-climacteric fruit; however, the underlying mechanism of ripening and the role of abscisic acid involved in this process are not yet understood for this species.

RESULTS

In the present study, a positive correlation between dynamic changes in endogenous ABA and the onset of jujube ripening was determined. Transcript analyses suggested that the expression balance among genes encoding nine-cis-epoxycarotenoid dioxygenase (ZjNCED3), ABA-8'-hydroxylase (ZjCYP707A2), and beta-glucosidase (ZjBG4, ZjBG5, ZjBG8, and ZjBG9) has an important role in maintaining ABA accumulation, while the expression of a receptor (ZjPYL8), protein phosphatase 2C (ZjPP2C4-8), and sucrose nonfermenting 1-related protein kinase 2 (ZjSnRK2-2 and ZjSnRK2-5) is important in regulating fruit sensitivity to ABA applications. In addition, white mature 'Dongzao' fruit were harvested and treated with 50 mg L- 1 ABA or 50 mg L- 1 nordihydroguaiaretic acid (NDGA) to explore the role of ABA in jujube fruit ripening. By comparative transcriptome analyses, 1103 and 505 genes were differentially expressed in response to ABA and NDGA applications on the 1st day after treatment, respectively. These DEGs were associated with photosynthesis, secondary, lipid, cell wall, and starch and sugar metabolic processes, suggesting the involvement of ABA in modulating jujube fruit ripening. Moreover, ABA also exhibited crosstalk with other phytohormones and transcription factors, indicating a regulatory network for jujube fruit ripening.

CONCLUSIONS

Our study further elucidated ABA-associated metabolic and regulatory processes. These findings are helpful for improving strategies for jujube fruit storage and for gaining insights into understand complex non-climacteric fruit ripening processes.

Biogenic Synthesis and Spatial Distribution of Endogenous Phytohormones and Ginsenosides Provide Insights on Their Intrinsic Relevance in Panax ginseng

Ginseng, the root and rhizome of Panax ginseng C. A. Mey., is a well-known and valuable traditional Chinese medicine. The pharmacological activities of ginseng are mainly attributed to the presence of ginsenosides, which are considered to be critical biomarkers for evaluating ginseng quality. The biosynthesis of triterpenes, which serve defensive functions in plants, is regulated by endogenous phytohormones that play key roles in growth and defense of plant populations. However, the role of major hormones that are closely related to secondary metabolism pathways in P. ginseng is poorly understood. To gain insight into their potential correlation, we performed a spatial synthesis analysis and studied the distribution of endogenous phytohormones and ginsenosides in different tissue regions of the entire P. ginseng plant. Gibberellins are growth hormones that accumulate in the fiber root. In contrast, abscisic acid (ABA), salicylic acid (SA), and jasmonic acid (JA), which are considered stress hormones, were predominantly found in the leaf and leaf peduncle. We observed a tissue-specific distribution of phytohormones consistent with the expression of genes involved in hormone biosynthesis that influenced ginsenoside synthesis and distribution. The aim of this study was to investigate the role of different endogenous phytohormones on triterpene metabolites in ginseng innate immunity.

Gene expression profiling of Bothriochloa ischaemum leaves and roots under drought stress

Drought is a common environmental factor that limits plant growth, development and productivity. To understand the effect of drought on the perennial grass Bothriochloa ischaemum, we applied high-throughput Illumina sequencing technology and analyzed the transcriptional expression profile of Bothriochloa ischaemum leaves and roots under drought and normal growth conditions. Compared to the controls, drought-treated samples had 7989 differentially expressed genes in leaves and 15,675 differentially expressed genes in roots. Of these, 4489 and 5010 genes were up-regulated genes in leaves and roots, respectively. Of the 2012 differentially expressed genes that were shared between leaves and roots, 1068 were up-regulated. We identified common and distinct biological processes and metabolic pathways involved in drought stress between the two tissues. Most notably, there was a dramatic up-regulation of genes involved in plant hormone signal transduction especially ABA signal transduction components and flavonoid biosynthesis enzymes or regulation factors in drought stress treated leaves. Therefore, these two cellular processes likely confer resistance to drought stress in Bothriochloa ischaemum. Overall, our findings provided new insights into a mechanism involving the synergistic interaction between ABA signaling and secondary metabolism during the drought adaptation of Bothriochloa ischaemum.

MaMADS2 repression in banana fruits modifies hormone synthesis and signalling pathways prior to climacteric stage

BACKGROUND

While the role of ethylene in fruit ripening has been widely studied, the contributions of additional plant hormones are less clear. Here we examined the interactions between the transcription factor MaMADS2-box which plays a major role in banana fruit ripening and hormonal regulation. Specifically, we used MaMADS2 repressed lines in transcriptome and hormonal analyses throughout ripening and assessed hormone and gene expression perturbations as compared to wild-type (WT) control fruit.

RESULTS

Our analyses revealed major differences in hormones levels and in expression of hormone synthesis and signaling genes mediated by MaMADS2 especially in preclimacteric pulp. Genes encoding ethylene biosynthesis enzymes had lower expression in the pulp of the repressed lines, consistent with reduced ethylene production. Generally, the expression of other hormone (auxin, gibberellins, abscisic acid, jasmonic acid and salicylic acid) response pathway genes were down regulated in the WT pulp prior to ripening, but remained high in MaMADS2 repressed lines. Hormone levels of abscisic acid were also higher, however, active gibberellin levels were lower and auxin levels were similar with MaMADS2 repression as compared to WT. Although abscisic level was higher in MaMADS2 repression, exogenous abscisic acid shortened the time to ethylene production and increased MaMADS2 mRNA accumulation in WT. Exogenous ethylene did not influence abscisic acid level. CRE - a cytokinin receptor, increased its expression during maturation in WT and was lower especially at prebreaker in the repressed line and zeatin level was lower at mature green of the repressed line in comparison to WT.

CONCLUSIONS

In addition to previously reported effects of MaMADS2 on ethylene, this transcription factor also influences other plant hormones, particularly at the pre-climacteric stage. The cytokinin pathway may play a previously unanticipated role via MaMADS2 in banana ripening. Finally, abscisic acid enhances MaMADS2 expression to promote ripening, but the transcription factor in turn auto inhibits ABA synthesis and signaling. Together, these results demonstrate a complex interaction of plant hormones and banana fruit ripening mediated by MaMADS2.

Below versus above Ground Plant Sources of Abscisic Acid (ABA) at the Heart of Tropical Forest Response to Warming

Warming surface temperatures and increasing frequency and duration of widespread droughts threaten the health of natural forests and agricultural crops. High temperatures (HT) and intense droughts can lead to the excessive plant water loss and the accumulation of reactive oxygen species (ROS) resulting in extensive physical and oxidative damage to sensitive plant components including photosynthetic membranes. ROS signaling is tightly integrated with signaling mechanisms of the potent phytohormone abscisic acid (ABA), which stimulates stomatal closure leading to a reduction in transpiration and net photosynthesis, alters hydraulic conductivities, and activates defense gene expression including antioxidant systems. While generally assumed to be produced in roots and transported to shoots following drought stress, recent evidence suggests that a large fraction of plant ABA is produced in leaves via the isoprenoid pathway. Thus, through stomatal regulation and stress signaling which alters water and carbon fluxes, we highlight the fact that ABA lies at the heart of the Carbon-Water-ROS Nexus of plant response to HT and drought stress. We discuss the current state of knowledge of ABA biosynthesis, transport, and degradation and the role of ABA and other isoprenoids in the oxidative stress response. We discuss potential variations in ABA production and stomatal sensitivity among different plant functional types including isohydric/anisohydric and pioneer/climax tree species. We describe experiments that would demonstrate the possibility of a direct energetic and carbon link between leaf ABA biosynthesis and photosynthesis, and discuss the potential for a positive feedback between leaf warming and enhanced ABA production together with reduced stomatal conductance and transpiration. Finally, we propose a new modeling framework to capture these interactions. We conclude by discussing the importance of ABA in diverse tropical ecosystems through increases in the thermotolerance of photosynthesis to drought and heat stress, and the global importance of these mechanisms to carbon and water cycling under climate change scenarios.

Salinity reduces 2,4-D efficacy in Echinochloa crusgalli by affecting redox balance, nutrient acquisition, and hormonal regulation

Distinct salinity levels have been reported to enhance plants tolerance to different types of stresses. The aim of this research is to assess the interaction of saline stress and the use of 2,4-D as a means of controlling the growth of Echinochloa crusgalli. The resultant effect of such interaction is vital for a sustainable approach of weed management and food production. The results showed that 2,4-D alone treatment reduces the chlorophyll contents, photosynthetic capacity, enhanced MDA, electrolyte leakage, and ROS production (H₂O₂, O₂^·-) and inhibited the activities of ROS scavenging enzymes. Further analysis of the ultrastructure of chloroplasts indicated that 2,4-D induced severe damage to the ultrastructure of chloroplasts and thylakoids. Severe saline stress (8 dS m^-1) followed by mild saline stress treatments (4 dS m^-1) also reduced the E. crusgalli growth, but had the least impact as compared to the 2,4-D alone treatment. Surprisingly, under combined treatments (salinity + 2,4-D), the phytotoxic effect of 2,4-D was reduced on saline-stressed E. crusgalli plants, especially under mild saline + 2,4-D treatment. This stimulated growth of E. crusgalli is related to the higher activities of enzymatic and non-enzymatic antioxidants and dynamic regulation of IAA, ABA under mild saline + 2,4-D treatment. This shows that 2,4-D efficacy was affected by salinity in a stress intensity-dependent manner, which may result in the need for greater herbicide application rates, additional application times, or more weed control operations required for controlling salt-affected weed.

Abscisic Acid Regulates Anthocyanin Biosynthesis and Gene Expression Associated With Cell Wall Modification in Ripening Bilberry (Vaccinium myrtillus L.) Fruits

Ripening of non-climacteric bilberry (Vaccinium myrtillus L.) fruit is characterized by a high accumulation of health-beneficial anthocyanins. Plant hormone abscisic acid (ABA) and sucrose have been shown to be among the central signaling molecules coordinating non-climacteric fruit ripening and anthocyanin accumulation in some fruits such as strawberry. Our earlier studies have demonstrated an elevation in endogenous ABA level in bilberry fruit at the onset of ripening indicating a role for ABA in the regulation of bilberry fruit ripening. In the present study, we show that the treatment of unripe green bilberry fruits with exogenous ABA significantly promotes anthocyanin biosynthesis and accumulation both in fruits attached and detached to the plant. In addition, ABA biosynthesis inhibitor, fluridone, delayed anthocyanin accumulation in bilberries. Exogenous ABA also induced the expression of several genes involved in cell wall modification in ripening bilberry fruits. Furthermore, silencing of VmNCED1, the key gene in ABA biosynthesis, was accompanied by the down-regulation in the expression of key anthocyanin biosynthetic genes. In contrast, the treatment of unripe green bilberry fruits with exogenous sucrose or glucose did not lead to an enhancement in the anthocyanin accumulation neither in fruits attached to plant nor in post-harvest fruits. Moreover, sugars failed to induce the expression of genes associated in anthocyanin biosynthesis or ABA biosynthesis while could elevate expression of some genes associated with cell wall modification in post-harvest bilberry fruits. Our results demonstrate that ABA plays a major role in the regulation of ripening-related processes such as anthocyanin biosynthesis and cell wall modification in bilberry fruit, whereas sugars seem to have minor regulatory roles in the processes. The results indicate that the regulation of bilberry fruit ripening differs from strawberry that is currently considered as a model of non-climacteric fruit ripening. In this study, we also identified transcription factors, which expression was enhanced by ABA, as potential regulators of ABA-mediated bilberry fruit ripening processes.