Metabolite profiling and quantitative genetics of natural variation for flavonoids in Arabidopsis

Metabolite analysis reveals flavonoids accumulation during flower development in Rhododendron pulchrum sweet (Ericaceae)

The azalea (Rhododendron simsii Planch.) is an important ornamental woody plant with various medicinal properties due to its phytochemical compositions and components. However little information on the metabolite variation during flower development in Rhododendron has been provided. In our study, a comparative analysis of the flavonoid profile was performed in Rhododendron pulchrum sweet at three stages of flower development, bud (stage 1), partially open flower (stage 2), and full bloom (stage 3). A total of 199 flavonoids, including flavone, flavonol, flavone C-glycosides, flavanone, anthocyanin, and isoflavone were identified. In hierarchical clustering analysis (HCA) and principal component analysis (PCA), the accumulation of flavonoids displayed a clear development stage variation. During flower development, 78 differential accumulated metabolites (DAMs) were identified, and most were enriched to higher levels at the full bloom stage. A total of 11 DAMs including flavone (chrysin, chrysoeriol O-glucuronic acid, and chrysoeriol O-hexosyl-O-pentoside), isoflavone (biochanin A), and flavonol (3,7-di-O-methyl quercetin and isorhamnetin) were significantly altered at three stages. In particular, 3,7-di-O-methyl quercetin was the top increased metabolite during flower development. Furthermore, integrative analyses of metabolomic and transcriptomic were conducted, revealing that the contents of isoflavone, biochanin A, glycitin, and prunetin were correlated with the expression of 2-hydroxyisoflavanone dehydratase (HIDH), which provide insight into the regulatory mechanism that controls isoflavone biosynthesis in R. pulchrum. This study will provide a new reference for increasing desired metabolites effectively by more accurate or appropriate genetic engineering strategies.

Functional analyses of the NRT2 family of nitrate transporters in Arabidopsis

Nitrogen is an essential macronutrient for plant growth and development. Nitrate is the major form of nitrogen acquired by most crops and also serves as a vital signaling molecule. Nitrate is absorbed from the soil into root cells usually by the low-affinity NRT1 NO3 - transporters and high-affinity NRT2 NO3 - transporters, with NRT2s serving to absorb NO3 - under NO3 -limiting conditions. Seven NRT2 members have been identified in Arabidopsis, and they have been shown to be involved in various biological processes. In this review, we summarize the spatiotemporal expression patterns, localization, and biotic and abiotic responses of these transporters with a focus on recent advances in the current understanding of the functions of the seven AtNRT2 genes. This review offers beneficial insight into the mechanisms by which plants adapt to changing environmental conditions and provides a theoretical basis for crop research in the near future.

Genome-wide association studies identify loci controlling specialized seed metabolites in Arabidopsis

Plants synthesize specialized metabolites to facilitate environmental and ecological interactions. During evolution, plants diversified in their potential to synthesize these metabolites. Quantitative differences in metabolite levels of natural Arabidopsis (Arabidopsis thaliana) accessions can be employed to unravel the genetic basis for metabolic traits using genome-wide association studies (GWAS). Here, we performed metabolic GWAS on seeds of a panel of 315 A. thaliana natural accessions, including the reference genotypes C24 and Col-0, for polar and semi-polar seed metabolites using untargeted ultra-performance liquid chromatography-mass spectrometry. As a complementary approach, we performed quantitative trait locus (QTL) mapping of near-isogenic introgression lines between C24 and Col-0 for specific seed specialized metabolites. Besides common QTL between seeds and leaves, GWAS revealed seed-specific QTL for specialized metabolites, indicating differences in the genetic architecture of seeds and leaves. In seeds, aliphatic methylsulfinylalkyl and methylthioalkyl glucosinolates associated with the ALKENYL HYDROXYALKYL PRODUCING loci (GS-ALK and GS-OHP) on chromosome 4 containing alkenyl hydroxyalkyl producing 2 (AOP2) and 3 (AOP3) or with the GS-ELONG locus on chromosome 5 containing methylthioalkyl malate synthase (MAM1) and MAM3. We detected two unknown sulfur-containing compounds that were also mapped to these loci. In GWAS, some of the annotated flavonoids (kaempferol 3-O-rhamnoside-7-O-rhamnoside, quercetin 3-O-rhamnoside-7-O-rhamnoside) were mapped to transparent testa 7 (AT5G07990), encoding a cytochrome P450 75B1 monooxygenase. Three additional mass signals corresponding to quercetin-containing flavonols were mapped to UGT78D2 (AT5G17050). The association of the loci and associating metabolic features were functionally verified in knockdown mutant lines. By performing GWAS and QTL mapping, we were able to leverage variation of natural populations and parental lines to study seed specialized metabolism. The GWAS data set generated here is a high-quality resource that can be investigated in further studies.

Targeted mutagenesis of flavonoid biosynthesis pathway genes reveals functional divergence in seed coat colour, oil content and fatty acid composition in Brassica napus L

Yellow-seed is widely accepted as a good-quality trait in Brassica crops. Previous studies have shown that the flavonoid biosynthesis pathway is essential for the development of seed colour, but its function in Brassica napus, an important oil crop, is poorly understood. To systematically explore the gene functions of the flavonoid biosynthesis pathway in rapeseed, several representative TRANSPARENT TESTA (TT) genes, including three structural genes (BnaTT7, BnaTT18, BnaTT10), two regulatory genes (BnaTT1, BnaTT2) and a transporter (BnaTT12), were selected for targeted mutation by CRISPR/Cas9 in the present study. Seed coat colour, lignin content, seed quality and yield-related traits were investigated in these Bnatt mutants together with Bnatt8 generated previously. These Bnatt mutants produced seeds with an elevated seed oil content and decreased pigment and lignin accumulation in the seed coat without any serious defects in the yield-related traits. In addition, the fatty acid (FA) composition was also altered to different degrees, i.e., decreased oleic acid and increased linoleic acid and α-linolenic acid, in all Bnatt mutants except Bnatt18. Furthermore, gene expression analysis revealed that most of BnaTT mutations resulted in the down-regulation of key genes related to flavonoid and lignin synthesis, and the up-regulation of key genes related to lipid synthesis and oil body formation, which may contribute to the phenotype. Collectively, our study generated valuable resources for breeding programs, and more importantly demonstrated the functional divergence and overlap of flavonoid biosynthesis pathway genes in seed coat colour, oil content and FA composition of rapeseed.

Targeted mutagenesis of BnTTG1 homologues generated yellow-seeded rapeseed with increased oil content and seed germination under abiotic stress

Yellow seed is one desirable trait with great potential to improve seed oil quality and yield. The present study surveys the redundant role of BnTTG1 genes in the proanthocyanidins (PA) biosynthesis, oil content and abiotic stress resistance. Stable yellow seed mutants were generated after mutating BnTTG1 by CRISPR/Cas9 genome editing system. Yellow seed phenotype could be obtained only when both functional homologues of BnTTG1 were simultaneously knocked out. Homozygous mutants of BnTTG1 homologues showed decreased thickness and PA accumulation in seed coat. Transcriptome and qRT-PCR analysis indicated that BnTTG1 mutation inhibited the expression of genes involved in phenylpropanoid and flavonoid biosynthetic pathways. Increased seed oil content and alteration of fatty acid (FA) composition were observed in homozygous mutants of BnTTG1 with enriched expression of genes involved in FA biosynthesis pathway. In addition, target mutation of BnTTG1 accelerated seed germination rate under salt and cold stresses. Enhanced seed germination capacity in BnTTG1 mutants was correlated with the change of expression level of ABA responsive genes. Overall, this study elucidated the redundant role of BnTTG1 in regulating seed coat color and established an efficient approach for generating yellow-seeded oilseed rape genetic resources with increase oil content, modified FA composition and resistance to multiple abiotic stresses.

QT-GWAS: A novel method for unveiling biosynthetic loci affecting qualitative metabolic traits

Although the plant kingdom provides an enormous diversity of metabolites with potentially beneficial applications for humankind, a large fraction of these metabolites and their biosynthetic pathways remain unknown. Resolving metabolite structures and their biosynthetic pathways is key to gaining biological understanding and to allow metabolic engineering. In order to retrieve novel biosynthetic genes involved in specialized metabolism, we developed a novel untargeted method designated as qualitative trait GWAS (QT-GWAS) that subjects qualitative metabolic traits to a genome-wide association study, while the conventional metabolite GWAS (mGWAS) mainly considers the quantitative variation of metabolites. As a proof of the validity of QT-GWAS, 23 and 15 of the retrieved associations identified in Arabidopsis thaliana by QT-GWAS and mGWAS, respectively, were supported by previous research. Furthermore, seven gene-metabolite associations retrieved by QT-GWAS were confirmed in this study through reverse genetics combined with metabolomics and/or in vitro enzyme assays. As such, we established that CYTOCHROME P450 706A5 (CYP706A5) is involved in the biosynthesis of chroman derivatives, UDP-GLYCOSYLTRANSFERASE 76C3 (UGT76C3) is able to hexosylate guanine in vitro and in planta, and SULFOTRANSFERASE 202B1 (SULT202B1) catalyzes the sulfation of neolignans in vitro. Collectively, our study demonstrates that the untargeted QT-GWAS method can retrieve valid gene-metabolite associations at the level of enzyme-encoding genes, even new associations that cannot be found by the conventional mGWAS, providing a new approach for dissecting qualitative metabolic traits.

Manipulation of light spectrum is an effective tool to regulate biochemical traits and gene expression in lettuce under different replacement methods of nutrient solution

The use of light-emitting diode (LED) technology represents a promising approach to improve plant growth and metabolic activities. The aim of this study was to investigate the effect of different light spectra: red (656 nm), blue (450 nm), red/blue (3:1), and white (peak at 449 nm) on biochemical properties, photosynthesis and gene expression in two lettuce cultivars (Lollo Rossa and Lollo Bionda) grown under different methods of nutrient solution replacement in hydroponics. Complete replacement and EC-based replacement of nutrient solution increased content of proline and soluble sugars and activity of antioxidant enzymes (CAT, GPX and SOD) under the red/blue LED and red LED light treatments in both cultivars. In addition, the red/blue and the monochromatic red light increased the soluble protein content and the antioxidant activity in the Lollo Rosa cultivar under the replacement method according to the needs of the plant. An increase in flavonoid content in the EC-based method in the Lollo Rosa variety treated with a combination of red and blue light was also observed. The red/blue light had the greatest induction effect on anthocyanin content, expression of the UFGT, CHS, and Rubisco small subunit genes, and the net photosynthetic rate. Data presented here will directly contribute to the development of nutrient solution and LED spectrum management strategies to significantly improve plant growth and metabolism, while avoiding water and nutrient waste, and environmental pollution.

Kaempferol-3-rhamnoside overaccumulation in flavonoid 3'-hydroxylase tt7 mutants compromises seed coat outer integument differentiation and seed longevity

Seeds slowly accumulate damage during storage, which ultimately results in germination failure. The seed coat protects the embryo from the external environment, and its composition is critical for seed longevity. Flavonols accumulate in the outer integument. The link between flavonol composition and outer integument development has not been explored. Genetic, molecular and ultrastructural assays on loss-of-function mutants of the flavonoid biosynthesis pathway were used to study the effect of altered flavonoid composition on seed coat development and seed longevity. Controlled deterioration assays indicate that loss of function of the flavonoid 3' hydroxylase gene TT7 dramatically affects seed longevity and seed coat development. Outer integument differentiation is compromised from 9 d after pollination in tt7 developing seeds, resulting in a defective suberin layer and incomplete degradation of seed coat starch. These distinctive phenotypes are not shared by other mutants showing abnormal flavonoid composition. Genetic analysis indicates that overaccumulation of kaempferol-3-rhamnoside is mainly responsible for the observed phenotypes. Expression profiling suggests that multiple cellular processes are altered in the tt7 mutant. Overaccumulation of kaempferol-3-rhamnoside in the seed coat compromises normal seed coat development. This observation positions TRANSPARENT TESTA 7 and the UGT78D1 glycosyltransferase, catalysing flavonol 3-O-rhamnosylation, as essential players in the modulation of seed longevity.

Metabolomics Analysis Reveals Metabolites and Metabolic Pathways Involved in the Growth and Quality of Water Dropwort [Oenanthe javanica (Blume) DC.] under Nutrient Solution Culture

Water dropwort (Oenanthe javanica (Blume) DC.) is an important vegetable crop. Nutrient liquid culture has become an important cultivation method in the production of water dropwort. However, the effects of different nutrient solution cultivation methods on the growth and quality of water dropwort remains unclear. In this study, to screen the most suitable nutrient solution formula for the cultivation of water dropwort, the effects of different nutrient solution formulas (Hoagland, Cooper, Dutch greenhouse, Garden-style, Yamasaki and SCAU) on plant physiological and quality characteristics are investigated. The plant height, root length, water content (%), distribution rate of dry matter (%), chlorophyll, VC, flavonoid, total phenolic, DPPH and dietary fiber of water dropwort under different nutrient solutions were determined. According to the analytic hierarchy process (AHP) of the growth index and quality index of water dropwort under different nutrient solutions, the Yamazaki nutrient solution was considered to be the most suitable nutrient solution formula for water dropwort. To further confirm the differences of water dropwort under nutrient solution culture and soil culture, the broadly targeted metabolomics were performed. A total of 485 metabolites were detected in water dropwort under optimal nutrient solution and soil cultivation. Metabolomics analysis showed that flavonoids were the most abundant differential accumulated metabolites, and most flavonoids were up-regulated. A qRT-PCR assay indicated that the structural genes of the flavonoid biosynthesis pathway (PAL, C4H, CHS, CHI, F3H, DFR, UFGT) were significantly higher under the Yamasaki nutrient solution treatment. The current study provided a theoretical basis and technical guidance for the nutrient solution cultivation of water dropwort. Meanwhile, this study provides new insights into the study of flavonoids in water dropwort.

Spatiotemporal transcriptomics and metabolic profiling provide insights into gene regulatory networks during lentil seed development

Lentil (Lens culinaris Medik.) is a nutritious legume with seeds rich in protein, minerals and an array of diverse specialized metabolites. The formation of a seed requires regulation and tight coordination of developmental programs to form the embryo, endosperm and seed coat compartments, which determines the structure and composition of mature seed and thus its end-use quality. Understanding the molecular and cellular events and metabolic processes of seed development is essential for improving lentil yield and seed nutritional value. However, such information remains largely unknown, especially at the seed compartment level. In this study, we generated high-resolution spatiotemporal gene expression profiles in lentil embryo, seed coat and whole seeds from fertilization through maturation. Apart from anatomic differences between the embryo and seed coat, comparative transcriptomics and weighted gene co-expression network analysis revealed embryo- and seed coat-specific genes and gene modules predominant in specific tissues and stages, which highlights distinct genetic programming. Furthermore, we investigated the dynamic profiles of flavonoid, isoflavone, phytic acid and saponin in seed compartments across seed development. Coupled with transcriptome data, we identified sets of candidate genes involved in the biosynthesis of these metabolites. The global view of the transcriptional and metabolic changes of lentil seed tissues throughout development provides a valuable resource for dissecting the genetic control of secondary metabolism and development of molecular tools for improving seed nutritional quality.

Fine mapping of genes controlling pigment accumulation in oilseed rape (Brassica napus L.)

Purple/red appearance is one of the common phenotypic variations in leaves, stems, and siliques of oilseed rape (Brassica napus L.) but very rare in flowers. In this study, the causal genes for the purple/red traits in stems and flowers in two accessions of oilseed rape (DH_PR and DH_GC001, respectively) derived from the wide hybridization were fine mapped, and candidate genes were determined by methods combined with bulked segregant analysis (BSA) and RNA-seq analysis. Both traits of purple stem and red flowers were mapped to the locus as AtPAP2 homologous genes (BnaPAP2.C6a and BnaPAP2.A7b, respectively) belonging to the R2R3-MYB family. Sequence comparisons of full-length allelic genes revealed several InDels and SNPs in intron 1 as well as exons, and completely different promoter region of BnaPAP2.C6a and a 211 bp insertion was identified in the promoter region of BnaPAP2.A7b of DH_GC001. Our results not only contribute to a better understanding of anthocyanin inheritance in B. napus, but also provide a useful toolbox for future breeding of cultivars with purple/red traits through the combination of different functional alleles and homologs.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01365-5.

Novel molecules and target genes for vegetative heat tolerance in wheat

To prevent yield losses caused by climate change, it is important to identify naturally tolerant genotypes with traits and related pathways that can be targeted for crop improvement. Here we report on the characterization of contrasting vegetative heat tolerance in two UK bread wheat varieties. Under chronic heat stress, the heat-tolerant cultivar Cadenza produced an excessive number of tillers which translated into more spikes and higher grain yield compared to heat-sensitive Paragon. RNAseq and metabolomics analyses revealed that over 5000 genotype-specific genes were differentially expressed, including photosynthesis-related genes, which might explain the observed ability of Cadenza to maintain photosynthetic rate under heat stress. Around 400 genes showed a similar heat-response in both genotypes. Only 71 genes showed a genotype × temperature interaction. As well as known heat-responsive genes such as heat shock proteins (HSPs), several genes that have not been previously linked to the heat response, particularly in wheat, have been identified, including dehydrins, ankyrin-repeat protein-encoding genes, and lipases. Contrary to primary metabolites, secondary metabolites showed a highly differentiated heat response and genotypic differences. These included benzoxazinoid (DIBOA, DIMBOA), and phenylpropanoids and flavonoids with known radical scavenging capacity, which was assessed via the DPPH assay. The most highly heat-induced metabolite was (glycosylated) propanediol, which is widely used in industry as an anti-freeze. To our knowledge, this is the first report on its response to stress in plants. The identified metabolites and candidate genes provide novel targets for the development of heat-tolerant wheat.

Overexpression of a Senescence-Related Gene CpSRG1 from Wintersweet (Chimonanthus praecox) Promoted Growth and Flowering, and Delayed Senescence in Transgenic Arabidopsis

Plant senescence is a complex process that is controlled by developmental regulation and genetic programs. A senescence-related gene CpSRG1, which belongs to the 2OG-Fe(II) dioxygenase superfamily, was characterized from wintersweet, and the phylogenetic relationship of CpSRG1 with homologs from other species was investigated. The expression analysis by qRT-PCR (quantitative real-time PCR) indicated that CpSRG1 is abundant in flower organs, especially in petals and stamens, and the highest expression of CpSRG1 was detected in stage 6 (withering period). The expression patterns of the CpSRG1 gene were further confirmed in CpSRG1pro::GUS (β-glucuronidase) plants, and the activity of the CpSRG1 promoter was enhanced by exogenous Eth (ethylene), SA (salicylic acid), and GA₃ (gibberellin). Heterologous overexpression of CpSRG1 in Arabidopsis promoted growth and flowering, and delayed senescence. Moreover, the survival rates were significantly higher and the root lengths were significantly longer in the transgenic lines than in the wild-type plants, both under low nitrogen stress and GA₃ treatment. This indicated that the CpSRG1 gene may promote the synthesis of assimilates in plants through the GA pathway, thereby improving growth and flowering, and delaying senescence in transgenic Arabidopsis. Our study has laid a satisfactory foundation for further analysis of senescence-related genes in wintersweet and wood plants. It also enriched our knowledge of the 2OG-Fe(II) dioxygenase superfamily, which plays a variety of important roles in plants.

Comparative transcriptomic responses of European and Japanese larches to infection by Phytophthora ramorum

BACKGROUND AND OBJECTIVES

Phytophthora ramorum severely affects both European larch (EL) and Japanese larch (JL) trees as indicated by high levels of mortality particularly in the UK. Field observations suggested that EL is less severely affected and so may be less susceptible to P. ramorum than JL; however, controlled inoculations have produced inconsistent or non-statistically significant differences. The present study aimed to compare RNA transcript accumulation profiles in EL and JL in response to inoculation with P. ramorum to improve our understanding of their defence responses.

METHODOLOGY

RNA-sequencing was carried out on bark tissues following the inoculation with P. ramorum of potted saplings in both EL and JL carried out under controlled environment conditions, with sampling at 1, 3, 10, and 25 days post inoculation in infected and control plants.

RESULTS

All of the inoculated trees rapidly developed lesions but no statistically significant differences were found in lesion lengths between EL and JL. RNA-Sequencing comparing control and inoculate saplings identified key differences in differentially expressed genes (DEGs) between the two larch species. European larch had rapid induction of defence genes within 24 hours of infection followed by sustained expression until 25 days after inoculation. Results in JL were more varied; upregulation was stronger but more transient and represented fewer defence pathways. Gene enrichment analyses highlighted differences in jasmonate signalling and regulation including NPR1 upregulation in EL only, and specific aspects of secondary metabolism. Some DEGs were represented by multiple responsive copies including lipoxygenase, chalcone synthase and nucleotide-binding, leucine-rich-repeat genes.

CONCLUSION

The variations between EL and JL in responsive DEGs of interest as potentially related to differences seen in the field and should be considered in the selection of trees for planting and future breeding.

Metabolic signatures of rhizobacteria-induced plant growth promotion

Various root-colonizing bacterial species can promote plant growth and trigger systemic resistance against aboveground leaf pathogens and herbivore insects. To date, the underlying metabolic signatures of these rhizobacteria-induced plant phenotypes are poorly understood. To identify core metabolic pathways that are targeted by growth-promoting rhizobacteria, we used combinations of three plant species and three rhizobacterial species and interrogated plant shoot chemistry by untargeted metabolomics. A substantial part (50%-64%) of the metabolites detected in plant shoot tissue was differentially affected by the rhizobacteria. Among others, the phenylpropanoid pathway was targeted by the rhizobacteria in each of the three plant species. Differential regulation of the various branches of the phenylpropanoid pathways showed an association with either plant growth promotion or growth reduction. Overall, suppression of flavonoid biosynthesis was associated with growth promotion, while growth reduction showed elevated levels of flavonoids. Subsequent assays with 12 Arabidopsis flavonoid biosynthetic mutants revealed that the proanthocyanidin branch plays an essential role in rhizobacteria-mediated growth promotion. Our study also showed that a number of pharmaceutically and nutritionally relevant metabolites in the plant shoot were significantly increased by rhizobacterial treatment, providing new avenues to use rhizobacteria to tilt plant metabolism towards the biosynthesis of valuable natural plant products.

EbMYBP1, a R2R3-MYB transcription factor, promotes flavonoid biosynthesis in Erigeron breviscapus

Erigeron breviscapus, a traditional Chinese medicinal plant, is enriched in flavonoids that are beneficial to human health. While we know that R2R3-MYB transcription factors (TFs) are crucial to flavonoid pathway, the transcriptional regulation of flavonoid biosynthesis in E. breviscapus has not been fully elucidated. Here, EbMYBP1, a R2R3-MYB transcription factor, was uncovered as a regulator involved in the regulation of flavonoid accumulation. Transcriptome and metabolome analysis revealed that a large group of genes related to flavonoid biosynthesis were significantly changed, accompanied by significantly increased concentrations of the flavonoid in EbMYBP1-OE transgenic tobacco compared with the wild-type (WT). In vitro and in vivo investigations showed that EbMYBP1 participated in flavonoid biosynthesis, acting as a nucleus-localized transcriptional activator and activating the transcription of flavonoid-associated genes like FLS, F3H, CHS, and CHI by directly binding to their promoters. Collectively, these new findings are advancing our understanding of the transcriptional regulation that modulates the flavonoid biosynthesis.

SlMBP22 overexpression in tomato affects flower morphology and fruit development

MADS-domain transcription factors have been identified as key regulators involved in proper flower and fruit development in angiosperms. As members of the MADS-box subfamily, B_sister (B_s) genes have been observed to play an important role during the evolution of the reproductive organs in seed plants. However, their effects on reproductive development in fruit crops, such as tomato (Solanum lycopersicum), remain unclear. Here, we found that SlMBP22 overexpression (SlMBP22-OE) resulted in considerable alterations in floral morphology and affected the expression levels of several floral homeotic genes. Further analysis by yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays demonstrated that SlMBP22 forms dimers with class A protein MACROCALYX (MC) and SEPALLATA (SEP) floral homeotic proteins TM5 and TM29, respectively. In addition, pollen viability and cross-fertilization assays suggested that the defect in female reproductive development was responsible for the infertility phenotype observed in the strong overexpression transgenic plants. Transgenic fruits with mild overexpression exhibited reduced size as a result of reduced cell expansion, rather than impaired cell division. Additionally, SlMBP22 overexpression in tomato not only affected proanthocyanidin (PA) accumulation but also altered seed dormancy. Taken together, these findings may provide new insights into the knowledge of B_s MADS-box genes in flower and fruit development in tomato.

Light Induced Regulation Pathway of Anthocyanin Biosynthesis in Plants

Anthocyanins are natural pigments with antioxidant effects that exist in various fruits and vegetables. The accumulation of anthocyanins is induced by environmental signals and regulated by transcription factors in plants. Numerous evidence has indicated that among the environmental factors, light is one of the most signal regulatory factors involved in the anthocyanin biosynthesis pathway. However, the signal transduction of light and molecular regulation of anthocyanin synthesis remains to be explored. Here, we focus on the research progress of signal transduction factors for positive and negative regulation in light-dependent and light-independent anthocyanin biosynthesis. In particular, we will discuss light-induced regulatory pathways and related specific regulators of anthocyanin biosynthesis in plants. In addition, an integrated regulatory network of anthocyanin biosynthesis controlled by transcription factors is discussed based on the significant progress.

Combined transcriptomic and metabolic analyses reveal potential mechanism for fruit development and quality control of Chinese raspberry (Rubus chingii Hu)

Combined transcriptomic and metabolic analyses reveal that fruit of Rubus chingii Hu launches biosynthesis of phenolic acids and flavonols at beginning of fruit set and then coordinately accumulated or converted to their derivatives. Rubus chingii Hu (Chinese raspberry) is an important dual functional food with nutraceutical and pharmaceutical values. Comprehensively understanding the mechanisms of fruit development and bioactive components synthesis and regulation could accelerate genetic analysis and molecular breeding for the unique species. Combined transcriptomic and metabolic analyses of R. chingii fruits from different developmental stages, including big green, green-to-yellow, yellow-to-orange, and red stages, were conducted. A total of 89,188 unigenes were generated and 57,545 unigenes (64.52%) were annotated. Differential expression genes (DEGs) and differentially accumulated metabolites (DAMs) were mainly involved in the biosynthesis of secondary metabolites. The fruit launched the biosynthesis of phenolic acids and flavonols at the very beginning of fruit set and then coordinately accumulated or converted to their derivatives. This was tightly regulated by expressions of the related genes and MYB and bHLH transcription factors. The core genes products participated in the biosynthesis of ellagic acid (EA) and kaempferol-3-O-rutinoside (K-3-R), such as DAHPS, DQD/SDH, PAL, 4CL, CHS, CHI, F3H, F3'H, FLS, and UGT78D2, and their corresponding metabolites were elaborately characterized. Our research reveals the molecular and chemical mechanisms of the fruit development of R. chingii. The results provide a solid foundation for the genetic analysis, functional genes isolation, fruit quality improvement and modifiable breeding of R. chingii.

Sterol Glucosyltransferases Tailor Polysaccharide Accumulation in Arabidopsis Seed Coat Epidermal Cells

The conjugation of sterols with a Glc moiety is catalyzed by sterol glucosyltransferases (SGTs). A portion of the resulting steryl glucosides (SG) are then esterified with a long-chain fatty acid to form acyl-SG (ASG). SG and ASG are prevalent components of plant cellular membranes and influence their organization and functional properties. Mutant analysis had previously inferred that two Arabidopsis SGTs, UGT80A2 and UGT80B1/TT15, could have specialized roles in the production of SG in seeds, despite an overlap in their enzymatic activity. Here, we establish new roles for both enzymes in the accumulation of polysaccharides in seed coat epidermal cells (SCEs). The rhamnogalacturonan-I (RG-I) content of the inner layer of seed mucilage was higher in ugt80A2, whereas RG-I accumulation was lower in mutants of UGT80B1, with double mutant phenotypes indicating that UGT80A2 acts independently from UGT80B1. In contrast, an additive phenotype was observed in double mutants for increased galactoglucomannan (GGM) content. Double mutants also exhibited increased polymer density within the inner mucilage layer. In contrast, cell wall defects were only observed in mutants defective for UGT80B1, while more mucilage cellulose was only observed when UGT80A2 was mutated. The generation of a range of phenotypic effects, simultaneously within a single cell type, demonstrates that the adjustment of the SG and ASG composition of cellular membranes by UGT80A2 and UGT80B1 tailors polysaccharide accumulation in Arabidopsis seeds.

Biosynthetic Pathway of Proanthocyanidins in Major Cash Crops

Proanthocyanidins (PAs) are a group of oligomers or polymers composed of monomeric flavanols. They offer many benefits for human fitness, such as antioxidant, anticancer, and anti-inflammatory activities. To date, three types of PA have been observed in nature: procyanidins, propelargonidins, and prodelphinidins. These are synthesized as some of the end-products of the flavonoid pathway by different consecutive enzymatic activities, from the same precursor—naringenin. Although the general biosynthetic pathways of PAs have been reported in a few model plant species, little is known about the species-specific pathways in major crops containing different types of PA. In the present study, we identified the species-specific pathways in 10 major crops, based on the presence/absence of flavanol-based intermediates in the metabolic pathway, and found 202 orthologous genes in the reference genomic database of each species, which may encode for key enzymes involved in the biosynthetic pathways of PAs. Parallel enzymatic reactions in the pathway are responsible for the ratio between PAs and anthocyanins, as well as among the three types of PAs. Our study suggests a promising strategy for molecular breeding, to regulate the content of PAs and anthocyanins and improve the nutritional quality of food sources globally.

Regulatory Mechanisms of Anthocyanin Biosynthesis in Apple and Pear

Anthocyanins contribute to the quality and flavour of fruits. They are produced through the phenylpropanoid pathway, which is regulated by specific key genes that have been identified in many species. The dominant anthocyanin forms are reversibly transformed at different pH states, thus forming different colours in aqueous solutions. In plants, anthocyanins are controlled by specific factors of the biosynthetic pathway: light, temperature, phytohormones and transcription factors. Although great progress in research on anthocyanin structures and the regulation of anthocyanin biosynthesis has been made, the molecular regulatory mechanisms of anthocyanin biosynthesis in different plants remain less clear. In addition, the co-regulation of anthocyanin biosynthesis is poorly understood. In this review, we summarise previous findings on anthocyanin biosynthesis, including the biochemical and biological features of anthocyanins; differences in anthocyanin biosynthesis among fruit species, i.e., apple, red pear, and the model plant Arabidopsis thaliana; and the developmental and environmental regulation of anthocyanin accumulation. This review reveals the molecular mechanisms underlying anthocyanin biosynthesis in different plant species and provides valuable information for the development of anthocyanin-rich red-skinned and red-fleshed apple and pear varieties.

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.

Impact of Betaine Under Salinity on Accumulation of Phenolic Compounds in Safflower (Carthamus tinctorius L.) Sprouts

It has been assumed that abiotic stresses often lead to osmotic and ionic stress in plants either inducing or reducing secondary plant metabolites. Therefore, the influence of NaCl, glycinebetaine (betaine), and NaCl with betaine on the growth and variation in the accumulation of phenolic compounds was investigated in safflower ( Carthamus tinctorius L.). The growth pattern of safflower sprouts was significantly influenced by these treatments. It was found that with increases in the concentration of NaCl, all growth parameters steadily decreased, but growth was markedly increased by adding different concentrations of betaine, especially at 0.5 mM, which produced the highest growth in terms of different growth parameters. High-performance liquid chromatographic (HPLC) analysis revealed changes in 7 different phenolic compounds in response to different treatments. After treatment with up to 200 mM NaCl, the levels of catechin, ferulic acid, benzoic acid, and kaempferol increased, whereas the levels of the remaining phenolic compounds, especially chlorogenic acid, and p-coumaric acid were reduced. Our results suggest that the growth suppression due to salinity stress is decreased in the sprouts of safflower by adding betaine.

Pre-harvest sprouting in cereals: genetic and biochemical mechanisms

With the growth of the global population and the increasing frequency of natural disasters, crop yields must be steadily increased to enhance human adaptability to risks. Pre-harvest sprouting (PHS), a term mainly used to describe the phenomenon in which grains germinate on the mother plant directly before harvest, is a serious global problem for agricultural production. After domestication, the dormancy level of cultivated crops was generally lower than that of their wild ancestors. Although the shortened dormancy period likely improved the industrial performance of cereals such as wheat, barley, rice, and maize, the excessive germination rate has caused frequent PHS in areas with higher rainfall, resulting in great economic losses. Here, we systematically review the causes of PHS and its consequences, the major indicators and methods for PHS assessment, and emphasize the biological significance of PHS in crop production. Wheat quantitative trait loci functioning in the control of PHS are also comprehensively summarized in a meta-analysis. Finally, we use Arabidopsis as a model plant to develop more complete PHS regulatory networks for wheat. The integration of this information is conducive to the development of custom-made cultivated lines suitable for different demands and regions, and is of great significance for improving crop yields and economic benefits.

Identification and Quantification of Coumarins by UHPLC-MS in Arabidopsis thaliana Natural Populations

Coumarins are phytochemicals occurring in the plant kingdom, which biosynthesis is induced under various stress factors. They belong to the wide class of specialized metabolites well known for their beneficial properties. Due to their high and wide biological activities, coumarins are important not only for the survival of plants in changing environmental conditions, but are of great importance in the pharmaceutical industry and are an active source for drug development. The identification of coumarins from natural sources has been reported for different plant species including a model plant Arabidopsis thaliana. In our previous work, we demonstrated a presence of naturally occurring intraspecies variation in the concentrations of scopoletin and its glycoside, scopolin, the major coumarins accumulating in Arabidopsis roots. Here, we expanded this work by examining a larger group of 28 Arabidopsis natural populations (called accessions) and by extracting and analysing coumarins from two different types of tissues-roots and leaves. In the current work, by quantifying the coumarin content in plant extracts with ultra-high-performance liquid chromatography coupled with a mass spectrometry analysis (UHPLC-MS), we detected a significant natural variation in the content of simple coumarins like scopoletin, umbelliferone and esculetin together with their glycosides: scopolin, skimmin and esculin, respectively. Increasing our knowledge of coumarin accumulation in Arabidopsis natural populations, might be beneficial for the future discovery of physiological mechanisms of action of various alleles involved in their biosynthesis. A better understanding of biosynthetic pathways of biologically active compounds is the prerequisite step in undertaking a metabolic engineering research.

Spinescence and Total Phenolic Content Do Not Influence Diet Preference of a Critically Endangered Megaherbivore, but the Mix of Compounds Does

In contrast to understanding spinescence in savanna woody species, little is known about the functions of plant secondary metabolites (PSM). Negative effects of PSMs on individual animal performance potentially translate into negative effects on herbivore population growth. Hence, understanding PSM functions is important for the conservation of savanna megafauna. We tested the view that black rhinoceros (Diceros bicornis) diet preference is not affected by spinescence or total phenolic abundance. We hypothesized that the composition of phenolic mixtures, however, would affect preference. Furthermore, we tested our data from 71 woody species for a trade-off between structural and chemical defenses. Spinescence type, and spinescence generally, did not deter black rhino feeding. Using eco-metabolomic data, we found that total abundance of phenolics did not affect preference, but mixture composition did and that the probability of spinescence trading off against phenolics depended on the mixture. We note that our study was restricted to black rhino and that diet preferences of other mammal herbivores might be influenced by subtle differences in phenolic mixtures. However, our results did support a previous, more detailed study of phenolic profiles of six species showing the same patterns in relation to preference generalised across mammal herbivore species in savannas. Our results represent substantial advancement in the understanding of the roles of PSMs, especially flavonoid compounds, in the functioning of savanna ecosystems, and highlight the need to dig deeper into broad groups of traits such as spinescence or total phenolics to improve understanding of woody plant defenses in savannas.

Combining QTL Mapping and Transcriptomics to Decipher the Genetic Architecture of Phenolic Compounds Metabolism in the Conifer White Spruce

Conifer forests worldwide are becoming increasingly vulnerable to the effects of climate change. Although the production of phenolic compounds (PCs) has been shown to be modulated by biotic and abiotic stresses, the genetic basis underlying the variation in their constitutive production level remains poorly documented in conifers. We used QTL mapping and RNA-Seq to explore the complex polygenic network underlying the constitutive production of PCs in a white spruce (Picea glauca) full-sib family for 2 years. QTL detection was performed for nine PCs and differentially expressed genes (DEGs) were identified between individuals with high and low PC contents for five PCs exhibiting stable QTLs across time. A total of 17 QTLs were detected for eight metabolites, including one major QTL explaining up to 91.3% of the neolignan-2 variance. The RNA-Seq analysis highlighted 50 DEGs associated with phenylpropanoid biosynthesis, several key transcription factors, and a subset of 137 genes showing opposite expression patterns in individuals with high levels of the flavonoids gallocatechin and taxifolin glucoside. A total of 19 DEGs co-localized with QTLs. Our findings represent a significant step toward resolving the genomic architecture of PC production in spruce and facilitate the functional characterization of genes and transcriptional networks responsible for differences in constitutive production of PCs in conifers.

Advances in Biosynthesis and Biological Functions of Proanthocyanidins in Horticultural Plants

Proanthocyanidins are colorless flavonoid polymers condensed from flavan-3-ol units. They are essential secondary plant metabolites that contribute to the nutritional value and sensory quality of many fruits and the related processed products. Mounting evidence has shown that the accumulation of proanthocyanidins is associated with the resistance of plants against a broad spectrum of abiotic and biotic stress conditions. The biosynthesis of proanthocyanidins has been examined extensively, allowing for identifying and characterizing the key regulators controlling the biosynthetic pathway in many plants. New findings revealed that these specific regulators were involved in the proanthocyanidins biosynthetic network in response to various environmental conditions. This paper reviews the current knowledge regarding the control of key regulators in the underlying proanthocyanidins biosynthetic and molecular mechanisms in response to environmental stress. Furthermore, it discusses the directions for future research on the metabolic engineering of proanthocyanidins production to improve food and fruit crop quality.

Specialized phenolic compounds in seeds: structures, functions, and regulations

Plants produce a huge diversity of specialized metabolites (SM) throughout their life cycle that play important physiological and ecological functions. SM can protect plants and seeds against diseases, predators, and abiotic stresses, or support their interactions with beneficial or symbiotic organisms. They also have strong impacts on human nutrition and health. Despite this importance, the biosynthesis and biological functions of most of the SM remain elusive and their diversity and/or quantity have been reduced in most crops during domestication. Seeds present a large number of SM that are important for their physiological, agronomic, nutritional or industrial qualities and hence, provide interesting models for both studying biosynthesis and producing large amounts of specialized metabolites. For instance, phenolics are abundant and widely distributed in seeds. More specifically, flavonoid pathway has been instrumental for understanding environmental or developmental regulations of specialized metabolic pathways, at the molecular and cellular levels. Here, we summarize current knowledge on seed phenolics as model, and discuss how recent progresses in omics approaches could help to further characterize their diversity, regulations, and the underlying molecular mechanisms involved.

Melatonin Represses Oil and Anthocyanin Accumulation in Seeds

Previous studies have clearly demonstrated that the putative phytohormone melatonin functions directly in many aspects of plant growth and development. In Arabidopsis (Arabidopsis thaliana), the role of melatonin in seed oil and anthocyanin accumulation, and corresponding underlying mechanisms, remain unclear. Here, we found that serotonin N-acetyltransferase1 (SNAT1) and caffeic acid O-methyltransferase (COMT) genes were ubiquitously and highly expressed and essential for melatonin biosynthesis in Arabidopsis developing seeds. We demonstrated that blocking endogenous melatonin biosynthesis by knocking out SNAT1 and/or COMT significantly increased oil and anthocyanin content of mature seeds. In contrast, enhancement of melatonin signaling by exogenous application of melatonin led to a significant decrease in levels of seed oil and anthocyanins. Further gene expression analysis through RNA sequencing and reverse-transcription quantitative PCR demonstrated that the expression of a series of important genes involved in fatty acid and anthocyanin accumulation was significantly altered in snat1-1 comt-1 developing seeds during seed maturation. We also discovered that SNAT1 and COMT significantly regulated the accumulation of both mucilage and proanthocyanidins in mature seeds. These results not only help us understand the function of melatonin and provide valuable insights into the complicated regulatory network controlling oil and anthocyanin accumulation in seeds, but also divulge promising gene targets for improvement of both oil and flavonoids in seeds of oil-producing crops and plants.

Conservation and diversification of flavonoid metabolism in the plant kingdom

Flavonoids are by far the largest class of polyphenols with huge structural and functional diversity. However, the mystery regarding the exact evolutionary pressures which lead to the amazing diversity in plant flavonoids has yet to be completely uncovered. Here we review recent advances in understanding the conservation and diversification of flavonoid pathway from algae and early land plants to vascular plants including the model plant Arabidopsis and economically important species such as cereals, legumes, and medicinal plants. Studies on the origin and evolution of R2R3-MYB regulatory system demonstrated its highly conserved function of regulating flavonoid production in land plants and this innovation appears to have been crucial in boosting the overall levels of these compounds in land plants. Convergent evolution has occurred as different flavonoids independently which emerged in distant taxa resulting in similar defense and tolerance characteristics against environmental stresses. Future studies on an increasing number of plant species taking advantage of newly developed genomic and metabolite profiling technologies are envisaged to provide comprehensive insight into flavonoid biosynthesis as well as pathway diversification and the underlying evolutionary mechanisms.

Stimulated biosynthesis of delphinidin-related anthocyanins in tea shoots reducing the quality of green tea in summer

BACKGROUND

Greater proportions of purple tea buds and leaves usually appear in the summer, which seriously affects the color and taste quality of green tea products, yet the metabolism of purple tea shoots in summer remains unclear. Here, the metabolomic profiles and gene expression of related flavonoid metabolic pathways in the purple and normal green shoots of 'Longjing 43', and the quality of green tea made with these two phenotypes, were analyzed and compared.

RESULTS

Differential metabolites identified using high-performance liquid chromatography-Orbitrap/mass spectrometry indicated that anthocyanin biosynthesis in purple leaves was enriched, with higher levels of anthocyanidins (delphinidin-hexose-coumaroyl showed the greatest increase), proanthocyanidins (oligomers of catechins) and kaempferol glycoside. Expression patterns of the genes ANR, ANS, FLS, LAR, C4H, PAL, CHI, CHS and DFR revealed that the metabolism of anthocyanin is positively regulated by high temperature and/or light levels in summer. Gas chromatography-mass spectrometry results showed that, in purple tea shoots, the metabolism of carbohydrates was enriched whereas that of amino acids was diminished, while their mannose, fructose, d-galactose, sorbose and d-glucose contents were more than double those found in green leaves. A sensory evaluation confirmed that a greater quantity of purple shoots had a greater negative impact on green tea quality because of a bitter taste and dark color (leaves and infusions were tested).

CONCLUSIONS

These results highlight the need for and possibility of improving commercial tea quality via cultivation that controls the temperature or light of tea gardens during the summer. © 2019 Society of Chemical Industry.

CsCYT75B1, a Citrus CYTOCHROME P450 Gene, Is Involved in Accumulation of Antioxidant Flavonoids and Induces Drought Tolerance in Transgenic Arabidopsis

CYTOCHROME P450s genes are a large gene family in the plant kingdom. Our earlier transcriptome data revealed that a CYTOCHROME P450 gene of Citrus sinensis (CsCYT75B1) was associated with flavonoid metabolism and was highly induced after drought stress. Here, we characterized the function of CsCYT75B1 in drought tolerance by overexpressing it in Arabidopsis thaliana. Our results demonstrated that the overexpression of the CsCYT75B1 gene significantly enhanced the total flavonoid contents with increased antioxidant activity in transgenic Arabidopsis. The gene expression results showed that several genes that are responsible for the biosynthesis of antioxidant flavonoids were induced by 2-12 fold in transgenic Arabidopsis lines. After 14 days of drought stress, all transgenic lines displayed an enhanced tolerance to drought stress along with accumulating antioxidant flavonoids with lower superoxide radicals and reactive oxygen species (ROS) than wild type plants. In addition, drought-stressed transgenic lines possessed higher antioxidant enzymatic activities than wild type transgenic lines. Moreover, the stressed transgenic lines had significantly lower levels of electrolytic leakage than wild type transgenic lines. These results demonstrate that the CsCYT75B1 gene of sweet orange functions in the metabolism of antioxidant flavonoid and contributes to drought tolerance by elevating ROS scavenging activities.

Arabidopsis MYB4 plays dual roles in flavonoid biosynthesis

Flavonoids are major secondary metabolites derived from the plant phenylpropanoid pathway that play important roles in plant development and also have benefits for human health. So-called MBW ternary complexes involving R2R3-MYB and basic helix-loop-helix (bHLH) transcription factors along with WD-repeat proteins have been reported to regulate expression of the biosynthetic genes in the flavonoid pathway. MYB4 and its closest homolog MYB7 have been suggested to function as repressors of phenylpropanoid metabolism. However, the detailed mechanism by which they act has not been fully elucidated. Here, we show that Arabidopsis thaliana MYB4 and its homologs MYB7 and MYB32 interact with the bHLH transcription factors TT8, GL3 and EGL3 and thereby interfere with the transcriptional activity of the MBW complexes. In addition, MYB4 can also inhibit flavonoid accumulation by repressing expression of the gene encoding Arogenate Dehydratase 6 (ADT6), which catalyzes the final step in the biosynthesis of phenylalanine, the precursor for flavonoid biosynthesis. MYB4 potentially represses not only the conventional ADT6 encoding the plastidial enzyme but also the alternative isoform encoding the cytosolic enzyme. We suggest that MYB4 plays dual roles in modulating the flavonoid biosynthetic pathway in Arabidopsis.

Genome-wide Dissection of Co-selected UV-B Responsive Pathways in the UV-B Adaptation of Qingke

Qingke (Tibetan hulless barley) has long been cultivated and exposed to long-term and strong UV-B radiation on the Tibetan Plateau, which renders it an ideal species for elucidating novel UV-B responsive mechanisms in plants. Here we report a comprehensive metabolite profiling and metabolite-based genome-wide association study (mGWAS) using 196 diverse qingke and barley accessions. Our results demonstrated both constitutive and induced accumulation, and common genetic regulation, of metabolites from different branches of the phenylpropanoid pathway that are involved in UV-B protection. A total of 90 significant mGWAS loci for these metabolites were identified in barley-qingke differentiation regions, and a number of high-level metabolite trait alleles were found to be significantly enriched in qingke, suggesting co-selection of various phenylpropanoids. Upon dissecting the entire phenylpropanoid pathway, we identified some key determinants controlling natural variation of phenylpropanoid content, including three novel proteins, a flavone C-pentosyltransferase, a tyramine hydroxycinnamoyl acyltransferase, and a MYB transcription factor. Our study, furthermore, demonstrated co-selection of both constitutive and induced phenylpropanoids for UV-B protection in qingke.

Functional characterization of a HD-ZIP IV transcription factor NtHDG2 in regulating flavonols biosynthesis in Nicotiana tabacum

The HD-ZIP Ⅳ transcription factors have been identified and functional characterized in many plant species. However, no tobacco HD-ZIP IV gene has been isolated, and it is not yet known whether HD-ZIP IV genes are involved in controlling flavonols accumulation in plants. Here, we cloned a HD ZIP gene named NtHDG2 from Nicotiana tabacum, which belongs to the class IV of HD-ZIP family, and the NtHDG2-GFP fusion protein is localized to the nucleus. We further observed that the flavonols contents in the NtHDG2 overexpression leaves increase to 1.9-4.5 folds of that in WT plants, but in the NtHDG2-RNAi plants the flavonols contents reduce to 20.9%-52.7% of that in WT plants. The transcriptions of one regulatory gene NtMYB12, and three structural genes (NtPAL, NtF3'H, NtF3GT), contributing to flavonols biosynthesis, were significantly induced by NtHDG2. However, the transcription level of NtNAC002, a flavonols biosynthesis repressor, was also significantly up-regulated in NtHDG2-overexpression lines, but significantly down-regulated in the RNAi lines, indicating that HDG2 regulates the synthesis of flavonols as a complex regulatory network. Moreover, ectopic expression of NtHDG2 gene promoted the transcription of several AP2/ERF genes, including NtERF1-5, NtERF109, NtDREB1, and NtCIPK11, which participate in regulating root development and resistance to abiotic stresses. Our findings reveal the new function of HD-ZIP IV transcription factors in flavonoids biosynthesis, and indicate that HD-ZIP IV members may play an important role in plant resistance to abiotic stress. The NtHDG2 gene provides a promising target for genetically manipulating to increase the amounts of flavonols in tobacco leaves.

Ectopic expression of citrus UDP-GLUCOSYL TRANSFERASE gene enhances anthocyanin and proanthocyanidins contents and confers high light tolerance in Arabidopsis

BACKGROUND

Citrus fruits are consumed freshly or as juice to directly provide various dietary flavonoids to humans. Diverse metabolites are present among Citrus genera, and many flavonoids biosynthetic genes were induced after abiotic stresses. To better understand the underlying mechanism, we designed experiments to overexpress a UDP-GLUCOSYL TRANSFERASE gene from sweet orange (Citrus sinensis) to evaluate its possible function in metabolism and response to stress.

RESULTS

Our results demonstrated that overexpression of Cs-UGT78D3 resulted in high accumulation of proanthocyanidins in the seed coat and a dark brown color to transgenic Arabidopsis seeds. In addition, the total contents of flavonoid and anthocyanin were significantly enhanced in the leaves of overexpressed lines. Gene expression analyses indicated that many flavonoid (flavonol) and anthocyanin genes were up-regulated by 4-15 folds in transgenic Arabidopsis. Moreover, after 14 days of high light stress, the transgenic Arabidopsis lines showed strong antioxidant activity and higher total contents of anthocyanins and flavonoids in leaves compared with the wild type.

CONCLUSION

Our study concluded that the citrus Cs-UGT78D3 gene contributes to proanthocyanidins accumulation in seed coats and confers tolerance to high light stress by accumulating the total anthocyanin and flavonoid contents with better antioxidant potential (due to photoprotective activity of anthocyanin) in the transgenic Arabidopsis.

Transcriptome analysis reveals candidate genes related to phosphorus starvation tolerance in sorghum

BACKGROUND

Phosphorus (P) deficiency in soil is a worldwide issue and a major constraint on the production of sorghum, which is an important staple food, forage and energy crop. The depletion of P reserves and the increasing price of P fertilizer make fertilizer application impractical, especially in developing countries. Therefore, identifying sorghum accessions with low-P tolerance and understanding the underlying molecular basis for this tolerance will facilitate the breeding of P-efficient plants, thereby resolving the P crisis in sorghum farming. However, knowledge in these areas is very limited.

RESULTS

The 29 sorghum accessions used in this study demonstrated great variability in their tolerance to low-P stress. The internal P content in the shoot was correlated with P tolerance. A low-P-tolerant accession and a low-P-sensitive accession were chosen for RNA-seq analysis to identify potential underlying molecular mechanisms. A total of 2089 candidate genes related to P starvation tolerance were revealed and found to be enriched in 11 pathways. Gene Ontology (GO) enrichment analyses showed that the candidate genes were associated with oxidoreductase activity. In addition, further study showed that malate affected the length of the primary root and the number of tips in sorghum suffering from low-P stress.

CONCLUSIONS

Our results show that acquisition of P from soil contributes to low-P tolerance in different sorghum accessions; however, the underlying molecular mechanism is complicated. Plant hormone (including auxin, ethylene, jasmonic acid, salicylic acid and abscisic acid) signal transduction related genes and many transcriptional factors were found to be involved in low-P tolerance in sorghum. The identified accessions will be useful for breeding new sorghum varieties with enhanced P starvation tolerance.

Anti-Inflammatory Activity of A Polyphenolic Extract from Arabidopsis thaliana in In Vitro and In Vivo Models of Alzheimer's Disease

Alzheimer’s disease (AD) is the most common neurodegenerative disorder and the primary form of dementia in the elderly. One of the main features of AD is the increase in amyloid-beta (Aβ) peptide production and aggregation, leading to oxidative stress, neuroinflammation and neurodegeneration. Polyphenols are well known for their antioxidant, anti-inflammatory and neuroprotective effects and have been proposed as possible therapeutic agents against AD. Here, we investigated the effects of a polyphenolic extract of Arabidopsis thaliana (a plant belonging to the Brassicaceae family) on inflammatory response induced by Aβ. BV2 murine microglia cells treated with both Aβ_25–35 peptide and extract showed a lower pro-inflammatory (IL-6, IL-1β, TNF-α) and a higher anti-inflammatory (IL-4, IL-10, IL-13) cytokine production compared to cells treated with Aβ only. The activation of the Nrf2-antioxidant response element signaling pathway in treated cells resulted in the upregulation of heme oxygenase-1 mRNA and in an increase of NAD(P)H:quinone oxidoreductase 1 activity. To establish whether the extract is also effective against Aβ-induced neurotoxicity in vivo, we evaluated its effect on the impaired climbing ability of AD Drosophila flies expressing human Aβ_1–42. Arabidopsis extract significantly restored the locomotor activity of these flies, thus confirming its neuroprotective effects also in vivo. These results point to a protective effect of the Arabidopsis extract in AD, and prompt its use as a model in studying the impact of complex mixtures derived from plant-based food on neurodegenerative diseases.

Evolutionary and functional analyses of the 2-oxoglutarate-dependent dioxygenase genes involved in the flavonoid biosynthesis pathway in tobacco

MAIN CONCLUSION

This study illustrates the differences in the gene structure of 2-oxoglutarate-dependent oxygenase involved in flavonoid biosynthesis (2ODD-IFB), and their potential roles in regulating tobacco flavonoid biosynthesis and plant growth. Flavonol synthase (FLS), anthocyanidin synthase (ANS), and flavanone 3β-hydroxylase belong to the 2-oxoglutarate-dependent (2ODD) oxygenase family, and each performs crucial functions in the biosynthesis of flavonoids. We identified two NtFLS genes, two NtANS genes, and four NtF3H genes from Nicotiana tabacum genome, as well as their homologous genes in the N. sylvestris and N. tomentosiformis genomes. Our phylogenetic analysis indicated that these three types of genes split from each other before the divergence of gymnosperms and angiosperms. FLS evolved faster in the eudicot plants, whereas ANS evolved faster in the monocot plants. Gene structure analysis revealed two fragment insertions occurred at different times in the intron one position of tobacco FLS genes. Homologous protein modeling revealed distinct structures in the N terminus of the tobacco 2ODD oxygenases. We found that the expression patterns of genes encoding tobacco 2ODD oxygenases in flavonoids biosynthesis (2ODD-IFB) did not determine the accumulation patterns of flavonoids among various tobacco tissues, but strongly affected the concentration of flavonoids in the tissues, where they were biosynthesized. More carbon resource flowed to the flavonol biosynthesis when NtANS gene was silenced, otherwise more anthocyanidin accumulated when NtFLS gene was repressed. This study illustrates the 2ODD-IFB gene structure evolution, differences among their protein structures, and provides a foundation for regulating plant development and altering flavonoid content and/or composition through the manipulation of plant 2ODD-IFB genes.

The Diversity of Nutritional Metabolites: Origin, Dissection, and Application in Crop Breeding

The chemical diversity of plants is very high, and plant-based foods provide almost all the nutrients necessary for human health, either directly or indirectly. With advancements in plant metabolomics studies, the concept of nutritional metabolites has been expanded and updated. Because the concentration of many nutrients is usually low in plant-based foods, especially those from crops, metabolome-assisted breeding techniques using molecular markers associated with the synthesis of nutritional metabolites have been developed and used to improve nutritional quality of crops. Here, we review the origins of the diversity of nutrient metabolites from a genomic perspective and the role of gene duplication and divergence. In addition, we systematically review recent advances in the metabolomic and genetic basis of metabolite production in major crops. With the development of genome sequencing and metabolic detection technologies, multi-omic integrative analysis of genomes, transcriptomes, and metabolomes has greatly facilitated the deciphering of the genetic basis of metabolic pathways and the diversity of nutrient metabolites. Finally, we summarize the application of nutrient diversity in crop breeding and discuss the future development of a viable alternative to metabolome-assisted breeding techniques that can be used to improve crop nutrient quality.

Four flavonoid glycosyltransferases present in tea overexpressed in model plants Arabidopsis thaliana and Nicotiana tabacum for functional identification

Tea possesses a distinctive flavor profile and can have health benefits owing to the high levels of flavonoids in its leaves. However, the mechanism of the flavonoid glycosylation hasn't been well studied in tea plants, especially glycosylation at the 7-OH site has rarely been reported. In this study, four UGT genes CsUGT73A20, CsUGT75L12, CsUGT78A14 and CsUGT78A15 were isolated from tea leaves and overexpressed in the model plants Arabidopsis thaliana and Nicotiana tabacum for the functional identification of genes in vivo. In order to characterize the CsUGT functions in model plants, flavonoids in seeds of Arabidopsis and the flowers of tobacco were identified first. In CsUGT73A20-overexpressing Arabidopsis and tobacco, the level of certain flavonol glycosides involved in glycosylation reactions at the 3-OH and 7-OH sites increased considerably, but the level of flavan-3-ols decreased. In CsUGT75L12 transgenic Arabidopsis, the level of flavonol glycosides exhibiting glucosyltransferase activity at the 7-OH position increased markedly, but the concentrations of quercetin and kaempferol and flavan-3-ols decreased. In both transgenic Arabidopsis and tobacco, CsUGT78A14 promoted the synthesis of more flavonol glucosides with UDP-glucose as a sugar donor at the 3-OH glycosylation site. In CsUGT78A15 transgenic plants, flavonol galactosides at the 3-OH glycosylation site with UDP-galactose as a sugar donor were increased. In the tea plant, the corresponding flavonoid glycosides such as kaempferol‑3‑O‑β‑d‑glucosides, kaempferol‑3‑O‑β‑d‑galactosides, kaempferol‑7‑O‑β‑d‑glucoside, and luteolin‑7‑O‑β‑d‑glucoside were identified. And it could be possible that they were products of CsUGT78A14, CsUGT78A15, CsUGT73A20 and CsUGT75L12, respectively.

Metabolome variability for two Mediterranean sponge species of the genus Haliclona: specificity, time, and space

INTRODUCTION

The study of natural variation of metabolites brings valuable information on the physiological state of the organisms as well as their phenotypic traits. In marine organisms, metabolome variability has mostly been addressed through targeted studies on metabolites of ecological or pharmaceutical interest. However, comparative metabolomics has demonstrated its potential to address the overall and complex metabolic variability of organisms.

OBJECTIVES

In this study, the intraspecific (temporal and spatial) variability of two Mediterranean Haliclona sponges (H. fulva and H. mucosa) was investigated through an untargeted and then targeted metabolomics approach and further compared to their interspecific variability.

METHODS

Samples of both species were collected monthly during 1 year in the coralligenous habitat of the Northwestern Mediterranean sae at Marseille and Nice. Their metabolomic profiles were obtained by UHPLC-QqToF analyses.

RESULTS

Marked variations were noticed in April and May for both species including a decrease in Shannon's diversity and concentration in specialized metabolites together with an increase in fatty acids and lyso-PAF like molecules. Spatial variations across different sampling sites could also be observed for both species, however in a lesser extent.

CONCLUSIONS

Synchronous metabolic changes possibly triggered by physiological factors like reproduction and/or environmental factors like an increase in the water temperature were highlighted for both Mediterranean Haliclona species inhabiting close habitats but displaying different biosynthetic pathways. Despite significative intraspecific variations, metabolomic variability remains minor when compared to interspecific variations for these congenerous species, therefore suggesting the predominance of genetic information of the holobiont in the observed metabolome.

A Maternally Deposited Endosperm Cuticle Contributes to the Physiological Defects of transparent testa Seeds

Mature dry seeds are highly resilient plant structures where the encapsulated embryo is kept protected and dormant to facilitate its ultimate dispersion. Seed viability is heavily dependent on the seed coat's capacity to shield living tissues from mechanical and oxidative stress. In Arabidopsis (Arabidopsis thaliana), the seed coat, also called the testa, arises after the differentiation of maternal ovular integuments during seed development. We recently described a thick cuticle tightly embedded in the mature seed's endosperm cell wall. We show here that it is produced by the maternal inner integument 1 layer and, remarkably, transferred to the developing endosperm. Arabidopsis transparent testa (tt) mutations cause maternally derived seed coat pigmentation defects. TT gene products encode proteins involved in flavonoid metabolism and regulators of seed coat development. tt mutants have abnormally high seed coat permeability, resulting in lower seed viability and dormancy. However, the biochemical basis of this high permeability is not fully understood. We show that the cuticles of developing tt mutant integuments have profound structural defects, which are associated with enhanced cuticle permeability. Genetic analysis indicates that a functional proanthocyanidin synthesis pathway is required to limit cuticle permeability, and our results suggest that proanthocyanidins could be intrinsic components of the cuticle. Together, these results show that the formation of a maternal cuticle is an intrinsic part of the normal integumental differentiation program leading to testa formation and is essential for the seed's physiological properties.

Sergeeva L, Vreugdenhil D. Natural variation of hormone levels in Arabidopsis roots and correlations with complex root architecture

Studies on natural variation are an important tool to unravel the genetic basis of quantitative traits in plants. Despite the significant roles of phytohormones in plant development, including root architecture, hardly any studies have been done to investigate natural variation in endogenous hormone levels in plants. Therefore, in the present study a range of hormones were quantified in root extracts of thirteen Arabidopsis thaliana accessions using a ultra performance liquid chromatography triple quadrupole mass spectrometer. Root system architecture of the set of accessions was quantified, using a new parameter (mature root unit) for complex root systems, and correlated with the phytohormone data. Significant variations in phytohormone levels among the accessions were detected, but were remarkably small, namely less than three-fold difference between extremes. For cytokinins, relatively larger variations were found for ribosides and glucosides, as compared to the free bases. For root phenotyping, length-related traits-lateral root length and total root length-showed larger variations than lateral root number-related ones. For root architecture, antagonistic interactions between hormones, for example, indole-3-acetic acid to trans-zeatin were detected in correlation analysis. These findings provide conclusive evidence for the presence of natural variation in phytohormone levels in Arabidopsis roots, suggesting that quantitative genetic analyses are feasible.

Transcriptome Analysis Reveals Candidate Genes Associated with Leaf Etiolation of a Cytoplasmic Male Sterility Line in Chinese Cabbage (Brassica Rapa L. ssp. Pekinensis)

Cytoplasmic male sterility (CMS) is universally utilized in cruciferous vegetables. However, the Chinese cabbage hau CMS lines, obtained by interspecific hybridization and multiple backcrosses of the Brassica juncea (B. juncea) CMS line and Chinese cabbage, show obvious leaf etiolation, and the molecular mechanism of etiolation remains elusive. Here, the ultrastructural and phenotypic features of leaves from the Chinese cabbage CMS line 1409A and maintainer line 1409B are analyzed. The results show that chloroplasts of 1409A exhibit abnormal morphology and distribution. Next, RNA-sequencing (RNA-Seq) is used to identify 485 differentially expressed genes (DEGs) between 1409A and 1409B, and 189 up-regulated genes and 296 down-regulated genes are found. Genes that affect chloroplasts development, such as GLK1 and GLK2, and chlorophyll biosynthesis, such as PORB, are included in the down-regulated DEGs. Quantitative real-time PCR (qRT-PCR) analysis validate that the expression levels of these genes are significantly lower in 1409A than in 1409B. Taken together, these results demonstrate that leaf etiolation is markedly affected by chloroplast development and pigment biosynthesis. This study provides an effective foundation for research on the molecular mechanisms of leaf etiolation of the hau CMS line in Chinese cabbage (Brassica rapa L. ssp. pekinensis).

Mapping the Arabidopsis Metabolic Landscape by Untargeted Metabolomics at Different Environmental Conditions

Metabolic genome-wide association studies (mGWAS), whereupon metabolite levels are regarded as traits, can help unravel the genetic basis of metabolic networks. A total of 309 Arabidopsis accessions were grown under two independent environmental conditions (control and stress) and subjected to untargeted LC-MS-based metabolomic profiling; levels of the obtained hydrophilic metabolites were used in GWAS. Our two-condition-based GWAS for more than 3000 semi-polar metabolites resulted in the detection of 123 highly resolved metabolite quantitative trait loci (p ≤ 1.0E-08), 24.39% of which were environment-specific. Interestingly, differently from natural variation in Arabidopsis primary metabolites, which tends to be controlled by a large number of small-effect loci, we found several major large-effect loci alongside a vast number of small-effect loci controlling variation of secondary metabolites. The two-condition-based GWAS was followed by integration with network-derived metabolite-transcript correlations using a time-course stress experiment. Through this integrative approach, we selected 70 key candidate associations between structural genes and metabolites, and experimentally validated eight novel associations, two of them showing differential genetic regulation in the two environments studied. We demonstrate the power of combining large-scale untargeted metabolomics-based GWAS with time-course-derived networks both performed under different abiotic environments for identifying metabolite-gene associations, providing novel global insights into the metabolic landscape of Arabidopsis.

Genetic Mapping Populations for Conducting High-Resolution Trait Mapping in Plants

Fine mapping of quantitative trait loci (QTL) is the route to more detailed molecular characterization and functional studies of the relationship between polymorphism and trait variation. It is also of direct relevance to breeding since it makes QTL more easily integrated into marker-assisted breeding and into genomic selection. Fine mapping requires that marker-trait associations are tested in populations in which large numbers of recombinations have occurred. This can be achieved by increasing the size of mapping populations or by increasing the number of generations of crossing required to create the population. We review the factors affecting the precision and power of fine mapping experiments and describe some contemporary experimental approaches, focusing on the use of multi-parental or multi-founder populations such as the multi-parent advanced generation intercross (MAGIC) and nested association mapping (NAM). We favor approaches such as MAGIC since these focus explicitly on increasing the amount of recombination that occurs within the population. Whatever approaches are used, we believe the days of mapping QTL in small populations must come to an end. In our own work in MAGIC wheat populations, we started with a target of developing 1,000 lines per population: that number now looks to be on the low side. Graphical Abstract.