MATE transporters facilitate vacuolar uptake of epicatechin 3'-O-glucoside for proanthocyanidin biosynthesis in Medicago truncatula and Arabidopsis

The Seed Coat’s Impact on Crop Performance in Pea (Pisum sativum L.)

Seed development in angiosperms produces three genetically and developmentally distinct sub-compartments: the embryo, endosperm, and seed coat. The maternally derived seed coat protects the embryo and interacts closely with the external environment especially during germination and seedling establishment. Seed coat is a key contributor to seed composition and an important determinant of nutritional value for humans and livestock. In this review, we examined pea crop productivity through the lens of the seed coat, its contribution to several valued nutritional traits of the pea crop, and its potential as a breeding target. Key discoveries made in advancing the knowledge base for sensing and transmission of external signals, the architecture and chemistry of the pea seed coat, and relevant insights from other important legumes were discussed. Furthermore, for selected seed coat traits, known mechanisms of genetic regulation and efforts to modulate these mechanisms to facilitate composition and productivity improvements in pea were discussed, alongside opportunities to support the continued development and improvement of this underutilized crop. This review describes the most important features of seed coat development in legumes and highlights the key roles played by the seed coat in pea seed development, with a focus on advances made in the genetic and molecular characterization of pea and other legumes and the potential of this key seed tissue for targeted improvement and crop optimization.

Identification of two chickpea multidrug and toxic compound extrusion transporter genes transcriptionally upregulated upon aluminum treatment in root tips

Aluminum (Al) toxicity poses a significant challenge for the yield improvement of chickpea, which is an economically important legume crop with high nutritional value in human diets. The genetic basis of Al-tolerance in chickpea remains unclear. Here, we assessed the Al-tolerance of 8 wild Cicer and one cultivated chickpea (PBA Pistol) accessions by measuring the root elongation in solution culture under control (0 μM Al³⁺) and Al treatments (15, 30 μM Al³⁺). Compared to PBA Pistol, the wild Cicer accessions displayed both tolerant and sensitive phenotypes, supporting wild Cicer as a potential genetic pool for Al-tolerance improvement. To identify potential genes related to Al-tolerance in chickpea, genome-wide screening of multidrug and toxic compound extrusion (MATE) encoding genes was performed. Fifty-six MATE genes were identified in total, which can be divided into 4 major phylogenetic groups. Four chickpea MATE genes (CaMATE1-4) were clustered with the previously characterized citrate transporters MtMATE66 and MtMATE69 in Medicago truncatula. Transcriptome data showed that CaMATE1-4 have diverse expression profiles, with CaMATE2 being root-specific. qRT-PCR analyses confirmed that CaMATE2 and CaMATE4 were highly expressed in root tips and were up-regulated upon Al treatment in all chickpea lines. Further measurement of carboxylic acids showed that malonic acid, instead of malate or citrate, is the major extruded acid by Cicer spp. root. Protein structural modeling analyses revealed that CaMATE2 has a divergent substrate-binding cavity from Arabidopsis AtFRD3, which may explain the different acid-secretion profile for chickpea. Pangenome survey showed that CaMATE1-4 have much higher genetic diversity in wild Cicer than that in cultivated chickpea. This first identification of CaMATE2 and CaMATE4 responsive to Al³⁺ treatment in Cicer paves the way for future functional characterization of MATE genes in Cicer spp., and to facilitate future design of gene-specific markers for Al-tolerant line selection in chickpea breeding programs.

Root-secreted bitter triterpene modulates the rhizosphere microbiota to improve plant fitness

Underground microbial ecosystems have profound impacts on plant health^1-5. Recently, essential roles have been shown for plant specialized metabolites in shaping the rhizosphere microbiome^6-9. However, the potential mechanisms underlying the root-to-soil delivery of these metabolites remain to be elucidated¹⁰. Cucurbitacins, the characteristic bitter triterpenoids in cucurbit plants (such as melon and watermelon), are synthesized by operon-like gene clusters¹¹. Here we report two Multidrug and Toxic Compound Extrusion (MATE) proteins involved in the transport of their respective cucurbitacins, a process co-regulated with cucurbitacin biosynthesis. We further show that the transport of cucurbitacin B from the roots of melon into the soil modulates the rhizosphere microbiome by selectively enriching for two bacterial genera, Enterobacter and Bacillus, and we demonstrate that this, in turn, leads to robust resistance against the soil-borne wilt fungal pathogen, Fusarium oxysporum. Our study offers insights into how transporters for specialized metabolites manipulate the rhizosphere microbiota and thereby affect crop fitness.

Response of Anthocyanin Accumulation in Pepper (Capsicum annuum) Fruit to Light Days

Light is the key factor affecting the synthesis of anthocyanins in pepper. In this study, pepper fruit under different light days was used as experimental material to explore the synthesis of anthocyanins in purple pepper. A total of 38 flavonoid metabolites were identified in the purple pepper germplasm HNUCA21 by liquid chromatography–tandem mass spectrometry (LC-MS/MS), of which 30 belong to anthocyanins. The detected anthocyanin with the highest content was Delphinidin-3-O-glucoside (17.13 µg/g), which reached the maximum after 168 h of light treatment. Through weighted gene co-expression network analysis (WGCNA), the brown module was identified to be related to the early synthesis of anthocyanins. This module contains many structural genes related to flavonoid synthesis, including chalcone synthase (CHS 107871256, 107864266), chalcone isomerase (CHI 107871144, 107852750), dihydroflavonol 4-reductase (DFR 107860031), flavonoid 3′ 5′-hydroxylase (F3’5’H 107848667), flavonoid 3′-monooxygenase (F3M 107862334), leucoanthocyanidin dioxygenase (LDOX 107866341), and trans-cinnamate 4-monooxygenase (TCM 107875406, 107875407). The module also contained some genes related to anthocyanin transport function, such as glutathione S-transferase (GST 107861273), anthocyanidin 3-O-glucosyltransferase (UDPGT 107861697, 107843659), and MATE (107863234, 107844661), as well as some transcription factors, such as EGL1 (107865400), basic helix-loop-helix 104 (bHLH104 107864591), and WRKY44 (107843538, 107843524). The co-expression regulatory network indicated the involvement of CHS, DFR, CHI, and EGL1, as well as two MATE and two WRKY44 genes in anthocyanin synthesis. The identified genes involved in early, middle, and late light response provided a reference for the further analysis of the regulatory mechanism of anthocyanin biosynthesis in pepper.

SK, Sheoran S, K. UB, K. BN, Kumar S, Singh AN, Singh HV. Seed Longevity in Legumes: Deeper Insights Into Mechanisms and Molecular Perspectives

Sustainable agricultural production largely depends upon the viability and longevity of high-quality seeds during storage. Legumes are considered as rich source of dietary protein that helps to ensure nutritional security, but associated with poor seed longevity that hinders their performance and productivity in farmer's fields. Seed longevity is the key determinant to assure proper seed plant value and crop yield. Thus, maintenance of seed longevity during storage is of prime concern and a pre-requisite for enhancing crop productivity of legumes. Seed longevity is significantly correlated with other seed quality parameters such as germination, vigor, viability and seed coat permeability that affect crop growth and development, consequently distressing crop yield. Therefore, information on genetic basis and regulatory networks associated with seed longevity, as well as molecular dissection of traits linked to longevity could help in developing crop varieties with good storability. Keeping this in view, the present review focuses towards highlighting the molecular basis of seed longevity, with special emphasis on candidate genes and proteins associated with seed longevity and their interplay with other quality parameters. Further, an attempt was made to provide information on 3D structures of various genetic loci (genes/proteins) associated to seed longevity that could facilitate in understanding the interactions taking place within the seed at molecular level. This review compiles and provides information on genetic and genomic approaches for the identification of molecular pathways and key players involved in the maintenance of seed longevity in legumes, in a holistic manner. Finally, a hypothetical fast-forward breeding pipeline has been provided, that could assist the breeders to successfully develop varieties with improved seed longevity in legumes.

MtGSTF7, a TT19-like GST gene, is essential for accumulation of anthocyanins, but not proanthocyanins in Medicago truncatula

Anthocyanins and proanthocyanins (PAs) are two end products of the flavonoid biosynthesis pathway. They are believed to be synthesized in the endoplasmic reticulum and then sequestered into the vacuole. In Arabidopsis thaliana, TRANSPARENT TESTA 19 (TT19) is necessary for both anthocyanin and PA accumulation. Here, we found that MtGSTF7, a homolog of AtTT19, is essential for anthocyanin accumulation but not required for PA accumulation in Medicago truncatula. MtGSTF7 was induced by the anthocyanin regulator LEGUME ANTHOCYANIN PRODUCTION 1 (LAP1), and its tissue expression pattern correlated with anthocyanin deposition in M. truncatula. Tnt1-insertional mutants of MtGSTF7 lost anthocyanin accumulation in vegetative organs, and introducing a genomic fragment of MtGSTF7 could complement the mutant phenotypes. Additionally, the accumulation of anthocyanins induced by LAP1 was significantly reduced in mtgstf7 mutants. Yeast-one-hybridization and dual-luciferase reporter assays revealed that LAP1 could bind to the MtGSTF7 promoter to activate its expression. Ectopic expression of MtGSTF7 in tt19 mutants could rescue their anthocyanin deficiency, but not their PA defect. Furthermore, PA accumulation was not affected in the mtgstf7 mutants. Taken together, our results show that the mechanism of anthocyanin and PA accumulation in M. truncatula is different from that in A. thaliana, and provide a new target gene for engineering anthocyanins in plants.

Capturing acyltransferase(s) transforming final step in the biosynthesis of a major Iridoid Glycoside, (Picroside-II) in a Himalayan Medicinal Herb, Picrorhiza kurroa

BACKGROUND

Picrorhiza kurroa has been reported as an age-old ayurvedic hepato-protection to treat hepatic disorders due to the presence of iridoids such as picroside-II (P-II), picroside-I, and kutkoside. The acylation of catalpol and vanilloyl coenzyme A by acyltransferases (ATs) is critical step in P-II biosynthesis. Since accumulation of P-II occurs only in roots, rhizomes and stolons in comparison to leaves uprooting of this critically endangered herb has been the only source of this compound. Recently, we reported that P-II acylation likely happen in roots, while stolons serve as the vital P-II storage compartment. Therefore, developing an alternate engineered platform for P-II biosynthesis require identification of P-II specific AT/s.

METHODS AND RESULTS

In that direction, egg-NOG function annotated 815 ATs from de novo RNA sequencing of tissue culture based 'shoots-only' system and nursery grown shoots, roots, and stolons varying in P-II content, were cross-compared in silico to arrive at ATs sequences unique and/or common to stolons and roots. Verification for organ and accession-wise upregulation in gene expression of these ATs by qRT-PCR has shortlisted six putative 'P-II-forming' ATs. Further, six-frame translation, ab initio protein structure modelling and protein-ligand molecular docking of these ATs signified one MBOAT domain containing AT with preferential binding to the vanillic acid CoA thiol ester as well as with P-II, implying that this could be potential AT decorating final structure of P-II.

CONCLUSIONS

Organ-wise comparative transcriptome mining coupled with reverse transcription real time qRT-PCR and protein-ligand docking led to the identification of an acyltransferases, contributing to the final structure of P-II.

Integrative Analysis of Metabolome and Transcriptome Identifies Potential Genes Involved in the Flavonoid Biosynthesis in Entada phaseoloides Stem

Entada phaseoloides stem is known for its high medicinal benefits and ornamental value. Flavonoids are one of the main active constituents in E. phaseoloides stem. However, the regulatory mechanism of flavonoids accumulation in E. phaseoloides is lacking. Here, phytochemical compounds and transcripts from stems at different developmental stages in E. phaseoloides were investigated by metabolome and transcriptome analysis. The metabolite profiling of the oldest stem was obviously different from young and older stem tissues. A total of 198 flavonoids were detected, and flavones, flavonols, anthocyanins, isoflavones, and flavanones were the main subclasses. The metabolome data showed that the content of acacetin was significantly higher in the young stem and older stem than the oldest stem. Rutin and myricitrin showed significantly higher levels in the oldest stem. A total of 143 MYBs and 143 bHLHs were identified and classified in the RNA-seq data. Meanwhile, 34 flavonoid biosynthesis structural genes were identified. Based on the expression pattern of structural genes involved in flavonoid biosynthesis, it indicated that flavonol, anthocyanin, and proanthocyanin biosynthesis were first active during the development of E. phaseoloides stem, and the anthocyanin or proanthocyanin biosynthesis branch was dominant; the flavone biosynthesis branch was active at the late developmental stage of the stem. Through the correlation analysis of transcriptome and metabolome data, the potential candidate genes related to regulating flavonoid synthesis and transport were identified. Among them, the MYBs, bHLH, and TTG1 are coregulated biosynthesis of flavonols and structural genes, bHLH and transporter genes are coregulated biosynthesis of anthocyanins. In addition, the WDR gene TTG1-like (AN11) may regulate dihydrochalcones and flavonol biosynthesis in specific combinations with IIIb bHLH and R2R3-MYB proteins. Furthermore, the transport gene protein TRANSPARENT TESTA 12-like gene is positively regulated the accumulation of rutin, and the homolog of ABC transporter B family member gene is positively correlated with the content of flavone acacetin. This study offered candidate genes involved in flavonoid biosynthesis, information of flavonoid composition and characteristics of flavonoids accumulation, improved our understanding of the MYBs and bHLHs-related regulation networks of flavonoid biosynthesis in E. phaseoloides stem, and provided references for the metabolic engineering of flavonoid biosynthesis in E. phaseoloides stem.

Diverse roles of MYB transcription factors in regulating secondary metabolite biosynthesis, shoot development, and stress responses in tea plants (Camellia sinensis)

Tea (Camellia sinensis) is concocted from tea plant shoot tips that produce catechins, caffeine, theanine, and terpenoids, which collectively determine the rich flavors and health benefits of the infusion. However, little is known about the integrated regulation of shoot tip development and characteristic secondary metabolite biosynthesis in tea plants. Here, we demonstrate that MYB transcription factors (TFs) play key and yet diverse roles in regulating leaf and stem development, secondary metabolite biosynthesis, and environmental stress responses in tea plants. By integrating transcriptomic and metabolic profiling data in different tissues at a series of developmental stages or under various stress conditions, alongside biochemical and genetic analyses, we predicted the MYB TFs involved in regulating shoot development (CsMYB2, 98, 107, and 221), epidermal cell initiation (CsMYB184, 41, 139, and 219), stomatal initiation (CsMYB113 and 153), and the biosynthesis of flavonoids (including catechins, anthocyanins, and flavonols; CsMYB8 and 99), caffeine (CsMYB85 and 86), theanine (CsMYB9 and 49), carotenoids (CsMYB110), mono-/sesquiterpenoid volatiles (CsMYB68, 147, 148, and 193), lignin (CsMYB164 and 192), and indolic compounds (CsMYB139, 162, and 198), as well as the MYB TFs that are likely involved in hormone signaling-mediated environmental stress and defense responses. We characterized the functions of some key MYBs in regulating flavonoid and carotenoid biosynthesis for tea quality and flavor. This study provides a cross-family analysis of MYBs in tea alongside new insights into the coordinated regulation of tea plant shoot development and secondary metabolism, paving the way towards understanding of tea quality trait formation and genetic improvement of quality tea plants.

Biochemistry and Molecular Basis of Intracellular Flavonoid Transport in Plants

Flavonoids are a biochemically diverse group of specialized metabolites in plants that are derived from phenylalanine. While the biosynthesis of the flavonoid aglycone is highly conserved across species and well characterized, numerous species-specific decoration steps and their relevance remained largely unexplored. The flavonoid biosynthesis takes place at the cytosolic side of the endoplasmatic reticulum (ER), but accumulation of various flavonoids was observed in the central vacuole. A universal explanation for the subcellular transport of flavonoids has eluded researchers for decades. Current knowledge suggests that a glutathione S-transferase-like protein (ligandin) protects anthocyanins and potentially proanthocyanidin precursors during the transport to the central vacuole. ABCC transporters and to a lower extend MATE transporters sequester anthocyanins into the vacuole. Glycosides of specific proanthocyanidin precursors are sequestered through MATE transporters. A P-ATPase in the tonoplast and potentially other proteins generate the proton gradient that is required for the MATE-mediated antiport. Vesicle-mediated transport of flavonoids from the ER to the vacuole is considered as an alternative or additional route.

Chemical Diversity of Flavan-3-Ols in Grape Seeds: Modulating Factors and Quality Requirements

Grape seeds are a rich source of flavan-3-ol monomers, oligomers, and polymers. The diverse profile of compounds includes mainly B-type procyanidins (especially C4→C8 linked molecules) and the key monomers, catechin, and epicatechin that are positively implicated in the 'French Paradox'. Today grape seed nutraceuticals have become a multi-million-dollar industry. This has created incentives to elucidate the variations in chemistry across cultivars, to identify signs of adulteration, and to understand the intrinsic and extrinsic factors controlling the expression of metabolites in the seeds' metabolome. This review provides a critical overview of the existing literature on grape seed chemistry. Although the biosynthetic pathways for polymeric procyanidins in seeds have not yet been explained, abiotic factors have been shown to modulate associated genes. Research of extrinsic factors has demonstrated that the control of procyanidin expression is strongly influenced, in order of importance, by genotype (species first, then variety) and environment, as claimed anecdotally. Unfortunately, research outcomes on the effects of abiotic factors have low certainty, because effects can be specific to genotype or variety, and there is limited control over physical metrics in the field. Thus, to gain a fuller understanding of the effects of abiotic factors and biosynthetic pathways, and realise potential for optimisation, a more fundamental research approach is needed. Nevertheless, the current synthesis offers insight into the selection of species or varieties according to the profile of polyphenols, as well as for optimisation of horticultural practices, with a view to produce products that contain the compounds that support health claims.

A Systematic Phylogenomic Classification of the Multidrug and Toxic Compound Extrusion Transporter Gene Family in Plants

Multidrug and toxic compound extrusion (MATE) transporters comprise a multigene family that mediates multiple functions in plants through the efflux of diverse substrates including organic molecules, specialized metabolites, hormones, and xenobiotics. MATE classification based on genome-wide studies remains ambiguous, likely due to a lack of large-scale phylogenomic studies and/or reference sequence datasets. To resolve this, we established a phylogeny of the plant MATE gene family using a comprehensive kingdom-wide phylogenomic analysis of 74 diverse plant species. We identified more than 4,000 MATEs, which were classified into 14 subgroups based on a systematic bioinformatics pipeline using USEARCH, blast+ and synteny network tools. Our classification was performed using a four-step process, whereby MATEs sharing ≥ 60% protein sequence identity with a ≤ 1E-05 threshold at different sequence lengths (either full-length, ≥ 60% length, or ≥ 150 amino acids) or retaining in the similar synteny blocks were assigned to the same subgroup. In this way, we assigned subgroups to 95.8% of the identified MATEs, which we substantiated using synteny network clustering analysis. The subgroups were clustered under four major phylogenetic groups and named according to their clockwise appearance within each group. We then generated a reference sequence dataset, the usefulness of which was demonstrated in the classification of MATEs in additional species not included in the original analysis. Approximately 74% of the plant MATEs exhibited synteny relationships with angiosperm-wide or lineage-, order/family-, and species-specific conservation. Most subgroups evolved independently, and their distinct evolutionary trends were likely associated with the development of functional novelties or the maintenance of conserved functions. Together with the systematic classification and synteny network profiling analyses, we identified all the major evolutionary events experienced by the MATE gene family in plants. We believe that our findings and the reference dataset provide a valuable resource to guide future functional studies aiming to explore the key roles of MATEs in different aspects of plant physiology. Our classification framework can also be readily extendable to other (super) families.

UGT72, a Major Glycosyltransferase Family for Flavonoid and Monolignol Homeostasis in Plants

Simple Summary

Phenylpropanoids are specialized metabolites playing crucial roles in plant developmental processes and in plant defense towards pathogens. The attachment of sugar moieties to these small hydrophobic molecules renders them more hydrophilic and increases their solubility. The UDP-glycosyltransferase 72 family (UGT72) of plants has been shown to glycosylate mainly two classes of phenylpropanoids, (i) the monolignols that are the building blocks of lignin, the second most abundant polymer after cellulose, and (ii) the flavonoids, which play determinant roles in plant interactions with other organisms and in response to stress. The purpose of this review is to bring an overview of the current knowledge of the UGT72 family and to highlight its role in the homeostasis of these molecules. Potential applications in pharmacology and in wood, paper pulp, and bioethanol production are given within the perspectives.

Abstract

Plants have developed the capacity to produce a diversified range of specialized metabolites. The glycosylation of those metabolites potentially decreases their toxicity while increasing their stability and their solubility, modifying their transport and their storage. The UGT, forming the largest glycosyltransferase superfamily in plants, combine enzymes that glycosylate mainly hormones and phenylpropanoids by using UDP-sugar as a sugar donor. Particularly, members of the UGT72 family have been shown to glycosylate the monolignols and the flavonoids, thereby being involved in their homeostasis. First, we explore primitive UGTs in algae and liverworts that are related to the angiosperm UGT72 family and their role in flavonoid homeostasis. Second, we describe the role of several UGT72s glycosylating monolignols, some of which have been associated with lignification. In addition, the role of other UGT72 members that glycosylate flavonoids and are involved in the development and/or stress response is depicted. Finally, the importance to explore the subcellular localization of UGTs to study their roles in planta is discussed.

Hierarchical regulation of MYBPA1 by anthocyanin- and proanthocyanidin-related MYB proteins is conserved in Vaccinium species

Members of the Vaccinium genus bear fruits rich in anthocyanins, a class of red-purple flavonoid pigments that provide human health benefits, although the localization and concentrations of anthocyanins differ between species: blueberry (V. corymbosum) has white flesh, while bilberry (V. myrtillus) has red flesh. Comparative transcriptomics between blueberry and bilberry revealed that MYBPA1.1 and MYBA1 strongly correlated with the presence of anthocyanins, but were absent or weakly expressed in blueberry flesh. MYBPA1.1 had a biphasic expression profile, correlating with both proanthocyanidin biosynthesis early during fruit development and anthocyanin biosynthesis during berry ripening. MYBPA1.1 was unable to induce anthocyanin or proanthocyanidin accumulation in Nicotiana benthamiana, but activated promoters of flavonoid biosynthesis genes. The MYBPA1.1 promoter is directly activated by MYBA1 and MYBPA2 proteins, which regulate anthocyanins and proanthocyanidins, respectively. Our findings suggest that the lack of VcMYBA1 expression in blueberry flesh results in an absence of VcMYBPA1.1 expression, which are both required for anthocyanin regulation. In contrast, VmMYBA1 is well expressed in bilberry flesh, up-regulating VmMYBPA1.1, allowing coordinated regulation of flavonoid biosynthesis genes and anthocyanin accumulation. The hierarchal model described here for Vaccinium may also occur in a wider group of plants as a means to co-regulate different branches of the flavonoid pathway.

Identifying Quantitative Trait Loci and Candidate Genes Conferring Resistance to Soybean Mosaic Virus SC7 by Quantitative Trait Loci-Sequencing in Soybean

Soybean mosaic virus (SMV) is detrimental to soybean (Glycine max) breeding, seed quality, and yield worldwide. Improving the basic resistance of host plants is the most effective and economical method to reduce damage from SMV. Therefore, it is necessary to identify and clone novel SMV resistance genes. Here, we report the characterization of two soybean cultivars, DN50 and XQD, with different levels of resistance to SMV. Compared with XQD, DN50 exhibits enhanced resistance to the SMV strain SC7. By combining bulked-segregant analysis (BSA)-seq and fine-mapping, we identified a novel resistance locus, R _SMV -11, spanning an approximately 207-kb region on chromosome 11 and containing 25 annotated genes in the reference Williams 82 genome. Of these genes, we identified eleven with non-synonymous single-nucleotide polymorphisms (SNPs) or insertion-deletion mutations (InDels) in their coding regions between two parents. One gene, GmMATE68 (Glyma.11G028900), harbored a frameshift mutation. GmMATE68 encodes a multidrug and toxic compound extrusion (MATE) transporter that is expressed in all soybean tissues and is induced by SC7. Given that MATE transporter families have been reported to be linked with plant disease resistance, we suggest that GmMATE68 is responsible for SC7 resistance in DN50. Our results reveal a novel SMV-resistance locus, improving understanding of the genetics of soybean disease resistance and providing a potential new tool for marker-assisted selection breeding in soybean.

Response of anthocyanin biosynthesis to light by strand-specific transcriptome and miRNA analysis in Capsicum annuum

BACKGROUND

Anthocyanins have distinct biological functions in plant coloring, plant defense against strong light, UV irradiation, and pathogen infection. Aromatic hydroxyl groups and ortho-dihydroxyl groups in anthocyanins are able to inhibit free-radical chain reactions and hydroxyl radicals. Thus, anthocyanins play an antioxidative role by removing various types of ROS. Pepper is one of the solanaceous vegetables with the largest cultivation area in China. The purple-fruited pepper is rich in anthocyanins, which not only increases the ornamental nature of the pepper fruit but also benefits the human body. In this experiment, light-induced regulatory pathways and related specific regulators of anthocyanin biosynthesis were examined through integrative transcriptomic and metabolomic analysis.

RESULTS

Results revealed that delphinium 3-O-glucoside significantly accumulated in light exposed surface of pepper fruit after 48 h as compared to shaded surface. Furthermore, through strand-specific sequencing technology, 1341 differentially expressed genes, 172 differentially expressed lncRNAs, 8 differentially expressed circRNAs, and 28 differentially expressed miRNAs were identified significantly different among both surfaces. The flavonoid synthesis pathway was significantly enriched by KEGG analysis including SHT (XM_016684802.1), AT-like (XM_016704776.1), CCoAOMT (XM_016698340.1, XM_016698341.1), CHI (XM_016697794.1, XM_016697793.1), CHS2 (XM_016718139.1), CHS1B (XM_016710598.1), CYP98A2-like (XM_016688489.1), DFR (XM_016705224.1), F3'5'H (XM_016693437.1), F3H (XM_016705025.1), F3'M (XM_016707872.1), LDOX (XM_016712446.1), TCM (XM_016722116.1) and TCM-like (XM_016722117.1). Most of these significantly enriched flavonoid synthesis pathway genes may be also regulated by lncRNA. Some differentially expressed genes encoding transcription factors were also identified including MYB4-like (XM_016725242.1), MYB113-like (XM_016689220.1), MYB308-like (XM_016696983.1, XM_016702244.1), and EGL1 (XM_016711673.1). Three 'lncRNA-miRNA-mRNA' regulatory networks with sly-miR5303, stu-miR5303g, stu-miR7997a, and stu-miR7997c were constructed, including 28 differentially expressed mRNAs and 6 differentially expressed lncRNAs.

CONCLUSION

Possible light regulated anthocyanin biosynthesis and transport genes were identified by transcriptome analysis, and confirmed by qRT-PCR. These results provide important data for further understanding of the anthocyanin metabolism in response to light in pepper.

The Poly-Glutamate Motif of GmMATE4 Regulates Its Isoflavone Transport Activity

Multidrug and toxic compound extrusion (MATE) transporters in eukaryotes have been characterized to be antiporters that mediate the transport of substrates in exchange for protons. In plants, alkaloids, phytohormones, ion chelators, and flavonoids have been reported to be the substrates of MATE transporters. Structural analyses have been conducted to dissect the functional significance of various motifs of MATE proteins. However, an understanding of the functions of the N- and C-termini has been inadequate. Here, by performing phylogenetic analyses and protein sequence alignment of 14 representative plant species, we identified a distinctive N-terminal poly-glutamate motif among a cluster of MATE proteins in soybean. Amongst them, GmMATE4 has the most consecutive glutamate residues at the N-terminus. A subcellular localization study showed that GmMATE4 was localized at the vacuolar membrane-like structure. Protein charge prediction showed that the mutation of the glutamate residues to alanine would reduce the negative charge at the N-terminus. Using yeast as the model, we showed that GmMATE4 mediated the transport of daidzein, genistein, glycitein, and glycitin. In addition, the glutamate-to-alanine mutation reduced the isoflavone transport capacity of GmMATE4. Altogether, we demonstrated GmMATE4 as an isoflavone transporter and the functional significance of the N-terminal poly-glutamate motif of GmMATE4 for regulating the isoflavone transport activity.

The Identification of MATE Antisense Transcripts in Soybean Using Strand-Specific RNA-Seq Datasets

Natural antisense transcripts (NATs) have been generally reported as negative regulators of their sense counterparts. Multidrug and toxic compound extrusion (MATE) proteins mediate the transport of various substrates. Although MATEs have been identified genome-wide in various plant species, their transcript regulators remain unclear. Here, using the publicly available strand-specific RNA-seq datasets of Glycine soja (wild soybean) which have the data from various tissues including developing pods, developing seeds, embryos, cotyledons and hypocotyls, roots, apical buds, stems, and flowers, we identified 35 antisense transcripts of MATEs from 28 gene loci after transcriptome assembly. Spearman correlation coefficients suggested the positive expression correlations of eight MATE antisense and sense transcript pairs. By aligning the identified transcripts with the reference genome of Glycine max (cultivated soybean), the MATE antisense and sense transcript pairs were identified. Using soybean C08 (Glycine max), in developing pods and seeds, the positive correlations between MATE antisense and sense transcript pairs were shown by RT-qPCR. These findings suggest that soybean antisense transcripts are not necessarily negative transcription regulators of their sense counterparts. This study enhances the existing knowledge on the transcription regulation of MATE transporters by uncovering the previously unknown MATE antisense transcripts and their potential synergetic effects on sense transcripts.

The Euscaphis japonica genome and the evolution of malvids

Malvids is one of the largest clades of rosids, includes 58 families and exhibits remarkable morphological and ecological diversity. Here, we report a high-quality chromosome-level genome assembly for Euscaphis japonica, an early-diverging species within malvids. Genome-based phylogenetic analysis suggests that the unstable phylogenetic position of E. japonica may result from incomplete lineage sorting and hybridization event during the diversification of the ancestral population of malvids. Euscaphis japonica experienced two polyploidization events: the ancient whole genome triplication event shared with most eudicots (commonly known as the γ event) and a more recent whole genome duplication event, unique to E. japonica. By resequencing 101 samples from 11 populations, we speculate that the temperature has led to the differentiation of the evergreen and deciduous of E. japonica and the completely different population histories of these two groups. In total, 1012 candidate positively selected genes in the evergreen were detected, some of which are involved in flower and fruit development. We found that reddening and dehiscence of the E. japonica pericarp and long fruit-hanging time promoted the reproduction of E. japonica populations, and revealed the expression patterns of genes related to fruit reddening, dehiscence and abscission. The key genes involved in pentacyclic triterpene synthesis in E. japonica were identified, and different expression patterns of these genes may contribute to pentacyclic triterpene diversification. Our work sheds light on the evolution of E. japonica and malvids, particularly on the diversification of E. japonica and the genetic basis for their fruit dehiscence and abscission.

A Talk between Flavonoids and Hormones to Reorient the Growth of Gymnosperms

Plants reorient the growth of affected organs in response to the loss of gravity vector. In trees, this phenomenon has received special attention due to its importance for the forestry industry of conifer species. Sustainable management is a key factor in improving wood quality. It is of paramount importance to understand the molecular and genetic mechanisms underlying wood formation, together with the hormonal and environmental factors that affect wood formation and quality. Hormones are related to the modulation of vertical growth rectification. Many studies have resulted in a model that proposes differential growth in the stem due to unequal auxin and jasmonate allocation. Furthermore, many studies have suggested that in auxin distribution, flavonoids act as molecular controllers. It is well known that flavonoids affect auxin flux, and this is a new area of study to understand the intracellular concentrations and how these compounds can control the gravitropic response. In this review, we focused on different molecular aspects related to the hormonal role in flavonoid homeostasis and what has been done in conifer trees to identify molecular players that could take part during the gravitropic response and reduce low-quality wood formation.

Microscale Thermophoresis Reveals Oxidized Glutathione as High-Affinity Ligand of Mal d 1

Pathogenesis-related (PR)-10 proteins, due to their particular secondary structure, can bind various ligands which could be important for their biological function. Accordingly, the PR-10 protein Mal d 1, the major apple allergen, probably also binds molecules in the hydrophobic cavity of its secondary structure, but it has not yet been investigated in this respect. In this study, various natural products found in apples such as flavonoids, glutathione (GSH), and glutathione disulfide (GSSG) were investigated as possible ligands of Mal d 1 using microscale thermophoresis. Dissociation constants of 16.39 µM, 29.51 µM, 35.79 µM, and 0.157 µM were determined for catechin, quercetin-3-O-rhamnoside, GSH, and GSSG, respectively. Molecular docking was performed to better understand the underlying binding mechanism and revealed hydrophobic interactions that stabilize the ligands within the pocket while hydrophilic interactions determine the binding of both GSH derivatives. The binding of these ligands could be important for the allergenicity of the PR-10 protein and provide further insights into its physiological role.

MATE-Type Proteins Are Responsible for Isoflavone Transportation and Accumulation in Soybean Seeds

Soybeans are nutritionally important as human food and animal feed. Apart from the macronutrients such as proteins and oils, soybeans are also high in health-beneficial secondary metabolites and are uniquely enriched in isoflavones among food crops. Isoflavone biosynthesis has been relatively well characterized, but the mechanism of their transportation in soybean cells is largely unknown. Using the yeast model, we showed that GmMATE1 and GmMATE2 promoted the accumulation of isoflavones, mainly in the aglycone forms. Using the tobacco BrightYellow-2 (BY-2) cell model, GmMATE1 and GmMATE2 were found to be localized in the vacuolar membrane. Such subcellular localization supports the notion that GmMATE1 and GmMATE2 function by compartmentalizing isoflavones in the vacuole. Expression analyses showed that GmMATE1 was mainly expressed in the developing soybean pod. Soybean mutants defective in GmMATE1 had significantly reduced total seed isoflavone contents, whereas the overexpression of GmMATE1 in transgenic soybean promoted the accumulation of seed isoflavones. Our results showed that GmMATE1, and possibly also GmMATE2, are bona fide isoflavone transporters that promote the accumulation of isoflavones in soybean seeds.

Loss of LaMATE impairs isoflavonoid release from cluster roots of phosphorus-deficient white lupin

White lupin (Lupinus albus L.) forms brush-like root structures called cluster roots under phosphorus-deficient conditions. Clusters secrete citrate and other organic compounds to mobilize sparingly soluble soil phosphates. In the context of aluminum toxicity tolerance mechanisms in other species, citrate is released via a subgroup of MATE/DTX proteins (multidrug and toxic compound extrusion/detoxification). White lupin contains 56 MATE/DTX genes. Many of these are closely related to gene orthologs with known substrates in other species. LaMATE is a marker gene for functional, mature clusters and is, together with its close homolog LaMATE3, a candidate for the citrate release. Both were highest expressed in mature clusters and when expressed in oocytes, induced inward-rectifying currents that were likely carried by endogenous channels. No citrate efflux was associated with LaMATE and LaMATE3 expression in oocytes. Furthermore, citrate secretion was largely unaffected in P-deficient composite mutant plants with genome-edited or RNAi-silenced LaMATE in roots. Moderately lower concentrations of citrate and malate in the root tissue and consequently less organic acid anion secretion and lower malate in the xylem sap were identified. Interestingly, however, less genistein was consistently found in mutant exudates, opening the possibility that LaMATE is involved in isoflavonoid release.

Plant Secondary Metabolite Transporters: Diversity, Functionality, and Their Modulation

Secondary metabolites (SMs) play crucial roles in the vital functioning of plants such as growth, development, defense, and survival via their transportation and accumulation at the required site. However, unlike primary metabolites, the transport mechanisms of SMs are not yet well explored. There exists a huge gap between the abundant presence of SM transporters, their identification, and functional characterization. A better understanding of plant SM transporters will surely be a step forward to fulfill the steeply increasing demand for bioactive compounds for the formulation of herbal medicines. Thus, the engineering of transporters by modulating their expression is emerging as the most viable option to achieve the long-term goal of systemic metabolic engineering for enhanced metabolite production at minimum cost. In this review article, we are updating the understanding of recent advancements in the field of plant SM transporters, particularly those discovered in the past two decades. Herein, we provide notable insights about various types of fully or partially characterized transporters from the ABC, MATE, PUP, and NPF families including their diverse functionalities, structural information, potential approaches for their identification and characterization, several regulatory parameters, and their modulation. A novel perspective to the concept of "Transporter Engineering" has also been unveiled by highlighting its potential applications particularly in plant stress (biotic and abiotic) tolerance, SM accumulation, and removal of anti-nutritional compounds, which will be of great value for the crop improvement program. The present study creates a roadmap for easy identification and a better understanding of various transporters, which can be utilized as suitable targets for transporter engineering in future research.

Elusive partners: a review of the auxiliary proteins guiding metabolic flux in flavonoid biosynthesis

Flavonoids are specialized metabolites widely distributed across the plant kingdom. They are involved in the growth and survival of plants, conferring the ability to filter ultra-violet rays, conduct symbiotic partnerships, and respond to stress. While many branches of flavonoid biosynthesis have been resolved, recent discoveries suggest missing auxiliary components. These overlooked elements can guide metabolic flux, enhance production, mediate stereoselectivity, transport intermediates, and exert regulatory functions. This review describes several families of auxiliary proteins from across the plant kingdom, including examples from specialized metabolism. In flavonoid biosynthesis, we discuss the example of chalcone isomerase-like (CHIL) proteins and their non-catalytic role. CHILs mediate the cyclization of tetraketides, forming the chalcone scaffold by interacting with chalcone synthase (CHS). Loss of CHIL activity leads to derailment of the CHS-catalyzed reaction and a loss of pigmentation in fruits and flowers. Similarly, members of the pathogenesis-related 10 (PR10) protein family have been found to differentially bind flavonoid intermediates, guiding the composition of anthocyanins. This role comes within a larger body of PR10 involvement in specialized metabolism, from outright catalysis (e.g., (S)-norcoclaurine synthesis) to controlling stereochemistry (e.g., enhancing cis-trans cyclization in catnip). Both CHILs and PR10s hail from larger families of ligand-binding proteins with a spectrum of activity, complicating the characterization of their enigmatic roles. Strategies for the discovery of auxiliary proteins are discussed, as well as mechanistic models for their function. Targeting such unanticipated components will be crucial in manipulating plants or engineering microbial systems for natural product synthesis.

Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa)

Multidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice. In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. The rice MATE family was divided into four subfamilies based on the phylogenetic tree. Tandem repeats and fragment replication contribute to the expansion of the rice MATE gene family. Gene structure and cis-regulatory elements reveal the potential functions of MATE genes. Analysis of gene expression showed that most of MATE genes were constitutively expressed and the expression patterns of genes in different tissues were analyzed using RNA-seq. Furthermore, qRT-PCR-based analysis showed differential expression patterns in response to salt and drought stress. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

Ionomic Approaches for Discovery of Novel Stress-Resilient Genes in Plants

Plants, being sessile, face an array of biotic and abiotic stresses in their lifespan that endanger their survival. Hence, optimized uptake of mineral nutrients creates potential new routes for enhancing plant health and stress resilience. Recently, minerals (both essential and non-essential) have been identified as key players in plant stress biology, owing to their multifaceted functions. However, a realistic understanding of the relationship between different ions and stresses is lacking. In this context, ionomics will provide new platforms for not only understanding the function of the plant ionome during stresses but also identifying the genes and regulatory pathways related to mineral accumulation, transportation, and involvement in different molecular mechanisms under normal or stress conditions. This article provides a general overview of ionomics and the integration of high-throughput ionomic approaches with other "omics" tools. Integrated omics analysis is highly suitable for identification of the genes for various traits that confer biotic and abiotic stress tolerance. Moreover, ionomics advances being used to identify loci using qualitative trait loci and genome-wide association analysis of element uptake and transport within plant tissues, as well as genetic variation within species, are discussed. Furthermore, recent developments in ionomics for the discovery of stress-tolerant genes in plants have also been addressed; these can be used to produce more robust crops with a high nutritional value for sustainable agriculture.

Comprehensive genome-wide identification, characterization, and expression profiling of MATE gene family in Nicotiana tabacum

The transporters belonging to the MATE family are involved in the transportation of diverse ligands, including metal ions and small organic molecules, and, therefore, play an important role in plant biology. Our genome-wide analysis led to the identification of 138 MATE genes in N. tabacum, which were grouped into four major phylogenetic clades. The expression of several NtMATE genes was reported to be differential in different tissues, namely young leaf, mature leaf, stem, root, and mature flower. The upstream regions of the NtMATE genes were predicted to contain several cis-acting elements associated with hormonal, developmental, and stress responses. Some of the genes were found to display induced expression following methyl jasmonate treatment. The co-expression analysis revealed 126 candidate transcription factor genes that might be involved in the transcriptional regulation of 21 NtMATE genes. Certain MATE genes (NtMATE81, NtMATE82, NtMATE88, and NtMATE89) were predicted to be targeted by micro RNAs (nta-miR167a, nta-miR167b, nta-miR167c, nta-miR167d and nta-miR167e). The computational analysis of MATE transporters provided insights into the key amino acid residues involved in the binding of the alkaloids. Further, the putative function of some of the NtMATE transporters was also revealed. The present study develops a solid foundation for the functional characterization of MATE transporter genes in N. tabacum.

Genome-Wide Association Study Reveals Genomic Regions Associated with Fusarium Wilt Resistance in Common Bean

Fusarium wilt (Fusarium oxysporum f. sp. phaseoli, Fop) is one of the main fungal soil diseases in common bean. The aim of the present study was to identify genomic regions associated with Fop resistance through genome-wide association studies (GWAS) in a Mesoamerican Diversity Panel (MDP) and to identify potential common bean sources of Fop's resistance. The MDP was genotyped with BARCBean6K_3BeadChip and evaluated for Fop resistance with two different monosporic strains using the root-dip method. Disease severity rating (DSR) and the area under the disease progress curve (AUDPC), at 21 days after inoculation (DAI), were used for GWAS performed with FarmCPU model. The p-value of each SNP was determined by resampling method and Bonferroni test. For UFV01 strain, two significant single nucleotide polymorphisms (SNPs) were mapped on the Pv05 and Pv11 for AUDPC, and the same SNP (ss715648096) on Pv11 was associated with AUDPC and DSR. Another SNP, mapped on Pv03, showed significance for DSR. Regarding IAC18001 strain, significant SNPs on Pv03, Pv04, Pv05, Pv07 and on Pv01, Pv05, and Pv10 were observed. Putative candidate genes related to nucleotide-binding sites and carboxy-terminal leucine-rich repeats were identified. The markers may be important future tools for genomic selection to Fop disease resistance in beans.

Metabolome and transcriptome profiling reveals anthocyanin contents and anthocyanin-related genes of chimeric leaves in Ananas comosus var. bracteatus

BACKGROUND

Ananas comosus var. bracteatus is a colorful plant used as a cut flower or landscape ornamental. The unique foliage color of this plant includes both green and red leaves and, as a trait of interest, deserves investigation. In order to explore the pigments behind the red section of the chimeric leaves, the green and red parts of chimeric leaves of Ananas comosus var. bracteatus were sampled and analyzed at phenotypic, cellular and molecular levels in this study.

RESULTS

The CIELAB results indicated that the a* values and L* values samples had significant differences between two parts. Freehand sections showed that anthocyanin presented limited accumulation in the green leaf tissues but obviously accumulation in the epidermal cells of red tissues. Transcriptomic and metabolomic analyses were performed by RNA-seq and LC-ESI-MS/MS. Among the 508 identified metabolites, 10 kinds of anthocyanins were detected, with 6 significantly different between the two samples. The cyanidin-3,5-O-diglucoside content that accounts for nearly 95.6% in red samples was significantly higher than green samples. RNA-Seq analyses showed that 11 out of 40 anthocyanin-related genes were differentially expressed between the green and red samples. Transcriptome and metabolome correlations were determined by nine quadrant analyses, and 9 anthocyanin-related genes, including MYB5 and MYB82, were correlated with 7 anthocyanin-related metabolites in the third quadrant in which genes and metabolites showing consistent change. Particularly, the PCCs between these two MYB genes and cyanidin-3,5-O-diglucoside were above 0.95.

CONCLUSION

Phenotypic colors are closely related to the tissue structures of different leaf parts of Ananas comosus var. bracteatus, and two MYB transcription factors might contribute to differences of anthocyanin accumulation in two parts of Ananas comosus var. bracteatus chimeric leaves. This study lay a foundation for further researches on functions of MYBs in Ananas comosus var. bracteatus and provides new insights to anthocyanin accumulation in different parts of chimeric leaves.

DcTT8, a bHLH transcription factor, regulates anthocyanin biosynthesis in Dendrobium candidum

Dendrobium candidum stems are used as Chinese medicine and functional food. Red stems of D. candidum are rich in anthocyanins, which attract pollinator insects, protect the plants against environmental stress, and improve human health. The regulatory mechanisms of anthocyanin biosynthesis and stem color differentiation in D. candidum are not fully understood. Using transcriptome profiling, we identified a basic helix-loop-helix transcription factor (DcTT8) involved in anthocyanin biosynthesis in D. candidum stems. Ultraperformance liquid chromatography-tandem mass spectrometry was used to determine pigment contents and compositions in red and green stems, revealing that cyanidin is responsible for the red color. DcTT8 could bind the DcF3'H and DcUFGT promoters and finely regulate DcF3'H and DcUFGT expression. Our data indicate that DcTT8 participates in anthocyanin biosynthesis and offers novel insights into the transcriptional regulation of anthocyanin biosynthesis in D. candidum.

Computational and Transcriptomic Analysis Unraveled OsMATE34 as a Putative Anthocyanin Transporter in Black Rice (Oryza sativa L.) Caryopsis

Anthocyanin is a flavonoid compound with potential antioxidant properties beneficial to human health and sustains plant growth and development under different environmental stresses. In black rice, anthocyanin can be found in the stems, leaves, stigmas, and caryopsis. Although the anthocyanin biosynthesis in rice has been extensively studied, limited knowledge underlying the storage mechanism and transporters is available. This study undertook the complementation of computational and transcriptome analysis to decipher a potential multidrug and toxic compound extrusion (MATE) gene candidate for anthocyanin transportation in black rice caryopsis. The phylogenetic analysis showed that OsMATE34 has the same evolutionary history and high similarities with VvAM1, VvAM3, MtMATE2, SlMATE/MTP77, RsMATE8, AtFFT, and AtTT12 involved in anthocyanin transportation. RNA sequencing analysis in black caryopsis (Bc; Bc11, Bc18, Bc25) and white caryopsis (Wc; Wc11, Wc18, Wc25), respectively, at 11 days after flowering (DAF), 18 DAF, and 25 DAF revealed a total of 36,079 expressed genes, including 33,157 known genes and 2922 new genes. The differentially expressed genes (DEGs) showed 15,573 genes commonly expressed, with 1804 and 1412 genes uniquely expressed in Bc and Wc, respectively. Pairwise comparisons showed 821 uniquely expressed genes out of 15,272 DEGs for Wc11 vs. Bc11, 201 uniquely expressed genes out of 16,240 DEGs for Wc18 vs. Bc18, and 2263 uniquely expressed genes out of 16,240 DEGs for Wc25 vs. Bc25. Along with anthocyanin biosynthesis genes (OsPAL, OsCHS, OsCHI, OsF3H, OsDFR, OsANS, and OsUFGT/Os3GT), OsMATE34 expression was significantly upregulated in all Bc but not in Wc. OsMATE34 expression was similar to OsGSTU34, a transporter of anthocyanin in rice leaves. Taken together, our results highlighted OsMATE34 (Os08g0562800) as a candidate anthocyanin transporter in rice caryopsis. This study provides a new finding and a clue to enhance the accumulation of anthocyanin in rice caryopsis.

Spotlight on the overlapping routes and partners for anthocyanin transport in plants

Secondary metabolites are produced by plants and are classified based on their chemical structure or the biosynthetic routes through which they are synthesized. Among them, flavonoids, including anthocyanins and pro-anthocyanidins (PAs), are abundant in leaves, flowers, fruits, and seed coats in plants. The anthocyanin biosynthetic pathway has been intensively studied, but the molecular mechanism of anthocyanin transport from the synthesis site to the storage site needs attention. Although the major transporters are well defined yet, the redundancy of these transporters for structurally similar or dis-similar anthocyanins motivates additional research. Herein, we reviewed the role of membrane transporters involved in anthocyanin transport, including ATP-binding cassette, multidrug and toxic compound extrusion (MATE), Bilitranslocase-homolog (BTL), and vesicle-mediated transport. We also highlight the ability of transporters to cater distinct anthocyanins or their chemically-modified forms with overlapping transport mechanisms and sequestration into the vacuoles. Our understanding of the anthocyanin transporters could provide anthocyanin-rich crops and fruits with a benefit on human health at a large scale.

Genome-wide identification and expression analysis of detoxification efflux carriers (DTX) genes family under abiotic stresses in flax

The detoxification efflux carriers (DTX)/multidrug and toxic compound extrusion (MATE) transporters encompass an ancient gene family of secondary transporters involved in the process of plant detoxification. A genome-wide analysis of these transporters was carried out in order to better understand the transport of secondary metabolites in flaxseed genome (Linum usitassimum). A total of 73 genes coding for DTX/MATE transporters were identified. Gene structure, protein domain and motif organization were found to be notably conserved over the distinct phylogenetic groups, showing the evolutionary significant role of each class. Gene ontology (GO) annotation revealed a link to transporter activities, response to stimulus and localizations. The presence of various hormone and stress-responsive cis-regulatory elements in promoter regions could be directly correlated with the alteration of their transcripts. Tertiary structure showed conservation for pore size and constrains in the pore, which indicate their involvement in the exclusion of toxic substances from the cell. MicroRNA target analysis revealed that LuDTXs genes were targeted by different classes of miRNA families. Twelve LuDTX genes were chosen for further quantitative real-time polymerase chain reaction analysis in response to cold, salinity and cadmium stress at 0, 6, 12 and 24 hours after treatment. Altogether, the identified members of the DTX gene family, their expression profile, phylogenetic and miRNAs analysis might provide opportunities for future functional validation of this important gene family in flax.

Exploring genetic architecture for pod-related traits in soybean using image-based phenotyping

Mature pod color (PC) and pod size (PS) served as important characteristics are used in the soybean breeding programs. However, manual phenotyping of such complex traits is time-consuming, laborious, and expensive for breeders. Here, we collected pod images from two different populations, namely, a soybean association panel (SAP) consisting of 187 accessions and an inter-specific recombinant inbred line (RIL) population containing 284 RILs. An image-based phenotyping method was developed and used to extract the pod color- and size-related parameters from images. Genome-wide association study (GWAS) and linkage mapping were performed to decipher the genetic control of pod color- and size-related traits across 2 successive years. Both populations exhibited wide phenotypic variations and continuous distribution in pod color- and size-related traits, indicating quantitative polygenic inheritance of these traits. GWAS and linkage mapping approaches identified the two major quantitative trait loci (QTL) underlying the pod color parameters, i.e., qPC3 and qPC19, located to chromosomes 3 and 19, respectively, and 12 stable QTLs for pod size-related traits across nine chromosomes. Several genes residing within the genomic region of stable QTL were identified as potential candidates underlying these pod-related traits based on the gene annotation and expression profiling data. Our results provide the useful information for fine-mapping/map-based cloning of QTL and marker-assisted selection of elite varieties with desirable pod traits.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01223-2.

The Light-Induced WD40-Repeat Transcription Factor DcTTG1 Regulates Anthocyanin Biosynthesis in Dendrobium candidum

Dendrobium candidum is used as a traditional Chinese medicine and as a raw material in functional foods. D. candidum stems are green or red, and red stems are richer in anthocyanins. Light is an important environmental factor that induces anthocyanin accumulation in D. candidum. However, the underlying molecular mechanisms have not been fully unraveled. In this study, we exposed D. candidum seedlings to two different light intensities and found that strong light increased the anthocyanin content and the expression of genes involved in anthocyanin biosynthesis. Through transcriptome profiling and expression analysis, we identified a WD40-repeat transcription factor, DcTTG1, whose expression is induced by light. Yeast one-hybrid assays showed that DcTTG1 binds to the promoters of DcCHS2, DcCHI, DcF3H, and DcF3'H, and a transient GUS activity assay indicated that DcTTG1 can induce their expression. In addition, DcTTG1 complemented the anthocyanin deficiency phenotype of the Arabidopsis thaliana ttg1-13 mutant. Collectively, our results suggest that light promotes anthocyanin accumulation in D. candidum seedlings via the upregulation of DcTTG1, which induces anthocyanin synthesis-related gene expression.

Light and CO2 Modulate the Accumulation and Localization of Phenolic Compounds in Barley Leaves

Barley (Hordeum vulgare) accumulates phenolic compounds (PhCs), which play a key role in plant defense against environmental stressors as antioxidants or UV screening compounds. The influence of light and atmospheric CO2 concentration ([CO2]) on the accumulation and localization of PhCs in barley leaves was examined for two varieties with different tolerances to oxidative stress. PhC localization was visualized in vivo using fluorescence microscopy. Close relationships were found between fluorescence-determined localization of PhCs in barley leaves and PhC content estimated using liquid chromatography coupled with mass spectroscopy detection. Light intensity had the strongest effect on the accumulation of PhCs, but the total PhC content was similar at elevated [CO2], minimizing the differences between high and low light. PhCs localized preferentially near the surfaces of leaves, but under low light, an increasing allocation of PhCs in deeper mesophyll layers was observed. The PhC profile was significantly different between barley varieties. The relatively tolerant variety accumulated significantly more hydroxycinnamic acids, indicating that these PhCs may play a more prominent role in oxidative stress prevention. Our research presents novel evidence that [CO2] modulates the accumulation of PhCs in barley leaves. Mesophyll cells, rather than epidermal cells, were most responsive to environmental stimuli in terms of PhC accumulation.

Isoflavone malonyl-CoA acyltransferase GmMaT2 is involved in nodulation of soybean by modifying synthesis and secretion of isoflavones

Malonyl-CoA:flavonoid acyltransferases (MaTs) modify isoflavones, but only a few have been characterized for activity and assigned to specific physiological processes. Legume roots exude isoflavone malonates into the rhizosphere, where they are hydrolyzed into isoflavone aglycones. Soybean GmMaT2 was highly expressed in seeds, root hairs, and nodules. GmMaT2 and GmMaT4 recombinant enzymes used isoflavone 7-O-glucosides as acceptors and malonyl-CoA as an acyl donor to generate isoflavone glucoside malonates. GmMaT2 had higher activity towards isoflavone glucosides than GmMaT4. Overexpression in hairy roots of GmMaT2 and GmMaT4 produced more malonyldaidzin, malonylgenistin, and malonylglycitin, and resulted in more nodules than control. However, only GmMaT2 knockdown (KD) hairy roots showed reduced levels of malonyldaidzin, malonylgenistin, and malonylglycitin, and, likewise, reduced nodule numbers. These were consistent with the up-regulation of only GmMaT2 by rhizobial infection, and higher expression levels of early nodulation genes in GmMaT2- and GmMaT4-overexpressing roots, but lower only in GmMaT2-KD roots compared with control roots. Higher malonyl isoflavonoid levels in transgenic hairy roots were associated with higher levels of isoflavones in root exudates and more nodules, and vice versa. We suggest that GmMaT2 participates in soybean nodulation by catalyzing isoflavone malonylation and affecting malonyl isoflavone secretion for activation of Nod factor and nodulation.

Linking anthocyanin diversity, hue, and genetics in purple corn

While maize with anthocyanin-rich pericarp (purple corn) is rising in popularity as a source of natural colorant for foods and beverages, information on color range and stability-factors associated with anthocyanin decorations and compositional profiles-is currently limited. Furthermore, to maximize the scalability and meet growing demands, both anthocyanin concentrations and agronomic performance must improve in purple corn varieties. Using the natural anthocyanin diversity present in a purple corn landrace, Apache Red, we generated a population with variable flavonoid profiles-flavanol-anthocyanin condensed forms (0-83%), acylated anthocyanins (2-72%), pelargonidin-derived anthocyanins (5-99%), C-glycosyl flavone co-pigments up to 1904 µg/g, and with anthocyanin content up to 1598 µg/g. Each aspect of the flavonoid profiles was found to play a role in either the resulting extract hue or intensity. With genotyping-by-sequencing of this population, we mapped aspects of the flavonoid profile. Major quantitative trait loci (QTLs) for anthocyanin type were found near loci previously identified only in aleurone-pigmented maize varieties [Purple aleurone1 (Pr1) and Anthocyanin acyltransferase1 (Aat1)]. A QTL near P1 (Pericarp color1) was found for both flavone content and flavanol-anthocyanin condensed forms. A significant QTL associated with peonidin-derived anthocyanins near a candidate S-adenosylmethionine-dependent methyltransferase was also identified, warranting further investigation. Mapping total anthocyanin content produced signals near Aat1, the aleurone-associated bHLH R1 (Colored1), the plant color-associated MYB, Pl1 (Purple plant1), the aleurone-associated recessive intensifier, In1 (Intensifier1), and several previously unidentified candidates. This population represents one of the most anthocyanin diverse pericarp-pigmented maize varieties characterized to date. Moreover, the candidates identified here will serve as branching points for future research studying the genetic and molecular processes determining anthocyanin profile in pericarp.

Enhanced Biosynthesis of Chlorogenic Acid and Its Derivatives in Methyl-Jasmonate-Treated Gardenia jasminoides Cells: A Study on Metabolic and Transcriptional Responses of Cells

Chlorogenic acid and its derivatives (CQAs) are considered as important bioactive secondary metabolites in Gardenia jasminoides Ellis (G. jasminoides). However, few studies have investigated the biosynthesis and regulation of CQAs in G. jasminoides. In this study, methyl jasmonate (MeJA) was used to enhance CQAs accumulation in cultured G. jasminoides cells. Moreover, the possible molecular mechanism of MeJA-mediated accumulation of CQAs is also explored. To this end, time-course transcriptional profiles of G. jasminoides cells responding to MeJA were used to investigate the mechanism from different aspects, including jasmonate (JAs) biosynthesis, signal transduction, biosynthesis of precursor, CQAs biosynthesis, transporters, and transcription factors (TFs). A total of 57,069 unigenes were assembled from the clean reads, in which 80.7% unigenes were successfully annotated. Furthermore, comparative transcriptomic results indicated that differentially expressed genes (DEGs) were mainly involved in JAs biosynthesis and signal transduction (25 DEGs), biosynthesis of precursor for CQAs (18 DEGs), CQAs biosynthesis (19 DEGs), and transporters (29 DEGs). Most of these DEGs showed continuously upregulated expressions over time, which might activate the jasmonic acid (JA) signal transduction network, boost precursor supply, and ultimately stimulate CQAs biosynthesis. Additionally, various TFs from different TF families also responded to MeJA elicitation. Interestingly, 38 DEGs from different subgroups of the MYB family might display positive or negative regulations on phenylpropanoids, especially on CQAs biosynthesis. Conclusively, our results provide insight into the possible molecular mechanism of regulation on CQAs biosynthesis, which led to a high CQAs yield in the G. jasminoides cells under MeJA treatment.

Membrane transporters: the key drivers of transport of secondary metabolites in plants

This review summarizes the recent updates in the area of transporters of plant secondary metabolites, including their applied aspects in metabolic engineering of economically important secondary metabolites. Plants have evolved biosynthetic pathways to produce structurally diverse secondary metabolites, which serve distinct functions, including defense against pathogens and herbivory, thereby playing a pivotal role in plant ecological interactions. These compounds often display interesting bioactivities and, therefore, have been used as repositories of natural drugs and phytoceuticals for humans. At an elevated level, plant secondary metabolites could be cytotoxic to the plant cell itself; therefore, plants have developed sophisticated mechanisms to sequester these compounds to prevent cytotoxicity. Many of these valuable natural compounds and their precursors are biosynthesized and accumulated at diverse subcellular locations, and few are even transported to sink organs via long-distance transport, implying the involvement of compartmentalization via intra- and intercellular transport mechanisms. The transporter proteins belonging to different families of transporters, especially ATP binding cassette (ABC) and multidrug and toxic compound extrusion (MATE) have been implicated in membrane-mediated transport of certain plant secondary metabolites. Despite increasing reports on the characterization of transporter proteins and their genes, our knowledge about the transporters of several medicinally and economically important plant secondary metabolites is still enigmatic. A comprehensive understanding of the molecular mechanisms underlying the whole route of secondary metabolite transportome, in addition to the biosynthetic pathways, will aid in systematic and targeted metabolic engineering of high-value secondary metabolites. The present review embodies a comprehensive update on the progress made in the elucidation of transporters of secondary metabolites in view of basic and applied aspects of their transport mechanism.

MiR858b Inhibits Proanthocyanidin Accumulation by the Repression of DkMYB19 and DkMYB20 in Persimmon

Persimmon proanthocyanidin (PA) biosynthesis is controlled by structural genes and regulated by transcription factors (TFs). MicroRNAs are a key factor involved in regulating gene expression at the posttranscriptional level whose functions in persimmon PA biosynthesis are poorly understood. Here, we identified a microRNA, miR858b, that putatively targets two R2R3-MYB TFs, DkMYB19 and DkMYB20. DkMYB19, DkMYB20, and miR858b showed divergent expression patterns during fruit development, and the interaction between miR858b and DkMYB19 or DkMYB20 was experimentally validated by 5' RNA ligase-mediated RACE, LUC enzyme activity analysis, and GFP signal detection. The DkMYB19 localized to the nucleus as well as the cytoplasm and DkMYB20 localized to the nucleus. The overexpression of miR858b led to the downregulation of DkMYB19 and DkMYB20, which reduced the content of PA, whereas a reduction in miR858b activity upregulated DkMYB19 and DkMYB20, resulting in a high content of PA in leaves transiently expressing a small tandem target mimic construct for blocking miR858 (STTM858b) in vivo. The transient transformation of miR858b in fruit discs in vitro also reduced the content of PA, while the content of PA increased under the transient transformation of fruit discs with STTM858b, DkMYB19, or DkMYB20. A similar phenomenon was observed upon the overexpression of miR858b in wild-type (WT) Arabidopsis and DkMYB19 or DkMYB20 in persimmon leaf calli. These findings suggested that miR858b repressed the expression of DkMYB19 and DkMYB20, which contributed to the PA accumulation in persimmon.

Comprehensive characterization of the ALMT and MATE families on Populus trichocarpa and gene co-expression network analysis of its members during aluminium toxicity and phosphate starvation stresses

Aluminium (Al) toxicity and phosphate deficit on soils are some of the main problems of modern agriculture and are usually associated. Some plants are able to overcome these stresses through exuding organic acids on the rhizosphere, such as citrate and malate, which are exported by MATE (Multi drug and toxin extrusion) and ALMT (Aluminium-activated malate transporter) transporters, respectively. Despite its co-action on acidic soils, few studies explore these two families' correlation, especially on tree crops, therefore we performed a comprehensive description of MATE and ALMT families on Populus trichocarpa as a model species for arboreal plants. We found 20 and 56 putative members of ALMT and MATE families, respectively. Then, a gene co-expression network analysis was performed using broad transcriptomic data to analyze which members of each family were transcriptionally associated. Four independent networks were generated, one of which is composed of members putatively related to phosphate starvation and aluminum toxicity stresses. The PoptrALMT10 and PoptrMATE54 genes were selected from this network for a deeper analysis, which revealed that in roots under phosphate starvation stress the two genes have independent transcriptional profiles, however, on the aluminum toxicity stress they share some common correlations with other genes. The data presented here help on the description of these gene families, of which some members are potentially involved in plant responses to acid soil-related stresses and its exploration is an important step towards using this knowledge on breeding programs for P. trichocarpa and other tree crops.

Diurnal metabolic regulation of isoflavones and soyasaponins in soybean roots

Isoflavones and soyasaponins are major specialized metabolites accumulated in soybean roots and secreted into the rhizosphere. Unlike the biosynthetic pathway, the transporters involved in metabolite secretion remain unknown. The developmental regulation of isoflavone and soyasaponin secretions has been recently reported, but the diurnal regulation of their biosynthesis and secretion still needs to be further studied. To address these challenges, we conducted transcriptome and metabolite analysis using hydroponically grown soybean plants at 6-hr intervals for 48 hr in a 12-hr-light/12-hr-dark condition. Isoflavone and soyasaponin biosynthetic genes showed opposite patterns in the root tissues; that is, the former genes are highly expressed in the daytime, while the latter ones are strongly induced at nighttime. GmMYB176 encoding a transcription factor of isoflavone biosynthesis was upregulated from ZT0 (6:00 a.m.) to ZT6 (12:00 a.m.), followed by the induction of isoflavone biosynthetic genes at ZT6. The isoflavone aglycone content in the roots accordingly increased from ZT6 to ZT18 (0:00 a.m.). The isoflavone aglycone content in root exudates was kept consistent throughout the day, whereas that of glucosides increased at ZT6, which reflected the decreased expression of the gene encoding beta-glucosidase involved in the hydrolysis of apoplast-localized isoflavone conjugates. Co-expression analysis revealed that those isoflavone and soyasaponin biosynthetic genes formed separate clusters, which exhibited a correlation to ABC and MATE transporter genes. In summary, the results in this study indicated the diurnal regulation of isoflavone biosynthesis in soybean roots and the putative transporter genes responsible for isoflavone and soyasaponin transport.

Postharvest seed coat darkening in pinto bean (Phaseolus vulgaris) is regulated by Psd , an allele of the basic helix-loop-helix transcription factor P

Pinto bean (Phaseolus vulgaris) is one of the leading market classes of dry beans that is most affected by postharvest seed coat darkening. The process of seed darkening poses a challenge for bean producers and vendors as they encounter significant losses in crop value due to decreased consumer preference for darker beans. Here, we identified a novel allele of the P gene, Psd , responsible for the slow darkening seed coat in pintos, and identified trait-specific sequence polymorphisms which are utilized for the development of new gene-specific molecular markers for breeding. These tools can be deployed to help tackle this economically important issue for bean producers.

SUMMARY

Postharvest seed coat darkening in pinto bean is an undesirable trait that reduces the market value of the stored crop. Regular darkening (RD) pintos darken faster after harvest and accumulate higher level of proanthocyanidins (PAs) compared to slow darkening (SD) cultivars. Although the markers cosegregating with the SD trait have been known for some time, the SLOW DARKENING (Sd) gene identity had not been proven.Here, we identified Psd as a candidate for controlling the trait. Genetic complementation, transcript abundance, metabolite analysis, and inheritance study confirmed that Psd is the Sd gene. Psd is another allele of the P (Pigment) gene, whose loss-of-function alleles result in a white seed coat. Psd encodes a bHLH transcription factor with two transcript variants but only one is involved in PA biosynthesis. An additional glutamate residue in the activation domain, and/or an arginine to histidine substitution in the bHLH domain of the Psd-1 transcript in the SD cultivar is likely responsible for the reduced activity of this allele compared to the allele in a RD cultivar, leading to reduced PA accumulation.Overall, we demonstrate that a novel allele of P, Psd , is responsible for the SD phenotype, and describe the development of new, gene-specific, markers that could be utilized in breeding to resolve an economically important issue for bean producers.

Identification and Expression of the Multidrug and Toxic Compound Extrusion (MATE) Gene Family in Capsicum annuum and Solanum tuberosum

Multidrug and Toxic Compound Extrusion (MATE) proteins are essential transporters that extrude metabolites and participate in plant development and the detoxification of toxins. Little is known about the MATE gene family in the Solanaceae, which includes species that produce a broad range of specialized metabolites. Here, we identified and analyzed the complement of MATE genes in pepper (Capsicum annuum) and potato (Solanum tuberosum). We classified all MATE genes into five groups based on their phylogenetic relationships and their gene and protein structures. Moreover, we discovered that tandem duplication contributed significantly to the expansion of the pepper MATE family, while both tandem and segmental duplications contributed to the expansion of the potato MATE family, indicating that MATEs took distinct evolutionary paths in these two Solanaceous species. Analysis of ω values showed that all potato and pepper MATE genes experienced purifying selection during evolution. In addition, collinearity analysis showed that MATE genes were highly conserved between pepper and potato. Analysis of cis-elements in MATE promoters and MATE expression patterns revealed that MATE proteins likely function in many stages of plant development, especially during fruit ripening, and when exposed to multiple stresses, consistent with the existence of functional differentiation between duplicated MATE genes. Together, our results lay the foundation for further characterization of pepper and potato MATE gene family members.

Proanthocyanidin Biosynthesis-a Matter of Protection

Proanthocyanidins are the second most abundant plant phenolic polymer, but, despite intensive investigation, several aspects of their biosynthesis and functions remain unclear.

Metabolic and transcriptomic analysis related to flavonoid biosynthesis during the color formation of Michelia crassipes tepal

Michelia crassipes is the only plant with purple flowers amongst Michelia species, and its tepals exhibit an obvious color change from green to purple. In this study, a combination of metabolic and transcriptomic analyses was conducted at three stages of tepals in Michelia crassipes: green tepal, purple spot-containing tepal, and totally purple tepal. Several classes of flavonoid compounds were detected and cyanidin 3-rutinoside and delphinidin 3-glucoside were the major anthocyanins underlying the purple color formation, along with co-pigmentation of flavone compounds represented by luteolin derivatives and flavonol compounds represented by kaempferol and quercetin derivatives. Transcriptome analysis revealed up-regulation of genes encoding enzymes involved in the conversion of phenylpropanoid for flavonoid biosynthesis in Stage 1 vs. Stage 2, whereas up-regulation of most flavonoid biosynthesis genes was observed in Stage 1 vs. Stage 3. MYB, bHLH, and WD40 isoforms, as well as other classes of transcriptional factors, also exhibited differential expression. In addition, differentially expressed genes putatively related to the transport of flavonoids were also identified. The results of the current study provide insight into the regulatory mechanism underlying the color transition from green to purple in Michelia crassipes tepals and describe a complicated network involving PAL, transporter genes, and transcription factors, specifically responsible for the emergence of purple color in Stage 1 vs. Stage 2.

Arabidopsis ECHIDNA protein is involved in seed coloration, protein trafficking to vacuoles, and vacuolar biogenesis

Flavonoids are a major group of plant-specific metabolites that determine flower and seed coloration. In plant cells, flavonoids are synthesized at the cytosolic surface of the endoplasmic reticulum and are sequestered in the vacuole. It is possible that membrane trafficking, including vesicle trafficking and organelle dynamics, contributes to flavonoid transport and accumulation. However, the underlying mechanism has yet to be fully elucidated. Here we show that the Arabidopsis ECHIDNA protein plays a role in flavonoid accumulation in the vacuole and protein trafficking to the vacuole. We found defective pigmentation patterns in echidna seed, possibly caused by reduced levels of proanthocyanidins, which determine seed coloration. The echidna mutant has defects in protein sorting to the protein storage vacuole as well as vacuole morphology. These findings indicate that ECHIDNA is involved in the vacuolar trafficking pathway as well as the previously described secretory pathway. In addition, we found a genetic interaction between echidna and green fluorescent seed 9 (gfs9), a membrane trafficking factor involved in flavonoid accumulation. Our findings suggest that vacuolar trafficking and/or vacuolar development, both of which are collectively regulated by ECHIDNA and GFS9, are required for flavonoid accumulation, resulting in seed coat pigmentation.