Overexpression of herbaceous peony miR156e-3p improves anthocyanin accumulation in transgenic Arabidopsis thaliana lateral branches

Painting the plant body: pigment biosynthetic pathways regulated by small RNAs

Plant pigments are diverse natural molecules involved in numerous biological functions such as development, growth, and metabolism. As plants age, not only new organs will be formed, but also, they will acquire the necessary pigments in response to the environment and endogenous programming in order to achieve reproductive success. Among the endogenous cues, the small RNAs (sRNAs), an endogenous group of ubiquitous regulatory molecules, may regulate the pigments-associated biosynthetic pathways at posttranscriptional level. Although plant pigments and sRNAs have been comprehensively studied in several processes throughout the entire plant cycle in model and nonmodel species, connections among these central players must be revised. Studying these complex networks allow us not only to know the progress that has been made in this area, but also generate research questions to be explored in order to unravel novel mechanisms for improving plant yield; therefore, in this review we have summarized the emerging roles of sRNAs-regulated nodes in mediating plant pigmentation-associated biosynthetic pathways, focused on chlorophylls, flavonoids, carotenoids, and betalains. In addition, we discuss perspectives related to the manipulation of those genes associated with plant pigments for obtaining genetically improved plants.

Research advances of coloring mechanism regulated by MicroRNAs in plants

In plants, microRNAs (miRNAs) are a class of important small RNAs involved in their growth and development, and play a very significant role in regulating their tissue coloring. In this paper, the mechanisms on miRNA regulation of plant coloring are mainly reviewed from three aspects: macroscopic physiological and molecular foundations related to tissue coloring, miRNA biosynthesis and function, and specific analysis of miRNA regulation studies on leaf color, flower color, fruit color, and other tissue color formation in plants. Furthermore, we also systematically summarize the miRNA regulatory mechanisms identified on pigments biosynthesis and color formation in plants, and the regulatory mechanisms of these miRNAs mentioned on the existing researches can be divided into four main categories: directly targeting the related transcription factors, directly targeting the related structural genes, directly targeting the related long noncoding RNAs (LncRNAs) and miRNA-mediated production of trans-acting small interfering RNAs (ta-siRNAs). Together, these research results aim to provide a theoretical reference for the in-depth study of plant coloring mechanism and molecular breeding study of related plants in the future.

Fine-tuning plant valuable secondary metabolite biosynthesis via small RNA manipulation: strategies and potential

Plants produce secondary metabolites that serve various functions, including defense against biotic and abiotic stimuli. Many of these secondary metabolites possess valuable applications in diverse fields, including medicine, cosmetic, agriculture, and food and beverage industries, exhibiting their importance in both plant biology and various human needs. Small RNAs (sRNA), such as microRNA (miRNA) and small interfering RNA (siRNA), have been shown to play significant roles in regulating the metabolic pathways post-transcriptionally by targeting specific key genes and transcription factors, thus offering a promising tool for enhancing plant secondary metabolite biosynthesis. In this review, we summarize current approaches for manipulating sRNAs to regulate secondary metabolite biosynthesis in plants. We provide an overview of the latest research strategies for sRNA manipulation across diverse plant species, including the identification of potential sRNAs involved in secondary metabolite biosynthesis in non-model plants. We also highlight the potential future research directions, focusing on the manipulation of sRNAs to produce high-value compounds with applications in pharmaceuticals, nutraceuticals, agriculture, cosmetics, and other industries. By exploring these advanced techniques, we aim to unlock new potentials for biotechnological applications, contributing to the production of high-value plant-derived products.

Small RNA and Degradome Sequencing Reveal Roles of miRNAs in the Petal Color Fading of Malus Crabapple

The Malus crabapple is an important woody ornamental plant. The fading of petals during its development significantly affects their ornamental value. Petal color is related to anthocyanin content and miRNAs play an important role in the post-transcriptional regulation of anthocyanin synthesis. However, the mechanisms underlying miRNA regulation of petal fading have rarely been studied. Transcriptome and small RNA sequencing of petals from the blooming phases of Malus. 'Indian Summer' varieties S1 (small bud), S2 (initial-flowering), and S3 (late-flowering) allowed us to identify 230 known miRNAs and 17 novel miRNAs, including 52 differentially expressed miRNAs which targeted 494 genes and formed 823 miRNA-target pairs. Based on the target gene annotation results, miRNA-target pairs were screened that may be involved in the fading process of Malus crabapple petals through three different pathways: anthocyanin synthesis, transport, and degradation, involving mcr-miR858-MYB1\MYB5 and mcr-miR396-McCHI inhibiting anthocyanin synthesis; mcr-miR167, mcr-miR390, mcr-miR535, and mcr-miR858 inhibiting anthocyanin transport from the cytoplasm to the vacuole by targeting ABC transporter genes (ABCB, ABCC, ABCD, and ABCG); and mcr-miR398 targeting the superoxide dismutase genes (CZSOD2 and CCS) to accelerate anthocyanin degradation. These findings offer a novel approach to understanding the mechanism of petal fading and serve as a reference for other plants with floral fading.

The Role of Anthocyanins in Plant Tolerance to Drought and Salt Stresses

Drought and salinity affect various biochemical and physiological processes in plants, inhibit plant growth, and significantly reduce productivity. The anthocyanin biosynthesis system represents one of the plant stress-tolerance mechanisms, activated by surplus reactive oxygen species. Anthocyanins act as ROS scavengers, protecting plants from oxidative damage and enhancing their sustainability. In this review, we focus on molecular and biochemical mechanisms underlying the role of anthocyanins in acquired tolerance to drought and salt stresses. Also, we discuss the role of abscisic acid and the abscisic-acid-miRNA156 regulatory node in the regulation of drought-induced anthocyanin production. Additionally, we summarise the available knowledge on transcription factors involved in anthocyanin biosynthesis and development of salt and drought tolerance. Finally, we discuss recent progress in the application of modern gene manipulation technologies in the development of anthocyanin-enriched plants with enhanced tolerance to drought and salt stresses.

The MdmiR156n Regulates Drought Tolerance and Flavonoid Synthesis in Apple Calli and Arabidopsis

Drought is the major abiotic stress that limits apple productivity and quality. To date, many important and divergent regulatory functions of miR156/SBP genes in plant growth and development have been well understood. However, little is known about the role of apple miR156 in response to abiotic stress. To better understand the functions of MdmiR156 in abiotic stress tolerance, we constructed the overexpression (OE) and short tandem target mimic (STTM) vector of MdmiR156n and performed its functional analysis through the characterization of transgenic apple calli and Arabidopsis thaliana plants. In this study, MdmiR156n overexpression significantly increased the length of primary roots and the number of lateral roots in transgenic Arabidopsis plants under drought stress. In addition, MdmiR156n transgenic Arabidopsis and apple calli had a lower electrolyte leakage rate and less cell membrane damage than WT and STTM156 after drought stress. Further studies showed that MdmiR156n overexpression promoted the accumulation of flavonoids and scavenging of reactive oxygen species (ROS) under drought conditions in transgenic apple calli and A. thaliana plants. Taken together, overexpression MdmiR156n enhances drought tolerance by regulating flavonoid synthesis and ROS signaling cascades in apple calli and A. thaliana.

Identification of differentially expressed miRNAs and their target genes in response to brassinolide treatment on flowering of tree peony (Paeonia ostii)

Tree peony is a famous flower plant in China, but the short and concentrated flowering period limits its ornamental value and economic value. Brassinolide (BR) plays an important role in plant growth and development including flowering. There have been a large number of reports on the molecular aspects of the flowering process, but the genetic mechanism that was responsible for miRNA-guided regulation of tree peony is almost unclear. In this study, the leaves of tree peony cultivar, 'Feng Dan', were sprayed with different concentrations of BR, and the obvious bloom delay was found at the treatment with BR 50 μg/L. The small RNA sequencing and transcriptome sequencing were performed on the petals of tree peony under an untreated control (CK) and the treatment with BR 50 μg/L during four consecutive flowering development stages. A total of 22 known miRNAs belonging to 12 families were identified and 84 novel miRNAs were predicted. Combined with transcriptome data, a total of 376 target genes were predicted for the 18 differentially expressed known miRNAs and 177 target genes were predicted for the 23 differentially expressed novel miRNAs. Additionally, the potential miRNAs and their target genes were identified, including miR156b targeting SPL, miR172a_4 targeting AP2 and four novel miRNAs targeting SPA1, and revealed that they might affect the flowering time in tree peony. Collectively, these results would provide a theoretical basis for further analysis of miRNA-guided regulation on flowering period in tree peony.

Integrated analysis of miRNAome transcriptome and degradome reveals miRNA-target modules governing floral florescence development and senescence across early- and late-flowering genotypes in tree peony

As a candidate national flower of China, tree peony has extremely high ornamental, medicinal and oil value. However, the short florescence and rarity of early-flowering and late-flowering varieties restrict further improvement of the economic value of tree peony. Specific miRNAs and their target genes engaged in tree peony floral florescence, development and senescence remain unknown. This report presents the integrated analysis of the miRNAome, transcriptome and degradome of tree peony petals collected from blooming, initial flowering, full blooming and decay stages in early-flowering variety Paeonia ostii 'Fengdan', an early-flowering mutant line of Paeonia ostii 'Fengdan' and late-flowering variety Paeonia suffruticosa 'Lianhe'. Transcriptome analysis revealed a transcript ('psu.G.00014095') which was annotated as a xyloglucan endotransglycosylase/hydrolase precursor XTH-25 and found to be differentially expressed across flower developmental stages in Paeonia ostii 'Fengdan' and Paeonia suffruticosa 'Lianhe'. The miRNA-mRNA modules were presented significant enrichment in various pathways such as plant hormone signal transduction, indole alkaloid biosynthesis, arachidonic acid metabolism, folate biosynthesis, fatty acid elongation, and the MAPK signaling pathway. Multiple miRNA-mRNA-TF modules demonstrated the potential functions of MYB-related, bHLH, Trihelix, NAC, GRAS and HD-ZIP TF families in floral florescence, development, and senescence of tree peony. Comparative spatio-temporal expression investigation of eight floral-favored miRNA-target modules suggested that transcript 'psu.T.00024044' and microRNA mtr-miR166g-5p are involved in the floral florescence, development and senescence associated agronomic traits of tree peony. The results might accelerate the understanding of the potential regulation mechanism in regards to floral florescence, development and abscission, and supply guidance for tree peony breeding of varieties with later and longer florescence characteristics.

Genome-Wide Identification and Comparative Profiling of MicroRNAs Reveal Flavonoid Biosynthesis in Two Contrasting Flower Color Cultivars of Tree Peony

MicroRNA (miRNA)-mediated gene regulation is involved in various physiological processes in plants. Flower color is one of the vital ornamental traits of tree peony (Paeonia suffruticosa Andr.). However, the yellow-flowered tree peony cultivars are particularly rare. To elucidate the miRNA-mediated gene regulatory mechanism underlying yellow pigmentation in tree peony, we combined pigment assessment, miRNA identification, expression analysis, and gene functional verification in two contrasting flower color cultivars "High Noon" and "Roufurong." Flavones/flavonols and anthocyanins were found to be the main contributors to the coloration of "High Noon" and "Roufurong" petals, respectively. Subsequently, miRNA analysis based on available genome data identified 9 differentially expressed miRNAs and 12 relevant target genes implicated in flavonoid biosynthesis. Their dynamic expression patterns determined the key role of mdm-miR156b-PsSPL2 module in yellow pigmentation of tree peony flowers. The sequence analysis and subcellular localization validated that PsSPL2 might function as a nuclear-localized transcription factor. Overexpression of PsSPL2 in tobacco resulted in a decrease of anthocyanin content and down-regulation of NtF3'H and NtDFR transcripts. PsSPL2-silenced petals exhibited lighter yellow color, and the contents of THC, Ap, and Ch decreased significantly. Meanwhile, expression levels of PsCHS, PsCHI, and PsF3H were significantly decreased in the petals with PsSPL2 silencing, while those of PsF3'H and PsDFR were remarkably increased. This study offers a novel insight into yellow pigmentation-related miRNA regulation network in tree peony, and further provides the valuable information on physiological changes during yellow coloring process of tree peony.

Rice microRNA171f/SCL6 module enhances drought tolerance by regulation of flavonoid biosynthesis genes

Plants have evolved sophisticated defense systems to enhance drought tolerance. These include the microRNA (miRNA) group of small noncoding RNAs that act as post-transcriptional regulators; however, details of the mechanisms by which they confer drought tolerance are not well understood. Here, we show that osa-MIR171f, a member of osa-MIR171 gene family, is mainly expressed in response to drought stress and regulates the transcript levels of SCARECROW-LIKE6-I (SCL6-I) and SCL6-II in rice (Oryza sativa). The SCL6 genes are known to be involved in shoot branching and flag leaf morphology. Osa-MIR171f-overexpressing (osa-MIR171f-OE) transgenic plants showed reduced drought symptoms compared with non-transgenic (NT) control plants under both field drought and polyethylene glycol (PEG)-mediated dehydration stress conditions. Transcriptome analysis of osa-MIR171f-OE plants and osa-mir171f-knockout (K/O) lines generated by clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) revealed that osa-mature-miR171a-f (osa-miR171) regulates the expression of flavonoid biosynthesis genes, consequently leading to drought tolerance. This upregulation in the osa-MIR171f-OE plants, which did not occur in NT control plants, was observed under both normal and drought conditions. Our findings indicate that osa-miR171 plays a role in drought tolerance by regulating SCL6-I and SCL6-II transcript levels.

MicroRNA Profiling During Mulberry (Morus atropurpurea Roxb) Fruit Development and Regulatory Pathway of miR477 for Anthocyanin Accumulation

To understand the mechanism of small non-coding RNAs (miRNA)-mediated development and ripening of mulberry fruits, three small RNA libraries from mulberry fruits at different development stages were constructed, and 159 conserved miRNAs as well as 86 novel miRNAs were successfully identified. Among the miRNAs identified, there were 90 miRNAs which showed differential expression patterns at different stages of fruit development and ripening. The target genes of these differential expressed (DE) miRNAs were involved in growth and development, transcription and regulation of transcription, metabolic processes, and etc. Interestingly, it was found that the expression level of mul-miR477 was increased with fruit ripening, and it can target the antisense lncRNA (Mul-ABCB19AS) of the ATP binding cassette (ABC) transporter B 19 gene (Mul-ABCB19). Our results showed that mul-miR477 can repress the expression of Mul-ABCB19AS and increase the expression of Mul-ABCB19, and it acted as a positive regulator participating anthocyanin accumulation through the regulatory network of mul-miR477-Mul-ABCB19AS-Mul-ABCB19.

Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis

miRNAs are involved in various biological processes, including adaptive responses to abiotic stress. To understand the role of miRNAs in the response to ABA, ABA-responsive miRNAs were identified by small RNA sequencing in wild-type Arabidopsis, as well as in abi1td, mkkk17, and mkkk18 mutants. We identified 10 novel miRNAs in WT after ABA treatment, while in abi1td, mkkk17, and mkkk18 mutants, three, seven, and nine known miRNAs, respectively, were differentially expressed after ABA treatment. One novel miRNA (miRn-8) was differentially expressed in the mkkk17 mutant. Potential target genes of the miRNA panel were identified using psRNATarget. Sequencing results were validated by quantitative RT-PCR of several known and novel miRNAs in all genotypes. Of the predicted targets of novel miRNAs, seven target genes of six novel miRNAs were further validated by 5' RLM-RACE. Gene ontology analyses showed the potential target genes of ABA-responsive known and novel miRNAs to be involved in diverse cellular processes in plants, including development and stomatal movement. These outcomes suggest that a number of the identified miRNAs have crucial roles in plant responses to environmental stress, as well as in plant development, and might have common regulatory roles in the core ABA signaling pathway.

Advances in molecular biology of Paeonia L

Molecular biology can serve as a tool to solve the limitations of traditional breeding and cultivation techniques related to flower patterns, the improvement of flower color, and the regulation of flowering and stress resistance. These characteristics of molecular biology ensured its significant role in improving the efficiency of breeding and germplasm amelioration of Paeonia. This review describes the advances in molecular biology of Paeonia, including: (1) the application of molecular markers; (2) genomics, transcriptomics, proteomics, metabolomics, and microRNA studies; (3) studies of functional genes; and (4) molecular biology techniques. This review also points out select limitations in current molecular biology, analyzes the direction of Paeonia molecular biology research, and provides advice for future research objectives.

Exploration of miRNA-mediated fertility regulation network of cytoplasmic male sterility during flower bud development in soybean

Cytoplasmic male sterility (CMS) plays an important role in the production of soybean hybrid seeds. MicroRNAs (miRNAs) are a class of non-coding endogenous ~ 21 nt small RNAs that play crucial roles in flower and pollen development by targeting genes in plants. To dissect the function of miRNAs in soybean CMS, a total of 558 known miRNAs, 10 novel miRNAs, and 466 target genes were identified in flower buds of the soybean CMS line NJCMS1A and its restorer line NJCMS1C through small RNA sequencing and degradome analysis. In addition, miRNA-mediated editing events were also observed, and the two most frequently observed editing types (A → G and C → U) were validated by cloning and sequencing. And as the base editing occurred, some targets were filtered, such as gma-miR2118b-P6GT with Glyma.08G122000.2. Further integrated analysis of transcriptome and small RNA found some miRNAs and their targets' expression patterns showing a negative correlation, such as gma-miR156b/GmSPL9a and gma-miR4413b/GmPPR. Furthermore, opposite expression pattern was observed between gma-miR156b and GmSPL9 during early stage of flower bud development. Taken together, the regulatory network of gma-miR156b/GmSPL9 and gma-miR4413b/GmPPR with flower bud development in soybean CMS was developed. Most importantly, previous reports showed that these targets might be related to pollen development and male sterility, suggesting that both conserved and species-specific miRNAs might act as regulators of flower bud development in soybean CMS. These findings may provide a better understanding of the miRNA-mediated regulatory networks of CMS mechanisms in soybean.

Understanding the genetic regulation of anthocyanin biosynthesis in plants - Tools for breeding purple varieties of fruits and vegetables

Anthocyanins are naturally occurring flavonoids derived from the phenylpropanoid pathway. There is increasing evidence of the preventative and protective roles of anthocyanins against a broad range of pathologies, including different cancer types and metabolic diseases. However, most of the fresh produce available to consumers typically contains only small amounts of anthocyanins, mostly limited to the epidermis of plant organs. Therefore, transgenic and non-transgenic approaches have been proposed to enhance the levels of this phytonutrient in vegetables, fruits, and cereals. Here, were review the current literature on the anthocyanin biosynthesis pathway in model and crop species, including the structural and regulatory genes involved in the differential pigmentation patterns of plant structures. Furthermore, we explore the genetic regulation of anthocyanin biosynthesis and the reasons why it is strongly repressed in specific cell types, in order to create more efficient breeding strategies to boost the biosynthesis and accumulation of anthocyanins in fresh fruits and vegetables.

Identification of exosome-like nanoparticle-derived microRNAs from 11 edible fruits and vegetables

Edible plant-derived exosome-like nanoparticles (EPDELNs) are novel naturally occurring plant ultrastructures that are structurally similar to exosomes. Many EPDELNs have anti-inflammatory properties. MicroRNAs (miRNAs) play a critical role in mediating physiological and pathological processes in animals and plants. Although miRNAs can be selectively encapsulated in extracellular vesicles, little is known about their expression and function in EPDELNs. In this study, we isolated nanovesicles from 11 edible fruits and vegetables and subjected the corresponding EPDELN small RNA libraries to Illumina sequencing. We identified a total of 418 miRNAs-32 to 127 per species-from the 11 EPDELN samples. Target prediction and functional analyses revealed that highly expressed miRNAs were closely associated with the inflammatory response and cancer-related pathways. The 418 miRNAs could be divided into three classes according to their EPDELN distributions: 26 "frequent" miRNAs (FMs), 39 "moderately present" miRNAs (MPMs), and 353 "rare" miRNAs (RMs). FMs were represented by fewer miRNA species than RMs but had a significantly higher cumulative expression level. Taken together, our in vitro results indicate that miRNAs in EPDELNs have the potential to regulate human mRNA.