MiR160 and its target genes ARF10, ARF16 and ARF17 modulate hypocotyl elongation in a light, BRZ, or PAC-dependent manner in Arabidopsis: miR160 promotes hypocotyl elongation

Function of floral fragrance-related microRNAs and their targets in Hedychium coronarium

BACKGROUND

Hedychium coronarium is highly valued for its intense fragrance, which may be influenced by the expression of microRNAs (miRNAs). miRNAs are a class of small RNAs that play conserved and pivotal regulatory roles throughout plant growth and development, modulating various aspects of plant metabolism. However, the specific roles of miRNAs in the growth and development of H. coronarium remain largely uncharacterized.

RESULTS

To identify miRNAs in H. coronarium and assess their potential role in the synthesis of floral fragrance compounds, we analyzed the volatile compounds and miRNA expression patterns at three developmental stages (F1, F5, F6). Our findings revealed that the volatile emissions of major floral compounds, including eucalyptol, ocimene, and linalool, increased as the flowers progressed through development. Small RNA sequencing identified 171 conserved miRNAs from 24 miRNA families, along with 32 novel miRNAs. Degradome sequencing uncovered 102 mRNA degradation sites corresponding to 90 target genes from 30 miRNA families. Quantitative RT-PCR (qRT-PCR) analysis showed that the expression of hco-miR393a and hco-miR167n mirrored the release pattern of floral fragrance compounds, while the expression of HcTIR1 and HcARF8 inversely correlated with those of hco-miR393a and hco-miR167n. Co-transformation experiments in tobacco confirmed that HcTIR1 and HcARF8 are direct targets of hco-miR393a and hco-miR167n, respectively. Additionally, treatments with exogenous IAA and the auxin inhibitor PCIB modulated both the release of floral volatiles and the expression of hco-miR393a and hco-miR167n. STTM and VIGS experiments further indicated that hco-miR167n and hco-miR393a positively regulate floral fragrance metabolism, while HcARF8 and HcTIR1 act as negative regulators. Finally, dual-luciferase and yeast one-hybrid assays demonstrated that HcARF8 binds to the promoter of the terpene synthase gene HcTPS8, thereby regulating the biosynthesis of floral fragrance compounds.

CONCLUSIONS

This study represents the first comprehensive identification of miRNAs in H. coronarium and the characterization of their expression profiles in petal tissues at various developmental stages. These findings offer novel insights into the molecular mechanisms governing the synthesis of floral fragrance compounds and highlight the critical role of miRNAs in the regulation of metabolic processes within the Zingiberaceae family.

Branching angles in the modulation of plant architecture: Molecular mechanisms, dynamic regulation, and evolution

Plants develop branches to expand areas for assimilation and reproduction. Branching angles coordinate with branching types, creating diverse plant shapes that are adapted to various environments. Two types of branching angle-the angle between shoots and the angle in relation to gravity or the gravitropic set-point angle (GSA) along shoots-determine the spacing between shoots and the shape of the aboveground plant parts. However, it remains unclear how these branching angles are modulated throughout shoot development and how they interact with other factors that contribute to plant architecture. In this review, we systematically focus on the molecular mechanisms that regulate branching angles across various species, including gravitropism, anti-gravitropic offset, phototropism, and other regulatory factors, which collectively highlight comprehensive mechanisms centered on auxin. We also discuss the dynamics of branching angles during development and their relationships with branching number, stress resistance, and crop yield. Finally, we provide an evolutionary perspective on the conserved role of auxin in the regulation of branching angles.

Identification and characterization of auxin response factor (ARF) gene family in five Bambusoideae species reveals the role of PedARF 23 in regulating lignin synthesis through auxin signaling

Auxin plays a critical role in plant growth and development, mediating responses to environmental stimuli and directing organ growth by establishing and maintaining auxin concentration gradients. Auxin Response Factors (ARFs) are key transcription factors that regulate the expression of auxin-responsive genes. Different ARF genes can act as transcriptional activators or repressors, functioning through various auxin signaling pathways at different developmental stages and under various environmental conditions. Studying the ARF gene family in bamboo is essential for uncovering the molecular mechanisms underlying rapid growth, maintenance of apical dominance, and root development in bamboo. However, research on the function of ARF genes in bamboo is still limited. In this study, we utilized the latest bamboo genome data to comprehensively analyze the genomes of five representative bamboo species, identifying a total of 216 ARF genes and classifying them into 12 subfamilies based on phylogenetic relationships. Through a combination of transcriptome date and RT-qPCR analysis, we observed that the PedARF23 gene in Moso bamboo was significantly upregulated following NAA treatment. To further explore the mechanisms by which PedARF23 modulates plant growth and development via auxin signaling, we developed PedARF23 overexpression lines. By measuring auxin and lignin levels, the expression of key genes (4CL3, 4CL7, and CCoAOMT1) in the lignin biosynthesis pathway in both Moso bamboo and transgenic Arabidopsis, as well as the Yeast one-hybrid assay and LUC activation assay, study discovered that PedARF23 could enhances auxin synthesis and activates the auxin signaling pathway, thereby regulating lignin biosynthesis. Overall, this study provides a foundation for understanding the classification, characteristics, and functions of the ARF gene family in the Bambusoideae. It elucidates the role of ARFs in regulating lignin synthesis, offering valuable insights into the regulation of lignin content in bamboo.

Functional Genomics of Legumes in Bulgaria-Advances and Future Perspectives

Members of the Leguminosae family are important crops that provide food, animal feed and vegetable oils. Legumes make a substantial contribution to sustainable agriculture and the nitrogen cycle through their unique ability to fix atmospheric nitrogen in agricultural ecosystems. Over the past three decades, Medicago truncatula and Lotus japonicus have emerged as model plants for genomic and physiological research in legumes. The advancement of innovative molecular and genetic tools, particularly insertional mutagenesis using the retrotransposon Tnt1, has facilitated the development of extensive mutant collections and enabled precise gene tagging in plants for the identification of key symbiotic and developmental genes. Building on these resources, twelve years ago, our research team initiated the establishment of a platform for functional genomic studies of legumes in Bulgaria. In the framework of this initiative, we conducted systematic sequencing of selected mutant lines and identified genes involved in plant growth and development for detailed functional characterization. This review summarizes our findings on the functions of selected genes involved in the growth and development of the model species, discusses the molecular mechanisms underlying important developmental processes and examines the potential for the translation of this fundamental knowledge to improve commercially important legume crops in Bulgaria and globally.

RNA Metabolism and the Role of Small RNAs in Regulating Multiple Aspects of RNA Metabolism

RNA metabolism is focused on RNA molecules and encompasses all the crucial processes an RNA molecule may or will undergo throughout its life cycle. It is an essential cellular process that allows all cells to function effectively. The transcriptomic landscape of a cell is shaped by the processes such as RNA biosynthesis, maturation (RNA processing, folding, and modification), intra- and inter-cellular transport, transcriptional and post-transcriptional regulation, modification, catabolic decay, and retrograde signaling, all of which are interconnected and are essential for cellular RNA homeostasis. In eukaryotes, sRNAs, typically 20-31 nucleotides in length, are a class of ncRNAs found to function as nodes in various gene regulatory networks. sRNAs are known to play significant roles in regulating RNA population at the transcriptional, post-transcriptional, and translational levels. Along with sRNAs, such as miRNAs, siRNAs, and piRNAs, new categories of ncRNAs, i.e., lncRNAs and circRNAs, also contribute to RNA metabolism regulation in eukaryotes. In plants, various genetic screens have demonstrated that sRNA biogenesis mutants, as well as RNA metabolism pathway mutants, exhibit similar growth and development defects, misregulated primary and secondary metabolism, as well as impaired stress response. In addition, sRNAs are both the "products" and the "regulators" in broad RNA metabolism networks; gene regulatory networks involving sRNAs form autoregulatory loops that affect the expression of both sRNA and the respective target. This review examines the interconnected aspects of RNA metabolism with sRNA regulatory pathways in plants. It also explores the potential conservation of these pathways across different kingdoms, particularly in plants and animals. Additionally, the review highlights how cellular RNA homeostasis directly impacts adaptive responses to environmental changes as well as different developmental aspects in plants.

Revealing critical mechanisms involved in carbon nanosol-mediated tobacco growth using small RNA and mRNA sequencing in silico approach

Nanomaterials have been shown to promote crop growth, yield and stress resistance. Carbon nanosol (CNS), a type of nanomaterial, is used to regulate tobacco shoot and root growth. However, information about the application of CNS to crop plants, especially tobacco, is still limited. Based on differential expression analysis and trend analysis, several miRNAs (miRN21-Novel-5p-mature, miR319b-Probable-5p-mature, miR160a-c-Known/Probable-5p-mature and miR156c-e-Known-5p-mature/star) and their target genes, including transcription factors (TFs), are likely responsible for the effect of CNS on promoting the growth of tobacco plants. In addition, we characterized nine TFs [Nitab4.5_00001789g0110 (NbbZIP), Nitab4.5_00001176g0010 (NbMYB), Nitab4.5_0001366g0010 (NbNAC), Nitab4.5_00000895g013 (NbMYB), Nitab4.5_0001225g0120 (NbNAC), Nitab4.5_0000202g0230 (NbDof), Nitab4.5_0002241g0010 (NbMYB-related), Nitab4.5_0000410g0060 (NbTCP), and Nitab4.5_0000159g0180 (NbC2H2)] associated with the response of tobacco to CNS according to the differential expression analysis, TF‒gene interaction network analysis and weighted correlation network analysis (WGCNA). Taken together, the findings of our study help understand CNS-mediated growth promotion in tobacco plants. The identification of candidate miRNAs and genes will provide potential support for the use of CNS in tobacco.

Integrated analysis of microRNAs and lncRNAs expression profiles reveals regulatory modules during adventitious shoot induction in Moringa oleifera Lam

BACKGROUND

Embryogenic callus (EC) has strong regenerative potential, useful for propagation and genetic transformation. miRNAs have been confirmed to play key regulatory roles in EC regeneration across various plants. However, challenges in EC induction have hindered the breeding of drumstick (Moringa oleifera Lam.), a tree with significant commercial potential. Understanding the regulatory networks of miRNAs-lncRNAs during EC formation in drumstick is crucial for overcoming these barriers.

RESULTS

In this study, three drumstick EC small RNA libraries were sequenced using an Illumina Nova 6000 system. We identified 50 known miRNAs and 233 novel miRNAs. Target prediction and functional analysis showed that these miRNAs are involved in plant hormone signal transduction. Notably, miR319a and miR319b were upregulated throughout the entire process, while miR171 and miR160 were downregulated in the earlier stage but upregulated in the later stage. The expression patterns of 6 miRNAs detected by qRT-PCR were consistent with those observed in RNA-seq. The regulatory relationships between 6 selected highly expressed miRNAs and their target genes generally conformed to a negative regulatory pattern. Furthermore, miR156 and MolncRNA2275 were identified as key regulators in miRNA-mRNA-lncRNA network.

CONCLUSIONS

In summary, our study provides valuable insights into the molecular mechanisms underlying EC formation and enhances the understanding of the miRNA networks involved in this process.

Characterization and expression analysis of the B3 gene family during seed development in Akebia trifoliata

BACKGROUND

B3 genes encode transcription factors that play key roles in plant growth and development. However, the specific B3 genes involved in the seed development of Akebia trifoliata remain unexplored.

RESULTS

A total of 72 AktB3 genes were identified and classified into five subfamilies (ARF, LAV, RAV, HSI, and REM) based on phylogenetic analysis. These 72 AktB3 genes were unevenly distributed across 16 chromosomes. Collinear analysis indicated that segmental duplication has played a significant role in the evolution of AktB3 genes, and underwent purification selection. Expression profiling across seed development stages revealed that seven AktB3 genes, particularly from the LAV subfamily (AktABI3, AktFUS3, AktLEC2), were up-regulated at 70 days after flowering (DAF). Notably, the expression of oleosin exhibited a strong positive correlation with LAV subfamily genes, highlighting their potential roles as hub genes in lipid metabolism and seed development. Yeast two-hybrid (Y2H) and yeast one-hybrid (Y1H) experiments confirmed that AktFUS3-1, AktFUS3-2, and AktLEC2 form protein complexes and individually bind to the AktOLE1 promoter, thereby regulating downstream gene expression. These results provide direct evidence of the cooperative role these transcription factors play in controlling lipid metabolism, particularly related to oleosin proteins. Additionally, miRNA sequencing across three seed developmental stages identified 591 miRNAs and 1,673 target gene pairs. A total of 23 AktB3 genes were predicted to be targets of 20 miRNAs, with 11 miRNAs specifically targeting the ARF subfamily genes. Particularly, miR160-x, miR160-z, and miR167-z were predicted to target ARF subfamily genes, potentially influencing seed development. Moreover, the miRNA-B3 regulatory modules, especially involving ARF genes and miR160/167, require further study to clarify their roles in seed development.

CONCLUSIONS

These findings contribute valuable resources for future functional studies of the molecular regulatory networks governing seed development in A. trifoliata.

Molecular Insights into MpAGO1 and Its Regulatory miRNA, miR11707, in the High-Temperature Acclimation of Marchantia polymorpha

As a model plant for bryophytes, Marchantia polymorpha offers insights into the role of RNA silencing in aiding early land plants navigate the challenges posed by high-temperature environments. Genomic analysis revealed unique ARGONAUTE1 ortholog gene (MpAGO1) in M. polymorpha, which is regulated by two species-specific microRNAs (miRNAs), miR11707.1 and miR11707.2. Comparative studies of small RNA profiles from M. polymorpha cellular and MpAGO1 immunoprecipitation (MpAGO1-IP) profiles at various temperatures, along with analyses of Arabidopsis AGO1 (AtAGO1), revealed that MpAGO1 has a low selectivity for a diverse range of small RNA species than AtAGO1. Protein structural comparisons revealed no discernible differences in the guide strand small RNA recognition middle domain, MID domain, of MpAGO1 and AtAGO1, suggesting the complexity of miRNA species specificity and necessitating further exploration. Small RNA profiling and size exclusion chromatography have pinpointed a subset of M. polymorpha miRNAs, notably miR11707, that remain in free form within the cell at 22°C but are loaded into MpAGO1 at 28°C to engage in RNA silencing. Investigations into the mir11707 gene editing (mir11707ge) mutants provided evidence of the regulation of miR11707 in MpAGO1. Notably, while MpAGO1 mRNA expression decreases at 28°C, the stability of the MpAGO1 protein and its associated miRNAs is essential for enhancing the RNA-inducing silencing complex (RISC) activity, revealing the importance of RNA silencing in enabling M. polymorpha to survive thermal stress. This study advances our understanding of RNA silencing in bryophytes and provides groundbreaking insights into the evolutionary resilience of land plants to climatic adversities.

The Biosynthesis Process of Small RNA and Its Pivotal Roles in Plant Development

In the realm of plant biology, small RNAs (sRNAs) are imperative in the orchestration of gene expression, playing pivotal roles across a spectrum of developmental sequences and responses to environmental stressors. The biosynthetic cascade of sRNAs is characterized by an elaborate network of enzymatic pathways that meticulously process double-stranded RNA (dsRNA) precursors into sRNA molecules, typically 20 to 30 nucleotides in length. These sRNAs, chiefly microRNAs (miRNAs) and small interfering RNAs (siRNAs), are integral in guiding the RNA-induced silencing complex (RISC) to selectively target messenger RNAs (mRNAs) for post-transcriptional modulation. This regulation is achieved either through the targeted cleavage or the suppression of translational efficiency of the mRNAs. In plant development, sRNAs are integral to the modulation of key pathways that govern growth patterns, organ differentiation, and developmental timing. The biogenesis of sRNA itself is a fine-tuned process, beginning with transcription and proceeding through a series of processing steps involving Dicer-like enzymes and RNA-binding proteins. Recent advances in the field have illuminated the complex processes underlying the generation and function of small RNAs (sRNAs), including the identification of new sRNA categories and the clarification of their involvement in the intercommunication among diverse regulatory pathways. This review endeavors to evaluate the contemporary comprehension of sRNA biosynthesis and to underscore the pivotal role these molecules play in directing the intricate performance of plant developmental processes.

Knockdown of microRNA390 Enhances Maize Brace Root Growth

Brace root architecture is a critical determinant of maize's stalk anchorage and nutrition uptake, influencing root lodging resistance, stress tolerance, and plant growth. To identify the key microRNAs (miRNAs) in control of maize brace root growth, we performed small RNA sequencing using brace root samples at emergence and growth stages. We focused on the genetic modulation of brace root development in maize through manipulation of miR390 and its downstream regulated auxin response factors (ARFs). In the present study, miR167, miR166, miR172, and miR390 were identified to be involved in maize brace root growth in inbred line B73. Utilizing short tandem target mimic (STTM) technology, we further developed maize lines with reduced miR390 expression and analyzed their root architecture compared to wild-type controls. Our findings show that STTM390 maize lines exhibit enhanced brace root length and increased whorl numbers. Gene expression analyses revealed that the suppression of miR390 leads to upregulation of its downstream regulated ARF genes, specifically ZmARF11 and ZmARF26, which may significantly alter root architecture. Additionally, loss-of-function mutants for ZmARF11 and ZmARF26 were characterized to further confirm the role of these genes in brace root growth. These results demonstrate that miR390, ZmARF11, and ZmARF26 play crucial roles in regulating maize brace root growth; the involved complicated molecular mechanisms need to be further explored. This study provides a genetic basis for breeding maize varieties with improved lodging resistance and adaptability to diverse agricultural environments.

Like mother like son: Transgenerational memory and cross-tolerance from drought to heat stress are identified in chloroplast proteome and seed provisioning in Pinus radiata

How different stressors impact plant health and memory when they are imposed in different generations in wild ecosystems is still scarce. Here, we address how different environments shape heritable memory for the next generation in seeds and seedlings of Pinus radiata, a long-lived species with economic interest. The performance of the seedlings belonging to two wild clonal subpopulations (optimal fertirrigation vs. slightly stressful conditions) was tested under heat stress through physiological profiling and comparative time-series chloroplast proteomics. In addition, we explored the seeds conducting a physiological characterization and targeted transcriptomic profiling in both subpopulations. Our results showed differential responses between them, evidencing a cross-stress transgenerational memory. Seedlings belonging to the stressed subpopulation retained key proteins related to Photosystem II, chloroplast-to-nucleus signalling and osmoprotection which helped to overcome the applied heat stress. The seeds also showed a differential gene expression profile for targeted genes and microRNAs, as well as an increased content of starch and secondary metabolites, molecules which showed potential interest as biomarkers for early selection of primed plants. Thus, these finds not only delve into transgenerational cross-stress memory in trees, but also provide a new biotechnological tool for forest design.

HD-Zip II transcription factors control distal stem cell fate in Arabidopsis roots by linking auxin signaling to the FEZ/SOMBRERO pathway

In multicellular organisms, specialized tissues are generated by specific populations of stem cells through cycles of asymmetric cell divisions, where one daughter undergoes differentiation and the other maintains proliferative properties. In Arabidopsis thaliana roots, the columella - a gravity-sensing tissue that protects and defines the position of the stem cell niche - represents a typical example of a tissue whose organization is exclusively determined by the balance between proliferation and differentiation. The columella derives from a single layer of stem cells through a binary cell fate switch that is precisely controlled by multiple, independent regulatory inputs. Here, we show that the HD-Zip II transcription factors (TFs) HAT3, ATHB4 and AHTB2 redundantly regulate columella stem cell fate and patterning in the Arabidopsis root. The HD-Zip II TFs promote columella stem cell proliferation by acting as effectors of the FEZ/SMB circuit and, at the same time, by interfering with auxin signaling to counteract hormone-induced differentiation. Overall, our work shows that HD-Zip II TFs connect two opposing parallel inputs to fine-tune the balance between proliferation and differentiation in columella stem cells.

A novel miR160a-GmARF16-GmMYC2 module determines soybean salt tolerance and adaptation

Salt stress is a major challenge that has a negative impact on soybean growth and productivity. Therefore, it is important to understand the regulatory mechanism of salt response to ensure soybean yield under such conditions. In this study, we identified and characterized a miR160a-GmARF16-GmMYC2 module and its regulation during the salt-stress response in soybean. miR160a promotes salt tolerance by cleaving GmARF16 transcripts, members of the Auxin Response Factor (ARF) family, which negatively regulates salt tolerance. In turn, GmARF16 activates GmMYC2, encoding a bHLH transcription factor that reduces salinity tolerance by down-regulating proline biosynthesis. Genomic analysis among wild and cultivated soybean accessions identified four distinct GmARF16 haplotypes. Among them, the GmARF16H3 haplotype is preferentially enriched in localities with relatively saline soils, suggesting GmARF16H3 was artificially selected to improve salt tolerance. Our findings therefore provide insights into the molecular mechanisms underlying salt response in soybean and provide valuable genetic targets for the molecular breeding of salt tolerance.

Plant non-coding RNAs: The new frontier for the regulation of plant development and adaptation to stress

Most plant transcriptomes constitute functional non-coding RNAs (ncRNAs) that lack the ability to encode proteins. In recent years, more research has demonstrated that ncRNAs play important regulatory roles in almost all plant biological processes by modulating gene expression. Thus, it is important to study the biogenesis and function of ncRNAs, particularly in plant growth and development and stress tolerance. In this review, we systematically explore the process of formation and regulatory mechanisms of ncRNAs, particularly those of microRNAs (miRNAs), small interfering RNAs (siRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). Additionally, we provide a comprehensive overview of the recent advancements in ncRNAs research, including their regulation of plant growth and development (seed germination, root growth, leaf morphogenesis, floral development, and fruit and seed development) and responses to abiotic and biotic stress (drought, heat, cold, salinity, pathogens and insects). We also discuss research challenges and provide recommendations to advance the understanding of the roles of ncRNAs in agronomic applications.

FvemiR160-FveARF18A-FveAP1/FveFUL module regulates flowering time in woodland strawberry

Flowering is an indicator of plant transformation from vegetative to reproductive growth. miR160 has been shown to have a significant effect on the growth and development of fruits, leaves, and roots of plants or their stress response to environment, but the participation of miR160 in regulating flowering time in plants is unclear. In this study, we found that two FvemiR160s (FvemiR160a/FvemiR160b) mature sequences in strawberry (Fragaria vesca) were consistent. It was displayed that the miR160 mature sequence is highly conserved in various species, and the miR160 mature sequence formed by the 5' arm of the MIR160 precursor was more conserved. Three FveARFs in woodland strawberry were negatively regulated by FvemiR160a, among which FveARF18A was the most significant. Phylogenetic analysis indicated that FvemiR160 is closely related to apple (Malus domestica), grape (Vitis vinifera), and Arabidopsis thaliana, while FveARF18A is closely related to RcARF18. Subsequently, we demonstrated that FvemiR160a can target cutting FveARF18A to negatively regulate its expression by RLM-5' RACE, cleavage site mutation, and GFP fluorescence assay. Moreover, we observed that FveMIR160a overexpressed plants have advanced flowering, while mFveARF18A overexpressed plants have delayed flowering. We also verified that FveARF18A negatively regulates the expression of FveAP1 and FveFUL by binding their promoters by yeast one-hybrid, LUC, and GUS assay, and FveAP1 and FveFUL transgenic Arabidopsis showed early flowering phenotype. In addition, the expression level of FvemiR160a was decreased obviously while that of FveARF18A was increased obviously by MeJA, GA and IAA. In conclusion, our study reveals the important role of the FvemiR160-FveARF18A-FveAP1/FveFUL module in the flowering process of woodland strawberry and provides a new pathway for studying flowering.

RNA Polymerase III-Dependent BoNR8 and AtR8 lncRNAs Contribute to Hypocotyl Elongation in Response to Light and Abscisic Acid

Hypocotyl elongation is inhibited by light and promoted by darkness. The plant hormone abscisic acid (ABA) also inhibits hypocotyl elongation. However, details of the molecular mechanism that regulates the integrated effects of light and ABA signaling on hypocotyl elongation remain unclear. Long non-coding RNAs (lncRNAs; >200 nt) do not encode proteins but play many physiological roles in organisms. Until now, only a few lncRNAs related to hypocotyl elongation have been reported. The lncRNAs BoNR8 (272 nt) and AtR8 (259 nt), both of which are transcribed by RNA polymerase III, are homologous lncRNAs that are abundantly present in cabbage and Arabidopsis, respectively. These lncRNAs shared 77% sequence identity, and their predicted RNA secondary structures were similar; the non-conserved nucleotides in both sequences were positioned mainly in the stem-loop regions of the secondary structures. A previous study showed that BoNR8 regulated seed germination along with ABA and that AtR8 may be involved in innate immune function in Arabidopsis. Our results show that the expression levels of BoNR8 and AtR8 were differentially affected by light and ABA and that overexpression (OX) of both BoNR8 and AtR8 in Arabidopsis regulated hypocotyl elongation depending on light and ABA.. The expression levels of light-related genes PHYB, COP1, HY5 and PIF4 and ABA-related genes ABI3 and ABI5 were altered in the AtR8-OX and BoNR8-OX lines, and, in an ABI3-defective mutant, hypocotyl elongation was greatly increased under dark condition with the addition of ABA. These results indicate that BoNR8 and AtR8 regulate hypocotyl elongation together with ABI3 and key downstream light signaling genes.

Identification and Characterization of PRE Genes in Moso Bamboo (Phyllostachys edulis)

Basic helix-loop-helix (bHLH)/HLH transcription factors are involved in various aspects of the growth and development of plants. Here, we identified four HLH genes, PePRE1-4, in moso bamboo plants that are homologous to Arabidopsis PRE genes. In bamboo seedlings, PePRE1/3 were found to be highly expressed in the internode and lamina joint by using quantitative RT-PCR analysis. In the elongating internode of bamboo shoots, PePRE genes are expressed at higher levels in the basal segment than in the mature top segment. Overexpression of PePREs (PePREs-OX) in Arabidopsis showed longer petioles and hypocotyls, as well as earlier flowering. PePRE1 overexpression restored the phenotype due to the deficiency of AtPRE genes caused by artificial micro-RNA. PePRE1-OX plants showed hypersensitivity to propiconazole treatment compared with the wild type. In addition, PePRE1/3 but not PePRE2/4 proteins accumulated as punctate structures in the cytosol, which was disrupted by the vesicle recycling inhibitor brefeldin A (BFA). PePRE genes have a positive function in the internode elongation of moso bamboo shoots, and overexpression of PePREs genes promotes flowering and growth in Arabidopsis. Our findings provided new insights about the fast-growing mechanism of bamboo shoots and the application of PRE genes from bamboo.

Integrative Analysis of Transcriptome, Proteome, and Phosphoproteome Reveals Potential Roles of Photosynthesis Antenna Proteins in Response to Brassinosteroids Signaling in Maize

Brassinosteroids are a recently discovered group of substances that promote plant growth and productivity. Photosynthesis, which is vital for plant growth and high productivity, is strongly influenced by brassinosteroid signaling. However, the molecular mechanism underlying the photosynthetic response to brassinosteroid signaling in maize remains obscure. Here, we performed integrated transcriptome, proteome, and phosphoproteomic analyses to identify the key photosynthesis pathway that responds to brassinosteroid signaling. Transcriptome analysis suggested that photosynthesis antenna proteins and carotenoid biosynthesis, plant hormone signal transduction, and MAPK signaling in CK VS EBR and CK VS Brz were significantly enriched in the list of differentially expressed genes upon brassinosteroids treatment. Consistently, proteome and phosphoproteomic analyses indicated that photosynthesis antenna and photosynthesis proteins were significantly enriched in the list of differentially expressed proteins. Thus, transcriptome, proteome, and phosphoproteome analyses showed that major genes and proteins related to photosynthesis antenna proteins were upregulated by brassinosteroids treatment in a dose-dependent manner. Meanwhile, 42 and 186 transcription factor (TF) responses to brassinosteroid signals in maize leaves were identified in the CK VS EBR and CK VS Brz groups, respectively. Our study provides valuable information for a better understanding of the molecular mechanism underlying the photosynthetic response to brassinosteroid signaling in maize.

Profiling of phytohormone-specific microRNAs and characterization of the miR160-ARF1 module involved in glandular trichome development and artemisinin biosynthesis in Artemisia annua

MicroRNAs (miRNAs) play crucial roles in plant development and secondary metabolism through different modes of sequence-specific interaction with their targets. Artemisinin biosynthesis is extensively regulated by phytohormones. However, the function of phytohormone-responsive miRNAs in artemisinin biosynthesis remains enigmatic. Thus, we combined the analysis of transcriptomics, small RNAs, and the degradome to generate a comprehensive resource for identifying key miRNA-target circuits involved in the phytohormone-induced process of artemisinin biosynthesis in Artemisia annua. In total, 151 conserved and 52 novel miRNAs and their 4132 targets were determined. Based on the differential expression analysis, miR160 was selected as a potential miRNA involved in artemisinin synthesis. Overexpressing MIR160 significantly impaired glandular trichome formation and suppressed artemisinin biosynthesis in A. annua, while repressing its expression resulted in the opposite effect, indicating that miR160 negatively regulates glandular trichome development and artemisinin biosynthesis. RNA ligase-mediated 5' RACE and transient transformation assays showed that miR160 mediates the RNA cleavage of Auxin Response Factor 1 (ARF1) in A. annua. Furthermore, ARF1 was shown to increase artemisinin synthesis by activating AaDBR2 expression. Taken together, our results reveal the intrinsic link between the miR160-ARF1 module and artemisinin biosynthesis, and may expedite the innovation of metabolic engineering approaches for high and stable production of artemisinin in the future.

Integrative Analysis of miRNAs and Their Targets Involved in Ray Floret Growth in Gerbera hybrida

MicroRNAs (miRNAs) are involved in regulating many aspects of plant growth and development at the post-transcriptional level. Gerbera (Gerbera hybrida) is an important ornamental crop. However, the role of miRNAs in the growth and development of gerbera is still unclear. In this study, we used high-throughput sequencing to analyze the expression profiles of miRNAs in ray floret during inflorescence opening. A total of 164 miRNAs were obtained, comprising 24 conserved miRNAs and 140 novel miRNAs. Ten conserved and 15 novel miRNAs were differentially expressed during ray floret growth, and 607 differentially expressed target genes of these differentially expressed miRNAs were identified using psRNATarget. We performed a comprehensive analysis of the expression profiles of the miRNAs and their targets. The changes in expression of five miRNAs (ghy-miR156, ghy-miR164, ghy-miRn24, ghy-miRn75 and ghy-miRn133) were inversely correlated with the changes in expression of their eight target genes. The miRNA cleavage sites in candidate target gene mRNAs were determined using 5′-RLM-RACE. Several miRNA-mRNA pairs were predicted to regulate ray floret growth and anthocyanin biosynthesis. In conclusion, the results of small RNA sequencing provide valuable information to reveal the mechanisms of miRNA-mediated ray floret growth and anthocyanin accumulation in gerbera.

Identification of ARF family in blueberry and its potential involvement of fruit development and pH stress response

Background

Auxin responsive factor (ARF) family is one of core components in auxin signalling pathway, which governs diverse developmental processes and stress responses. Blueberry is an economically important berry-bearing crop and prefers to acidic soil. However, the understandings of ARF family has not yet been reported in blueberry.

Results

In the present study, 60 ARF genes (VcARF) were identified in blueberry, and they showed diverse gene structures and motif compositions among the groups and similar within each group in the phylogenetic tree. Noticeably, 9 digenic, 5 trigenic and 6 tetragenic VcARF pairs exhibited more than 95% identity to each other. Computational analysis indicated that 23 VcARFs harbored the miRNA responsive element (MRE) of miR160 or miR167 like other plant ARF genes. Interestingly, the MRE of miR156d/h-3p was observed in the 5’UTR of 3 VcARFs, suggesting a potentially novel post-transcriptional control. Furthermore, the transcript accumulations of VcARFs were investigated during fruit development, and three categories of transcript profiles were observed, implying different functional roles. Meanwhile, the expressions of VcARFs to different pH conditions (pH4.5 and pH6.5) were surveyed in pH-sensitive and tolerant blueberry species, and a number of VcARFs showed different transcript accumulations. More importantly, distinct transcriptional response to pH stress (pH6.5) were observed for several VcARFs (such as VcARF6s and VcARF19-3/19–4) between pH-sensitive and tolerant species, suggesting their potential roles in adaption to pH stress.

Conclusions

Sixty VcARF genes were identified and characterized, and their transcript profiles were surveyed during fruit development and in response to pH stress. These findings will contribute to future research for eliciting the functional roles of VcARFs and regulatory mechanisms, especially fruit development and adaption to pH stress.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08556-y.

The Characters of Non-Coding RNAs and Their Biological Roles in Plant Development and Abiotic Stress Response

Plant growth and development are greatly affected by the environment. Many genes have been identified to be involved in regulating plant development and adaption of abiotic stress. Apart from protein-coding genes, more and more evidence indicates that non-coding RNAs (ncRNAs), including small RNAs and long ncRNAs (lncRNAs), can target plant developmental and stress-responsive mRNAs, regulatory genes, DNA regulatory regions, and proteins to regulate the transcription of various genes at the transcriptional, posttranscriptional, and epigenetic level. Currently, the molecular regulatory mechanisms of sRNAs and lncRNAs controlling plant development and abiotic response are being deeply explored. In this review, we summarize the recent research progress of small RNAs and lncRNAs in plants, focusing on the signal factors, expression characters, targets functions, and interplay network of ncRNAs and their targets in plant development and abiotic stress responses. The complex molecular regulatory pathways among small RNAs, lncRNAs, and targets in plants are also discussed. Understanding molecular mechanisms and functional implications of ncRNAs in various abiotic stress responses and development will benefit us in regard to the use of ncRNAs as potential character-determining factors in molecular plant breeding.

miR160 Interacts in vivo With Pinus pinaster AUXIN RESPONSE FACTOR 18 Target Site and Negatively Regulates Its Expression During Conifer Somatic Embryo Development

MicroRNAs (miRNAs) are key regulators of several plant developmental processes including embryogenesis. Most miRNA families are conserved across major groups of plant species, but their regulatory roles have been studied mainly in model species like Arabidopsis and other angiosperms. In gymnosperms, miRNA-dependent regulation has been less studied since functional approaches in these species are often difficult to establish. Given the fundamental roles of auxin signaling in somatic embryogenesis (SE) induction and embryo development, we investigated a previously predicted interaction between miR160 and a putative target encoding AUXIN RESPONSE FACTOR 18 in Pinus pinaster (PpARF18) embryonic tissues. Phylogenetic analysis of AUXIN RESPONSE FACTOR 18 (ARF18) from Pinus pinaster and Picea abies, used here as a model system of conifer embryogenesis, showed their close relatedness to AUXIN RESPONSE FACTOR (ARF) genes known to be targeted by miR160 in other species, including Arabidopsis ARF10 and ARF16. By using a luciferase (LUC) reporter system for miRNA activity in Arabidopsis protoplasts, we have confirmed that P. pinaster miR160 (ppi-miR160) interacts in vivo with PpARF18 target site. When the primary miR160 from P. pinaster was overexpressed in protoplasts under non-limiting levels of ARGONAUTE1, a significant increase of miR160 target cleavage activity was observed. In contrast, co-expression of the primary miRNA and the target mimic MIM160 led to a decrease of miR160 activity. Our results further support that this interaction is functional during consecutive stages of SE in the conifer model P. abies. Expression analyses conducted in five stages of development, from proembryogenic masses (PEMs) to the mature embryo, show that conifer ARF18 is negatively regulated by miR160 toward the fully developed mature embryo when miR160 reached its highest expression level. This study reports the first in vivo validation of a predicted target site of a conifer miRNA supporting the conservation of miR160 interaction with ARF targets in gymnosperms. The approach used here should be useful for future characterization of miRNA functions in conifer embryogenesis.

Feedback Inhibition Might Dominate the Accumulation Pattern of BR in the New Shoots of Tea Plants (Camellia sinensis)

Brassinosteroid (BR), a kind of polyhydroxylated steroid hormone, plays an important role in physiological and biochemical processes in plants. Studies were mainly focused on BR signaling and its exogenous spraying to help enhance crop yields. Few research studies are centered on the accumulation pattern of BR and its mechanism. Yet, it is crucial to unlock the mystery of the function of BR and its cross action with other hormones. Tea (Camellia sinensis (L.) O. Kuntze) is one of the important economic crops in some countries, and new shoots are the raw materials for the preparation of various tea products. Different concentrations of exogenous BR were reported to have different effects on growth and development. New shoots of tea plants can thus be considered a valuable research object to study the accumulation pattern of BR. In this study, the quantity of five BR components (brassinolide, 28-norbrassinolide, 28-homobrassinolide, castasterone, and 28-norcastasterone) in different tissues of tea plants, including buds (Bud), different maturity of leaves (L1, L2), and stems (S1, S2) were determined by UPLC-MS/MS. A total of 15 cDNA libraries of the same tissue with three repetitions for each were constructed and sequenced. The BR-accumulation pattern and gene expression pattern were combined together for weighted gene co-expression network analysis (WGCNA). BR-accumulation-relative genes were then screened using two methods, based on the K.in value and BR biosynthetic pathway (ko00905), respectively. The result showed that photosynthesis-related genes and CYP450 family genes were actively involved and might play important roles in BR accumulation and/or its accumulation pattern. First and foremost, feedback inhibition was more likely to dominate the accumulation pattern of BR in the new shoots of tea plants. Moreover, three conserved miRNAs with their target transcriptional factors and target mRNAs had been figured out from negative correlation modules that might be strongly linked to the BR-accumulation pattern. Our study provided an experimental basis for the role of BR in tea plants. The excavation of genes related to the accumulation pattern of BR provided the possibility of cross-action studies on the regulation of BR biosynthesis and the study between BR and other hormones.

microRNAs and Their Roles in Plant Development

Small RNAs are short non-coding RNAs with a length ranging between 20 and 24 nucleotides. Of these, microRNAs (miRNAs) play a distinct role in plant development. miRNAs control target gene expression at the post-transcriptional level, either through direct cleavage or inhibition of translation. miRNAs participate in nearly all the developmental processes in plants, such as juvenile-to-adult transition, shoot apical meristem development, leaf morphogenesis, floral organ formation, and flowering time determination. This review summarizes the research progress in miRNA-mediated gene regulation and its role in plant development, to provide the basis for further in-depth exploration regarding the function of miRNAs and the elucidation of the molecular mechanism underlying the interaction of miRNAs and other pathways.

miR160: An Indispensable Regulator in Plant

MicroRNAs (miRNA), recognized as crucial regulators of gene expression at the posttranscriptional level, have been found to be involved in the biological processes of plants. Some miRNAs are up- or down-regulated during plant development, stress response, and secondary metabolism. Over the past few years, it has been proved that miR160 is directly related to the developments of different tissues and organs in multifarious species, as well as plant-environment interactions. This review highlights the recent progress on the contributions of the miR160-ARF module to important traits of plants and the role of miR160-centered gene regulatory network in coordinating growth with endogenous and environmental factors. The manipulation of miR160-guided gene regulation may provide a new method to engineer plants with improved adaptability and yield.

Integration of small RNA, degradome, and transcriptome sequencing data illustrates the mechanism of low phosphorus adaptation in Camellia oleifera

Phosphorus (P) is an indispensable macronutrient for plant growth and development, and it is involved in various cellular biological activities in plants. Camellia oleifera is a unique high-quality woody oil plant that grows in the hills and mountains of southern China. However, the available P content is deficient in southern woodland soil. Until now, few studies focused on the regulatory functions of microRNAs (miRNAs) and their target genes under low inorganic phosphate (Pi) stress. In this study, we integrated small RNA, degradome, and transcriptome sequencing data to investigate the mechanism of low Pi adaptation in C. oleifera. We identified 40,689 unigenes and 386 miRNAs by the deep sequencing technology and divided the miRNAs into four different groups. We found 32 miRNAs which were differentially expressed under low Pi treatment. A total of 414 target genes of 108 miRNAs were verified by degradome sequencing. Gene ontology (GO) functional analysis of target genes found that they were related to the signal response to the stimulus and transporter activity, indicating that they may respond to low Pi stress. The integrated analysis revealed that 31 miRNA-target pairs had negatively correlated expression patterns. A co-expression regulatory network was established based on the profiles of differentially expressed genes. In total, three hub genes (ARF22, WRKY53, and SCL6), which were the targets of differentially expressed miRNAs, were discovered. Our results showed that integrated analyses of the small RNA, degradome, and transcriptome sequencing data provided a valuable basis for investigating low Pi in C. oleifera and offer new perspectives on the mechanism of low Pi tolerance in woody oil plants.

Biogenesis, Trafficking, and Function of Small RNAs in Plants

Small RNAs (sRNAs) encoded by plant genomes have received widespread attention because they can affect multiple biological processes. Different sRNAs that are synthesized in plant cells can move throughout the plants, transport to plant pathogens via extracellular vesicles (EVs), and transfer to mammals via food. Small RNAs function at the target sites through DNA methylation, RNA interference, and translational repression. In this article, we reviewed the systematic processes of sRNA biogenesis, trafficking, and the underlying mechanisms of its functions.

Plant RNA-mediated gene regulatory network

Not all transcribed RNAs are protein-coding RNAs. Many of them are non-protein-coding RNAs in diverse eukaryotes. However, some of them seem to be non-functional and are resulted from spurious transcription. A lot of non-protein-coding transcripts have a significant function in the translation process. Gene expressions depend on complex networks of diverse gene regulatory pathways. Several non-protein-coding RNAs regulate gene expression in a sequence-specific system either at the transcriptional level or post-transcriptional level. They include a significant part of the gene expression regulatory network. RNA-mediated gene regulation machinery is evolutionarily ancient. They well-evolved during the evolutionary time and are becoming much more complex than had been expected. In this review, we are trying to summarizing the current knowledge in the field of RNA-mediated gene silencing.

Comparative Transcriptome Analysis Reveals Regulatory Networks during the Maize Ear Shank Elongation Process

In maize, the ear shank is a short branch that connects the ear to the stalk. The length of the ear shank mainly affects the transportation of photosynthetic products to the ear, and also influences the dehydration of the grain by adjusting the tightness of the husks. However, the molecular mechanisms of maize shank elongation have rarely been described. It has been reported that the maize ear shank length is a quantitative trait, but its genetic basis is still unclear. In this study, RNA-seq was performed to explore the transcriptional dynamics and determine the key genes involved in maize shank elongation at four different developmental stages. A total of 8145 differentially expressed genes (DEGs) were identified, including 729 transcription factors (TFs). Some important genes which participate in shank elongation were detected via function annotation and temporal expression pattern analyses, including genes related to signal transduction hormones (auxin, brassinosteroids, gibberellin, etc.), xyloglucan and xyloglucan xyloglucosyl transferase, and transcription factor families. The results provide insights into the genetic architecture of maize ear shanks and developing new varieties with ideal ear shank lengths, enabling adjustments for mechanized harvesting in the future.