Arabidopsis miR171-targeted scarecrow-like proteins bind to GT cis-elements and mediate gibberellin-regulated chlorophyll biosynthesis under light conditions

ScRNA-seq reveals dark- and light-induced differentially expressed gene atlases of seedling leaves in Arachis hypogaea L

Although the regulatory mechanisms of dark and light-induced plant morphogenesis have been broadly investigated, the biological process in peanuts has not been systematically explored on single-cell resolution. Herein, 10 cell clusters were characterized using scRNA-seq-identified marker genes, based on 13 409 and 11 296 single cells from 1-week-old peanut seedling leaves grown under dark and light conditions. 6104 genes and 50 transcription factors (TFs) displayed significant expression patterns in distinct cell clusters, which provided gene resources for profiling dark/light-induced candidate genes. Further pseudo-time trajectory and cell cycle evidence supported that dark repressed the cell division and perturbed normal cell cycle, especially the PORA abundances correlated with 11 TFs highly enriched in mesophyll to restrict the chlorophyllide synthesis. Additionally, light repressed the epidermis cell developmental trajectory extending by inhibiting the growth hormone pathway, and 21 TFs probably contributed to the different genes transcriptional dynamic. Eventually, peanut AHL17 was identified from the profile of differentially expressed TFs, which encoded protein located in the nucleus promoted leaf epidermal cell enlargement when ectopically overexpressed in Arabidopsis through the regulatory phytohormone pathway. Overall, our study presents the different gene atlases in peanut etiolated and green seedlings, providing novel biological insights to elucidate light-induced leaf cell development at the single-cell level.

Molecular Mimicry of Transposable Elements in Plants

Transposable elements (TEs) are mobile DNA elements that are particularly abundant in the plant genomes. They have long been considered as junk DNA; however, a growing body of evidence suggests that TE insertions promote genetic diversity that is essential for the adaptive evolution of a species. Thus far, studies have mainly investigated the cis-acting regulatory roles of TEs generated by their insertions nearby or within the host genes. However, the trans-acting effects of TE-derived RNA and DNA remained obscure to date. TEs contain various regulatory elements within their sequences that can accommodate the binding of specific RNAs and proteins. Recently, it was suggested that some of these cellular regulators are shared between TEs and the host genes, and the competition for the common host factors underlies the fine-tuned developmental reprogramming. In this review, we will highlight and discuss the latest discoveries on the biological functions of plant TEs, with a particular focus on their competitive binding with specific developmental regulators.

Transcriptome and small RNA analysis unveils novel insights into the C4 gene regulation in sugarcane

MAIN CONCLUSION

This study reveals miRNA indirect regulation of C4 genes in sugarcane through transcription factors, highlighting potential key regulators like SsHAM3a. C4 photosynthesis is crucial for the high productivity and biomass of sugarcane, however, the miRNA regulation of C4 genes in sugarcane remains elusive. We have identified 384 miRNAs along the leaf gradients, including 293 known miRNAs and 91 novel miRNAs. Among these, 86 unique miRNAs exhibited differential expression patterns, and we identified 3511 potential expressed targets of these differentially expressed miRNAs (DEmiRNAs). Analyses using Pearson correlation coefficient (PCC) and Gene Ontology (GO) enrichment revealed that targets of miRNAs with positive correlations are integral to chlorophyll-related photosynthetic processes. In contrast, negatively correlated pairs are primarily associated with metabolic functions. It is worth noting that no C4 genes were predicted as targets of DEmiRNAs. Our application of weighted gene co-expression network analysis (WGCNA) led to a gene regulatory network (GRN) suggesting miRNAs might indirectly regulate C4 genes via transcription factors (TFs). The GRAS TF SsHAM3a emerged as a potential regulator of C4 genes, targeted by miR171y and miR171am, and exhibiting a negative correlation with miRNA expression along the leaf gradient. This study sheds light on the complex involvement of miRNAs in regulating C4 genes, offering a foundation for future research into enhancing sugarcane's photosynthetic efficiency.

GRAS gene family in rye (Secale cereale L.): genome-wide identification, phylogeny, evolutionary expansion and expression analyses

BACKGROUND

The GRAS transcription factor family plays a crucial role in various biological processes in different plants, such as tissue development, fruit maturation, and environmental stress. However, the GRAS family in rye has not been systematically analyzed yet.

RESULTS

In this study, 67 GRAS genes in S. cereale were identified and named based on the chromosomal location. The gene structures, conserved motifs, cis-acting elements, gene replications, and expression patterns were further analyzed. These 67 ScGRAS members are divided into 13 subfamilies. All members include the LHR I, VHIID, LHR II, PFYRE, and SAW domains, and some nonpolar hydrophobic amino acid residues may undergo cross-substitution in the VHIID region. Interested, tandem duplications may have a more important contribution, which distinguishes them from other monocotyledonous plants. To further investigate the evolutionary relationship of the GRAS family, we constructed six comparative genomic maps of homologous genes between rye and different representative monocotyledonous and dicotyledonous plants. The response characteristics of 19 ScGRAS members from different subfamilies to different tissues, grains at filling stages, and different abiotic stresses of rye were systematically analyzed. Paclobutrazol, a triazole-based plant growth regulator, controls plant tissue and grain development by inhibiting gibberellic acid (GA) biosynthesis through the regulation of DELLA proteins. Exogenous spraying of paclobutrazol significantly reduced the plant height but was beneficial for increasing the weight of 1000 grains of rye. Treatment with paclobutrazol, significantly reduced gibberellin levels in grain in the filling period, caused significant alteration in the expression of the DELLA subfamily gene members. Furthermore, our findings with respect to genes, ScGRAS46 and ScGRAS60, suggest that these two family members could be further used for functional characterization studies in basic research and in breeding programmes for crop improvement.

CONCLUSIONS

We identified 67 ScGRAS genes in rye and further analysed the evolution and expression patterns of the encoded proteins. This study will be helpful for further analysing the functional characteristics of ScGRAS genes.

Network of GRAS transcription factors in plant development, fruit ripening and stress responses

The plant-specific family of GRAS transcription factors has been wide implicated in the regulation of transcriptional reprogramming associated with a diversity of biological functions ranging from plant development processes to stress responses. Functional analyses of GRAS transcription factors supported by in silico structural and comparative analyses are emerging and clarifying the regulatory networks associated with their biological roles. In this review, a detailed analysis of GRAS proteins' structure and biochemical features as revealed by recent discoveries indicated how these characteristics may impact subcellular location, molecular mechanisms, and function. Nomenclature issues associated with GRAS classification into different subfamilies in diverse plant species even in the presence of robust genomic resources are discussed, in particular how it affects assumptions of biological function. Insights into the mechanisms driving evolution of this gene family and how genetic and epigenetic regulation of GRAS contributes to subfunctionalization are provided. Finally, this review debates challenges and future perspectives on the application of this complex but promising gene family for crop improvement to cope with challenges of environmental transition.

Conserved and non-conserved RNA-target modules in plants: lessons for a better understanding of Marchantia development

A wide variety of functional regulatory non-coding RNAs (ncRNAs) have been identified as essential regulators of plant growth and development. Depending on their category, ncRNAs are not only involved in modulating target gene expression at the transcriptional and post-transcriptional levels but also are involved in processes like RNA splicing and RNA-directed DNA methylation. To fulfill their molecular roles properly, ncRNAs must be precisely processed by multiprotein complexes. In the case of small RNAs, DICER-LIKE (DCL) proteins play critical roles in the production of mature molecules. Land plant genomes contain at least four distinct classes of DCL family proteins (DCL1-DCL4), of which DCL1, DCL3 and DCL4 are also present in the genomes of bryophytes, indicating the early divergence of these genes. The liverwort Marchantia polymorpha has become an attractive model species for investigating the evolutionary history of regulatory ncRNAs and proteins that are responsible for ncRNA biogenesis. Recent studies on Marchantia have started to uncover the similarities and differences in ncRNA production and function between the basal lineage of bryophytes and other land plants. In this review, we summarize findings on the essential role of regulatory ncRNAs in Marchantia development. We provide a comprehensive overview of conserved ncRNA-target modules among M. polymorpha, the moss Physcomitrium patens and the dicot Arabidopsis thaliana, as well as Marchantia-specific modules. Based on functional studies and data from the literature, we propose new connections between regulatory pathways involved in Marchantia's vegetative and reproductive development and emphasize the need for further functional studies to understand the molecular mechanisms that control ncRNA-directed developmental processes.

Genome-wide identification and expression analysis of the GRAS gene family under abiotic stresses in wheat (Triticum aestivum L.)

The GRAS transcription factors are multifunctional proteins involved in various biological processes, encompassing plant growth, metabolism, and responses to both abiotic and biotic stresses. Wheat is an important cereal crop cultivated worldwide. However, no systematic study of the GRAS gene family and their functions under heat, drought, and salt stress tolerance and molecular dynamics modeling in wheat has been reported. In the present study, we identified the GRAS gene in Triticum aestivum through systematically performing gene structure analysis, chromosomal location, conserved motif, phylogenetic relationship, and expression patterns. A total of 177 GRAS genes were identified within the wheat genome. Based on phylogenetic analysis, these genes were categorically placed into 14 distinct subfamilies. Detailed analysis of the genetic architecture revealed that the majority of TaGRAS genes had no intronic regions. The expansion of the wheat GRAS gene family was proven to be influenced by both segmental and tandem duplication events. The study of collinearity events between TaGRAS and analogous orthologs from other plant species provided valuable insights into the evolution of the GRAS gene family in wheat. It is noteworthy that the promoter regions of TaGRAS genes consistently displayed an array of cis-acting elements that are associated with stress responses and hormone regulation. Additionally, we discovered 14 miRNAs that target key genes involved in three stress-responsive pathways in our study. Moreover, an assessment of RNA-seq data and qRT-PCR results revealed a significant increase in the expression of TaGRAS genes during abiotic stress. These findings highlight the crucial role of TaGRAS genes in mediating responses to different environmental stresses. Our research delved into the molecular dynamics and structural aspects of GRAS domain-DNA interactions, marking the first instance of such information being generated. Overall, the current findings contribute to our understanding of the organization of the GRAS genes in the wheat genome. Furthermore, we identified TaGRAS27 as a candidate gene for functional research, and to improve abiotic stress tolerance in the wheat by molecular breeding.

Small RNA sequencing provides insights into molecular mechanism of flower development in Rhododendron pulchrum Sweet

Rhododendron pulchrum sweet, a member of the Ericaceae family possessing valuable horticultural properties, is widely distributed in the temperate regions. Though serving as bioindicator of metal pollution, the molecular mechanism regulating flowering in R. pulchrum is very limited. Illumina sequencing was performed to identify critical miRNAs in the synthesis of flavonoids at different developmental stages. Totally, 722 miRNAs belonging to 104 families were screened, and 84 novel mature miRNA sequences were predicted. The miR166, miR156, and miR167-1 families were dominant. In particular, 126 miRNAs were significantly differentially expressed among four different flowering stages. Totally, 593 genes were differentially regulated by miRNAs during the flower development process, which were mostly involved in "metabolic pathways", "plant hormone signal transduction", and "mitosis and regulation of biosynthetic processes". In pigment biosynthesis and signal transduction processes, gra-miR750 significantly regulated the expression of flavonoid 3',5'-hydroxylase; aof-miR171a, aof-miR171b, aof-miR171c, cas-miR171a-3p, and cas-miR171c-3p could regulate the expression of DELLA protein; aof-miR390, aof-miR396b, ath-miR3932b-5p, cas-miR171a-3p, aof-miR171a, and aof-miR171b regulated BAK1 expression. This research showed great potentials for genetic improvement of flower color traits for R. pulchrum and other Rhododendron species.

The cotton miR171a-SCL6 module mediates plant resistance through regulating GhPR1 expression

Plants have developed intricate defense mechanisms in response to fluctuating environmental cues, including the use of microRNA (miRNA) as post-transcriptional regulators. However, the specific mechanisms through which miRNA contributes to disease resistance remain largely elusive. While the miR171-SCLs have been investigated in an eclectic array of plants, there has been a notable scarcity of research specifically focused on cotton (Gossypium hirsutum). In our previous miRNA-sequencing analysis, we found that ghr-miR171a displayed a differential response to infections by Verticillium dahliae. In this study, we further investigated the function of the miR171a-SCL6 module in cotton during V. dahliae infection. The ghr-miR171a was confirmed to direct the cleavage of GhSCL6 mRNA in the post-transcriptional process, as evidenced by 5' RLM-RACE, β-glucuronidase (GUS) histochemical staining and enzyme activity assay. Interestingly, we found that overexpressing ghr-miR171a reduced cotton plants' resistance to V. dahliae, while suppressing ghr-miR171a increased the plants' defense capacity. The GhSCL6 protein, when fused with green fluorescent protein (GFP), localizes in the cell nucleus, indicating its potential role in gene regulation. This was further corroborated by yeast two-hybrid assays, which verified GhSCL6's transcriptional activation ability. Through quantitative reverse transcriptase PCR (qRT-PCR), luciferase (LUC) fluorescence, and yeast one-hybrid assays, we found that GhSCL6 binds to the GT-box element of the GhPR1 promoter, activating its expression and thereby enhancing plant disease resistance. Taken together, our findings demonstrate that the cotton miR171a-SCL6 module regulates Verticillium wilt resistance in plants through the post-transcriptional process. This insight may offer new perspectives for disease resistance strategies in cotton.

mRNA-Seq and miRNA-Seq Analyses Provide Insights into the Mechanism of Pinellia ternata Bulbil Initiation Induced by Phytohormones

Pinellia ternata (Thunb.) Breit (abbreviated as P. ternata) is a plant with an important medicinal value whose yield is restricted by many factors, such as low reproductive efficiency and continuous cropping obstacles. As an essential breeding material for P. ternata growth and production, the bulbils have significant advantages such as a high survival rate and short breeding cycles. However, the location effect, influencing factors, and molecular mechanism of bulbil occurrence and formation have not been fully explored. In this study, exogenously applied phytohormones were used to induce in vitro petiole of P. ternata to produce bulbil structure. Transcriptome sequencing of mRNA and miRNA were performed in the induced petiole (TCp) and the induced bulbil (TCb). Gene Ontology (GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed for the identification of key genes and pathways involved in bulbil development. A total of 58,019 differentially expressed genes (DEGs) were identified. The GO and KEGG analysis indicated that DEGs were mainly enriched in plant hormone signal transduction and the starch and sucrose metabolism pathway. The expression profiles of miR167a, miR171a, and miR156a during bulbil induction were verified by qRT-PCR, indicating that these three miRNAs and their target genes may be involved in the process of bulbil induction and play an important role. However, further molecular biological experiments are required to confirm the functions of the identified bulbil development-related miRNAs and targets.

Role of microRNA miR171 in plant development

MicroRNAs (miRNAs) are endogenous non-coding small RNA with 19-24 nucleotides (nts) in length, which play an essential role in regulating gene expression at the post-transcriptional level. As one of the first miRNAs found in plants, miR171 is a typical class of conserved miRNAs. The miR171 sequences among different species are highly similar, and the vast majority of them have both "GAGCCG" and "CAAUAU" fragments. In addition to being involved in plant growth and development, hormone signaling and stress response, miR171 also plays multiple and important roles in plants through interactions with microbe and other small-RNAs. The miRNA functions by regulating the expression of target genes. Most of miR171's target genes are in the GRAS gene family, but also include some NSP, miRNAs, lncRNAs, and other genes. This review is intended to summarize recent updates on miR171 regarding its function in plant life and hopefully provide new ideas for understanding miR171 function and regulatory mechanisms.

Role of plant microRNAs and their corresponding pathways in fluctuating light conditions

In recent years, it has been established that microRNAs (miRNAs) are critical for various plant physiological regulations in numerous species. Next-generation sequencing technologies have aided to our understandings related to the critical role of miRNAs during environmental stress conditions and plant development. Light influences not just miRNA accumulation but also their biological activities via regulating miRNA gene transcription, biosynthesis, and RNA-induced silencing complex (RISC) activity. Light-regulated routes, processes, and activities can all be affected by miRNAs. Here, we will explore how light affects miRNA gene expression and how conserved and novel miRNAs exhibit altered expression across different plant species in response to variable light quality. Here, we will mainly discuss recent advances in understanding how miRNAs are involved in photomorphogenesis, and photoperiod-dependent plant biological processes such as cell proliferation, metabolism, chlorophyll pigment synthesis and axillary bud growth. The review concludes by presenting future prospects via hoping that light-responsive miRNAs can be exploited in a better way to engineer economically important crops to ensure future food security.

Silencing of SlMYB50 affects tolerance to drought and salt stress in tomato

High salinity and drought stresses often cause plants to produce ROS, including hydrogen peroxide (H₂O₂) and superoxide (O₂^-), which interfere with plant growth and affect crop yield. The transcription factors of the MYB family are involved in responses to biotic and abiotic stresses. Here, we isolated the R2R3-MYB transcription factor gene SlMYB50 and found that silencing of SlMYB50 increased resistance to PEG 6000, mannitol and salt. In addition, the resistance of transgenic tomatoes increased under high salt and drought stress. After stress treatment, the relative water content, chlorophyll content (critical for carbon fixation) and root vitality of the SlMYB50-RNAi lines were higher than those of the wild-type (WT). The opposite was true the water loss rate, relative conductivity, and MDA (as a sign of cell wall disruption). Under drought stress conditions, SlMYB50-silenced lines exhibited less H₂O₂ and less O₂^- accumulation, as well as higher CAT enzyme activity, than were exhibited by the WT. Notably, after stress treatment, the expression levels of chlorophyll-synthesis-related, flavonoid-synthesis-related, carotenoid-related, antioxidant-enzyme-related and ABA-biosynthesis-related genes were all upregulated in SlMYB50-silenced lines compared to those of WT. A dual-luciferase reporter system was used to verify that SlMYB50 could bind to the CHS1 promoter. In summary, this study identified essential roles for SlMYB50 in regulating drought and salt tolerance.

Unveiling gene expression regulation of the Bacillus thuringiensis Cry3Aa toxin receptor ADAM10 by the potato dietary miR171c in Colorado potato beetle

BACKGROUND

The Colorado potato beetle (CPB) is a worldwide devastating pest of potato plants and other Solanaceae characterized by its remarkable ability to evolve resistance to insecticides. Bacillus thuringiensis (Bt) Cry3Aa toxin represents an environmentally safe alternative for CPB control but larvae susceptibility to this toxin has been reported to vary depending on the host plant on which larvae feed. To gain more insight into how nutrition mediates Bt tolerance through effects on gene expression, here we explored the post-transcriptional regulation by microRNAs (miRNAs) of the CPB-ADAM10 gene encoding the Cry3Aa toxin functional receptor ADAM10.

RESULTS

The lower CPB-ADAM10 gene expression in CPB larvae fed on potato plants cv. Vivaldi than those fed on potato cv. Monalisa or tomato plants was inversely related to Cry3Aa toxicity. By high-throughput sequencing we identified seven CPB miRNAs and one potato miRNA predicted to base pair with the CPB-ADAM10 messenger RNA. No differential expression of the endogenous lde-miR1175-5p was found in larvae feeding on any of the two potato plant varieties. However, statistically significant increased amounts of potato stu-miR171c-5p were detected in CPB larvae fed on potato cv. Vivaldi compared to larvae fed on potato cv. Monalisa.

CONCLUSION

Our results support a role for dietary miRNAs in Bt toxicity by regulating the CPB-ADAM10 gene encoding the Cry3Aa toxin receptor ADAM10 in CPB larvae and opening up the possibility of exploiting plant natural variation in miRNAs to provide more sustainable potato crop protection against CPB. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Arabidopsis ETHYLENE INSENSITIVE 3 directly regulates the expression of PG1β-like family genes in response to aluminum stress

The genes in the subfamily PG1β (beta subunit of poly-galacturonase isoenzyme 1) have a clear effect on the biosynthesis pathway of pectin, a main component of the cell wall. However, the detailed functions of the PG1β-like gene members in Arabidopsis (AtPG1-3) have not yet been determined. In this study, we investigated their functional roles in response to aluminum (Al) stress. Our results indicate that the PG1β-like gene members are indeed involved in the Al-stress response and they can modulate its accumulation in roots to achieve optimum root elongation and hence better seedling growth. We found that transcription factor EIN3 (ETHYLENE INSENSITIVE 3) alters pectin metabolism and the EIN3 gene responds to Al stress to affect the pectin content in the root cell walls, leading to exacerbation of the inhibition of root growth, as reflected by the phenotypes of overexpressing lines. We determined that EIN3 can directly bind to the promoter regions of PG1-3, which act downstream of EIN3. Thus, our results show that EIN3 responds to Al stress in Arabidopsis directly through regulating the expression of PG1-3. Hence, EIN3 mediates their functions by acting as a biomarker in their molecular biosynthesis pathways, and consequently orchestrates their biological network in response to Al stress.

Uncovering a Phenomenon of Active Hormone Transcriptional Regulation during Early Somatic Embryogenesis in Medicago sativa

Somatic embryogenesis (SE) is a developmental process in which somatic cells undergo dedifferentiation to become plant stem cells, and redifferentiation to become a whole embryo. SE is a prerequisite for molecular breeding and is an excellent platform to study cell development in the majority of plant species. However, the molecular mechanism involved in M. sativa somatic embryonic induction, embryonic and maturation is unclear. This study was designed to examine the differentially expressed genes (DEGs) and miRNA roles during somatic embryonic induction, embryonic and maturation. The cut cotyledon (ICE), non-embryogenic callus (NEC), embryogenic callus (EC) and cotyledon embryo (CE) were selected for transcriptome and small RNA sequencing. The results showed that 17,251 DEGs, and 177 known and 110 novel miRNAs families were involved in embryonic induction (ICE to NEC), embryonic (NEC to EC), and maturation (EC to CE). Expression patterns and functional classification analysis showed several novel genes and miRNAs involved in SE. Moreover, embryonic induction is an active process of molecular regulation, and hormonal signal transduction related to pathways involved in the whole SE. Finally, a miRNA–target interaction network was proposed during M. sativa SE. This study provides novel perspectives to comprehend the molecular mechanisms in M. sativa SE.

Integrated Analysis of Microarray, Small RNA, and Degradome Datasets Uncovers the Role of MicroRNAs in Temperature-Sensitive Genic Male Sterility in Wheat

Temperature-sensitive genic male sterile (TGMS) line Beijing Sterility 366 (BS366) has been utilized in hybrid breeding for a long time, but the molecular mechanism underlying male sterility remains unclear. Expression arrays, small RNA, and degradome sequencing were used in this study to explore the potential role of miRNA in the cold-induced male sterility of BS366. Microspore observation showed defective cell plates in dyads and tetrads and shrunken microspores at the vacuolated stage. Differential regulation of Golgi vesicle transport, phragmoplast formation, sporopollenin biosynthesis, pollen exine formation, and lipid metabolism were observed between cold and control conditions. Pollen development was significantly represented in the 352 antagonistic miRNA-target pairs in the integrated analysis of miRNA and mRNA profiles. The specific cleavage of ARF17 and TIR1 by miR160 and miR393 were found in the cold-treated BS366 degradome, respectively. Thus, the cold-mediated miRNAs impaired cell plate formation through repression of Golgi vesicle transport and phragmoplast formation. The repressed expression of ARF17 and TIR1 impaired pollen exine formation. The results of this study will contribute to our understanding of the roles of miRNAs in male sterility in wheat.

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.

An organ-specific transcriptomic atlas of the medicinal plant Bletilla striata: Protein-coding genes, microRNAs, and regulatory networks

As one of the important species belonging to the Bletilla genus of Orchidaceae, Bletilla striata (Thunb.) Rchb. f., possesses both ornamental and medicinal values. Its dried tubers are used as a traditional Chinese medicine, and several secondary metabolites have been indicated to be the active ingredients. However, the molecular mechanisms related to the regulation of secondary metabolism have not been characterized in B. striata. In this study, integrated analysis of RNA sequencing (RNA-seq), small RNA sequencing (sRNA-seq), and degradome sequencing (degradome-seq) data from three organs (leaf, root, and tuber) of B. striata provided us with a comprehensive view of the microRNA (miRNA)-mediated regulatory network. Firstly, based on the RNA-seq data, the organ-specific expression patterns of the protein-coding genes, especially for those related to secondary metabolism, were investigated. Secondly, 342 conserved miRNA candidates were identified from B. striata. These miRNAs were assigned to 88 families, some of which were selected for expression pattern analysis. Additionally, 31 hairpin-structured precursors encoding 23 novel miRNAs were uncovered from the transcriptome assembly. Thirdly, based on the degradome signatures, 1,142 validated miRNA-target pairs (involving 167 conserved miRNAs and six novel miRNAs and 51 target genes) were included in the regulatory network. Organ-specific expression level comparison between the miRNAs and their targets revealed some interesting miRNA-target pairs. Fourthly, some valuable subnetworks were extracted for further functional studies. Additionally, some regulatory pathways were indicated to be monocot specific. Summarily, our results lay a solid basis for in-depth studies on the regulatory mechanisms underlying the production of the medicinal ingredients in B. striata.

miR171 modulates induction of somatic embryogenesis in citrus callus

Overexpression of miR171 restored SE competence in the recalcitrant citrus callus, and inhibition of miR171 function weakened SE competence in the strongly embryogenic citrus callus. Somatic embryogenesis (SE) is an important way of in vitro regeneration for plants. For perennial woody crops such as citrus, embryogenic callus is usually induced from unfertilized aborted ovules and widely used in biotechnology aided breeding. However, SE capacity always declines in callus during subculture, which makes regeneration difficult and hinders the application of biotechnology. We previously found that miR171 may be a regulator of SE in citrus, based on the abundant expression of csi-miR171c in the embryogenic callus and during SE of citrus. Here, we report that miR171 promotes SE and is required for SE in citrus. Overexpression of miR171 restored SE competence in the recalcitrant callus of 'Guoqing No.1' Satsuma mandarin (G1), whereas inhibition of miR171 function by Short Tandem Target Mimic (STTM) weakened SE competence in the strongly embryogenic callus of 'Valencia' sweet orange (V). The comparative transcriptomic analysis in miR171 overexpressed callus line (OE) and the wild type callus (WT) indicated that overexpression of miR171 decreased the expression level of its SCARECROW-LIKE (CsSCL) targets, and activated stress response related biological processes and metabolic processes that are required for cell differentiation. However, CsSCLs were up-regulated in the OE callus during SE induction process, which activated the cell division and developmental processes that are required for embryogenesis progress. Our results validate the function of miR171 in regulation of SE and reveal the biological responses provoked by miR171 in citrus that may promote SE.

Dosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize

The genomic imbalance caused by varying the dosage of individual chromosomes or chromosomal segments (aneuploidy) has more detrimental effects than altering the dosage of complete chromosome sets (ploidy). Previous analysis of maize (Zea mays) aneuploids revealed global modulation of gene expression both on the varied chromosome (cis) and the remainder of the genome (trans). However, little is known regarding the role of microRNAs (miRNAs) under genomic imbalance. Here, we report the impact of aneuploidy and polyploidy on the expression of miRNAs. In general, cis miRNAs in aneuploids present a predominant gene-dosage effect, whereas trans miRNAs trend toward the inverse level, although other types of responses including dosage compensation, increased effect, and decreased effect also occur. By contrast, polyploids show less differential miRNA expression than aneuploids. Significant correlations between expression levels of miRNAs and their targets are identified in aneuploids, indicating the regulatory role of miRNAs on gene expression triggered by genomic imbalance.

Identification of miRNAs in Response to Sweet Potato Weevil (Cylas formicarius) Infection by sRNA Sequencing

The sweet potato weevil (Cylas formicarius) is an important pest in the growing and storage of sweet potatoes. It is a common pest in the sweet potato production areas of southern China, causing serious harm to the development of the sweet potato industry. For the existing cultivars in China and abroad, there is no sweet potato variety with complete resistance to the sweet potato weevil. Thus, understanding the regulation mechanisms of sweet potato weevil resistance is the prerequisite for cultivating sweet potato varieties that are resistant to the sweet potato weevil. However, very little progress has been made in this field. In this study, we inoculated adult sweet potato weevils into sweet potato tubers. The infected sweet potato tubers were collected at 0, 24, 48, and 72 h. Then, a miRNA library was constructed for Eshu 6 and Guang 87 sweet potato tubers infected for different lengths of time. A total of 407 known miRNAs and 298 novel miRNAs were identified. A total of 174 differentially expressed miRNAs were screened out from the known miRNAs, and 247 differentially expressed miRNAs were screened out from the new miRNAs. Moreover, the targets of the differentially expressed miRNAs were predicted and their network was further investigated through GO analysis and KEGG analysis using our previous transcriptome data. More importantly, we screened 15 miRNAs and their target genes for qRT-PCR verification to confirm the reliability of the high-throughput sequencing data, which indicated that these miRNAs were detected and most of the expression results were consistent with the sequencing results. These results provide theoretical and data-based resources for the identification of miRNAs in response to sweet potato weevil infection and an analysis of the molecular regulatory mechanisms involved in insect resistance.

Genome-wide survey and expression analysis of GRAS transcription factor family in sweetpotato provides insights into their potential roles in stress response

BACKGROUND

The plant-specific GRAS transcription factors play pivotal roles in various adverse environmental conditions. Numerous GRAS genes have been explored and characterized in different plants, however, comprehensive survey on GRASs in sweetpotato is lagging.

RESULTS

In this study, 72 putative sweetpotato IbGRAS genes with uneven distribution were isolated on 15 chromosomes and classified into 12 subfamilies supported by gene structures and motif compositions. Moreover, both tandem duplication and segmental duplication events played critical roles in the expansion of sweetpotato GRAS genes, and the collinearity between IbGRAS genes and the related orthologs from nine other plants further depicted evolutionary insights into GRAS gene family. RNA-seq analysis under salt stress and qRT-PCR detection of 12 selected IbGRAS genes demonstrated their significant and varying inductions under multiple abiotic stresses (salt, drought, heat and cold) and hormone treatments (ABA, ACC and JA). Consistently, the promoter regions of IbGRAS genes harbored a series of stress- and hormone-associated cis-acting elements. Among them, IbGRAS71, the potential candidate for breeding tolerant plants, was characterized as having transactivation activity in yeasts, while IbGRAS-2/-4/-9 did not. Moreover, a complex interaction relationship between IbGRASs was observed through the interaction network analysis and yeast two-hybrid assays.

CONCLUSIONS

Our results laid a foundation for further functional identifications of IbGRAS genes, and multiple members may serve as potential regulators for molecular breeding of tolerant sweetpotato.

Research on lncRNA related to drought resistance of Shanlan upland rice

Background

Drought has become the major abiotic stress that causes losses in rice yields and consequently is one of the main environmental factors threatening food security. Long non-coding RNA (lncRNA) is known to play an important role in plant response to drought stress, while the mechanisms of competing endogenous RNA (ceRNA) in drought resistance in upland rice have been rarely reported.

Results

In our study, a total of 191 lncRNAs, 2115 mRNAs and 32 miRNAs (microRNAs) were found by strand-specific sequencing and small RNA sequencing to be differentially expressed in drought-stressed rice. Functional analysis of results indicate that they play important roles in hormone signal transduction, chlorophyll synthesis, protein synthesis and other pathways. Construction of a ceRNA network revealed that MSTRG.28732.3 may interact with miR171 in the chlorophyll biosynthesis pathway and affect the ability of plants to withstand drought stress by regulating Os02g0662700, Os02g0663100 and Os06g0105350. The accuracy of the regulatory network was verified by qRT-PCR.

Conclusion

Our results provide a theoretical basis for future studies on the potential function of lncRNA in plant drought resistance, and they provide new genetic resources for drought-resistant rice breeding.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08546-0.

Melatonin delays dark-induced leaf senescence by inducing miR171b expression in tomato

Melatonin functions in multiple aspects of plant growth, development, and stress response. Nonetheless, the mechanism of melatonin in plant carbon metabolism remains largely unknown. In this study, we investigated the influence of melatonin on the degradation of starch in tomato leaves. Results showed that exogenous melatonin attenuated carbon starvation-induced chlorophyll degradation and leaf senescence. In addition, melatonin delayed leaf starch degradation and inhibited the transcription of starch-degrading enzymes after sunset. Interestingly, melatonin-alleviated symptoms of leaf senescence and starch degradation were compromised when the first key gene for starch degradation, α-glucan water dikinase (GWD), was overexpressed. Furthermore, exogenous melatonin significantly upregulated the transcript levels of several microRNAs, including miR171b. Crucially, the GWD gene was identified as a target of miR171b, and the overexpression of miR171b ameliorated the carbon starvation-induced degradation of chlorophyll and starch, and inhibited the expression of the GWD gene. Taken together, these results demonstrate that melatonin promotes plant tolerance against carbon starvation by upregulating the expression of miR171b, which can directly inhibit GWD expression in tomato leaves.

Effect of aneuploidy of a non-essential chromosome on gene expression in maize

The non-essential supernumerary maize (Zea mays) B chromosome (B) has recently been shown to contain active genes and to be capable of impacting gene expression of the A chromosomes. However, the effect of the B chromosome on gene expression is still unclear. In addition, it is unknown whether the accumulation of the B chromosome has a cumulative effect on gene expression. To examine these questions, the global expression of genes, microRNAs (miRNAs), and transposable elements (TEs) of leaf tissue of maize W22 plants with 0-7 copies of the B chromosome was studied. All experimental genotypes with B chromosomes displayed a trend of upregulated gene expression for a subset of A-located genes compared to the control. Over 3000 A-located genes are significantly differentially expressed in all experimental genotypes with the B chromosome relative to the control. Modulations of these genes are largely determined by the presence rather than the copy number of the B chromosome. By contrast, the expression of most B-located genes is positively correlated with B copy number, showing a proportional gene dosage effect. The B chromosome also causes increased expression of A-located miRNAs. Differentially expressed miRNAs potentially regulate their targets in a cascade of effects. Furthermore, the varied copy number of the B chromosome leads to the differential expression of A-located and B-located TEs. The findings provide novel insights into the function and properties of the B chromosome.

Multifarious and Interactive Roles of GRAS Transcription Factors During Arbuscular Mycorrhiza Development

Arbuscular mycorrhiza (AM) is a mutualistic symbiotic interaction between plant roots and AM fungi (AMF). This interaction is highly beneficial for plant growth, development and fitness, which has made AM symbiosis the focus of basic and applied research aimed at increasing plant productivity through sustainable agricultural practices. The creation of AM requires host root cells to undergo significant structural and functional modifications. Numerous studies of mycorrhizal plants have shown that extensive transcriptional changes are induced in the host during all stages of colonization. Advances have recently been made in identifying several plant transcription factors (TFs) that play a pivotal role in the transcriptional regulation of AM development, particularly those belonging to the GRAS TF family. There is now sufficient experimental evidence to suggest that GRAS TFs are capable to establish intra and interspecific interactions, forming a transcriptional regulatory complex that controls essential processes in the AM symbiosis. In this minireview, we discuss the integrative role of GRAS TFs in the regulation of the complex genetic re-programming determining AM symbiotic interactions. Particularly, research being done shows the relevance of GRAS TFs in the morphological and developmental changes required for the formation and turnover of arbuscules, the fungal structures where the bidirectional nutrient translocation occurs.

Integrated analysis of the transcriptome, sRNAome, and degradome reveals the network regulating fruit skin coloration in sponge gourd (Luffa cylindrica)

Sponge gourd fruit skin color is an important quality-related trait because it substantially influences consumer preferences. However, little is known about the miRNAs and genes regulating sponge gourd fruit skin coloration. This study involved an integrated analysis of the transcriptome, sRNAome, and degradome of sponge gourd fruit skins with green skin (GS) and white skin (WS). A total of 4,331 genes were differentially expressed between the GS and WS, with 2,442 down-regulated and 1,889 up-regulated genes in WS. The crucial genes involved in chlorophyll metabolism, chloroplast development, and chloroplast protection were identified (e.g., HEMA, CHLM, CRD1, POR, CAO, CLH, SGR, CAB, BEL1-like, KNAT, ARF, and peroxidase genes). Additionally, 167 differentially expressed miRNAs were identified, with 70 up-regulated and 97 down-regulated miRNAs in WS. Degradome sequencing identified 125 differentially expressed miRNAs and their 521 differentially expressed target genes. The miR156, miR159, miR166, miR167, miR172, and miR393 targeted the genes involved in chlorophyll metabolism, chloroplast development, and chloroplast protection. Moreover, a flavonoid biosynthesis regulatory network was established involving miR159, miR166, miR169, miR319, miR390, miR396, and their targets CHS, 4CL, bHLH, and MYB. The qRT-PCR data for the differentially expressed genes were generally consistent with the transcriptome results. Subcellular localization analysis of selected proteins revealed their locations in different cellular compartments, including nucleus, cytoplasm and endoplasmic reticulum. The study findings revealed the important miRNAs, their target genes, and the regulatory network controlling fruit skin coloration in sponge gourd.

Function and Regulation of microRNA171 in Plant Stem Cell Homeostasis and Developmental Programing

MicroRNA171 (miR171), a group of 21-nucleotide single-strand small RNAs, is one ancient and conserved microRNA family in land plants. This review focuses on the recent progress in understanding the role of miR171 in plant stem cell homeostasis and developmental patterning, and the regulation of miR171 by developmental cues and environmental signals. Specifically, miR171 regulates shoot meristem activity and phase transition through repressing the HAIRYMERISTEM (HAM) family genes. In the model species Arabidopsis, miR171 serves as a short-range mobile signal, which initiates in the epidermal layer of shoot meristems and moves downwards within a limited distance, to pattern the apical-basal polarity of gene expression and drive stem cell dynamics. miR171 levels are regulated by light and various abiotic stresses, suggesting miR171 may serve as a linkage between environmental factors and cell fate decisions. Furthermore, miR171 family members also demonstrate both conserved and lineage-specific functions in land plants, which are summarized and discussed here.

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.

Small RNA and Degradome Sequencing Reveal Important MicroRNA Function in Nicotiana tabacum Response to Bemisia tabaci

MicroRNAs (miRNAs), a class of small non-coding regulatory RNAs, are key molecules in many biological and metabolic processes of plant growth, development and stress response via targeting mRNAs. The phloem-feeding insect whitefly Bemisia tabaci (Hemiptera, Aleyrodidae) is a serious pest that causes devastating harm to agricultural production worldwide. However, the function of host miRNAs in the response to whitefly infestation remains unclear. Here, we sequenced the small RNA and degradome of tobacco (Nicotiana tabacum L.), after and before infestation by B. tabaci. We identified 1291 miRNAs belonging to 138 miRNA families including 706 known miRNAs and 585 novel miRNAs. A total of 47 miRNAs were differentially expressed, of which 30 were upregulated and 17 were downregulated by whitefly exposure. Then, computational analysis showed that the target genes of differential miRNAs were involved in R gene regulation, plant innate immunity, plant pathogen defense, the plant hormone signal pathway and abiotic stress tolerance. Furthermore, degradome analysis demonstrated that 253 mRNAs were cleaved by 66 miRNAs. Among them, the targets cleaved by upregulated miR6025, miR160, miR171, miR166 and miR168 are consistent with our prediction, suggesting that pathogen-related miRNAs may function in plant defense against whitefly. Moreover, our results show that plant miRNA response and miRNA-mediated post-transcriptional regulation for phloem-feeding insect infestation are similar to pathogen invasion. Our study provides additional data to further elucidate how host plants respond and defend the phloem-feeding insects.

Integrated transcriptome and small RNA sequencing in revealing miRNA-mediated regulatory network of floral bud break in Prunus mume

MicroRNAs is one class of small non-coding RNAs that play important roles in plant growth and development. Though miRNAs and their target genes have been widely studied in many plant species, their functional roles in floral bud break and dormancy release in woody perennials is still unclear. In this study, we applied transcriptome and small RNA sequencing together to systematically explore the transcriptional and post-transcriptional regulation of floral bud break in P. mume. Through expression profiling, we identified a few candidate genes and miRNAs during different developmental stage transitions. In total, we characterized 1,553 DEGs associated with endodormancy release and 2,084 DEGs associated with bud flush. Additionally, we identified 48 known miRNAs and 53 novel miRNAs targeting genes enriched in biological processes such as floral organ morphogenesis and hormone signaling transudation. We further validated the regulatory relationship between differentially expressed miRNAs and their target genes combining computational prediction, degradome sequencing, and expression pattern analysis. Finally, we integrated weighted gene co-expression analysis and constructed miRNA-mRNA regulatory networks mediating floral bud flushing competency. In general, our study revealed the miRNA-mediated networks in modulating floral bud break in P. mume. The findings will contribute to the comprehensive understanding of miRNA-mediated regulatory mechanism governing floral bud break and dormancy cycling in wood perennials.

Impact of CuO nanoparticles on maize: Comparison with CuO bulk particles with special reference to oxidative stress damages and antioxidant defense status

The present study aimed to systematically investigate the particle size effects of copper (II) oxide [CuO nanoparticles (<50 nm) and CuO bulk particles (<10 μm)] on maize (Zea mays L.). Bioaccumulation of Cu, in vivo ROS generation, membrane damage, transcriptional modulation of antioxidant genes, cellular redox status of glutathione and ascorbate pool, expression patterns of COPPER TRANSPORTER 4 and stress responsive miRNAs (miR398a, miR171b, miR159f-3p) with their targets were investigated for better understanding of the underlying mechanisms and the extent of CuO nanoparticles and CuO bulk particles induced oxidative stress damages. More restricted seedling growth, comparatively higher membrane injury, marked decline in the levels of chlorophylls and carotenoids and severe oxidative burst were evident in CuO bulk particles challenged leaves. Dihydroethidium and CM-H2DCFDA staining further supported elevated reactive oxygen species generation in CuO bulk particles stressed roots. CuO bulk particles exposed seedlings accumulated much higher amount of Cu in roots as compared to CuO nanoparticles stressed plants with low root-to-shoot Cu translocation. Moderately high GR expression with maintenance of a steady GSH-GSSG ratio in CuO nanoparticles challenged leaves might be accountable for their rather improved performance under stressed condition. miR171b-mediated enhanced expression of SCARECROW 6 might participate in the marked decline of chlorophyll content in CuO bulk particles exposed leaves. Ineffective recycling of AsA pool is another decisive feature of inadequate performance of CuO bulk particles stressed seedlings in combating oxidative stress damages. Taken together, our findings revealed that toxicity of CuO bulk particles was higher than CuO nanoparticles and the adverse effects of CuO bulk particles on maize seedlings might be due to higher Cu ions dissolution.

Identification of miRNA and their target genes in Cestrum nocturnum L. and Cestrum diurnum L. in stress responses

MicroRNAs (miRNAs) are small, highly conserved non-coding RNA molecules and products of primary miRNAs that regulate the target gene expression. Homology-based approaches were employed to identify miRNAs and their targets in Cestrum nocturnum L. and Cestrum diurnum L. A total of 32 and 12 miRNA candidates were identified in C. nocturnum and C. diurnum. These miRNAs belong to 26 and 10 miRNA families and regulate 1024 and 1007 target genes in C. nocturnum, and C. diurnum, respectively. The functional roles of these miRNAs have not been earlier elucidated in Cestrum. MiR815a, miR849, miR1089 and miR172 have a strong propensity to target genes controlling phytochrome-interacting factor 1 (PIF1), ubiquitin-specific protease 12 (UBP12), leucine-rich repeat (LRR) protein kinase and GAI, RGA, SCR (GRAS) family transcription factor in C. nocturnum. While miR5205a, miR1436 and miR530 regulate PATATIN-like protein 6 (PLP6), PHD finger transcription factor and myb domain protein 48 (MYB48) in C. diurnum. Overall, these miRNAs have regulatory responses in biotic and abiotic stresses in both plant species. Eight putative miRNAs and their target genes were selected for qRT-PCR validation. The validated results suggested the importance of miR815a, miR849, miR5205a, miR1089, miR172, miR1436, and miR530 in exerting control over stress responses in C. nocturnum and C. diurnum.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01127-1.

Integrative genome, transcriptome, microRNA, and degradome analysis of water dropwort (Oenanthe javanica) in response to water stress

Water dropwort (Liyang Baiqin, Oenanthe javanica (BI.) DC.) is an aquatic perennial plant from the Apiaceae family with abundant protein, dietary fiber, vitamins, and minerals. It usually grows in wet soils and can even grow in water. Here, whole-genome sequencing of O. javanica via HiSeq 2000 sequencing technology was reported for the first time. The genome size was 1.28 Gb, including 42,270 genes, of which 93.92% could be functionally annotated. An online database of the whole-genome sequences of water dropwort, Water dropwortDB, was established to share the results and facilitate further research on O. javanica (database homepage: http://apiaceae.njau.edu.cn/waterdropwortdb ). Water dropwortDB offers whole-genome and transcriptome sequences and a Basic Local Alignment Search Tool. Comparative analysis with other species showed that the evolutionary relationship between O. javanica and Daucus carota was the closest. Twenty-five gene families of O. javanica were found to be expanded, and some genetic factors (such as genes and miRNAs) related to phenotypic and anatomic differentiation in O. javanica under different water conditions were further investigated. Two miRNA and target gene pairs (miR408 and Oja15472, miR171 and Oja47040) were remarkably regulated by water stress. The obtained reference genome of O. javanica provides important information for future work, thus making in-depth genetic breeding and gene editing possible. The present study also provides a foundation for the understanding of the O. javanica response to water stress, including morphological, anatomical, and genetic differentiation.

The GRAS gene family and its roles in seed development in litchi (Litchi chinensis Sonn)

BACKGROUND

The GRAS gene family plays crucial roles in multiple biological processes of plant growth, including seed development, which is related to seedless traits of litchi (Litchi chinensis Sonn.). However, it hasn't been fully identified and analyzed in litchi, an economic fruit tree cultivated in subtropical regions.

RESULTS

In this study, 48 LcGRAS proteins were identified and termed according to their chromosomal location. LcGRAS proteins can be categorized into 14 subfamilies through phylogenetic analysis. Gene structure and conserved domain analysis revealed that different subfamilies harbored various motif patterns, suggesting their functional diversity. Synteny analysis revealed that the expansion of the GRAS family in litchi may be driven by their tandem and segmental duplication. After comprehensively analysing degradome data, we found that four LcGRAS genes belong to HAM subfamily were regulated via miR171-mediated degradation. The various expression patterns of LcGRAS genes in different tissues uncovered they were involved in different biological processes. Moreover, the different temporal expression profiles of LcGRAS genes between abortive and bold seed indicated some of them were involved in maintaining the normal development of the seed.

CONCLUSION

Our study provides comprehensive analyses on GRAS family members in litchi, insight into a better understanding of the roles of GRAS in litchi development, and lays the foundation for further investigations on litchi seed development.

Identification and expression analysis of miRNAs in germination and seedling growth of Tibetan hulless barley

Germination and seedling growth are crucial for plant development and agricultural production. While, the regulatory mechanisms during these processes in Tibetan hulless barley (Hordeum vulgare L. var. nudum) are not well understood. Given the regulatory roles of microRNAs (miRNAs) in crop plants and the irreplaceability of barley in the highland area of China, we herein presented a genome-wide survey of miRNAs to reveal a potential regulatory network in the early developmental stages of two Tibetan hulless barleys, from which a total of 156 miRNAs was identified including 35 known and 121 novel ones. Six of the identified novel miRNAs were further experimentally validated. According to the evolutionary analysis, miR156, miR166, miR168, and miR171 were conserved across Tibetan hulless barleys and eight other seed plants. Expression profiles of ten known miRNAs showed that they were involved in phytohormone signaling, carbohydrate and lipid metabolism, as well as juvenile-adult transition during barley development. Moreover, a total of 1280 genes targeted by 101 miRNAs were predicted from both barley libraries. Three genes (PLN03212, MATE eukaryotic, and GRAS) were validated via the RNA ligase-mediated 5'-rapid amplification of cDNA ends (RLM-5' RACE) to be the targets of hvu-miR159a, hvu-miR166a, and hvu-miR171-3p, respectively. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of putative targets, the most abundant pathways were related to "metabolism". These results revealed that miRNA-target pairs participating in the regulation of multigene expression and the embryonic development of Tibetan hulless barleys were controlled by complex mechanisms involving the concordant expression of different miRNAs and feedback loops among miRNAs as well as their targets. The study provides insight into the regulatory network of barley miRNAs for better understanding of miRNA functions during germination and seedling growth.

Integrated Analysis of mRNA and Non-coding RNA Transcriptome in Pepper (Capsicum chinense) Hybrid at Seedling and Flowering Stages

Pepper is an important vegetable in the world. In this work, mRNA and ncRNA transcriptome profiles were applied to understand the heterosis effect on the alteration in the gene expression at the seedling and flowering stages between the hybrid and its parents in Capsicum chinense. Our phenotypic data indicated that the hybrid has dominance in leaf area, plant scope, plant height, and fruit-related traits. Kyoto Encyclopedia of Genes and Genomes analysis showed that nine members of the plant hormone signal transduction pathway were upregulated in the seedling and flowering stages of the hybrid, which was supported by weighted gene coexpression network analysis and that BC332_23046 (auxin response factor 8), BC332_18317 (auxin-responsive protein IAA20), BC332_13398 (ethylene-responsive transcription factor), and BC332_27606 (ethylene-responsive transcription factor WIN1) were candidate hub genes, suggesting the important potential role of the plant hormone signal transduction in pepper heterosis. Furthermore, some transcription factor families, including bHLH, MYB, and HSF were greatly over-dominant. We also identified 2,525 long ncRNAs (lncRNAs), 47 micro RNAs (miRNAs), and 71 circle RNAs (circRNAs) in the hybrid. In particular, downregulation of miR156, miR169, and miR369 in the hybrid suggested their relationship with pepper growth vigor. Moreover, we constructed some lncRNA–miRNA–mRNA regulatory networks that showed a multi-dimension to understand the ncRNA relationship with heterosis. These results will provide guidance for a better understanding of the molecular mechanism involved in pepper heterosis.

Genome-wide identification, expression analysis, and functional study of the GRAS transcription factor family and its response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]

Background

GRAS, an important family of transcription factors, have played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. Since the sequencing of the sorghum genome, a plethora of genetic studies were mainly focused on the genomic information. The indepth identification or genome-wide analysis of GRAS family genes, especially in Sorghum bicolor, have rarely been studied.

Results

A total of 81 SbGRAS genes were identified based on the S. bicolor genome. They were named SbGRAS01 to SbGRAS81 and grouped into 13 subfamilies (LISCL, DLT, OS19, SCL4/7, PAT1, SHR, SCL3, HAM-1, SCR, DELLA, HAM-2, LAS and OS4). SbGRAS genes are not evenly distributed on the chromosomes. According to the results of the gene and motif composition, SbGRAS members located in the same group contained analogous intron/exon and motif organizations. We found that the contribution of tandem repeats to the increase in sorghum GRAS members was slightly greater than that of fragment repeats. By quantitative (q) RT-PCR, the expression of 13 SbGRAS members in different plant tissues and in plants exposed to six abiotic stresses at the seedling stage were quantified. We further investigated the relationship between DELLA genes, GAs and grain development in S. bicolor. The paclobutrazol treatment significantly increased grain weight, and affected the expression levels of all DELLA subfamily genes. SbGRAS03 is the most sensitive to paclobutrazol treatment, but also has a high response to abiotic stresses.

Conclusions

Collectively, SbGRAs play an important role in plant development and response to abiotic stress. This systematic analysis lays the foundation for further study of the functional characteristics of GRAS genes of S. bicolor.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07848-z.

MicroRNAs Roles in Plants Secondary Metabolism

Plant growth and development is dependent on the regulation of classes of microRNAs (miRNAs) that have emerged as important gene regulators. These miRNAs can regulate plant gene expression to function. They play an important roles in biological homeostasis and environmental response controls. A wide range of plant biological and metabolic processes, including developmental timing, tissues specific development, and differentiation, depends on miRNAs. They perpetually regulate secondary metabolite functions in different plant family lines. Mapping of molecular phylogenies shows the distribution of secondary metabolism in the plant territory. More importantly, a lot of information related to miRNA regulatory processes in plants is revealed, but the role of miRNAs in secondary metabolism regulation and functions of the metabolites are still unclear. In this review, we pinnacle some potential miRNAs regulating the secondary metabolite biosynthesis activities in plants. This will provide an alternative knowledge for functional studies of secondary metabolism.

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.

Next-Generation Sequencing Identification and Characterization of MicroRNAs in Dwarfed Citrus Trees Infected With Citrus Dwarfing Viroid in High-Density Plantings

Citrus dwarfing viroid (CDVd) induces stunting on sweet orange trees [Citrus sinensis (L.) Osbeck], propagated on trifoliate orange rootstock [Citrus trifoliata (L.), syn. Poncirus trifoliata (L.) Raf.]. MicroRNAs (miRNAs) are a class of non-coding small RNAs (sRNAs) that play important roles in the regulation of tree gene expression. To identify miRNAs in dwarfed citrus trees, grown in high-density plantings, and their response to CDVd infection, sRNA next-generation sequencing was performed on CDVd-infected and non-infected controls. A total of 1,290 and 628 miRNAs were identified in stem and root tissues, respectively, and among those, 60 were conserved in each of these two tissue types. Three conserved miRNAs (csi-miR479, csi-miR171b, and csi-miR156) were significantly downregulated (adjusted p-value < 0.05) in the stems of CDVd-infected trees compared to the non-infected controls. The three stem downregulated miRNAs are known to be involved in various physiological and developmental processes some of which may be related to the characteristic dwarfed phenotype displayed by CDVd-infected C. sinensis on C. trifoliata rootstock field trees. Only one miRNA (csi-miR535) was significantly downregulated in CDVd-infected roots and it was predicted to target genes controlling a wide range of cellular functions. Reverse transcription quantitative polymerase chain reaction analysis performed on selected miRNA targets validated the negative correlation between the expression levels of these targets and their corresponding miRNAs in CDVd-infected trees. Our results indicate that CDVd-responsive plant miRNAs play a role in regulating important citrus growth and developmental processes that may participate in the cellular changes leading to the observed citrus dwarf phenotype.

PIF3/HY5 module regulates BBX11 to suppress protochlorophyllide levels in dark and promote photomorphogenesis in light

Greening of cotyledons during de-etiolation is critical for harvesting light energy and sustaining plant growth. PIF3 and HY5 antagonistically regulate protochlorophyllide synthesis in the dark. However, the mechanism by which the PIF3/HY5 module regulates genes involved in protochlorophyllide synthesis is not clear. Using genetic, molecular and biochemical techniques we identified that the B-BOX protein BBX11 acts directly downstream of PIF3 and HY5 to transcriptionally modulate genes involved in protochlorophyllide synthesis. Dark-grown bbx11 and 35S:BBX11 seedlings exhibit an enhanced and reduced ability to green, respectively, when exposed to light. Transcript levels of HEMA1 and CHLH are upregulated in 35S:BBX11 seedlings that accumulate high levels of protochlorophyllide in the dark and undergo photobleaching upon illumination. PIF3 inhibits BBX11 in the dark by directly binding to its promoter. bbx11 suppresses the cotyledon greening defect of pif3 after prolonged dark, indicating that the PIF3-mediated regulation of greening is dependent on BBX11. The enhanced greening of hy5 is also suppressed in hy5 lines overexpressing BBX11. In light, HY5 directly binds to the promoter of BBX11 and activates its expression to regulate BBX11-mediated hypocotyl inhibition. We show that a PIF3/HY5 module regulates BBX11 expression in opposite ways to optimise protochlorophyllide accumulation in the dark and promote photomorphogenesis in light.

sRNATargetDigger: A bioinformatics software for bidirectional identification of sRNA-target pairs with co-regulatory sRNAs information

Identification of the target genes of microRNAs (miRNAs), trans-acting small interfering RNAs (ta-siRNAs), and small interfering RNAs (siRNAs) is an important step for understanding their regulatory roles in plants. In recent years, many bioinformatics software packages based on small RNA (sRNA) high-throughput sequencing (HTS) and degradome sequencing data analysis have provided strong technical support for large-scale mining of sRNA-target pairs. However, sRNA-target regulation is achieved using a complex network of interactions since one transcript might be co-regulated by multiple sRNAs and one sRNA may also affect multiple targets. Currently used mining software can realize the mining of multiple unknown targets using known sRNA, but it cannot rule out the possibility of co-regulation of the same target by other unknown sRNAs. Hence, the obtained regulatory network may be incomplete. We have developed a new mining software, sRNATargetDigger, that includes two function modules, “Forward Digger” and “Reverse Digger”, which can identify regulatory sRNA-target pairs bidirectionally. Moreover, it has the ability to identify unknown sRNAs co-regulating the same target, in order to obtain a more authentic and reliable sRNA-target regulatory network. Upon re-examination of the published sRNA-target pairs in Arabidopsis thaliana, sRNATargetDigger found 170 novel co-regulatory sRNA-target pairs. This software can be downloaded from http://www.bioinfolab.cn/sRNATD.html.

Argonaute4 Modulates Resistance to Fusarium brachygibbosum Infection by Regulating Jasmonic Acid Signaling

Argonautes (AGOs) associate with noncoding RNAs to regulate gene expression during development and stress adaptation. Their role in plant immunity against hemibiotrophic fungal infection remains poorly understood. Here, we explore the function of AGOs in the interaction of wild tobacco (Nicotiana attenuata) with a naturally occurring hemibiotrophic pathogen, Fusarium brachygibbosum Among all AGOs, only transcripts of AGO4 were elicited after fungal infection. The disease progressed more rapidly in AGO4-silenced (irAGO4) plants than in wild type, and small RNA (smRNA) profiling revealed that 24-nucleotide smRNA accumulation was severely abrogated in irAGO4 plants. Unique microRNAs (miRNAs: 130 conserved and 208 novel, including 11 canonical miRNA sequence variants known as "isomiRs") were identified in infected plants; silencing of AGO4 strongly changed miRNA accumulation dynamics. Time-course studies revealed that infection increased accumulation of abscisic acid, jasmonates, and salicylic acid in wild type; in irAGO4 plants, infection accumulated lower jasmonate levels and lower transcripts of jasmonic acid (JA) biosynthesis genes. Treating irAGO4 plants with JA, methyl jasmonate, or cis-(+)-12-oxo-phytodienoic acid restored wild-type levels of resistance. Silencing expression of RNA-directed RNA polymerases RdR1 and RdR2 (but not RdR3) and Dicer-like3 (DCL3, but not DCL2 or DCL4) increased susceptibility to F brachygibbosum The relevance of AGO4, RdR1, RdR2, and DCL3 in a natural setting was revealed when plants individually silenced in their expression (and their binary combinations) were planted in a diseased field plot in the Great Basin Desert of Utah. These plants were more susceptible to infection and accumulated lower JA levels than wild type. We infer that AGO4-dependent smRNAs play a central role in modulating JA biogenesis and signaling during hemibiotrophic fungal infections.

The Apple microR171i-SCARECROW-LIKE PROTEINS26.1 Module Enhances Drought Stress Tolerance by Integrating Ascorbic Acid Metabolism

Drought stress severely restricts crop yield and quality. Small noncoding RNAs play critical roles in plant growth, development, and stress responses by regulating target gene expression, but their roles in drought stress tolerance in apple (Malus domestica) are poorly understood. Here, we identified various small noncoding RNAs and their targets from the wild apple species Malus sieversii via high-throughput sequencing and degradome analysis. Forty known microRNAs (miRNAs) and eight new small noncoding RNAs were differentially expressed in response to 2 or 4 h of drought stress treatment. We experimentally verified the expression patterns of five selected miRNAs and their targets. We established that one miRNA, mdm-miR171i, specifically targeted and degraded SCARECROW-LIKE PROTEINS26 1 (MsSCL26 1) transcripts. Both knockout of mdm-miR171i and overexpression of MsSCL26 1 improved drought stress tolerance in the cultivated apple line 'GL-3' by regulating the expression of antioxidant enzyme genes, especially that of MONODEHYDROASCORBATE REDUCTASE, which functions in metabolism under drought stress. Transient expression analysis demonstrated that MsSCL26.1 activates MsMDHAR transcription by positively regulating the activity of the P1 region in its promoter. Therefore, the miR171i-SCL26 1 module enhances drought stress tolerance in apple by regulating antioxidant gene expression and ascorbic acid metabolism.

SCARECROW gene function is required for photosynthetic development in maize

C4 photosynthesis in grasses relies on a specialized leaf anatomy. In maize, this "Kranz" leaf anatomy is patterned in part by the duplicated SCARECROW (SCR) genes ZmSCR1 and ZmSCR1h. Here we show that in addition to patterning defects, chlorophyll content and levels of transcripts encoding Golden2-like regulators of chloroplast development are significantly lower in Zmscr1; Zmscr1h mutants than in wild-type. These perturbations are not associated with changes in chloroplast number, size, or ultrastructure. However, the maximum rates of carboxylation by ribulose bisphosphate carboxylase/oxygenase (RuBisCO, V cmax) and phosphoenolpyruvate carboxylase (PEPC, V pmax) are both reduced, leading to perturbed plant growth. The CO2 compensation point and 13C‰ of Zmscr1;Zmscr1h plants are both normal, indicating that a canonical C4 cycle is operating, albeit at reduced overall capacity. Taken together, our results reveal that the maize SCR genes, either directly or indirectly, play a role in photosynthetic development.

SIGNIFICANCE STATEMENT

SCARECROW (SCR) is one of the best studied plant developmental regulators, however, its role in downstream plant physiology is less well-understood. Here, we have demonstrated that SCR is required to establish and/or maintain photosynthetic capacity in maize leaves.

Variation in Maize Chlorophyll Biosynthesis Alters Plant Architecture

Chlorophyll is a tetrapyrrole metabolite essential for photosynthesis in plants. The first committed step of chlorophyll biosynthesis is catalyzed by a multimeric enzyme, magnesium chelatase, the subunit I of which is encoded by the oil yellow1 (oy1) gene in maize (Zea mays). A range of chlorophyll contents and net CO2 assimilation rates can be achieved in maize by combining a semidominant mutant allele of oy1 (Oy1-N1989) and a cis-regulatory modifier named very oil yellow1 (vey1) that varies between different inbred lines. We previously demonstrated that these allelic interactions can delay reproductive maturity. In this study, we demonstrate that multiple gross morphological traits respond to a reduction in chlorophyll. We found that stalk width, number of lateral branches (tillers), and branching of the inflorescence decline with a decrease in chlorophyll level. Chlorophyll deficit suppressed tillering in multiple maize mutants, including teosinte branched1, Tillering1, and grassy tillers1 In contrast to these traits, plant height showed a nonlinear response to chlorophyll levels. Weak suppression of Oy1-N1989 by vey1 B73 resulted in a significant increase in mutant plant height. By contrast, enhancement of the severity of the Oy1-N1989 phenotype by the vey1 Mo17 allele resulted in reduced plant height. We demonstrate that the effects of reduced chlorophyll contents on plant growth and development are complex and depend on the trait being measured. We propose that the lack of chlorophyll exerts growth control via energy balance sensing, which is upstream of the known genetic networks for branching and architecture.