Constitutive Expression of miR408 Improves Biomass and Seed Yield in Arabidopsis

Redox regulation of epigenetic and epitranscriptomic gene regulatory pathways in plants

Developmental and environmental constraints influence genome expression through complex networks of regulatory mechanisms. Epigenetic modifications and remodelling of chromatin are some of the major actors regulating the dynamic of gene expression. Unravelling the factors relaying environmental signals that induce gene expression reprogramming under stress conditions is an important and fundamental question. Indeed, many enzymes involved in epigenetic and chromatin modifications are regulated by redox pathways, through post-translational modifications of proteins or by modifications of the flux of metabolic intermediates. Such modifications are potential hubs to relay developmental and environmental changes for gene expression reprogramming. In this review, we provide an update on the interaction between major redox mediators, such as reactive oxygen and nitrogen species and antioxidants, and epigenetic changes in plants. We detail how redox status alters post-translational modifications of proteins, intracellular epigenetic and epitranscriptional modifications, and how redox regulation interplays with DNA methylation, histone acetylation and methylation, miRNA biogenesis, and chromatin structure and remodelling to reprogram genome expression under environmental constraints.

MicroRNA257 promotes secondary growth in hybrid poplar

Populus, a significant fast-growing tree species with global afforestation and energy potential, holds considerable economic value. The abundant production of secondary xylem by trees, which serves as a vital resource for industrial purposes and human sustenance, necessitates the orchestration of various regulatory mechanisms, encompassing transcriptional regulators and microRNAs (miRNAs). Nevertheless, the investigation of microRNA-mediated regulation of poplar secondary growth remains limited. In this study, we successfully isolated a novel microRNA (Pag-miR257) from 84 K poplar and subsequently integrated it into the 35 S overexpression vector. The overexpression of Pag-miR257 resulted in notable increases in plant height, stem diameter, and fresh weight. Additionally, the overexpression of Pag-miR257 demonstrated a significant enhancement in net photosynthetic rate. The findings from the examination of cell wall autofluorescence indicated a substantial increase in both xylem area and the number of vessels in poplar plants overexpressing Pag-miR257. Furthermore, the cell wall of the Pag-miR257 overexpressing plants exhibited thickening as observed through transmission electron microscopy. Moreover, the Fourier Transforms Infrared (FTIR) analysis and phloroglucinol-HCl staining revealed an elevation in lignin content in Pag-miR257 overexpressing poplar plants. The findings of this study suggest that microRNA257 may play a role in the control of secondary growth in poplar stems, thereby potentially enhancing the development of wood engineering techniques for improved material and energy production.

Genome-wide analysis of plant specific YABBY transcription factor gene family in carrot (Dacus carota) and its comparison with Arabidopsis

YABBY gene family is a plant-specific transcription factor with DNA binding domain involved in various functions i.e. regulation of style, length of flowers, and polarity development of lateral organs in flowering plants. Computational methods were utilized to identify members of the YABBY gene family, with Carrot (Daucus carota) 's genome as a foundational reference. The structure of genes, location of the chromosomes, protein motifs and phylogenetic investigation, syntony and transcriptomic analysis, and miRNA targets were analyzed to unmask the hidden structural and functional characteristics YABBY gene family in Carrots. In the following research, it has been concluded that 11 specific YABBY genes irregularly dispersed on all 9 chromosomes and proteins assembled into five subgroups i.e. AtINO, AtCRC, AtYAB5, AtAFO, and AtYAB2, which were created on the well-known classification of Arabidopsis. The wide ranges of YABBY genes in carrots were dispersed due to segmental duplication, which was detected as prevalent when equated to tandem duplication. Transcriptomic analysis showed that one of the DcYABBY genes was highly expressed during anthocyanin pigmentation in carrot taproots. The cis-regulatory elements (CREs) analysis unveiled elements that particularly respond to light, cell cycle regulation, drought induce ability, ABA hormone, seed, and meristem expression. Furthermore, a relative study among Carrot and Arabidopsis genes of the YABBY family indicated 5 sub-families sharing common characteristics. The comprehensive evaluation of YABBY genes in the genome provides a direction for the cloning and understanding of their functional properties in carrots. Our investigations revealed genome-wide distribution and role of YABBY genes in the carrots with best-fit comparison to Arabidopsis thaliana.

Unveiling Innovative Approaches to Mitigate Metals/Metalloids Toxicity for Sustainable Agriculture

Due to anthropogenic activities, environmental pollution of heavy metals/metalloids (HMs) has increased and received growing attention in recent decades. Plants growing in HM-contaminated soils have slower growth and development, resulting in lower agricultural yield. Exposure to HMs leads to the generation of free radicals (oxidative stress), which alters plant morpho-physiological and biochemical pathways at the cellular and tissue levels. Plants have evolved complex defense mechanisms to avoid or tolerate the toxic effects of HMs, including HMs absorption and accumulation in cell organelles, immobilization by forming complexes with organic chelates, extraction via numerous transporters, ion channels, signaling cascades, and transcription elements, among others. Nonetheless, these internal defensive mechanisms are insufficient to overcome HMs toxicity. Therefore, unveiling HMs adaptation and tolerance mechanisms is necessary for sustainable agriculture. Recent breakthroughs in cutting-edge approaches such as phytohormone and gasotransmitters application, nanotechnology, omics, and genetic engineering tools have identified molecular regulators linked to HMs tolerance, which may be applied to generate HMs-tolerant future plants. This review summarizes numerous systems that plants have adapted to resist HMs toxicity, such as physiological, biochemical, and molecular responses. Diverse adaptation strategies have also been comprehensively presented to advance plant resilience to HMs toxicity that could enable sustainable agricultural production.

Mapping and Screening of Candidate Gene Regulating the Biomass Yield of Sorghum (Sorghum bicolor L.)

Biomass yield is one of the important traits of sorghum, which is greatly affected by leaf morphology. In this study, a lobed-leaf mutant (sblob) was screened and identified, and its F2 inbred segregating line was constructed. Subsequently, MutMap and whole-genome sequencing were employed to identify the candidate gene (sblob1), the locus of which is Sobic.003G010300. Pfam and homologous analysis indicated that sblob1 encodes a Cytochrome P450 protein and plays a crucial role in the plant serotonin/melatonin biosynthesis pathway. Structural and functional changes in the sblob1 protein were elucidated. Hormone measurements revealed that sblob1 regulates both leaf morphology and sorghum biomass through regulation of the melatonin metabolic pathway. These findings provide valuable insights for further research and the enhancement of breeding programs, emphasizing the potential to optimize biomass yield in sorghum cultivation.

Modulation of Plant MicroRNA Expression: Its Potential Usability in Wheat (Triticum aestivum L.) Improvement

Wheat, a crucial crop for the pursuit of food security, is faced with a plateauing yield projected to fall short of meeting the demands of the exponentially increasing human population. To raise global wheat productivity levels, strong efforts must be made to overcome the problems of (1) climate change-induced heat and drought stress and (2) the genotype-dependent amenability of wheat to tissue culture, which limits the success of recovering genetically engineered plants, especially in elite cultivars. Unfortunately, the mainstream approach of genetically engineering plant protein-coding genes may not be effective in solving these problems as it is difficult to map, annotate, functionally verify, and modulate all existing homeologs and paralogs within wheat's large, complex, allohexaploid genome. Additionally, the quantitative, multi-genic nature of most agronomically important traits furthers the complications faced by this approach. miRNAs are small, noncoding RNAs (sncRNAs) that repress gene expression at the post-transcriptional level, regulating various aspects of plant growth and development. They are gaining popularity as alternative targets of genetic engineering efforts for crop improvement due to their (1) highly conserved nature, which facilitates reasonable prediction of their gene targets and phenotypic effects under different expression levels, and (2) the capacity to target multiple genes simultaneously, making them suitable for enhancing complex and multigenic agronomic traits. In this mini-review, we will discuss the biogenesis, manipulation, and potential applications of plant miRNAs in improving wheat's yield, somatic embryogenesis, thermotolerance, and drought-tolerance in response to the problems of plateauing yield, genotype-dependent amenability to tissue culture, and susceptibility to climate change-induced heat and drought stress.  © His Majesty the King in Right of Canada, as represented by the Minister of Agriculture and Agri-Food, 2023.

A loss-of-function mutant allele of a glycosyl hydrolase gene has been co-opted for seed weight control during soybean domestication

The resultant DNA from loss-of-function mutation can be recruited in biological evolution and development. Here, we present such a rare and potential case of "to gain by loss" as a neomorphic mutation during soybean domestication for increasing seed weight. Using a population derived from a chromosome segment substitution line of Glycine max (SN14) and Glycine soja (ZYD06), a quantitative trait locus (QTL) of 100-seed weight (qHSW) was mapped on chromosome 11, corresponding to a truncated β-1, 3-glucosidase (βGlu) gene. The novel gene hsw results from a 14-bp deletion, causing a frameshift mutation and a premature stop codon in the βGlu. In contrast to HSW, the hsw completely lost βGlu activity and function but acquired a novel function to promote cell expansion, thus increasing seed weight. Overexpressing hsw instead of HSW produced large soybean seeds, and surprisingly, truncating hsw via gene editing further increased the seed size. We further found that the core 21-aa peptide of hsw and its variants acted as a promoter of seed size. Transcriptomic variation in these transgenic soybean lines substantiated the integration hsw into cell and seed size control. Moreover, the hsw allele underwent selection and expansion during soybean domestication and improvement. Our work cloned a likely domesticated QTL controlling soybean seed weight, revealed a novel genetic variation and mechanism in soybean domestication, and provided new insight into crop domestication and breeding, and plant evolution.

Riboflavin mediates m6A modification targeted by miR408, promoting early somatic embryogenesis in longan

Plant somatic embryogenesis (SE) is an in vitro biological process wherein bipolar structures are induced to form somatic cells and regenerate into whole plants. MicroRNA (miRNA) is an essential player in plant SE. However, the mechanism of microRNA408 (miR408) in SE remains elusive. Here, we used stable transgenic technology in longan (Dimocarpus longan) embryogenic calli to verify the mechanism by which miR408 promotes cell division and differentiation of longan early SE. dlo-miR408-3p regulated riboflavin biosynthesis by targeting nudix hydrolase 23 (DlNUDT23), a previously unidentified gene mediating N6-methyladenosine (m6A) modification and influencing RNA homeostasis and cell cycle gene expression during longan early SE. We showed that DlMIR408 overexpression (DlMIR408-OE) promoted 21-nt miRNA biosynthesis. In DlMIR408-OE cell lines, dlo-miR408-3p targeted and downregulated DlNUDT23, promoted riboflavin biosynthesis, decreased flavin mononucleotide (FMN) accumulation, promoted m6A level, and influenced miRNA homeostasis. DNA replication, glycosylphosphatidylinositol (GPI)-anchor biosynthesis, the pentose phosphate pathway, and taurine and hypotaurine metabolism were also closely associated with riboflavin metabolism. In a riboflavin feeding assay, dlo-miR408-3p and pre-miR408 were upregulated and DlNUDT23 was downregulated, increasing the m6A level and cell division and differentiation in longan globular embryos. When riboflavin biosynthesis was inhibited, dlo-miR408-3p was downregulated and DlNUDT23 was upregulated, which decreased m6A modification and inhibited cell division but did not inhibit cell differentiation. FMN artificial demethylated m6A modification affected the homeostasis of precursor miRNA and miRNA. Our results revealed a mechanism underlying dlo-miR408-3p-activated riboflavin biosynthesis in which DlNUDT23 is targeted, m6A modification is dynamically mediated, and cell division is affected, promoting early SE in plants.

microRNA408 and its encoded peptide regulate sulfur assimilation and arsenic stress response in Arabidopsis

MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in regulating various developmental and biological processes. The expression of miRNAs is differentially modulated in response to various biotic and abiotic stresses. Recent findings have shown that some pri-miRNAs encode small regulatory peptides known as microRNA-encoded peptides (miPEPs). miPEPs regulate the growth and development of plants by modulating corresponding miRNA expression; however, the role of these peptides under different stress conditions remains unexplored. Here, we report that pri-miR408 encodes a small peptide, miPEP408, that regulates the expression of miR408, its targets, and associated phenotype in Arabidopsis. We also report that miR408, apart from Plantacyanin (ARPN) and Laccase3 (LAC3), targets a glutathione S-transferase (GSTU25) that plays a role in sulfur assimilation and exhibits a range of detoxification activities with the environmental pollutant. Plants overexpressing miR408 showed severe sensitivity under low sulfur (LS), arsenite As(III), and LS + As(III) stress, while miR408 mutants developed using the CRISPR/Cas9 approach showed tolerance. Transgenic lines showed phenotypic alteration and modulation in the expression of genes involved in the sulfur reduction pathway and affect sulfate and glutathione accumulation. Similar to miR408 overexpressing lines, the exogenous application of synthetic miPEP408 and miPEP408OX lines led to sensitivity in plants under LS, As(III), and combined LS + As(III) stress compared to the control. This study suggests the involvement of miR408 and miPEP408 in heavy metal and nutrient deficiency responses through modulation of the sulfur assimilation pathway.

Delineating the tissue-mediated drought stress governed tuning of conserved miR408 and its targets in rice

Engineering drought tolerance in rice needs to focus on regulators that enhance tolerance while boosting plant growth and vigor. The present study delineated the concealed function and tissue-mediated interplay of the miR408/target module in imparting drought stress tolerance in rice. The plant miR408 family comprises three dominant mature forms (21 nt), including a distinct monocot variant (F-7 with 5' C) and is divided into six groups. miR408 majorly cleaves genes belonging to the blue copper protein in addition to several other species-specific targets in plants. Comparative sequence analysis in 4726 rice accessions identified 22 sequence variants (SNP and InDELs) in its promoter (15) and pre-miR408 region. Haplotype analysis of the sequence variants indicated eight haplotypes (three: Japonica-specific and five: Indica-specific) of the miR408 promoter. In drought-tolerant Nagina 22, miR408 follows flag leaf preferential expression. Under drought conditions, its levels are upregulated in flag leaf and roots which seems to be regulated by a differential fraction of methylated cytosines (mCs) in the precursor region. The active pool of miR408 regulated targets under control and drought conditions is impacted by the tissue type. Comparative expression analysis of the miR408/target module under different sets of conditions features 83 targets exhibiting antagonistic expression in rice, out of which 12 genes, including four PLANTACYANINS (OsUCL6, 7, 9 and 30), PIRIN, OsLPR1, OsCHUP1, OsDOF12, OsBGLU1, glycine-rich cell wall gene, OsDUT, and OsERF7, are among the high confidence targets. Further, overexpression of MIR408 in drought-sensitive rice cultivar (PB1) leads to the massive enhancement of vegetative growth in rice with improved ETR and Y(II) and enhanced dehydration stress tolerance. The above results suggest that miR408 is likely to act as a positive regulator of growth and vigor, as well as dehydration stress, making it a potential candidate for engineering drought tolerance in rice.

Whole transcriptome analysis and construction of a ceRNA regulatory network related to leaf and petiole development in Chinese cabbage (Brassica campestris L. ssp. pekinensis)

BACKGROUND

The growth and development of leaves and petioles have a significant effect on photosynthesis. Understanding the molecular mechanisms underlying leaf and petiole development is necessary for improving photosynthetic efficiency, cultivating varieties with high photosynthetic efficiency, and improving the yield of crops of which the leaves are foodstuffs. This study aimed to identify the mRNAs, long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) related to leaf and petiole development in Chinese cabbage (Brassica campestris L. ssp. pekinensis). The data were used to construct a competitive endogenous RNA (ceRNA) network to obtain insights into the mechanisms underlying leaf and petiole development.

RESULTS

The leaves and petioles of the 'PHL' inbred line of Chinese cabbage were used as research materials for whole transcriptome sequencing. A total of 10,646 differentially expressed (DE) mRNAs, 303 DElncRNAs, 7 DEcircRNAs, and 195 DEmiRNAs were identified between leaves and petioles. Transcription factors and proteins that play important roles in leaf and petiole development were identified, including xyloglucan endotransglucosylase/hydrolase, expansion proteins and their precursors, transcription factors TCP15 and bHLH, lateral organ boundary domain protein, cellulose synthase, MOR1-like protein, and proteins related to plant hormone biosynthesis. A ceRNA regulatory network related to leaf and petiole development was constructed, and 85 pairs of ceRNA relationships were identified, including 71 DEmiRNA-DEmRNA, 12 DEmiRNA-DElncRNA, and 2 DEmiRNA-DEcircRNA pairs. Three LSH genes (BrLSH1, BrLSH2 and BrLSH3) with significant differential expression between leaves and petioles were screened from transcriptome data, and their functions were explored through subcellular localization analysis and transgenic overexpression verification. BrLSH1, BrLSH2 and BrLSH3 were nuclear proteins, and BrLSH2 inhibited the growth and development of Arabidopsis thaliana.

CONCLUSIONS

This study identifies mRNAs and non-coding RNAs that may be involved in the development of leaves and petioles in Chinese cabbage, and establishes a ceRNA regulatory network related to development of the leaves and petioles, providing valuable genomic resources for further research on the molecular mechanisms underlying leaf and petiole development in this crop species.

Characterization of plant laccase genes and their functions

Laccase is a copper-containing polyphenol oxidase found in different organisms. The multigene family that encodes laccases is widely distributed in plant genomes. Plant laccases oxidize monolignols to produce lignin which is important for plant growth and stress responses. Industrial applications of fungal and bacterial laccases are extensively explored and addressed. Recently many studies have focused on the significance of plant laccase, particularly in crop yield, and its functions in different environmental conditions. This review summarizes the transcriptional and posttranscriptional regulation of plant laccase genes and their functions in plant growth and development. It especially describes the responses of laccase genes to various stresses and their contributions to plant biotic and abiotic stress resistance. In-depth explanations and scientific advances will serve as foundations for research into plant laccase genes' function, mechanism, and possible applications.

Tweaking the Small Non-Coding RNAs to Improve Desirable Traits in Plant

Plant transcriptome contains an enormous amount of non-coding RNAs (ncRNAs) that do not code for proteins but take part in regulating gene expression. Since their discovery in the early 1990s, much research has been conducted to elucidate their function in the gene regulatory network and their involvement in plants' response to biotic/abiotic stresses. Typically, 20-30 nucleotide-long small ncRNAs are a potential target for plant molecular breeders because of their agricultural importance. This review summarizes the current understanding of three major classes of small ncRNAs: short-interfering RNAs (siRNAs), microRNA (miRNA), and transacting siRNAs (tasiRNAs). Furthermore, their biogenesis, mode of action, and how they have been utilized to improve crop productivity and disease resistance are discussed here.

Understanding source-sink interactions: Progress in model plants and translational research to crops

Agriculture is facing a massive increase in demand per hectare as a result of an ever-expanding population and environmental deterioration. While we have learned much about how environmental conditions and diseases impact crop yield, until recently considerably less was known concerning endogenous factors, including within-plant nutrient allocation. In this review, we discuss studies of source-sink interactions covering both fundamental research in model systems under controlled growth conditions and how the findings are being translated to crop plants in the field. In this respect we detail efforts aimed at improving and/or combining C₃, C₄, and CAM modes of photosynthesis, altering the chloroplastic electron transport chain, modulating photorespiration, adopting bacterial/algal carbon-concentrating mechanisms, and enhancing nitrogen- and water-use efficiencies. Moreover, we discuss how modulating TCA cycle activities and primary metabolism can result in increased rates of photosynthesis and outline the opportunities that evaluating natural variation in photosynthesis may afford. Although source, transport, and sink functions are all covered in this review, we focus on discussing source functions because the majority of research has been conducted in this field. Nevertheless, considerable recent evidence, alongside the evidence from classical studies, demonstrates that both transport and sink functions are also incredibly important determinants of yield. We thus describe recent evidence supporting this notion and suggest that future strategies for yield improvement should focus on combining improvements in each of these steps to approach yield optimization.

Independent Responses of Photosynthesis and Plant Morphology to Alterations of PIF Proteins and Light-Dependent MicroRNA Contents in Arabidopsis thaliana pif Mutants Grown under Lights of Different Spectral Compositions

The effects of the quality of light on the content of phytochrome interacting factors (PIFs) such as PIF3, PIF4 and PIF5, as well as the expression of various light-dependent microRNAs, in adult Arabidopsis thaliana pif mutant plants (pif4, pif5, pif3pif5, pif4pif5, pif3pif4pif5) were studied. We demonstrate that under blue light, the pif4 mutant had maximal expression of most of the studied microRNAs (miR163, miR319, miR398, miR408, miR833) when the PIF4 protein in plants was reduced. This finding indicates that the PIF4 protein is involved in the downregulation of this group of microRNAs. This assumption is additionally confirmed by the fact that under the RL spectrum in pif5 mutants, practically the same miRNAs decrease expression against the background of an increase in the amount of PIF4 protein. Unlike the WT and other mutants, the pif4 mutant responded to the BL spectrum not only by activating the expression of light-dependent miRNAs, but also by a significant increase in the expression of transcription factors and key light signalling genes. These molecular reactions do not affect the activity of photosynthesis but may be involved in the formation of a light quality-dependent phenotype.

miR-4739/ITGA10/PI3K signaling regulates differentiation and apoptosis of osteoblast

Introduction

To probe the impacts and biological roles of miR-4739/ITGA10 on the proliferation, differentiation and apoptosis of osteoblasts.

Methods

Bioinformatics analysis was conducted to screen the key genes in osteoporosis. The upstream miRNAs of ITGA10 were predicted by TargetScan. KEGG pathway enrichment analysis was performed by DAVID database. The osteoblast proliferation and apoptosis were measured using CCK-8 and flow cytometry. The differentiation markers were measured by qRT-PCR and western blotting. The luciferase reporter assay was conducted to verify the binding of miR-4739 to ITGA10.

Results

ITGA10 was down-regulated in patients with osteoporosis and identified as the key gene in osteoporosis by the bioinformatics analysis. Then the prediction provided by TargetScan indicated that miR-4739 was the potential upstream miRNA for ITGA10. And the following luciferase reporter assay showed that miR-4739 could bind to ITGA10 3′UTR. Furthermore, the miR-4739 inhibitor promoted osteoblasts proliferation, differentiation, and inhibited cell apoptosis by increasing the expression of ITGA10 and subsequently activating the PI3K/AKT signaling pathway.

Conclusions

Overall, we proved that the higher expression of miR-4739 participated in the progression of osteoporosis by targeting ITGA10 and modulating PI3K/AKT signaling pathway, and perhaps miR-4739/ITGA10 axis could be potential diagnostic markers and therapeutic target for osteoporosis.

Analysis of Homologous Regions of Small RNAs MIR397 and MIR408 Reveals the Conservation of Microsynteny among Rice Crop-Wild Relatives

MIRNAs are small non-coding RNAs that play important roles in a wide range of biological processes in plant growth and development. MIR397 (involved in drought, low temperature, and nitrogen and copper (Cu) starvation) and MIR408 (differentially expressed in response to environmental stresses such as copper, light, mechanical stress, dehydration, cold, reactive oxygen species, and drought) belong to conserved MIRNA families that either negatively or positively regulate their target genes. In the present study, we identified the homologs of MIR397 and MIR408 in Oryza sativa and its six wild progenitors, three non-Oryza species, and one dicot species. We analyzed the 100 kb segments harboring MIRNA homologs from 11 genomes to obtain a comprehensive view of their community evolution around these loci in the farthest (distant) relatives of rice. Our study showed that mature MIR397 and MIR408 were highly conserved among all Oryza species. Comparative genomics analyses also revealed that the microsynteny of the 100 kb region surrounding MIRNAs was only conserved in Oryza spp.; disrupted in Sorghum, maize, and wheat; and completely lost in Arabidopsis. There were deletions, rearrangements, and translocations within the 100 kb segments in Oryza spp., but the overall microsynteny of the region was maintained. The phylogenetic analyses of the precursor regions of all MIRNAs under study revealed a bimodal clade of common origin. This comparative analysis of miRNA involved in abiotic stress tolerance in plants provides a powerful tool for future Oryza research. Crop wild relatives (CWRs) offer multiple traits with potential to decrease the amount of yield loss owing to biotic and abiotic stresses. Using a comparative genomics approach, the exploration of CWRs as a source of tolerance to these stresses by understanding their evolution can be further used to leverage their yield potential.

Genome-wide identification of miRNAs and targets associated with cell wall biosynthesis: Differential roles of dlo-miR397a and dlo-miR408-3p during early somatic embryogenesis in longan

The dynamic alterations in cell wall (CW) biosynthesis play an essential role in physiological isolation during the plant somatic embryogenesis (SE). However, the mechanisms underlying the functions of cell wall-associated miRNAs (CW-miRNA) remain poorly understood in plant SE. Here, we have identified 36 distinct candidate miRNAs associated with CW biosynthesis from longan third-generation genome as well as miRNA transcriptome, and modified RLM-RACE validated four distinct miRNA, which specifically targeted four CW-related genes. More importantly, we found that the dlo-miR397a-antagomir significantly enhanced DlLAC7 expression and improved laccase activity. Interestingly, inhibition of dlo-miR397a increased CW lignin deposition and promoted the tightening of protodermal cell by miRNA-mimic technology during early SE. Moreover, overexpression of dlo-miR408-3p (dlo-miR408-3p-agomir) markedly decreased DlLAC12 expression. dlo-miR408-3p-agomir activated rapid cell division, thus promoting the globular embryo (GE) development, which might be due to high DNA synthesis activity in protoepidermal cells, rather than affecting lignin synthesis. The subcellular location also indicated that both DlLAC7 and DlLAC12 proteins were primarily localized in CW and regulated CW biosynthesis. Overall, our findings provided new insight on the molecular regulatory networks comprising various miRNAs associated with cell wall, and established that dlo-miR397a and dlo-miR408-3p played differential roles during early SE in longan. The findings also shed some light on the potential role of miRNA target DlLAC regulating in vivo embryonic development of plant.

Integration of mRNA and miRNA analysis reveals the differentially regulatory network in two different Camellia oleifera cultivars under drought stress

Camellia oleifera Abel. (C. oleifera) is an edible oil tree species that provide an important guarantee for targeted poverty alleviation strategy in China. Severe difficulties in irrigation leading to drought stress have become a major obstacle to the development of the C. oleifera planting industry. Breeding of drought-tolerant cultivars is the main idea for solving the problem of water shortage stress in C. oleifera cultivation. The photosynthetic physiology traits of C. oleifera cultivars 'Xianglin No.1' and 'Hengdong No.2' were affected by drought stress to different degrees, which demonstrated that the two cultivars suffered different degrees of damage. In the present study, we applied mRNA-seq and miRNA-seq to analyze the difference in molecular responses between drought stress and control, drought-tolerant and -sensitive cultivars, at mRNA and miRNA levels. The differentially expressed genes (DEGs) involved in photosynthesis-related, porphyrin, and chlorophyll metabolism, circadian rhythm system, and plant hormone signal transduction pathways were identified that might be candidates for drought stress tolerance genes. Subsequently, the miRNA-mRNA regulatory networks connected the differentially expressed miRNAs (DEMs) to their predicted target genes were established. miR398 and miR408-3p in C. oleifera showed that associated with the response to drought stress by negatively regulating genes encoding Downy Mildew Resistance 6 (DMR6) and Enhanced Disease Resistance 2 (EDR2), respectively, which might further improve drought tolerance via crosstalk between different stress-responsive pathways. The quantitation results of miRNA and mRNA were validated by quantitative real-time PCR (qRT-PCR). In summary, the integrated mRNA-seq and miRNA-seq analysis deepen our understanding of the regulatory network response to drought stress and variety-specific responses improving drought tolerance in C. oleifera.

Preparation of a miR-155-activating nucleic acid nanoflower to study the molecular mechanism of miR-155 in inflammation

At present, the molecular mechanisms underlying inflammation remain unclear. In recent years, research on inflammation has focused on stimulating cell inflammation by using exogenous pro-inflammatory substances such as lipopolysaccharide (LPS) or inflammatory factors. To investigate the molecular mechanism of inflammation from a new perspective, we designed a nucleic acid nanoflowers (NFs) complex to directly activate inflammatory genes to study the inflammatory response without the need for external microbial factors to trigger an inflammatory response. An RNAa-type target gene-activated NFs was designed. Human umbilical vein endothelial cells (HUVECs) were transfected with NFs carrying small activating RNA (saRNAs) to directly co-activate microRNA (miR)-155 and SHIP1 genes. After RNA activation (RNAa)-type NFs were transferred into HUVECs, the expression of miR-155 and pro-inflammatory and cancer-related factors increased, anti-inflammatory factors were reduced, cell proliferation increased, and cell migration was promoted. IL-1β protein levels were decreased and SHIP1 expression was downregulated. When miR-155 and its target SHIP1 were both activated, the expression of both was unaltered, maintaining cell homeostasis. This points towards miR-155 overexpression can trigger inflammation, and that miR-155 and its target genes act as a molecular switch role in the development of inflammation.

Catalase (CAT) Gene Family in Wheat (Triticum aestivum L.): Evolution, Expression Pattern and Function Analysis

Catalases (CATs) are present in almost all living organisms and play important roles in plant development and response to various stresses. However, there is relatively little information on CAT genes in wheat and related Triticeae species. A few studies on CAT family genes in wheat have been reported. In this study, ten CAT proteins (TaCATs) were identified in wheat and classified into three groups based on their phylogenetic features and sequence analysis. The analysis of the structure and motif composition of the TaCAT proteins suggested that a segmental duplication event occurred in the TaCAT gene family. Collinearity relationship analysis among different species showed that there were three orthologous CAT genes in rice and in maize. By analyzing the cis-elements in the promoter regions, we speculated that TaCAT genes expression might be regulated by light, oxygen deficit, methyl jasmonate and abscisic acid, and by transcription factors such as MYB. A Gene Ontology (GO)-based analysis showed that TaCAT proteins may be related to the response to various stresses, are cytoplasm localized, and may function as antioxidant enzymes. RT-qPCR and transcriptome data analyses exhibited distinct expression patterns of TaCAT genes in different tissues and in response to various treatments. In this study, a comprehensive analysis of wheat CAT genes was performed, enriching our knowledge of CAT genes and providing a foundation for further functional analyses of this gene family in wheat.

The Evolution and Functional Roles of miR408 and Its Targets in Plants

MicroRNA408 (miR408) is an ancient and highly conserved miRNA, which is involved in the regulation of plant growth, development and stress response. However, previous research results on the evolution and functional roles of miR408 and its targets are relatively scattered, and there is a lack of a systematic comparison and comprehensive summary of the detailed evolutionary pathways and regulatory mechanisms of miR408 and its targets in plants. Here, we analyzed the evolutionary pathway of miR408 in plants, and summarized the functions of miR408 and its targets in regulating plant growth and development and plant responses to various abiotic and biotic stresses. The evolutionary analysis shows that miR408 is an ancient and highly conserved microRNA, which is widely distributed in different plants. miR408 regulates the growth and development of different plants by down-regulating its targets, encoding blue copper (Cu) proteins, and by transporting Cu to plastocyanin (PC), which affects photosynthesis and ultimately promotes grain yield. In addition, miR408 improves tolerance to stress by down-regulating target genes and enhancing cellular antioxidants, thereby increasing the antioxidant capacity of plants. This review expands and promotes an in-depth understanding of the evolutionary and regulatory roles of miR408 and its targets in plants.

Integrative small RNA and transcriptome analysis provides insight into key role of miR408 towards drought tolerance response in cowpea

Drought stress response studies and overexpression of vun-miR408 proved it to be essential for abiotic stress tolerance in cowpea. Small RNA and transcriptome sequencing of an elite high-yielding drought-tolerant Indian cowpea cultivar, Pusa Komal revealed a differential expression of 198 highly conserved, 21 legume-specific, 14 less-conserved, and 10 novel drought-responsive microRNAs (miRNAs) along with 3391 (up-regulated) and 3799 (down-regulated) genes, respectively, in the leaf and root libraries. Among the differentially expressed miRNAs, vun-miR408-3p, showed an up-regulation of 3.53-log₂-fold change under drought stress. Furthermore, laccase 12 (LAC 12) was identified as the potential target of vun-miR408-3p using 5' RNA ligase-mediated rapid amplification of cDNA ends. The stable transgenic cowpea lines overexpressing artificial vun-miR408-3p (OX-amiR408) displayed enhanced drought and salinity tolerance as compared to the wild-type plants. An average increase of 30.17% in chlorophyll, 26.57% in proline, and 27.62% in relative water content along with lesser cellular H₂O₂ level was observed in the transgenic lines in comparison with the wild-type plants under drought stress. Additionally, the scanning electron microscopic study revealed a decrease in the stomatal aperture and an increase in the trichome density in the transgenic lines. The expression levels of laccase 3 and laccase 12, the potential targets of miR408, related to lipid catabolic processes showed a significant reduction in the wild-type plants under drought stress and the transgenic lines, indicating the regulation of lignin content as a plausibly essential trait related to the drought tolerance in cowpea. Taken together, this study primarily focused on identification of drought-responsive miRNAs and genes in cowpea, and functional validation of role of miR408 towards drought stress response in cowpea.

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.

Non-Coding RNAs in Response to Drought Stress

Drought stress causes changes in the morphological, physiological, biochemical and molecular characteristics of plants. The response to drought in different plants may vary from avoidance, tolerance and escape to recovery from stress. This response is genetically programmed and regulated in a very complex yet synchronized manner. The crucial genetic regulations mediated by non-coding RNAs (ncRNAs) have emerged as game-changers in modulating the plant responses to drought and other abiotic stresses. The ncRNAs interact with their targets to form potentially subtle regulatory networks that control multiple genes to determine the overall response of plants. Many long and small drought-responsive ncRNAs have been identified and characterized in different plant varieties. The miRNA-based research is better documented, while lncRNA and transposon-derived RNAs are relatively new, and their cellular role is beginning to be understood. In this review, we have compiled the information on the categorization of non-coding RNAs based on their biogenesis and function. We also discuss the available literature on the role of long and small non-coding RNAs in mitigating drought stress in plants.

Genome-Wide Characterization of Salt-Responsive miRNAs, circRNAs and Associated ceRNA Networks in Tomatoes

Soil salinization is a major environmental stress that causes crop yield reductions worldwide. Therefore, the cultivation of salt-tolerant crops is an effective way to sustain crop yield. Tomatoes are one of the vegetable crops that are moderately sensitive to salt stress. Global market demand for tomatoes is huge and growing. In recent years, the mechanisms of salt tolerance in tomatoes have been extensively investigated; however, the molecular mechanism through which non-coding RNAs (ncRNAs) respond to salt stress is not well understood. In this study, we utilized small RNA sequencing and whole transcriptome sequencing technology to identify salt-responsive microRNAs (miRNAs), messenger RNAs (mRNAs), and circular RNAs (circRNAs) in roots of M82 cultivated tomato and Solanum pennellii (S. pennellii) wild tomato under salt stress. Based on the theory of competitive endogenous RNA (ceRNA), we also established several salt-responsive ceRNA networks. The results showed that circRNAs could act as miRNA sponges in the regulation of target mRNAs of miRNAs, thus participating in the response to salt stress. This study provides insights into the mechanisms of salt tolerance in tomatoes and serves as an effective reference for improving the salt tolerance of salt-sensitive cultivars.

miRNAs play critical roles in response to abiotic stress by modulating cross-talk of phytohormone signaling

One of the most interesting signaling molecules that regulates a wide array of adaptive stress responses in plants are the micro RNAs (miRNAs) that are a unique class of non-coding RNAs constituting novel mechanisms of post-transcriptional gene regulation. Recent studies revealed the role of miRNAs in several biotic and abiotic stresses by regulating various phytohormone signaling pathways as well as by targeting a number of transcription factors (TFs) and defense related genes. Phytohormones are signal molecules modulating the plant growth and developmental processes by regulating gene expression. Studies concerning miRNAs in abiotic stress response also show their vital roles in abiotic stress signaling. Current research indicates that miRNAs may act as possible candidates to create abiotic stress tolerant crop plants by genetic engineering. Yet, the detailed mechanism governing the dynamic expression networks of miRNAs in response to stress tolerance remains unclear. In this review, we provide recent updates on miRNA-mediated regulation of phytohormones combating various stress and its role in adaptive stress response in crop plants.

MicroRNAs in Woody Plants

MicroRNAs (miRNAs) are small (∼21-nucleotides) non-coding RNAs found in plant and animals. MiRNAs function as critical post-transcriptional regulators of gene expression by binding to complementary sequences in their target mRNAs, leading to mRNA destabilization and translational inhibition. Plant miRNAs have some distinct characteristics compared to their animal counterparts, including greater evolutionary conservation and unique miRNA processing methods. The lifecycle of a plant begins with embryogenesis and progresses through seed germination, vegetative growth, reproductive growth, flowering and fruiting, and finally senescence and death. MiRNAs participate in the transformation of plant growth and development and directly monitor progression of these processes and the expression of certain morphological characteristics by regulating transcription factor genes involved in cell growth and differentiation. In woody plants, a large and rapidly increasing number of miRNAs have been identified, but their biological functions are largely unknown. In this review, we summarize the progress of miRNA research in woody plants to date. In particular, we discuss the potential roles of these miRNAs in growth, development, and biotic and abiotic stresses responses in woody plants.

Overexpression of Os-microRNA408 enhances drought tolerance in perennial ryegrass

As a conserved microRNA (miRNA) family in plants, miR408 is known to be involved in different abiotic stress responses, including drought. Interestingly, some studies indicated a species- and/or cultivar-specific drought-responsive characteristic of miR408 in plant drought stress. Moreover, the functions of miR408 in perennial grass species are unknown. In this study, we investigated the role of miR408 in perennial ryegrass (Lolium perenne L.) by withholding water for 10 days for both wild type and transgenic plants with heterologous expression of rice (Oryza sativa L.) miR408 gene, Os-miR408. The results showed that transgenic perennial ryegrass plants displayed morphological changes under normal growth conditions, such as curl leaves and sunken stomata, which could be related to decreased leaf water loss. Moreover, transgenic perennial ryegrass exhibited improved drought tolerance, as demonstrated by maintaining higher leaf relative water content (RWC), lower electrolyte leakage (EL), and less lipid peroxidation compared to WT plants under drought stress. Furthermore, the transgenic plants showed higher antioxidative capacity under drought. These results showed that the improved drought tolerance in Os-miR408 transgenic plants could be due to leaf morphological changes favoring the maintenance of water status and to increased antioxidative capacity protecting against the reactive oxygen species damages under stress. These findings implied that miR408 could serve as a potential target for genetic manipulations to engineer perennial grass plants for improved water stress tolerance.

Efficient deletion of multiple circle RNA loci by CRISPR-Cas9 reveals Os06circ02797 as a putative sponge for OsMIR408 in rice

CRISPR-Cas9 is an emerging genome editing tool for reverse genetics in plants. However, its application for functional study of non-coding RNAs in plants is still at its infancy. Despite being a major class of non-coding RNAs, the biological roles of circle RNAs (circRNAs) remain largely unknown in plants. Previous plant circRNA studies have focused on identification and annotation of putative circRNAs, with their functions largely uninvestigated by genetic approaches. Here, we applied a multiplexed CRISPR-Cas9 strategy to efficiently acquire individual null mutants for four circRNAs in rice. We showed each of these rice circRNA loci (Os02circ25329, Os06circ02797, Os03circ00204 and Os05circ02465) can be deleted at 10% or higher efficiency in both protoplasts and stable transgenic T0 lines. Such high efficiency deletion enabled the generation of circRNA null allele plants without the CRISPR-Cas9 transgene in the T1 generation. Characterization of the mutants reveals these circRNAs' participation in salt stress response during seed germination and in particular the Os05circ02465 null mutant showed high salt tolerance. Notably, the seedlings of the Os06circ02797 mutant showed rapid growth phenotype after seed germination with the seedlings containing higher chlorophyll A/B content. Further molecular and computational analyses suggested a circRNA-miRNA-mRNA regulatory network where Os06circ02797 functions to bind and sequester OsMIR408, an important and conserved microRNA in plants. This study not only presents genetic evidence for the first time in plants that certain circRNAs may serve as sponges to negatively regulate miRNAs, a phenomenon previously demonstrated in mammalian cells, but also provides important insights for improving agronomic traits through gene editing of circRNA loci in crops.

Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean

BACKGROUND

Castor bean (Ricinus communis L.) is an important oil crop, which belongs to the Euphorbiaceae family. The seed oil of castor bean is currently the only commercial source of ricinoleic acid that can be used for producing about 2000 industrial products. However, it remains largely unknown regarding the origin, domestication, and the genetic basis of key traits of castor bean.

RESULTS

Here we perform a de novo chromosome-level genome assembly of the wild progenitor of castor bean. By resequencing and analyzing 505 worldwide accessions, we reveal that the accessions from East Africa are the extant wild progenitors of castor bean, and the domestication occurs ~ 3200 years ago. We demonstrate that significant genetic differentiation between wild populations in Kenya and Ethiopia is associated with past climate fluctuation in the Turkana depression ~ 7000 years ago. This dramatic change in climate may have caused the genetic bottleneck in wild castor bean populations. By a genome-wide association study, combined with quantitative trait locus analysis, we identify important candidate genes associated with plant architecture and seed size.

CONCLUSIONS

This study provides novel insights of domestication and genome evolution of castor bean, which facilitates genomics-based breeding of this important oilseed crop and potentially other tree-like crops in future.

PCirc: random forest-based plant circRNA identification software

Background

Circular RNA (circRNA) is a novel type of RNA with a closed-loop structure. Increasing numbers of circRNAs are being identified in plants and animals, and recent studies have shown that circRNAs play an important role in gene regulation. Therefore, identifying circRNAs from increasing amounts of RNA-seq data is very important. However, traditional circRNA recognition methods have limitations. In recent years, emerging machine learning techniques have provided a good approach for the identification of circRNAs in animals. However, using these features to identify plant circRNAs is infeasible because the characteristics of plant circRNA sequences are different from those of animal circRNAs. For example, plants are extremely rich in splicing signals and transposable elements, and their sequence conservation in rice, for example is far less than that in mammals. To solve these problems and better identify circRNAs in plants, it is urgent to develop circRNA recognition software using machine learning based on the characteristics of plant circRNAs.

Results

In this study, we built a software program named PCirc using a machine learning method to predict plant circRNAs from RNA-seq data. First, we extracted different features, including open reading frames, numbers of k-mers, and splicing junction sequence coding, from rice circRNA and lncRNA data. Second, we trained a machine learning model by the random forest algorithm with tenfold cross-validation in the training set. Third, we evaluated our classification according to accuracy, precision, and F1 score, and all scores on the model test data were above 0.99. Fourth, we tested our model by other plant tests, and obtained good results, with accuracy scores above 0.8. Finally, we packaged the machine learning model built and the programming script used into a locally run circular RNA prediction software, Pcirc (https://github.com/Lilab-SNNU/Pcirc).

Conclusion

Based on rice circRNA and lncRNA data, a machine learning model for plant circRNA recognition was constructed in this study using random forest algorithm, and the model can also be applied to plant circRNA recognition such as Arabidopsis thaliana and maize. At the same time, after the completion of model construction, the machine learning model constructed and the programming scripts used in this study are packaged into a localized circRNA prediction software Pcirc, which is convenient for plant circRNA researchers to use.

Involvement of Arabidopsis Multi-Copper Oxidase-Encoding LACCASE12 in Root-to-Shoot Iron Partitioning: A Novel Example of Copper-Iron Crosstalk

Numerous central biological processes depend on the participation of the essential elements iron (Fe) or copper (Cu), including photosynthesis, respiration, cell wall remodeling and oxidative stress protection. Yet, both Fe and Cu metal cations can become toxic when accumulated in excess. Because of the potent ligand-binding and redox chemistries of these metals, there is a need for the tight and combined homeostatic control of their uptake and distribution. Several known examples pinpoint an inter-dependence of Fe and Cu homeostasis in eukaryotes, mostly in green algae, yeast and mammals, but this is less well understood in multicellular plants to date. In Arabidopsis, Cu deficiency causes secondary Fe deficiency, and this is associated with reduced in vitro ferroxidase activity and decreased root-to-shoot Fe translocation. Here we summarize the current knowledge of the cross-talk between Cu and Fe homeostasis and present a partial characterization of LACCASE12 (LAC12) that encodes a member of the multicopper oxidase (MCO) protein family in Arabidopsis. LAC12 transcript levels increase under Fe deficiency. The phenotypic characterization of two mutants carrying T-DNA insertions suggests a role of LAC12 in root-to-shoot Fe partitioning and in maintaining growth on Fe-deficient substrates. A molecular understanding of the complex interactions between Fe and Cu will be important for combating Fe deficiency in crops and for advancing biofortification approaches.

Genome-Wide Identification of Tannase Genes and Their Function of Wound Response and Astringent Substances Accumulation in Juglandaceae

Tannins are important polyphenol compounds with different component proportions in different plant species. The plants in the Juglandaceae are rich in tannins, including condensed tannins and hydrolyzable tannins. In this study, we identified seven tannase genes (TAs) responsible for the tannin metabolism from walnut, pecan, and Chinese hickory, and three nut tree species in the Juglandaceae, which were divided into two groups. The phylogenetic and sequence analysis showed that TA genes and neighboring clade genes (TA-like genes) had similar sequences compared with other carboxylesterase genes, which may be the origin of TA genes produced by tandem repeat. TA genes also indicated higher expressions in leaf than other tissues and were quickly up-regulated at 3 h after leaf injury. During the development of the seed coat, the expression of the synthesis-related gene GGTs and the hydrolase gene TAs was continuously decreased, resulting in the decrease of tannin content in the dry sample of the seed coat of Chinese hickory. However, due to the reduction in water content during the ripening process, the tannin content in fresh sample increased, so the astringent taste was obvious at the mature stage. In addition, the CcGGTs' expression was higher than CiGGTs in the initiation of development, but CcTAs continued to be down-regulated while CiTA2a and CiTA2b were up-regulated, which may bring about the significant differences in tannin content and astringent taste between Chinese hickory and pecan. These results suggested the crucial role of TAs in wound stress of leaves and astringent ingredient accumulation in seed coats of two nut tree species in the Juglandaceae.

Identification of genuine and novel miRNAs in Amaranthus hypochondriacus from high-throughput sequencing data

Amaranth has been proposed as an exceptional alternative for food security and climate change mitigation. Information about the distribution, abundance, or specificity of miRNAs in amaranth species is scare. Here, small RNAs from seedlings under control, drought, heat, and cold stress conditions of the Amaranthus hypocondriacus variety "Gabriela" were sequenced and miRNA loci identified in the amaranth genome using the ShortStack software. Fifty-three genuine miRNA clustersthirty-nine belonging to conserved families, and fourteen novel, were identified. Identification of their target genes suggests that conserved amaranth miRNAs are involved in growth and developmental processes, as well as stress responses. MiR0005, an amaranth-specific miRNA, exhibited an unusual high level of expression, akin to that of conserved miRNAs. Overall, our results broaden our knowledge regarding the distribution, abundance and expression of miRNAs in amaranth, providing the basis for future research on miRNAs and their functions in this important species.

MicroRNA transcriptomic analysis of the sixth leaf of maize (Zea mays L.) revealed a regulatory mechanism of jointing stage heterosis

BACKGROUND

Zhengdan 958 (Zheng 58 × Chang 7-2), a commercial hybrid that is produced in a large area in China, is the result of the successful use of the heterotic pattern of Reid × Tang-SPT. The jointing stage of maize is the key period from vegetative to reproductive growth, which determines development at later stages and heterosis to a certain degree. MicroRNAs (miRNAs) play vital roles in the regulation of plant development, but how they function in the sixth leaf at the six-leaf (V6) stage to influence jointing stage heterosis is still unclear.

RESULT

Our objective was to study miRNAs in four hybrid combinations developed in accordance with the Reid × Tang-SPT pattern, Zhengdan 958, Anyu 5 (Ye 478 × Chang 7-2), Ye 478 × Huangzaosi, Zheng 58 × Huangzaosi, and their parental inbred lines to explore the mechanism related to heterosis. A total of 234 miRNAs were identified in the sixth leaf at the V6 stage, and 85 miRNAs were differentially expressed between the hybrid combinations and their parental inbred lines. Most of the differentially expressed miRNAs were non-additively expressed, which indicates that miRNAs may participate in heterosis at the jointing stage. miR164, miR1432 and miR528 families were repressed in the four hybrid combinations, and some miRNAs, such as miR156, miR399, and miR395 families, exhibited different expression trends in different hybrid combinations, which may result in varying effects on the heterosis regulatory mechanism.

CONCLUSIONS

The potential targets of the identified miRNAs are related to photosynthesis, the response to plant hormones, and nutrient use. Different hybrid combinations employ different mature miRNAs of the same miRNA family and exhibit different expression trends that may result in enhanced or repressed gene expression to regulate heterosis. Taken together, our results reveal a miRNA-mediated network that plays a key role in jointing stage heterosis via posttranscriptional regulation.

Global identification and characterization of miRNA family members responsive to potassium deprivation in wheat (Triticum aestivum L.)

Potassium (K) is essential for plant growth and stress responses. MicroRNAs (miRNAs) are involved in adaptation to nutrient deprivation through modulating gene expression. Here, we identified the miRNAs responsive to K deficiency in Triticum aestivum based on high-throughput small RNA sequencing analyses. Eighty-nine miRNAs, including 68 previously reported ones and 21 novel ones, displayed differential expression under K deficiency. In Gene Ontology and Kyoto Encyclopedia and Genome analyses, the putative target genes of the differentially expressed miRNAs were categorized into functional groups associated with ADP-binding activity, secondary metabolic pathways, and biosynthesis and metabolism. Functional characterization of tae-miR408, an miRNA significantly down-regulated under K deficiency, revealed its important role in mediating low-K tolerance. Compared with wild type, transgenic tobacco lines overexpressing tae-miR408 showed significantly improved K uptake, biomass, photosynthesis, and reactive oxygen species scavenging under K deficiency. These results show that distinct miRNAs function in the plant response to K deficiency through regulating target genes involved in energy metabolism and various secondary metabolic pathways. Our findings shed light on the plant response to K deficiency mediated by miRNAs in T. aestivum. Distinct miRNAs, such as tae-miR408, are valuable targets for generating crop varieties with improved K-use efficiency.

Identification of candidate miRNAs related in storage root development of sweet potato by high throughput sequencing

Sweet potato (Ipomoea batatas L.) is a food consumed worldwide, an industrial raw material and new energy crop. The storage root is the most economical part of the crop. However, the mechanism of storage root initiation and development is still unclear. In this study, conserved and novel miRNAs during storage root development were identified by high-throughput sequencing technology by constructing small RNA libraries from sweet potato fibrous roots (F) and storage roots at four different developmental stages (storage roots with different diameters: 1 cm, D1; 3 cm, D3; 5 cm, D5 and 10 cm, D10). A total of 61 known miRNAs and 471 novel miRNAs were identified. In addition, 145 differentially expressed miRNAs were identified in the F library compared with the four storage root libraries, with 30 known miRNAs and 115 novel miRNAs. Moreover, the targets of the differentially expressed miRNAs were predicted and their network was further investigated by GO analysis using our previous transcriptome data. The GO analysis revealed that antioxidant activity and binding process were the most enriched terms of the target genes. The secondary structure and expression of six candidate miRNAs including three conserved miRNAs and three novel miRNAs were investigated and their predicted targets were validated by qRT-PCR. The results showed that the expression levels of the miRNAs were all consistent with the sequencing data. Most of the miRNAs and their corresponding targets had obvious negative correlations. This study contributed to elucidating the potential miRNA mediated regulatory mechanism of storage root development in sweet potato. The specific differentially expressed miRNAs in sweet potato storage roots can be used to breed high-yield sweet potatoes and other tuberous root crops.

MicroRNAs Are Involved in Maize Immunity Against Fusarium verticillioides Ear Rot

Fusarium ear rot (FER) caused by Fusarium verticillioides is one of the most common diseases affecting maize production worldwide. FER results in severe yield losses and grain contamination with health-threatening mycotoxins. Although most studies to date have focused on comprehensive analysis of gene regulation in maize during defense responses against F. verticillioides infection, less is known about the role of microRNAs (miRNAs) in this process. We used deep sequencing to compare small RNA libraries from the maize kernels of susceptible (N6) or resistant (BT-1) inbred lines from uninfected plants and upon F. verticillioides infection. We found that pathogen exposure was accompanied by dynamic alterations in expression levels of multiple miRNAs, including new members of previously annotated miRNA families. A combination of transcriptomic, degradomic, and bioinformatics analyses revealed that F. verticillioides-responsive miRNAs and their potential target genes displayed opposite expression patterns in the susceptible and resistant genotypes. Functional category analysis uncovered preferential enrichment of the pathogen-responsive miRNAs and their targets in the phenylpropanoid metabolic processes, plant-pathogen interactions, and plant phytohormone signal transduction pathways. Furthermore, transgenic maize plants overexpressing miR408b exhibited reduced resistance to F. verticillioides infection in a susceptible maize line. These findings provide new insights into the regulatory roles of miRNAs in maize immunity against FER and new resources for breeding disease resistance into maize.

Genome-wide identification of miRNAs and their targets during early somatic embryogenesis in Dimocarpus longan Lour

miRNAs are endogenous regulatory factors that play pivotal roles in post-transcriptional regulation. However, their specific roles in early somatic embryogenesis (SE) remain unclear. Study of the SE system is fundamental for clarifying the molecular mechanisms in Dimocarpus longan. We identified 289 known miRNAs from 106 different miRNA families and 1087 novel miRNAs during early longan SE, including embryogenic callus (EC), incomplete pro-embryogenic culture (ICpEC), globular embryo (GE), and non-embryogenic callus (NEC). The abundances of known miRNAs were concentrated in GE. The differentially expression (DE) miRNAs showed five expression patterns during early SE. Largely miRNAs were expressed highly and specially in EC, ICpEC, and GE, respectively. Some miRNAs and putative target genes were enriched in lignin metabolism. Most potential targets were related to the pathways of plant hormone signal transduction, alternative splicing, tyrosine metabolism and sulfur metabolism in early longan SE. The regulatory relationships between dlo-miR166a-3p and DlHD-zip8, dlo-miR397a and DlLAC7, dlo-miR408-3p and DlLAC12 were confirmed by RNA ligase-mediated rapid amplification of cDNA ends. The expression patterns of eight DE miRNAs detected by qRT-PCR were consistent with RNA-seq. Finally, the miRNA regulatory network in early SE was constructed, which provided new insight into molecular mechanism of early SE in longan.

Biotechnological strategies for improved photosynthesis in a future of elevated atmospheric CO2

The improvement of photosynthesis using biotechnological approaches has been the focus of much research. It is now vital that these strategies be assessed under future atmospheric conditions. The demand for crop products is expanding at an alarming rate due to population growth, enhanced affluence, increased per capita calorie consumption, and an escalating need for plant-based bioproducts. While solving this issue will undoubtedly involve a multifaceted approach, improving crop productivity will almost certainly provide one piece of the puzzle. The improvement of photosynthetic efficiency has been a long-standing goal of plant biotechnologists as possibly one of the last remaining means of achieving higher yielding crops. However, the vast majority of these studies have not taken into consideration possible outcomes when these plants are grown long-term under the elevated CO₂ concentrations (e[CO₂]) that will be evident in the not too distant future. Due to the considerable effect that CO₂ levels have on the photosynthetic process, these assessments should become commonplace as a means of ensuring that research in this field focuses on the most effective approaches for our future climate scenarios. In this review, we discuss the main biotechnological research strategies that are currently underway with the aim of improving photosynthetic efficiency and biomass production/yields in the context of a future of e[CO₂], as well as alternative approaches that may provide further photosynthetic benefits under these conditions.

Integrated Analysis of Small RNA, Transcriptome and Degradome Sequencing Provides New Insights into Floral Development and Abscission in Yellow Lupine (Lupinus luteus L.)

The floral development in an important legume crop yellow lupine (Lupinus luteus L., Taper cv.) is often affected by the abscission of flowers leading to significant economic losses. Small non-coding RNAs (sncRNAs), which have a proven effect on almost all developmental processes in other plants, might be of key players in a complex net of molecular interactions regulating flower development and abscission. This study represents the first comprehensive sncRNA identification and analysis of small RNA, transcriptome and degradome sequencing data in lupine flowers to elucidate their role in the regulation of lupine generative development. As shedding in lupine primarily concerns flowers formed at the upper part of the inflorescence, we analyzed samples from extreme parts of raceme separately and conducted an additional analysis of pedicels from abscising and non-abscising flowers where abscission zone forms. A total of 394 known and 28 novel miRNAs and 316 phased siRNAs were identified. In flowers at different stages of development 59 miRNAs displayed differential expression (DE) and 46 DE miRNAs were found while comparing the upper and lower flowers. Identified tasiR-ARFs were DE in developing flowers and were strongly expressed in flower pedicels. The DEmiR-targeted genes were preferentially enriched in the functional categories related to carbohydrate metabolism and plant hormone transduction pathways. This study not only contributes to the current understanding of how lupine flowers develop or undergo abscission but also holds potential for research aimed at crop improvement.

Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos

Regulation of seed development by small non-coding RNAs (sRNAs) is an important mechanism controlling a crucial phase of the life cycle of seed plants. In this work, sRNAs from seed tissues (zygotic embryos and megagametophytes) and from somatic embryos of Pinus pinaster were analysed to identify putative regulators of seed/embryo development in conifers. In total, sixteen sRNA libraries covering several developmental stages were sequenced. We show that embryos and megagametophytes express a large population of 21-nt sRNAs and that substantial amounts of 24-nt sRNAs were also detected, especially in somatic embryos. A total of 215 conserved miRNAs, one third of which are conifer-specific, and 212 high-confidence novel miRNAs were annotated. MIR159, MIR171 and MIR394 families were found in embryos, but were greatly reduced in megagametophytes. Other families, like MIR397 and MIR408, predominated in somatic embryos and megagametophytes, suggesting their expression in somatic embryos is associated with in vitro conditions. Analysis of the predicted miRNA targets suggests that miRNA functions are relevant in several processes including transporter activity at the cotyledon-forming stage, and sulfur metabolism across several developmental stages. An important resource for studying conifer embryogenesis is made available here, which may also provide insightful clues for improving clonal propagation via somatic embryogenesis.

Construction and analysis of degradome-dependent microRNA regulatory networks in soybean

BACKGROUND

Usually the microRNA (miRNA)-mediated gene regulatory network (GRN) is constructed from the investigation of miRNA expression profiling and target predictions. However, the higher/lower expression level of miRNAs does not always indicate the higher/lower level of cleavages and such analysis, thus, sometimes ignores the crucial cleavage events. In the present work, the degradome sequencing data were employed to construct the complete miRNA-mediated gene regulatory network in soybean, unlike the traditional approach starting with small RNA sequencing data.

RESULTS

We constructed the root-, cotyledon-, leaf- and seed-specific miRNA regulatory networks with the degradome sequencing data and the forthcoming verification of miRNA profiling analysis. As a result, we identified 205 conserved miRNA-target interactions (MTIs) involved with 6 conserved gma-miRNA families and 365 tissue-specific MTIs containing 24 root-specific, 45 leaf-specific, 63 cotyledon-specific and 225 seed-specific MTIs. We found a total of 156 miRNAs in tissue-specific MTIs including 18 tissue-specific miRNAs, however, only 3 miRNAs have consistent tissue-specific expression. Our study showed the degradome-dependent miRNA regulatory networks (DDNs) in four soybean tissues and explored their conservations and specificities.

CONCLUSIONS

The construction of DDNs may provide the complete miRNA-Target interactions in certain plant tissues, leading to the identification of the conserved and tissue-specific MTIs and sub-networks. Our work provides a basis for further investigation of the roles and mechanisms of miRNA-mediated regulation of tissue-specific growth and development in soybean.

Conserved Cu-MicroRNAs in Arabidopsis thaliana Function in Copper Economy under Deficiency

Copper (Cu) is a micronutrient for plants. Three small RNAs, which are up-regulated by Cu deficiency and target transcripts for Cu proteins, are among the most conserved microRNAs in plants. It was hypothesized that these Cu-microRNAs help save Cu for the most essential Cu-proteins under deficiency. Testing this hypothesis has been a challenge due to the redundancy of the Cu microRNAs and the properties of the regulatory circuits that control Cu homeostasis. In order to investigate the role of Cu-microRNAs in Cu homeostasis during vegetative growth, we used a tandem target mimicry strategy to simultaneously inhibit the function of three conserved Cu-microRNAs in Arabidopsis thaliana. When compared to wild-type, transgenic lines that express the tandem target mimicry construct showed reduced Cu-microRNA accumulation and increased accumulation of transcripts that encode Cu proteins. As a result, these mimicry lines showed impaired photosynthesis and growth compared to wild type on low Cu, which could be ascribed to a defect in accumulation of plastocyanin, a Cu-containing photosynthetic electron carrier, which is itself not a Cu-microRNA target. These data provide experimental support for a Cu economy model where the Cu-microRNAs together function to allow maturation of essential Cu proteins under impending deficiency.

Plant Cell Wall Proteomics: A Focus on Monocot Species, Brachypodium distachyon, Saccharum spp. and Oryza sativa

Plant cell walls mostly comprise polysaccharides and proteins. The composition of monocots' primary cell walls differs from that of dicots walls with respect to the type of hemicelluloses, the reduction of pectin abundance and the presence of aromatic molecules. Cell wall proteins (CWPs) differ among plant species, and their distribution within functional classes varies according to cell types, organs, developmental stages and/or environmental conditions. In this review, we go deeper into the findings of cell wall proteomics in monocot species and make a comparative analysis of the CWPs identified, considering their predicted functions, the organs analyzed, the plant developmental stage and their possible use as targets for biofuel production. Arabidopsis thaliana CWPs were considered as a reference to allow comparisons among different monocots, i.e., Brachypodium distachyon, Saccharum spp. and Oryza sativa. Altogether, 1159 CWPs have been acknowledged, and specificities and similarities are discussed. In particular, a search for A. thaliana homologs of CWPs identified so far in monocots allows the definition of monocot CWPs characteristics. Finally, the analysis of monocot CWPs appears to be a powerful tool for identifying candidate proteins of interest for tailoring cell walls to increase biomass yield of transformation for second-generation biofuels production.