Roles of miR319-regulated TCPs in plant development and response to abiotic stress

A viral small interfering RNA-host plant mRNA pathway modulates virus-induced drought tolerance by enhancing autophagy

Virus-induced drought tolerance presents a fascinating facet of biotic-abiotic interaction in plants, yet its molecular intricacies remain unclear. Our study shows that cowpea mild mottle virus (CPMMV) infection enhances drought tolerance in common bean (Phaseolus vulgaris) plants through a virus-derived small interfering RNA (vsiRNA)-activated autophagy pathway. Specifically, a 21 nt vsiRNA originating from the CPMMV Triple Gene Block1 (TGB1) gene targeted the 5' untranslated region (UTR) of the host Teosinte branched 1, Cycloidea, Proliferating Cell Factor (TCP) transcription factor gene PvTCP2, independent of the known role of TGB1 as an RNA silencing suppressor. This targeting attenuated the expression of PvTCP2, which encodes a transcriptional repressor, and in turn upregulated the core autophagy-related gene (ATG) PvATG8c, leading to activated autophagy activity surpassing the level induced by drought or CPMMV infection alone. The downstream EARLY RESPONSIVE TO DEHYDRATION (ERD) effector PvERD15 is a homologue of Arabidopsis thaliana AtERD15, which positively regulates stomatal aperture. PvERD15 was degraded in PvATG8c-mediated autophagy. Therefore, we establish a TGB1-PvTCP2-PvATG8c-PvERD15 module as a trans-kingdom fine-tuning mechanism that contributes to virus-induced drought tolerance in plant-drought-virus interactions.

Identification and Analysis of WRKY Transcription Factors in Response to Cowpea Fusarium Wilt in Cowpea

In plants, WRKY transcription factors play a crucial role in plant growth, development, and response to abiotic and biotic stress. Cowpea (Vigna unguiculata) is an important legume crop. However, cowpea Fusarium wilt (CFW), caused by Fusarium oxysporum f. sp. tracheiphilum (Fot), poses a serious threat to its production. In this study, we systematically identified members of the cowpea WRKY (VuWRKY) gene family and analyzed their expression patterns under CFW stress. A total of 91 WRKY transcription factors were identified in the cowpea genome. Phylogenetic and synteny analyses indicated that the expansion of VuWRKY genes in cowpea is primarily due to recent duplication events. Transcriptome analysis of cowpea inoculated with Fo revealed 31 differentially expressed VuWRKY genes, underscoring their role in the response to CFW infection. Four differentially expressed WRKY genes were selected for validation. Subcellular localization and Western blot assays showed their nuclear localization and normal expression in N. benthamiana. Additionally, yeast one-hybrid assays demonstrated that VuWRKY2 can bind to the promoter region of the Catalase (CAT) gene, indicating its potential role in transcriptional regulation. This study establishes a foundation for further exploration of the role and regulatory mechanisms of VuWRKY genes in response to CFW stress.

Salicylic acid-mediated alleviation of salt stress: Insights from physiological and transcriptomic analysis in Asarum sieboldii Miq

As global agriculture faces the pressing threat of salt stress, innovative solutions are imperative for sustainable agriculture. The remarkable potential of salicylic acid (SA) in enhancing plant resilience against environmental stressors has recently gained attention. However, the specific molecular mechanisms by which SA mitigates salt stress in Asarum sieboldii Miq., a valuable medicinal plant, remain poorly understood. Here, we evaluated the physiological and transcriptomic regulatory responses of A. sieboldii under salt stress (100 mM NaCl), both in the presence (1 mM SA) and absence of exogenous SA. The results highlighted that SA significantly alleviates salt stress, primarily through enhancing antioxidant activities as evidenced by increased superoxide dismutase, and peroxidase activities. Additionally, we observed an increment in chlorophyll (a and b), proline, total soluble sugar, and plant fresh weight, along with a decrease in malondialdehyde contents. Transcriptome analysis suggested consistency in the regulation of many differentially expressed genes and transcription factors (TFs); however, genes targets (GSTs, TIR1, and NPR1), and TFs (MYB, WRKY, TCP, and bHLH) possessed expressional uniqueness, and majority had significantly up-regulated trends in SA-coupled salt stress treatments. Further, bioinformatics and KEGG enrichment analysis indicated several SA-induced significantly enriched biological pathways. Specifically, plant hormone signal transduction was identified as being populated with key genes distinctive to auxin, cytokinin, ethylene, and salicylic acid signaling, suggesting their important role in salt stress alleviation. Inclusively, this report presents a comprehensive analysis encompassing gene targets, TFs, and biological pathways, and these insights may offer a valuable contribution to our knowledge of SA-mediated regulation and its crucial role in enhancing plant defense against diverse abiotic stressors.

Amaranth's Growth and Physiological Responses to Salt Stress and the Functional Analysis of AtrTCP1 Gene

Amaranth species are C4 plants that are rich in betalains, and they are tolerant to salinity stress. A small family of plant-specific TCP transcription factors are involved in the response to salt stress. However, it has not been investigated whether amaranth TCP1 is involved in salt stress. We elucidated that the growth and physiology of amaranth were affected by salt concentrations of 50-200 mmol·L-1 NaCl. The data showed that shoot and root growth was inhibited at 200 mmol·L-1, while it was promoted at 50 mmol·L-1. Meanwhile, the plants also showed physiological responses, which indicated salt-induced injuries and adaptation to the salt stress. Moreover, AtrTCP1 promoted Arabidopsis seed germination. The germination rate of wild-type (WT) and 35S::AtrTCP1-GUS Arabidopsis seeds reached around 92% by the seventh day and 94.5% by the second day under normal conditions, respectively. With 150 mmol·L-1 NaCl treatment, the germination rate of the WT and 35S::AtrTCP1-GUS plant seeds was 27.0% by the seventh day and 93.0% by the fourth day, respectively. Under salt stress, the transformed 35S::AtrTCP1 plants bloomed when they grew 21.8 leaves after 16.2 days of treatment, which was earlier than the WT plants. The transformed Arabidopsis plants flowered early to resist salt stress. These results reveal amaranth's growth and physiological responses to salt stress, and provide valuable information on the AtrTCP1 gene.

Insertion of a miniature inverted-repeat transposable element into the promoter of OsTCP4 results in more tillers and a lower grain size in rice

A class I PCF type protein, TCP4, was identified as a transcription factor associated with both grain size and tillering through a DNA pull-down-MS assay combined with a genome-wide association study. This transcription factor was found to have a significant role in the variations among the 533 rice accessions, dividing them into two main subspecies. A Tourist-like miniature inverted-repeat transposable element (MITE) was discovered in the promoter of TCP4 in japonica/geng accessions (TCP4M+), which was found to suppress the expression of TCP4 at the transcriptional level. The MITE-deleted haplotype (TCP4M-) was mainly found in indica/xian accessions. ChIP-qPCR and EMSA demonstrated the binding of TCP4 to promoters of grain reservoir genes such as SSIIa and Amy3D in vivo and in vitro, respectively. The introduction of the genomic sequence of TCP4M+ into different TCP4M- cultivars was found to affect the expression of TCP4 in the transgenic rice, resulting in decreased expression of its downstream target gene SSIIa, increased tiller number, and decreased seed length. This study revealed that a Tourist-like MITE contributes to subspecies divergence by regulating the expression of TCP4 in response to environmental pressure, thus influencing source-sink balance by regulating starch biosynthesis in rice.

The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling

Plant species utilize a variety of regulatory mechanisms to ensure sustainable productivity. Within this intricate framework, numerous non-coding RNAs (ncRNAs) play a crucial regulatory role in plant biology, surpassing the essential functions of RNA molecules as messengers, ribosomal, and transfer RNAs. ncRNAs represent an emerging class of regulators, operating directly in the form of small interfering RNAs (siRNAs), microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). These ncRNAs exert control at various levels, including transcription, post-transcription, translation, and epigenetic. Furthermore, they interact with each other, contributing to a variety of biological processes and mechanisms associated with stress resilience. This review primarily concentrates on the recent advancements in plant ncRNAs, delineating their functions in growth and development across various organs such as root, leaf, seed/endosperm, and seed nutrient development. Additionally, this review broadens its scope by examining the role of ncRNAs in response to environmental stresses such as drought, salt, flood, heat, and cold in plants. This compilation offers updated information and insights to guide the characterization of the potential functions of ncRNAs in plant growth, development, and stress resilience in future research.

Identification and Profiling Analysis of microRNAs in Guava Fruit (Psidium guajava L.) and Their Role during Ripening

The guava (Psidium guajava L.) is a climacteric fruit with an accelerated post-harvest overripening. miRNAs are small RNA sequences that function as gene regulators in eukaryotes and are essential for their survival and development. In this study, miRNA libraries were constructed, sequenced and analyzed from the breaker and ripe stages of guava fruit cv. Siglo XXI. One hundred and seventy-four mature miRNA sequences from 28 miRNA families were identified. The taxonomic distribution of the guava miRNAs showed a high level of conservation among the dicotyledonous plants. Most of the predicted miRNA target genes were transcription factors and genes involved in the metabolism of phytohormones such as abscisic acid, auxins, and ethylene, as revealed through an ontology enrichment analysis. The miRNA families miR168, miR169, miR396, miR397, and miR482 were classified as being directly associated with maturation, whereas the miRNA families miR160, miR165, miR167, miR3930, miR395, miR398, and miR535 were classified as being indirectly associated. With this study, we intended to increase our knowledge and understanding of the regulatory process involved in the ripening process, thereby providing valuable information for future research on the ripening of guava fruit.

Exploring the Seasonal Dynamics and Molecular Mechanism of Wood Formation in Gymnosperm Trees

Forests, comprising 31% of the Earth's surface, play pivotal roles in regulating the carbon, water, and energy cycles. Despite being far less diverse than angiosperms, gymnosperms account for over 50% of the global woody biomass production. To sustain growth and development, gymnosperms have evolved the capacity to sense and respond to cyclical environmental signals, such as changes in photoperiod and seasonal temperature, which initiate growth (spring and summer) and dormancy (fall and winter). Cambium, the lateral meristem responsible for wood formation, is reactivated through a complex interplay among hormonal, genetic, and epigenetic factors. Temperature signals perceived in early spring induce the synthesis of several phytohormones, including auxins, cytokinins, and gibberellins, which in turn reactivate cambium cells. Additionally, microRNA-mediated genetic and epigenetic pathways modulate cambial function. As a result, the cambium becomes active during the summer, resulting in active secondary xylem (i.e., wood) production, and starts to become inactive in autumn. This review summarizes and discusses recent findings regarding the climatic, hormonal, genetic, and epigenetic regulation of wood formation in gymnosperm trees (i.e., conifers) in response to seasonal changes.

Genome-wide identification and functional analysis of the TCP gene family in rye (Secale cereale L.)

TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) proteins are plant-specific transcription factors that play significant roles in plant growth, development, and stress response. Rye is a high-value crop with strong resistance to adverse environments. However, the functions of TCP proteins in rye are rarely reported. Based on a genome-wide analysis, the present study identified 26 TCP genes (ScTCPs) in rye. Mapping showed an uneven distribution of the ScTCP genes on the seven rye chromosomes and detected three pairs of tandem duplication genes. Phylogenetic analysis divided these genes into PCF (Proliferrating Cell Factors), CIN (CINCINNATA), and CYC (CYCLOIDEA)/TB1 (Teosinte Branched1) classes, which showed the highest homology between rye and wheat genes. Analysis of miRNA targeting sites indicated that five ScTCP genes were identified as potential targets of miRNA319. Promoter cis-acting elements analysis indicated that ScTCPs were regulated by light signals. Further analysis of the gene expression patterns and functional annotations suggested the role of a few ScTCPs in grain development and stress response. In addition, two TB1 homologous genes (ScTCP9 and ScTCP10) were identified in the ScTCP family. Synteny analysis showed that TB1 orthologous gene pairs existed before the ancestral divergence. Finally, the yeast two-hybrid assay and luciferase complementation imaging assay proved that ScTCP9, localized in the nucleus, interacts with ScFT (Flowering locus T), indicating their role in regulating flowering time. Taken together, this comprehensive study of ScTCPs provides important information for further research on gene function and crop improvement.

Simultaneous detection of miRNA and mRNA at the single-cell level in plant tissues

Detecting the simultaneous presence of a microRNA (miRNA) and a mRNA in a specific tissue can provide support for the prediction that the miRNA regulates the mRNA. Although two such methods have been developed for mammalian tissues, they have a low signal-noise ratio and/or poor resolution at the single-cell level. To overcome these drawbacks, we develop a method that uses sequence-specific miRNA-locked nucleic acid (LNA) and mRNA-LNA probes. Moreover, it augments the detection signal by rolling circle amplification, achieving a high signal-noise ratio at the single-cell level. Dot signals are counted for determining the expression levels of mRNA and miRNA molecules in specific cells. We show a high sequence specificity of our miRNA-LNA probe, revealing that it can discriminate single-base mismatches. Numerical quantification by our method is tested in transgenic rice lines with different gene expression levels. We conduct several applications. First, the spatial expression profiling of osa-miR156 and OsSPL12 in rice leaves reveals their specific expression in mesophyll cells. Second, studying rice and its mutant lines with our method reveals opposite expression patterns of miRNA and its target mRNA in tissues. Third, the dynamic expression profiles of ZmGRF8 and zma-miR396 during maize leaf development provide evidence that zma-miR396 regulates the preferential spatial expression of ZmGRF8 in bundle sheath cells. Finally, our method can be scaled up to simultaneously detect multiple miRNAs and mRNAs in a tissue. Thus, it is a sensitive and versatile technique for studying miRNA regulation of plant tissue development.

miR319 and its target TCP4 involved in plant architecture regulation in Brassica napus

Plant architecture is a collection of genetically controlled crop productivity and adaptation. MicroRNAs (miRNAs) have been proved to function in various biological processes, but little is known about how miRNA regulates plant architecture in rapeseed (Brassica napus L.). In this study, four small RNA libraries and two degradome libraries from shoot apex of normal and rod-like plants were sequenced. A total of 639 miRNA precursors and 16 differentially expressed miRNAs were identified in this study. In addition, 322 targets were identified through degradome sequencing. Among them, 14 targets were further validated via RNA ligase-mediated 5' rapid amplification of cDNA ends. Transgenic approach showed that increased TCP4 activity in Arabidopsis resulted in premature onset of maturation and reduced plant size along with early flowering and shortened flowering time. miR319-OE lines in Brassica napus exhibited serrated leaves and abnormal development of shoot apical meristem (SAM), which led to the deformed growth of stem and reduced plant height. In conclusion, our study lays the foundation for elucidating miRNA regulate plant architecture and provides new insight into the miR319/TCP4 module regulates plant architecture in rapeseed.

Characterization of PsmiR319 during flower development in early- and late-flowering tree peonies cultivars

The flowering period is the most important ornamental trait of tree peony, while industrial development of tree peony has been limited by short flowering period. miR319 plays an important regulatory role in plant flowering. In the current study, the expression characteristics and evolution of PsmiR319 in tree peony flowering was explored using 'Feng Dan' and 'Lian He', which are early-flowering and late-flowering varieties of tree peony, respectively. The structure, evolution, and target(s) of PsmiR319 were analyzed by bioinformatics. Evolution analysis showed that pre-PsmiR319 was distributed in 41 plant species, among which the length of the precursor sequence exhibited marked differences (between 52 and 308 bp). Pre-PsmiR319 of tree peony was located close to the corresponding sequences of Linum usitatissimum and Picea abies in the phylogenetic tree, and in addition, could form a typical hairpin structure including a mature body with a length of 20 bp located on the 3p arm and part of the loop sequence. The mature sequence of miR319 was highly conserved among different species. Target genes of PsmiR319 include MYB-related transcription factor in tree peony. Expression of PsmiR319, assayed by qRT-PCR, differed between 'Feng Dan' and 'Lian He' during different flower development periods. PsmiR319 and its target gene showed a negative expression regulation relationship during the periods of CE (color exposure), BS (blooming stage), IF (initial flowering), and HO (half opening) in the early-flowering 'Feng Dan', and the same in FB (Full blooming) periods of late-flowering 'Lian He'. Findings from this study provide a reference for further investigation into the mechanism of miR319 in the development of different varieties of tree peony.

Overexpression of Mtr-miR319a Contributes to Leaf Curl and Salt Stress Adaptation in Arabidopsis thaliana and Medicago truncatula

Salt stress is a worldwide agronomic issue that limits crop yield and quality. Improving salt stress tolerance via genetic modification is the most efficient method to conquer soil salinization problems in crops. Crop miRNAs have been declared to be tightly associated with responding and adapting to salt stress and are advantageous for salt tolerance modification. However, very few studies have validated vital salt tolerance miRNAs and coupled potent target genes in Medicago species, the most economically important forage legume species. In this study, Mtr-miR319a, a miRNA that was identified from the previous next-generation sequencing assay of salt-treated Medicago truncatula, was overexpressed in M. truncatula and Arabidopsis thaliana, inducing the curly leaves and salt stress tolerance phenotypes. Combining the elevated expression level of Mtr-miR319a in the M. truncatula overexpression lines under normal and salt-treatment conditions, the regulatory roles of Mtr-miR319a in leaf development and salt stress adaptation were demonstrated. Several predicted target genes of Mtr-miR319a were also regulated by Mtr-miR319a and were associated with the aforementioned phenotypes in M. truncatula plants, most notably MtTCP4. Our study clarified the functional role of Mtr-miR319a and its target genes in regulating leaf development and defending salt stress, which can help to inform crop breeding efforts for improving salt tolerance via genetic engineering.

Genomic survey of TCP transcription factors in plants: Phylogenomics, evolution and their biology

The TEOSINTE BRANCHED1 (TBI1), CYCLOIDEA (CYC), and PROLIFERATING CELL NUCLEAR ANTIGEN FACTORS (PCF1 and PCF2) proteins truncated as TCP transcription factors carry conserved basic-helix-loop-helix (bHLH) structure, related to DNA binding functions. Evolutionary history of the TCP genes has shown their presence in early land plants. In this paper, we performed a comparative discussion on the current knowledge of the TCP Transcription Factors in lower and higher plants: their evolutionary history based on the phylogenetics of 849 TCP proteins from 37 plant species, duplication events, and biochemical roles in some of the plants species. Phylogenetics investigations confirmed the classification of TCP TFs into Class I (the PCF1/2), and Class II (the C- clade) factors; the Class II factors were further divided into the CIN- and CYC/TB1- subclade. A trace in the evolution of the TCP Factors revealed an absence of the CYC/TB1subclade in lower plants, and an independent evolution of the CYC/TB1subclade in both eudicot and monocot species. 54% of the total duplication events analyzed were biased towards the dispersed duplication, and we concluded that dispersed duplication events contributed to the expansion of the TCP gene family. Analysis in the TCP factors functional roles confirmed their involvement in various biochemical processes which mainly included promoting cell proliferation in leaves in Class I TCPs, and cell division during plant development in Class II TCP Factors. Apart from growth and development, the TCP Factors were also shown to regulate hormonal and stress response pathways. Although this paper does not exhaust the present knowledge of the TCP Transcription Factors, it provides a base for further exploration of the gene family.

The Arabidopsis transcription factor TCP9 modulates root architectural plasticity, reactive oxygen species-mediated processes, and tolerance to cyst nematode infections

Infections by root-feeding nematodes have profound effects on root system architecture and consequently shoot growth of host plants. Plants harbor intraspecific variation in their growth responses to belowground biotic stresses by nematodes, but the underlying mechanisms are not well understood. Here, we show that the transcription factor TEOSINTE BRANCHED/CYCLOIDEA/PROLIFERATING CELL FACTOR-9 (TCP9) modulates root system architectural plasticity in Arabidopsis thaliana in response to infections by the endoparasitic cyst nematode Heterodera schachtii. Young seedlings of tcp9 knock-out mutants display a significantly weaker primary root growth inhibition response to cyst nematodes than wild-type Arabidopsis. In older plants, tcp9 reduces the impact of nematode infections on the emergence and growth of secondary roots. Importantly, the altered growth responses by tcp9 are most likely not caused by less biotic stress on the root system, because TCP9 does not affect the number of infections, nematode development, and size of the nematode-induced feeding structures. RNA-sequencing of nematode-infected roots of the tcp9 mutants revealed differential regulation of enzymes involved in reactive oxygen species (ROS) homeostasis and responses to oxidative stress. We also found that root and shoot growth of tcp9 mutants is less sensitive to exogenous hydrogen peroxide and that ROS accumulation in nematode infection sites in these mutants is reduced. Altogether, these observations demonstrate that TCP9 modulates the root system architectural plasticity to nematode infections via ROS-mediated processes. Our study further points at a novel regulatory mechanism contributing to the tolerance of plants to root-feeding nematodes by mitigating the impact of belowground biotic stresses.

MicroRNAs Mediated Plant Responses to Salt Stress

One of the most damaging issues to cultivatable land is soil salinity. While salt stress influences plant growth and yields at low to moderate levels, severe salt stress is harmful to plant growth. Mineral shortages and toxicities frequently exacerbate the problem of salinity. The growth of many plants is quantitatively reduced by various levels of salt stress depending on the stage of development and duration of stress. Plants have developed various mechanisms to withstand salt stress. One of the key strategies is the utilization of microRNAs (miRNAs) that can influence gene regulation at the post-transcriptional stage under different environmental conditions, including salinity. Here, we have reviewed the miRNA-mediated adaptations of various plant species to salt stress and other abiotic variables. Moreover, salt responsive (SR)-miRNAs, their targets, and corresponding pathways have also been discussed. The review article concludes by suggesting that the utilization of miRNAs may be a vital strategy to generate salt tolerant crops ensuring food security in the future.

Genome-wide analysis of citrus TCP transcription factors and their responses to abiotic stresses

BACKGROUND

Citrus is one of the most important fruit crops in the world, and it is worthy to conduct more research on artificially controlling citrus plant growth and development to adapt to different cultivation patterns and environmental conditions. The plant-specific TEOSINTE BRANCHED1, CYCOLOIDEA, and PROLIFERATING CELL FACTORS (TCP) transcription factors are crucial regulators controlling plant growth and development, as well as responding to abiotic stresses. However, the information about citrus TCP transcription factors remains unclear.

RESULTS

In this study, twenty putative TCP genes (CsTCPs) with the TCP domain were explored from Citrus sinensis genome, of which eleven (CsTCP3, - 4, - 5, - 6, - 10, - 11, - 15, - 16, - 18, - 19, - 20), five (CsTCP1, - 2, - 7, - 9, - 13), and four genes (CsTCP8, - 12, - 14, - 17) were unevenly distributed on chromosomes and divided into three subclades. Cis-acting element analysis indicated that most CsTCPs contained many phytohormone- and environment-responsive elements in promoter regions. All of CsTCPs were predominantly expressed in vegetative tissues or organs (stem, leaf, thorn, and bud) instead of reproductive tissues or organs (flower, fruit, and seed). Combined with collinearity analysis, CsTCP3, CsTCP9, and CsTCP13 may take part in leaf development; CsTCP12 and CsTCP14 may function in shoot branching, leaf development, or thorn development; CsTCP15 may participate in the development of stem, leaf, or thorn. In mature leaf, transcript levels of two CsTCPs (CsTCP19, - 20) were significantly increased while transcript levels of eight CsTCPs (CsTCP2, - 5, - 6, - 7, - 8, - 9, - 10, - 13) were significantly decreased by shading; except for two CsTCPs (CsTCP11, - 19), CsTCPs' transcript levels were significantly influenced by low temperature; moreover, transcript levels of two CsTCPs (CsTCP11, - 12) were significantly increased while five CsTCPs' (CsTCP14, - 16, - 18, - 19, - 20) transcript levels were significantly reduced by drought.

CONCLUSIONS

This study provides significant clues for research on roles of CsTCPs in regulating citrus plant growth and development, as well as responding to abiotic stresses.

Genome-Wide Identification of Binding Sites for SmTCP7a Transcription Factors of Eggplant during Bacterial Wilt Resistance by ChIP-Seq

Teosinte branched 1/cycloidea/proliferating cell factor (TCP) transcription factors play a key role in the regulation of plant biotic and abiotic stresses. In this study, our results show that SmTCP7a positively regulated bacterial wilt that was caused by Ralstonia solanacearum. ChIP-seq was conducted to analyze the transcriptional regulation mechanism of SmTCP7a before (R0 h) and 48 h after infection (R48 h). SmTCP7a regulated a total of 92 and 91 peak-associated genes in R0 h and R48 h, respectively. A KEGG (Kyoto encyclopedia of genes and genomes) pathway analysis showed that phenylpropanoid biosynthesis, MAPK (mitogen-activated protein kinas) signaling pathway, plant hormone signal transduction and plant-pathogen interactions were involved. The difference in peaks between R0 h and R48 h showed that there were three peak-associated genes that were modulated by infection. A better understanding of the potential target genes of SmTCP7a in response to R. solanacearum will provide a comprehensive understanding of the SmTCP7a regulatory mechanism during the eggplant defense response to bacterial wilt.

TCP Transcription Factors Involved in Shoot Development of Ma Bamboo (Dendrocalamus latiflorus Munro)

Ma bamboo (Dendrocalamus latiflorus Munro) is the most widely cultivated clumping bamboo in Southern China and is valuable for both consumption and wood production. The development of bamboo shoots involving the occurrence of lateral buds is unique, and it affects both shoot yield and the resulting timber. Plant-specific TCP transcription factors are involved in plant growth and development, particularly in lateral bud outgrowth and morphogenesis. However, the comprehensive information of the TCP genes in Ma bamboo remains poorly understood. In this study, 66 TCP transcription factors were identified in Ma bamboo at the genome-wide level. Members of the same subfamily had conservative gene structures and conserved motifs. The collinear analysis demonstrated that segmental duplication occurred widely in the TCP transcription factors of Ma bamboo, which mainly led to the expansion of a gene family. Cis-acting elements related to growth and development and stress response were found in the promoter regions of DlTCPs. Expression patterns revealed that DlTCPs have tissue expression specificity, which is usually highly expressed in shoots and leaves. Subcellular localization and transcriptional self-activation experiments demonstrated that the five candidate TCP proteins were typical self-activating nuclear-localized transcription factors. Additionally, the transcriptome analysis of the bamboo shoot buds at different developmental stages helped to clarify the underlying functions of the TCP members during the growth of bamboo shoots. DlTCP12-C, significantly downregulated as the bamboo shoots developed, was selected to further verify its molecular function in Arabidopsis. The DlTCP12-C overexpressing lines exhibited a marked reduction in the number of rosettes and branches compared with the wild type in Arabidopsis, suggesting that DlTCP12-C conservatively inhibits lateral bud outgrowth and branching in plants. This study provides useful insights into the evolutionary patterns and molecular functions of the TCP transcription factors in Ma bamboo and provides a valuable reference for further research on the regulatory mechanism of bamboo shoot development and lateral bud growth.

Integrated Analysis of Physiological, mRNA Sequencing, and miRNA Sequencing Data Reveals a Specific Mechanism for the Response to Continuous Cropping Obstacles in Pogostemon cablin Roots

Pogostemon cablin (patchouli) is a commercially important medicinal and industrial crop grown worldwide for its medicinal and aromatic properties. Patchoulol and pogostone, derived from the essential oil of patchouli, are considered valuable components in the cosmetic and pharmaceutical industries. Due to its high application value in the clinic and industry, the demand for patchouli is constantly growing. Unfortunately, patchouli cultivation has suffered due to severe continuous cropping obstacles, resulting in a significant decline in yield and quality. Moreover, the physiological and transcriptional changes in patchouli in response to continuous cropping obstacles remain unclear. This has greatly restricted the development of the patchouli industry. To explore the mechanism underlying the rapid response of patchouli roots to continuous cropping stress, integrated analysis of the transcriptome and miRNA profiles of patchouli roots under continuous and noncontinuous cropping conditions in different growth periods was conducted using RNA sequencing (RNA-seq) and miRNA-seq and complemented with physiological data. The physiological and biochemical results showed that continuous cropping significantly inhibited root growth, decreased root activity, and increased the activity of antioxidant enzymes (superoxide dismutase, peroxidase, and catalase) and the levels of osmoregulators (malondialdehyde, soluble protein, soluble sugar, and proline). Subsequently, we found 4,238, 3,494, and 7,290 upregulated and 4,176, 3,202, and 8,599 downregulated differentially expressed genes (DEGs) in the three growth periods of continuously cropped patchouli, many of which were associated with primary carbon and nitrogen metabolism, defense responses, secondary metabolite biosynthesis, and transcription factors. Based on miRNA-seq, 927 known miRNAs and 130 novel miRNAs were identified, among which 67 differentially expressed miRNAs (DEMIs) belonging to 24 miRNA families were induced or repressed by continuous cropping. By combining transcriptome and miRNA profiling, we obtained 47 miRNA-target gene pairs, consisting of 18 DEMIs and 43 DEGs, that likely play important roles in the continuous cropping response of patchouli. The information provided in this study will contribute to clarifying the intricate mechanism underlying the patchouli response to continuous cropping obstacles. In addition, the candidate miRNAs and genes can provide a new strategy for breeding continuous cropping-tolerant patchouli.

Controlling flowering of Medicago sativa (alfalfa) by inducing dominant mutations

Breeding plants with polyploid genomes is challenging because functional redundancy hampers the identification of loss-of-function mutants. Medicago sativa is tetraploid and obligate outcrossing, which together with inbreeding depression complicates traditional breeding approaches in obtaining plants with a stable growth habit. Inducing dominant mutations would provide an alternative strategy to introduce domestication traits in plants with high gene redundancy. Here we describe two complementary strategies to induce dominant mutations in the M. sativa genome and how they can be relevant in the control of flowering time. First, we outline a genome-engineering strategy that harnesses the use of microProteins as developmental regulators. MicroProteins are small proteins that appeared during genome evolution from genes encoding larger proteins. Genome-engineering allows us to retrace evolution and create microProtein-coding genes de novo. Second, we provide an inventory of genes regulated by microRNAs that control plant development. Making respective gene transcripts microRNA-resistant by inducing point mutations can uncouple microRNA regulation. Finally, we investigated the recently published genomes of M. sativa and provide an inventory of breeding targets, some of which, when mutated, are likely to result in dominant traits.

CINCINNATA-Like TCP Transcription Factors in Cell Growth - An Expanding Portfolio

Post-mitotic cell growth is a key process in plant growth and development. Cell expansion drives major growth during morphogenesis and is influenced by both endogenous factors and environmental stimuli. Though both isotropic and anisotropic cell growth can contribute to organ size and shape at different degrees, anisotropic cell growth is more likely to contribute to shape change. While much is known about the mechanisms that increase cellular turgor and cell-wall biomass during expansion, the genetic factors that regulate these processes are less studied. In the past quarter of a century, the role of the CINCINNATA-like TCP (CIN-TCP) transcription factors has been well documented in regulating diverse aspects of plant growth and development including flower asymmetry, plant architecture, leaf morphogenesis, and plant maturation. The molecular activity of the CIN-TCP proteins common to these biological processes has been identified as their ability to suppress cell proliferation. However, reports on their role regulating post-mitotic cell growth have been scanty, partly because of functional redundancy among them. In addition, it is difficult to tease out the effect of gene activity on cell division and expansion since these two processes are linked by compensation, a phenomenon where perturbation in proliferation is compensated by an opposite effect on cell growth to keep the final organ size relatively unaltered. Despite these technical limitations, recent genetic and growth kinematic studies have shown a distinct role of CIN-TCPs in promoting cellular growth in cotyledons and hypocotyls, the embryonic organs that grow solely by cell expansion. In this review, we highlight these recent advances in our understanding of how CIN-TCPs promote cell growth.

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.

Combined Stress Conditions in Melon Induce Non-additive Effects in the Core miRNA Regulatory Network

Climate change has been associated with a higher incidence of combined adverse environmental conditions that can promote a significant decrease in crop productivity. However, knowledge on how a combination of stresses might affect plant development is still scarce. MicroRNAs (miRNAs) have been proposed as potential targets for improving crop productivity. Here, we have combined deep-sequencing, computational characterization of responsive miRNAs and validation of their regulatory role in a comprehensive analysis of response of melon to several combinations of four stresses (cold, salinity, short day, and infection with a fungus). Twenty-two miRNA families responding to double and/or triple stresses were identified. The regulatory role of the differentially expressed miRNAs was validated by quantitative measurements of the expression of the corresponding target genes. A high proportion (ca. 60%) of these families (mainly highly conserved miRNAs targeting transcription factors) showed a non-additive response to multiple stresses in comparison with that observed under each one of the stresses individually. Among those miRNAs showing non-additive response to stress combinations, most interactions were negative, suggesting the existence of functional convergence in the miRNA-mediated response to combined stresses. Taken together, our results provide compelling pieces of evidence that the response to combined stresses cannot be easily predicted from the study individual stresses.

Integrated analysis of miRNA-mRNA regulatory networks of potato (Solanum tuberosum L.) in response to cadmium stress

Cadmium (Cd) stress is a ubiquitous abiotic stress affecting plant growth worldwide and negatively impacting crop yield and food safety. Potato is the most important non-grain crop globally, but there is limited research available on the response of this crop to Cd stress. This study explored the coping mechanism for Cd stress in potato through analyses of miRNA and mRNA. Tissue culture seedlings (20-day-old) of potato variety 'Atlantic' were cultured for up to 48 h in liquid medium containing 5 mmol/L CdCl2, and phenotypic, physiological, and transcriptomic changes were observed at specific times. With the extension of Cd stress time, the potato leaves gradually wilted and curled, and root salicylic acid (SA), glutathione (GSH), and lignin contents and peroxidase (POD) activity increased, while indole-3-acetic acid (IAA) and zeatin (ZT) contents decreased. Using miRNA-seq, 161 existing miRNAs, 383 known miRNAs, and 7361 novel miRNAs were identified, and, 18 miRNAs were differentially expressed in response to Cd stress. Based on mRNA-seq, 7340 differentially expressed mRNAs (DEGs) were found. Through mRNA-miRNA integrated analysis, miRNA-target gene pairs consisting of 23 DEGs and 33 miRNAs were identified. Furthermore, "glutathione metabolism" "plant hormone signal transduction" and "phenylpropanoid biosynthesis" were established as crucial pathways in the Cd stress response of potato. Novel miRNAs novel-m3483-5p and novel-m2893-5p participate in these pathways through targeted regulation of cinnamic alcohol dehydrogenase (CAD; PG0005359) and alanine aminotransferase (POP; PG0024281), respectively. This study provides information that will help elucidate the complex mechanism of the Cd stress response in potato. Moreover, candidate miRNAs and mRNAs could yield new strategies for the development of Cd-tolerant potato breeding.

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.