The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis

Arabidopsis RGLG1/2 regulate flowering time under different soil moisture conditions by affecting the protein stability of TOE1/2

Drought constitutes a significant environmental factor influencing the growth and development of plants. Consequently, terrestrial plants have evolved a range of strategies to mitigate the adverse effects of soil water deficit. One such strategy, known as drought escape, involves the acceleration of flowering under drought, thereby enabling plants to complete their life cycle rapidly. However, the molecular mechanisms underlying this adaptive response remain largely unclear. Using genetic, molecular, and biochemical techniques, we demonstrated that the AP2 family proteins TARGET OF EAT 1/2 (TOE1/2) are essential for the drought escape response in Arabidopsis, with a significant reduction in their protein stability observed during this process. Our findings indicate that the RING-type E3 ubiquitin ligases RING DOMAIN LIGASE 1/2 (RGLG1/2) interact with TOE1/2 and facilitate their degradation within the nucleus. Under water deficit conditions, there is increased expression of RGLG1/2, and their protein products translocate to the nucleus to ubiquitinate and degrade TOE1/2, thereby enhancing the drought escape response. Furthermore, the loss of TOE1/2 in drought conditions directly results in a reduction of drought resistance in plants, suggesting that drought escape is a high-risk behaviour for plants and that the RGLG1/2-TOE1/2 signalling cascade may serve as a central regulatory mechanism governing the trade-off between drought escape and drought tolerance in plants.

Stem trichome polarity development in Gossypium hirsutum: insights into GhPRP gene regulation

KEY MESSAGE

Cotton stem trichomes exhibit a distinct polarity distribution, which may be regulated by GhPRP genes and temperature. Stem trichomes in cotton are essential for pest resistance and stress tolerance, yet their molecular regulation remains poorly understood. Significant differences in trichome number and length were observed under 25 °C and 30 °C, with more and longer trichomes at the first stem node under 25 °C. The side above the first true leaf (M side) showed more number of trichomes than the opposite side (L side), indicating polarity distribution. Transcriptome sequencing (RNA-seq) identified differentially expressed genes (DEGs), and 17 key DEGs were selected for further analysis, including 9 upregulated genes encoding proline-rich cell wall proteins (PRPs), flavonol synthase (FLS), prolyl endopeptidase (PREP), and diacylglycerol O-acyltransferase 3 (DGAT3). Quantitative real-time PCR (qRT-PCR) confirmed higher GhPRP expression on the M side. When GhPRP1, GhPRP2, or GhPRP10 was silenced using virus-induced gene silencing (VIGS) technique, trichome density decreased, and polarity was disrupted, highlighting their regulatory roles. Bioinformatics analysis revealed hormone signal transduction-related domains in PRP gene promoters, potentially linking them to trichome polarity regulation. This study advances understanding the mechanisms of trichome polarity distribution and offers insights for improving pest resistance and stress adaptation in cotton.

The microRNA Pathway of Macroalgae: Its Similarities and Differences to the Plant and Animal microRNA Pathways

In plants and animals, the microRNA (miRNA) class of small regulatory RNA plays an essential role in controlling gene expression in all aspects of development, to respond to environmental stress, or to defend against pathogen attack. This well-established master regulatory role for miRNAs has led to each protein-mediated step of both the plant and animal miRNA pathways being thoroughly characterized. Furthermore, this degree of characterization has led to the development of a suite of miRNA-based technologies for gene expression manipulation for fundamental research or for use in industrial or medical applications. In direct contrast, molecular research on the miRNA pathway of macroalgae, specifically seaweeds (marine macroalgae), remains in its infancy. However, the molecular research conducted to date on the seaweed miRNA pathway has shown that it shares functional features specific to either the plant or animal miRNA pathway. In addition, of the small number of seaweed species where miRNA data is available, little sequence conservation of individual miRNAs exists. These preliminary findings show the pressing need for substantive research into the seaweed miRNA pathway to advance our current understanding of this essential gene expression regulatory process. Such research will also generate the knowledge required to develop novel miRNA-based technologies for use in seaweeds. In this review, we compare and contrast the seaweed miRNA pathway to those well-characterized pathways of plants and animals and outline the low degree of miRNA sequence conservation across the polyphyletic group known as the seaweeds.

The GhWRKY46-GhGAI Module Mediates Cotton Flowering by Regulating the Expression of Flowering Promotion Factors

Flowering represents a pivotal developmental transition stage in the life cycle of a plant, and the occurrence of flowering at the optimal time is critical for reproductive success. WRKY transcription factors play a vital role in a signaling network that governs a multitude of plant processes. Here, a gene, GhWRKY46, that was differentially expressed in early and late maturing materials was identified via association analysis, and it was specifically expressed in flower buds. Under natural light and temperature conditions, compared to Jin668, the flowering time of OE-GhWRKY46 plants was advanced by approximately 6 days, while the flowering time of CR-GhWRKY46 plants was delayed by approximately 8 days. Transcriptomic data indicated that overexpression or knockout of GhWRKY46 resulted in the activation or repression, respectively, of the photoperiod gene CO-Like and genes related to bud differentiation. Combined RNA-seq and DAP-seq analysis revealed that three genes, namely, GhCOL4, GhCOL2 and GhFPF1-like, may be expressed downstream of GhWRKY46. Dual-luciferase assays and electrophoretic mobility shift assays (EMSAs) demonstrated that GhWRKY46 could directly bind to the W-box and promote the expression of these genes. Similarly, GhFT was also found to be activated by GhWRKY46. Both in vivo and in vitro biochemical analyses demonstrated that GhWRKY46 interacted with GhGAI, and GhGAI could interfere with the transcriptional activation of GhWRKY46, which in turn inhibited the expression of GhCOL4, GhCOL2, GhFPF1-like, and GhFT. In conclusion, this study accurately predicted the GhWRKY46 binding motif, which is important for the construction of regulatory networks of the WRKY family in other crops and introduces a novel regulatory module for the flowering regulation pathway in cotton.

Genome-Wide Analysis and Expression Profiles of AhCOLs Family in Peanut (Arachis hypogaea L.)

The CONSTANS-like (COL) gene family plays critical roles in plant growth, development, stress responses, and light signal transduction. However, its functions in peanut (Arachis hypogaea) remain poorly understood. In this study, we identified 18 AhCOL genes in the peanut genome, all localized in the nucleus. Phylogenetic analysis classified these genes into three subfamilies, with Group I containing eight members and Groups II and III each comprising five. Conserved domain analysis revealed that all AhCOL proteins possess at least one B-box and one CCT domain. Most of the AhCOL members in peanuts contain a large number of ABA and MeJA elements. Additionally, some members have low-temperature response elements, anaerobic induction, circadian control, and defense stress elements. Expression profiling indicated that most AhCOL genes are abundantly expressed in leaves, flowers, and fruit needles. Notably, genes such as AhCOL4, AhCOL8, AhCOL13, and AhCOL14 were upregulated under light induction and mechanical stress, highlighting their involvement in pod development. AhCOL1 interacts with AhNF-YC1, while AhCOL3 interacts with both AhNF-YC1 and AhCOP1 proteins. This study identifies key AhCOL genes implicated in light and mechanical stress responses, offering insights into their potential roles in peanut flowering and abiotic stress tolerance.

Regulation of storage organ formation by long-distance tuberigen signals in potato

Potatoes are valued as reliable crops due to their high carbohydrate content and relatively low farming demands. Consequently, significant attention has been directed towards understanding and controlling the life cycle of potato tubers in recent years. Notably, recent studies have identified self-pruning 6A (StSP6A) as a key component of the tuberigen, the mobile signal for tuber formation, produced in leaves and then transported underground to induce tuber formation in potatoes. Recent progress in comprehending the signaling mechanisms that regulate StSP6A by photoperiod and ambient temperature components, its long-distance transport into underground tissue, and its involvement in regulating stolon tuberization has advanced significantly. Consequently, the modulation of StSP6A and other possible tuberigen signals, along with their regulatory pathways, significantly impacts potato domestication and crop yield. This progress highlights the differential regulation of tuberigen signals and their potential functions in promoting tuber formation.

Circular RNAs derived from MIR156D promote rice heading by repressing transcription elongation of pri-miR156d through R-loop formation

In angiosperms, microRNA156 (miR156) acts as an intrinsic, endogenous developmental timer for the age-dependent transition from the juvenile to the adult phase1-3. However, the mechanisms modulating the age-dependent expression pattern of miR156 are still poorly understood4. In this Article, we report that circular RNAs (ciMIR156Ds) derived from pri-miR156d negatively regulate miR156 levels in an aging-dependent manner in rice. The ciMIR156D levels increase as plants age, which is inversely correlated with the changes of pri-miR156d and miR156 abundance. Consistent with this observation, ciMIR156Ds deficiency caused by a spontaneous mutation increases pri-miR156d and miR156 levels, resulting in a delayed heading phenotype, whereas ciMIR156Ds overexpression has opposite effects, demonstrating that ciMIR156Ds are negative regulators of miR156. We further show that ciMIR156Ds form R-loops with MIR156D at the region where they derive in an aging-dependent manner, which reduces the occupancy of DNA-dependent RNA polymerase II at that location and hence impedes pri-miR156d elongation. These findings reveal a mechanism for regulating heading date by refining the aging-dependent expression of miR156.

A space for time. Exploring temporal regulation of plant development across spatial scales

Plants continuously undergo change during their life cycle, experiencing dramatic phase transitions altering plant form, and regulating the assignment and progression of cell fates. The relative timing of developmental events is tightly controlled and involves integration of environmental, spatial, and relative age-related signals and actors. While plant phase transitions have been studied extensively and many of their regulators have been described, less is known about temporal regulation on a smaller, cell-level scale. Here, using examples from both plant and animal systems, we outline time-dependent changes. Looking at systemic scale changes, we discuss the timing of germination, juvenile-to-adult transition, flowering, and senescence, together with regeneration timing. Switching to temporal regulation on a cellular level, we discuss several instances from the animal field in which temporal control has been examined extensively at this scale. Then, we switch back to plants and summarize examples where plant cell-level changes are temporally regulated. As time cannot easily be separated from signaling derived from the environment and tissue context, we next discuss factors that have been implicated in controlling the timing of developmental events, reviewing temperature, photoperiod, nutrient availability, as well as tissue context and mechanical cues on the cellular scale. Afterwards, we provide an overview of mechanisms that have been shown or implicated in the temporal control of development, considering metabolism, division control, mobile signals, epigenetic regulation, and the action of transcription factors. Lastly, we look at remaining questions for the future study of developmental timing in plants and how recent technical advancement can enable these efforts.

Profiling of Known and Novel microRNAs in an Oleaginous Crop Native to the Amazon Basin, Sacha Inchi (Plukenetia volubilis), Through smallRNA-Seq

BACKGROUND

MicroRNAs (miRNAs) play crucial roles in regulating tissue-specific gene expression and plant development. This study explores the identification and functional characterization of miRNAs in Plukenetia volubilis (sacha inchi), an economically and nutritionally significant crop native to the Amazon basin, across three organs: root, stem, and leaf.

METHODS

Small RNA libraries were sequenced on the Illumina Novaseq 6000 platform, yielding high-quality reads that facilitated the discovery of known and novel miRNAs using miRDeep-P.

RESULTS

A total of 277 miRNAs were identified, comprising 71 conserved and 206 novel miRNAs, across root, stem, and leaf tissues. In addition, differential expression analysis using DESeq2 identified distinct miRNAs exhibiting tissue-specific regulation. Notably, novel miRNAs like novel_1, novel_88, and novel_189 showed significant roles in processes such as auxin signaling, lignin biosynthesis, and stress response. Functional enrichment analysis of miRNA target genes revealed pathways related to hormonal regulation, structural reinforcement, and environmental adaptation, highlighting tissue-specific functions. The Principal Component Analysis and PERMANOVA confirmed clear segregation of miRNA expression profiles among tissues, underlining organ-specific regulation. Differential expression patterns emphasized unique regulatory roles in each organ: roots prioritized stress response and nutrient uptake, leaves focused on photosynthesis and UV protection, and stems contributed to structural integrity and nutrient transport, suggesting evolutionary adaptations in P. volubilis.

CONCLUSIONS

This study identified novel miRNA-mediated networks that regulate developmental and adaptive processes in P. volubilis, underscoring its molecular adaptations for resilience and productivity. By characterizing both conserved and novel miRNAs, the findings lay a foundation for genetic improvement and molecular breeding strategies aimed at enhancing agronomic traits, stress tolerance, and the production of bioactive compounds.

A review of MicroRNAs and flavonoids: New insights into plant secondary metabolism

Flavonoids, essential plant secondary metabolites, play crucial roles in growth regulation, stress responses, and applications in medicine, agriculture, and industry. However, the complexity of their biosynthetic pathways and regulatory networks poses challenges for industrial-scale production. MicroRNAs (miRNAs), as pivotal post-transcriptional regulators, play significant roles in fine-tuning flavonoid metabolism by targeting key enzyme genes and transcription factors. This review provides a comprehensive analysis of miRNA biogenesis and their molecular mechanisms, emphasizing miRNA-mediated regulation of flavonoid biosynthesis. We introduce the concept of "miRNA-multifactorial synergistic networks", which elucidates the collaborative interactions between miRNAs, non-coding RNAs, transcription factors, and epigenetic regulators. The review explores emerging strategies, including artificial miRNA design and CRISPR/Cas technologies, to precisely manipulate miRNA activity for enhancing flavonoid production. Additionally, integrating CRISPR/Cas13, synthetic biology, and multi-omics technologies offers new opportunities to construct efficient flavonoid metabolic systems. Artificial intelligence (AI) is proposed as a powerful tool to analyze omics data, identify regulatory nodes, and simulate environmental impacts on miRNA networks, thereby optimizing metabolic pathways. By integrating these multidisciplinary approaches, this review provides a novel theoretical framework and technical roadmap for understanding and improving flavonoid metabolism. The insights presented here aim to facilitate breakthroughs in metabolic engineering, offering significant potential for practical applications in plant breeding, functional food production, and pharmaceutical development.

Molecular genetic regulation of the vegetative-generative transition in wheat from an environmental perspective

The key to the wide geographical distribution of wheat is its high adaptability. One of the most commonly used methods for studying adaptation is investigation of the transition between the vegetative-generative phase and the subsequent intensive stem elongation process. These processes are determined largely by changes in ambient temperature, the diurnal and annual periodicity of daylength, and the composition of the light spectrum. Many genes are involved in the perception of external environmental signals, forming a complex network of interconnections that are then integrated by a few integrator genes. This hierarchical cascade system ensures the precise occurrence of the developmental stages that enable maximum productivity. This review presents the interrelationship of molecular-genetic pathways (Earliness per se, circadian/photoperiod length, vernalization - cold requirement, phytohormonal - gibberellic acid, light perception, ambient temperature perception and ageing - miRNA) responsible for environmental adaptation in wheat. Detailed molecular genetic mapping of wheat adaptability will allow breeders to incorporate new alleles that will create varieties best adapted to local environmental conditions.

Exploring the drought-responsive miRNAs and their corresponding target genes in chickpea root tissue

Chickpea is an important pulse crop globally, with major production in Southeast Asia. However, the production of chickpea is hampered due to various biotic and abiotic stressors. In response to such stressors, microRNAs which are small non-coding regulatory RNA molecules have been observed as key players. The present study evaluates the role of drought-responsive microRNAs in the root tissues of chickpea genotypes contrasting for drought tolerance. This study led to the generation of 146.7 million short-read sequences from small RNA libraries constructed from the root tissues of the two genotypes. Upon analysis, 224 conserved and 155 novel miRNA sequences were identified. The miR156 family was found to be the most abundant among the 51 families identified for the conserved miRNAs. Quantitative real-time PCR (qRT-PCR) was used to validate eleven conserved and six novel miRNAs. The identification of drought-induced expression of specific miRNAs and their related target genes suggests miRNA-mediated response mechanisms in chickpea. Furthermore, this research investigated the role of drought-responsive miRNAs, specifically miR171 and miR166 and their target genes, SCL27 (scarecrow-like protein 27) and ATHB15 (Homeobox-leucine zipper family protein), respectively. The study validated the miR171 and miR166 directed cleavage of SCL27 and ATHB15, respectively, in drought-stressed root tissues using 5´RLM-RACE (5' RNA Ligase-Mediated Rapid Amplification of cDNA Ends) analysis. The study highlights the role of diverse miRNAs in chickpea for mitigating drought.

GmHSP40.1, a nuclear-localized soybean J domain protein, participates in regulation of flowering time through interacting with EMF1 and JMJ14

Heat shock protein 40s (HSP40s) are a group of J domain proteins (JDPs), which serve as co-chaperones for heat shock protein 70s. We previously reported that over-expression of a soybean class C JDP, GmHSP40.1, in Arabidopsis activated defense responses. Surprisingly, a significantly delayed flowering phenotype was also observed for the GmHSP40.1-overexpressing (OE) lines. We provided evidence that the late-flowering phenotype observed in the GmHSP40.1-OE lines was not due to impaired pri-miRNA processing and pre-mRNA splicing. Instead, we found that GmHSP40.1 interacted and co-localized with both EMF1 and JMJ14, two major components in the EMF1 complex (EMF1c), which plays a key role in depositing and maintaining the H3K27me3 modification in the FT locus. Consistent with these interactions, the H3K27me3 modification at FT chromatin was significantly increased, whereas the H3K27me3 modification at FLC locus was significantly decreased in the GmHSP40.1-OE line compared with the wde-type Col-0. Interestingly, the H3K4me3 modification was just opposite to H3K27me3 modification at FT and FLC loci, suggesting an antagonistic relationship between these two modifications. Accordingly, the expression of FT and FLC was significantly reduced and increased, respectively, in the GmHSP40.1-OE line compared with that of Col-0. Lastly, we showed that both EMF1 and JMJ14 are genetically epistatic to GmHSP40.1-overexpression. Together, our results revealed that GmHSP40.1 negatively regulates flowering time through promoting the function of EMF1c via interacting with both EMF1 and JMJ14.

An organ-specific transcriptome atlas of Curcuma wenyujin: MicroRNAs, phasiRNAs, and metabolic pathways

Curcuma wenyujin Y. H. Chen et C. Ling (C. wenyujin) is a medicinal plant widely used for clinical treatments. In this study, integrated omics data analyses enabled us to discover the microRNAs (miRNAs) and the phased small interfering RNAs (phasiRNAs) on a transcriptome-wide scale. A total of 186 mature miRNAs and 23 precursors were reported. Besides, 31 miRNAs of 14 families were organ-specifically expressed, and 13 of these miRNAs could perform organ-specific target regulation. More than 80% of the phasiRNA loci were organ-specifically expressed, especially in tubers. In some cases, phasiRNAs with distinct increments, but with accordant organ-specific expression patterns, were generated from a highly overlapped region, indicating that different machineries might be synchronously engaged in phasiRNA processing. Based on the transcriptome assembly, 28 and 56 tuber-specific genes were identified to be involved in alkaloid and terpenoid metabolisms, respectively. Analysis of the enzyme-coding genes of the β-elemene biosynthetic pathway showed that the downstream genes were tuber-specific, while the upstream genes were not. We assumed that the precursor metabolites produced in the other organs might be delivered to the tubers for the final steps of β-elemene biosynthesis. Summarily, our report provided an organ-specific transcriptome atlas of C. wenyujin, which could serve as the basis for the molecular studies on organ development and secondary metabolisms in this plant.

Effects of cold and methyl jasmonate on the expression of miRNAs and target genes in response to vernalisation in two wheat cultivars (Triticum aestivum L.)

Wheat undergoes significant physiological changes during winter, driven by processes such as cold acclimation and vernalisation that are regulated by gene expression and phytohormones. We investigate the effects of methyl jasmonate (MeJA) and cold treatments on the expression of three specific miRNAs and the associated target genes in Baz spring wheat and Norstar winter wheat using qRT-PCR analysis. Our objective was to examine the impact of MeJA on vernalisation and cold adaptation in these genotypes. Results showed that MeJA had no significant impact on vernalisation and acclimation in Baz, while the compound decreased these traits in Norstar. Additionally, the expression of miRNAs in Norstar was significantly reduced after a 2-day cold treatment, particularly for miR156 and further reduced after 14days for miR172 and miR319 . In contrast, Baz showed varied gene expression responses, with an increase in miRNA levels after the 14-day cold treatment. MeJA combined with a 2-day cold treatment suppressed the expression of SPL , AP2 and MYB3 target genes, with the most pronounced suppression observed in SPL . However, AP2 was induced after 14-day cold treatment in both cultivars. The study highlighted an inverse relationship between miRNAs and target genes under vernalisation conditions, underscoring the complex regulatory interactions between genotype, miRNAs and the associated target genes. Therefore, these findings provide new insights into how MeJA and cold treatments modulate miRNA and gene expression, enhancing our understanding of wheat's adaptive response mechanisms.

Study of the SPL gene family and miR156-SPL module in Populus tomentosa: Potential roles in juvenile-to-adult phase transition and reproductive phase

Populus tomentosa, a deciduous tree species distinguished by its significant economic and ecological value, enjoys a wide-ranging natural distribution. However, its long juvenile period severely restricts the advancement of breeding work. The SPL gene family, a distinctive class of transcription factors exclusive to the plant kingdom, is critical in various processes of plant growth and development. The miR156-SPL molecular module stands as an indispensable regulatory mechanism in the transition from the vegetative juvenile phase to the adult phase in plants. Consequently, this research endeavored a methodical and exhaustive exploration of the SPL gene family within the P.tomentosa species, synergistically integrating the miR156 family into the analysis. A total of 56 PtSPL genes were identified and subjected to a comprehensive analysis of their gene structure, conserved motifs, collinearity relationships, chromosomal localization, and promoter cis-acting elements. Further analysis of gene expression profiles confirmed the pivotal role of PtSPLs in the reproductive phase and tissue development of P. tomentosa. In addition, 11 members of miR156 in P. tomentosa were identified and their sequences analyzed, elucidating the miR156-SPL regulatory network. The target relationship between miR156k and PtSPLs was further validated by detecting the expression levels of PtSPLs in transgenic poplars overexpressing 35S::MIR156k. This comprehensive study lays a robust theoretical foundation for the continued exploration and application of the SPL genes in P. tomentosa, opening avenues for future research and potential advancements in plant biology and breeding strategies.

Aging-dependent temporal regulation of MIR156 epigenetic silencing by CiLDL1 and CiNF-YB8 in chrysanthemum

Temporal decline in microRNA miR156 expression is crucial for the transition to, and maintenance of, the adult phase and flowering competence in flowering plants. However, the molecular mechanisms underlying the temporal regulation of miR156 reduction remain largely unknown. Here, we investigated the epigenetic mechanism regulating the temporal silencing of cin-MIR156 in wild chrysanthemum (Chrysanthemum indicum), focusing on the role of the lysine-specific demethylase CiLDL1 and the nuclear factor Y complex. CiLDL1 and CiNF-YB8 interact with the classical histone-like fold domain (HFD) of CiNF-YC1 and CiNF-YA3, which form distinct heterotrimers binding to the 'CCAAT' box in the promoter region of cin-MIR156ab. CiLDL1 and CiNF-YB8 have opposing effects on cin-MIR156ab expression, with influencing histone 3 lysine 4 demethylation (H3K4me2) levels at the cin-MIR156ab locus. During aging, decreased CiNF-YB8 expression leads to a quantitative switch from the CiNF-YA3-CiNF-YC1-CiNF-YB8 heterotrimer to the CiNF-YA3-CiNF-YC1-CiLDL1 heterotrimer, which reduces H3K4me2 levels at the cin-MIR156ab locus, thus temporal silencing its expression. Our results thus reveal that the dynamic regulatory shift between CiLDL1 and CiNF-YB8 ensures proper aging-dependent flowering in chrysanthemum.

Proper activity of the age-dependent miR156 is required for leaf heteroblasty and extrafloral nectary development in Passiflora spp

Passion flower extrafloral nectaries (EFNs) protrude from leaves and facilitate mutualistic interactions with insects; however, how age cues control EFN growth remains poorly understood. Here, we examined leaf and EFN morphology and development of two Passiflora species with distinct leaf shapes, and compared the phenotype of these to transgenics with manipulated activity of the age-dependent miR156, which targets several SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL) transcription factors. Low levels of miR156 correlated with leaf maturation and EFN formation in Passiflora edulis and P. cincinnata. Accordingly, manipulating miR156 activity affected leaf heteroblasty and EFN development. miR156-overexpressing leaves exhibited less abundant and tiny EFNs in both Passiflora species. EFN abundance remained mostly unchanged when miR156 activity was reduced, but it led to larger EFNs in P. cincinnata. Transcriptome analysis of young leaf primordia revealed that miR156-targeted SPLs may be required to properly express leaf and EFN-associated genes. Importantly, altered miR156 activity impacted sugar profiles of the nectar and modified ecological relationships between EFNs and ants. Our work provides evidence that the miR156/SPL module indirectly regulates EFN development in an age-dependent manner and that the EFN development program is closely associated with the heteroblastic developmental program of the EFN-bearing leaves.

Trichome development of systemic developing leaves is regulated by a nutrient sensor-relay mechanism within mature leaves

Trichome initiation and development is regulated by a diverse range of environmental signals. However, how leaf carbohydrate status determines the trichome initiation and development of systemic developing leaves remains unclear. Here, we found that a specific organ (such as a mature leaf) could function as a nutrient sensor, subsequently promoting or suppressing nonautonomous regulation of trichome initiation and development in response to alternations in nutrient levels. This physical phenomenon was regulated by a sucrose ⟶ ACS7 ⟶ ethylene ⟶ EIN3 ⟶ SUC4 ⟶ sucrose pathway in mature leaves, with a remote control of trichome production in newly developing leaves via a sucrose ⟶ ACS7 ⟶ ethylene ⟶ EIN3 ⟶ TTG1 pathway. These data provide insights into how mature leaves function as nutrient sensors that control trichome formation within distant developing leaves through a nutrient sensor-relay mechanism. Our findings uncover both a previously unidentified, nutrient sensing-regulatory mechanism and the cognate underpinning molecular architecture.

Deciphering the impact of microRNAs in plant biology: a review of computational insights and experimental validation

Exploring the complex world of microRNA (miRNA) biogenesis and functions in plants is essential for understanding their diverse regulatory mechanisms. This review highlights the processes involved in miRNA biogenesis and their crucial roles in growth and development of plant, stress responses, and nutrient homeostasis. miRNAs play a central role in various developmental processes, including the transition from the juvenile to adult stage, the growth of shoot apical meristem, leaf and floral morphogenesis, and the determination of flowering time. By presenting the current state of research, we focus on the vital role of computational tools and databases in deciphering the regulatory networks controlled by miRNAs, which helps us navigate the intricate world of plant biology. Furthermore, it stresses the importance of experimental validation techniques in confirming computational predictions, ensuring that miRNA research is reliable and robust. As the field continues to grow, this review emphasizes the urgent need for integrated approaches, to deepen our knowledge of plant miRNA biology and its implications. These insights will pave the way for advancements in crop improvement, stress resilience, and biotechnological innovations.

GhCOL2 Positively Regulates Flowering by Activating the Transcription of GhHD3A in Upland Cotton (Gossypium hirsutum L.)

Plants have evolved sophisticated signaling networks to adjust flowering time, ensuring successful reproduction. Two crucial flowering regulators, FLOWERING LOCUS T (FT) and CONSTANS (CO), play pivotal roles in regulating flowering across various species. Previous studies have indicated that suppressing Gossypium hirsutum CONSTANS-LIKE 2 (GhCOL2), a homolog of Arabidopsis CO, leads to delayed flowering in cultivated cotton. However, the underlying regulatory mechanisms remain unknown. In this study, a yeast one-hybrid and dual-LUC expression assays were used to elucidate the molecular mechanism through which GhCOL2 regulates the transcription of GhHD3A. RT-qPCR was used to examine the expression of GhCOL2 and GhHD3A. Our findings reveal that GhCOL2 directly binds to CCACA cis-elements and atypical CORE (TGTGTATG) cis-elements in the promoter regions of HEADING DATE 3 A (HD3A), thereby activating GhHD3A transcription. Notably, GhCOL2 and GhHD3A exhibited high expression levels in the adult stage and low levels in the juvenile stage. Interestingly, the expression of GhCOL2 and GhHD3A varied significant between the two cotton varieties (Tx2094 and Maxxa). In summary, our study enhances the understanding of the molecular mechanism by which cotton GhCOL2-GhHD3A regulates flowering at the molecular level. Furthermore, it contributes to a broader comprehension of the GhCOL2-GhHD3A model in G. hirsutum.

Identification and expression analysis of the SPL gene family during flower bud differentiation in Rhododendron molle

BACKGROUND

The family of SQUAMOSA promoter binding protein-like (SPL) transcription factors is essential for regulating plant growth and development. While this SPL gene functional research has been limited in Rhododendron molle (R. molle).

OBJECTIVE

To preliminarily explore the regulatory mechanism of the SPL gene in flower bud development of R. molle.

METHODS

In this study, for R. molle, the flower bud differentiation period was determined by observing the morphological anatomy of the flower bud. The SPL gene family members were identified based on the R. molle genome, Additionally, the expressions of RmSPL genes at five flower bud differentiation stages were analyzed via Quantitative reverse transcription PCR (RT-qPCR).

RESULTS

We first characterized 20 SPL family members in the reference genome of R. molle. The phylogenetic analysis of plant SPL proteins separated them into eight subfamilies (G1-G8) according to conserved gene structures and protein motifs. Cis-elements of promoter region analysis showed that RmSPL genes were regulated by light, phytohormones, stress response, and plant growth and development and may play a critical role in the photoresponse, abasic acid, anaerobic induction, and meristematic expression. Gene expression analysis showed that 18 RmSPL genes were differentially expressed in different developing flower buds. In particular, RmSPL1/7/8/12/13 exhibited significantly different expressions, suggesting that they were likely essential genes for regulating the differentiation of flower buds.

CONCLUSION

In conclusion, our analysis of RmSPL genes provides a theoretical basis and reference for future functional analysis of RmSPL genes in the flower bud differentiation of R. molle.

MicroRNAs in Plant Genetic Regulation of Drought Tolerance and Their Function in Enhancing Stress Adaptation

Adverse environmental conditions, including drought stress, pose a significant threat to plant survival and agricultural productivity, necessitating innovative and efficient approaches to enhance their resilience. MicroRNAs (miRNAs) are recognized as key elements in regulating plant adaptation to drought stress, with a notable ability to modulate various physiological and molecular mechanisms. This review provides an in-depth analysis of the role of miRNAs in drought response mechanisms, including abscisic acid (ABA) signaling, reactive oxygen species (ROS) detoxification, and the optimization of root system architecture. Additionally, it examines the effectiveness of bioinformatics tools, such as those employed in in silico analyses, for studying miRNA-mRNA interactions, as well as the potential for their integration with experimental methods. Advanced methods such as microarray analysis, high-throughput sequencing (HTS), and RACE-PCR are discussed for their contributions to miRNA target identification and validation. Moreover, new data and perspectives are presented on the role of miRNAs in plant responses to abiotic stresses, particularly drought adaptation. This review aims to deepen the understanding of genetic regulatory mechanisms in plants and to establish a robust scientific foundation for the development of drought-tolerant crop varieties.

Genome-wide analysis of the SPL family in Zanthoxylum armatum and ZaSPL21 promotes flowering and improves salt tolerance in transgenic Nicotiana benthamiana

Z. armatum is an economically valued crop known for its rich aroma and medicinal properties. This study identified 45 members of the SQUAMOSA-PROMOTER BINDING PROTEIN LIKE (SPL) gene family in the genome of Z. armatum. Phylogenetic and collinearity analyzes demonstrated a close relationship between ZaSPLs and ZbSPLs from B subgenomes of Zanthoxylum bungeanum. Our miRNA sequencing revealed a high degree of conservation of miR156a within Z. armatum, with the za-miR156a sequence identical to miR156-5p in Arabidopsis thaliana and Citrus sinensis. Of the 45 genes identified by ZaSPLs, 21 were targeted by za-miR156a, transient co-expression experiments in N. benthamiana demonstrated the targeting relationship between za-miR156 and ZaSPL21. Furthermore, RNA-seq and qRT-PCR analysis revealed that ZaSPL genes exhibited elevated expression levels in juvenile tissues of Z. armatum. The expression of nine representative ZaSPL genes were upregulated under polyethylene glycol (PEG) and abscisic acid (ABA). Overexpression of ZaSPL21 delayed the germination of transgenic tobacco and facilitated the flowering process in transgenic N. benthamiana. Significant up-regulation in the expression levels of flowering-related genes such as NbFT1, NbPIP2;1, NbTCP1, NbCOL1, NbGI2, NbGAI1, NbCKX2, and NbARR4 was observed in transgenic plants, suggesting that ZaSPL21 may stimulate plant flowering by regulation of these genes. Furthermore, ZaSPL21 also increased the germination speed of transgenic tobacco seeds during drought and salt stress conditions, and improved the salt tolerance of transgenic seedlings. In conclusion, our study contributes to understanding the functional analysis of the SPL gene family in Z. armatum and emphasizes the crucial role of ZaSPL21 in improving tolerance to salt and promoting flowering. The results offer potential strategies for the further utilization of these genes to improve the salt tolerance of Z. armatum.

Differential Stress Responses to Rice Blast Fungal Infection Associated with the Vegetative Growth Phase in Rice

During vegetative growth, plants undergo various morphological and physiological changes in the transition from the juvenile phase to the adult phase. In terms of stress resistance, it has been suggested that plants gain or reinforce disease resistance during the process of maturation, which is recognized as adult plant resistance or age-related resistance. While much knowledge has been obtained about changes in disease resistance as growth stages progress, knowledge about changes in plant responses to pathogens with progressing age in plants is limited. In this study, we experimentally compared rice blast resistance in rice leaves sampled from plants at different growth phases. The results indicate differential infection progression and fungal status depending on growth stage. Transcriptome analysis following blast fungus infection revealed that several genes involved in the defense response were upregulated in both the juvenile and intermediate stage, but the expression changes of many genes were growth phase-specific. These findings highlight differences in rice leaf stress responses to blast infection at different growth stages.

Transcriptional regulation of miR528-PPO module by miR156 targeted SPLs orchestrates chilling response in banana

Banana is sensitive to cold stress and often suffers from chilling injury with browning peel and failure to normal ripening. We have previously reported that banana chilling injury is accompanied by a reduction of miR528 accumulation, alleviating the degradation of its target gene MaPPO and raising ROS levels that cause peel browning. Here, we further revealed that the miR528-MaPPO cold-responsive module was regulated by miR156-targeted SPL transcription factors, and the miR156c-MaSPL4 module was also responsive to cold stress in banana. Transient overexpression of miR156c resulted in a more severe chilling phenotype by decreasing the expression of MaSPL4 and miR528. Conversely, the browning was alleviated in STTM-miR156c silencing and OE-MaSPL4 samples. Furthermore, DNA affinity purification sequencing and MaSPL4-overexpressing transcriptome jointly revealed that MaSPL4 may mediate the transcription of genes related to lipid metabolism and antioxidation, in addition to the miR528-MaPPO module, demonstrating MaSPL4 as a master regulator in the fruit cold response network. In summary, our results suggest that the miR156c-MaSPL4 module can mediate the chilling response in banana by regulating the miR528-MaPPO module and multiple other pathways, which provides evidence for the crosstalk between TFs and miRNAs that can be used for the molecular breeding of fruit cold tolerance.

Endogenous H2S promotes Arabidopsis flowering through the regulation of GA20ox4 in the gibberellin pathway

Flowering time is a critical determinant of plant reproductive success and agricultural yield. Hydrogen sulfide (H₂S), as a signaling molecule, regulates various aspects of plant growth and development. In this study, we examined the role of endogenous H₂S in regulating flowering time in Arabidopsis. The O-acetylserine thiol lyase a1 (oasa1) mutant, which has elevated H₂S levels due to impaired OASA1 activity that catalyzes the synthesis of Cys from H2S, flowers earlier than wild type (WT). The OASA1 overexpression lines (OE-OASA1-#33/#142), characterized by reduced H₂S levels, show delayed flowering, accompanied by decreased expression of key flowering regulators, FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), and AGAMOUS-LIKE24 (AGL24). Notably, vernalization and short-day (SD) conditions did not affect their flowering patterns. Exogenous H₂S and GA₃ treatment rescued the delayed flowering phenotype of OE-OASA1-#33/#142. In oasa1, levels of GA intermediates (GA15 and GA53) were elevated, while their levels were reduced in OE-OASA1-#33/#142. RT-qPCR analysis showed a significant reduction in the expression of GIBBERELLIN 20-OXIDASE 4 (GA20ox4) in OE-OASA1-#33/#142 compared to WT. Overexpression of GA20ox4 (OE-GA20ox4-#20/#30) resulted in earlier flowering and partially rescued the delayed flowering phenotype of OE-OASA1-#33/#142. Additionally, the expression of age pathway-related genes, including miRNA172b and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3/4/5/9/15 (SPL3/4/5/9/15), was significantly reduced in OE-OASA1-#33/#142 seedlings. These findings suggest that endogenous H₂S positively regulates GA20ox4 expression, thereby promoting gibberellin synthesis and advancing flowering in Arabidopsis through the GA pathway. Furthermore, the promotion of flowering by H₂S appears to be linked to the age pathway.

Transcriptome analyses at specific plastochrons reveal timing and involvement of phytosulfokine in maize vegetative phase change

Successive developmental stages of representative early and late juvenile, transition, and adult maize leaves were compared using machine-learning-aided analyses of gene expression patterns to characterize vegetative phase change (VPC), including identification of the timing of this developmental transition in maize. We used t-SNE to organize 32 leaf samples into 9 groups with similar patterns of gene expression. oposSOM yielded clusters of co-expressed genes from key developmental stages. TO-GCN supported a sequence of events in maize in which germination-associated ROS triggers a JA response, both relieving oxidative stress and inducing miR156 production, which in turn spurs juvenility. Patterns of expression of MIR395, which regulates sulfur assimilation, led to the hypothesis that phytosulfokine, a sulfated peptide, is involved in the transition to adult patterns of differentiation.

DNA self-assembly-boosted transcription amplification coupled with CRISPR/Cas13a system for plant microRNA analysis

MicroRNAs (miRNAs) play important roles in the growth process of plants, and some food-originated plant miRNAs have potential impacts on human health, which makes the detection of plant miRNAs of great significance. However, plant miRNAs are naturally modified with 2'-O-methyl at the 3'-terminal, which is difficult to be directly quantified by enzyme-catalyzed terminal polymerization protocols. Herein, we have proposed a simple strategy by coupling DNA self-assembly-boosted transcription amplification with CRISPR/Cas13a platform (termed as Cas13a-SATA) for the specific and sensitive detection of plant miRNA. In the Cas13a-SATA, the plant miRNA will mediate DNA self-assembly on the surface of microbeads and then trigger efficient transcription amplification to yield numerous single-stranded RNA (ssRNA) molecules, which can effectively activate the Cas13a trans-cleavage activity to generate intense fluorescence signal in a plant miRNA dosage-responsive manner. Using the Cas13a-SATA, we have realized the sensitive detection of plant miR156a with the limit of detection (LOD) down to 3.8 fM. Furthermore, Cas13a-SATA has been successfully applied to the accurate quantification of miR156a in Arabidopsis and maize, demonstrating its feasibility in analyzing plant miRNAs in real biological samples.

Genome-Wide Identification and Expression Profiling of the SPL Transcription Factor Family in Response to Abiotic Stress in Centipedegrass

SQUAMOSA promoter-binding protein-like (SPL) transcription factors play a critical role in the regulation of gene expression and are indispensable in orchestrating plant growth and development while also improving resistance to environmental stressors. Although it has been identified across a wide array of plant species, there have been no comprehensive studies on the SPL gene family in centipedegrass [Eremochloa ophiuroides (Munro) Hack.], which is an important warm-season perennial C4 turfgrass. In this study, 19 potential EoSPL genes in centipedegrass were identified and assigned the names EoSPL1-EoSPL19. Gene structure and motif analysis demonstrated that there was relative consistency among the branches of the phylogenetic tree. Five pairs of segmental duplication events were detected within centipedegrass. Ten EoSPL genes were predicted to be targeted by miR156. Additionally, the EoSPL genes were found to be predominantly expressed in leaves and demonstrated diverse responses to abiotic stress (salt, drought, glufosinate ammonium, aluminum, and cold). This study offers a comprehensive insight into the SPL gene family in centipedegrass, creating a foundation for elucidating the functions of EoSPL genes and investigating their involvement in abiotic stress responses.

microRNA858 represses the transcription factor gene SbMYB47 and regulates flavonoid biosynthesis in Scutellaria baicalensis

MicroRNAs (miRNAs) are noncoding endogenous single-stranded RNAs that regulate target gene expression by reducing their transcription and translation. Several miRNAs in plants function in secondary metabolism. The dried root of Scutellaria baicalensis Georgi is a traditional Chinese medicine that contains flavonoids (baicalin, wogonoside, and baicalein) as its main active ingredients. Although the S. baicalensis genome sequence has been published, information regarding its miRNAs is lacking. In this study, 12 small RNA libraries of different S. baicalensis tissues were compiled, including roots, stems, leaves, and flowers. A total of 129 miRNAs were identified, including 99 miRNAs from 27 miRNA families and 30 predicted miRNAs. Furthermore, 46 reliable target genes of 15 miRNA families were revealed using psRNATarget and confirmed by degradome sequencing. It was speculated that the microRNA858 (miR858)-SbMYB47 module might be involved in flavonoid biosynthesis. Transient assays in Nicotiana benthamiana leaves indicated that miR858 targets SbMYB47 and suppresses its expression. Artificial miRNA-mediated knockdown of miR858 and overexpression of SbMYB47 significantly increased the flavonoid content in S. baicalensis hairy roots, while SbMYB47 knockdown inhibited flavonoid accumulation. Yeast one-hybrid and dual-luciferase assays indicated that SbMYB47 directly binds to and activates the S. baicalensis phenylalanine ammonia-lyase 3 (SbPAL-3) and flavone synthase II (SbFNSⅡ-2) promoters. Our findings reveal the link between the miR858-SbMYB47 module and flavonoid biosynthesis, providing a potential strategy for the production of flavonoids with important pharmacological activities through metabolic engineering.

The potato sugar transporter SWEET1g affects apoplasmic sugar ratio and phloem-mobile tuber- and flower-inducing signals

The main phloem loader in potato, sucrose transporter StSUT1, is coexpressed with 2 members of the SWEET gene family: StSWEET11b, a clade III member of SWEET carriers assumed to be involved in sucrose efflux, and StSWEET1g, a clade I member involved in glucose efflux into the apoplast, that physically interacts with StSUT1. We investigated the functionality of SWEET carriers via uptake experiments with fluorescent glucose or sucrose analogs. Inhibition or overexpression of StSWEET1g/SlSWEET1e affected tuberization and flowering in transgenic potato plants. Isolation of the apoplasmic fluid by vacuum infiltration centrifugation revealed changes in the apoplasmic hexose composition and mono-to-disaccharide ratio, affecting sink strength. Downregulation of StSWEET1g expression affected the expression of SP6A, a tuberigen, and miR172 under long-day conditions, leading to early flowering and tuberization. A systematic screen for StSWEET1g-interacting protein partners revealed several proteins affecting cell wall integrity and strengthening. StSWEET1g and the main interaction partners were strongly downregulated during tuber development. We discuss whether StSWEET1g activity might be linked to cell wall remodeling during tuber development and the switch from apoplasmic to symplasmic phloem unloading.

Advantage looping: Gene regulatory circuits between microRNAs and their target transcription factors in plants

The 20 to 24 nucleotide microRNAs (miRNAs) and their target transcription factors (TF) have emerged as key regulators of diverse processes in plants, including organ development and environmental resilience. In several instances, the mature miRNAs degrade the TF-encoding transcripts, while their protein products in turn bind to the promoters of the respective miRNA-encoding genes and regulate their expression, thus forming feedback loops (FBLs) or feedforward loops (FFLs). Computational analysis suggested that such miRNA-TF loops are recurrent motifs in gene regulatory networks (GRNs) in plants as well as animals. In recent years, modeling and experimental studies have suggested that plant miRNA-TF loops in GRNs play critical roles in driving organ development and abiotic stress responses. Here, we discuss the miRNA-TF FBLs and FFLs that have been identified and studied in plants over the past decade. We then provide some insights into the possible roles of such motifs within GRNs. Lastly, we provide perspectives on future directions for dissecting the functions of miRNA-centric GRNs in plants.

Functional characterization of protein SUMOylation in the miRNA transcription regulation during heat stress in Arabidopsis

MicroRNAs (miRNAs) play an essential role as non-coding-RNA-type epigenetic regulators in response to high-temperature stress in plants. There are crucial roles for global transcriptional regulation under SUMO (small ubiquitin-related MOdifier) stress response (SSR). However, the molecular mechanisms underlying its downstream regulation remain unclear. In this study, SUMO-specific chromatin immunoprecipitation sequencing analysis detected specific binding in the promoter region of miRNAs under high-temperature stress. A correlation analysis between this binding and miRNA profiling revealed that the location of SUMO on the chromosome was correlated with the expression pattern of miRNAs, particularly miR398a and miR824a. In contrast, knockout mutants of the SSR-dependent SUMO E3 ligase SAP AND MIZ 1 in Arabidopsis exhibited opposing trends in target gene expression for the SUMO-related miRNAs compared to the wild type. Multi-omics correlation analyses identified 34 SUMO-candidate proteins that might be involved in the regulation of miRNA response to high-temperature stress. Therefore, we propose a potential model whereby high-temperature exposure induces nuclear entry of SUMO molecules, modifying specific transcription factors that bind to miRNA gene promoters and potentially regulate miRNA expression.

Sucrose induces flowering by degradation of the floral repressor Ghd7 via K48-linked polyubiquitination in rice

Sucrose functions as a signaling molecule in several metabolic pathways as well as in various developmental processes. However, the molecular mechanisms by which sucrose regulates these processes remain largely unknown. In the present study, we demonstrate that sucrose promotes flowering by mediating the stability of a regulatory protein that represses flowering in rice. Exogenous application of sucrose promoted flowering by inducing florigen gene expression. Reduction of sucrose levels in the phloem through genetic modifications, such as the overexpression of the vacuolar invertase OsVIN2 or the mutation of OsSUT2, a sucrose transporter, delayed flowering. Analysis of relative transcript levels of floral regulatory genes showed that sucrose activated Ehd1 upstream of the florigen, with no significant effect on the expression of other upstream genes. Examination of protein stability after sucrose treatment of major floral repressors revealed that the Ghd7 protein was specifically degraded. The Ghd7 protein interacted with the E3 ligase IPA INTERACTING PROTEIN1 (IPI1), and sucrose-induced K48-linked polyubiquitination of Ghd7 via IPI1, leading to protein degradation. Mutants defective in IPI1 delayed flowering, confirming its role in modulating proteins involved in flowering. We conclude that sucrose acts as a signaling molecule to induce flowering by promoting Ghd7 degradation via IPI1.

Genome-Wide Dissection of Selection on microRNA Target Genes Involved in Rice Flower Development

Although genome-wide studies have identified a number of candidate regions evolving under selection in domesticated animals and cultivated plants, few attempts have been made, from the point of a definite biological process, to assess sequence variation and characterize the regimes of the selection on miRNA-associated motifs. Here, we performed a genome-wide dissection of nucleotide variation and selection of miRNA targets associated with rice flower development. By sampling and resequencing 26 miRNA targets for globally diverse representative populations of Asian cultivated rice and wild relatives, we found that purifying selection has reduced genetic variation at the conserved miRNA binding sites on the whole, and highly conserved miRNA binding sequences were maintained in the studied rice populations. Conversely, non-neutral evolution of positive and/or artificial selection accelerates the elevated variations at nonconserved binding sites in a population-specific behavior which may have contributed to flower development-related phenotypic variation. Taken together, our results elucidate that miRNA targets involved in flower development are under distinctive selection regimes during rice evolution.

Integrated Transcriptome and sRNAome Analysis Reveals the Molecular Mechanisms of Piriformospora indica-Mediated Resistance to Fusarium Wilt in Banana

Bananas (Musa spp.) are among the most important fruit and staple food crops globally, holding a significant strategic position in food security in tropical and subtropical regions. However, the industry is grappling with a significant threat from Fusarium wilt, a disease incited by Fusarium oxysporum f. sp. cubense (Foc). In this study, we explored the potential of Piriformospora indica (Pi), a mycorrhizal fungus renowned for bolstering plant resilience and nutrient assimilation, to fortify bananas against this devastating disease. Through a meticulous comparative analysis of mRNA and miRNA expression in control, Foc-inoculated, Pi-colonized, and Pi-colonized followed by Foc-inoculated plants via transcriptome and sRNAome, we uncovered a significant enrichment of differentially expressed genes (DEGs) and DE miRNAs in pathways associated with plant growth and development, glutathione metabolism, and stress response. Our findings suggest that P. indica plays a pivotal role in bolstering banana resistance to Foc. We propose that P. indica modulates the expression of key genes, such as glutathione S-transferase (GST), and transcription factors (TFs), including TCP, through miRNAs, thus augmenting the plant's defensive capabilities. This study offers novel perspectives on harnessing P. indica for the management of banana wilt disease.

SPL13 controls a root apical meristem phase change by triggering oriented cell divisions

Oriented cell divisions are crucial for determining the overall morphology and size of plants, but what controls the onset and duration of this process remains largely unknown. Here, we identified a small molecule that activates root apical meristem (RAM) expression of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE13 (SPL13) a known player in the shoot's juvenile-to-adult transition. This expression leads to oriented cell divisions in the RAM through SHORT ROOT (SHR) and cell cycle regulators. We further show that the RAM has distinct juvenile and adult phases typed by morphological and molecular characteristics and that SPL factors are crucially required for this transition in Arabidopsis and rice (Oryza sativa). In summary, we provide molecular insights into the age-dependent morphological changes occurring in the RAM during phase change.

Aging drives a program of DNA methylation decay in plant organs

How organisms age is a question with broad implications for human health. In mammals, DNA methylation is a biomarker for biological age, which may predict age more accurately than date of birth. However, limitations in mammalian models make it difficult to identify mechanisms underpinning age-related DNA methylation changes. Here, we show that the short-lived model plant Arabidopsis thaliana exhibits a loss of epigenetic integrity during aging, causing heterochromatin DNA methylation decay and the expression of transposable elements. We show that the rate of epigenetic aging can be manipulated by extending or curtailing lifespan, and that shoot apical meristems are protected from this aging process. We demonstrate that a program of transcriptional repression suppresses DNA methylation maintenance pathways during aging, and that mutants of this mechanism display a complete absence of epigenetic decay. This presents a new paradigm in which a gene regulatory program sets the rate of epigenomic information loss during aging.

Integrated Analysis of microRNAs and Transcription Factor Targets in Floral Transition of Pleioblastus pygmaeus

Bamboo plants have erratic flowering habits with a long vegetative growth and an uncertain flowering cycle. The process of floral transition has always been one of the hot and intriguing topics in bamboo developmental biology. As master modulators of gene expression at the post-transcriptional level, miRNAs play a crucial role in regulating reproductive growth, especially in floral transition of flowering plants. Pleioblastus pygmaeus is a kind of excellent ground cover ornamental bamboo species. In this study, we performed miRNA expression profiling of the shoot buds and flower buds from the bamboo species, to investigate flowering-related miRNAs in bamboo plants. A total of 179 mature miRNAs were identified from P. pygmaeus, including 120 known miRNAs and 59 novel miRNAs, of which 96 (61 known miRNAs and 35 novel miRNAs) were differentially expressed in the shoots at different growth stages. Based on target gene (TG) prediction, a total of 2099 transcription factors (TFs) were annotated to be TGs of the 96 differentially expressed miRNAs (DEMs), corresponding to 839 recordings of DEM-TF pairs. In addition, we identified 23 known DEMs involved in flowering and six known miRNAs related to floral organ development based on previous reports. Among these, there were 11 significantly differentially expressed miRNAs, with 124 TF targets corresponding to 132 DEM-TF pairs in P. pygmaeus. In particular, we focused on the identification of miR156a-SPL (SQUAMOSA Promoter-Binding protein-Like) modules in the age pathway, which are well-known to regulate the vegetative-to-reproductive phase transition in flowering plants. A total of 36 TF targets of miR156a were identified, among which there were 11 SPLs. The Dual-Luciferase transient expression assay indicated miR156a mediated the repression of the PpSPL targets in P. pygmaeus. The integrated analysis of miRNAs and TGs at genome scale in this study provides insight into the essential roles of individual miRNAs in modulating flowering transition through regulating TF targets in bamboo plants.

MYB transcription factors, their regulation and interactions with non-coding RNAs during drought stress in Brassica juncea

BACKGROUND

Brassica juncea (L.) Czern is an important oilseed crop affected by various abiotic stresses like drought, heat, and salt. These stresses have detrimental effects on the crop's overall growth, development and yield. Various Transcription factors (TFs) are involved in regulation of plant stress response by modulating expression of stress-responsive genes. The myeloblastosis (MYB) TFs is one of the largest families of TFs associated with various developmental and biological processes such as plant growth, secondary metabolism, stress response etc. However, MYB TFs and their regulation by non-coding RNAs (ncRNAs) in response to stress have not been studied in B. juncea. Thus, we performed a detailed study on the MYB TF family and their interactions with miRNAs and Long non coding RNAs.

RESULTS

Computational investigation of genome and proteome data presented a comprehensive picture of the MYB genes and their protein architecture, including intron-exon organisation, conserved motif analysis, R2R3 MYB DNA-binding domains analysis, sub-cellular localization, protein-protein interaction and chromosomal locations. Phylogenetically, BjuMYBs were further classified into different subclades on the basis of topology and classification in Arabidopsis. A total of 751 MYBs were identified in B. juncea corresponding to 297 1R-BjuMYBs, 440 R2R3-BjuMYBs, 12 3R-BjuMYBs, and 2 4R-BjuMYBs types. We validated the transcriptional profiles of nine selected BjuMYBs under drought stress through RT-qPCR. Promoter analysis indicated the presence of drought-responsive cis-regulatory components. Additionally, the miRNA-MYB TF interactions was also studied, and most of the microRNAs (miRNAs) that target BjuMYBs were involved in abiotic stress response and developmental processes. Regulatory network analysis and expression patterns of lncRNA-miRNA-MYB indicated that selected long non-coding RNAs (lncRNAs) acted as strong endogenous target mimics (eTMs) of the miRNAs regulated expression of BjuMYBs under drought stress.

CONCLUSIONS

The present study has established preliminary groundwork of MYB TFs and their interaction with ncRNAs in B. juncea and it will help in developing drought- tolerant Brassica crops.

Overexpression of lily MicroRNA156-resistant SPL13A stimulates stem elongation and flowering in Lilium formosanum under non-inductive (non-chilling) conditions

Flowering plants undergo juvenile vegetative, adult vegetative, and reproductive phases. Lily plants (Lilium spp.) develop scaly leaves during their juvenile vegetative phase. Stem elongation occurs in the adult vegetative phase and is followed by floral transition. As the duration of the juvenile vegetative phase is long in lilies, the microRNA156 (miR156) and SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL) modules are expected to play a major role in vegetative phase change and flower induction. In the present study, we aimed to explore the functions of lily SLP13A. We evaluated phenotypic changes and gene expression in L. formosanum plants overexpressing miR156-resistant SPL13A (rSPL13A) and examined the accumulation levels of gene transcripts and mature miRNAs in non-transformed L. longiflorum plants. Lily plants overexpressing rSPL13A exhibited stem elongation under non-inductive conditions, and FLOWERING LOCUS T (FT) genes were poorly involved in this stem elongation. Flowering was induced in the transformed plants with elongated stems, and the accumulation of MADS5 (APETALA1) transcripts and mature miR172 was elevated in these plants. In non-transformed lilies, SPL13A transcripts were highly accumulated in the shoot apices of both juvenile and adult plants. As mature miR156 was poorly accumulated in the shoot apices of the adult plants, SPL13A was active enough to stimulate stem elongation and flower induction. In contrast, mature miR156 was reliably detected in shoot apices of the juvenile plants. Because our transient assay using tobacco plants expressing a SPL13A-GFP fusion protein indicated that miR156 repressed SPL13A expression mainly at the translational level, SPL13A activity should be insufficient to stimulate stem elongation in the juvenile plants. In addition, the accumulation of MADS5 transcripts and mature miR172 in the shoot apices increased with plant growth and peaked before the transition to the reproductive phase. Therefore, we conclude that SPL13A regulates stem elongation in the adult vegetative phase, which differs from the mechanisms evaluated in Arabidopsis and rice, wherein stem elongation proceeds in a reproductive phase and FT genes are heavily involved in it, and that SPL13A induces flowering by the activation of genes related to the age pathway underlying floral transition, as APETALA1 and primary-MIR172 are mainly involved in this pathway.

Age-associated growth control modifies leaf proximodistal symmetry and enabled leaf shape diversification

Biological shape diversity is often manifested in modulation of organ symmetry and modification of the patterned elaboration of repeated shape elements.1,2,3,4,5 Whether and how these two aspects of shape determination are coordinately regulated is unclear.5,6,7 Plant leaves provide an attractive system to investigate this problem, because they often show asymmetries along the proximodistal (PD) axis of their blades, along which they can also produce repeated marginal outgrowths such as serrations or leaflets.1 One aspect of leaf shape diversity is heteroblasty, where the leaf form in a single genotype is modified with progressive plant age.8,9,10,11 In Arabidopsis thaliana, a plant with simple leaves, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9 (SPL9) controls heteroblasty by activating CyclinD3 expression, thereby sustaining proliferative growth and retarding differentiation in adult leaves.12,13 However, the precise significance of SPL9 action for leaf symmetry and marginal patterning is unknown. By combining genetics, quantitative shape analyses, and time-lapse imaging, we show that PD symmetry of the leaf blade in A. thaliana decreases in response to an age-dependent SPL9 expression gradient, and that SPL9 action coordinately regulates the distribution and shape of marginal serrations and overall leaf form. Using comparative analyses, we demonstrate that heteroblastic growth reprogramming in Cardamine hirsuta, a complex-leafed relative of A. thaliana, also involves prolonging the duration of cell proliferation and delaying differentiation. We further provide evidence that SPL9 enables species-specific action of homeobox genes that promote leaf complexity. In conclusion, we identified an age-dependent layer of organ PD growth regulation that modulates leaf symmetry and has enabled leaf shape diversification.

Harnessing miRNA156: A molecular Toolkit for reshaping plant development and achieving ideal architecture

Achieving ideal plant architecture is of utmost importance for plant improvement to meet the demands of ever-increasing population. The wish list of ideal plant architecture traits varies with respect to its utilization and environmental conditions. Late seed development in woody plants poses difficulties for their propagation, and an increase in regeneration capacity can overcome this problem. The transition of a plant through sequential developmental stages e.g., embryonic, juvenile, and maturity is a well-orchestrated molecular and physiological process. The manipulation in the timing of phase transition to achieve ideal plant traits and regulation of metabolic partitioning will unlock new plant potential. Previous studies demonstrate that micro RNA156 (miR156) impairs the expression of its downstream genes to resist the juvenile-adult-reproductive phase transition to prolonged juvenility. The phenomenon behind prolonged juvenility is the maintenance of stem cell integrity and regeneration is an outcome of re-establishment of the stem cell niche. The previously reported vital and diverse functions of miR156 make it a more important case of study to explore its functions and possible ways to use it in molecular breeding. In this review, we proposed how genetic manipulation of miR156 can be used to reshape plant development phase transition and achieve ideal plant architecture. We have summarized recent studies on miR156 to describe its functional pattern and networking with up and down-stream molecular factors at each stage of the plant developmental life cycle. In addition, we have highlighted unaddressed questions, provided insights and devised molecular pathways that will help researchers to design their future studies.

CpSPL10-CpELF4 module involves in the negative regulation of flower bud differentiation in Chinese cherry

SQUAMOSA promoter-binding protein-like (SPL) genes play a crucial role in regulating floral induction. Despite such importance, a comprehensive study of SPLs in Chinese cherry flower bud development has been absent. In this study, 32 CpSPL genes were identified. According to expression profiling, CpSPLs exhibited tissue-specific expression and distinct trends throughout flower bud differentiation. Specifically, CpSPL10 was greatly expressed at the beginning of the differentiation, and its role was further investigated. Its overexpression extended the vegetative growth of transgenic tobacco plants, delayed flowering by about 20 days. Moreover, the accumulation of NbELF4 (Early flowering 4) transcripts was enhanced due to the up-regulated levels of CpSPL10 in tobacco plants. ELF4 functions as a major element of the circadian clock; its high expression typically delays the transition from vegetative-to-reproductive growth. Further experiments revealed that CpSPL10 interacts with CpSPL9 or a transposase-derived transcription factor CpFRS5 (FAR1-RELATED SEQUENCE 5) and activates the expression of the downstream gene CpELF4. Notably, the GUS fusing reporter assay detected the activation of CpSPL10 and CpELF4 promoters in shoot apical meristems of transgenic Arabidopsis. These findings revealed the negative regulation of the CpSPL10-CpELF4 module in flower bud differentiation, providing references for supplementing the specific relationships among SPL, FRS, and ELF4.

Genome-Wide Characterization and Analysis of the SPL Gene Family in Eucalyptus grandis

SQUAMOSA promoter-binding protein-like (SPL) gene family, a group of plant-specific transcription factors, played crucial roles in regulating plant growth, development, signal transduction, and stress response. This study focuses on the SPL gene family in the fast-growing Eucalyptus grandis, employing bioinformatics approaches to identify and analyze the gene physiochemical characteristics, conserved domains, structural composition, chromosomal distribution, phylogenetic relationships, cis-acting elements, and their expression patterns in various tissues and stress treatments. Twenty-three SPL genes were identified in E. grandis, which uneven distributed across seven chromosomes and classified into five groups. Prediction of cis-acting elements revealed that these genes might be related to light, hormone, and stress responses. Furthermore, EgSPL9 and EgSPL23, mainly expressed in the stem apex and lateral branches, seem to be involved in hormone stress resistance. Our study provides insights into the potential functions of the EgSPL genes in plant growth, stress response, and hormone transduction, offering valuable perspectives for subsequent research into their biological roles.

Deciphering the Role of SVP-Like Genes and Their Key Regulation Networks During Reproductive Cone Development in Pinus tabuliformis

Reproductive development plays an essential role in the perpetuation of genetic material and environmental adaptation. In angiosperms, the Short Vegetative Phase (SVP) serves as a flowering repressor, influencing the development of floral organs. In this study, heterologous transformation of Arabidopsis thaliana with SVP-like genes (PtSVL1 and PtSVL2) derived from Pinus tabuliformis significantly impacted stamen formation and pollen fertility, without altering flowering time. Gene co-expression networks revealed that SVP-like and SOC1-like genes function as key coregulatory transcription factors during the initial stages of cone development in P. tabuliformis. Interestingly, the regulatory module of SOC1 regulated by SVP in angiosperms is absent in conifers and conifer SVP-like exercises its function in a form that is physically bound to SOC1-like. Furthermore, combining the yeast one-hybrid scanning with co-expression network analysis, revealed that SPLs and TPSs were the principal downstream target genes of PtSVL1. Notably, the PtSPL16 promoter is positively regulated by PtSVL1, and overexpression of PtSPL16 results in delayed flowering in Arabidopsis, suggesting that the PtSVL1-PtSPL16 module plays a crucial role in regulating reproductive development in conifers. Collectively, these findings enhance our understanding of the roles of SVP-like genes in conifers and the key regulatory networks centred on PtSVL1 during reproductive cone development.

Genome-wide identification and expression analysis of the SPL gene family and its response to abiotic stress in barley (Hordeum vulgare L.)

BACKGROUND

Squamosa promoter-binding protein-like (SPL) is a plant-specific transcription factor that is widely involved in the regulation of plant growth and development, including flower and grain development, stress responses, and secondary metabolite synthesis. However, this gene family has not been comprehensively evaluated in barley, the most adaptable cereal crop with a high nutritional value.

RESULTS

In this study, a total of 15 HvSPL genes were identified based on the Hordeum vulgare genome. These genes were named HvSPL1 to HvSPL15 based on the chromosomal distribution of the HvSPL genes and were divided into seven groups (I, II, III, V, VI, VII, and VIII) based on the phylogenetic tree analysis. Chromosomal localization revealed one pair of tandem duplicated genes and one pair of segmental duplicated genes. The HvSPL genes exhibited the highest collinearity with the monocotyledonous plant, Zea mays (27 pairs), followed by Oryza sativa (18 pairs), Sorghum bicolor (16 pairs), and Arabidopsis thaliana (3 pairs), and the fewest homologous genes with Solanum lycopersicum (1 pair). The distribution of the HvSPL genes in the evolutionary tree was relatively scattered, and HvSPL proteins tended to cluster with SPL proteins from Z. mays and O. sativa, indicating a close relationship between HvSPL and SPL proteins from monocotyledonous plants. Finally, the spatial and temporal expression patterns of the 14 HvSPL genes from different subfamilies were determined using quantitative real-time polymerase chain reaction (qRT-PCR). Based on the results, the HvSPL gene family exhibited tissue-specific expression and played a regulatory role in grain development and abiotic stress. HvSPL genes are highly expressed in various tissues during seed development. The expression levels of HvSPL genes under the six abiotic stress conditions indicated that many genes responded to stress, especially HvSPL8, which exhibited high expression under multiple stress conditions, thereby warranting further attention.

CONCLUSION

In this study, 15 SPL gene family members were identified in the genome of Hordeum vulgare, and the phylogenetic relationships, gene structure, replication events, gene expression, and potential roles of these genes in millet development were studied. Our findings lay the foundation for exploring the HvSPL genes and performing molecular breeding of barley.

ALTERED MERISTEM PROGRAM1 sustains cellular differentiation by limiting HD-ZIP III transcription factor gene expression

Plants show remarkable developmental and regenerative plasticity through the sustained activity of stem cells in meristems. Under certain conditions, pluripotency can even be reestablished in cells that have already entered differentiation. Mutation of the putative carboxypeptidase ALTERED MERISTEM PROGRAM1 (AMP1) in Arabidopsis (Arabidopsis thaliana) causes a set of hypertrophic phenotypes, indicating a defect in the suppression of pluripotency. A role of AMP1 in the miRNA-mediated inhibition of translation has previously been reported; however, how this activity is related to its developmental functions is unclear. Here, we examined the functional interaction between AMP1 and the Class III homeodomain-leucine zipper (HD-ZIP III) transcription factors, which are miRNA-controlled determinants of shoot meristem specification. We found that the HD-ZIP III transcriptional output is enhanced in the amp1 mutant and that plant lines with increased HD-ZIP III activity not only developed amp1 mutant-like phenotypes but also showed a synergistic genetic interaction with the mutant. Conversely, the reduction of HD-ZIP III function suppressed the shoot hypertrophy defects of the amp1 mutant. We further provide evidence that the expression domains of HD-ZIP III family members are expanded in the amp1 mutant and that this misexpression occurs at the transcriptional level and does not involve the function of miRNA165/166. Finally, amp1 mutant-specific phenotypes cannot be mimicked by a general inhibition of miRNA function in the AMP1 expression domain. These findings lead us to a model in which AMP1 restricts cellular pluripotency upstream of HD-ZIP III proteins, and this control appears to be not directly mediated by the canonical miRNA pathway.

Natural allelic diversity of the calcium signaling regulators in plants

Calcium ions act as secondary messengers in diverse signaling pathways in plants throughout their life cycle. Studies have revealed that calcium is involved in developmental events and in responses to external stimuli, such as biotic and abiotic stresses. Cellular calcium ion levels are tightly controlled by intricate molecular machinery such as calcium channels and pumps. Transient and spatial fluctuations in calcium levels are subsequently recognized by diverse calcium-decoding molecules, resulting in signal transduction. In this review, we highlight recent findings on natural variations in genes controlling calcium signaling in diverse plant biological processes. We then show how the calcium ion context is utilized by fine-tuning the natural variation in centrally important genes.