The noncoding RNA HIDDEN TREASURE 1 promotes phytochrome B-dependent seed germination by repressing abscisic acid biosynthesis

AtR8 lncRNA integrates WRKY46 into ABA signaling to regulate seed and seeding growth in Arabidopsis

Seed germination plays a vital role in ensuring plant survival under unfavorable conditions. Abscisic acid (ABA) signaling is important for integrating environmental information to regulate seed germination. Despite the identification of numerous regulatory factors in ABA signaling pathways during seed germination, the transcriptional regulatory mechanisms influencing ABA signaling remain largely uncharacterized. Long non-coding RNAs (lncRNAs) have many physiological functions in diverse organisms. To date, only a few seed germination-related lncRNAs have been reported. The AtR8 lncRNA (259 nt) in Arabidopsis is transcribed by the RNA polymerase III. We previously determined that the AtR8 lncRNA affects the innate immunity of seedlings as well as hypocotyl elongation. It is also highly expressed in the germinating seeds and induced by ABA. In this study, its loss-of-function mutant (atr8) had incompletely formed siliques and seeds and a relatively low germination rate. The germination efficiency and primary root elongation were strongly affected by the ABA level. In addition, ABA signaling and AtEM6 expression were significantly induced in the atr8 mutant. Moreover, the AtEM6-overexpressing Arabidopsis plants and the atr8 mutant had similar ABA-dependent phenotypes. Genetic analyses clarified the relationship between AtR8 and AtEM6 during ABA signaling. The stress-dependent transcription of WRKY46 in the germinating atr8 seeds was significantly upregulated by ABA. AtEM6 expression increased in a wrky46 background. WRKY46 promoted AtEM6 expression by binding to the gene promoter W-boxes in a yeast one-hybrid assay. These results suggest the AtR8 lncRNA integrates WRKY46 into the ABA signaling pathway to regulate AtEM6 expression and influences seed germination and silique development in Arabidopsis. The study elucidated the mechanism of AtR8 lncRNA in regulating seed germination and seedling growth through mediate ABA signaling.

Genome-Wide-Association-Analysis-Based Identification of Genetic Loci and Candidate Genes Associated with Cold Germination in Sweet Corn

Sweet corn is highly susceptible to low temperatures, especially during seed germination, which severely affects plant growth and crop yield. This study used 100 sweet corn micro-core germplasms to evaluate two key germination traits under cold stress: seed storage material utilization efficiency (SRUE) and mobilization weight (WMSR). To investigate the genetic basis of cold germination in sweet corn, we selected the BLINK model for GWAS due to its ability to minimize false positives. A total of nine SNPs were found to be significantly associated with cold germination. These SNPs explained between 9.8% and 17.2% of the phenotypic variance (PVE). Within the confidence interval, 63 functionally annotated genes were identified. Fourteen candidate genes associated with cold germination were identified through GO functional analysis and the functional expression of homologous genes. A literature analysis indicated that these genes are primarily involved in seed germination, cold tolerance, and responses to other abiotic stresses. These findings enhance our understanding of the genetic and molecular mechanisms underlying cold germination, establishing a theoretical foundation for breeding cold-tolerant sweet corn varieties.

Transcription factors CsWRKY53 and CsWRKY40 synergistically regulate l-theanine hydrolysis via the abscisic acid signaling pathway during tea withering

l-Theanine hydrolysis in tea (Camellia sinensis) leaves not only reduces the quality of tea products but also decreases their health benefits. Postharvest dehydration-induced abscisic acid (ABA) contributes to l-theanine hydrolysis, but the specific underlying mechanism has not been explored. Based on transcriptome analysis and gene silencing experiments, CsNCED3a was shown to be a key gene for ABA synthesis in harvested tea leaves, and CsABF7 up-regulated the expression of CsWRKY40, which encodes a transcription factor that directly regulates a l-theanine hydrolysis gene, resulting in the loss of l-theanine. CsWRKY53 and CsWRKY40 activated the expression of CsNCED3a. The CsWRKY53-CsWRKY40 complex exhibited a stronger regulatory effect than the individual transcription factors. These findings reveal an ABA-mediated regulatory pathway for l-theanine hydrolysis, and highlight the pivotal role of ABA in the postharvest metabolism of critical flavor-contributing metabolites in tea leaves.

Light and high temperatures control epigenomic and epitranscriptomic events in Arabidopsis

Light and temperature are two key environmental factors that control plant growth and adaptation by influencing biomolecular events. This review highlights the latest milestones on the role of light and high temperatures in modulating the epigenetic and epitranscriptomic landscape of Arabidopsis to trigger developmental and adaptive responses to a changing environment. Recent discoveries on how light and high temperature signals are integrated in the nucleus to modulate gene expression are discussed, as well as highlighting research gaps and future perspectives in further understanding how to promote plant resilience in times of climate change.

Warm temperature perceived at the vegetative stage affects progeny seed germination in natural accessions of Arabidopsis thaliana

Temperatures perceived early in the life cycle of mother plants can affect the germination of the offspring seeds. In Arabidopsis thaliana, vernalisation-insensitive mutants showed altered germination response to elevated maternal temperature, hence revealing a strong genetic determinism. However, the genetic control of this maternal effect and its prevalence across natural populations remain unclear. Here, we exposed a collection of European accessions of A. thaliana to increased temperature during the vegetative phase and assessed germination in their progeny to identify the genetic basis of transgenerational germination response. We found that genotypes with rapidly germinating progeny after early maternal exposure to elevated temperature originated from regions with low-light radiation. Combining genome-wide association, expression analysis and functional assays across multiple genetic backgrounds, we show a central role for PHYB in mediating the response to maternally perceived temperature at the vegetative stage. Differential gene expression analysis in leaves identified a similar genetic network as previously found in seed endosperm under elevated temperature, supporting the pleiotropic involvement of PHYB signalling across different tissues and stages. This provides evidence that complex environmental responses modulated by the maternal genotype can rely on a consistent set of genes yet produce different effects at the different stages of exposure.

miR827 orchestrates the regulation of SPX-MFS1 and SPX-MFS5 with the assistance of lncRNA767 to enhance phosphate starvation tolerance and maize development

MicroRNA827 (miR827) is functionally conserved among different plant species and displays species-specific characteristics, but the mechanisms by which miR827 regulates phosphate (Pi) starvation tolerance and maize development remain elusive. We found that miR827 selectively targets the Pi transporter genes SPX-MFS1 and SPX-MFS5. miR827 overexpression improved the Pi starvation tolerance, plant architecture and grain yield and quality, whereas miR827 suppression yielded a contrasting phenotype. In addition, we identified a specific long noncoding RNA (lncRNA767) that serves as a direct target and a facilitator of miR827 and can stabilize the SPX-MFS1 and SPX-MFS5 transcripts, leading to their translation inhibition. The orchestrated regulation of SPX-MFS1 and SPX-MFS5 modulates PHR1; 1 and PHR1; 2, which are critical transcription factors in Pi signalling, and thereby affects the expression of downstream Pi starvation-induced genes. Together, these findings demonstrate that miR827, assisted by lncRNA767, enhances SPX-MFS1 and SPX-MFS5 suppression and thus exerts a significant impact on Pi homeostasis and several essential agronomic traits of maize.

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

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

Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition

Translation of seed stored mRNAs is essential to trigger germination. However, when RNAPII re-engages RNA synthesis during the seed-to-seedling transition has remained in question. Combining csRNA-seq, ATAC-seq and smFISH in Arabidopsis thaliana we demonstrate that active transcription initiation is detectable during the entire germination process. Features of non-coding regulation such as dynamic changes in chromatin accessible regions, antisense transcription, as well as bidirectional non-coding promoters are widespread throughout the Arabidopsis genome. We show that sensitivity to exogenous ABSCISIC ACID (ABA) during germination depends on proximal promoter accessibility at ABA-responsive genes. Moreover, we provide genetic validation of the existence of divergent transcription in plants. Our results reveal that active enhancer elements are transcribed producing non-coding enhancer RNAs (eRNAs) as widely documented in metazoans. In sum, this study defining the extent and role of coding and non-coding transcription during key stages of germination expands our understanding of transcriptional mechanisms underlying plant developmental transitions.

Long Non-Coding RNAs: Discoveries, Mechanisms, and Research Strategies in Seeds

Seeds provide nutrients for the embryo and allow for dormancy in stressed environments to better adapt the plant to its environment. In addition, seeds are an essential source of food for human survival and are the basis for the formation of food production and quality. Therefore, the research on the genetic mechanism of seed development and germination will provide a theoretical basis and technical support for the improvement of crop yield and quality. Recent studies have shown that long non-coding RNAs (lncRNAs) occupy a pivotal position in seed development and germination. In this review, we describe the key processes in seed biology and examine discoveries and insights made in seed lncRNA, with emphasis on lncRNAs that regulate seed biology through multiple mechanisms. Given that thousands of lncRNAs are present in the seed transcriptome, characterization has lagged far behind identification. We provide an overview of research strategies and approaches including some exciting new techniques that may uncover the function of lncRNAs in seed. Finally, we discuss the challenges facing the field and the opening questions. All in all, we hope to provide a clear perspective on discoveries of seed lncRNA by linking discoveries, mechanisms, and technologies.

The plant noncoding transcriptome: a versatile environmental sensor

Plant noncoding RNA transcripts have gained increasing attention in recent years due to growing evidence that they can regulate developmental plasticity. In this review article, we comprehensively analyze the relationship between noncoding RNA transcripts in plants and their response to environmental cues. We first provide an overview of the various noncoding transcript types, including long and small RNAs, and how the environment modulates their performance. We then highlight the importance of noncoding RNA secondary structure for their molecular and biological functions. Finally, we discuss recent studies that have unveiled the functional significance of specific long noncoding transcripts and their molecular partners within ribonucleoprotein complexes during development and in response to biotic and abiotic stress. Overall, this review sheds light on the fascinating and complex relationship between dynamic noncoding transcription and plant environmental responses, and highlights the need for further research to uncover the underlying molecular mechanisms and exploit the potential of noncoding transcripts for crop resilience in the context of global warming.

Dynamics of epigenetic control in plants via SET domain containing proteins: Structural and functional insights

Plants control expression of their genes in a way that involves manipulating the chromatin structural dynamics in order to adapt to environmental changes and carry out developmental processes. Histone modifications like histone methylation are significant epigenetic marks which profoundly and globally modify chromatin, potentially affecting the expression of several genes. Methylation of histones is catalyzed by histone lysine methyltransferases (HKMTs), that features an evolutionary conserved domain known as SET [Su(var)3-9, E(Z), Trithorax]. This methylation is directed at particular lysine (K) residues on H3 or H4 histone. Plant SET domain group (SDG) proteins are categorized into different classes that have been conserved through evolution, and each class have specificity that influences how the chromatin structure operates. The domains discovered in plant SET domain proteins have typically been linked to protein-protein interactions, suggesting that majority of the SDGs function in complexes. Additionally, SDG-mediated histone mark deposition also affects alternative splicing events. In present review, we discussed the diversity of SDGs in plants including their structural properties. Additionally, we have provided comprehensive summary of the functions of the SDG-domain containing proteins in plant developmental processes and response to environmental stimuli have also been highlighted.

From molecular basics to agronomic benefits: Insights into noncoding RNA-mediated gene regulation in plants

The development of plants is largely dependent on their growth environment. To better adapt to a particular habitat, plants have evolved various subtle regulatory mechanisms for altering gene expression. Non coding RNAs (ncRNAs) constitute a major portion of the transcriptomes of eukaryotes. Various ncRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycles of plants. In this review, we summarize the current understanding of the biogenesis and contributions of small nucle olar RNA (snoRNA)- and regulatory long non coding RNA (lncRNA)-mediated gene regulation in plant development and environmental responses. Many regulatory ncRNAs appear to be associated with increased yield, quality and disease resistance of various species and cultivars. These ncRNAs may potentially be used as genetic resources for improving agronomic traits and for molecular breeding. The challenges in understanding plant ncRNA biology and the possibilities to make better use of these valuable gene resources in the future are discussed in this review.