Transposable elements have long been recognised as critical drivers of genetic diversity and evolution in plant genomes, influencing various physiological and developmental processes. The transcription factor family FAR-RED ELONGATED HYPOCOTYLS3 (FHY3), and its homologue FAR-RED IMPAIRED RESPONSE1 (FAR1), initially identified as key components of phytochrome A (phyA)-mediated far-red (FR) light signalling in Arabidopsis thaliana, are derived from transposases and are essential for light signal transduction, plant growth, and development. FHY3 and FAR1 are also the founding members of the FAR1-RELATED SEQUENCE (FRS) family, which is conserved across terrestrial plants. While the coding sequences of many putative FRS and FAR1-RELATED FACTOR (FRF) orthologs have been identified in various angiosperm clades, their physiological functions remain largely unexplored. The FRF genes are considered truncated forms of FRS proteins that compete with FRS for DNA binding sites, thereby regulating gene expression. This review highlights recent advances in characterising the molecular mechanisms of FHY3, FAR1, and other members of the FRS-FRF protein family. We examine their roles in key processes such as regulating flowering time, controlling branching, integrating leaf aging and senescence, modulating the circadian clock, maintaining meristem function, starch synthesis, seed germination, and responding to Starch synthesis and carbon starvation. Additionally, we explore their contributions to plant immunity under biotic and abiotic stresses. Finally, we suggest future directions for functional characterising other FRS-FRF family proteins in plants, which could provide deeper insights into their regulatory roles in plant biology.

Premature senescence has a significant impact on the yield and quality of wheat crops. The process is controlled by multiple and intricate genetic pathways and regulatory elements, whereby the discovery of additional mutants provides important insights into the molecular basis of this important trait. Here, we developed a premature senescence wheat mutant je0874, its leaves started to show yellow before heading stage; with plant growth and development, the degree of yellowing worsened rapidly, and chlorophyll content in flag leaf was reduced by 93.8 % at 15 days after heading, all other leaves became dryness at the grain filling stage. In the mutant, the reactive oxygen species (ROS) and its metabolites increased up to 34.8-47.3 %, while activities of ROS scavenging enzymes were reduced by 62.7-96.7 %. Premature senescence resulted in a reduction of thousand grain weight by over 50 %. Genetic analysis showed the mutation of senescence was controlled by a single recessive gene, and target gene was finely mapped to a 338 kb region of the long arm of chromosome 2D. This region contained a total of 6 annotated genes, while only gene TraesFLD2D01G513900 carried a SNP mutation. The gene contained an NBS-LRR domain, we named it Taps1. Allelic mutants of Taps1 exhibited a lesion mimic phenotype, and the mutant allele resulted in cell death in tobacco, which represent a novel gene controlling wheat senescence. Two haplotypes were identified in 180 accessions, which did not lead to cell death. These results contribute to increase our understanding of the regulation of premature plant senescence.

Rice (Oryza sativa L.) is one of the most important grain crops in the world. Abiotic stress such as low temperature is an important factor affecting the yield and quality of rice. To explore the endogenous stress-resistant genes and apply them to the breeding of new stress-resistant varieties is an effective way to improve the stress tolerance and adaptability of rice. PHD-finger transcription factor is a kind of zinc-finger structural protein that exists widely in eukaryotes. Its function is mainly focused on gene transcription and regulation of chromatin state, but there are few reports about its involvement in stress response. In the present study, a total of 58 PHD-finger transcription factors were identified, and two genes OsPHD13 and OsPHD52 were significantly up-regulated under low temperature stress. After low temperature induction, GUS driven by OsPHD13 and OsPHD52 promoters had different expression activities in roots, stems and leaves of transgenic plants. Further functional analysis of the pOsPHD13 and pOsPHD52 showed that each of them had a cis-acting element of CRT/DRE in response to low temperature stress. Both in yeast one-hybrid assays and in in vitro gel-shift analysis, CBF protein could specifically bind to the CRT/DRE element in the promoter.

Nuclear factor Y (NF-Y) is an evolutionarily conserved heterotrimeric transcription factor in eukaryotes. In a previous study, OsNF-YB12 was confirmed to be associated with drought tolerance using the Ecotilling method. In this study, real-time quantitative RT-PCR revealed that OsNF-YB12 was induced by various abiotic stresses and phytohormones, with expression levels differing between leaves and roots. Rice overexpressing OsNF-YB12 was more sensitive to salinity and PEG osmotic stresses at seed germination stage, as well as reduced drought tolerance at seedling stage. Notably, the accumulation of free proline and photosynthetic efficiency was significantly declined in OsNF-YB12 transgenic plants following osmotic stimuli. Transcriptomic analysis of transgenic OsNF-YB12 plants indicated that OsNF-YB12 could upregulate terpene metabolism related to defense responses and the expression levels of JAZ proteins under normal conditions, while downregulating osmotic stress-related regulatory genes under osmotic stress, in comparison to the wild type. Further analysis revealed that overexpressing OsNF-YB12 promoted JA biosynthesis and inhibit seed germination. Haplotype analysis suggested that OsNF-YB12 may have been selected during the differentiation of indica and japonica rice varieties. Therefore, this research provides a potential molecular target for exploring and harnessing the haplotype diversity of OsNF-YB12 to enhance yield stability under drought stress during rice domestication and improvement.

Abiotic stresses adversely impact plants survival and growth, which in turn affect plants especially crop yields worldwide. To cope with these stresses, plant responses depend on the activation of molecular networks cascades, including stress perception, signal transduction, and the expression of specific stress-related genes. Plant bZIP (basic leucine zipper) transcription factors are important regulators that respond to diverse abiotic stresses.By binding to specific cis-elements, bZIPs can control the transcription of target genes, giving plants stress resistance. This review describes the structural characteristics of bZIPs and summarizes recent progress in analyzing the molecular mechanisms regulating plant responses to salinity, drought, and cold in different plant species. The main goal is to deepen the understanding of bZIPs and explore their value in genetic improvement of plants.

The presence of anthocyanins imparts vibrant hues to plants, whose biosynthesis and accumulation is a complex process and are influenced by numerous factors. In plants, sugar acts as a primary energy source and signaling molecule regulating anthocyanins biosynthesis. In this review, we provides a comprehensive overview of the relationship between sugar and anthocyanin. We delved into the intricate biosynthetic pathway of anthocyanins, outlining the key structural genes involved and their functions. Furthermore, we summarized how various environmental factors such as sugar, light, abiotic stresses, etc., affect anthocyanin biosynthesis. Notably, Most notably, we emphasized that sugars can independently regulate anthocyanin biosynthesis by modulating the expression of the MBW complex or structural genes, as well as through cascades involving hormones. These findings offer valuable insights into understanding the molecular mechanisms underlying anthocyanin accumulation and present potential avenues for enhancing anthocyanin content in plants through targeted manipulations that could have applications in agriculture and nutrition.

The JAZ protein family, serving as a key negative regulator in the jasmonic acid signaling pathway, interacts with transcription factors to play an essential role in plant growth, development, and stress responses. However, minimal research has focused on the role of JAZ transcription factors in regulating the growth, development, and stress responses of maize. In this study, we cloned the JAZ gene ZmJAZ13 from maize (Zea mays L.) and conducted a preliminary analysis of its biological function. ZmJAZ13 was highly expressed in maize immature embryos and was induced by abiotic stress and plant hormone treatments. Y2H and BiFC assays revealed interactions between ZmJAZ13 and ZmbHLH161, as well as ZmA0A1D6GLB9. Heterologous expression of ZmJAZ13 in Arabidopsis significantly enhanced plant tolerance to drought and salt stress, increased chlorophyll content, decreased malondialdehyde content, and enhanced peroxidase activity. Under abiotic stress, heterologous expression of ZmJAZ13 in Arabidopsis upregulated the expression levels of stress-related genes (RD22, RD29-A). Together, these results suggested that ZmJAZ13 may respond to abiotic stress, providing a foundation for further investigation into the mechanism of action of ZmJAZ13 in maize.

Flooding induces hypoxia in plant tissues, impacting various physiological and biochemical processes. This study investigates the adaptive response of the roots and nitrogen-fixing nodules of Medicago truncatula in symbiosis with Sinorhizobium meliloti under short-term hypoxia caused by flooding. Four-week-old plants were subjected to flooding for 1-4 days. Physiological parameters as well as the expression of the senescence marker gene MtCP6 remained unchanged after 4 days of flooding, indicating no senescence onset. Hypoxia was evident from the first day, as indicated by the upregulation of hypoxia marker genes (MtADH, MtPDC, MtAlaAT, MtERF73). Nitrogen-fixing capacity was unaffected after 1 day but markedly decreased after 4 days, while energy state (ATP/ADP ratio) significantly decreased from 1 day and was more affected in nodules than in roots. Nitric oxide (NO) production increased in roots but decreased in nodules after prolonged flooding. Nitrate reductase (NR) activity and expression of genes associated with Phytoglobin-NO (Pgb-NO) respiration (MtNR1, MtNR2, MtPgb1.1) were upregulated, suggesting a role in maintaining energy metabolism under hypoxia, but the use of M. truncatula nr1 and nr2 mutants, impaired in nitrite production, indicated the involvement of these two genes in ATP regeneration during initial flooding response. The addition of sodium nitroprusside or tungstate revealed that Pgb-NO respiration contributes significantly to ATP regeneration in both roots and nodules under flooding. Altogether, these results highlight the importance of NR1 and Pgb1.1 in the hypoxic response of legume root systems and show that nodules are more sensitive than roots to hypoxia.

Low temperatures severely threaten the growth and development of kiwifruit. Research has demonstrated that proteins belonging to the 14-3-3 family play a pivotal regulatory function in the ability of plants to resist stress. However, this specific roles of the genes in kiwifruit cold tolerance remain unclear. It had been identified that β-amylase gene, AaBAM3.1, exhibits a positive regulatory effect on kiwifruit's tolerance to low temperature. In our research, we obtained the Actinidia arguta 14-3-3 gene general regulatory factor 1 (AaGRF1) from yeast one-hybrid (Y1H) screening library of the AaBAM3.1 promoter; the expression level of AaGRF1 was enhanced by low-temperature stress. Subcellular localization, Y1H and dual-LUC assay indicated that the AaGRF1 protein resides within the nucleus and possesses the ability to interact with the AaBAM3.1 promoter. Moreover, we also studied the role of AaGRF1 gene in cold resistance of kiwifruit. When AaGRF1 was overexpressed in kiwifruit, the transgenic plants exhibited enhanced cold tolerance. The level of antioxidants and soluble sugars (SS) in these plants were elevated compared to wild-type (WT) lines. RNA-seq of the transgenic and WT lines revealed that AaGRF1 might interact with genes in the 'ascorbate-glutathione' and 'starch and sucrose' pathways, thereby enhancing the cold resistance of kiwifruit. In summary, we hypothesize that the 14-3-3 gene AaGRF1 may positively modulate the cold resistance in kiwifruit by accumulating more antioxidants and SS.

The stem gall fly (Procecidochares utilis) significantly impacts host-plant biology by inhabiting specific parts of stem tissue, ensuring its own survival. Despite this, comprehensive identification of the primary bioactive compounds within host plants that are involved in gall formation remains elusive. This study aims to elucidate the crucial volatile compounds utilized by gall flies to alter host-plant defenses, either through direct or indirect manipulation via the release of an enticing volatile compound attractive to the fly. Employing Y-tube olfactometer assays, we examined the response of Procecidochares utilis to host plants from three Asteraceae weed species-Ageratina adenophora, Ageratum conyzoides, and Praxelis clematidea. Volatile compounds were extracted using headspace solid-phase microextraction (HS-SPME) and SPME-FIBER. Subsequently, gas chromatography-electroantennography and electroantennography were employed to analyze the antennal responses to individual odorants. The analysis revealed that the primary bioactive compound varied among the three weed species. Out of a total of 805 known volatiles, 65 main active compounds were exclusive to Ageratina adenophora (host plant). Remarkably, only 8 bioactive compounds were identified to elicit an antennal response from Procecidochares utilis. Notably, caryophyllene, β-bisabolene, and 4-thujen-2-α-yl acetate exhibited the remarkable ability to elicit an attraction response from both sexes of Procecidochares utilis. Among these, β-bisabolene emerged as the key compound, eliciting the most significant response from the gall fly antenna. Our findings offer novel insights into the specific attraction of the stem gall fly to Ageratina adenophora, utilizing key odorants as unique cues for initiating gall formation on its host plant. This discovery highlights how these cues enable the gall fly to exert direct or indirect control over its host. Additionally, these findings underscore the potential of this approach in the development of sustainable pest management strategies in the context of field trials.

N-malonyl 1-aminocyclopropane-1-carboxylic acid (MACC) is a major conjugate of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) and may therefore play an important role in regulating ethylene production, as well as ethylene-independent ACC signalling. While the enzyme responsible for this derivatization, ACC malonyltransferase (AMT), has been studied in the past, its identity remains unknown. Methods to assay AMT activity are not well established, and no standardized assay has been described.

Nitrogen (N) supply is critical for apple yield and quality. Improving nitrogen use efficiency (NUE) could reduce fertilizer application for maintaining apple yield at the cost of environmental pollution in infertile soil. The molecular mechanisms underlying nitrate (NO) uptake are foundational for breeding high NUE cultivars. The two-month low N treatment mimicking infertile soil dramatically induced the accumulation of transcription factor MdWRKY17 in apple. Overexpression of MdWRKY17 conferred enhanced long-term low nitrogen tolerance in transgenic apple plants and calli, while RNA interference of MdWRKY17 reduced this tolerance. MdNRT2.5 encoding a high-affinity nitrate transporter was identified by chromatin immunoprecipitation sequencing (ChIP-seq) as the direct target of MdWRKY17. This is confirmed by in vitro EMSA and in vivo ChIP-qPCR assay. Notably, overexpression of MdNRT2.5 increased NO uptake under long-term N-deficiency conditions. RNA interference of MdNRT2.5 in roots decreased NO uptake efficiency of MdWRKY17-OE transgenic apple plants, indicating that MdWRKY17 improves NO uptake mainly by activating MdNRT2.5 expression. Our study identified an important MdWRKY17-MdNRT2.5 module in response to long-term low N stress, which will contribute to the molecular breeding of high NUE apple cultivars.

Jasmonic acid (JA), as a defensive plant hormone, can synergistically or antagonistically interact with common hormones such as gibberellin (GA), abscisic acid (ABA), indole-3-acetic hormone acid (IAA), and ethylene (ETH) during the plant growth process, as well as interact with hormones such as melatonin (MT), brassinolide (BR), and resveratrol to regulate plant growth and development processes such as metabolite synthesis, pest and disease defense, and organ growth. The core regulatory factor MYC2 of JA mainly mediates the signal transduction pathways of these hormone interactions by interacting with other genes or regulating transcription. This article reviews the mechanism of cross-talk between JA and hormones such as ABA, GA, and salicylic acid (SA), and discusses the role of MYC2 in hormone interactions.

Senescence is a crucial and highly active process in plants, optimising resource allocation and promoting phenotypic plasticity under restricted conditions. It involves global metabolic reprogramming for the organised disintegration and remobilization of resources. Polyamines (PAs) are polycationic biogenic amines prevalent in all eukaryotes and are necessary for cell survival. The commonly used PAs in plants include putrescine, spermidine, and spermine. Notably, the leaf's expression of S-adenosylmethionine decarboxylase and spermidine synthase gene family transcripts significantly changes during senescence. This suggests these genes are critical in spermidine metabolism and may condition metabolic reprogramming. One key role of spermidine in eukaryotes is to provide the 4-aminobutyl group for the posttranslational modification of lysine in eukaryotic translation factor 5A (eIF5A). This modification is catalysed by two sequential enzymatic steps leading to the activation of eIF5A by converting lysine to the unusual amino acid hypusine. Although eIF5A is well characterised to be involved in the translation of proline-rich repeat proteins and other hard-to-read motifs, the biological role of eIF5A has recently been clarified only in mammals. It could be better described at the plant functional level. The expression patterns of eIF5A isoforms and genes encoding machinery responsible for hypusination, differ between induced and developmental leaf senescence. In this paper, we summarise the existing knowledge on spermidine-dependent senescence control mechanisms in plants, raising the possibility that spermidine could be an element of a biological switch controlling the onset of a different type of senescence in an eIF5A-independent and dependent manner.

Agricultural production is severely affected by environmental stresses such as drought, and deep rooting is an important factor enhancing crop drought avoidance. H-ATPases provide a transmembrane proton gradient and are thought to play a crucial role in plant growth and abiotic stress responses. However, their expression under abiotic stress and function on deep rooting is poorly understood in rice. In this study, the conserved domains, potential phosphorylation sites, and three-dimensional structures of ten Oryza sativa PM H-ATPases (OSAs) were analyzed. Quantitative PCR analysis revealed different expression patterns of these OSA genes under hormone treatment conditions (e.g., abscisic acid) and abiotic stress conditions (e.g., drought and salt stress). Subcellular localization analysis revealed that most OSA proteins were localized to the cell membrane. Phenotype determination of OSA mutants indicated that the ratio of deep rooting (RDR) of both osa7 and osa8 mutants was significantly reduced compared to that of wild-type rice plants. Additionally, OSA haplotypes in 268 rice accessions were analyzed, and the haplotypes associated with RDR were identified. The present results provide valuable information on crucial domains, expression patterns, and functional identification of OSA paralogs to reveal their role in rice responses to abiotic stress.

Cold stress has a huge impact on the growth and development of cotton, presenting a significant challenge to its productivity. Comprehending the complex molecular mechanisms that control the reaction to CS is necessary for developing tactics to improve cold tolerance in cotton. This review paper explores how cotton responds to cold stress by regulating gene expression, focusing on both activating and repressing specific genes. We investigate the essential roles that transcription factors and regulatory elements have in responding to cold stress and controlling gene expression to counteract the negative impacts of low temperatures. Through a comprehensive examination of new publications, we clarify the intricacies of transcriptional reprogramming induced by cold stress, emphasizing the connections between different regulatory elements and signaling pathways. Additionally, we investigate the consecutive effects of cold stress on cotton yield, highlighting the physiological and developmental disturbances resulting from extended periods of low temperatures. The knowledge obtained from this assessment allows for a more profound comprehension of the molecular mechanisms that regulate cold stress responses, suggesting potential paths for future research to enhance cold tolerance in cotton by utilizing targeted genetic modifications and biotechnological interventions.

Theanine, specifically biosynthesized and accumulated in Camellia sinensis (L.) O. Kuntze, is widely recognized as the most positive ingredient related to the quality of tea. Therefore, genetic factors related to the biosynthesis of theanine in tea plant, CsAlaDC, CsGGTs and CsMYBs, etc., were elaborated and proved to be influential. Oppositely, TFs acting on the growth and development of tea plants, CsPIF, CsHO as well as CsGDH were demonstrated to be negative for biosynthesis of theanine. Since root is the original assembly site, transportation is indispensable for the accumulation of theanine in leaf. CsAAP7.2 was elucidated to be involved in the transportation of theanine crossing the vascular system to vegetative tissues. In order to promote the accumulation of theanine, strategies were proposed in aspect of processing, cultivation, fertilizer as well as germplasm innovation. Appropriate processing technology, scientific planting manner and fertilizer application, coupling with domestication of excellent varieties portrayed out the future orientation of theanine. Purpose of the review was to summarize advantages achieved in related to metabolism of theanine, and to motivate more intensive and more effective means to promote the accumulation of theanine in tea plant.

Low phosphate (LP) availability significantly impacts crop yield and quality. PHOSPHATE STARVATION RESPONSE1 (PHR1) along with PHR1-like 1 (PHL1) act as a key transcriptional regulator in a plant's adaptive response to LP conditions. Abscisic acid (ABA) plays an important role in how plants respond to environmental stresses like salinity and drought. However, the involvement of PHR1 and PHL1 in ABA response and signalling mechanisms remains to be fully understood. Our findings reveal that PHR1 and PHR1/PHL1 knockout mutations enhance the responsiveness of seed germination, early seedling growth, and stomatal opening to ABA in Arabidopsis. Furthermore, these mutations increase sensitivity to combined LP and ABA stress. In contrast, overexpression of PHR1 or PHL1 reduces this sensitivity in Arabidopsis. Knockout mutations of PHR1 and PHR1/PHL1 also increase sensitivity to salt and osmotic stresses, as well as to combined LP and salinity/osmotic stress, while overexpression of PHR1 or PHL1 reduces their sensitivity in seed germination and early seedling development. Knockout mutations of SPX1 and SPX2, negative regulators of PHR1 and PHL1, decrease sensitivity to ABA and salt/osmotic stresses in Arabidopsis. A group of genes related to ABA metabolism and signalling is significantly affected by the knockout or overexpression of PHR1 and PHL1, with a large proportion of these genes containing PHR1 binding site (P1BS) in their promoters. Moreover, the ABA-sensitive phenotype of phr1 or phr1 phl1 mutants can be rescued by PHR1 homologs from chlorophyte algae, liverwort and rice, suggesting their conserved roles in ABA signalling. These results indicate that PHR1 and its homologs negatively regulate plant responses to ABA in seed germination and stomatal aperture. This study provides new insights into the interplay between Pi homeostasis, abiotic stress and ABA signaling. Moderately increasing the expression of PHR1 or its homologs in crops could be a potential strategy to enhance plant resistance to combined LP and osmotic stress.

Amino acids are crucial nutrients for growth in crops. In this study, we found an amino acid transporter-like 13 (OsATL13), that coordinately determined rice yield and quality. OsATL13 was primarily expressed in the root and panicle, its protein was localized on plasma membrane, and it principally transported phenylalanine and methionine. Overexpression (OE) of OsATL13 increased the tiller number by 31.4%, resulting in a 16.18% increase in grain yield compared to Zhonghua 11 (ZH11). It also decreased amylose content and increased protein content in OsATL13 OE lines compared to ZH11, whereas the OsATL13 mutant exhibited opposite effects. RNA-seq analysis revealed that upregulation of OsATL13 influenced the expression of genes associated with nitrogen and starch metabolism pathways. Notably, exogenous treatment with phenylalanine and methionine promoted axillary buds outgrowth, increased tiller number and rice yield, improved milled and head rice rates, and decreased chalky rice rate. Furthermore, rapid viscosity analysis supported the observation that phenylalanine and methionine treatments influenced rice eating and cooking quality. This research offers new perspectives on the synchronized enhancement of both rice yield and quality with amino acid transporter OsATL13.

Tryptophan-arginine-lysine-tyrosine (WRKY) transcription factors are essential regulators of drought tolerance in multiple plants. However, whether and how GhWRKY207 modulates cotton response to drought stress is unclear. In this study, we determined that GhWRKY207 expression was high in leaves and induced by drought stress. The gene encoded a nuclear protein that had transcriptional activation activity. Silencing GhWRKY207 by virus-induced gene silencing (VIGS) caused significant reduction in drought tolerance of cotton plants. Consistently, overexpression of GhWRKY207 in Arabidopsis thaliana wild type (WT) plants clearly enhanced their drought tolerance. Moreover, GhWRKY207 VIGS plants had notably increased malondialdehyde (MDA) contents, electrolyte leakage percentages and O accumulation rates whereas GhWRKY207 overexpression lines showed markedly decreased levels of the three parameters compared to their corresponding controls under water deficit conditions. Additionally, GhWRKY207 enhanced superoxide dismutase (SOD) activity by directly activating the expression of GhCu/Zn-SOD3 (GhCSD3) and GhFe-SOD2 (GhFSD2) genes. Silencing GhCSD3 or GhFSD2 also markedly reduced drought tolerance of cotton plants. Taken together, these results suggest that GhWRKY207 positively regulates drought tolerance by inducing the expression of GhCSD3 and GhFSD2 in Gossypium hirsutum.

Plant A/T-rich sequence- and zinc-binding (PLATZ) family proteins represent a novel class of plant-specific transcription factors that bind to A/T-rich sequences. Advances in high-throughput sequencing and bioinformatics analyses have facilitated the identification of numerous PLATZ proteins across various plant species. Over the last decade, accumulating evidence from omics analyses, genetics studies, and gain- and loss-of function investigations has indicated that PLATZ proteins play crucial roles in the complex regulatory networks governing plant development and adaptation to environmental stress. Recently, an excellent review has been published highlighting the roles of PLATZ proteins in controlling plant developmental processes. However, a comprehensive review specifically addressing the molecular mechanisms by which these proteins drive their functions in plant responses to environmental cues is currently lacking. In this review, we summarize the characteristics and identification of PLATZ proteins, emphasizing their significance in stress responses. We also highlight the crosstalk between PLATZ proteins and phytohormones. Furthermore, we discuss the downstream target genes, interacting partners, and upstream regulatory mechanisms associated with PLATZ proteins, providing a thorough understanding of their multifaceted roles in plants.