Hormone Signaling Research Articles

A brief history of insect neuropeptide and peptide hormone research.

This review briefly summarizes 50years of research on insect neuropeptide and peptide hormone (collectively abbreviated NPH) signaling, starting with the sequencing of proctolin in 1975. The first 25years, before the sequencing of the Drosophila genome, were characterized by efforts to identify novel NPHs by biochemical means, mapping of their distribution in neurons, neurosecretory cells, and endocrine cells of the intestine. Functional studies of NPHs were predominantly dealing with hormonal aspects of peptides and many employed ex vivo assays. With the annotation of the Drosophila genome, and more specifically of the NPHs and their receptors in Drosophila and other insects, a new era followed. This started with matching of NPH ligands to orphan receptors, and studies to localize NPHs with improved detection methods. Important advances were made with introduction of a rich repertoire of innovative molecular genetic approaches to localize and interfere with expression or function of NPHs and their receptors. These methods enabled cell- or circuit-specific interference with NPH signaling for in vivo assays to determine roles in behavior and physiology, imaging of neuronal activity, and analysis of connectivity in peptidergic circuits. Recent years have seen a dramatic increase in reports on the multiple functions of NPHs in development, physiology and behavior. Importantly, we can now appreciate the pleiotropic functions of NPHs, as well as the functional peptidergic "networks" where state dependent NPH signaling ensures behavioral plasticity and systemic homeostasis.

Signaling pathways mediating the induction of preharvest fruit drop in litchi

Certain litchi varieties, such as “Nuomici”, are highly susceptible to preharvest fruit drop, which leads to significant losses in fruit yield and economic value. However, the precise molecular mechanisms underlying this issue are not yet fully understood. In this study, we aimed to elucidate the signaling pathways that facilitate preharvest fruit drop in litchi, using “Nuomici” and “Huaizhi” cultivars as examples, which demonstrate high and low preharvest fruit drop rates, respectively. Our findings revealed that “Nuomici” experienced a substantial preharvest fruit drop, with a cumulative rate of 41.68%, significantly higher than the 1.44% observed in “Huaizhi”. Cellulase activity assays showed a significant increase in cellulase activity in the abscission zone of “Nuomici”, which coincided with the occurrence of preharvest fruit drop, in contrast to the relatively low levels in “Huaizhi”. Phytohormone assays indicated lower indole-3-acetic acid content in the pericarp, aril, and seeds of “Nuomici” during the preharvest stage compared to “Huaizhi”, coupled with higher abscisic acid levels in the seeds of “Nuomici”. Furthermore, transcriptomic analysis identified 180, 282, 655, and 241 differentially expressed genes (DEGs) in the pericarp, aril, seed, and abscission zone, respectively, between the two cultivars during preharvest fruit drop. These DEGs are intricately involved in the generation and transmission of abscission signals from fruit tissues, encompassing PIN, PIN-LIKES, LAX, and SAUR genes related to polar auxin transport, ethylene diffusion, as well as perceiving these signals and activating the abscission process within the abscission zone. This includes ACO and ILR genes involved in hormone biosynthesis and signal transduction, regulation by WRKY, NAC, and bHLH transcription factors, AAO genes involved in response to reactive oxygen species, and EXP, EG, and PG genes involved in cell wall degradation in the abscission zone. Based on these comprehensive findings, we propose a model for preharvest fruit drop triggered by a series of molecular events in litchi, providing valuable insights into the complex mechanisms governing this phenomenon.

Growth and physiological response of Yulu Hippophae rhamnoides to drought stress and its omics analysis

ABSTRACT Hippophae rhamnoides (H. rhamnoides) is the primary tree species known for its ecological and economic benefits in arid and semi-arid regions. Understanding the response of H. rhamnoides roots to drought stress is essential for promoting the development of varieties. One-year-old Yulu H. rhamnoides was utilized as the experimental material, and three water gradients were established: control (CK), moderate (T1) and severe (T2), over a period of 120 days. The phenotypic traits and physiological indies were assessed and analyzed, while the roots were subjected by RNA-Seq transcriptome and Tandem Mass Tags (TMT) proteome analysis. Drought stress significantly reduced the plant height, ground diameter, root biomass and superoxide dismutase activity; however, the main root length increased. In comparison with CK, a total of 5789 and 5594 differential genes, as well as 63 and 1012 differential proteins, were identified in T1 and T2, respectively. The combined analysis of transcriptome and proteome showed that the number of differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) associated with T1, T2 and CK was 28 and 126, respectively, with 7 and 36 genes achieving effective KEGG annotation. In T1 and T2, the differential genes were significantly enriched in the plant hormone signal transduction pathway, but there was no significant enrichment in the protein expression profile. In T2, 38 plant hormone signal transduction function genes and 10 peroxisome related genes were identified. With the increase of drought stress, the combined expression of DEGs and DEPs increased. Yulu H. rhamnoides may allocate more resources toward CAT while simultaneously decreasing SOD and POD to mitigate the oxidative stress induced by drought. Furthermore, the molecular mechanisms underlying plant hormone signal transduction and peroxisome-related genes in the roots of H. rhamnoides were discussed in greater detail.

A Comparative Transcriptome Analysis Revealing the Mechanism Underlying the Effect of Maternal Plant Age on Adventitious Rooting of Euryodendron excelsum Cuttings

Euryodendron excelsum H. T. Chang, a monotypic plant endemic to China, exhibits significant variations in adventitious root formation in cuttings across different age groups through unclear molecular mechanisms. In this study, we performed RNA-sequencing (RNA-seq) and data analysis at three stages—initial excision (S0), root primordia (S1), and emergence of adventitious roots (S2)—for lateral buds from transplanted triennial tissue culture seedlings and decennial E. excelsum plants. We identified 13,424 differentially expressed genes (DEGs) between different rooting stages and age groups, including 8216 upregulated and 5208 downregulated genes. A Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis indicated that the S1 and S2 DEGs identified were mainly involved in phenylpropanoid biosynthesis, plant hormone signal transduction, plant–pathogen interactions, biosynthesizing various secondary plant metabolites, and starch and sucrose metabolism. Key auxin-pathway genes were expressed at significantly higher levels in culture seedlings than in adult plants, as were WUSCHEL-related homeobox and LATERAL ORGAN BOUNDARIES DOMAIN genes (related to adventitial root growth and development), which together promote the formation, growth, and development of adventitial root primordia. The dysregulated expression of 15 DEGs identified by RNA-seq were verified via real-time quantitative polymerase chain reaction analysis. This study investigates the morphological processes of adventitious root formation in cuttings of E. excelsum of different ages, and the potential molecular mechanisms involved. Our finding provides a basis for research on cutting propagation, conservation applications, and optimization of tissue culture for E. excelsum, and may help improve the rooting rate of E. excelsum cuttings.

Thyroid function and brain structure: insight from a Mendelian randomization study.

Thyroid hormones play a critical role in brain development. However, the precise causal associations between thyroid function and structural changes in specific brain regions remain uncertain. We applied the univariate Mendelian randomization (UVMR) method to assess the causal effects of thyroid function on brain structure. Genome-wide association study (GWAS) data on thyroid-related traits from the ThyroidOmics consortium, including free thyroxine (FT4), free triiodothyronine (FT3), thyroid-stimulating hormone (TSH), FT3/FT4 ratio, as well as dichotomized high and low TSH levels were used as exposures. GWAS data on cortical thickness, surface area, and volume of subcortical structures served as outcomes. Inverse-variance weighted (IVW) was the main estimate method. Subsequently, multivariable MR (MVMR) was conducted to validate significant causal associations identified in UVMR. UVMR analysis identified 1 significant and 13 nominal significant causal relationships (P<0.05). Genetically predicted FT4 showed a statistically significant inverse association with putamen volume (β= -71.91, 95% confidence interval: -112.11 to -31.71). These findings were robust in sensitivity analysis. MVMR analysis further confirmed a persistent causal relationship between FT4 and putamen volume after adjusting for FT3, TSH, and neuropsychiatric disorders. Functional enrichment analyses indicated the pathways by which FT4 influences putamen volume may be related to thyroid hormone signaling pathway, sodium-independent organic anion transport, and Rap1 signaling pathway. MR analysis provides evidence for causal relationships between thyroid function and brain structural alterations, particularly highlighting the impact of FT4 on putamen volume. Further research is warranted to elucidate the underlying mechanisms by which thyroid hormones modulate brain structure.

Physiological characteristics and transcriptomic analyses of alfalfa root crown in wintering

BackgroundAlfalfa, scientifically identified as Medicago sativa, is repeatedly referred to as the “king of forages”. Because of its tight relationship to winter hardiness, the alfalfa’s root crown plays a significant role as a storage organ over the winter. At present, it is still unknown what molecular process makes the alfalfa root crown resistant to cold. This study was aimed to study these knowledge gaps. Using RNA sequencing (RNA-Seq) technology, significant genes associated with cold hardiness were found.MethodsAccording to the random block design, Longmu 806 alfalfa and Sardi alfalfa were planted in regional experiments. Under the condition of low-temperature treatment in winter, the differentially expressed genes (DEGs), winter survival rate (WSR), and physiological characteristics were, in turn, calculated by RNA-Seq, chemical analysis, and field investigation.ResultsThe WSR of the Longmu 806 alfalfa was 3.68-fold greater than that of the Sardi alfalfa. The jasmonic acid (JA), soluble sugar (SS), proline (Pro), and glutathione (GSH) concentration in the roots of Longmu 806 alfalfa was more than the same amount in Sardi alfalfa in other words P is less than 0.05. An entire set of 878 DEGs related to winter hardiness was found by statistical analysis. Among them, 463 DEGs showed an increase in expression, whereas 415 DEGs showed a decrease in expression. The metabolic pathways’ examination presented that the DEGs (MsERF1, MsCHIB, MsJAZ, MsAOC, MsGST, MsINV, MsTPS, and MsOAT) were linked to the pathways of “plant hormone signaling transduction”, “Amino sugar and nucleotide sugar metabolism”, and “glutathione metabolism”. Furthermore, the physiological changes in JA, SS, Pro content, and GSH were influenced by the dynamic transcription profile of LT (low- temperature) resistance-related genes.

Unveiling the Role of β-Glucosidase Genes in Bletilla striata’s Secondary Metabolism: A Genome-Wide Analysis

β-glucosidases (BGLUs) are abundant enzymes in plants that play pivotal roles in cell wall modification, hormone signal transduction, secondary metabolism, defense against herbivores, and volatile compound release. Bletilla striata, a perennial herb revered for its therapeutic properties, lacks a comprehensive analysis of its BGLU gene family despite the critical role these genes play in plant secondary metabolism. This study aims to perform a genome-wide analysis of the BGLU gene family in B. striata (BsBGLU) to elucidate their functions and regulatory mechanisms in secondary metabolite biosynthesis. We conducted a genome-wide screening to identify BsBGLU, followed by phylogenetic analysis to classify these genes into groups. Sequence characteristics were analyzed to predict functional roles. Simple sequence repeat (SSR) markers were examined to assess conservation and polymorphism among different landraces. Expression profiles of BsBGLUs were evaluated under sodium acetate and salicylic acid elicitor treatments and across different tissues. The accumulation of phylogenetic metabolites in different treatments and tissues was also analyzed by HPLC and LCMS detection to explore the correlation between gene expression and metabolite accumulation. A total of 23 BsBGLU genes were identified and classified into eight distinct groups. Sequence analysis suggested diverse functions related to hormone responses, secondary metabolism, and stress resistance. BsBGLUs with SSR sequences were conserved yet showed polymorphism among different B. striata landraces. Under elicitor treatments, expression profiling revealed that BsBGLUs significantly modulate the synthesis of secondary metabolites such as dactylorhin A and militarine. Tissue-specific expression analysis indicated that BsBGLU15 and BsBGLU28 were highly expressed in tubers compared to other tissues, suggesting their central role and a potential negative regulatory effect in metabolite accumulation. The elicitor NaAc can regulate metabolite synthesis by modulating the expression of BsBGLUs. The BsBGLU gene family in B. striata is integral to the modulation of secondary metabolite biosynthesis and accumulation and can respond to elicitors to promote the synthesis of militarine. These findings provide a theoretical foundation for the further exploration of BsBGLU gene functions and their regulatory mechanisms, advancing the production of medicinally active compounds in B. striata.

Exploring Microgravity’s Effect on Seed Germination and Growth of Plants

The study of the effects of microgravity on plant cells has gained significant attention, especially in the context of space experiments, which necessitates a comprehensive understanding of plant growth and development in altered gravitational conditions. Understanding the impact of microgravity on seed germination, seedling establishment, and overall plant development is essential for future space agriculture and the development of sustainable food production systems. In microgravity, plants encounter unique physical and physiological challenges, making it essential to explore the physiological and biochemical responses of plant cells to this environment. Various factors contribute to the alterations observed in plant behavior under microgravity, including changes in water and nutrient distribution, disruptions in hormone signaling, and modifications in the expression of secondary metabolites. Physiological and biochemical in plants due to microgravity caused by the influence on the phytochrome system, gas exchange photosynthesis, and the production of secondary metabolites. Microgravity affects mechanocellular responses of plants which elucidates how the absence of gravity can disrupt cytoplasmic streaming, impact cell wall rigidity, and cause damage to cell membranes. These alterations in plant cell behavior under microgravity conditions can have profound implications for plant growth and development. Space farming faces challenges and constraints of cultivating plants in space, such as managing water distribution, temperature fluctuations, and radiation exposure, are addressed. Innovative methods for planting crops in space, including plant pillows, greenhouse cultivation, and soil-less systems, are discussed. In the future, research efforts should focus on selecting or genetically modifying plant varieties with enhanced tolerance to the diverse stress encountered in space environments. Thus, it is concluded that space farming underscores the importance of comprehensive studies on plant responses to microgravity, offering valuable insights for both space exploration and terrestrial agriculture.

Peripherally Restricted Activation of Opioid Receptors Influences Anxiety-Related Behaviour and Alters Brain Gene Expression in a Sex-Specific Manner

Although effects of stress-induced anxiety on the gastrointestinal tract and enteric nervous system (ENS) are well studied, how ENS dysfunction impacts behaviour is not well understood. We investigated whether ENS modulation alters anxiety-related behaviour in rats. We used loperamide, a potent μ-opioid receptor agonist that does not cross the blood–brain barrier, to manipulate ENS function and assess changes in behaviour, gut and brain gene expression, and microbiota profile. Sprague Dawley (male/female) rats were acutely dosed with loperamide (subcutaneous) or control solution, and their behavioural phenotype was examined using open field and elevated plus maze tests. Gene expression in the proximal colon, prefrontal cortex, hippocampus, and amygdala was assessed by RNA-seq and caecal microbiota composition determined by shotgun metagenome sequencing. In female rats, loperamide treatment decreased distance moved and frequency of supported rearing, indicating decreased exploratory behaviour and increased anxiety, which was associated with altered hippocampal gene expression. Loperamide altered proximal colon gene expression and microbiome composition in both male and female rats. Our results demonstrate the importance of the ENS for communication between gut and brain for normo-anxious states in female rats and implicate corticotropin-releasing hormone and gamma-aminobutyric acid gene signalling pathways in the hippocampus. This study also sheds light on sexually dimorphic communication between the gut and the brain. Microbiome and colonic gene expression changes likely reflect localised effects of loperamide related to gut dysmotility. These results suggest possible ENS pharmacological targets to alter gut to brain signalling for modulating mood.

Anionic phospholipid-mediated transmembrane transport and intracellular membrane trafficking in plant cells.

Cellular membranes primarily consist of proteins and lipids. These proteins perform cellular functions such as metabolic regulation, environmental and hormonal signal sensing, and nutrient transport. There is increasing experimental evidence that certain lipids, particularly anionic phospholipids, can act as signaling molecules. Specific examples of functional regulation by anionic phospholipids in plant cells have been reported for transporters, channels, and even receptors. By regulating the structure and activity of membrane-integral proteins, these phospholipids mediate the transport of phytohormones and ions, and elicit physiological responses to developmental and environmental cues. Phospholipids also control membrane protein abundance and lipid composition and abundance by facilitating vesicular trafficking. In this review, we discuss recent research that elucidates the mechanisms by which membrane-integral transporters and channels are controlled via phospholipid signaling, as well as the regulation of membrane protein accumulation by phospholipids through coordinated removal, recycling, and degradation processes.

Comparative transcriptome analysis provides novel insights into the seed germination of Panax japonicus, an endangered species in China

Panax japonicus, an endangered species in China, is usually used as a traditional medicine with functions of hemostasis, pain relief, and detoxify. However, the seeds of P. japonicus are hard to germinate in natural conditions, and the molecular events and systematic changes occurring in seed germination are still largely unknown. In this study, we compared the seeds in different germination stages in terms of morphological features, antioxidant enzyme activities, and transcriptomics. The results indicated that sand storage at 25℃ for 120 d effectively released the seed dormancy of P. japonicus and promoted the seed germination. Moreover, sand storage treatment increased the antioxidant capacity of P. japonicus seeds through increasing the activities of SOD, POD, and CAT. The RNA-seq identified 28,908 differentially expressed genes (DEGs) between different germination stages, of which 1697 DEGs significantly changed throughout the whole germination process. Functional annotations showed that the seed germination of P. japonicus was mainly regulated by the DEGs related to pathways of ROS-scavenging metabolism, plant hormonal signal transduction, starch and sucrose metabolism, energy supply (glycolysis, pyruvate metabolism, and oxidative phosphorylation), and phenylpropanoid biosynthesis, as well as the transcription factors such as bHLHs, MYBs, WRKYs, and bZIPs. This study provides a foundation for unveiling molecular mechanisms underlying the seed germination and is beneficial for accelerating the development of P. japonicus industry.

The effect of early weaning on feeding behavior parameters in rodents: A systematic review.

Breastfeeding is essential for somatic development, especially neurodevelopment. The abrupt termination of the mother-child bond, early weaning, is a stressful event during the neonatal period. This has lifelong consequences. The impact on neural plasticity will be reflected in behavioral expression, including feeding behavior. This behavior is modulated by encephalic and peripheral structures, such as the serotonergic and dopaminergic neurotransmission systems, as well as hormonal signaling, leptin, and ghrelin. The central nervous system, particularly the hypothalamus, receives information from the gastrointestinal tract to regulate hunger and satiety. Early weaning alters these mechanisms that control feeding behavior. The alterations most commonly reported in the literature are hyperphagia, increased body mass, and molecular alterations related to the control of feeding behavior. Studies have attempted to identify the factors involved in the changes in feeding behavior control caused by early weaning. Furthermore, pharmacological interventions, herbal medicines, calcium supplementation, and physical activity have been investigated as potential means of reversing these changes. Consequently, the objective of this literature review was to analyze the effects of early weaning on the modulation of parameters that act to control feeding behavior.

Unlocking the Growth Potential of Poplar: A Novel Transcriptomic-Metabolomic Approach to Evaluating the Impact of Divergent Pruning Strategies

Pruning is a common forest-tending method; its purpose is to promote growth and improve the overall stand quality. Poplar is a fast-growing, broad-leaved tree species with high ecological and economic value. It is a common management method to promote its growth by pruning and adjusting the spatial structure of the stand, but its potential regulatory mechanism remains unclear. In this study, transcriptome and metabolome data of different parts at all pruning intensities were determined and analyzed. The results showed that 7316 differentially expressed genes were identified in this study. In the plant hormone signal transduction pathway, candidate genes were found in eight kinds of plant hormones, among which the main expression was gibberellin, auxin, and brassinosteroid. Some candidate gene structures (beta-glucosidase, endoglucanase, hexokinase, glucan endo-1, 3-beta-D-glucosidase, beta-fructofuranosidase, fructokinase, maltase-glucoamylase, phosphoglucomutase, and sucrose) were specifically associated with starch and sucrose biosynthesis. In the starch and sucrose biosynthesis pathway, D-fructose 6-phosphate, D-glucose 1,6-bisphosphate, and glucose-1-phosphate were the highest in stems and higher in the first round of pruning than in no pruning. The bHLH plays a key role in the starch and sucrose synthetic pathway, and AP2/ERF-ERF is important in the plant hormone signal transduction pathway. These results laid a foundation for understanding the molecular mechanism of starch and sucrose biosynthesis and provided a theoretical basis for promoting tree growth through pruning.

Ubiquitin Ligase U-Box51 Positively Regulates Drought Stress in Potato (Solanum tuberosum L.)

The ubiquitin-proteasome system (UPS) is a key protein degradation pathway in eukaryotes, in which E3 ubiquitin ligases mediate protein ubiquitination, directly or indirectly targeting substrate proteins to regulate various biological processes, including plant growth, hormone signaling, immune responses, and adaptation to abiotic stress. In this study, we identified plant U-box protein 51 in Solanum tuberosum (StPUB51) as an E3 ubiquitin ligase through transcriptomic analysis, and used it as a candidate gene for gene-function analysis. Quantitative real-time PCR (qRT-PCR) was used to examine StPUB51 expression across different tissues, and its expression patterns under simulated drought stress induced by polyethylene glycol (PEG 6000) were assessed. Transgenic plants overexpressing StPUB51 and plants with down-regulated StPUB51 expression were generated to evaluate drought tolerance. The activities of key antioxidant enzymes-superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) as well as malondialdehyde (MDA) content in transgenic plants’ leaves were measured under drought conditions. Protein–protein interactions involving StPUB51 were explored via yeast two-hybrid (Y2H) screening, with interaction verification by bimolecular fluorescence complementation (BiFC). StPUB51 was predominantly expressed in stems, with lower expression observed in tubers, and its expression was significantly upregulated in response to 20% PEG-6000 simulated drought. Subcellular localization assays revealed nuclear localization of the StPUB51 protein. Under drought stress, StPUB51-overexpressing plants exhibited enhanced SOD, POD, and CAT activities and reduced MDA levels, in contrast to plants with suppressed StPUB51 expression. Y2H and BiFC analyses identified two interacting proteins, StSKP2A and StGATA1, which may be functionally linked to StPUB51. Collectively, these findings suggest that StPUB51 plays a positive regulatory role in drought tolerance, enhancing resilience in potato growth and stress adaptation.

The background sodium leak channel NALCN is a major controlling factor in pituitary cell excitability

AbstractThe pituitary gland produces and secretes a variety of hormones that are essential to life, such as for the regulation of growth and development, metabolism, reproduction, and the stress response. This is achieved through an intricate signalling interplay between the brain and peripheral feedback signals that shape pituitary cell excitability by regulating the ion channel properties of these cells. In addition, endocrine anterior pituitary cells spontaneously fire action potentials to regulate the intracellular calcium ([Ca2+]i) level, an essential signalling conduit for hormonal secretion. To this end, pituitary cells must regulate their resting membrane potential (RMP) close to the firing threshold, but the molecular identity of the ionic mechanisms responsible for this remains largely unknown. Here, we revealed that the sodium leak channel NALCN, known to modulate neuronal excitability elsewhere in the brain, regulates excitability in the mouse anterior endocrine pituitary cells. Using viral transduction combined with powerful electrophysiology methods and calcium imaging, we show that NALCN forms the major Na+ leak conductance in these cells, appropriately tuning cellular RMP for sustaining spontaneous firing activity. Genetic depletion of NALCN channel activity drastically hyperpolarised these cells, suppressing their firing and [Ca2+]i oscillations. Remarkably, despite this profound function of NALCN conductance in controlling pituitary cell excitability, it represents a very small fraction of the total cell conductance. Because NALCN responds to hypothalamic hormones, our results also provide a plausible mechanism through which hormonal feedback signals from the brain and body could powerfully affect pituitary activity to influence hormonal function. imageKey points Pituitary hormones are essential to life as they regulate important physiological processes, such as growth and development, metabolism, reproduction and the stress response. Pituitary hormonal secretion relies on the spontaneous electrical activity of pituitary cells and co‐ordinated inputs from the brain and periphery. This appropriately regulates intracellular calcium signals in pituitary cells to trigger hormonal release. Using viral transduction in combination with electrophysiology and calcium imaging, we show that the activity of the background leak channel NALCN is a major controlling factor in eliciting spontaneous electrical activity and intracellular calcium signalling in pituitary cells. Remarkably, our results revealed that a minute change in NALCN activity could have a major influence on pituitary cell excitability. Our study provides a plausible mechanism through which the brain and body could intricately control pituitary activity to influence hormonal function.

Comparative genomics analysis of the MYB gene family in barley: preliminary insights into evolution and biological function in Blue Qingke.

The Myeloblastosis related (MYB) family is one of the most widely distributed transcription factor families in plants and plays a significant role in plant growth and development, hormone signal transduction, and stress response. There are many reports on MYB family species, but the research on Qingke is still limited. This study used comparative genomics methods to analyze gene and protein structure, protein physicochemical properties, chromosome localization, and evolution. A bioinformatics approach was used to systematically analyze the HvMYB gene family. At the milk stage, soft dough stage, and mature stage, White and Blue Qingke grains were selected for RNA sequencing (RNA-seq), among which two proteins interacted (HvMYB and HvMYC). The expression of this gene family was analyzed through RNA-seq, and the expression levels of HvMYB and HvMYC in the grains of two different color varieties were analyzed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Finally, the interaction between HvMYB and HvMYC was verified by bimolecular fluorescence complementation (BiFC) experiments. A total of 92 Qingke HvMYB genes were identified and analyzed, and 92 HvMYB proteins were classified into five categories. Cis-acting elements associated with abscisic acid response, light response, and methyl jasmonate (MeJA) response were found in the promoter regions of most MYB genes. Using qRT-PCR combined with RNA-seq analysis showed that MYB gene was highly expressed in the soft dough stage and was varietal specific. Subcellular localization indicated that HvMYB was located in the nucleus and cell membrane, HvMYC was located in the nucleus, cell membrane, and cytoplasm. Through BiFC analysis, it has been proven that HvMYB in the MYB family and HvMYC in the basic helix-loop-helix (bHLH) family can interact. This study provides a preliminary theoretical basis for understanding the function and role of the Qingke MYB gene family and provides a reference for the molecular mechanism of Qingke gene evolution.

Unraveling the genetic basis of Rhizobium rhizogenes-mediated transformation and hairy root formation in rose using a genome-wide association study

Key MessageMultiple QTLs reveal the polygenic nature of R. rhizogenes-mediated transformation and hairy root formation in roses, with five key regions explaining 12.0–26.9% of trait variability and transformation-related candidate genes identified.Understanding genetic mechanisms of plant transformation remains crucial for biotechnology. This is particularly relevant for roses and other woody ornamentals that exhibit recalcitrant behavior in transformation procedures. Rhizobium rhizogenes-mediated transformation leading to hairy root (HR) formation provides an excellent model system to study transformation processes and host–pathogen interactions. Therefore, this study aimed to identify quantitative trait loci (QTLs) associated with HR formation and explore their relationship with adventitious root (AR) formation in rose as a model for woody ornamentals. A diversity panel of 104 in vitro grown rose genotypes was transformed with R. rhizogenes strain ATCC 15834 carrying a green fluorescent protein reporter gene. Phenotypic data on callus and root formation were collected for laminae and petioles. A genome-wide association study using 23,419 single-nucleotide polymorphism markers revealed significant QTLs on chromosomes one and two for root formation traits. Five key genomic regions explained 12.0–26.9% of trait variability, with some peaks overlapping previously reported QTLs for AR formation. This genetic overlap was supported by weak to moderate correlations between HR and AR formation traits, particularly in petioles. Candidate gene identification through literature review and transcriptomic data analysis revealed ten candidate genes involved in bacterial response, hormone signaling, and stress responses. Our findings provide new insights into the genetic control of HR formation in roses and highlight potential targets for improving transformation efficiency in ornamental crops, thereby facilitating future research and breeding applications.

Transcriptome analysis and transcription factors response to transplanting and topping time of upper leaf in tobacco (Nicotiana tabacum L.)

Tobacco, as an annual industrial crop, is significantly affected by agronomic practices such as transplanting and topping, which can influence the yield and quality of the upper leaves. However, the processes by which transcription factors integrate both agronomic practices remain unclear. In this study, eight treatments were designed based on varying transplanting and topping periods. RNA-seq was employed to analyze the transcriptional expression and identify key differentially expressed genes (DEGs) and transcription factors (TFs). Subsequently, a rigorous quality inspection and data cleaning process yielded 1,302,152,358 high-quality reads. The comparative analysis of 8 treatments identified a total of 4265 DEGs. Utilizing K-means analysis, these DEGs demonstrated 9 distinct expression patterns. GO and KEGG annotation revealed a significant association of these DEGs with photosynthesis and secondary metabolism. 10 hub genes including AFC2, SIGB, PGSIP8, BIG5, OSP1, RL13, PDC1, NtORF and EBG were identified through WGCNA analysis. 41 differentially expressed TFs were identified through transcription factor analysis. Among them, 10 TFs namely ABR1, ERF26, HAT5, HSF24, LUH, AGL8, TIFY5A, TIFY10A, WRKY4, and WRKY40 are directly associated with plant stress resistance. 5 TFs such as ERF110, IDD7, ATB40, NAC81, and NAC83 have been identified as positive regulators of growth and development, while 3 TFs such as BH130, TCP4, and WRKY53 have been found to negatively impact growth and development. Furthermore, 4 TFs have been implicated in hormone and light signaling pathways, namely CIGR1, BLH1, WRKY42, and EIN4. The identified hub genes and TFs suggest that early transplanting and topping (B1D1C) contribute to enhanced stress resistance in tobacco. This may result in more developed stomata on tobacco leaves, as well as an increase in leaf thickness and a reduction in leaf size.

Regulation and application of hormone signals on flowering of Cymbidium sinense

Regulation and application of hormone signals on flowering of <i>Cymbidium sinense</i>

Metabolomic and Transcriptomic Analysis Revealed the Maturation Mechanism of White-Fleshed Strawberry

Strawberry (Fragaria ananassa) is a widely grown horticultural crop, which exists in red, yellow, and white varieties. In recent years, the white-fleshed strawberry variety is gaining more attention from consumers for its unique taste and appearance, but a comprehensive understanding of the molecular processes governing the ripening of white-fleshed strawberry remains undisclosed. In this study, based on the joint analysis of physiology, metabolome, and transcriptome, we screened and identified the key metabolites that were highly correlated to the maturation of white-fleshed strawberry (cv. ‘snow white’, SW for short) fruits. In contrast to red-fleshed strawberries, SW fruits exhibited three main ripening stages during the maturation, accompanied by the increases in total soluble solid and total sugar and the declines in total anthocyanin and total acid. Metabolomic analysis identified 832 differential accumulated metabolites (DAMs) at the secondary level of LC-MS/MS, and further investigations suggested that the increase in sucrose, citric acid, and epicatechin levels potentially play a role in the ripening process of SW fruits. Furthermore, abscisic acid and methyl jasmonate were recognized as the primary phytohormones involved in the production of these metabolites. The enrichment analysis of RNA-Seq data revealed that the differential expressed genes (DEGs) were primarily attributed to the pathways of ‘Starch and sucrose metabolism’ and ‘Plant hormone signal transduction’ but were undetected in ‘Flavonoid biosynthesis’ at the late ripening stage. Moreover, the de novo biosynthesis pathway, WGCNA, and Pearson correlation analysis indicated a direct relationship between FaSPS1, FaSPP1, and FaSPP2 with sucrose, FaPEPC1, FaV-PPase2, and FaV-PPase3 with citric acid, and Fa4CL2, Fa4CL3, and FaANR1 with anthocyanin. Further analysis revealed a co-expression of MYBs, bHLHs, NACs, and WRKYs with the structural genes mentioned. Overall, our findings uncovered a molecular mechanism regulating the maturation of white-fleshed strawberry, providing valuable insights for enhancing the flavor of white-fleshed strawberry through the gene-editing technique.