Serotonin (5-hydroxytryptamine (5-HT)) is a pineal hormone and a secondary metabolite related to various hormonal and physiological functions at the organ, tissue, and cellular levels. It is considered increasingly important in regulating animal behavior, but the function of serotonin in plants is far less known. According to recent research, serotonin is vital for plant growth, development, and stress responses, achieved through transcriptional and phytohormonal interplay. Specifically, this review addresses critical gaps in the understanding of serotonin's function in plants by examining its biosynthesis, metabolism, and its multifaceted role in mitigating both abiotic stresses (salinity, drought, heat, cold, and heavy metals) as well as biotic challenges (pathogens, pests, and herbivores). As a pivotal player, it engages in a variety of significant cellular and molecular interactions, including those with reactive oxygen and nitrogen species (RONS), and various phytohormones such as auxin, abscisic acid (ABA), salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and cytokinin (CK). Advances in serotonin-related research are anticipated to offer a valuable basis for uncovering the regulatory pathways by which serotonin impacts the resilience of crops against abiotic stress.

Bamboo is a fast-growing and ecologically significant plant with immense economic value due to its applications in construction, textiles, and bioenergy. However, research on bamboo has been hindered by its long vegetative period, unpredictable flowering cycles, and challenges in genetic transformation. Recent developments in advanced sequencing and genetic engineering technologies have provided new insights into bamboo's evolutionary history, developmental biology, and stress resilience, paving the way for improved conservation and sustainable utilization. This review synthesizes the latest findings on bamboo's genomics, biotechnology, and the molecular mechanisms governing its growth, development, and stress response. Key genes and regulatory pathways controlling its rapid growth, internode elongation, rhizome development, culm lignification, flowering, and abiotic stress responses have been identified through multi-omics and functional studies. Complex interactions among transcription factors, epigenetic regulators, and functionally important genes shape bamboo's unique growth characteristics. Moreover, progress in genetic engineering techniques, including clustered regularly interspaced short palindromic repeats-based genome editing, has opened new avenues for targeted genetic improvements. However, technical challenges, particularly the complexity of polyploid bamboo genomes and inefficient regeneration systems, remain significant barriers to functional studies and large-scale breeding efforts. By integrating recent genomic discoveries with advancements in biotechnology, this review proposes potential strategies to overcome existing technological limitations and to accelerate the development of improved bamboo varieties. Continued efforts in multi-omics research, gene-editing applications, and sustainable cultivation practices will be essential for harnessing bamboo as a resilient and renewable resource for the future. The review presented here not only deepens our understanding of bamboo's genetic architecture but also provides a foundation for future research aimed at optimizing its ecological and industrial potential.

Light is a fundamental environmental cue that dynamically orchestrates plant growth and development through spatiotemporally regulated molecular networks. Among these, phosphorylation, a key post-translational modification, plays a crucial role in controlling the function, stability, subcellular localization, and protein–protein interactions of light signaling components. This review systematically examines phosphorylation-dependent regulatory events within the Arabidopsis light signaling cascade, focusing on its regulatory mechanisms, downstream functional consequences, and crosstalk with other signaling pathways. We underscore the pivotal role of phosphorylation in light signaling transduction, elucidating how the phosphorylation-decoding framework transduces light information into growth and developmental plasticity to modulate plant–environment interactions.

Pitaya is an important perennial herbaceous fruit tree. The color of fruit determines pitaya nutritive (and attractive) value, which is considered as an important objective in breeding improvement. In this study, we reported the first telomere-to-telomere (T2T) gap-free genome of “Shuangse No. 1” pitaya (Hylocereus polyrhizus; red peel). Two high-quality genomes for “Dahong” (H. polyrhizus; red peel) and “Honghuaqinglong” (H. stenopterus; stay-green) were further assembled, aiming to explore the genetic diversity of pitaya genomes. In further analysis, we noticed a high proportion of viral contamination in pitaya tissues, which hindered the efficient utilization of transcriptomic data. To address this issue, we analyzed 111 pitaya transcriptome data from different geographic regions to characterize and separate viral components. Then we developed an efficient, novel, and universal transcript purification system for pitaya transcriptomes by applying it to 27 samples from different tissues and species, thereby enhancing the utility for transcriptomic and broader biological research. Combining the purified transcriptomic data with comparative genomic analyses, we identified HuERF72, a transcription factor (TF) that potentially regulates chlorophyll degradation in pitaya. Interaction assays and plant transformation elucidated that HuERF72 acts as a repressive TF by directly binding to the promoter of HuSGR1, a key structural gene in the chlorophyll degradation pathway. This study provides high-quality genomic resources and novel methodologies for molecular investigations in pitaya. Additionally, the proposed regulatory network advances our understanding of the transcriptional regulatory mechanisms underlying chlorophyll degradation, offering valuable insights into the genetic improvement of pitaya.

The calcineurin B-like protein (CBL)-CBL-interacting protein kinase (CIPK) Ca²⁺ sensors play crucial roles in the plant's response to drought stress. However, there have been few reports on the synergistic regulation of drought stress by CBL-CIPK and abscisic acid (ABA) core signaling components. In this study, we discovered that ZmCIPK33 positively regulates drought resistance in maize. ZmCIPK33 physically interacts with and is enhanced by phosphorylation from ZmSnRK2.10. Drought stress can activate ZmCIPK33, which is partially dependent on ZmSnRK2.10. ZmCIPK33 in combination with ZmSnRK2.10 can activate the slow anion channel ZmSLAC1 in Xenopus laevis oocytes independently of CBLs, whereas ZmCIPK33 or ZmSnRK2.10 alone is unable to do so. Furthermore, ZmCIPK33 phosphorylates ZmPP2C11 at Ser60, which leads to a reduction in the interaction between ZmPP2C11 and ZmEAR1 (the ortholog of Arabidopsis Enhancer of ABA co-Receptor 1) and weakens the phosphatase activity of ZmPP2C11, consequently, enhancing the activity of ZmSnRK2.10 in an in vitro assay and in the in-gel assay of the zmcipk33 mutant. Our findings provide novel insights into the molecular mechanisms underlying the reciprocal enhancement of Ca²⁺ and ABA signaling under drought stress in maize.

Leaf curvature significantly contributes to important economic traits in vegetable crops. The upward-curling leaf phenotype has been consistently observed upon overexpression of a miR156/157-resistant version of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 10 (SPL10) transcription factor (rSPL10). However, the role of SPL10 in regulating leaf curvature has not been well characterized. In this study, using DNA affinity purification sequencing followed by transient transactivation assays, we found that SPL10 can bind to the promoter and gene body of REVOLUTA (REV), augmenting its expression. The rSPL10 rev-6 double mutant plant displayed a downward-curling leaf phenotype similar to the rev-6 plant, supporting the notion that REV functions downstream of SPL10. Importantly, the SPL10 protein physically interacts with the REV protein, which attenuates the expression of REV promoted by SPL10, leading to the downregulation of REV-regulated genes involved in leaf curvature, such as HB2 and HB4. These findings suggest that the SPL10–REV module acts as a molecular rheostat to prevent excessive amplification of REV transcripts in Arabidopsis. Furthermore, overexpression of the BrpREV1 gene in Chinese cabbage caused the transformation of rosette leaves from flat to upward-curving and accelerated heading. Taken together, our findings reveal the role of SPL10–REV module in orchestrating leaf curvature, which could potentially be utilized for molecular breeding of economical traits in vegetable crops.

Radish (Raphanus sativus L.) is a globally important root vegetable crop known for its diverse varieties and unique taproot characteristics. The LBD (LATERAL ORGAN BOUNDARIES DOMAIN) gene family, specific to plants, plays a pivotal role in the development of lateral plant organs. Nonetheless, the precise biological functions and molecular regulatory mechanisms of LBD genes in radish taproot development remain largely unexplored. In this study, the RsLBD3 gene was identified as a potential candidate affecting taproot size in radish through a genome-wide association study. Further investigation revealed two insertions in the C-terminal region of RsLBD3, with insertion³⁶³ notably enhancing the transcriptional activation capability of RsLBD3. It was observed that radish taproots with RsLBD3^Ins-363 haplotype displayed significantly greater length and weight compared to those with RsLBD3^Del-363 haplotype. RNA in situ hybridization and reverse transcription quantitative polymerase chain reaction analysis revealed that the RsLBD3 gene exhibits high expression level in the vascular cambium and is induced by cytokinin treatment. Silencing the RsLBD3 gene resulted in the inhibition of vascular cambium activity in the taproot, thereby impeding thickening. Exogenous cytokinin treatment could partially rescue the small-taproot phenotypes caused by RsLBD3 silencing. Moreover, RsARF5 (AUXIN RESPONSE FACTOR 5), RsRR7b (RESPONSE REGULATOR 7), and RsCYCD3-1 (CYCLIN D3;1) were identified as target genes of RsLBD3. Notably, RsARF5 was found to directly regulate the expression of RsWOX4 (WUSCHEL-RELATED HOMEOBOX 4). Additionally, biochemical analysis demonstrated that RsTCP14 interacts with RsLBD3, contributing to the binding of RsLBD3 to its target genes. Collectively, these findings contribute to a better understanding of the regulatory mechanisms underlying taproot morphogenesis, and provide novel allelic variations for the genetic enhancement of taproot shape traits in radish.

Transgenic and gene-editing technologies are essential for gene functional analysis and crop improvement. However, the pleiotropic effects and unknown mechanisms of morphogenic genes have hindered their broader application. In this study, we employed the one-step de novo shoot organogenesis (DNSO) method, and demonstrated that overexpression of the morphogenic gene Arabidopsis thanalia GROWTH-REGULATING FACTOR 5 (AtGRF5) significantly enhanced genetic transformation efficiency in cucurbit crops by promoting callus proliferation and increasing dense cells during regeneration. High-resolution time-series transcriptomics and single-cell RNA sequencing revealed that AtGRF5 overexpression induced auxin-related genes and expanded stem cell populations during cucumber DNSO. Using DNA-affinity purification sequencing (DAP-seq) in combination with spatiotemporal differential gene expression analysis, we identified CsIAA19 as a key downstream target of AtGRF5, with its modulation playing a pivotal role in regeneration. Rescuing CsIAA19 in AtGRF5-overexpressing explant reversed the enhanced callus proliferation and regeneration. To address growth defects caused by AtGRF5 overexpression, we developed an abscisic acid-inducible AtGRF5 expression system, significantly improving transformation and gene-editing efficiency across diverse genotypes while minimizing pleiotropic effects. In summary, this research provides mechanistic insights into AtGRF5-mediated transformation and offers a practical solution to overcome challenges in cucurbit crop genetic modification.

Budding speciation is a process wherein a new species arises from a small, isolated population within or at the margin of an ancestral species. Well-documented cases of budding speciation are rare, and the roles of various evolutionary factors in this process remain controversial. Based on whole-genome resequencing data from 272 individuals across 27 populations, we reconstructed the evolutionary history of Rhodiola sect. Trifida and explored the relative contributions of natural selection, genetic drift, and chromosomal rearrangements as drivers of lineage divergence. We found that all samples of R. chrysanthemifolia (including R. alterna and R. sinuata) were clustered into three clades. Rhodiola liciae was sister to all other samples in the section, likely due to post-divergence gene flow and the minimal population structure of the progenitor species, while it shared the same ancestry with R. ch-I in population structure analyses. The two populations of R. sinuata were not monophyletic, instead clustering with geographically proximate populations of R. ch-III. Demographic analyses revealed that R. liciae underwent a contraction in population size following its divergence from R. ch-I approximately 0.34 million years ago (Mya), and has remained stable since around 0.1 Mya. Genomic islands and genotype-environment association analyses suggested that genetic drift and the assorting of ancestral polymorphism may have played a more significant role in the speciation of R. liciae than nature selection or chromosomal rearrangements. We propose that R. liciae diverged from R. chrysanthemifolia through budding speciation, although post-divergence gene flow has obscured its phylogenetic signal. Additionally, we identified two potential parallel budding speciation events in R. sinuata at an earlier stage than R. liciae. Our study highlights budding speciation as a prevalent yet poorly characterized mode of plant speciation, with assorting of ancestral polymorphism as a key stochastic mechanism in the process.

Sweetpotato (Ipomoea batatas) starch is in high demand globally as a food and industrial product. However, the regulatory mechanisms governing starch biosynthesis and starch properties in this important crop remain largely unknown. Here we identified a natural allelic variant in the promoter of IbNAC22, encoding a NAC (NAM, ATAF1/2, and CUC2) transcription factor, which is closely linked to starch content in sweetpotato. In high-starch sweetpotato varieties, the T/C haplotype and a 13-bp deletion in the IbNAC22 promoter resulted in higher transcriptional activity. The high-starch IbNAC22 haplotype is more prevalent in regions of China where the sweetpotato starch industry is well developed, indicating that this advantageous allele type has been utilized in breeding starchy sweetpotato varieties in China. IbNAC22 is highly expressed in storage roots and starch-rich sweetpotato accessions. Overexpression of IbNAC22 significantly improved starch and amylose contents, as well as granule size and gelatinization temperature, and decreased starch crystallinity, whereas IbNAC22 knockdown had the opposite effects. IbNAC22 directly activates the expression of IbGBSSI, a key gene for amylose biosynthesis, but suppresses the expression of IbSBEI, a key gene for amylopectin biosynthesis. IbNAC22 directly interacts with IbNF-YA10. Overexpressing of IbNF-YA10 significantly improved starch and amylose contents, and starch gelatinization temperature, but decreased granule size, crystallinity, and amylopectin chain length distribution. IbNF-YA10 directly activates IbAGPL and IbGBSSI, which are key genes involved in starch and amylose biosynthesis. IbNAC22–IbNF-YA10 heterodimers further enhance the IbNF-YA10-induced activation of IbAGPL and IbGBSSI. These findings increase our understanding of starch biosynthesis and starch properties and provide strategies and candidate genes for the improvement of starchy root and tuber crops.

Late blight, caused by the oomycete plant pathogen Phytophthora infestans, is a destructive disease that leads to significant yield loss in potatoes and tomatoes. The introgression of disease resistance (R) genes, which encode nucleotide-binding domain leucine-rich repeat-containing receptors (NLRs), into cultivated potatoes, is highly effective in controlling late blight. Here, we generated transgenic 2R and 3R potato lines by stacking R genes Rpi-blb2/Rpi-vnt1.1 and Rpi-vnt1.1/RB/R8, respectively, in the susceptible cv. Desiree background. The resulting 2R and 3R transgenic potato plants showed resistance to highly virulent P. infestans field isolates. We hypothesized that stacking R genes either resulted in up-regulation of a broader range of immune-related genes, or, more importantly, increase in the fold change of gene expression. To test our hypotheses, we performed transcriptome analysis and identified a subset of core immune-related genes that are induced in response to P. infestans in transgenic lines carrying single R genes versus lines carrying stacks of multiple R genes. In our analysis, stacking R genes resulted not only in the induction of a broader range of defense-associated genes but also a global increase in gene expression fold change, caused by the pathogen. We further demonstrated that the calcium-dependent protein kinase 16 (StCDPK16) gene significantly contributed to resistance to a virulent P. infestans strain, in the R gene background, in a kinase activity-dependent manner. Thus, our data suggest that stacking the R genes enhances late blight resistance through modulating the expression of a broader range of defense-related genes and highlights CDPK16 as a novel player in potato R gene-mediated resistance.

Gram-negative bacteria are known to release extracellular vesicles (EVs) into their surrounding environment. However, the biological functions of the proteins contained within these vesicles remain largely unknown. Here, we used tandem mass tag (TMT) proteomic analysis to characterize protein cargoes within EVs of the phytopathogen Pseudomonas syringae pv. tomato DC3000 (Pto DC3000). Our investigation revealed that one catalase, KatB, is enriched in bacterial EVs. This enzyme confers EVs with the capacity to detoxify both exogenous and plant-produced H₂O₂, thereby contributing to the pathogen's proliferation within the plants. Interestingly, reactive oxygen species (ROS) stress stimulates bacterial EV secretion and enhances the package of KatB into these vesicles. This regulatory process depends on a periplasmic ankyrin-like protein, AnkB. Both AnkB and KatB are encoded within a small operon, and their mutant strains exhibit impaired growth in plant hosts. Furthermore, the treatment of EVs pelleted from bacterial culture supernatants activates the immune responses of plants, and the absence of KatB in EVs further enhances this protective activity. Collectively, our findings indicate that bacteria secreted KatB via EVs to interact with and reduce the host's oxidative environment, thereby promoting their proliferation within plants.