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Carotenoids are essential components of the photosynthetic apparatus and precursors of plant hormones, such as strigolactones (SLs). SLs are involved in various aspects of plant development and stress-response processes, including the establishment of root and shoot architecture. SL biosynthesis begins with the reversible isomerization of all-trans-carotene into 9-cis-β-carotene, catalysed by DWARF27 β-carotene isomerase (D27). Sequence comparisons have revealed the presence of D27-related proteins in photosynthetic eukaryotes and cyanobacteria lacking SLs. To gain insight into the evolution of SL biosynthesis, we characterized the activity of a cyanobacterial D27 protein (CaD27) from Cyanobacterim aponinum, using carotenoid-accumulating Escherichia coli cells and in vitro enzymatic assays. Our results demonstrate that CaD27 is an all-trans/cis and cis/cis-β-carotene isomerase, with a cis/cis conversion preference. CaD27 catalysed 13-cis/15-cis-, all-trans/9-cis-β-carotene, and neurosporene isomerization. Compared with plant enzymes, it exhibited a lower 9-cis-/all-trans-β-carotene conversion ratio. A comprehensive genome survey revealed the presence of D27 as a single-copy gene in the genomes of 20 out of 200 cyanobacteria species analysed. Phylogenetic and enzymatic analysis of CaD27 indicated that cyanobacterial D27 genes form a single orthologous group, which is considered an ancestral type of those found in photosynthetic eukaryotes. This article is part of the theme issue 'The evolution of plant meta‌bolism'. [ABSTRACT FROM AUTHOR]

Phenolic compounds of land plants are varied: they are chemodiverse, are sourced from different biosynthetic routes and fulfil a broad spectrum of functions that range from signalling phytohormones, to protective shields against stressors, to structural compounds. Their action defines the biology of land plants as we know it. Often, their roles are tied to environmental responses that, however, impacted already the algal progenitors of land plants, streptophyte algae. Indeed, many streptophyte algae successfully dwell in terrestrial habitats and have homologues for enzymatic routes for the production of important phenolic compounds, such as the phenylpropanoid pathway. Here, we synthesize what is known about the production of specialized phenolic compounds across hundreds of millions of years of streptophyte evolution. We propose an evolutionary scenario in which selective pressures borne out of environmental cues shaped the chemodiversity of phenolics in streptophytes. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

Societal Impact Statement Summary The root‐parasitic plant Striga hermonthica can cause severe crop failure, leading to significant agricultural and economic losses in Africa. Despite the promising target offered by the Striga seed germination mechanism for developing control methods, effective control methods have yet to be established. For seed germination, Striga must undergo an incubation under warm and humid conditions, a process termed conditioning, which allows it to germinate. Here, we report that the plant hormone gibberellin stimulates the conditioning process in Striga seeds. Our findings suggest that the quantitative control of gibberellin in plants is a promising approach for controlling Striga infestations and may help alleviate substantial threats to food security. The root‐parasitic plant S. hermonthica is a serious agricultural threat in Africa. Although a number of control methods have been employed to combat Striga, there is still a need to develop more effective control methods. Striga seeds germinate only in the presence of host plants, owing to the need for host‐released stimulants, primarily strigolactone. To detect signals from the host, Striga seeds must be exposed to a specific warm, dark, and moist environment, which is known as conditioning. Gibberellin directly promotes germination in many nonparasitic plants, but Striga seeds are insensitive to exogenous gibberellin. Consequently, the role of gibberellin in the germination of Striga seeds is unclear. We demonstrated that the effect of the gibberellin biosynthesis inhibitor paclobutrazol was higher in seeds during the conditioning, compared with those already conditioned, suggesting that gibberellin primarily regulates conditioning rather than germination. The content of an active form gibberellin, gibberellin A4 (GA4) exhibited an increase throughout the conditioning period, and we quantified the elevated expression levels of some gibberellin biosynthesis genes. The GA4 treatment shortened the conditioning period required for strigolactone‐induced seed germination. We also discovered that gibberellin upregulated ShACO1, the gene responsible for ethylene synthesis, during conditioning, and that the inhibition of GR24‐induced germination by the ethylene biosynthesis inhibitor α‐aminoisobutyric acid was gradually alleviated by GA4. Our findings demonstrate that gibberellin is critical for conditioning and germination processes but acts as a minor stimulant in Striga seeds. This study demonstrates the potential of quantitative endogenous gibberellin control for Striga management, providing valuable insights for alleviating food security issues. [ABSTRACT FROM AUTHOR]

Super absorbent polymers (SAP) provide moisture conditions that allow plant growth-promoting rhizobacteria (PGPR) to enter the soil for acclimatization and strain propagation. However, the effects of SAP co-applied with PGPR on the physiological characteristics of leaves and rhizosphere soil enzyme activities of poplar seedlings are not well understood. Here, a pot experiment using one-year-old poplar seedlings with five treatments, normal watering, drought stress (DR), drought stress + SAP (DR+SAP), drought stress + Priestia megaterium (DR +PGPR) and drought stress + SAP + P. megaterium (DR+S+P), was performed to analyze the contents of non-enzymatic antioxidants, osmotic regulators and hormones in leaves, as well as rhizosphere soil enzyme activities. Compared with normal watering, the DR treatment significantly decreased the contents of dehydroascorbate (DHA; 19.08%), reduced glutathione (GSH; 14.18%), oxidized glutathione, soluble protein (26.84%), indoleacetic acid (IAA; 9.47%), gibberellin (GA) and zeatin (ZT), the IAA/abscisic acid (ABA), GA/ABA, ZT/ABA and (IAA+GA+ZT)/ABA (34.67%) ratios in leaves, and the urease and sucrase activities in the rhizosphere soil. Additionally, it significantly increased the soluble sugar, proline and ABA contents in leaves. However, in comparison with the DR treatment, the DR+S+P treatment significantly increased the DHA (29.63%), GSH (15.13%), oxidized glutathione, soluble protein (29.15%), IAA (12.55%) and GA contents, the IAA/ABA, GA/ABA, ZT/ABA and (IAA+GA+ZT)/ABA (46.85%) ratios in leaves, and the urease, sucrose and catalase activities in rhizosphere soil to different degrees. The soluble sugar, proline and ABA contents markedly reduced in comparison to the DR treatment. The effects of the DR+SAP and DR+PGPR treatments were generally weaker than those of the DR+S+P treatment. Thus, under drought-stress conditions, the simultaneous addition of SAP and P. megaterium enhanced the drought adaptive capacities of poplar seedlings by regulating the non-enzymatic antioxidants, osmotic regulators, and endogenous hormone content and balance in poplar seedling leaves, as well as by improving the rhizosphere soil enzyme activities. [ABSTRACT FROM AUTHOR]

Huangjing is becoming a new generation of crop. Polygonatum kingianum var. grandifolium (XHJ) is a variant of P. kingianum (DHJ), and they are treated as Huangjing. Unlike other Polygonatum species, the rhizome bud of XHJ can germinate both in spring and autumn, which contributes to its high rhizome yield. However, the molecular mechanism of the autumn shooting of XHJ was still unknown. In the present study, cellular observation, comparative targeted metabolome of phytohormones, and transcriptome analysis between XHJ and DHJ in autumn were conducted. Interestingly, 'Diterpenoid biosynthesis' (ko00904) and 'Plant hormone signal transduction' (ko04075) were commonly enriched by differentially accumulated phytohormones (DAPs) and differentially expressed genes (DEGs) in all tissues, which indicated the high auxin content, low cytokinin (CTK) content, and low abscisic acid/gibberellin (ABA/GA) ratio might contribute to the XHJ rhizome buds' differentiation and germination in autumn. Moreover, according to the weighted gene co-expression network analysis (WCGNA), transcript factors (TFs) related to auxin, CTK, GA, and jasmonic acid (JA) metabolism were screened, such as AP2/ERFs , WRKY , and NAC , which deserve further research. In conclusion, we comprehensively illustrated the mechanism of XHJ natural autumn shooting through cytological, metabolic, and transcriptomic analysis, which improves our understanding of the high yield of XHJ rhizomes and the diversity of shooting mechanisms in Polygonatum to lay the foundation for the further development of the Huangjing industry. [ABSTRACT FROM AUTHOR]

Introduction: Melatonin, a tryptophan-derived indoleamine metabolite with important roles in plant growth and defense, has recently been regarded as a new plant hormone. Maize is one of the most important cereal crops in the world. Although the melatonin receptor gene, ZmPMTR1 , has already been identified, the genetic basis of melatonin biosynthesis in maize has still not been elucidated. Serotonin N-acetyltransferase (SNAT) is the enzyme that converts serotonin to N-acetylserotonin (NAS) or 5-methoxytryptamine (5MT) to melatonin in Arabidopsis and rice, but no SNAT encoding gene has been identified yet in maize. Methods: The bioinformatics analysis was used to identify maize SNAT genes and the enzyme activity of the recombinant proteins was determined through in vitro assay. The expression levels of ZmSNAT1 and ZmSNAT3 under drought and heat stresses were revealed by public RNA-seq datasets and qRT-PCR analysis. Results: We first identified three maize SNAT genes, ZmSNAT1, ZmSNAT2, and ZmSNAT3, through bioinformatics analysis, and demonstrated that ZmSNAT2 was present in only eight of the 26 cultivars analyzed. We then determined the enzyme activity of ZmSNAT1 and ZmSNAT3 using their recombinant proteins through in vitro assay. The results showed that both ZmSNAT1 and ZmSNAT3 could convert serotonin to NAS and 5-MT to melatonin. Recombinant ZmSNAT1 catalyzed serotonin into NAS with a higher catalytic activity (K m, 8.6 mM; V max, 4050 pmol/min/mg protein) than ZmSNAT3 (K m, 11.51 mM; V max, 142 pmol/min/mg protein). We further demonstrated that the 228th amino acid Tyr (Y228) was essential for the enzymatic activity of ZmSNAT1. Finally, we revealed that the expression of ZmSNAT1 and ZmSNAT3 varied among different maize cultivars and different tissues of a plant, and was responsive to drought and heat stresses. Discussion: In summary, the present study identified and characterized the first two functional SNAT genes in maize, laying the foundation for further research on melatonin biosynthesis and its regulatory role in plant growth and response to abiotic stresses. [ABSTRACT FROM AUTHOR]

The kiwifruit canker disease caused by Pseudomonas syringae pv. actinidiae (Psa) seriously threatens the development of kiwifruit industry. So far, only a limited number of Psa-resistant kiwifruit varieties have been identified, and the underlying molecular mechanisms are still largely unknown. In this study, we evaluated the Psa resistance of six hybrid populations and screened a resistant segregation population R1F2. Then, transcriptome analysis on the Psa extremely high-resistant (HR) and extremely high-susceptible (HS) plants of the R1F2 population was performed. KEGG enrichment analysis revealed that differentially expressed genes (DEGs) were significantly enriched in plant hormone signal transduction pathways, including auxin, abscisic acid, zeatin, jasmonic acid and salicylic acid. Furthermore, several transcription factors (TFs), especially WRKY TFs, were identified among the DEGs. The qRT-PCR showed that AcWRKY75 was highly expressed in the HS plants. Additionally, AcWRKY75 was significantly induced in the HS cultivar 'Hongyang' after Psa inoculation. Sequence amplification analysis showed that there was polymorphism in the DNA sequence of AcWRKY75 gene, but no HR or HS-specific differences were observed. Subcellular localization and transcriptional activity analysis confirmed that AcWRKY75 functions as a nucleus-located transcriptional activator. Transient overexpression of AcWRKY75 in kiwifruit leaves reduced the resistance to Psa, while silencing AcWRKY75 by virus-induced gene silencing (VIGS) slightly enhanced the resistance to Psa. Furthermore, AcWRKY75 exhibited a weak interaction with the promoter of the ABA-related DEG AcBet V1 (Acc27163). Our findings elucidated that AcWRKY75 may negatively regulate the Psa resistance of kiwifruit through the hormone signaling pathway, which laid a foundation for the analysis of the disease resistance mechanism of kiwifruit canker. [ABSTRACT FROM AUTHOR]

Background: Trihliex transcription factors (TFs) play crucial roles in plant growth and development, stress response, and plant hormone signaling network transmission. In order to comprehensively investigate the functions of trihliex genes in eggplant development and the abiotic stress response, we conducted an extensive analysis of the trihliex gene family in the eggplant genome. Results: In this study, 30 trihelix gene family members were unevenly distributed on 12 chromosomes. On the basis of their phylogenetic relationships, these genes were conserved in different plant species and could be divided into six subfamilies, with trihelix genes within the same subfamily sharing similar structures. The promoter regions of trihelix genes contained cis-acting elements related to plant growth and development, plant hormones, and abiotic stress responses, suggesting potential applications in the development of more resistant crops. Selective pressure assessments indicated that trihliex genes have undergone purifying selection pressure. Expression analysis on the basis of transcriptomic profiles revealed that SmGT18, SmGT29, SmGT6, and SmGT28 are highly expressed in roots, leaves, flowers, and fruits, respectively. Expression analysis via quantitative real-time PCR (qRT‒PCR) revealed that most trihelix genes respond to low temperature, abscisic acid (ABA), and salicylic acid (SA), with SmGT29 exhibiting significant upregulation under cold stress conditions. The SmGT29 gene was subsequently successfully cloned from eggplant, which was located in the nucleus, robust transcriptional activity, and a protein molecular weight of 74.59 kDa. On the basis of these findings, SmGT29 was postulated to be a pivotal candidate gene that actively responds to biotic stress stimuli, thereby supporting the plant's innate stress resistance mechanisms. Conclusion: In summary, this study was the first report on trihelix genes and their potential roles in eggplant plants. These results provided valuable insights for enhancing stress resistance and quality traits in eggplant breeding, thereby serving as a crucial reference for future improvement efforts. [ABSTRACT FROM AUTHOR]

Background: Pumpkin (Cucurbita moschata) is an important vegetable crop that often suffers from low-temperature stress during growth. However, the molecular mechanism involved in its response to chilling stress remains unknown. In this study, we comprehensively investigated the effect of chilling stress in pumpkin seedlings by conducting physiological, transcriptomic, and metabolomic analyses. Results: Under chilling stress, there was an overall increase in relative electrical conductivity, along with malondialdehyde, soluble sugar, and soluble protein contents, but decreased superoxide dismutase and peroxidase activities and chlorophyll contents in seedling leaves compared with controls. Overall, 5,780 differentially expressed genes (DEGs) and 178 differentially expressed metabolites (DEMs) were identified under chilling stress. Most DEGs were involved in plant hormone signal transduction and the phenylpropanoid biosynthesis pathway, and ERF, bHLH, WRKY, MYB, and HSF transcription factors were induced. Metabolomic analysis revealed that the contents of salicylic acid (SA), phenylalanine, and tyrosine increased in response to chilling stress. The findings indicated that the SA signaling and phenylpropanoid biosynthesis pathways are key to regulating the responses to chilling stress in pumpkins. Conclusion: Overall, our study provides valuable insights into the comprehensive response of C. moschata to chilling stress, enriching the theoretical basis of this mechanism and facilitating the development of molecular breeding strategies for pumpkin tolerance to chilling stress. [ABSTRACT FROM AUTHOR]

Abscisic acid (ABA) is a key plant hormone that regulates plant growth and response to stress. Pyrabactin resistance 1-like (PYR/PYL) proteins are ABA receptors involved in the initial steps of ABA signaling. Triticum monococcum L. subsp. aegilopoides is an important germplasm resource for wheat. In this study, we identified 15 PYL genes from T. monococcum L. subsp. aegilopoides and found that they were distributed across five chromosomes. Based on phylogenetic analysis, we classified these genes into three subfamilies. Members of each subfamily have similar gene structures and contain a common motif. Further analysis revealed that the promoters have multiple hormone-related elements. We found 7, 33, and 49 collinear gene pairs in three different ploidy wheat species (T. urartu, T. turgidum and T. aestivum), indicating that PYL genes are relatively conserved during the process of wheat polyploidization. Additionally, interaction networks and miRNA targets were predicted, revealing interactions between PYL proteins and key components of the abscisic acid signaling network. miR9666b-3p may serve as a central factor in PYL involvement in the abscisic acid network. Through RNA-seq analysis and qPCR validation, three genes (TbPYL2, TbPYL5, and TbPYL12) were found to potentially play a role in cold stress. These findings lay the groundwork for further research on PYL genes in T. monococcum L. subsp. aegilopoides. [ABSTRACT FROM AUTHOR]

Salicornia europaea, commonly known as glasswort, thrives in reclaimed land and coastal areas with high salinity, demonstrating remarkable adaptation to the arid conditions of such environments. Two aerobic, Gram-stain-negative, non-motile, rod-shaped bacterial strains, designated TR-M5T and TR-M9, were isolated from the root of Salicornia europaea plants. These bacteria exhibit plant growth-promoting and salt tolerance-enhancing abilities, which have not been reported in other species of the genus. Both strains produce indole-3-acetic acid (IAA), a plant growth hormone, and synthesize proline, which functions as an osmoprotectant. Additionally, they possess gelatinase and cellulase activities. Cells grow in temperatures from 4 to 42°C (optimum 25°C), pH levels from 6.0 to 9.0 (optimum 7.0), and NaCl concentrations from 0 to 8.0% (optimum 6.0%). The average nucleotide identity and digital DNA-DNA hybridization values of strain TR-M5T with the most closely related type strains for which whole genomes are publicly available were 74.05-77.78% and 18.6-23.1%, respectively. Phylogenetic analysis of their 16S rRNA gene sequences revealed that strains TR-M5T and TRM9 belong to the genus Algoriphagus. A. locisalis exhibited the highest similarity, sharing a sequence identity of 98.1%. The genomes of TR-M5T and TR-M9 exhibit a G + C content of 43 mol%. This study specifically focuses on the identification and characterization of strain TR-M5T as a novel species within the genus Algoriphagus, which we propose to name Algoriphagus halophytocola sp. nov., highlighting its potential role in enhancing plant growth and salt tolerance in saline environments. The type strain is TR-M5T (KCTC 92720T = GDMCC 1.3797T). [ABSTRACT FROM AUTHOR]

Peptide hormones regulate plant development, growth, and stress responses. Sulfated peptides represent a class of proteins that undergo posttranslational modification by tyrosylprotein sulfotransferase (TPST), followed by specific enzymatic cleavage to generate mature peptides. This process contributes to the formation of various bioactive peptides, including PSKs (PHYTOSULFOKINEs), PSYs (PLANT PEPTIDE CONTAINING SULFATED TYROSINE), CIFs (CASPARIAN STRIP INTEGRITY FACTOR), and RGFs (ROOT MERISTEM GROWTH FACTOR). In the past three decades, significant progress has been made in understanding the molecular mechanisms of sulfated peptides that regulate plant development, growth, and stress responses. In this review, we explore the sequence properties of precursors, posttranslational modifications, peptide receptors, and signal transduction pathways of the sulfated peptides, analyzing their functions in plants. The cross-talk between PSK/RGF peptides and other phytohormones, such as brassinosteroids, auxin, salicylic acid, abscisic acid, gibberellins, ethylene, and jasmonic acid, is also described. The significance of sulfated peptides in crops and their potential application for enhancing crop productivity are discussed, along with future research directions in the study of sulfated peptides. [ABSTRACT FROM AUTHOR]

Quercus variabilis (Q. variabilis), a significant broadleaf species used in afforestation across high, sandy, and mountainous regions, presents unique challenges for transplantation. This species is characterized by its slow above-ground growth and rapid taproot development, which suppresses the proliferation of lateral and fibrous roots, negatively impacting post-transplant survival. Research indicates that targeted root pruning—specifically, the removal of one-third of the roots—promotes the development of lateral roots in these seedlings. This study involved pruning the root systems of Q. variabilis and assessing the subsequent root development in comparison to an unpruned control group. Our analysis, which included transcriptome sequencing and plant hormone metabolism assays conducted at 2, 12, and 25 days post-pruning, yielded 126.02 Gb of clean data and identified 7662 differentially expressed genes (DEGs). These genes were primarily enriched in the plant hormone signal transduction pathway. Further investigation of this pathway, along with hormone content measurements, elucidated the mechanisms that contribute to enhanced root growth following pruning. Additionally, through a weighted correlation network analysis (WGCNA), we identified 20 key genes that are instrumental in promoting root development in Q. variabilis saplings. This research advances the theoretical framework for forestry seedling production and afforestation, laying the groundwork for scientifically informed vegetation restoration techniques. [ABSTRACT FROM AUTHOR]

The growth hormone export PIN-FORMED (PIN) is an important carrier for regulating the polar transport of plant growth hormones and plays an important role in plant growth and development. However, little is known about the characteristics and functions of PINs in potatoes. In this study, 10 PIN members were identified from potatoes and named StPIN1, StPIN2, StPIN3, StPIN4, StPIN5, StPIN6, StPIN7, StPIN8, StPIN9, and StPIN10 according to their positions in the potato chromosome In addition, the expression of 10 StPINs was analyzed by qRT-PCR during potato root development. The results showed that the StPIN4 gene plays an important regulatory role in potato root development, and its tissue expression varied greatly. Several cis-regulatory elements related to growth factors were also detected in the promoter region of the StPIN gene. The transgenic overexpressing StPIN4 in potato showed suppressed growth in root length and lateral root number, and StPIN4-interfering plants showed the opposite. These results suggested that StPIN4 plays a key role in the regulation of the potato root architecture. [ABSTRACT FROM AUTHOR]

The phospholipase A (PLA) gene family plays a crucial role in the regulation of plant growth, development and stress response. Although PLA genes have been identified in various plant species, their specific functions and characteristics in oil quality formation of rice grains (Oryza sativa L.) have not been studied yet. Here, we identified and characterized 35 rice PLA genes, which were divided into three subgroups based on gene structures and phylogenetic relationships. These genes are distributed unevenly across 11 rice chromosomes. The promoter sequence of rice PLAs contain multiple plant hormones and stress-related elements. Gene expression analyses in various tissues and under stress conditions indicated that PLAs may be involved in rice growth, development and stress response. In addition, metabolomics, transcriptomics and qRT-PCR analyses between two rice varieties Guang8B (G8B, high oil content) and YueFengB (YFB, low oil content) revealed that the different expressional levels of rice PLA genes were closely related to the differences in the oil content between 'G8B' and 'YFB' grains. The findings of this study provide potential novel insights into the molecular information of the phospholipase A gene family in rice, and underscore the potential functions of PLA genes in rice oil content accumulation, providing valuable resources for future genetic improvement and breeding strategies. [ABSTRACT FROM AUTHOR]

Abiotic stress affects the growth and development of maize (Zea mays). The regulator of chromosome condensation 1 (RCC1)-containing proteins (RCPs) plays crucial roles in plant growth and development and response to abiotic stresses. However, a comprehensive analysis of the maize RCP family has not been reported in detail. This study presents a systematic bioinformatics analysis of the ZmRCP family, identifying a total of 30 members distributed across nine chromosomes. The physicochemical properties and cis-acting elements in the promoters of ZmRCP members are predicted. The results of subcellular localization showed that ZmRCP3 and ZmRCP10 are targeted to mitochondria and ZmRCP2 is localized in the nucleus. A heatmap of expression levels among family members under abiotic stress conditions revealed varying degrees of induced expression, and the expression levels of 10 ZmRCP members were quantified using RT-qPCR under abiotic stress and plant hormone treatments. The results showed that ZmRCP members exhibit induced or inhibited responses to these abiotic stresses and plant hormones. These results contribute to a better understanding of the evolutionary history and potential role of the ZmRCP family in mediating responses to abiotic stress in maize. [ABSTRACT FROM AUTHOR]

• The PvPR-1 gene family consists of 13 members, which segregate into two distinct clusters. • Analyses of gene characteristics, biochemical properties, and structural features suggest these genes are well-suited to respond to biotic stress. • The resistant common bean variety exhibited up-regulation or constitutive expression of a greater number of PvPR-1 genes following inoculation with Colletotrichum lindemuthianum. • Based on their structural features and transcriptional regulation, PvPR-1-4, PvPR-1-5, and PvPR-1-10 are promising candidates for future biotechnological applications. Pathogenesis-related Protein 1 (PR-1) plays a crucial role in plant defense responses, particularly against fungal pathogens. Despite its significance, comprehensive studies characterizing this gene family in the common bean (Phaseolus vulgaris) are currently lacking. Therefore, the objective of this study was to conduct genomic mining and characterization of the PR-1 in common bean (PvPR-1) genome. Additionally, we assessed the transcriptional expression of all its isoforms in response to inoculation with the fungus Colletotrichum lindemuthianum. This evaluation was performed on leaf tissue samples obtained from both sensitive (Rosinha) and resistant (Africano 4) common bean varieties at 24-, 48-, and 96-hours post inoculation. Thirteen PvPR-1 genes were consistently identified, forming two major clusters across the clustering analyses. Physicochemical characterization indicated that the PvPR-1 proteins are predominantly basic, hydrophilic, and extracellularly localized. Moreover, their promoter regions contain putative cis-regulatory elements that respond to a broad spectrum of plant hormones, including jasmonic acid, gibberellin, and ethylene, which are key regulators of both biotic and abiotic stress responses. This discovery implies a multifaceted role for the studied proteins in common bean physiology. KEGG pathway analysis implicated PvPR-1 proteins in hormonal signaling (corroborating the anchored cis-regulatory elements) and plant-pathogen interaction networks. Secondary structure evaluation revealed the predominance of α-helices and coiled structures within these proteins. Subsequent 3D modeling demonstrated a conserved 'α-β-α' sandwich architecture characterized by a central cavity. This structural motif suggests potential functional versatility, particularly in pathogen recognition and responses. Additionally, the study provided insight into the potential interactions of PvPR-1 with Chitinase II (PR-3) and Rab-18, as suggested by the STRING platform. Temporal differences in PvPR-1 gene expression were observed between the common bean contrasting varieties following C. lindemuthianum inoculation. Africano-4, the resistant one, showed a higher abundance of up-regulated and constitutively expressed PvPR-1 transcripts compared to its sensitive counterpart (Rosinha), indicating a more effective role of this gene family against the pathogen. Furthermore, based on PCA analyses and interaction networks of differentially expressed genes, three key targets within the PvPR-1 family (PvPR-1-4, PvPR-1-5, and PvPR-1-10) emerged as promising candidates for future functional characterization. These molecular actors displayed differential transcriptional patterns between the studied varieties without compromising the transcript abundance of PvPR-1 protein synthesis in the resistant one. Consequently, they may represent key components of resistance mechanisms that contribute to the differentiation between the two organisms. These findings deepen our understanding of PvPR-1 genes and their roles in common bean defense responses. They also emphasized the potential of PvPR-1 genes as candidates for breeding stress-resistant common bean varieties, which are crucial for bolstering crop resilience to environmental adversities. [ABSTRACT FROM AUTHOR]

Small peptides produced by plants (SPPs) and microbes (SPMs) function as crucial mediators in plant–rhizosphere microbe interactions, with SPPs facilitating long-distance signaling through extracellular vesicles and SPMs modulating plant immunity and hormone signaling to enhance communication. SPPs may directly alter the rhizosphere microbiomes by modifying microbial gene expression or indirectly by influencing root morphology, exudate release, and immune responses, thus affecting microbial community structure and composition. Leveraging the bidirectional signaling facilitated by SPPs and SPMs between plants and their rhizosphere microbes offers a novel strategy in holobiont engineering, and the potential of exploring transgenic microbes to synthesize small peptides on a large scale merits further investigations. The crucial role of rhizosphere microbes in plant growth and their resilience to environmental stresses underscores the intricate communication between microbes and plants. Plants are equipped with a diverse set of signaling molecules that facilitate communication across different biological kingdoms, although our comprehension of these mechanisms is still evolving. Small peptides produced by plants (SPPs) and microbes (SPMs) play a pivotal role in intracellular signaling and are essential in orchestrating various plant development stages. In this review, we posit that SPPs and SPMs serve as crucial signaling agents for the bidirectional cross-kingdom communication between plants and rhizosphere microbes. We explore several potential mechanistic pathways through which this communication occurs. Additionally, we propose that leveraging small peptides, inspired by plant–rhizosphere microbe interactions, represents an innovative approach in the field of holobiont engineering. [ABSTRACT FROM AUTHOR]

The hormonal variation essential for fruit set differs regarding crop species. Parthenocarpy is a key trait to reduce the climate dependency of fruit crops. Two distinct molecular mechanisms lead to a gibberellin-induced fruit setting. Transcription factors and miRNA interactions control parthenocarpy in several species. Fruit development is essential for flowering plants' reproduction and a significant food source. Climate change threatens fruit yields due to its impact on pollination and fertilization processes, especially vulnerable to extreme temperatures, insufficient light, and pollinator decline. Parthenocarpy, the development of fruit without fertilization, offers a solution, ensuring yield stability in adverse conditions and enhancing fruit quality. Parthenocarpic fruits not only secure agricultural production but also exhibit improved texture, appearance, and shelf life, making them desirable for food processing and other applications. Recent research unveils the molecular mechanisms behind parthenocarpy, implicating transcription factors (TFs), noncoding RNAs, and phytohormones such as auxin, gibberellin (GA), and cytokinin (CK). Here we review recent findings, construct regulatory models, and identify areas for further research. [ABSTRACT FROM AUTHOR]

Graft healing involves a series of cytological and molecular events including wound responses, callus formation and vascular bundle remodelling. Hormones are important signalling molecules regulating plant development and responses to environmental stimuli. However, the detailed dynamics of phytohormones in graft healing remain elusive. In this research, internodes above and below the graft site were harvested from 0 to 168 h after grafting (HAG), and liquid chromatography tandem mass spectrometry (LC-MS/MS) was used to determinate jasmonic acid, auxin, cytokinin, ethylene, salicylic acid, abscisic acid and gibberellin levels during the graft healing process. Uniform manifold approximation and projection (UMAP) and k-means analyses were performed to explore hormone spatio-temporal dynamics. We found the stage-specific and asymmetric accumulation of phytohormones in the tomato graft healing process. At the early healing stage (before vascular bundle reconnection), IAA, cZ, ABA, JA and SA mainly accumulated above the graft site, while tZ and ACC mainly accumulated below the graft site. MEIAA, ICAld and IP mainly accumulated at the later stage. Comminated with the healing process, we suggested that JA is mainly involved in wound responses, IAA is beneficial to the formation of callus and vascular cell development, tZ promotes cell division, and IP is linked to vascular bundle remodelling. In addition, expression of JA-related genes SlMYC2 and SlJAZ2, IAA-related gene SlIAA1, tZ-related genes SlHP2 and SlRR8, and IP-related gene SlRR9 correlated with hormone accumulation. The findings provide important information about the hormones and genes involved in the tomato graft healing process. [ABSTRACT FROM AUTHOR]

Abscisic acid (ABA), a type of sesquiterpenoid plant hormone, has high application value in agriculture, nutrition and medicine. Herein, we constructed an efficient ABA-producing yeast cell factory by combining multidimensional engineering strategies. Starting from a suitable strain, YS010 was selected from 11 varieties of S. cerevisiae strains by evaluating ergosterol content and growth ability, then the biosynthetic pathway of ABA derived from Botris cinerea was constructed, resulting in 1.93 mg L−1 ABA. Next, the metabolic flux of the mevalonic acid (MVA) pathway was increased to enhance the synthesis of the precursor farnesyl pyrophosphate (FPP). To further increase the FPP competitiveness of the ABA synthesis pathway, we attempted to enhance the catalytic performance of BcABA3 through enzyme engineering, and the ABA yield of the mutant strain YS036-ABAPA206D reached 2.64 mg L−1 in SC-ura medium. In addition, we developed a multi-copy integration strategy, TPI1-delta driven CRISPR-Cas9 (TDI-CRISPR) integration system, to realize the high copy and stable expression of bcaba1 , bcaba2 and bcaba3 , which enabled the titer of ABA to reach 17.47 mg L−1. Finally, by optimising the fermentation medium, the ABA titer reached 30.30 mg L−1, which was the highest level ever reported for de novo ABA biosynthesis in S. cerevisiae. [Display omitted] • The engineered strain produced 30.30 mg L−1 of abscisic acid (ABA). • Rational design of α-ionylideneethane synthase (BcABA3) improved its activity. • ABA production significantly increased using the developed integration system. [ABSTRACT FROM AUTHOR]

Powdery mildew is a serious fungal disease in protected melon cultivation that affects the growth, development and production of melon plants. Previous studies have shown that red light can improve oriental melon seedlings resistance to powdery mildew. Here, after inoculation with Podosphaera xanthii, an obligate fungal pathogen eliciting powdery mildew, we found that red light pretreatment increased ethylene production and this improved the resistance of melon seedlings to powdery mildew, and the ethylene biosynthesis gene CmACS10 played an important role in this process. By analysing the CmACS10 promoter, screening yeast one‐hybrid library, it was found that CmERF27 positively regulated the expression of CmACS10, increased powdery mildew resistance and interacted with PHYTOCHROME INTERACTING FACTOR8 (CmPIF8) at the protein level to participate in the regulation of ethylene biosynthesis to respond to the red light‐induced resistance to P. xanthii, Furthermore, CmPIF8 also directly targeted the promoter of CmACS10, negatively participated in this process. In summary, this study revealed the specific mechanism by which the CmPIF8‐CmERF27‐CmACS10 module regulates red light‐induced ethylene biosynthesis to resist P. xanthii infection, elucidate the interaction between light and plant hormones under biological stress, provide a reference and genetic resources for breeding of disease‐resistant melon plants. Summary Statement: We found that ethylene was induced by red light and plays a positive role in the resistance of melon to powdery mildew. CmERF27 and CmPIF8 activate and inhibit the transcription of CmACS10, respectively, and regulate ethylene biosynthesis. Moreover, CmERF27 and CmPIF8 proteins interact, and this interaction interferes with the transcriptional activation of CmACS10 by CmERF27. [ABSTRACT FROM AUTHOR]

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Phytohormones are organic compounds produced in trace amounts within plants that regulate their physiological processes. Their physiological effects are highly complex and diverse. They influence processes ranging from cell division, elongation, and differentiation to plant germination and rooting. Therefore, phytohormones play a crucial regulatory role in plant growth and development. Recently, various studies have highlighted the role of PHs, such as auxin, cytokinin (CK), and abscisic acid (ABA), and newer classes of PHs, such as brassinosteroid (BR) and peptide hormone, in the plant responses toward environmental stresses. These hormones not only have distinct roles at different stages of plant growth but also interact to promote or inhibit each other, thus effectively regulating plant development. Roots are the primary organs for water and mineral absorption in plants. During seed germination, the radicle breaks through the seed coat and grows downward to form the primary root. This occurs because the root needs to quickly penetrate the soil to absorb water and nutrients, providing essential support for the plant's subsequent growth. Root development is a highly complex and precisely regulated process influenced by various signals. Changes in root architecture can affect the plant's ability to absorb nutrients and water, which in turn impacts crop yield. Thus, studying the regulation of root development is of great significance. Numerous studies have reported on the role of phytohormones, particularly auxins, in root regulation. This paper reviews recent studies on the regulation of root development by various phytohormones, both individually and in combination, providing a reference for researchers in this field and offering perspectives on future research directions for improving crop yields. [ABSTRACT FROM AUTHOR]

Cullins are crucial components of the ubiquitin–proteasome system, playing pivotal roles in the regulation of protein metabolism. This review provides insight into the wide-ranging functions of cullins, particularly focusing on their impact on plant growth, development, and environmental stress responses. By modulating cullin-mediated protein mechanisms, researchers can fine-tune hormone-signaling networks to improve various agronomic traits, including plant architecture, flowering time, fruit development, and nutrient uptake. Furthermore, the targeted manipulation of cullins that are involved in hormone-signaling pathways, e.g., cytokinin, auxin, gibberellin, abscisic acids, and ethylene, can boost crop growth and development while increasing yield and enhancing stress tolerance. Furthermore, cullins also play important roles in plant defense mechanisms through regulating the defense-associated protein metabolism, thus boosting resistance to pathogens and pests. Additionally, this review highlights the potential of integrating cullin-based strategies with advanced biological tools, such as CRISPR/Cas9-mediated genome editing, genetic engineering, marker-associated selections, gene overexpression, and gene knockout, to achieve precise modifications for crop improvement and sustainable agriculture, with the promise of creating resilient, high-yielding, and environmentally friendly crop varieties. [ABSTRACT FROM AUTHOR]

Cannabis sativa L. has a variety of uses, including fiber production, food, oil, and medicine. In response to environmental concerns regarding chemical fertilizers, Bacillus velezensis S141 was examined as a plant-growth-promoting bacterium (PGPB) for cannabis. This study evaluated the effects of S141 on cannabis growth and utilized transcriptomic analysis to identify the responsive pathways. Inoculation with S141 significantly increased growth in laboratory and field environments, with most of the bacteria residing in the leaves, followed by the stems and roots, as determined by quantitative polymerase chain reaction (qPCR). Transcriptomic analysis revealed 976 differentially expressed genes. Upregulated genes were associated with metabolism, cellular processes, and catalytic activities, especially in the biosynthesis of phenylpropanoid, plant–pathogen interactions, and hormone signaling pathways. S141 mutants deficient in the production of auxin and cytokinin displayed reduced growth enhancement, which affirmed the roles of these hormones in cannabis development. These findings emphasize the potential of S141 as a sustainable growth promoter for cannabis and provide insights into the underlying pathways it influences. [ABSTRACT FROM AUTHOR]

Main conclusion: The GhEB1C gene of the EB1 protein family functions as microtubule end-binding protein and may be involved in the regulation of microtubule-related pathways to enhance resistance to Verticillium wilt. The expression of GhEB1C is induced by SA, also contributing to Verticillium wilt resistance. Cotton, as a crucial cash and oil crop, faces a significant threat from Verticillium wilt, a soil-borne disease induced by Verticillium dahliae, severely impacting cotton growth and development. Investigating genes associated with resistance to Verticillium wilt is paramount. We identified and performed a phylogenetic analysis on members of the EB1 family associated with Verticillium wilt in this work. GhEB1C was discovered by transcriptome screening and was studied for its function in cotton defense against V. dahliae. The RT-qPCR analysis revealed significant expression of the GhEB1C gene in cotton leaves. Subsequent localization analysis using transient expression demonstrated cytoplasmic localization of GhEB1C. VIGS experiments indicated that silencing of the GhEB1C gene significantly increased susceptibility of cotton to V. dahliae. Comparative RNA-seq analysis showed that GhEB1C silenced plants exhibited altered microtubule-associated protein pathways and flavonogen-associated pathways, suggesting a role for GhEB1C in defense mechanisms. Overexpression of tobacco resulted in enhanced resistance to V. dahliae as compared to wild-type plants. Furthermore, our investigation into the relationship between the GhEB1C gene and plant disease resistance hormones salicylic axid (SA) and jasmonic acid (JA) revealed the involvement of GhEB1C in the regulation of the SA pathway. In conclusion, our findings demonstrate that GhEB1C plays a crucial role in conferring immunity to cotton against Verticillium wilt, providing valuable insights for further research on plant adaptability to pathogen invasion. [ABSTRACT FROM AUTHOR]

The foliar application of plant growth regulators to sugarcane can increase crop growth and yield per cultivated area, improve crop productivity and quality, and mitigate possible abiotic stresses by optimizing photosynthesis. The productive potential of sugarcane has not been fully tapped, and plant growth regulator technology via foliar application could greatly benefit the production of food and renewable energy from the sugarcane production chain. In this study, we conducted 15 sugarcane field trials to evaluate the effects of plant growth regulators (17 ppm GA3 activity, 817 ppm IAA activity and 43 ppm zeatin) via foliar application at the vegetative stage (V) or vegetative and maturation stages (VM) on the photosynthetic and antioxidant enzyme activities, carbohydrate production and yield production of three harvest periods (early, mid-late and late harvest sugarcane). In general, foliar application increased the enzymatic, agronomic, quality and energy parameters of sugarcane. The application of plant growth regulators in V and VM increased the activities of the photosynthetic enzymes phosphoenolpyruvate carboxylase and ribulose-1,5-bisphosphate carboxylase-oxygenase, decreased the contents of malondialdehyde and hydrogen peroxide, and increased superoxide dismutase, catalase, ascorbate peroxidase, and proline content. The average stalk yield over the three harvest times increased by 5.4 and 8.0% in V and VM, respectively, compared to the control (101 Mg ha−1). In addition, V and VM increased the sucrose concentration, theoretical recoverable sugars (TRS), and sugar productivity by averages of 2.9%, 2.6% and 9.3%, respectively compared to the control (13.9% of sucrose, 139 kg sugar stalk−1 of TRS, and 13.9 Mg ha−1 of stalk yield), across all harvest seasons. The best results for straw, bagasse and energy production were observed in VM, with average increases of 8.0%, 7.7% and 8.0% compared with the control (14.1 Mg ha−1, 6.1 Mg ha−1 and 69.8 kWh, respectively). Thus, plant growth regulator application can increase sugarcane metabolism, growth and development. Although single plant growth regulator application in the vegetative stage improved all sugarcane parameters, the double application of plant growth regulators in the vegetative and maturation stages ensured improvements in yield and product quality. [ABSTRACT FROM AUTHOR]

Amorphophallus muelleri, a naturally occurring variant of the commercially valuable Amorphophallus species grown in Southeast Asia, stands out for its desirable traits: high konjac glucomannan (KGM) content, apomictic properties, and strong disease resistance. However, the mechanisms governing KGM maturation and biosynthesis within A. muelleri seeds remain poorly understood. Accordingly, wide-targeted metabolomics and RNA-seq were used in the present study to analyze differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs). Importantly, we sought to identify changes during A. muelleri seed maturation and KGM biosynthesis. Our findings indicated that DAMs associated with amino acids and secondary metabolites were elevated in mature seeds. Moreover, the expression of several genes was also upregulated, including those involved in flavonoid biosynthesis and plant hormone signal transduction pathways, specifically TPS5, TPS6, C4H (CYP73A12), and key genes encoding auxin and abscisic acid (ABA) synthesis (IAA10, ARF11, SAPK7). Our findings suggest that these genes play positive roles in regulating seed maturation. Additionally, seven genes encoding key enzymes involved in KGM biosynthesis were upregulated during the first two stages of seed maturation compared to the third stage of seed ripening. This indicates a potential correlation between KGM content and the expression of these genes at the post-transcript level. Finally, a strong correlation was identified between key DAMs and DEGs. Collectively, these results provide valuable insights for researchers seeking to understand the molecular mechanisms underlying A. muelleri seed maturation and KGM synthesis. [ABSTRACT FROM AUTHOR]

Peach (Prunus persica (L.) Batsch) trees are prone to heavy cropping, but crop load management options are limited. 1-aminocyclopropane-1-carboxylic acid (ACC) has been suggested to reduce crop load and improve fruit quality in peaches, but many questions remain concerning the role of endogenous ethylene in the abscission response and other side effects. Here, the use of ACC as a chemical thinner in peach trees was studied at different rates (350, 500, and 750 mg L−1) and timings [at full bloom (FB) and after petal fall (AP) when the fruit was approximately 15–20 mm in diameter] by comparing the results to those of an untreated control and a hand-thinning treatment as a reference. The abscission response and ethylene emission were related to the ACC concentration. ACC-induced ethylene production, as well as some degree of defoliation, was time-dependent, with the highest ethylene emission peaks and the lowest defoliation degree occurring when ACC was applied at FB. On the other hand, the intra-annual differences in the abscission response between the FBs and APs varied depending on the season. AP-treated fruits produced more endogenous ethylene than did untreated fruits up to harvest, which could have influenced fruit color. Finally, our results indicate that ACC in the range of 500 and 350 mg L−1 can be used in 'Flatbeauti' peaches at FB and AP, respectively, to induce adequate levels of fruit crop load without or with minor undesired effects. [ABSTRACT FROM AUTHOR]

Strigolactones are phytohormones that influence arbuscular mycorrhizal fungal (AMF) spore germination, pre-symbiotic hyphal branching, and metabolic rates. Historically, strigolactone effects have been tested on single AMF strains. An open question is whether intraspecific variation in strigolactone effects and intraspecific interactions can influence AMF competition. Using the Rhizophagus irregularis strains A5 and C2, we tested for intraspecific variation in the response of germination and pre-symbiotic growth (i.e., hyphal length and branching) to the strigolactones GR24 and 5-deoxystrigol. We also tested if interactions between these strains modified their germination rates and pre-symbiotic growth. Spore germination rates were consistently high (> 90%) for C2 spores, regardless of treatment and the presence of the other strain. For A5 spores, germination was increased by strigolactone presence from approximately 30 to 70% but reduced when grown in mixed culture. When growing together, branching increased for both strains compared to monocultures. In mixed cultures, strigolactones increased the branching for both strains but led to an increase in hyphal length only for the strain A5. These strain-specific responses suggest that strigolactones may have the potential to shift competitive dynamics among AMF species with direct implications for the establishment of the AMF community. [ABSTRACT FROM AUTHOR]

Introduction: Nitraria tangutorum Bobr., a prominent xerophytic shrub, exhibits remarkable adaptability to harsh environment and plays a significant part in preventing desertification in northwest China owing to its exceptional drought and salinity tolerance. Methods: To investigate the drought-resistant mechanism underlying N. tangutorum, we treated 8-week-old seedlings with polyethylene glycol (PEG)- 6000 (20%, m/m) to induce drought stress. 27 samples from different tissues (leaves, roots and stems) of N. tangutorum at 0, 6 and 24 h after drought stress treatment were sequenced using PacBio single-molecule real-time (SMRT) sequencing and Illumina RNA sequencing to obtain a comprehensive transcriptome. Results: The PacBio SMRT sequencing generated 44,829 non-redundant transcripts and provided valuable reference gene information. In leaves, roots and stems, we identified 1162, 2024 and 232 differentially expressed genes (DEGs), respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that plant hormone signaling and mitogen-activated protein kinase (MAPK) cascade played a pivotal role in transmitting stress signals throughout the whole N. tangutorum plant following drought stress. The interconversion of starch and sucrose, as well as the biosynthesis of amino acid and lignin, may represent adaptive strategies employed by N. tangutorum to effectively cope with drought. Transcription factor analysis showed that AP2/ ERF-ERF, WRKY, bHLH, NAC and MYB families were mainly involved in the regulation of drought response genes. Furthermore, eight physiological indexes, including content of proline, hydrogen peroxide (H2O2), malondialdehyde (MDA), total amino acid and soluble sugar, and activities of three antioxidant enzymes were all investigate after PEG treatment, elucidating the drought tolerance mechanism from physiological perspective. The weighted gene co-expression network analysis (WGCNA) identified several hub genes serve as key regulator in response to drought through hormone participation, ROS cleavage, glycolysis, TF regulation in N. tangutorum. Discussion: These findings enlarge genomic resources and facilitate research in the discovery of novel genes research in N. tangutorum, thereby establishing a foundation for investigating the drought resistance mechanism of xerophyte. [ABSTRACT FROM AUTHOR]

Phytochrome-interacting factors (PIFs) are a subgroup of transcription factors within the basic helix-loop-helix (bHLH) family, playing a crucial role in integrating various environmental signals to regulate plant growth and development. Despite the significance of PIFs in these processes, a comprehensive genome-wide analysis of PIFs in conifers has yet to be conducted. In this investigation, three PtPIF genes were identified in Chinese pine, categorized into three subgroups, with conserved motifs indicating the presence of the APA/APB motif and bHLH domain in the PtPIF1 and PtPIF3 proteins. Phylogenetic analysis revealed that the PtPIF1 and PtPIF3 proteins belong to the PIF7/8 and PIF3 groups, respectively, and were relatively conserved among gymnosperms. Additionally, a class of PIF lacking APA/APB motif was identified in conifers, suggesting its function may differ from that of traditional PIFs. The cis-elements of the PtPIF genes were systematically examined, and analysis of PtPIF gene expression across various tissues and under different light, temperature, and plant hormone conditions demonstrated similar expression profiles for PtPIF1 and PtPIF3. Investigations into protein-protein interactions and co-expression networks speculated the involvement of PtPIFs and PtPHYA/Bs in circadian rhythms and hormone signal transduction. Further analysis of transcriptome data and experimental validation indicated an interaction between PtPIF3 and PtPHYB1, potentially linked to diurnal rhythms. Notably, the study revealed that PtPIF3 may be involved in gibberellic acid (GA) signaling through its interaction with PtDELLAs, suggesting a potential role for PtPIF3 in mediating both light and GA responses. Overall, this research provides a foundation for future studies investigating the functions of PIFs in conifer growth and development. [ABSTRACT FROM AUTHOR]

In plants, vegetative growth is controlled by synergistic and/or antagonistic effects of many regulatory factors. Here, the authors demonstrate that the ubiquitin ligase seven in absentia1 (SINA1) mammalian BTF2‐like transcription factors, Drosophila synapse‐associated proteins, and yeast DOS2‐like proteins (BSD1) function as a regulatory module to control vegetative growth in tomato via regulation of the production of plant growth hormone gibberellin (GA). SINA1 negatively regulates the protein level of BSD1 through ubiquitin‐proteasome‐mediated degradation, and the transgenic tomato over‐expressing SINA1 (SINA1‐OX) resembles the dwarfism phenotype of the BSD1‐knockout (BSD1‐KO) tomato plant. BSD1 directly activates expression of the BSD1‐regulated gene 1 (BRG1) via binding to a novel core BBS (standing for BSD1 binding site) binding motif in the BRG1 promoter. Knockout of BRG1 (BRG1‐KO) in tomato also results in a dwarfism phenotype, suggesting BRG1 plays a positive role in vegetative growth as BSD1 does. Significantly, GA contents are attenuated in transgenic SINA1‐OX, BSD1‐KO, and BRG1‐KO plants exhibiting dwarfism phenotype and exogenous application of bioactive GA3 restores their vegetative growth. Moreover, BRG1 is required for the expression of multiple GA biosynthesis genes and BSD1 activates three GA biosynthesis genes promoting GA production. Thus, this study suggests that the SINA1‐BSD1 module controls vegetative growth via direct and indirect regulation of GA biosynthesis in tomato. [ABSTRACT FROM AUTHOR]

ABSTRACT The sucrose yield in sugarcane largely depends on stem morphology, including length, diameter and sugar content, making sugarcane stem a key trait in breeding. The “Bainianzhe” variety from Songxi County, Fujian Province, possesses both aerial stems and rhizomes, providing a unique model for studying stem development. We performed a spatiotemporal transcriptomic analysis of the base, middle and apical sections of both aerial stems and rhizomes. The analysis categorized transcriptomes by developmental stage—base, middle and apical—rather than environmental differences. Apical segments were enriched with genes related to cell proliferation, while base segments were linked to senescence and fibrosis. Gene regulatory networks revealed key TFs involved in stem development. Orphan genes may be involved in rhizome development through coexpression networks. Plant hormones, especially genes involved in ABA and GAs synthesis, were highly expressed in rhizomes. Thiamine‐related genes were also more prevalent in rhizomes. Furthermore, the apical segments of rhizomes enriched in photosynthesis‐related genes suggest adaptations to light exposure. Low average temperatures in Songxi have led to unique cold acclimation in Bainianzhe, with rhizomes showing higher expression of genes linked to unsaturated fatty acid synthesis and cold‐responsive calcium signalling. This indicates that rhizomes may have enhanced cold tolerance, aiding in the plant's overwintering success. [ABSTRACT FROM AUTHOR]

Background: Two-line hybrid wheat technology system is one way to harness wheat heterosis both domestically and internationally. Seed vigor is a crucial parameter for assessing seed quality, as enhanced seed vigor can lead to yield increments of over 20% to a certain extent. MicroRNAs (miRNAs) were known to participate in the development and vigor of seed in plants, but its impact on seed vigor in two-line hybrid wheat remains poorly elucidated. Results: The hybrid (BS1453/11GF5135) wheat exhibited superiority in seed vigor and anti-aging capacity, compared to its male parent (11GF5135, MP) and female parent (BS1453, FP). We identified four miRNAs associated with seed vigor, all of which are novel miRNAs. The majority of targets of miRNAs were related to ubiquitin ligases, kinases, sucrose synthases and hydrolases, involving in starch and sucrose metabolism, hydrolysis, catalysis, plant hormone signal transduction, and other pathways, which played crucial roles in seed development. Additionally, we also found miR531 was differentially expressed in both male parent and hybrid, and its target gene was a component of the E1 subunit of α-ketoate dehydrogenase complex, which interacted with dihydrolipoamide acetyltransferase (E2) and dihydrolipoyl dehydrogenase (E3). Finally, We established a presumptive interaction model to speculate the relationship of miR531 and seed vigor. Conclusions: This study analyzed the seed vigor of two-line hybrid wheat, and screened seed vigor-related miRNAs. Meanwhile speculated the genetic relationship of hybrid and parents, in terms of miRNAs. Consequently, the present study provides new insights into the miRNA-mediated gene and protein interaction network that regulates seed vigor. These findings hold significance for enhancing the yield and quality of two-line hybrid wheat, facilitating its future applications. [ABSTRACT FROM AUTHOR]

Introduction: Phytohormones play a crucial role in regulating the abscission of plant organs and tissues. Methods: In this study, the ultrastructure of the sepals of Korla fragrant pears was observed using a transmission electron microscope, and high-performance liquid and gas chromatography were used to analyze the dynamic changes of phytohormones in the abscission zone during the calyx abscission process of Korla fragrant pears, and mass spectrometry imaging was applied to ascertain the spatial distribution of phytohormones. Results: The results revealed that the mitochondria in the abscission zone of the decalyx fruits were regularly distributed around the cell wall, and the chloroplasts were moderately present. In contrast, in the persistent calyx fruit, the corresponding parts of the abscission zone showed a scattered distribution of mitochondria within the cells, and there was a higher number of chloroplasts, which also contained starch granules inside. Mass spectrometry imaging revealed that ABA was enriched in the abscission zone of the decalyx fruit, and their ionic signal intensities were significantly stronger than those of the persistent calyx fruit. However, the ionic signal intensities of Indole-3-acetic acid (IAA) and Gibberellin A3 (GA3) of the persistent calyx fruit were significantly stronger than those in the abscission zone of the decalyx fruit and were concentrated in the persistent calyx fruit. 1-Aminocyclopropanecarboxylic Acid (ACC) did not show distinct regional distribution in both the decalyx and persistent calyx fruits. Furthermore, before the formation of the abscission zone, the levels of IAA, GA3, and zeatin (ZT) in the abscission zone of the decalyx fruits were significantly lower than those in the persistent calyx fruits by 37.9%, 57.7%, and 33.0%, respectively, while the levels of abscisic acid (ABA) and ethylene (ETH) were significantly higher by 21.9% and 25.0%, respectively. During the formation of the abscission zone, the levels of IAA, GA3, and ZT in the abscission zone of the decalyx fruits were significantly lower than those in the persistent calyx fruits by 41.7%, 71.7%, and 24.6%, respectively, while the levels of ABA and ETH were significantly higher by 15.2% and 80.0%, respectively. After the formation of the abscission zone, the levels of IAA and GA3 in the abscission zone of the decalyx fruits were lower than those in the persistent calyx fruits by 20.8% and 47.8%, respectively, while the levels of ABA and ETH were higher by 271.8% and 26.9%, respectively. In summary, during the calyx abscission process of Korla fragrant pears, IAA and GA3 in the abscission zone inhibited abscission, while ABA and ETH promoted calyx abscission. These research findings enrich the understanding of the regulatorymechanism of plant hormones on calyx abscission and provide a theoretical basis for the study of exogenous plant growth regulators for regulating calyx abscission in Korla fragrant pear. [ABSTRACT FROM AUTHOR]

Plant somatic embryogenesis (SE) is an efficient regeneration system for propagation. It involves the regulation of a complex molecular regulatory network encompassing endogenous hormone synthesis, metabolism, and signal transduction processes, induced through exogenous plant growth regulators. Previous studies have focused primarily on traditional propagation methods for Tectona grandis, but there is limited knowledge on SE and its hormonal regulatory mechanisms. In our study, different SE stages, including the nonembryogenic callus (NEC), embryogenic callus (EC), and globular and heartshaped embryo (E-SEs) stages, were induced in teak cotyledons incubated on MS medium supplemented with 0.1 mg/L thidiazuron (TDZ). Morphological and histological observations indicated that EC primarily originates from the development of embryogenic cell clusters. During SE induction, the levels of six classes of endogenous hormones, IAA, CTK, ETH, ABA, SA, and JA, changed significantly. Transcriptome analysis revealed that endogenous hormones participate in SE induction in teak through various biological processes, such as biosynthesis, metabolism, and signal transduction pathways. We found that IAA biosynthesis primarily occurs through the IAM pathway during these three stages. The ETH receptor kinase gene SERF1 exhibited the highest expression levels in E-SEs. The ABA-, SA-, and JA-related signal transduction genes ABI3, NPR1, and JAZ exhibited no differential expression during different stages. Moreover, key encoding genes of SE regulators, including WUS, WOX and SERK, were differentially expressed during SE. In conclusion, this study offers insights into the roles of endogenous hormones and their interactions during SE induction. [ABSTRACT FROM AUTHOR]

Background: Castor is an important industrial raw material. Drought-induced oxidative stress leads to slow growth and decreased yields in castor. However, the mechanisms of drought-induced oxidative stress in castor remain unclear. Therefore, in this study, physiological, biochemical, and RNA-seq analyses were conducted on the roots of castor plants under PEG-6000 stress for 3 d and 7 d followed by 4 d of hydration. Results: The photosynthetic rate of castor leaves was inhibited under PEG-6000 stress for 3 and 7 d. Biochemical analysis of castor roots stressed for 3 d and 7 d, and rehydrated for 4 d revealed that the activities of APX and CAT were highest after only 3 d of stress, whereas the activities of POD, GR, and SOD peaked after 7 d of stress. RNA-seq analysis revealed 2926, 1507, and 111 differentially expressed genes (DEGs) in the roots of castor plants under PEG-6000 stress for 3 d and 7 d and after 4 d of rehydration, respectively. GO analysis of the DEGs indicated significant enrichment in antioxidant activity. Furthermore, KEGG enrichment analysis of the DEGs revealed significantly enriched metabolic pathways, including glutathione metabolism, fatty acid metabolism, and plant hormone signal transduction. WGCNA identified the core genes PP2C39 and GA2ox4 in the navajowhite1 module, which was upregulated under PEG-6000 stress. On the basis of these results, we propose a model for the response to drought-induced oxidative stress in castor. Conclusions: This study provides valuable antioxidant gene resources, deepening our understanding of antioxidant regulation and paving the way for further molecular breeding of castor plants. [ABSTRACT FROM AUTHOR]

Inter-kingdom communication through small molecules is essential to the coexistence of organisms in an ecosystem. In soil communities, the plant root is a nexus of interactions for a remarkable number of fungi and is a source of small-molecule plant hormones that shape fungal compositions. Although hormone signaling pathways are established in plants, how fungi perceive and respond to molecules is unclear because many plant-associated fungi are recalcitrant to experimentation. Here, we develop an approach using the model fungus, Saccharomyces cerevisiae , to elucidate mechanisms of fungal response to plant hormones. Two plant hormones, strigolactone and methyl jasmonate, produce unique transcript profiles in yeast, affecting phosphate and sugar metabolism, respectively. Genetic analysis in combination with structural studies suggests that SLs require the high-affinity transporter Pho84 to modulate phosphate homeostasis. The ability to study small-molecule plant hormones in a tractable genetic system should have utility in understanding fungal-plant interactions. [Display omitted] • The plant hormone strigolactone hijacks phosphate metabolism in baker's yeast • Strigolactone allosterically inhibits the high-affinity phosphate transporter Pho84 • A conserved transmembrane pocket in Pho84 is required for strigolactone function • Strigolactone modulates phosphate homeostasis in plant-associated fungi Strigolactones act as both plant hormones and as environmental communication signals to plant-associated fungi. Bradley et al. show that strigolactone modulates phosphate homeostasis in baker's yeast by antagonizing the phosphate transporter Pho84. This strigolactone response is conserved in other fungi, suggesting that yeast will facilitate our understanding of natural plant-fungal communication. [ABSTRACT FROM AUTHOR]

Blueberries (Vaccinium spp.) are extremely sensitive to drought stress. Flavonoids are crucial secondary metabolites that possess the ability to withstand drought stress. Therefore, improving the drought resistance of blueberries by increasing the flavonoid content is crucial for the development of the blueberry industry. To explore the underlying molecular mechanism of blueberry in adaptation to drought stress, we performed an integrated analysis of the metabolome and transcriptome of blueberry leaves under drought stress. We found that the most enriched drought-responsive genes are mainly involved in flavonoid biosynthesis and plant hormone signal transduction pathways based on transcriptome data and the main drought-responsive metabolites come from the flavonoid class based on metabolome data. The UDP-glucose flavonoid 3-O-glucosyl transferase (UFGT), flavonol synthase (FLS), and anthocyanidin reductase (ANR-2) genes may be the key genes for the accumulation of anthocyanins, flavonols, and flavans in response to drought stress in blueberry leaves, respectively. Delphinidin 3-glucoside and delphinidin-3-O-glucoside chloride may be the most important drought-responsive flavonoid metabolites. VcMYB1, VcMYBPA1, MYBPA1.2, and MYBPA2.1 might be responsible for drought-induced flavonoid biosynthesis and VcMYB14, MYB14, MYB102, and MYB108 may be responsible for blueberry leaf drought tolerance. ABA responsive elements binding factor (ABF) genes, MYB genes, bHLH genes, and flavonoid biosynthetic genes might form a regulatory network to regulate drought-induced accumulation of flavonoid metabolites in blueberry leaves. Our study provides a useful reference for breeding drought-resistant blueberry varieties. [ABSTRACT FROM AUTHOR]

Broomcorn millet (Panicum miliaceum L.) is one of the earliest crops, domesticated nearly 8000 years ago in northern China. It gradually spread across the entire Eurasian continent, as well as to America and Africa, with recent improvement in various reproductive and vegetative traits. To identify the genes that were selected during the domestication and improvement processes, we performed a comparative transcriptome analysis based on wild types, landraces, and improved cultivars of broomcorn millet at both seeding and filling stages. The variations in gene expression patterns between wild types and landraces and between landraces and improved cultivars were further evaluated to explore the molecular mechanisms underlying the domestication and improvement of broomcorn millet. A total of 2155 and 3033 candidate genes involved in domestication and a total of 84 and 180 candidate genes related to improvement were identified at seedling and filling stages of broomcorn millet, respectively. The annotation results suggested that the genes related to metabolites, stress resistance, and plant hormones were widely selected during both domestication and improvement processes, while some genes were exclusively selected in either domestication or improvement stages, with higher selection pressure detected in the domestication process. Furthermore, some domestication- and improvement-related genes involved in stress resistance either lost their functions or reduced their expression levels due to the trade-offs between stress resistance and productivity. This study provided novel genetic materials for further molecular breeding of broomcorn millet varieties with improved agronomic traits. [ABSTRACT FROM AUTHOR]

SUMMARY: Mature embryos are the main explants of tissue culture used in rice transgenic technology. However, the mechanism of mature embryo callus formation remains unclear. In this study, a microRNA‐mediated gene regulatory network of rice calli was established using degradome sequencing. We identified a microRNA, OsmiR408, that regulates the formation of the callus derived from the mature rice embryo. OsUCLACYANIN 30 (OsUCL 30), a target gene of OsmiR408, was the most abundant cleavage mRNA in rice callus. OsUCL17 was verified as a target gene of OsmiR408 using RNA ligase‐mediated 5′‐RACE. In analysis of the OsmiR408 promoter reporter line and pri‐miR408 transcript level, the promoter activity and transcript level of MIR408 were increased dramatically during callus formation. In phenotypic observations, OsmiR408 knockout caused severe defects in mature embryo callus formation, whereas OsmiR408 overexpression promoted callus formation. Transcriptome analysis demonstrated that OsUCLs and certain genes related to the plant hormone signal transduction and phenylpropanoid‐flavonoid biosynthesis pathway had different differential expression patterns between OsmiR408 knockout and overexpression calli. Thus, OsmiR408 may regulate callus formation mainly by affecting plant hormone signal transduction and phenylpropanoid‐flavonoid biosynthesis pathway. Our findings provide insight into OsmiR408/UCLs module function in callus formation. Significance Statement: A novel function for the miR408 was determined, and its target genes OsUCL8, OsUCL17, and OsUCL30 were verified. miR408 regulates rice callus initiation through affecting plant hormone signal transduction and phenylpropanoid‐flavonoid biosynthesis pathway. This study expands our understanding of the function of OsmiR408 in the process of callus formation and will facilitate genetic manipulation based on callus explants in rice breeding. [ABSTRACT FROM AUTHOR]

SUMMARY: Plant hormones are chemical signals governing almost every aspect of a plant's life cycle and responses to environmental cues. They are enmeshed within complex signaling networks that can only be deciphered by using broad‐scale analytical methods to capture information about several plant hormone classes simultaneously. Methods used for this purpose are all based on reversed‐phase (RP) liquid chromatography and mass spectrometric detection. Hydrophilic interaction chromatography (HILIC) is an alternative chromatographic method that performs well in analyses of biological samples. We therefore developed and validated a HILIC method for broad‐scale plant hormone analysis including a rapid sample preparation procedure; moreover, derivatization or fractionation is not required. The method enables plant hormone screening focused on polar and moderately polar analytes including cytokinins, auxins, jasmonates, abscisic acid and its metabolites, salicylates, indoleamines (melatonin), and 1‐aminocyclopropane‐1‐carboxylic acid (ACC), for a total of 45 analytes. Importantly, the major pitfalls of ACC analysis have been addressed. Furthermore, HILIC provides orthogonal selectivity to conventional RP methods and displays greater sensitivity, resulting in lower limits of quantification. However, it is less robust, so procedures to increase its reproducibility were established. The method's potential is demonstrated in a case study by employing an approach combining hormonal analysis with phenomics to examine responses of three Arabidopsis ecotypes toward three abiotic stress treatments: salinity, low nutrient availability, and their combination. The case study showcases the value of the simultaneous determination of several plant hormone classes coupled with phenomics data when unraveling processes involving complex cross‐talk under diverse plant‐environment interactions. [ABSTRACT FROM AUTHOR]

Bud dormancy is a survival strategy that plants have developed in their native habitats. It helps them endure harsh seasonal changes by temporarily halting growth and activity until conditions become more favorable. Research has primarily focused on bud dormancy in tree species and the ability to halt growth in vegetative tissues, particularly in meristems. Various plant species, such as potato, have developed specialized storage organs, enabling them to become dormant during their yearly growth cycle. Deciduous trees and potato tubers exhibit a similar type of bud endodormancy, where the bud meristem will not initiate growth, even under favorable environmental conditions. Chilling accumulation activates C-repeat/dehydration responsive element binding (DREB) factors (CBFs) transcription factors that modify the expression of dormancy-associated genes. Chilling conditions shorten the duration of endodormancy by influencing plant hormones and sugar metabolism, which affect the timing and rate of bud growth. Sugar metabolism and signaling pathways can interact with abscisic acid, affecting the symplastic connection of dormant buds. This review explores how chilling affects endodormancy duration and explores the similarity of the chilling response of dormant buds in potato tubers and woody perennials. [ABSTRACT FROM AUTHOR]

ABSTRACT Plant growth and development are governed via signal networks that connect inputs from nutrient status, hormone signals, and environmental cues. Substantial researches have indicated a pivotal role of sugars as signalling molecules in plants that integrate external environmental cues and other nutrients with intrinsic developmental programmes regulated via multiple plant hormones. Therefore, plant growth and development are controlled through complication signalling networks. However, in many studies, to obtain more obviously experimental findings, excess concentrations of applied exogenous sugars have aggravated the complexity of this signalling networks. Once researchers underestimate this complexity, a series of contradictory or contrasting findings will be generated. More importantly, in terms of these contradictory findings, more contradictory study outcomings are derived. In this review, we carefully analyze some reports, and find that these reports have confused or neglected that the sugar‐antagonism of ethylene signalling is specific or conditional. As a result, many contradictory conclusions are generated, which will in turn misdirect the scientific community. [ABSTRACT FROM AUTHOR]

Background: The NAC transcription factor family, which is recognized as one of the largest plant-specific transcription factor families, comprises numerous members that are widely distributed among various higher plant species and play crucial regulatory roles in plant immunity. Results: In this paper, we provided a detailed summary of the roles that NAC transcription factors play in plant immunity via plant hormone pathways and reactive oxygen species pathways. In addition, we conducted in-depth investigations into the interactions between NAC transcription factors and pathogen effectors to summarize the mechanism through which they regulate the expression of defense-related genes and ultimately affect plant disease resistance. Conclusions: This paper presented a comprehensive overview of the crucial roles that NAC transcription factors play in regulating plant disease resistance through their involvement in diverse signaling pathways, acting as either positive or negative regulators, and thus provided references for further research on NAC transcription factors. [ABSTRACT FROM AUTHOR]

Auxin is the first plant hormone found to play a dominant role in fruit growth, from fruit set to fruit ripening. Strawberry plants represent a suitable model for studying auxin's biosynthesis, sensing, and signaling machinery. Aux/IAA genes are a classical rapid auxin-responsive family. However, the Aux/IAA gene family in Fragaria genus is poorly understood. In this study, a total of 287 Aux/IAA genes were identified in the eight strawberry genomes. Their physicochemical properties, domain structure, and cis-regulatory elements revealed the functional multiplicity of the strawberry Aux/IAAs. We used a phylogenetic analysis to classify these genes into 12 classes. In addition, based on synteny analysis, gene duplications, and calculation of the Ka/Ks ratio, we found that segmental duplications promote the evolution of Aux/IAAs in Fragaria species, which is followed by purifying selection. Furthermore, the expression pattern and protein–protein interaction network of these genes in Fragaria vesca revealed various tissue-specific expressions and probable regulatory functions. Taken together, these results provide basic genomic information and a functional analysis of these genes, which will serve to expand our understanding of the direction in which the Aux/IAA gene family is evolving in Fragaria species. [ABSTRACT FROM AUTHOR]

Bud-notching in pear varieties with weak-branches enhances branch development, hormone distribution, and germination, promoting healthier growth and improving early yield. To examine the regulatory mechanisms of endogenous hormones on lateral bud germination in Pyrus spp. (cv. 'Huangguan') (Pyrus bretschneideri Rehd.), juvenile buds were collected from 2-year-old pear trees. Then, a comprehensive study, including assessments of endogenous hormones, germination and branching rates, RNA-seq analysis, and gene function analysis in these lateral buds was conducted. The results showed that there was no significant difference in germination rate between the control and bud-notching pear trees, but the long branch rate was significantly increased in bud-notching pear trees compared to the control (p < 0.05). After bud-notching, there was a remarkable increase in IAA and BR levels in the pruned section of shoots, specifically by 141% and 93%, respectively. However, the content of ABA in the lateral buds after bud-notching was not significantly different from the control. Based on RNA-seq analysis, a notable proportion of the differentially expressed genes (DEGs) were linked to the plant hormone signal transduction pathway. Notably, the brassinosteroid signaling pathway seemed to have the closest connection with the branching ability of pear with the related genes encoding BRI1 and CYCD3, which showed significant differences between lateral buds. Finally, the heterologous expression of PyCYCD3 has a positive regulatory effect on the increased Arabidopsis growth and branching numbers. Therefore, the PyCYCD3 was identified as an up-regulated gene that is induced via brassinosteroid (BR) and could act as a conduit, transforming bud-notching cues into proliferative signals, thereby governing lateral branching mechanisms in pear trees. [ABSTRACT FROM AUTHOR]