Search Results (32)

Peach trees exhibit vigorous growth that is often difficult to manage, frequently leading to canopy closure and the outward migration of fruiting positions, which ultimately results in diminished yield and fruit quality. Therefore, it is of great importance to study the key genes regulating peach tree vigor. Preliminary experiments identified PpNAC036 as a candidate gene potentially associated with vigor. In this study, we characterized the expression profile of PpNAC036 across various peach tissues. Our results demonstrate that PpNAC036 is most highly expressed in stems and responds rapidly to hormonal treatments, with expression levels increasing 3.6-fold and 3.9-fold under IAA and NPA treatments, respectively (5 min to 1 h). Subsequently, the PpNAC036 gene was cloned and overexpressed in Arabidopsis thaliana. Compared to the wild type, transgenic Arabidopsis exhibited a 28–50% reduction in primary root length and a 31.6–36.8% decrease in hypocotyl length. Conversely, at maturity, the transgenic Arabidopsis displayed enhanced vegetative vigor, with fresh and dry weights increasing by 37–48% and 29–46%, respectively. This growth was accompanied by a nearly two-fold increase in stem diameter and a 1.5- to 2-fold elevation in lignin content; simultaneously, genes related to lignin biosynthesis were upregulated. Hormonal profiling revealed that PpNAC036 overexpression led to a 7-fold increase in IAA, a 22–60% rise in GAs, and a 97–106% increase in CTKs, whereas ABA levels decreased by 5–6%. Furthermore, the transgenic Arabidopsis exhibited delayed germination and flowering, along with alterations in the number of floral organs. Transcriptomic analysis identified 2797 common DEGs, which were enriched in pathways related to cell wall organization and hormone signaling. Collectively, these findings elucidate the function of PpNAC036 as a pivotal regulator of plant vigor and secondary cell wall development, positioning it as a promising candidate gene for molecular breeding and architectural optimization in peach. Full article

Waterlogging is a major abiotic stress that restricts plant growth, productivity, and survival by disrupting root aeration and altering hormonal homeostasis. To elucidate the physiological and molecular responses associated with flooding tolerance in Liriodendron hybrids (Liriodendron chinense × Liriodendron tulipifera), this study investigated its morphological, physiological, and transcriptomic changes under 0, 1, 3, and 6 days of waterlogging. Roots exhibited rapid decay, while leaves showed delayed chlorosis and reduced chlorophyll content. Changes in antioxidant enzyme activities reflected enhanced antioxidant capacity, with superoxide dismutase (SOD) activity decreasing and peroxidase (POD) and catalase (CAT) activities increasing. Hormone measurements indicated organ-specific patterns, including abscisic acid (ABA) accumulation in leaves and decreased indole-3-acetic acid (IAA) and gibberellin (GA) levels in both roots and leaves. Transcriptome profiling revealed extensive transcriptional adjustments in hormone biosynthesis, signaling, and stress-responsive pathways, including divergent regulation of ABA-associated genes in leaves and roots and broad downregulation of auxin- and gibberellin-related genes. Key ABA biosynthetic genes (NCED1, ABA2) and signaling components (PYL4, PP2C, ABF) were upregulated in leaves but downregulated in roots, whereas auxin (YUC6) and gibberellin (GA20ox) genes were generally suppressed. These coordinated physiological and molecular responses suggest organ-differentiated adaptation to waterlogging in Liriodendron hybrids, highlighting candidate pathways and genes for further investigation and providing insights for improving flooding tolerance in woody species. Full article

Camellia drupifera is an important woody oil crop with high economic and medicinal value. Fruit maturation is a complex process regulated by hormones and gene networks, yet its molecular basis remains unclear. Here, we integrated hormone profiling (IAA, GA₃, ABA), transcriptomics, and miRNA-omics across three key stages: nutrient synthesis (S1), lipid accumulation (S4), and maturation (S7). During early development (S1), IAA and GA₃ levels peaked, accompanied by the upregulation of growth-related genes (AUX1, ARF, GID1), which promote fruit growth. By maturation (S7), ABA content increased markedly, activating PYR/PYL, PP2C, and ABF, while IAA and GA₃ declined. Transcriptome analysis revealed 45 key differentially expressed genes correlated with hormone levels. In parallel, miRNAs such as miR393-z (targeting TIR1) and novel-m0146-5p (targeting ARF1) were identified as regulators of hormone signaling and fruit maturation. Collectively, our results highlight a coordinated “hormone–miRNA–mRNA” regulatory network underlying C. drupifera fruit development. These findings provide new insights into the molecular regulation of fruit maturation and lipid accumulation in woody oil crops, offering a foundation for genetic improvement and efficient utilization of this species. Full article

Irregular rooting in vitro is a major problem in the micropropagation of culinary rhubarb (Rheum rhaponticum), a vegetable crop rich in bioactive compounds. To date, little is known about the factors and mechanisms underlying adventitious root (AR) formation in rhubarb under in vitro conditions. Here, we studied the effects of indole-3-butyric acid (IBA) and its interaction with ethylene (ET) on AR development in rhubarb ‘Raspberry’ selection. To evaluate the ET-effect, we applied a precursor of ET biosynthesis—1 aminocyclopropane-1-carboxylic acid (ACC); an inhibitor of ET synthesis—aminoethoxyvinylglycine (AVG); and an inhibitor of ET action—silver nitrate (AgNO₃). The best results (96.9% rooting frequency, 12.7 roots/shoot) were obtained after adding ACC to the IBA-containing medium. The positive effect of ET was linked to decreased levels of cytokinin and auxins in the rhubarb shoot bases at the initiation and expression stages of rooting. Moreover, the enhanced expression levels of genes involved in auxin signalling and homeostasis (IAA17, GH3.1) and ABA catabolism (CYP707A1) were observed. The blocking of ethylene synthesis significantly increased JA production, and the rooting frequency decreased to 29.8%. The presence of AgNO₃ in the auxin medium resulted in a significant reduction in root number, which was consistent with the enhanced levels of ABA and the expression of genes related to ABA biosynthesis and signalling (PP2C49 and CBF4), as well as ET synthesis (ACO5). Full article

Fruit shape is an important quality and yield trait of pear, and the fruit shape of ‘Laiyang Cili’ presents a spindle shape which seriously affects its commercial value. Calyx excision treatment could change the fruit shape, while the underlying genes and their regulatory mechanism remain poorly understood. In this study, we constructed RNA-seq libraries of pear treated with calyx excision to explore underlying regulatory mechanisms. At the early stage of the calyx excision treatment, the numbers of differentially expressed genes (DEGs) between each comparison group were relatively high and gradually decreased along with fruit development. The expression pattern of the DEGs ranked in the top 30 of the six groups had obvious divergence, and DEGs were mainly distributed in the “after calyx excision treatment (0 days)” (AC0d) and AC2d groups. The DEGs were mainly enriched in plant hormone signal transduction and plant defense response. We identified 17 candidate genes related to fruit shape and tested their expression patterns along with fruit development. Among them, nine candidate genes expression trends were consistent with fragments per kilobase of exon model per million mapped fragment (FPKM) values, including MYB62, outer envelope pore protein 62 (OEP62), auxin response factor 3 (ARF3), auxin-responsive protein 50 (SAUR50), protein phosphatase 2C 51 (PP2C 51), major allergen Pyr c 1 (PYRC1), aquaporin TIP1-3 (TIP1-3), transcription factor TGA4 (TGA4) and auxin-responsive protein 17 (IAA17). And then, weighted gene co-expression network analysis (WGCNA) analysis revealed that the OVATE family protein (OFP) and SUN domain-containing protein (SUN) were divided into the MEblue model, which had a positive correlation with calyx excision treatment, and the expression trend of LOC103960706 (OFP8) appeared cohesive with FPKM values. Pbr014104.1 and Pbr016952.1, which were the ortholog genes of LOC103960706, were further identified from the pear genome, and were found to be highly expressed in pear fruit through RT-PCR analysis. Taken together, the key stage determining the development of fruit shape was in the early stage after calyx excision treatment, and fruit shape regulation and development were co-regulated by multiple genes. Full article

The phosphofructokinase (PFK) gene family plays a pivotal role in glycolysis and energy metabolism in plants. This study aimed to systematically characterize the PFK gene family in Arabidopsis thaliana at the genome-wide level and to investigate the function of AtPFK2 (ATP-dependent phosphofructokinase 2) in response to salt and drought stress. Through bioinformatics analysis, 11 AtPFK genes were identified. Phylogenetic analysis revealed that these PFK genes can be classified into two subfamilies: PFK and PFP. Notably, AtPFK2 possesses a unique structure, containing only a single intron, and its promoter is enriched with stress- and hormone-responsive elements, such as ABRE and MBS. T-DNA insertion mutants (pfk2) exhibited slightly shorter roots but slightly higher fresh weight under stress conditions, whereas Arabidopsis lines AtPFK2-overexpressing (OE-PFK2) showed increased stress sensitivity, with inhibited root and leaf growth, leaf wilting, reduced malondialdehyde and chlorophyll content, and enhanced accumulation of proline and soluble sugars. Weighted gene co-expression network analysis (WGCNA) identified 14 stress-related modules, from which six core genes—LBD41, TRP3, PP2-A3, SAUR10, IAA6, and JAZ1—were selected. These genes are involved in glycine metabolism and plant hormone signaling. The results of this study indicate that AtPFK2 mediates stress responses by regulating osmoregulatory substances and hormone signaling pathways, offering new insights into the mechanisms of stress resistance in crops. Full article

Soil, rhizosphere, and plant-associated microorganisms can enhance plant growth and health. A genomic analysis of these microbes revealed the key characteristics contributing to their beneficial effects. Following a field survey in Panama, four bacterial isolates with plant growth-promoting traits (PGPT) in rice (Oryza sativa L.) were identified. In this study, we sequenced, assembled, and annotated the genomes of Lysinibacillus fusiformis C6 and 24, and Bacillus cereus D23 and 59. The C6 genome was 4,754,472 bp long with 10 contigs, 37.62% guanine-cytosine (GC) content, and 4657 coding sequences (CDS). The 24 genome was 4,683,219 bp with five contigs, 37.65% GC content, and 4550 CDS. The D23 genome was 6,199,908 bp long with 18 contigs, 34.84% GC content, and 6141 CDS. The 59 genome was 6,194,462 bp with 21 contigs, 34.87% GC content, and 6122 CDS. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) confirmed that C6 and 24 belong to Lysinibacillus fusiformis, whereas D23 and 59 belong to the Bacillus cereus species. Further results revealed that these bacteria contained genes characteristic of plant growth-promoting bacteria, such as siderophore, phytohormone auxin (IAA) production, and nitrogen-fixing abilities that promote plant growth. Moreover, the antiSMASH database identified gene clusters involved in secondary metabolite production (biosynthetic gene clusters), such as betalactone, NRPS-like, NRP-siderophore, terpene, and RiPP-like clusters. Moreover, diverse and novel biosynthetic clusters (BCGs) have included non-ribosomal peptides (NRPs), polyketides (PKs), bacteriocins, and ribosomally synthesized and post-transcriptionally modified peptides (RiPPs). This work offers new insights into the genomic basis of the studied strains’ plant growth-promoting capabilities. Full article

This article methodically reveals how, in woody plants (poplar), the interaction between N and P coordinates root structure and nutrient absorption through a complex hormone signaling network. This study bridges a significant gap in our knowledge of nutrient interaction networks. The results demonstrate that NO₃⁻ significantly enhances the gene expression and enzymatic activity of organic acid synthases (MDH, PEPC) and APs. Furthermore, it synergizes with IAA/ABA signals to refine root structure, enhancing the surface area for P absorption. In low Pi availability environments, NO₃⁻ further promotes P recycling by simultaneously boosting the levels of Pi transport proteins (notably, the PHO family), facilitating myo-inositol phosphate metabolism (via IMP3/ITPK1-mediated PP-InsPs degradation), and augmenting IAA/SA signals. Pi induces the activity of N assimilation enzymes (GS/GOGAT/GDH), facilitating nitrogen metabolism. However, in the absence of N, it leads to a metabolic imbalance characterized by high enzymatic activity but low efficiency. Alternatively, adequate N availability allows Pi to improve root robustness and N assimilation efficiency, mediated by IAA/GA accumulation and ABA signaling (e.g., SNRK2/ABF). We propose the existence of an intricate network in poplar, orchestrated by transcriptional cascades, metabolic regulation, and hormonal synergism. Key modules such as SPX-PHR, NLA, HHO2, and MYB59 are likely central to this network’s function. These findings offer a foundational framework for the development of molecular breeding and precise fertilization strategies, enhancing the efficient use of N and P in forestry. Full article

Paclobutrazol (PAC) is a significant inhibitor of gibberellin biosynthesis that profoundly influences grape seed development (GSD) through the modulation of key molecular pathways. Here, we identified 6659 differentially expressed genes (DEGs) in GSD under PAC treatment, with 3601 up-regulated and 3058 down-regulated. An analysis of hormone-associated DEGs revealed that auxin-related genes (16) were the most up-regulated, followed by genes associated with brassinosteroid and ABA. In contrast, cytokinin- and gibberellin-related genes exhibited a suppressive response. PAC treatment also triggered extensive reprogramming of metabolic pathways, including 44 genes involved in starch and sucrose metabolism (24 up-regulated, 20 down-regulated), 101 cell wall-related genes (53 up-regulated, 48 down-regulated), and 110 transcription factors (77 up-regulated, 33 down-regulated). A cis-element analysis of the promoters of 76 hormone-responsive genes identified 14 types of hormone-responsive cis-elements, with ABRE being the most prevalent. Genes responsible for inactivating active hormones, such as ABA-VvPP2CA, IAA-VvGH3.1, and CK-VvARR9-1, were also identified. Concurrently, PAC negatively regulated hormone-active genes, including BR-VvXTH25, SA-VvTGA21-3, and JA-VvTIFY3B, leading to reduced levels of these hormones. PAC modulates GSD by mediating the dynamic balance of multi-hormone accumulations. Furthermore, development-related cis-elements such as the AACA-motif, AAGAA-motif, AC-I, AC-II, O2-site, as-1, CAT-box, CCAAT-box, circadian, GCN4-motif, RY-element, HD-Zip 1, HD-Zip 3, MSA-like, MYB-like sequence, MYB-binding site, and MYB recognition site, were found in key DEGs involved in starch and sucrose metabolism, cell wall remodeling, and epigenetic regulation. This indicates that these pathways are responsive to PAC modulation during GSD. Finally, we developed a comprehensive regulatory network to illustrate the PAC-mediated pathways involved in GSD. This network integrates multi-hormonal signaling, cell wall remodeling, epigenetic regulation, and transcription factors, highlighting PAC’s pivotal role in GSD. Our findings provide new insights into the complex mechanisms underlying PAC’s effects on grapevine development. Full article

Parthenocarpy, the development of fruit without fertilization, is a significant trait in fingered citron (Citrus medica L. var. sarcodactylis Swingle). This study aims to elucidate the regulatory mechanisms underlying parthenocarpy through comparative transcriptome analysis and phytohormone profiling between fingered citron and its non-parthenocarpic counterpart, citron. A total of 66 differentially expressed hormone-related genes were identified, with the auxin pathway emerging as the most prominent in fingered citron. Protein–protein interaction analysis revealed a potential interaction between auxin and abscisic acid (ABA). Phytohormone content analysis indicated that fingered citron exhibited higher levels of indole-3-acetic acid (IAA) and lower levels of ABA compared to citron. A weighted gene co-expression network analysis (WGCNA) suggested that the interplay between auxin and ABA is crucial for triggering parthenocarpy. Virus-induced gene silencing (VIGS) experiments demonstrated that silencing CmsABI5 led to decreased ABA levels, while auxin levels remained unchanged, resulting in disrupted parthenocarpy and increased ethylene levels, indicating a secondary hormonal response. Additionally, gene expression changes associated with failed parthenocarpy showed down-regulation of SAUR50 and up-regulation of PP2C 56, linking these changes to ABA signaling. Our findings highlight the central regulatory role of auxin in parthenocarpy in fingered citron, with ABA acting as a critical modulator. The suppression of ABA alone disrupts parthenocarpy despite stable auxin levels, emphasizing the necessity of balanced hormone interactions. This research underscores the significant role of auxin, rather than gibberellin (GA), in regulating parthenocarpy in fingered citron, contributing valuable insights to the understanding of fruit development mechanisms. Full article

The hairy roots of Rehmannia glutinosa (Gaertn.) Libosch. ex Fisch. & C. A. Mey. are capable of producing active compounds such as iridoid glycoside, and phenylethanoid glycosides, which have potential applications in the pharmaceutical industry. Silver nanoparticles (AgNPs) have been used as novel elicitors in the induced cultivation of hairy roots, but there is a lack of research regarding their effects on R. glutinosa hairy roots. In the present study, silver nanoparticles (Pp-AgNPs) synthesized by the endophytic fungus Penicillium polandii PG21 were adopted to elicit hairy roots of R. glutinosa, to investigate their influences on the biomass, color, secondary metabolites, antioxidant activity, sucrose metabolism, and phytohormone-related gene expression. The results revealed that the dry weight and fresh weight of R. glutinosa hairy roots were both higher in the treated group than in the control group after addition of 2 mg/L Pp-AgNPs for 20 d. The content of verbascoside, total phenylethanol glycosides and total cycloartenoid in the treatment group reached the highest level at 20 d, which were 1.75, 1.51, 1.44 times more than those in the control group, respectively. Pp-AgNPs significantly stimulated the enzyme activities of catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD). The growth-promoting effect of Pp-AgNPs may be accomplished by increasing sucrose metabolism, and regulating the synthesis and signal transduction of gibberellin (GA) and indoleacetic acid (IAA). Moreover, expressed sequence tags-simple sequence repeat (EST-SSR)-based genetic diversity analyses indicated that there was little possibility of genetic variation among samples under different treatment conditions. In conclusion, the appropriate concentration of Pp-AgNPs can be used as an effective elicitor to improve the biomass and secondary metabolites content in R. glutinosa hairy roots. Full article

Euterpe oleracea Mart., also known for its fruit açaí, is a palm native to the Amazon region. The state of Pará, Brazil, accounts for over 90% of açaí production. Demand for the fruit in national and international markets is increasing; however, climate change and diseases such as anthracnose, caused by the fungus Colletotrichum sp., lead to decreased production. To meet demand, measures such as expanding cultivation in upland areas are often adopted, requiring substantial economic investments, particularly in irrigation. Therefore, the aim of this study was to evaluate the potential of açaí rhizobacteria in promoting plant growth (PGPR). Rhizospheric soil samples from floodplain and upland açaí plantations were collected during rainy and dry seasons. Bacterial strains were isolated using the serial dilution method, and subsequent assays evaluated their ability to promote plant growth. Soil analyses indicated that the sampling period influenced the physicochemical properties of both areas, with increases observed during winter for most soil components like organic matter and C/N ratio. A total of 177 bacterial strains were isolated from rhizospheres of açaí trees cultivated in floodplain and upland areas across dry and rainy seasons. Among these strains, 24% produced IAA, 18% synthesized ACC deaminase, 11% mineralized organic phosphate, and 9% solubilized inorganic phosphate, among other characteristics. Interestingly, 88% inhibited the growth of phytopathogenic fungi of the genera Curvularia and Colletotrichum. Analysis under simulated water stress using Polyethylene Glycol 6000 revealed that 23% of the strains exhibited tolerance. Two strains were identified as Bacillus proteolyticus (PP218346) and Priestia aryabhattai (PP218347). Inoculation with these strains increased the speed and percentage of açaí seed germination. When inoculated in consortium, 85% of seeds germinated under severe stress, compared to only 10% in the control treatment. Therefore, these bacteria show potential for use as biofertilizers, enhancing the initial development of açaí plants and contributing to sustainable agricultural practices. Full article

Sugarcane holds global promise as a biofuel feedstock, necessitating a deep understanding of factors that influence biomass yield. This study unravels the intricate dynamics of plant hormones that govern growth and development in sugarcane. Transcriptome analysis of F2 introgression hybrids, derived from the cross of Saccharum officinarum “LA Purple” and wild Saccharum robustum “MOL5829”, was conducted, utilizing the recently sequenced allele-specific genome of “LA Purple” as a reference. A total of 8059 differentially expressed genes were categorized into gene models (21.5%), alleles (68%), paralogs (10%), and tandemly duplicated genes (0.14%). KEGG analysis highlighted enrichment in auxin (IAA), jasmonic acid (JA), and abscisic acid (ABA) pathways, revealing regulatory roles of hormone repressor gene families (Aux/IAA, PP2C, and JAZ). Signaling pathways indicated that downregulation of AUX/IAA and PP2C and upregulation of JAZ repressor genes in high biomass segregants act as key players in influencing downstream growth regulatory genes. Endogenous hormone levels revealed higher concentrations of IAA and ABA in high biomass, which contrasted with lower levels of JA. Weighted co-expression network analysis demonstrated strong connectivity between hormone-related key genes and cell wall structural genes in high biomass genotypes. Expression analysis confirmed the upregulation of genes involved in the synthesis of structural carbohydrates and the downregulation of inflorescence and senescence-related genes in high biomass, which suggested an extended vegetative growth phase. The study underscores the importance of cumulative gene expression, including gene models, dominant alleles, paralogs, and tandemly duplicated genes and activators and repressors of disparate hormone (IAA, JA, and ABA) signaling pathways are the points of hormone crosstalk in contrasting biomass F2 segregants and could be applied for engineering high biomass acquiring varieties. Full article

Global sorghum production has been significantly reduced due to the occurrence of sorghum root rot caused by the fungus Fusarium graminearum. The utilization of biocontrol microorganisms has emerged as an effective strategy. However, the underlying mechanisms remain unclear. Therefore, the aim of this study was to investigate the effectiveness of biocontrol bacteria in inducing sorghum resistance against sorghum root rot and explore the potential induced resistance mechanisms through metabolomics analysis. The results revealed that the biocontrol bacteria Lnkb100, identified as Serratia marcescens (GenBank: PP152264), significantly enhanced the resistance of sorghum against sorghum root rot and promoted its growth, leading to increased seed weight. Targeted metabolomics analysis demonstrated that the highest concentration of the hormone IAA (indole-3-acetic acid) was detected in the metabolites of Lnkb100. Treatment with IAA enhanced the activity of disease-related enzymes such as SOD, CAT, POD and PPO in sorghum, thereby improving its resistance against sorghum root rot. Further untargeted metabolomic analysis revealed that IAA treatment resulted in higher concentrations of metabolites involved in the resistance against F. graminearum, such as geniposidic acid, 5-L-Glutamyl-taurine, formononetin 7-O-glucoside-6″-O-malonate, as well as higher concentrations of the defense-related molecules volicitin and JA. Additionally, “secondary bile acid biosynthesis” and “glycerophospholipid metabolism” pathways were found to play significant roles in the defense response of sorghum against fungal infection. These findings provide a reliable theoretical basis for utilizing biocontrol microorganisms to control sorghum root rot. Full article

Mealy peaches are dry and flavorless, which reduces their consumer acceptance. A deeper understanding of the mechanism underlying mealiness is crucial to enhancing peach fruit quality. In this study, comparative profiling was conducted on CP13, CP14, CM, and RM peaches. Sensory evaluation indicated that CP13 and CM are non-mealy clingstone and freestone peaches, respectively, and CP14 and RM are mealy freestone peaches. Both CP13 and CP14, identified as stony hard (SH) peaches, exhibited minimal ethylene release, whereas CM and RM, identified as melting flesh (MF) peaches, released high amounts of ethylene during the ripening process. Scanning electron microscopy (SEM) microstructure observation indicated that cells in the flesh tissue of mealy peaches, CP14 (SH) and RM (MF), were intact and separated, with large intercellular spaces and irregular arrangements. The main factor that promotes mealiness is differences in pectin metabolism, which impact cell wall composition. The fluctuations in polygalacturonase (PG) and pectin methylesterase (PME) activity between mealy and non-mealy peaches were the main factor contributing to mealiness. However, the changes in cell wall metabolism that caused these fluctuations did not have a clear direction. Using transcriptome analysis and weighted gene co-expression network analysis (WGCNA), we were able to identify forty differentially expressed genes (DEGs) that are associated with mealy patterns. Among these DEGs, genes encoding PG were significantly upregulated in mealy peaches (CP14 and RM) compared to non-mealy peaches (CP13 and CM). PpPG1 was the main effector gene for mealiness, while PpPG2, PpEGase2, PpEXP1, PpEXP3, PpAGP2, PpIAA4, and PpABA2 were identified as candidate genes regulating peach mealiness. These findings provide a solid experimental basis for understanding the textual distinctions between mealy and non-mealy peaches. Full article