Lotus, an economically significant aquatic crop within the genus Nelumbo (family Nelumbonaceae), includes the two extant species Nelumbo nucifera and Nelumbo lutea. Renowned for its ornamental, culinary, and medicinal value, lotus has seen notable advancements in genomics and molecular biology, particularly in reference genome sequencing and assembly, bioactive compound biosynthetic pathways, and molecular mechanisms underlying key traits. Critical genes linked to horticultural characteristics, edible quality, medicinal properties, and stress resilience have been identified and functionally validated. This review presents a thorough overview of recent molecular developments in lotus research, emphasizing genome sequencing and functional gene analysis. Additionally, it addresses prevailing challenges and future directions, providing valuable insights for foundational research and genetic enhancement of lotus.

Lysine acetylation is pivotal in regulating growth, development, and stress responses across numerous plant species. This modification, mediated by lysine acetyltransferases (KATs) and lysine deacetylases (KDACs), is both dynamic and reversible. Despite the economic significance of grape (Vitis vinifera) as a fruit crop, comprehensive insights into its KAT and KDAC gene families remain limited. In this study, 8 VvKATs and 14 VvKDACs were identified within the grape genome. Detailed analyses of their physicochemical properties, chromosomal distribution, phylogenetic synteny, evolutionary relationships, gene structures, and conserved motifs were conducted. Promoter region analysis revealed numerous cis-regulatory elements linked to light, hormone, and stress responsiveness. Transcriptomic data indicated that VvKATs and VvKDACs display distinct expression profiles across various tissues and developmental stages. Notably, VvSRT1, VvHDA19a, and VvHDA15 expression levels correlated strongly with anthocyanin accumulation in grape. Application of the deacetylase inhibitor sirtinol resulted in berry color changes and increased anthocyanin accumulation, suggesting that enhanced anthocyanin content in sirtinol-treated grape berry skins may result from post-translational modifications of genes involved in anthocyanin biosynthesis. These findings contribute to a deeper understanding of VvKAT and VvKDAC gene structures and properties, establishing a foundation for further exploration into lysine acetylation's role in fruit quality, particularly anthocyanin biosynthesis, in grape.

Model organisms have been instrumental in advancing discoveries in plant biology. Tomato (Solanum lycopersicum) is distinguished as a prominent model system due to its well-characterized genetics and economic significance as a crop. Micro-Tom (MT), an ornamental dwarf tomato variety, was adopted by the tomato research community as a model plant due to its short stature, fast life cycle, ease of genetic transformation, and ample genomic resources. Over the last 30 years, the use of MT has illuminated various facets of plant development, including the control of growth habit, glandular trichomes, leaf anatomy, and the formation of arbuscular mycorrhizal symbioses. We briefly summarize these contributions and point to further potential advances in the future.

Pathogenesis-related proteins (PRs) are essential for plant defense against both biotic and abiotic stresses. However, knowledge regarding PRs in pears remains limited. In this study, 637 PRs, classified into 16 families, were identified in Pyrus bretschneideri. Phylogenetic, sequence similarity, and secondary structure analyses enabled the classification of several PRs with conserved sequences, including PR-11, PR-8, PR-15, and PR-16. Genomic analysis revealed that the expansion of most PR families resulted from recent whole-genome duplication (WGD) events, occurring approximately 30–45 million years ago (Mya). Various gene duplication mechanisms have collectively contributed to the proliferation of PR families, with purifying selection indicated by the low Ka/Ks ratios. Examination of apoplastic fluid composition showed that only a subset of PRs was present in the apoplast. Transcriptomic data from Pyrus infected with Erwinia amylovora and Colletotrichum fructicola revealed the expression profiles of PR genes post-infection, underscoring the complexity of PR regulation. This study elucidates the evolutionary expansion, regulation, and functional roles of PRs in disease resistance, highlighting certain PRs as reliable markers of pear disease resistance. These findings offer valuable insights for future functional analyses and breeding strategies to enhance pear resistance to pathogens.

Late blight, caused by Phytophthora infestans, is one of the most devastative global plant threats. Pyramiding multiple resistance genes (R genes) was initially considered as a promising strategy for breeding broad-spectrum late blight-resistance potato varieties. However, stacking multiple R genes may induce detrimental effects on plant health. Fine-tuning the expression of R genes is critical for their effective stacking in potato breeding. This study confirms that low-level expression of individual potato late blight resistance genes like RB, R8, and Vnt1.1, controlled by the CaMV 35S promoter, does not trigger cell death (CD). However, co-expression of these genes in Nicotiana benthamiana leaves induces CD. Plant upstream open reading frames (uORFs) attenuate the translation of the downstream main ORF. We demonstrates that N. benthamiana open reading frame (NbuORF) and Solanumtuberosum L. open reading frame (StuORF) completely suppress green fluorescent protein (GFP) translation, whereas Arabidopsisthaliana open reading frames (AtuORFs) only partially inhibit GFP translation in N. benthamiana leaves. Simultaneous expression of AtuORFs or StuORF and RB, under the control of either pathogen-inducible potato vetispiradiene synthase gene 3 (PVS3) promoter or the 35S promoter, leads to inhibition of CD. Transgenic potatoes with 35S::RB exhibit superior late blight resistance compared to PVS3::RB transgenic lines. Plants expressing 35S::StuORF-RB show increased resistance, although slightly lower than that of 35S::RB transgenic plants. However, 35S::AtuORFs-RB and PVS3::AtuORFs-RB transgenic potatoes are susceptible to P. infestans, suggesting that AtuORFs and StuORF suppress RB translation in these plants. These findings highlight the potential of different promoter and uORF combinations for finely tuning R gene expression, which may optimize the balance between plant resistance and normal growth.

The SQUAMOUS PROMOTER BINDING PROTEIN-LIKE (SPL) gene family encodes plant-specific transcription factors that regulate diverse physiological processes, including growth, flowering, and stress responses. A total of 32 PaSPL genes were identified and characterized in the genome of Platanus × acerifolia, an ancient hexaploid species widely cultivated as a street tree. The PaSPL genes were classified into nine distinct groups based on their phylogenetic relationship. Gene structure examination revealed considerable variation in intron number and length among groups. Cis-regulatory element analysis indicated that the promoter regions of PaSPLs are enriched with light-responsive elements. Expression profiling across different tissues and developmental stages demonstrated that the PaSPL genes harboring a site targeted by microRNA156 exhibited stage-specific expression patterns, while those in the Groups II, III, V, and IX displayed tissue-specific expression. Notably, several PaSPL genes exhibited dynamic expression during floral transition, implicating their role in flowering regulation. Among them, PaSPL8a, a Group III member, was differentially expressed in flowerless germplasm resources. Functional characterization demonstrated that PaSPL8a overexpression in Arabidopsis thaliana accelerated flowering and upregulated key flowering regulators. These findings provide mechanistic insights into the function of PaSPLs in P. × acerifolia and establish PaSPL8a as a positive regulator of flowering.

Citrus canker, caused by Xanthomonas citri subsp. citri (Xcc), represents a significant threat to the global citrus industry. LATERAL ORGAN BOUNDARIES 1 (LOB1) has been identified as a key gene involved in the development of citrus canker in susceptible varieties. However, the role and molecular mechanisms of LOB1 in disease-resistant varieties, such as Kumquat (Fortunella spp.), remain poorly understood. In this study, transgenic kumquat plants with either Citrus sinensis LOB1 (CsLOB1) overexpression or RNAi-mediated silencing were obtained to investigate the function and molecular basis of LOB1 in kumquat resistance to Xcc. Overexpression of CsLOB1 in kumquats resulted in dwarf phenotype with reduced leaf size, increased branching, and numerous pustule-like bulges resembling citrus canker. Microscopic analysis revealed that these bulges were due to the excessive proliferation of mesophyll cells, along with spongy cell enlargement and palisade cell shortening. Resistance assays showed that CsLOB1 overexpression promoted kumquat susceptibility to Xcc, while the resistance remained stable in the RNAi lines. RNA-seq analysis revealed that CsLOB1 significantly upregulated immune response-related genes in kumquat. Furthermore, CsLOB1 was shown to regulate kumquat immunity through modulation of indole- 3-acetic acid-amido synthetase 3.17 (GH3.17), elongation factor tu receptor (EFR), mitogen-activated protein kinase kinase 5 (MKK5) and ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1). Taken together, these findings demonstrate that CsLOB1 not only promotes citrus canker development by altering cellular states and hormone signaling but also activates immune responses in kumquat. Our work offers insights into harnessing LOB1 in the breeding of canker-resistant varieties in citrus.

MicroRNA164 (miR164) is a highly conserved miRNA that targets NAC transcription factors in plants. This study explores its role in regulating stress responses in petunia by generating MIR164 overexpression (MIR164-ox) and miR164 suppression (miR164-STTM) lines. Under heat stress, MIR164-ox lines exhibited enhanced tolerance, while miR164-STTM lines showed reduced tolerance with growth reduction in both shoots and roots. Conversely, under salinity stress, miR164-STTM lines displayed improved tolerance, while MIR164-ox lines were more sensitive, suggesting that miR164 may have a differential regulatory effect on heat and salinity stress responses. To further investigate the molecular mechanisms underlying these differential stress responses mediated by miR164, we conducted a bioinformatic analysis of the NAC transcription factor family in Petunia, the primary targets of miR164. A genome-wide analysis of the NAC gene family in Petunia identified 80 NAC genes in P. axillaris and 91 in P. inflata. Phylogenetic analysis revealed nine distinct clades, indicating both conserved and divergent functions of NAC proteins. Expression analysis of miR164-targeted NAC genes showed tissue- and stress-specific patterns. Protein–protein interaction (PPI) network and Gene Ontology (GO) enrichment analyses provided insights into the potential functions of NAC proteins in petunia, particularly in secondary cell wall biogenesis and xylem development. Real-time qRT-PCR analysis revealed differential expression of specific NAC genes in miR164 transgenic lines under heat and salinity stress, with NAC06 and NAC39/NAC54 showing the most pronounced changes, suggesting their potential involvement in heat and salinity stress responses, respectively. Taken together, our findings suggest that miR164 plays a crucial role in regulating NAC gene expression and stress responses in petunia, providing a foundation for further functional characterization of miR164-NAC regulatory modules in plant stress adaptation.

The plant hormone abscisic acid (ABA) regulates fruit growth, development, and ripening, playing a pivotal role in fruit quality during non-climacteric ripening. As a typical non-climacteric fruit, strawberries rely on ABA to promote ripening. However, the optimal concentration for ABA treatment and the mechanisms through which ABA signaling influences gene targets that determine key quality attributes, such as sugar-acid balance and coloration, remain poorly understood. This study examined the effects of exogenous ABA and its inhibitor nordihydroguaiaretic acid (NDGA) on white-stage 'Benihoppe' strawberries. Phenotypic observations and quality measurements were conducted. Results revealed that 0.2 mM ABA treatment most significantly increased soluble sugar content, anthocyanin levels, and the sugar-acid ratio while decreasing fruit firmness and organic acid concentrations. In contrast, NDGA treatment produced opposite effects. RNA-seq analysis further identified differentially expressed genes primarily involved in flavonoid biosynthesis and fructose-mannitol metabolism, suggesting alterations in carbon metabolism within the fruit. These findings elucidate the role of ABA signaling in shaping strawberry quality during fruit development and highlight key genes as potential targets, providing a theoretical basis for advancing strawberry breeding and farming practices.

Chrysanthemum (Chrysanthemum ×  morifolium Ramat.) is a widely cultivated ornamental species, among which green-flowered cultivar representing rarity and distinctiveness. However, the underlying mechanisms governing the formation and regulation of green color remain poorly understood. In this study, exposure to high-intensity light resulted in the loss of green coloration in green chrysanthemum, while low-intensity light preserved it during flower opening in chrysanthemum ‘Lv Dingdang’. A R1-type MYB transcription factor, CmREVEILLE2 (CmRVE2), was identified through transcriptomic analysis of flowers subjected to different light intensities (3,000 Lux for low light, LL; 6,000 Lux for moderate light, ML; and 12,000 Lux for high light, HL). CmRVE2 expression was significantly upregulated under HL conditions, while its expression was lower under LL compared to ML. Additionally, CmRVE2 was upregulated by abscisic acid (ABA) and downregulated by gibberellin (GA). Virus-induced gene silencing (VIGS) of CmRVE2 led to a marked increase in chlorophyll content and the upregulation of chlorophyll biosynthesis-related genes, while CmRVE2 overexpression resulted in the opposite trend. Yeast one-hybrid, electrophoretic mobility shift assays (EMSA), and transient activation assays demonstrated that CmRVE2 directly bound to the promoter of CHLI1, a gene encodes magnesium chelatase I subunit in chlorophyll biosynthesis. Furthermore, CmRVE2 repressed the expression of MAGNESIUM-PROTOPORPHYRIN IX MONOMETHYL ESTER OXIDATIVE CYCLASE1 (CRD1) and PROTOCHLOROPHYLLIDE OXIDOREDUCTASE1 (PORA1), thereby inhibiting chlorophyll synthesis. These findings provide new insights into how CmRVE2 mediates light signaling to negatively regulate chlorophyll biosynthesis in chrysanthemum flowers.

Metabolomics, a rapidly evolving field, has revolutionized horticultural crop research by enabling comprehensive analysis of metabolites that influence plant yield, growth, quality and nutritional value. The integration of web-based resources, including databases, computational tools and analytical platforms has significantly enhanced metabolomics studies by facilitating data processing, metabolite identification and pathway analysis. Moreover, the application of machine learning algorithms to these web resources has further optimized data interpretation, enabling more accurate prediction of metabolic profiles. Publicly available reference libraries and bioinformatic tools support precision of breeding, postharvest quality assessment and ultimately improving crop yield and sustainability. In this mini-review, we explore the current status of the diverse range of plant metabolomics databases in horticultural crops, highlighting the synergy between machine learning and traditional bioinformatics methods, their applications, challenges and future prospects in advancing plant science and agricultural innovation.

Carnations (Dianthus spp.), among the most significant ornamental flowers globally, are widely appreciated for their aesthetic appeal. Floral scent, a key quality attribute, leaves a lasting impression on consumers. However, the release patterns and regulatory mechanisms of the major scent components in contemporary carnation cultivars remain poorly understood. Gas Chromatography-Mass Spectrometry (GC–MS) and RNA sequencing identified 14 volatile organic compounds (VOCs) as the primary aromatic constituents in the fragrant ‘Scarlet Queen’. Notably, eugenol, β-caryophyllene, and cis-3-hexenyl benzoate are the principal contributors. VOC emission in ‘Scarlet Queen’ predominantly occurs at the full bloom (S6) and early senescence (S7) stages. Additionally, this study elucidated the metabolic pathways of key aroma compounds and pinpointed crucial genes involved in their biosynthesis, including phenylalanine ammonia-lyase (PAL), coniferyl alcohol acyltransferase (CFAT), and two eugenol synthase (EGS) genes for eugenol, as well as isopentenyl diphosphate isomerase (IDI) and terpene synthase (TPS) genes for β-caryophyllene. Furthermore, the expression patterns of DcaMYB78, DcaMYB84, and DcaMYB90 correlated with the eugenol release profile, as confirmed by k-means clustering and co-expression network analysis. This study not only delineates the principal aromatic compounds and their biosynthetic pathways in carnations but also provides a vital framework for improving the scent quality of cut carnations.

Pepper (Capsicum annuum L.) is a globally significant vegetable crop, with China accounting for one-third of the world's total pepper production. The genetic diversity of pepper germplasm resources is critical for further research and breeding efforts. In this study, 50 pepper accessions were sampled and analyzed to assess genetic diversity. A comprehensive analysis was conducted using the coefficient of variation, principal component analysis (PCA), and cluster analysis to evaluate the diversity and variation in 33 phenotypic traits across the accessions. Coefficient of variation for average fruit weight reached 102.91%, highlighting significant differences among the pepper accessions. Correlation analysis revealed a strong negative relationship between average fruit weight and both soluble solids content and ascorbic acid content. PCA indicated that the first three principal components explained 92.73% of the total variation, with key traits such as leaf color, fruit weight, and fruit color being most influential. Cluster analysis classified the 50 pepper accessions into six distinct groups. Additionally, genetic diversity analysis using molecular markers offers notable advantages due to its insensitivity to environmental factors and tissue specificity. Eleven highly polymorphic simple sequence repeat (SSR) markers were employed to assess the genetic diversity of the accessions. These markers allow for the detection of target genes at the seedling stage, enabling early selection of individuals with desirable traits and significantly expediting the breeding process. The findings of this study provide a solid theoretical foundation for the selection, utilization, and breeding of pepper germplasm resources.

Nodal culture is a powerful plant tissue culture technique addressing critical challenges such as desiccation, microbial contamination, and the limited viability of explants, particularly in recalcitrant horticultural crops like Garcinia mangostana, Artocarpus heterophyllus, Cucumis melo, Citrus limon, Kinnow mandarin, and Coffea arabica. This method utilizes sterilized immature nodal explants, with regeneration induced through the precise application of growth regulators, primarily auxins and cytokinins, to media such as Driver-Kuniyuki (DKW), Woody Plant Media (WPM), and Murashige and Skoog (MS) under controlled conditions. These regulators significantly enhance both shoot and root regeneration, thus reducing the generation time for difficult-to-regenerate species. Reactive oxygen species (ROS) play a pivotal role in regulating cell division and hormone signaling during regeneration. Additionally, transcription factors such as wound-induced dedifferentiation 1 (WIND1), WUSCHEL (WUS), Enhancer of Shoot Regeneration 1 (ESR1), Cup-shaped Cotyledon 1 and 2 (CUC1, CUC2), and Lateral Organ Boundaries Domain 16 (LBD16) are integral to callus induction and organogenesis. Genetic variation observed in regenerated populations reflects the complexity of these regulatory networks and underscores the need for further investigation. Notably, nodal culture provides a promising alternative to conventional tissue culture methods, particularly in facilitating CRISPR/Cas9-mediated genetic modifications in recalcitrant crops. This technique enhances the efficient regeneration of transgenic horticultural crops, overcoming significant barriers to transformation. Future research should focus on refining nodal culture protocols across a broader spectrum of horticultural species, improving gene editing efficiency, and integrating this approach with advanced breeding technologies for targeted trait development and sustainable crop improvement.

The process of fruit development involves the initiation of fruit set, followed by growth, maturation, and ripening. Auxin, a key plant hormone, regulates nearly all aspects of plant growth and development. In concert with gibberellic acid (GA), auxin promotes cell division and expansion, crucially influencing fruit initiation and growth post-fertilization. Fruit ripening is a multifaceted process. While ethylene remains the dominant phytohormone in climacteric fruits, recent research highlights the increasing role of auxin. Although auxin inhibits the climacteric ripening of fruits like tomatoes, emerging studies suggest its stimulatory role in the ripening of other climacteric fruits, such as apples and peaches. This review examines auxin's involvement in the development of reproductive organs, fruit initiation and growth, ripening, shaping, and abscission, emphasizing its distinct regulatory effects in climacteric fruits. Furthermore, it explores potential molecular mechanisms and highlights future research avenues focused on auxin's role in fruit development and ripening.

Summer tea (Camellia sinensis) is less favored due to its inferior taste compared to spring tea. The application of selenium (Se) has proven effective in enhancing tea flavor. However, the specific mechanisms underlying the Se-mediated improvement of summer tea quality remain unclear. This study examines the alteration of trace elements, the metabolome, and the transcriptome in tea plants subjected to Se treatment. Se application increased the concentrations of B, Fe, Zn, and Se in the summer tea shoots of certain cultivars. Metabolomic analysis revealed that exogenous Se elevated the levels of theanine and flavonoids while reducing the catechin bitterness taste index in most of the selected cultivars. Transcriptomic analysis further demonstrated that Se treatment modulated the expression of CsSULTRs, CsPHTs, CsIRTs, CsZIPs, and CsBOTs, indicating a potential link between the accumulation of these elements and the corresponding transporter genes. Based on qRT-PCR results, CsSULTR1.1, 1.2, and 4.1 are likely involved in Se transport. Additionally, differentially expressed genes (DEGs) were predominantly enriched in the flavonoid and amino acid biosynthesis pathways following Se treatment. In conclusion, the addition of Se enhances the flavor profile of summer tea by modulating genes participating in flavonoid and amino acid metabolism, underpinning its potential for improving summer tea quality.

Tea plants (Camellia sinensis) demonstrate significant tolerance to aluminum (Al) and even require it for optimal growth. However, the mechanisms involved remain poorly understood. This study explored the responses of tea plants to varying Al concentrations at both metabolomic and transcriptomic levels. Compared to 0 mM Al treatment, low Al concentrations (0.4 mM) enhanced root vitality by 8.91%, while higher Al concentrations (10 and 100 mM) reduced root vigor by 19.31% and 76.81%, respectively. In a similar pattern, the electron transfer rate in leaves remained stable under low Al levels but significantly decreased under high Al conditions. Transcriptomic analysis showed a downregulation of genes associated with DNA replication in both Al-deficient and Al-toxic conditions, suggesting that Al may play an essential role in maintaining genomic stability during tea plant growth. Weighted gene co-expression network analysis (WGCNA) identified 84 hub genes potentially involved in Al tolerance, including aluminum sensitive 3 (CsALS3), xyloglucan endotransglucosylase/hydrolase protein 23 (CsXTH23), and arginine decarboxylase 2 (CsADC2). Metabolomic analysis revealed that high Al concentrations suppressed pathways related to amino acid, lipid, and carbohydrate metabolism, yet several metabolites, such as putrescine, histidine, and epigallocatechin, were upregulated under high Al conditions. Combined pathway analysis indicated an upregulation of the putrescine biosynthetic pathway under high Al, highlighting its critical role in Al detoxification in tea plants. Overall, this study provides a comprehensive understanding of effects from Al on tea plant physiology, offering molecular and physiological insights into Al tolerance mechanisms and theoretical bases for optimizing tea cultivation in acidic soils.

The centromere plays a pivotal role in the karyotype of citrus chromosomes. However, the development of markers capable of distinguishing individual chromosomes remains a challenge. Oligo-FISH provides an efficient method for generating citrus centromere-specific markers. Accurate identification of centromere positions is a prerequisite for marker development. In this study, centromere locations on each chromosome were recalibrated using previously published ChIP-seq data of CsCENH3, aligned with the high-quality sweet orange genome (SWO v3). A total of 16,827 45-nucleotide oligos spanning nine centromeric regions were screened, with each region containing between 868 and 5,965 oligos, yielding an approximate density of one oligo per kilobase. Oligos from the centromere regions of chromosomes 1 (Chr1) and 4 (Chr4) were randomly selected to synthesize centromere-specific probes. Dual-color FISH assays on mitotic and meiotic chromosomes revealed distinct signals from each probe on homologous chromosomes. These signals coincided with those from the previously identified centromeric marker CL34contig88, demonstrating the ability of the probes to differentiate centromeres of individual chromosomes. Furthermore, chromosome painting was conducted across several citrus species, including Citrus sinensis, C. reticulata, C. limon, C. grandis, Fortunella japonica, and Poncirus trifoliata, with centromeric signals for Chr1 and Chr4 observable in all species. Chr1 and Chr4 exhibited characteristics of submetacentric and metacentric chromosomes, respectively, based on arm ratios, reflecting the conserved karyotypic structure of these chromosomes across citrus species and their consistent centromeric oligo sequences. These findings underscore the potential of centromere-specific probes in advancing citrus cytology and provide a robust foundation for exploring centromeric sequence evolution in citrus.

Kiwifruit (Actinidia Lindl.) is a valuable fruit tree species, with its cold resistance being influenced by leaf structure and various cell types. Despite significant progress in understanding the cold stress response during the last decade, the mechanisms underlying the formation of distinct cold-resistant cell types in kiwifruit, particularly at the single-cell level, remain poorly understood. In this study, single-cell RNA sequencing (scRNA-seq) of leaves from ‘Hongyang’ (HY, A. chinensis, cold sensitive) and its transgenic line with overexpressed AaBAM3.1 (designated as HT, cold resistant) was employed to construct a single-cell transcriptional atlas to investigate the cell heterogeneity of two kiwifruit genotypes exhibiting different cold resistance capacities. A total of 5,611 and 13,466 single cells were obtained from HY and HT, respectively. The cells were classified into eight clusters based on gene expression patterns, and key genes associated with specific cell types in both genotypes were identified. Notably, pseudotime trajectory analysis revealed distinct developmental paths for guard cells and mesophyll cells. Additionally, a transcription factor, AaTIFY, exhibited genotype-specific expression and negatively regulated cold resistance. In summary, these results demonstrate that scRNA-seq offers valuable insights into cell differentiation and development in kiwifruit with varying cold resistance at the single-cell level and highlights novel genes related to cold tolerance in kiwifruit.

Eruca sativa, or arugula, a leafy vegetable from the Mediterranean region, is gaining popularity worldwide. However, its domestication history and genetic diversity remain poorly understood. This study investigates the genetic background of globally collected arugula accessions, their domestication history, and the implications for future breeding strategies. Among the 202 arugula accessions analysed, four distinct groups were identified. Group 1 (G1) appears to be misidentified as arugula and is more closely related to radish (Raphanus sativus) and Brassica spp. Group 2 (G2), Group 3 (G3), and Group 4 (G4) likely represent arugula populations evolved separately, with G4 showing greater genetic isolation and drifts. Geographically, G2 accessions cluster in Europe, G3 in North Africa, and G4 in South Asia (furthest from the Mediterranean region). Phylogenetic and demographic history analyses suggest that G2 is more ancient than G3 and G4. While G3 and G4 share a more recent common ancestor, small scale introgression between G2 and G3 was detected. Selective sweeps signatures revealed 12 genes under positive selection in G4 compared to G2, and these 12 genes are likely associated with adaptive divergency, suggesting that arugula has not undergone stringent artificial selection. A potential hybrid zone between Turkey, Israel, and Iran was identified. Accessions from this zone may serve as a valuable resource for screening new arugula varieties with superior traits. Although 202 accessions were studied, some exhibited high genetic similarity. To enhance germplasm diversity for breeding, future efforts should prioritize expanding collections in regions where arugula has naturalized.

Drought stress induces premature wilting and accelerates petal senescence, thereby diminishing the commercial value of roses. Rosa banksiae, renowned for its drought tolerance, serves as an optimal model for investigating drought-responsive mechanisms within the genus Rosa. In this study, a comparative analysis was conducted to evaluate the drought tolerance of petals from R. banksiae f. lutea (RbY) and R. banksiae var. banksiae (RbW) under treatment with 20% polyethylene glycol 6000. Physiological assessments demonstrated that RbY exhibited superior drought tolerance relative to RbW. Integrated transcriptomic and metabolomic analyses identified several drought-responsive pathways common to both genotypes, including isoflavonoid biosynthesis, glutathione metabolism, and betaine biosynthesis. Remarkably, pathways associated with flavonoid and coumarin biosynthesis, glutathione metabolism, betaine biosynthesis, and phytohormone signaling were implicated as major contributors to RbY’s enhanced dehydration tolerance. These pathways corresponded with elevated levels of metabolites such as γ-glutamylcysteine, celosianin II, 2''-(6''-p-coumaroylglucosyl) quercitrin, imperatorin, and jasmonic acid-isoleucine. Subsequent quantitative real-time polymerase chain reaction validation revealed that key genes within these pathways, including cinnamate 4-hydroxylase (C4H), chalcone synthase (CHS), chalcone isomerase (CHI), phospholipase A1 (LCAT3), allene oxide synthase (AOS), ascorbate peroxidase (APX), and glutathione S-transferase (GSTs), may underlie the intensified drought response observed in RbY. Collectively, the findings suggest that the superior drought tolerance of RbY is orchestrated through a coordinated defense system involving antioxidative mechanisms, hormonal regulation, and osmotic adjustment. These insights provide valuable knowledge for elucidating the molecular underpinnings of drought adaptation in rose petals and establish a foundation for breeding drought-resilient rose cultivars.

Guangchenpi (GCP, Citrus reticulata), a well-known traditional Chinese medicine and homology food condiment, is predominantly consumed in Asia. Extending its aging process enhances its medicinal properties, flavor, and profitability. However, pinpointing the aging year of GCP remains a bottleneck of the industry. This study represents the first comprehensive characterization of 32 glycosidically bound volatiles in GCP, employing a combination of Amberlite XAD-2 resin extraction and gas chromatography-mass spectrometry (GC–MS) analysis. The identified compounds include bioactive substances such as 5-hydroxymethylfurfural and acorenone B. Fourteen glycosidically bound volatiles exhibited a significant correlation with the aging duration of GCP. Additionally, the aging process was associated with dynamic shifts in the microbial community, notably an enrichment of Lactobacillus and Oceanobacillus, which potentially influenced the volatile compound profile. Machine learning integration revealed a model based on the content and relative weight of the 14 glycosidically bound volatiles, demonstrating high accuracy in determining aging years of GCP. This model could aid in detecting adulteration and standardizing the GCP market.