High salinity can severely inhibit the growth and development of watermelon (Citrullus lanatus L.). WRKY proteins are believed to mediate the adaptation of plants to abiotic stresses. Here, we identified the ClWRKY61 gene, which positively regulates the tolerance of watermelon to salt stress. Knockout of the ClWRKY61 reduced salt tolerance, while overexpression of the ClWRKY61 enhanced salt tolerance in watermelon according to phenotypic and physiological analyses. Yeast two-hybrid assays revealed that ClWRKY61 interacts with the ClLEA55 protein, and this interaction was further confirmed by luciferase complementation imaging, transient bimolecular fluorescence complementation, and GST pull-down assays. Knockout of the ClLEA55 resulted in lower salt tolerance compared to the wild-type plants. RNA-seq analysis indicated 421 up-regulated and 133 down-regulated genes in the ClWRKY61 knockout line under salt stress, containing 293 differentially expressed genes with W-box in their promoters. Thirteen genes encoding phytoene synthase, MYB transcription factor, sucrose synthase, alpha/beta-hydrolases superfamily protein, glutathione reductase, sugar transporter, LEA protein, WRKY transcription factor, ERF transcription factor, alpha-glucan water dikinase, and calcium-dependent protein kinase showed transcriptional changes in ClWRKY61 knockout line, ClWRKY61 overexpression line, and ClLEA55 knockout line under salt stress. These results provide an opportunity to mediate the regulation of salt stress in watermelon with WRKY proteins.

Mineral nutrients are essential for plant growth and development, playing a critical role in the mutualistic symbiosis between legumes and rhizobia. Legumes have evolved intricate signaling pathways that respond to various mineral nutrients, selectively activating genes involved in nodulation and nutrient uptake during symbiotic nitrogen fixation (SNF). Key minerals, including nitrogen, calcium, and phosphorus, are vital throughout the SNF process, influencing signal recognition, nodule formation, the regulation of nodule numbers, and the prevention of nodule early senescence. Here, we review recent advancements in nutrient-dependent regulation of root nodule symbiosis, focusing on the systemic autoregulation of nodulation in nitrate-dependent symbiosis, the roles of nodule inception-like proteins, and the function of essential nutrients and their associated transporters in legume symbiosis. Additionally, we discuss several key research areas that require further exploration to deepen our understanding of nutrient-dependent mechanisms in SNF.

Although it is well established that ethylene and light stimulate the process of chlorophyll degradation in mature apple peels, there is still a need for further exploration of the molecular mechanisms that regulate this process. This study identified MdEIL1 and MdHY5 as promoters of the chlorophyll degradation pathway in apple peels, activated by ethylene and light. Physiological and molecular tests demonstrated that MdEIL1 and MdHY5 are responsible for activating the expression of genes associated with chlorophyll degradation, including MdERF17, MdNYC1, MdPPH, and MdPAO. Furthermore, the interaction between MdEIL1 and MdHY5 proteins enhances their regulatory activity on the target gene MdERF17. Moreover, MdEIL1 binds to the promoter of MdHY5, resulting in the upregulation of its expression, which is further enhanced in the presence of the MdEIL1-MdHY5 protein complex. These findings indicate that MdEIL1-MdHY5 module acts as positive regulator mediating ethylene and light signals that promote chlorophyll degradation in apple peels.

The HAIRY MERISTEM (HAM) gene family encodes Type I and II GRAS domain transcriptional regulators in plants. Type II HAMs, predominantly expressed in meristems and regulated by microRNA171, are essential for maintaining undifferentiated meristems, a role conserved across various species. Conversely, the functions of Type I HAMs have been less characterized. In this study, we investigated the role of SlHAM4, a Type I HAM in tomato. CRISPR-induced SlHAM4 loss-of-function mutations (slham4CR) resulted in shoot and fruit abnormalities, which were fully reversed by reintroducing SlHAM4, driven by its native promoter, into the mutant background. Mutant abnormalities included simpler leaves and increased anthocyanin pigmentation in the leaf and sepal primordia, reminiscent of phenotypes observed in certain Arabidopsis mutants with compromised phloem. In addition, slham4CR plants produced significantly smaller fruits with a subset developing catface-like scars, attributed to tears that occurred in the pericarp of setting fruits. Using a GUS reporter gene driven by the native SlHAM4 promoter, we found that SlHAM4 is predominantly expressed in phloem tissues. Consistent with this, transcriptome analysis of mutant anthesis ovaries revealed specific downregulation of genes implicated in phloem development and function, particularly those expressed in companion cells. However, histological analysis showed no obvious abnormalities in phloem vasculature. Taken together, our data suggest that SlHAM4 plays a role in shoot and fruit development likely by regulating genes essential for phloem function.

The fading of flower color is caused by changes in anthocyanin content during flower development in many plants, including lilac (Syringa oblata). However, the molecular regulatory mechanism of this phenomenon is still poorly understood. UDP-glucose: flavonoid 3-O-glucosyltransferase (UFGT) has a pivotal role in the formation of stable anthocyanins. Here, SoUFGT1 and three transcription factors, SoMYB44, SobHLH130, and SoNAC72, were identified and verified to participate in anthocyanin production in lilac. Overexpressing SoMYB44 promoted SoUFGT1 expression in lilac petals. The yeast one-hybrid (Y1H) and dual-luciferase (Dual-LUC) assays demonstrated that SoMYB44 activated SoUFGT1, thereby bolstering anthocyanin accumulation. The overexpression and silencing of SoNAC72 in petals revealed that it facilitated anthocyanin accumulation. The Y1H and Dual-LUC assays verified that SoNAC72 was capable of directly binding to the SoMYB44 promoter to activate the latter's expression. In addition, SobHLH130 was also displayed to mediate anthocyanin accumulation in petals. By using yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays, the interaction between SoMYB44 and SobHLH130 was confirmed. These results corroborated that SoNAC72 regulates SoMYB44 expression, and SoMYB44 interacts with SobHLH130 to trigger SoUFGT1 expression in lilac, which then contributes to their anthocyanin accumulation. In sum, along with lilac flower development, the lower expression of SoNAC72 and SobHLH130 reduces SoMYB44 transcripts and depresses transcriptional regulation of SoUFGT1, thus diminishing anthocyanin biosynthesis, leading to the fading of petal color. These study's findings provide valuable new insight for understanding the formation and regulatory mechanisms of flower color in lilac.

The genus Paris, comprising a series of distinctive medicinal plants, has been utilized globally for its therapeutic properties over centuries. Modern pharmacological studies have demonstrated that secondary metabolites from Paris species exhibit significant pharmacological activities, including anticancer, hemostatic, anti-inflammatory, antimicrobial, and other effects. Additionally, the unique morphological traits and large genome size of Paris species have continuously captured the interest of botanists and horticulturalists. Nonetheless, the conservation of wild Paris populations is threatened due to the lengthy reproductive cycle and overexploitation, posing considerable challenges to their development and sustainable use. This review provides a comprehensive overview of the botanical characteristics, historical medicinal uses, pharmacological effects, and toxicity evaluation of secondary metabolites in Paris species. It also covers the molecular biological research conducted on the genus Paris and proposes key research questions and important directions for future solutions. We advocate the expansion and implementation of multi-omics approaches, as well as molecular and genetic technologies recently advanced in model plant research, to intensively study Paris species. This will facilitate the comprehensive understanding of gene function and molecular mechanisms underlying specialized metabolite formation in Paris.

Understanding how medicinal plants adapt to global warming, particularly through epigenetic mechanisms that modify phenotypes without changing DNA sequences is crucial. Scrophularia ningpoensis Hemsl., a traditional Chinese Medicine (TCM), produces bioactive compounds that are influenced by environmental temperatures, making it an ideal model for studying the biological basis of TCM geoherbalism. However, the adaptive potential of epigenetic marks in S. ningpoensis under varying temperatures remains understudied, partly due to the absence of a reference genome. Here, it was demonstrated that mild warm temperatures contribute to the metabolic accumulation and the cultivated migration of S. ningpoensis using a global dataset. A high-quality chromosome-level genome was assembled, and an atlas of epigenetic, metabolic, and transcriptomic profiles across different tissues. Transcriptome analysis identified 3401 allele-specific expressed genes (ASEGs) across nine tissues by comparing two haplotypes. ChIP-seq and BS-seq data from leaf and root tissues revealed that ASEGs are associated with distinct epigenetic patterns, particularly the active mark H3K36me3, which functions differently in these tissues. Notably, genes marked with H3K36me3 in iridoid synthesis pathway predominantly expressed in roots. Additionally, the histone methyltransferase SnSDG8 was identified to regulate ectopic H3K36me3 in iridoid biosynthesis in response to warming temperatures. Our results highlight the epigenetic mechanisms of global warming on herb-derived products, significant for medicinal plant breeding under temperature stress.

Grafting is a propagation method extensively utilized in cucurbits. However, the mechanisms underlying graft healing remain poorly understood. This study employed self-grafted watermelon plants to investigate how rootstock cotyledon affects healing. The complete removal of rootstock cotyledons significantly hindered scion growth, as evidenced by reductions in scion fresh weight and the area of true leaves. Physiological assessments revealed reduced callus formation, weaker adhesion forces, a more pronounced necrotic layer, and decreased rates of xylem and phloem reconnection at the graft junction when rootstock cotyledons were completely removed. Additionally, auxin levels at the rootstock graft junction notably decreased following cotyledon removal. In contrast, the exogenous application of indole-3-acetic acid (IAA) notably enhanced graft healing. Moreover, gene expression analysis of the PIN auxin efflux carriers in the rootstock cotyledons indicated significant activation of ClPIN1a postgrafting. Furthermore, we developed an improved Virus-Induced Gene Silencing (VIGS) system for cucurbits using seeds soaking method. This method achieved an infection success rate of 83% with 60%-75% gene silencing efficiency, compared to the 37% success rate with 40%-60% efficiency seen with traditional cotyledon infection. Combining our novel VIGS approach with cotyledon grafting techniques, we demonstrated that rootstock cotyledons regulate callus formation through ClPIN1a-mediated endogenous auxin release, thus facilitating graft union development. These findings suggest potential strategies for enhancing watermelon graft healing by manipulating rootstock cotyledons.

Incomplete lineage sorting (ILS) and introgression/hybridization (IH) are prevalent in nature and thus frequently result in discrepancies within phylogenetic tree topologies, leading to misinterpretation of phylogenomic data. Despite the availability of numerous tools for detecting ILS and IH among species, many of these tools lack effective visualization, or are time-consuming, or require prior predetermination. Here, we addressed these shortcomings by developing a fast-running, user-friendly tool called Phytop. By defining ILS and IH indices to quantify ILS and IH, this tool can detect the extent of ILS and IH among lineages with high reliability, and can visualize them based on the gene tree topology patterns constructed using ASTRAL. We tested Phytop extensively using both simulated and real data, and found that it enables users to quickly and conveniently estimate the extent of ILS and IH, thus clarifying the phylogenetic uncertainty. Phytop is available at https://github.com/zhangrengang/phytop and is expected to contribute to the intuitive and convenient inference of genetic relationships among lineages in future research.

Timed termination of floral meristem (FM) is crucial for proper development of floral organs and fruits. In Solanum lycopersicum, CLAVATA3 (CLV3)-WUSCHEL (WUS) feedback regulation maintains FM homeostasis in early stage of floral buds. It is known that the zinc finger protein SlKNUCKLES (SlKNU) functions to promote FM determinacy by directly repressing the stem cell identity gene SlWUS. However, how the robust FM activity is suppressed to secure fruit development is not fully understood in tomato. Here, we demonstrate that SlKNU also directly represses the stem cell marker gene SlCLV3 and the receptor gene SlCLV1 for FM determinacy control. Besides, loss-of-function mutants of SlKNU generated by CRISPR-Cas9 show increased fruit size of tomato. Moreover, overexpression of SlKNU attenuates the activities of the shoot apical meristem (SAM) and FM in Arabidopsis, but normal carpel development is still maintained. Hence, although the function of KNU in tomato and Arabidopsis may diverge during evolution, the role of KNU for FM determinacy and fruit size control is conserved and may potentially be useful for enhancing fruit yield of tomato.

Most Hydrangea species have inflorescences composed of two types of flowers: decorative flowers with showy sepals and plain nondecorative flowers. In wild plants of Hydrangea macrophylla, the decorative flowers are located at the periphery of the corymb, resulting in the lacecap phenotype. However, after the discovery of the mophead phenotype, in which decorative flowers are borne not only at the periphery but also on the entire inflorescence, it developed remarkably as a garden plant. In this study, we aimed to identify the gene controlling the inflorescence type and the mutations causing the mophead phenotype. Linkage analyses identified a SEPALLATA (SEP) homologous gene as a candidate gene, named TEMARY. We analyzed the genome sequences of TEMARY using several cultivars. The results revealed that the H. macrophylla cultivars had three types of loss-of-function alleles, and that the locus of the mophead cultivars consisted of only loss-of-function alleles. The phenotypes of 27 mophead cultivars could be explained by three types of loss-of-function TEMARY alleles. RNA-seq analysis and qRT-PCR analysis using two bud sport mutant lines related to the inflorescence type revealed that mophead mutants did not express TEMARY normally. These results suggest that TEMARY controls the inflorescence type and that mutations in this gene cause the mophead phenotype.

Shade tolerance is a key trait for cultivars in inter/relay-cropped soybeans in maize fields. Our previous genome-wide association study (GWAS) results on southern China soybean germplasm revealed that the shade tolerance was conferred by a complex of genes with multiple alleles. To complete our understanding of the shade tolerance gene system, GWAS with gene-allele sequences as markers (designated GASM-RTM-GWAS) was conducted in a recombinant inbred line (RIL) population between two extreme parents using the shade tolerance index (STI) and relative pith cell length (RCL) as indicators. Altogether, 211 genes, comprising 99 and 119 genes (seven shared) for STI and RCL, respectively, were identified and then annotated into a similar set of five biological categories. Furthermore, transcriptome analysis detected 7837 differentially expressed genes (DEGs), indicating plentiful DEGs involved in the expression of regulatory/causal GWAS genes. Protein-protein interaction (PPI) analysis and gene functional analysis for both GWAS genes and DEGs showed a group of interrelated causal genes and a group of interrelated DEGs; the former were included in the latter and their functions were interconnected as a gene network. For further understanding of the response of soybean to shade stress in a sequential connection, six chronological gene modules were grouped as signal activation and transport, signal-transduction, signal amplification, gene expression, regulated metabolites, and material transport. From the modules, 12 key genes were selected as entry points for further analysis. Our study provides an overview of the shade tolerance gene network as a new insight into a complex-trait genetic system, rather than the usual way of starting from a hand-picked single gene.

Despite the paramount importance in metal(loid) detoxification by phytochelatin synthase (PCS) genes, no comprehensive analysis of their evolutionary patterns has been carried out in land plants in general and in crops in particular. A phylogenetic large-scale analysis of gene duplication in angiosperms was carried out followed by in vitro recombinant protein assays as well as complementation analysis (growth, thiol-peptides, elements) of Arabidopsis cad1-3 mutant with four representative PCS genes from two model crop species, Malus domestica and Medicago truncatula. We uncovered a so far undetected ancient tandem duplication (D duplication) spanning the whole core eudicotyledon radiation. Complementation with PCS genes from both D-subclades from M. domestica and M. truncatula displayed clear in vivo conservation of the differences between D1 and D2 paralogous proteins in plant growth, phytochelatin, and glutathione pools, as well as element contents under metal(loid) stress. In vitro recombinant PCS analysis identified analogous patterns of differentiation, showing a higher activity of D2 PCS genes, so far largely overlooked, compared to their paralogs from the D1 clade. This suggests that in many other crop species where the duplication is present, the D2 copy might play a significant role in metal(loid) detoxification. The retention of both PCS paralogs and of their functional features for such long divergence time suggests that PCS copy number could be constrained by functional specialization and/or gene dosage sensitivity. These results uncover the patterns of PCS evolution in plant genomes and of functional specialization of their paralogs in the genomes of two important model crops.

Bottle gourd (Lagenaria siceraria (Molina) Standl) is a widely distributed Cucurbitaceae species, but gaps and low-quality assemblies have limited its genomic study. To address this, we assembled a nearly complete, high-quality genome of the bottle gourd (Pugua) using PacBio HiFi sequencing and Hi-C correction. The genome, being 298.67 Mb long with a ContigN50 of 28.55 Mb, was identified to possess 11 chromosomes, 11 centromeres, 18 telomeres, and 24 439 predicted protein-coding genes; notably, gap-free telomere-to-telomere assembly was accomplished for seven chromosomes. Based on the Pugua genome, the transcriptomic and metabolomic combined analyses revealed that amino acids and lipids accumulate during the expansion stage, while sugars and terpenoids increase during ripening. GA4 and genes of the Aux/IAA family mediate fruit expansion and maturation, while cell wall remodeling is regulated by factors such as XTHs, EXPs, polyphenols, and alkaloids, contributing to environmental adaptation. GGAT2 was positively correlated with glutamate, a source of umami, and SUS5 and SPS4 expression aligned with sucrose accumulation. This study provides a valuable genetic resource for bottle gourd research, enhancing the understanding of Cucurbitaceae evolution and supporting further studies on bottle gourd development, quality, and genetic improvement.

Mung bean (Vigna radiata), an essential annual legume, holds substantial value in global agriculture due to its short growth cycle, low input requirements, and nutritional benefits. Despite extensive domestication, the genetic mechanisms underlying its morphological and physiological evolution remain incompletely understood. In this study, we present a gap-free, telomere-to-telomere genome assembly of the mung bean cultivar 'Weilv-9′, achieved through the integration of PacBio HiFi, Oxford Nanopore, and high-throughput chromosome conformation capture (Hi-C) sequencing technologies. The 500-Mb assembly, encompassing 11 chromosomes and containing 28 740 protein-coding genes, reveals that 49.17% of the genome comprises repetitive sequences. Within the genome, we found the recent amplification of transposable elements significantly impacts the expression of nearby genes. Furthermore, integrating structural variation and single-nucleotide polymorphism (SNP) data from resequencing, we identified that the fatty acid synthesis, suberin biosynthetic, and phenylpropanoid metabolic processes have undergone strong selection during domestication. These findings provide valuable insights into the genetic mechanisms driving domestication and offer a foundation for future genetic enhancement and breeding programs in mung beans and related species.

Brassica rapa includes a variety of important vegetable and oilseed crops, yet it is significantly challenged by clubroot disease. Notably, the majority of genotypes of B. rapa with published genomes exhibit high susceptibility to clubroot disease. The present study presents a high-quality chromosome-level sequence of the genome of the DH40 clubroot-resistant (CR) line, a doubled haploid line derived from the hybrid progeny of a European turnip (ECD01) and two lines of Chinese cabbage. The assembled genome spans 420.92 Mb, with a contig N50 size of 11.97 Mb. Comparative genomics studies revealed that the DH40 line is more closely related to the Chinese cabbage Chiifu than to the turnip ECD04. The DH40 genome provided direct reference and greatly facilitate the map-based cloning of the clubroot resistance gene Crr5, encoding a nucleotide-binding leucine-rich repeat (NLR) protein. Further functional analysis demonstrated that Crr5 confers clubroot resistance in both Chinese cabbage and transgenic Arabidopsis. It responds to inoculation with Plasmodiophora brassicae and is expressed in both roots and leaves. Subcellular localization shows that Crr5 is present in the nucleus. Notably, the Toll/interleukin-1 receptor (TIR) domain of Crr5 can autoactivate and trigger cell death. In addition, we developed two Crr5-specific Kompetitive allele-specific PCR (KASP) markers and showcased their successful application in breeding CR Chinese cabbage through marker-assisted selection. Overall, our research offers valuable resources for genetic and genomic studies in B. rapa and deepens our understanding of the molecular mechanisms underlying clubroot resistance against P. brassicae.

The homeostasis of gibberellin (GA) is crucial for the normal development of anthers, but its underlying regulatory mechanisms are not clear. The GA-induced v-Myb myeloblastosis viral oncogene homolog (MYB) transcription factor LoMYB65 is involved in anther development. In this study, we screened and identified an interacting protein of LoMYB65, Lilium Oriental Hybrids BEL1-Like Homeodomain6 (LoBLH6). LoBLH6 was localized in both the nucleus and cytoplasm, and it interacted with LoMYB65 through its BELL domain, exhibiting transcriptional repression activity. LoBLH6 was continuously expressed during anther development, with particularly high expression in the mid and late stages. In situ hybridization revealed high expression of LoBLH6 in the tapetum and microspores, with the same tissue specificity as LoMYB65. Silencing of LoBLH6 in lilies resulted in abnormal anther development, reduced pollen, and increased GA content. The application of GA-induced phenotypes in the anthers and pollen of lily that were similar to the silencing of LoBLH6. Further research showed that LoBLH6 directly binds to the promoter of Lilium Oriental Hybrids GA 20-oxidase1 (LoGA20ox1) to suppress its expression, and coexpression with LoMYB65 enhances this repression. Additionally, GA treatment enhanced the interaction between LoBLH6 and LoMYB65 and their complex's inhibitory effect on downstream target genes. During the transition from microspores to mature pollen grains in lily anthers, GA levels maintain a steady state, which is disrupted by silencing LoBLH6, leading to abnormal pollen development. Overall, our results reveal that the interaction between LoBLH6 and LoMYB65 regulates anther development through feedback regulation of GA synthesis.

Commercial value of cucumber is primarily driven by fruit quality. However, breeding goals frequently focus on production constraints caused by biotic and abiotic stresses. As sources of resistances are often present in unadapted germplasm, we sought to provide morphological and genetic information characterizing the diversity of fruit quality traits present in the CucCAP cucumber core collection. These 388 accessions representing >96% of the genetic diversity for cucumber present in the US National Plant Germplasm System harbor important sources of resistances and extensive morphological diversity. Data were collected for skin color, length/diameter ratio (L/D), tapering, curvature, and spine density for young fruits [5-7 days postpollination (dpp)], and length, diameter, L/D, skin color, netting, seed cavity size, flesh thickness, hollowness, and flesh color for mature fruits (30-40 dpp). Significant associations of single nucleotide polymorphisms (SNPs) with each trait were identified from genome-wide association studies. In several cases, quantitative trait loci (QTL) for highly correlated traits were closely clustered. Principal component analysis, driven primarily by the highly correlated traits of fruit length, young and mature L/D ratios, and curvature showed a clear divergence of East Asian accessions. Significant SNPs contributing to the longest fruits, including development-stage specific QTL, were distributed across multiple chromosomes, indicating broad genomic effects of selection. Many of the SNPs identified for the various morphological traits were in close vicinity to previously identified fruit trait QTL and candidate genes, while several novel genes potentially important for these traits were also identified.

Cassava (Manihot esculenta Crantz) is a staple food of 800 million people in the tropical and subtropical regions of the world. Its industrial utilization for bioethanol, animal feed, and starch are still continuously expanding. It was not until the 1970s that significant scientific efforts were undertaken to improve cassava, despite its considerable economic and social significance. Shortening the breeding cycle and improving the breeding efficiency are always the focus of the cassava breeding study. In this review, we provide a global perspective on the current status of cassava germplasm resources and explore the diverse applications of cassava breeding methods from hybridization, polyploidy, and inbreeding to genomic selection and gene editing. Additionally, we overview at least six nearly complete cassava genome sequences established based on modern genomic techniques. These achievements have substantially supported the advancing of gene discovery and breeding of new cassava varieties. Furthermore, we provide a summary of the advancements in cassava’s functional genomics, concentrating on important traits such as starch quality and content, dry matter content, tolerance to postharvest physiological deterioration, nutritional quality, and stress resistance. We also provide a comprehensive summary of the milestone events and key advancements in cassava genetic improvement over the past 50 years. Finally, we put forward the perspective of developing genomic selection breeding model and super-hybrids of cassava through building inbreeding population and emphasize the generation of triploid cassavas, as well as using gene editing technology allowing cassava to be a tropical model plant to serve for basic biological research and molecular breeding.

Galloylated flavan-3-ols are key quality and health-related compounds in tea plants of Camellia section Thea. Camellia ptilophylla and Camellia sinensis are two representative species known for their high levels of galloylated flavan-3-ols. Building on our knowledge of galloyl catechin biosynthesis in C. sinensis, we now focus on the biosynthesis of galloylated phenolics in C. ptilophylla, aiming to elucidate the mechanisms underlying the high accumulation of these compounds in Camellia species. The phenolic compounds in C. ptilophylla were identified and quantified using chromatographic and colorimetric methods. Genes involved in polyphenol galloylation were identified by correlating gene expression with the accumulation of galloylated phenolics across 18 additional Camellia species and one related species using Weighted Gene Coexpression Network Analysis. Key findings include the coexpression of SCPL4/2 and SCPL5 subgroup enzymes as crucial for galloylation of catechins, while SCPL3 and SCPL8 showed enzymatic activity related to hydrolyzable tannin synthesis. Variations in the amino acid sequences of SCPL5, particularly in the catalytic triad (T-D-Y vs S-D-H) observed in C. ptilophylla and C. sinensis, were found to significantly affect enzymatic activity and epigallocatechin gallate (EGCG) production. In conclusion, this research provides important insights into the metabolic pathways of C. ptilophylla, emphasizing the critical role of SCPL enzymes in shaping the phenolic profile within the section Thea. The findings have significant implications for the cultivation and breeding of tea plants with optimized phenolic characteristics.

Tree and herbaceous peony are considerably important ornamental plants within the genus Paeonia, and hold substantial horticultural value. This review summarizes the progress in research on the senescence mechanisms of tree and herbaceous peony flowers, focusing on the regulation of gene expression, hormonal interactions, and the influence of environmental factors on senescence. Using high-throughput sequencing technologies, key genes displaying differential expression during senescence have been identified, and these play central roles in hormone signaling and cellular senescence. The interactions among plant hormones, including ethylene, abscisic acid, gibberellins, cytokinins, and auxins, also play key roles in the regulation of senescence. Adjustments in antioxidant levels, as well as water and energy metabolism, are critical factors in the delay of senescence. Environmental factors, including light, temperature, drought, and salt stress, also significantly affect senescence. Additionally, this review proposes future research directions, including the expansion of the molecular regulatory network of senescence in Paeonia, the use of gene editing technologies like CRISPR/Cas9, multiomics studies, and exploratory comparative research on spatial biology senescence mechanisms. These studies aim to deepen our understanding of the molecular mechanisms that underlie senescence in Paeonia and provide a scientific basis for cultivar improvement and postharvest management of these ornamental commodities in the horticultural industry.

The present research examined the regulatory function of MaEIL4 in the ripening process of banana. The findings demonstrated that MaEIL4 is a transcription factor with activity in the nucleus. The transient modulation of MaEIL4 expression in banana fruit slices has been found to exert a significant impact on maturation, either enhancing or inhibiting its progression, as shown by phenotype and endogenous gene expression. MaEIL4, MaMADS36, and MaACS7 were coexpressed in bananas. MaEIL4 interacted with both the MaMADS36 protein and the TGAA box of the MaMADS36 promoter to activate its expression. Moreover, MaMADS36 bound to the C(A/T)rG box of the MaACS7 promoter to regulate fruit ripening. The results have characterized the mechanism of MaMADS36’s response to upstream ethylene signals and established a new module, MaEIL4-MaMADS36-MaACS7, which transcriptionally regulates banana fruit ripening. This research has enhanced our comprehension of the pivotal function of MaMADS36 in controlling fruit maturation and thus suggests new strategies for fruit shelf life improvement and postharvest loss reduction.

Taxus L., an important ornamental, economic, and medicinal plant, is renowned for producing paclitaxel (Taxol®), a potent chemotherapeutic agent. The biosynthesis of paclitaxel involves intricate biosynthetic pathways, spanning multiple enzymatic steps. Despite advances, challenges remain in optimizing production methods. Microorganisms, particularly endophytic fungi, show potential in producing paclitaxel, though with limitations in yield and stability. The suspension culture of Taxus cells is a promising alternative, offering sustainable production, yet it requires further genetic and environmental optimization. Recent advancements in synthetic biology have enabled partial reconstitution of paclitaxel pathways in microbial and plant chassis. However, achieving complete biosynthesis remains an ongoing challenge. This review consolidates recent progress in paclitaxel biosynthesis, highlighting current limitations and future prospects for industrial-scale production.

Sandalwood (Santalum album), a culturally significant and economically valuable horticultural species, is renowned for its heartwood and essential oils enriched with sesquiterpene compounds such as santalol. Despite progress in elucidating the biosynthetic pathway of these valuable metabolites, the transcriptional regulation of this process, particularly under abiotic stress conditions, remains largely unexplored. Under drought conditions, we observed a marked increase in SaAREB6 expression, paralleled by elevated levels of santalols. Moreover, we identified SaCYP736A167, a cytochrome P450 mono-oxygenase gene, as a direct target of SaAREB6. Using electrophoretic mobility shift assays (EMSAs), microscale thermophoresis assays (MSTs), and dual luciferase assays (DLAs), we validated the precise and specific interaction of SaAREB6 with the promoter region of SaCYP736A167. This interaction leads to the upregulation of SaCYP736A167, which in turn catalyzes the final steps in the conversion of sesquiterpene precursors to santalols, thereby reinforcing the connection between SaAREB6 activity and increased santalol production during drought. Collectively, our work illuminates the previously uncharacterized role of SaAREB6 in orchestrating a transcriptional regulation that facilitates drought-induced santalol biosynthesis in sandalwood, presenting opportunities for genetic engineering strategies to improve heartwood and essential oil yields in this economically vital species.

Curcuma alismatifolia is an important ornamental plant of significant economic value, while the floral fragrance has been rarely investigated, leading to a lack of knowledge about the floral scent. By performing metabolomic and transcriptomic analyses, we investigated the variation of 906 volatile organic compounds (VOCs) in florets of eight C. alismatifolia cultivars and four different developmental stages of “Chiang Mai Pink” (CMP). The metabolite profiling revealed that the terpenoid group (213 out of 906) was the predominant VOC, accounting for 33.5% and 43.4% of total VOC contents in the florets of different cultivars and developmental stages, respectively. Sweet and woody were the predominant odors not only in different cultivars but also during developmental stages. The varied intensities of other odors contributed to forming odor diversities in C. alismatifolia floret. We uncovered seven terpenoid synthetase (TPS) genes and four MYB genes of significant association with the biosynthesis of terpenoids in eight cultivars and floret development, respectively. We performed an activity assay on four selected TPS genes and identified that Chr15HA1352 and Chr15HA2528 are responsible for the biosynthesis of α-farnesene. The significant association between the MYB gene (Chr03HA28) and seven terpenoids can be observed among different cultivars and during different developmental stages. These findings highlight the varying floral scents in different cultivars and floret development and suggest the potential roles of identified TPS and MYB genes in the biosynthesis of terpenoids in C. alismatifolia.

Polyphenols represent a significant class of nutrients in apples, contributing to human health and well-being. Among these, procyanidins stand out as the most prevalent polyphenolic compounds in apple fruits. These compounds are abundant in wild apples and generally low in modern apple cultivars. Therefore, it is crucial to identify and recover genetically lost genes that regulate polyphenol accumulation in order to improve the apple quality. To achieve this, we conducted a genome-wide association study (GWAS) on 15 traits related to polyphenol content, utilizing 134 Malus accessions. We identified 1204 marker-trait associations (MTAs) and 840 candidate genes, including known polyphenol biosynthetic and regulatory genes, such as MYB7, TT4, and HCT/HQT. Notably, we pinpointed a protein S-acyl transferase 10 (PAT10), which is significantly associated with procyanidin content. Through experiments with transgenic calli, we determined that apple (Malus domestica) MdPAT10 positively regulated procyanidin accumulation. Furthermore, we identified a 51-bp insertion variant (In-868) on the promoter of the PAT10, which influences its expression. Both a yeast one-hybrid (Y1H) assay and an electrophoretic mobility shift assay (EMSA) revealed that MdDof2.4 was able to bind to the promoter of MdPAT10 containing In-868 (MdPAT10_pro^In-868), but not to the promoter of MdPAT10 without In-868 (MdPAT10_pro). Moreover, MdDof2.4 promoted MdPAT10 (with MdPAT10_pro^In-868) expression and increased procyanidin accumulation in fruits. Overall, our results enhance the understanding of the biosynthetic regulation of apple polyphenols and provide a theoretical foundation and genetic resources for breeding apple varieties with optimal polyphenol content.

Pathogens significantly restrict the production of Brassica rapa (B. rapa L. ssp. Pekinensis), with climate change and evolving planting patterns exacerbating disease prevalence. Multichannel rapid diagnostic methods in the field can facilitate the early detection and control of diseases in B. rapa. Here, we established a multichannel lateral flow biosensor (LFB) combined with a CRISPR/Cas12a cleavage assay for the simultaneous detection of four B. rapa diseases. Key innovations of this study include: (1) High specificity and sensitivity, down to pathogen concentrations of 1.5 pg/μl—due to the optimization of crRNA secondary structure: the more stable the crRNA, the higher its detection sensitivity. (2) Optimized visual detection parameters. We identified ideal concentration ratios for the visual fluorescence detection system: 50 nM Cas12a, 50 nM crRNA, and 500 nM ssDNA fluorescent probe. Furthermore, the optimal concentrations of components on the LFB detection system were 3 μl SA-GNPs, 500 nM ssDNA test strip probe, 0.5 mg/ml biotin-BSA as the test line, and 1 mg/ml anti-FITC as the control line. (3) Field-Ready Cas-AIRPA Platform. We developed the on-site Cas-AIRPA platform for the simultaneous detection of B. rapa pathogens by combining rapid nucleic acid extraction and a four-channel lateral flow biosensor (4-LFB), which quickly provides disease-related information through a specific 2D barcode. Analysis of B. rapa samples in the field confirmed the suitability of the Cas-AIRPA platform for rapid (~25 min) and simultaneous on-site detection of four diseases of B. rapa. This platform can also be adapted to detect other plant diseases in the field.

Proanthocyanidins (PAs), anthocyanins, and flavonols are key flavonoids that play diverse roles in plant physiology and human health. Despite originating from a shared biosynthetic pathway, the regulatory mechanisms of PA biosynthesis and the cooperative regulation of different kinds of flavonoids remain elusive, particularly in flower tissues or organs. Here, we elucidated the regulatory network governing PA biosynthesis in Freesia hybrida ‘Red River®’ by characterizing four TT2-type MYB transcription factors, designated FhMYBPAs. Phylogenetic analysis, subcellular localization, and transactivation assays predicted their roles as PA-related activators. Pearson correlation analysis revealed significant correlations between FhMYBPAs and PA accumulation in various floral tissues and development stages. Functional studies demonstrated that FhMYBPAs activated PA biosynthesis by directly binding to the promoters of target genes, which can be enhanced by FhTT8L. Additionally, a hierarchical and feedback regulatory model involving FhTTG1, FhMYB27, and FhMYBx was proposed for PA biosynthesis. Furthermore, comparative analysis of flavonoid-related MYB factors involving FhPAP1, FhMYB5, FhMYBF1, and FhMYB21L2 highlighted their roles in regulating PA, anthocyanin, and flavonol biosynthesis, with some exhibiting versatile regulations. Overall, our findings provide insights into the spatio-temporal regulation of flavonoids in flowers and expand our understanding of MYB-mediated transcriptional regulation of specialized metabolites in plants.