In fruit crops, sugar accumulation is a highly orchestrated process that requires coordination among numerous sugar transporters and metabolic enzymes. However, much remains unknown about how the underlying mechanisms coordinating these genes contribute to controlling sugar movement across the apoplasmic gap and sugar accumulation in fruits. In this study, we identified a cytoplasmic membrane–localized sucrose transporter, VvSWEET15, from grapevine (Vitis vinifera L.), whose expression was associated with significant hexose accumulation during berry ripening and exhibited expression patterns similar to those of the sucrose synthase VvSUSY3. Although overexpressing VvSWEET15 increased fructose and glucose concentrations in transgenic grape calli, it unexpectedly decreased that of sucrose. RNA sequencing (RNA-seq) and expression analyses revealed that VvSUSY3 was up-regulated in the transgenic calli lines overexpressing VvSWEET15. Further analyses suggested that the increased hexose concentration in the transgenic lines correlated with the up-regulation of VvSUSY3 expression. Suppressing VvSUSY3 in the VvSWEET15-overexpressing grape calli reduced the positive effect of VvSWEET15 on sugar accumulation. These findings demonstrate that the increased sucrose transport into the cytosol, mediated by VvSWEET15, up-regulates sucrose synthase VvSUSY3 expression to promote hexose accumulation in the berries. Thus, our study establishes a framework for understanding how sugar transporters and metabolic genes are integrated to facilitate sugar partitioning and accumulation in plants.

The ATP-binding cassette (ABC) gene family plays a crucial role in plants by mediating the transport of various molecules, contributing to development, stress responses, and secondary metabolism. Here, 159077 ABC genes were identified from 1108 plant species. Comparative analysis revealed that higher plants had more ABC genes compared to algae plants. The ABCG1, ABCG4, and ABCG8 subfamilies originated in land plants and subsequently underwent distinct evolutionary pathways. Motif 1 and motif 9 demonstrated a conserved high-frequency pattern across different lineages. The expansion of ABC family mainly occurred through dispersed and whole-genome duplication in higher angiosperms, and full-length transposons may mediate the neofunctionalization of these genes. The pan-ABC family analysis of 12 tomato accessions revealed more relaxed selective pressures in dispensable ABC genes. The ABC genes of Arabidopsis thaliana exhibited stronger responsiveness and connectivity degree under salt stress. To facilitate further research, we established the PlantABC database (http://biodb.com.cn/PlantABC/index.html), which contains comprehensive genomic and evolutionary information about plant ABC genes. This study provides valuable perspective and resources for advancing research on the evolution and functions of plant ABC genes.

Rosa beggeriana is a Central Asiatic native ornamental shrub with extreme freezing tolerance, which has been applied to cold-tolerant rose breeding through interspecific hybridization. Over recent years, several rose genome assemblies have been released, revealing the mechanisms of genomics-based modern rose breeding and ornamental traits [1–3]. Despite the increasing availability of rose genomes, the practical utility of cold tolerance-associated genes unique to wild germplasm remains largely elusive. Our study addresses this gap by presenting complete and haplotype-resolved assemblies for cold resistance mechanisms and adaptation to habitats. This breakthrough elucidates the molecular mechanisms of cold tolerance in R. beggeriana and establishes a theoretical foundation for breeding cold-tolerant roses.

Drought stress severely limits apple cultivation. Malus sieversii, a wild ancestor of domesticated apple, provides a valuable genetic resource for improving drought tolerance in cultivated apple rootstocks. Although plant-specific GRAS [GIBBERELLIC-ACID INSENSITIVE (GAI), REPRESSOR of GAI, and SCARECROW] transcription factors (TFs) are known to regulate development and stress responses, their precise functions and mechanisms in apple remain largely unexplored. Here, we demonstrated that overexpression of MsSCL28.5, a GRAS TF from M. sieversii, substantially enhances drought tolerance of rootstock ‘M26’ (Malus domestica). Transgenic plants exhibited increased adventitious root (AR) growth and improved reactive oxygen species scavenging capacity. MsSCL28.5 directly binds to the promoters of MdLBD16a and MdLBD21b, key genes regulating AR growth. We further identified the TF MdMYB87 as an interacting partner of MsSCL28.5. The resulting MsSCL28.5–MdMYB87 complex synergistically activates the transcription of MdLBD16a/21b. Additionally, grafting experiments confirmed that MsSCL28.5-overexpressing rootstocks systemically enhance the drought resistance of non-transgenic scions. Furthermore, we discovered that comprising reduced methylation of the SCL28.5 promoter coupled with a TATA-box insertion in the MYB87 promoter collectively contributes to the superior drought tolerance observed in M. sieversii. Our findings present molecular insights into how transcriptional regulation of SCL28.5-MYB87 module are integrated into drought response of different apple rootstocks.

Humans cannot synthesize ascorbic acid (AsA), making dietary intake from fruits and vegetables crucial. Kiwifruit is a rich source of AsA; however, the genetic and regulatory basis for its accumulation is not fully elucidated. This study integrates quantitative trait locus (QTL) mapping, transcriptomics, and functional characterization to uncover a novel regulatory role of AaAGPase, encoding an ADP-glucose pyrophosphorylase, in determining AsA levels in kiwifruit. A significant QTL was mapped on chr10 in a tetraploid Actinidia arguta biparental population, explaining 11.46% of the variation in AsA levels. Based on gene annotation and expression differences between high-and low-AsA genotypes, ADP-glucose pyrophosphorylase (AGPase) was identified as a negative regulator. Our results indicated that a promoter variation in AGPase affects both AsA and starch levels. Overexpression of AaAGPase in transiently transformed fruit and transgenic kiwifruit plants led to reduced AsA levels via downregulation of key genes in the L-galactose pathway while increasing starch levels. Conversely, virus-induced gene silencing of AaAGPase resulted in increased AsA but decreased starch levels. Additionally, we identified the Golden 2-like transcription factor, AaGLK, which binds to and activates the AaAGPase promoter. Manipulating AaGLK expression resulted in variations in AsA levels by regulating AaAGPase expression. These findings reveal that the AaGLK-AaAGPase module negatively regulates AsA biosynthesis in kiwifruit. Additionally, we developed a molecular marker based on the sequence variation of AGPase promoter for marker assisted selection. In summary, our study revealed that AaAGPase, which is transcriptionally activated by AaGLK, plays a novel role in determining AsA levels through carbohydrates substrates competition.

Oceanian citrus species, including wild taxa native to Australia and Papua New Guinea, form a genetically distinct clade within the Citrus L. (1753) genus. These species remain largely underexplored, despite their adaptation to diverse environments and relevance for citrus improvement. To support their use in breeding and evolutionary studies, we generated a high-quality, chromosome-scale genome assembly of an Australian finger lime accession (SRA 1002), a natural interspecific hybrid. The genome was assembled using long-read sequencing, optical mapping, and a high-density genetic map, resulting in nine pseudomolecules covering over 97% of the genome. Using this reference, we analyzed whole-genome resequencing data from 132 accessions representing the diversity of Asian and Oceanian citrus. Variant calling across the dataset produced a high-resolution catalogue of single nucleotide polymorphisms (SNPs) and derived database of SNPs fully discriminant of 20 Citrus species (diagnostic SNPs, DSNPs), enabling detailed exploration of inter- and intraspecific diversity. The data reveal a strong population structure within the group with clear heterozygosity variation between ancestral species and admixed accessions, reflecting their complex evolutionary history and hybridization patterns. This study provides the first integrated genomic framework for Oceanian citrus diversity, offering essential tools for downstream applications in citrus breeding, conservation, and evolutionary genomics. The resources generated lay the groundwork for future association studies and the targeted introgression of beneficial traits into cultivated citrus.

The genus Zingiber represents an economically important group within Zingiberaceae, distinguished by its aromatic and bioactive rhizomes. Zingiber striolatum Diels is an endemic Chinese medicinal and edible plant highly valued for its flower buds, which are rich in natural red pigments (yanghe red pigment, YRP). Here, we present the first haplotype-resolved, chromosome-scale assembly of ‘Ziyanghe,’ a purplish-red-bud cultivar widely grown in Guizhou Province. The triploid genome was resolved into three haplotypes: subA (2.80 Gb), subB1 (2.66 Gb), and subB2 (2.64 Gb), with the latter two exhibiting strong collinearity. Comparative analysis across five Zingiberaceae genomes revealed a family-specific whole-genome duplication ~52.5 million years ago (Mya) and lineage-specific bursts of long terminal repeat retrotransposons occurring between 0.15 and 0.66 Mya. These events likely contributed to substantial genome expansion in Z. striolatum. Evolutionary analysis of gene families suggested parallel subgenome adaptation to montane shade environments and rhizome-specific volatile biosynthesis. Metabolomic profiling identified cyanidin-3-O-glucoside, peonidin-3-O-glucoside, delphinidin-3-O-glucoside, and delphinidin-3-O-rutinoside as the major YRP components, with quercetin-3-O-glucoside functioning as a co-pigment. Integrated multi-omics analysis provides a preliminary molecular framework for YRP biosynthesis. This high-quality genomic resource significantly enhances phylogenomic understanding of Zingiberaceae and provides a foundation for the genetic improvement and metabolic engineering of anthocyanin biosynthesis in this species.

Adverse environmental conditions severely limit plant growth and productivity, especially under an increasingly frequent and severe drought. Cultivated tomato is highly sensitive to drought, while wild tomato species exhibit remarkable drought tolerance. In this study, we identified SlERF26 as a drought-responsive gene that was differentially expressed between drought-tolerant Solanum pennellii introgression lines and the cultivated tomato background through combined introgression-line and transcriptomic analyses. SlERF26 encodes an AP2/ERF (APETALA2/Ethylene Response Factor) transcription factor. Under drought stress, overexpression of SlERF26 reduced the accumulation of reactive oxygen species (ROS), including H₂O₂ and O₂⁻, which is consistent with its positive role in regulating drought tolerance. Transcriptome profiling further indicated that SlERF26 regulated a series of drought-responsive genes involved in membrane transport and ROS scavenging, such as aquaporin and peroxidases. Specifically, SlERF26 directly bound to the promoter of SlPIP2;4, an aquaporin gene, and activated its transcription. The slpip2;4 mutant accumulated higher ROS levels and exhibited significantly reduced drought tolerance. Moreover, analysis of SlERF26 OE × slpip2;4 hybrid plants confirms that SlERF26 acts upstream of SlPIP2;4 in drought tolerance. Consistent with this genetic relationship, biochemical quantification and histochemical staining demonstrated that SlERF26 and SlPIP2;4 act together to maintain ROS homeostasis during drought stress. Collectively, our findings define a SlERF26–SlPIP2;4 regulatory module that enhances drought tolerance in tomato by modulating aquaporin expression and ROS homeostasis.

Sweetpotato (Ipomoea batatas [L.] Lam.) vines exhibit strong regenerative capacity, and their blades are rich in flavonoids, making them a promising target for nutritional biofortification. Here, we quantitatively assessed flavonoid contents and antioxidant capacities in blades from 90 genetically diverse sweetpotato genotypes. Integrated metabolomic and transcriptomic analyses identified IbWRKY24 as a key transcriptional regulator of flavonoid biosynthesis in sweetpotato blades. Overexpression of IbWRKY24 in stable transgenic sweetpotato lines significantly increased blade flavonoid accumulation (1.22–2.34-fold) and antioxidant activity (1.29–2.16-fold), whereas gene silencing caused marked reductions in both traits. Mechanistically, yeast one-hybrid, dual-luciferase, and electrophoretic mobility shift assays demonstrated that IbWRKY24 directly binds specific W-box elements in the promoters of core flavonoid biosynthetic genes, including IbCHS, IbCHI, and IbFLS, thereby activating their transcription. Moreover, developmental profiling revealed a strong concordance between IbWRKY24 transcript abundance and flavonoid accumulation in blades (r = 0.806, P < 0.0001). Together, these results establish IbWRKY24 as a positive regulator of flavonoid biosynthesis and provide insights into transcriptional control of specialized metabolism in sweetpotato. This work offers a molecular target for flavonoid biofortification and high-value utilization of sweetpotato blade resources.

Vaccinium is one of the most economically significant genera in the Ericaceae family, with breeding efforts substantially improving yield, fruit quality, and adaptation, contributing to the widespread consumption of this berry-bearing clade. Crops within this genus are valued for their high nutritional content, including antioxidants, dietary fiber, and vitamins, as well as their culinary versatility. Health benefits, such as anti-inflammatory activity, combined with advances in breeding and cultivation that enhance flavor and yield, have further boosted consumer demand. However, the application of traditional breeding methods in Vaccinium remains challenging, mostly due to their long juvenile period, polyploidy, and the complex genomes of both cultivated and wild plants. To overcome these constraints, new breeding techniques (NBTs), such as gene editing, offer tremendous potential for developing improved varieties with traits that are difficult to achieve through traditional methods. Over the past 30 years, significant advancements in Vaccinium biotechnology have been made, particularly in the field of transgenesis. These advancements, including the ability to introduce foreign genes and edit genomes, hold great promise for overcoming the challenges posed by traditional breeding techniques. Despite these developments, the implementation of NBTs in Vaccinium remains at an earlier stage compared with other horticultural crops, primarily due to: (i) recalcitrancy to stable genetic transformation and (ii) low editing efficiencies. In this review, we provide a detailed overview of advancements in regeneration and genetic transformation in Vaccinium species, along with a perspective on the major constraints and future strategies to improve Vaccinium through biotechnological methods.

Roses are globally important ornamental crops worldwide and are widely used as landscape plants in outdoor greening. However, cold stress limits their growth, development, and cultivation range, especially in northern and high-altitude regions. Nevertheless, the transcriptional networks mediating cold stress responses in roses have yet to be fully understood. In this study, we identified and characterized RcWRKY71, a cold-induced WRKY transcription factor from rose (Rosa chinensis). Our findings systematically establish that RcWRKY71 is a key positive regulator of cold hardiness in roses. Overexpressing of RcWRKY71 enhanced cold resistance, as indicated by improved growth performance of callus under low-temperature conditions. Conversely, silencing this gene reduced cold tolerance, resulting in reduced leaf photosynthetic capacity and lower soluble sugar content in roots. Furthermore, we provide conclusive evidence that RcWRKY71 directly binds to and tran- scriptionally activates its downstream gene RcGolS1. Virus -induced gene silencing of RcGolS1 led to reduced cold tolerance, while its overexpression increased cold resistance by activating raffinose family oligosaccharide biosynthesis, as evidenced by the accumulation of myo-inositol, galactinol, and raffinose. Our study reveals a novel RcWRKY71-RcGolS1 regulator y module within the cold hardiness signaling pathway and provides key molecular evidence explaining how cr yoprotective oligosaccha- rides accumulate to facilitate over wintering adaptation in perennial woody plants. These findings provide valuable genetic resources and a theoretical foundation for breeding new, cold-resistant rose germplasm through genetic engineering.

Citrate, the predominant organic acid in citrus fruits, is a major determinant of fruit acidity. While significant progress has been made in elucidating the mechanisms of citrate accumulation, the comprehensive molecular regulator y network remains incompletely understood. In this study, ‘Jinxiu’ Bingtang sweet orange (Citrus sinensis) is a bud mutant derived from ‘Qianyang’ Bingtang sweet orange and exhibits an extremely low-acidity phenotype. CsMAC9F1 expression was associated with citrate accumulation in both cultivars. Unlike previously characterized tonoplast-localized proteins, CsMAC9F1 localizes to the plasma membrane, suggesting its involvement in a novel pathway regulating citrate accumulation. Functional analyses demonstrated that CsMAC9F1 acts as a positive regulator of citrate accumulation in citrus. We further identified a bHLH tran- scription factor, CsbHLH113, which binds the CsMAC9F1 promoter and activates its expression. Overexpression and silencing analyses across citrus, kumquat, and heterologous tomato systems consistently supported the role of CsbHLH113 in promoting citrate accumulation through CsMAC9F1. Together, our findings reveal a CsbHLH113–CsMAC9F1 regulator y module that adds a plasma membrane–associated branch to the citrus acidity network and provides new insights into the transcriptional control of fruit acidity.

The involvement of plant hormones in the graft union healing process is significant; yet, how exogenous MeJA affects graft union healing and stress tolerance in cucurbit seedlings remains poorly understood at the molecular level. Exogenous MeJA treatment significantly accelerated the healing process of oriental melon grafted onto squash rootstocks. This treatment led to increased expression of CmWRKY23, CmWRKY69, and the cell adhesion-related gene CmGH9B3 at the graft union, providing evidence for the participation of the CmWRKY23/CmWRKY69-CmGH9B3 module in the MeJA-facilitated graft union-healing process. Furthermore, CmWRKY23 and CmWRKY69 function as transcriptional activators by directly binding to the promoter of CmAOC2, a key jasmonic acid (JA) biosynthesis gene, thereby upregulating CmAOC2 expression. Knockout mutants of CmWRKY23 or CmWRKY69 significantly decreased the low-temperature tolerance of grafted oriental melon seedlings, accompanied by decreased antioxidant enzyme (SOD, POD, CAT) activity, downregulated CmAOC2 expression, and reduced endogenous JA levels. These findings further supported the role of this transcriptional module in regulating low-temperature tolerance through the JA signaling pathway. Overall, our work established that exogenous MeJA promoted graft union healing and enhanced the low-temperature tolerance in grafted oriental melon seedlings. This coordination was achieved via the CmWRKY23/CmWRKY69-CmGH9B3 module for graft union healing and a CmWRKY23/CmWRKY69-CmAOC2 positive feedback loop for low-temperature adaptation. This study revealed a dual regulatory mechanism by which MeJA coordinated both graft union healing and low-temperature resistance, providing new theoretical foundations and practical targets for improving the quality and environmental adaptability of grafted oriental melon seedlings.

Watermelon (Citrullus lanatus) has undergone severe loss of genetic diversity due to domestication, necessitating the exploitation of wild relatives for trait improvement. While structural variations (SVs) represent a major source of genetic diversity, high-throughput SV genotyping remains technically challenging, and existing single-nucleotide polymorphism (SNP) arrays fail to capture presence/absence variations (PAVs) that differentiate wild from cultivated germplasm. Here, we developed the ‘Watermelon 40K SNP-SV Chip,’ the first liquid-phase genotyping chip enriched with SV markers, leveraging a telomere-to-telomere super-pangenome of seven Citrullus species. The chip comprises 7087 SV markers (enriched for PAVs) and 11 383 SNP/InDel markers. Technical validation in 12 accessions and large-scale genotyping of 228 diverse accessions demonstrated high reproducibility (≥98.5% concordance) and robust call rates (>97%), though performance declined in deeply divergent wild species. Genome-wide association studies revealed SV-specific signals for flesh color and rind pattern that co-localized with known quantitative trait loci (QTL), including a strong candidate regulator y PAV upstream of LCYB. The predominance of rare variants (74.3% SVs with minor allele frequency < 0.05) limits statistical power for detecting QTL underlying polygenic domestication traits such as yield but confers exceptional utility for tracking wild introgressions in early-generation breeding populations. The 40K SNP-SV chip bridges the gap between fundamental SV research and practical breeding, enabling SV-assisted genomic selection for watermelon improvement.

Sassafras tzumu (Hemsl.) Hemsl. is an endemic tree species in East Asia with considerable ecological and economic value. It is widely used for its fine-grained and durable wood, rich aromatic oils, and ornamental value. Despite its multifaceted importance, the absence of genomic resources has hindered our understanding of its evolutionary position and the molecular basis of its wood-related traits. To construct a high-continuity reference genome, we employed a comprehensive strategy. We combined PacBio HiFi long reads, Illumina short reads for polishing, and Hi-C data for chromosome-level scaffolding. The resulting assembly spans 929.18 Mb, anchored to 12 pseudochromosomes, and achieves an impressive contig N50 of 78.46 Mb. The assembly achieves a BUSCO completeness score of 98.8%, indicating that nearly all conserved core eukaryotic genes are present and intact. To experimentally verify the genome size of S. tzumu, flow cytometry (FCM) was performed using a Sysmex CyFlow ^® Cube6 instrument. Fresh leaf tissue was processed and stained with propidium iodide following standard protocols. Phyllostachys edulis (2048 Mb) was used as the reference species. The genome size was calculated based on the ratio of the geometric mean of the fluorescence intensity between the sample and the reference. A standout feature of this genome is its exceptional continuity: 10 of the 12 chromosomes are assembled as single contigs and are entirely gapless. The remaining two chromosomes (Chr08 and Chr12) each contain only a single gap of 100 bp located in the centromeric regions. Furthermore, telomeric motifs were identified at both ends of seven chromosomes (Chr01–06 and Chr09) and at one end of the remaining five, confirming a near-complete telomere-to-telomere reconstruction. This assembly represents one of the most complete genomes within Lauraceae to date, substantially surpassing previously published genomes, such as Cinnamomum kanehirae [1]. It provides a robust foundation for exploring the evolution and genetic regulation of wood formation in Lauraceae and offers reliable genomic evidence to investigating the evolutionary position of magnoliids among angiosperms (Fig. 1A). Through analyses of synonymous substitution rates (K_s) and 4-fold degenerate transversion (4DTv) sites, we identified two distinct whole-genome duplication (WGD) signals: an ancient WGD commonly referred to as a magnoliid-shared WGD [2], and a more recent WGD signal observed within Lauraceae in our sampling (Fig. 1B and C). These WGD events likely fueled the diversification and environmental adaptation of the lineage. Comparative synteny analyses between S. tzumu and C. camphora revealed extensive one-to-one chromosomal collinearity (Fig. 1D), suggesting that despite the long divergence time, the overall genome structure has remained remarkably stable following these shared WGD events. Phylogenetic reconstruction based on 130 single-copy orthologs from 13 representative angiosperm species robustly supports the basal placement of magnoliids as a sister lineage to the clade comprising eudicots and monocots, consistent with the studies on Magnolia biondii [3]. Molecular dating analysis further estimates that S. tzumu diverged from other Lauraceae lineages ~29.6 million years ago (Fig. 1E). To rule out gene count inflation, we performed a comprehensive repeat annotation combining ab initio prediction (using LTR_FINDER, RepeatModeler, etc.) and homology-based alignment (RepeatMasker). The results reveal that LTR retrotransposons (46.31% of the genome) experienced a recent burst (~2–6 Ma), which is temporally distinct from the ancient WGD events (K_s ≈ 0.5). This confirms that the expanded gene families are not artifacts of recent transposon activity. Beyond phylogenomics, the S. tzumu genome provides valuable insights into the genetic basis of wood-related traits. Of the 33 863 annotated protein-coding genes, we applied a birth–death probability model (CAFE 5, P < 0.05) and identified 174 significantly expanded gene families. Gene Ontology enrichment analysis revealed that these expansions are predominantly associated with biological processes related to cell wall organization, cellulose biosynthesis, and metabolic adaptation. Furthermore, genomic collinearity analysis between S. tzumu and P. trichocarpa visually illustrates the chromosomal distribution of the expanded CesA gene family, particularly highlighting the syntenic relationships of StCesA1 (Fig. 1F). Notably, the StCesA gene family exhibited the most pronounced expansion with 31 members identified in S. tzumu-a substantially higher count than in model woody species such as P. trichocarpa (17 members) and Eucalyptus grandis (20 members) (Fig. 1G). Detailed phylogenetic analysis classified these StCesA proteins into distinct clades, revealing that many expanded members fall into clades typically associated with primary cell wall (PCW) biosynthesis. Specifically, StCesA1 clustered closely with Arabidopsis AtCesA1, AtCesA3, and AtCesA10, which are essential for cellulose synthesis [4]. Transcriptomic profiling across various tissues-including tender leaves, phloem, xylem, roots, and seeds-demonstrated that StCesA1 is highly expressed specifically in the xylem tissue. To experimentally validate this function, we overexpressed StCesA1 in hybrid poplar P. × canescens, a transformable woody model for secondary growth and cell wall studies. After 3 months of growth under controlled conditions, the transgenic lines exhibited marked morphological enhancements compared to wild-type plants, including an 11%–15% increase in plant height and up to a 35.8% increase in stem diameter (Fig. 1H). Biochemical analysis revealed a remarkable 39.4% increase in stem cellulose content, while lignin levels remained unchanged. Importantly, this substantial gain in cellulose did not come at the expense of lignin content, which remained statistically unchanged compared to the control. Histochemical staining of stem cross-sections further confirmed enhanced cellulose deposition without any observable abnormalities in xylem structure. These findings suggest that StCesA1 may promote growth and cellulose accumulation in hybrid poplar under the tested conditions without significantly altering lignin content, indicating its potential value as a candidate gene for future studies of wood formation and molecular breeding. In conclusion, our study presents a near-gapless reference genome for S. tzumu, providing a valuable genomic resource for comparative analyses of Lauraceae and magnoliids. The genome assembly supports phylogenomic analyses relevant to the placement of magnoliids and reveals a lineage-specific expansion of the CesA gene family that may be associated with wood formation. Functional analysis of StCesA1 in hybrid poplar suggests a potential role in promoting growth and cellulose accumulation under the tested conditions. Together, these genomic resources and preliminary functional results provide useful candidates for future studies of wood formation and molecular breeding in woody plants [5].

Whether plant life form influences the long-term persistence of polyploid lineages remains an important unresolved question in plant evolution. Previous studies have suggested that perennial herbaceous plants harbor higher proportions of neo-polyploids, yet comprehensive phylogenetic validation across paleopolyploid lineages using genomic data remains limited. The rapid accumulation of plant genome sequences, particularly from horticultural and agricultural species, provides an unprecedented opportunity to investigate the evolutionary relationships among polyploidization, plant growth form, and plant stature across seed plants. Here, we analyzed 351 seed plant genomes, including major cereals, vegetables, fruits, and their wild relatives, to investigate the long-term evolutionary associations between paleopolyploidization and plant phenotypic diversity. Phylogenetically informed comparative analyses showed that lineages experiencing more paleopolyploidization events were significantly more likely to exhibit herbaceous rather than woody growth forms. We further found that paleopolyploidization frequency was negatively associated with plant height across seed plants after accounting for phylogenetic relatedness. In addition, evolutionary rates, estimated using synonymous substitution rates (Ks), were associated with paleopolyploidization, plant growth form, and species richness. Herbaceous species exhibited higher Ks values than woody and vine species, and plant families with higher evolutionary rates tended to contain more species. Together, these findings provide a phylogenetically informed evidence that paleopolyploidization is closely associated with plant growth form, plant stature, and evolutionary rate, offering new insights into the long-term evolutionary consequences of genome duplication in seed plants.

A s one of the world’s most important ornamental crops, rose (Rosa sp.) is highly susceptible to grey mold disease caused by Botrytis cinerea. Outbreaks of this disease during long-distance transportation often lead to substantial economic losses. This study identifies the WRKY transcription factor RcWRKY29 as a key regulator in the defense response against B. cinerea. Integrated RNA sequencing and DNA affinity purification sequencing analyses revealed RcERF98 as a direct target of RcWRKY29. Knockdown or overexpression RcWRKY29 correspondingly altered RcERF98 transcript levels, which in turn modulated ascorbic acid (AsA) accumulation and reactive oxygen species (ROS) scavenging in petals. expression. We demonstrated that the auxin response factor RcARF8, but not RcARF1, binds to the RcWRKY29 promoter and activates its transcription. Moreover, knocking down or overexpression of RcARF8 affected the expression of both RcWRKY29 and RcERF98, thereby regulating AsA biosynthesis and ROS homeostasis, and ultimately determining disease susceptibility. Collectively, our findings reveal a signaling module in which the auxin-mediated transcription cascade involving RcARF8- RcWRKY29-RcERF98 confers resistance to B. cinerea by coordinating AsA-dependent ROS scavenging in rose petals.

As one of the most globally cultivated vegetables, lettuce’s commercial yield is severely compromised by premature bolting, an undesirable agronomic trait that diminishes crop quality and market value. In this study, we genetically cloned the OVATE family protein 6 (LsOFP6) controlling bolting time in lettuce. LsOFP6 had a nonsense mutation in the late bolting parent. CRISPR/Cas9 knockout and complementary tests confirmed that LsOFP6 positively regulates bolting in lettuce. LsOFP6 physically interacts with the CONSTANS-LIKE 3 (LsCOL3). Genetic analyses suggest that LsOFP6 regulates bolting through an LsCOL3-dependent pathway in the Lsblh2 Lskn1 genotype background, where we have previously established that LsBLH2 and LsKN1, the positive and negative transcriptional regulators of bolting, respectively, both interact with LsOFP6 and exert their functions via the gibberellin pathway. LsCOL3 represses bolting development by directly binding to the promoters of TWIN SISTER OF FLOWERING LOCUS T (LsTSF1) and TERMINAL FLOWER 1 (LsTFL1), downregulating the former while upregulating the latter. These regulations are antagonized by LsOFP6, which promotes bolting by compromising the effects of LsCOL3 on LsTSF1 and LsTFL1. Therefore, loss of function of Lsofp6 decreases LsTSF1 and increases LsTFL1 expression, resulting in late bolting. In summary, the LsOFP6–LsCOL3 module regulates lettuce bolting development by controlling the transcript levels of LsTSF1 and LsTFL1 genes. This study deepens the molecular understanding of bolting development and provides valuable genetic resources and novel strategies for developing lettuce with improved resistance to premature bolting, highlighting the power of natural variation to address agricultural challenges.

Litchi (Litchi chinensis Sonn.) is a high-value subtropical fruit tree native to eastern Yunnan, China. Its cultivation was recorded in the second century BC. Ancient litchi trees are widespread across southern China, some over 1000 years old, yet their genetic potential remains largely uninvestigated. Here, we analyzed resequencing data from 93 in situ ancient litchi trees with integrated public datasets and simulated paleoclimate species distribution models (SDMs) using over 20 000 ancient litchi distribution records. This approach led to several significant findings. First, population analyses identified two wild lineages (Yunnan, Hainan) and five admixed clusters. SDMs indicate last glacial maximum contraction with a Hainan refugium, followed by postglacial expansion across South China while Yunnan lagged. Principal component analysis and runs of homozygosity further revealed fine-scale population structure. Second, several historical dispersal events of litchi were uncovered. Most ancient Sichuan trees were derived from the Yunnan wild lineage, with fragmented montane habitats supporting human-mediated introduction. Ancient Fujian and Guangdong trees are chiefly admixed cultivars, with genetic distances indicating clonal spread across regions. Third, we identified signals where variation in flowering time and disease resistance coincides with highly heterozygous genomic blocks and haplotype-biased transcription. This pattern is observed in flowering differences between cultivars ‘Feizixiao’ and ‘Nuomici’ and in disease responses between the ancient resistant cultivar ‘Heiye’ and the susceptible cultivar ‘Guiwei’. Our research provides a genomic resource for ancient litchi trees, offering new insights into litchi dispersal, cultivation, and priorities for breeding.

Drought stress is a major abiotic constraint on agricultural production, and cultivated tomato varieties are generally sensitive to water deficit. This review systematically summarizes the physiological, biochemical, and molecular mechanisms underlying tomato drought responses. It also integrates recent high-impact insights to advance our understanding of this topic. It then surveys multidimensional improvement strategies. These include biostimulants, chemical regulators, nanomaterials, grafting, water management, and genetic engineering approaches such as transgenesis and CRISPR/Cas9-based genome editing. Current research faces bottlenecks in translating laboratory findings to field applications, particularly due to the inherent trade-off between drought tolerance and fruit yield and quality. To address this challenge, we propose a framework that integrates several key components: precision editing tools (e.g. base editing and promoter editing), tissue-specific or stress-inducible expression systems, and parallel phenotyping of yield components and fruit quality traits under both well-watered and drought conditions. This framework is designed to balance stress resilience with productivity. Moving forward, a systematic multidisciplinary approach is required to overcome this trade-off, enabling water-efficient, stable-yielding, and high-quality sustainable tomato production. This review provides an integrative perspective and forward-looking guidance for future research and practical applications.

Lycium barbarum fruits are valued for bioactive carotenoids, yet the enzymatic basis underlying accumulation of their hallmark xanthophyll diester, zeaxanthin dipalmitate (ZD), remains unclear. Biosynthesis of ZD requires two sequential reactions: β-carotene hydroxylation catalyzed by β-carotene hydroxylase (BCH) to produce zeaxanthin, followed by xanthophyll esterification mediated by xanthophyll esterase (XES). However, the specific genes responsible for ZD formation in L. barbarum have not been functionally defined. Here, we integrated genome mining, phylogenetics, developmental metabolite profiling, tissue-and stage-resolved expression analysis, and functional validation using Escherichia coli complementation, transient expression in L. barbarum and tobacco, and fruit-specific co-expression in tomato. Carotenoid profiling revealed a ripening-associated transition from free xanthophylls to esters. Among the candidates, LbBCH1 and LbXES2 showed fruit-preferential expression, positively correlated with ZD accumulation, and both encoded plastid-localized proteins. In E. coli complementation assays, LbBCH1 converted β-carotene to zeaxanthin, and LbXES2 further catalyzed the formation of ZD from zeaxanthin. Transient expression assays showed that LbXES2 could esterify multiple xanthophylls and exhibited a preference for palmitoylation, while ZD production was enhanced by LbBCH1-mediated zeaxanthin supply. In tomato, fruit-specific co-expression of LbBCH1 and LbXES2 enabled de novo biosynthesis of xanthophyll ester, elevated total carotenoids, promoted chromoplast and plastoglobule development, and altered sugars, organic acids, and carotenoid-derived volatiles. Collectively, these results identify LbXES2 as a xanthophyll esterification enzyme associated with ZD biosynthesis and support a functional role for LbBCH1-mediated zeaxanthin supply in this process. Our study provides molecular tools and a heterologous engineering strategy for producing high-value esterified carotenoids in fleshy fruits.

Soil salinization and alkalinization threaten plant growth worldwide. In response, plants deploy various physiological and molecular defense mechanisms. Nanobiotechnology offers a potential strategy to enhance crop stress tolerance. Here, we found that nano-Fe₃O₄ increased salt–alkali tolerance in melon seedlings by suppressing the expression of the transcription factor CmBHLH93. Transcriptomic analysis revealed strong downregulation of CmBHLH93 upon nano-Fe₃O₄ application under salt–alkali stress. Functional assays showed that CmBHLH93 acted as a negative regulator of salt tolerance. It directly bound the promoters of key defense-related genes involved in abscisic acid (ABA) synthesis (CmNCED3), jasmonic acid (JA) synthesis (CmAOS), antioxidant activity (CmPOD-1), and Na⁺ transport (CmSOS1), thereby repressing their transcription. Taken together, nano-Fe₃O₄ enhanced melon salt tolerance by downregulating CmBHLH93 transcription and activating downstream responses associated with ABA/JA signaling, antioxidant capacity, and Na⁺/K⁺ homeostasis. These results define a regulatory mechanism through which nanomaterials modulate plant tolerance to salt–alkali stress and provide a conceptual basis for improving crop stress tolerance using nanotechnology.

Hygrophila difformis is an ornamental amphibious plant that develops distinct terrestrial (shallow-serrated) and submerged (deep-lobed) leaf forms in response to environmental conditions. Although previous studies have reported bicarbonate (HCO₃⁻) utilization and highlighted the involvement of carbonic anhydrase in inorganic carbon uptake, the photosynthetic strategy and carbon assimilation pathway operating under submergence remain unclear. Here, we applied an integrated framework combining physiological measurements, enzyme activity assays, transcriptomic, proteomic, and metabolomic profiling, stable carbon isotope analysis, and ultrastructural observations to compare terrestrial and submerged leaves. Submerged leaves displayed a δ¹³C value of −20.068 ‰, indicating a substantial shift toward C₄-like photosynthetic metabolism under aquatic conditions. Consistent with this signature, activities of key carboxylation and decarboxylation enzymes were significantly elevated, supporting a transition from C₃ photosynthesis toward an NAD-malic enzyme (NAD-ME)–type C₄ pathway. Multiomics analyses revealed extensive reprogramming of photosynthetic and starch metabolic networks in response to submergence, with strong upregulation of genes and metabolites associated with the NAD-ME–type C₄ cycle, including cytosolic aspartate aminotransferase and alanine aminotransferase, accompanied by coordinated downregulation of Calvin cycle components. By contrast, terrestrial leaves retained high Rubisco activity and strong expression of Calvin cycle genes, consistent with classical C₃ photosynthesis. Reverse-transcription quantitative PCR analyses demonstrated marked induction of carbonic anhydrase genes under submerged conditions, with Hd αCA9 showing a 194-fold increase in transcript abundance, highlighting its central role in underwater carbon utilization. Transmission electron microscopy further revealed dimorphic chloroplasts within submerged mesophyll cells. Collectively, results demonstrate plasticity in H. difformis and provide insights into C₄-like carbon assimilation strategies in amphibious plants.

Quinolizidine alkaloids restrict the use of lupin seeds as food and feed. In narrow-leafed lupin, low-alkaloid content in most cultivars has been traced to the recessive iucundus locus, with the RAP2-7 transcription factor as a candidate regulator. The molecular basis of alternative low-alkaloid sources remains unclear. The aim of this study was to elucidate the molecular determinants underlying low-alkaloid content through a comparative analysis of the classical iucundus and alternative Bryansk backgrounds, with particular emphasis on the molecular characterization of RAP2-7. This multiomic framework integrates alkaloid profiling and transcriptomics alongside RAP2-7 DNA binding characterization, and sequence-level motif and variant analyses. Alkaloid profiles revealed genotype-specific differences, with Bryansk lines showing a distinct, sparteine-enriched and lupanine-depleted chemotype relative to iucundus and Iucundus. Using Iucundus line as a reference, transcriptome analyses highlighted candidate genes associated with low-alkaloid iucundus and Bryansk lines, spanning enzymes, transporters and putative regulators. Consistent with a key role of RAP2-7, DAP-seq summits in Iucundus and Bryansk contained a clear AP2-like motif, whereas the iucundus background showed both strong depletion of high-confidence peaks and no defined motif. In silico modelling of RAP2-7 bound to its DNA motif, combined with DAP-seq and expression data, supported reduced binding of the iucundus variant relative to Iucundus, as well as a possible role for a mutation within the promoter of key acyltransferase LaAT. Collectively, these data extend lupin transcriptomic resources and refine models of alkaloid biosynthesis beyond the classical iucundus background, while also providing the first comprehensive molecular characterization of Bryansk low-alkaloid lines.

Cold stress inhibits the growth and development of melon. Exogenous trehalose (Tre) has been reported to alleviate cold damage in melon seedlings; however, it remains unclear whether plants respond to cold stress by activating endogenous Tre synthesis and the associated upstream and downstream pathways. Here, the results show that cold stress markedly increases endogenous Tre levels in melon leaves. Transcriptome analysis identified two trehalose-6-phosphate phosphatase (key enzymes in Tre synthesis, TPP) genes, CmTPP2 and CmTPP5, which were strongly induced by cold stress. Silencing CmTPP2/5 significantly reduced Tre content, lowered the activities of superoxide dismutase, ascorbate peroxidase and glutathione reductase, and exacerbated cold-induced lipid peroxidation damage; meanwhile, it inhibited apoplastic H₂O₂ accumulation, restricted H₂O₂ transport into the cytoplasm, and downregulated the expression of C-repeat binding factor 1/2 (CmCBF1/2) under cold stress. Protein–DNA interaction assays demonstrated that the transcription factor CmABF3 binds to the ABRE motif in the CmTPP2/5 promoter to activate their transcription. Silencing CmABF3 gene significantly reduced CmCBF1/2 and CmTPP2/5 expression and reduced Tre accumulation. Inhibition of trehalase activity by validamycin A elevated Tre content, enhanced antioxidant capacity under cold stress, promoted apoplastic H₂O₂ production and transport, and upregulated CmCBF1/2 expression. Silencing CmCBF1/2 also inhibited the production and transport of apoplastic H₂O₂ and reduced melon cold tolerance. These findings reveal that cold stress triggers CmABF3-mediated activation of CmTPP2/5, leading to Tre accumulation, which then enhanced antioxidant defenses via regulation of apoplastic H₂O₂ production and transport, and coordination with the CBF-dependent pathway to improve cold tolerance in melon seedlings.

Miniaturization and multiple branching are characteristic features of horticultural plants. Gibberellins participate in regulating the size and branching of plant architecture. Gibberellin 3β hydroxylase (GA3ox) and gibberellin 2β hydroxylase (GA2ox) are a pair of key enzymes for the homeostasis of active GA. However, the transcriptional regulation of GA3ox and GA2ox and the synthesis of active GAs remain unknown. Here the roles of narcissus NtMYB1 and NtbZIP53 in regulating the biosynthesis of diverse active GAs were addressed. Overexpression of NtMYB1 in Arabidopsis and Narcissus shows a tiny-type phenotype. The NtMYB1 co-expression network reveals that NtMYB1 or NtbZIP53 is closely related to NtKS1, NtGA20ox, NtGA2ox, and NtGA3ox in the GA biosynthetic pathway of narcissus. NtMYB1 can interact with NtbZIP53. Overexpression of NtMYB1 and NtMYB1/NtbZIP53 in transgenic narcissus upregulated the expression of upstream genes NtKS1 and NtGA20ox in the GA biosynthesis pathway; however, NtMYB1 and/or NtbZIP53 directly targeted the promoters of NtGA3ox2 and NtGA2ox8 and antagonistically controlled NtGA3ox2 and NtGA3ox8 transcription, respectively, and both decreased GA 1 accumulation. NtMYB1 recruiting NtbZIP53 enhanced the repression of NtGA3ox2 and the activation of NtGA2ox8, reducing the GA 1/GA 3 ratio and plant size in narcissus. This provides a conceptual basis for controlling the architecture of Chinese narcissus.

Complex regulatory networks formed by epigenetic modifications such as DNA, histones, and RNA can influence gene expression without altering DNA sequences, participating in ripening processes and quality changes in fruits. Although significant progress has been made in understanding epigenetic modifications and their roles in fruit ripening, the regulatory network underlying these complex relationships remains incompletely elucidated. Here, we summarize the key molecular regulatory networks involving DNA, histone, and RNA modifications in fruit ripening and secondary metabolite changes in recent years; review the research applications of epigenetic modification inhibitors and omics technologies, elucidating their advantages and limitations; and ultimately propose a comprehensive strategic model for future studies on epigenetic modification regulation of fruit ripening. These findings not only deepen our understanding of epigenetic modifications during fruit ripening but also raise new questions and research directions. It provides a deeper understanding of the ripening process and quality changes in fruits, offering insights for new strategies in fruit production and integrated regulation.