Anthracnose, caused by Colletotrichum species, poses a significant threat to global tea ( Camellia sinensis ) production, yet its inducible resistance mechanisms remain largely uncharacterized. Through integrated transcriptomic and metabolomic analyses of the anthracnose-resistant cultivar ‘Zijuan’ and the susceptible cultivar ‘Longjing43’, we identified sakuranetin as a key phytoalexin in tea plants and elucidated a complete jasmonic acid (JA)-mediated defense pathway. Our functional characterization revealed that CsNOMT (Cha09g008790), a naringenin 7-O-methyltransferase, catalyzes sakuranetin biosynthesis with high substrate specificity. Following infection with Colletotrichum camelliae , sakuranetin accumulated exclusively in resistant cultivars, exhibiting superior antifungal activity compared to major tea catechins. Functional validation demonstrated that overexpression of CsNOMT enhanced both sakuranetin accumulation and disease resistance, while gene silencing compromised both traits. Mechanistically, we established that the JA-responsive transcription factor CsMYC2.1 directly activates CsNOMT transcription via G-box binding, establishing a novel JA–CsMYC2.1–CsNOMT–sakuranetin defense axis that distinguishes resistant from susceptible tea cultivars. This study represents the first comprehensive characterization of inducible phytoalexin-mediated immunity in tea, providing immediate applications for sustainable tea production. CsNOMT serves as a valuable functional marker for resistance breeding, while sakuranetin emerges as a promising natural biopesticide to reduce reliance on synthetic fungicides.

Kiwifruit ( Actinidia spp.) is a globally significant horticultural crop, renowned for its exceptional nutritional value and high vitamin C content. The distinctive genetic features of this genus, including a dioecious sexual system (XY/XX) and a wide range of ploidy (2 x–10 x), have driven substantial genomic and phenotypic diversification, thereby constituting a valuable germplasm resource for systematic breeding. Recent advances in kiwifruit genomics are transforming the field and revolutionizing our understanding of its evolution, domestication, and the genetic mechanisms underlying agronomic traits. In this review, we highlight the key achievements in kiwifruit genome research over the past decades, chronologically spanning from the initial draft genome assembly to the recent super pan–genome construction. We further synthesize how multi-omics approaches have been leveraged for fine mapping, gene discovery, and the analysis of gene expression and metabolic pathways. Finally, we discuss future research directions and breeding strategies enabled by these genomic breakthroughs, particularly through the applications of genomic selection and gene editing in kiwifruit.

Elevated atmospheric [CO ₂] and nitrogen (N) availability are critical determinants of plant growth. This study investigated the underlying mechanisms of hormones in mediating elevated [CO ₂]-promoted shoot growth and leaf elongation under different N conditions in tall fescue ( Festuca arundinacea). Plants were grown under low N (LN, 0.25 mM) and moderate N (MN, 4 mM) conditions. Subsequently, the plants from each N treatment were divided and immediately transferred to ambient (400 μmol mol ⁻¹) or elevated [CO ₂] (800 μmol mol ⁻¹). Elevated [CO ₂] promoted plant growth under both LN and MN conditions through affecting cell division and cell elongation, with a more pronounced effect under MN supply levels. Elevated [CO ₂]-induced shoot growth and leaf elongation were associated with increased cytokinin level under LN and with enhanced cytokinin and auxin under MN conditions. Exogenous cytokinin inhibitor (lovastatin) and auxin inhibitor (2,3,5-triiodobenzoic acid) altered elevated [CO ₂]-enhanced growth in tall fescue regardless of N conditions. Elevation of [CO ₂]-enhanced growth by modulating cell growth-related genes OsCycD2, OsPCNA, and OsEXPA10 was counteracted and reduced in FaCKX11-OE lines under LN and MN conditions, respectively. However, this enhancement was counteracted in FaDAO-OE lines under MN but not under LN conditions. These results demonstrated that elevated [CO ₂]-enhanced shoot growth in perennial grass species could be primarily mediated by cytokinin under LN conditions, while both cytokinin and auxin were involved in regulating elevated [CO ₂]-enhanced growth under MN conditions.

Crotalaria is a genus of the Fabaceae family with agricultural and medicinal value, but to date the genome has not been fully sequenced. Although Crotalaria pallida is widely distributed in tropical and subtropical regions, the degree of genetic diversity and the specific traits influenced by geographic dispersal remain unknown. We here report a high-quality genome assembly of C. pallida with 98.52% coverage which is assembled into 8 chromosomes. C. pallida is closely related to Lupinus angustifolius , with genetic divergence occurring ∼42.5–57.4 million years ago (MYA). Re-sequencing of 236 C. pallida accessions revealed a genetic diversity decrease as C. pallida spread from Africa to America and Asia, and from Asia to China and finally to Hainan. Significant divergence was observed in seven traits between non-Hainan and Hainan accessions. Genome-wide association studies identified 73 loci for 18 agronomic traits, 25 of which overlapped with divergent sweeps between non-Hainan accessions and Hainan accessions. Furthermore, the dispersal of C. pallida in Hainan reduced genetic diversity, leading to a divergence in allelic frequencies at four candidate genes ( CpPTR , CpMYB , CpRLPK , and CpNADK ) associated with plant height. This study reveals the genetic basis of trait divergence driven by geographic dispersal and offers valuable resources for the strategic development of C. pallida breeding.

Plant elicitor peptides (Peps) are a class of endogenous phytocytokine that enhances plant innate immunity against diverse pathogens. They are widely distributed in the plant kingdom, yet their interfamily compatibility of Peps perception remains controversial. In this study, two pear ( Pyrus L.) Peps, PbePep4 ( Pyrus betulifolia) and PdrPep6 ( Pyrus ussuriensis × communis Zhongai), were identified and their function in eliciting interfamily immunity was dissected. We found that PbePep4 and PdrPep6 improved resistance of pear leaves to fire blight caused by Erwinia amylovora. Exogenous treatment with PbePep4 and PdrPep6 activated various immune responses in pear leaves, including burst of reactive oxygen species, deposition of callose, phosphorylation of mitogen-activated protein kinase, and up-regulation of defense genes. Intriguingly, these two pear peptides were able to interfamilially trigger immune responses of plants from Brassicaceae and Cucurbiaceae families. Application with PbePep4 and PdrPep6 enhanced the resistance of Brassicaceae species Arabidopsis thaliana and Brassica napus to Sclerotinia sclerotiorum, and that of Cucurbiaceae species Citrullus lanatus to Botrytis cinerea. We demonstrated that the key of these peptides to induce immunity in cross-family species is associated with the conservation of the conformed motif at the C-terminal of Pep peptides and their six active binding sites in PEPRs in cross-family species from the Rosaceae, Brassicaceae, and Cucurbiaceae. Taken together, our findings not only solved the debate whether plant Peps can only stimulate immunity within the family, but also clarified the exploitation potential of pear Peps as broad-spectrum immune inducers to control disease in crops of at least three families.

Soil salinization poses a serious threat to plant development and represents a major obstacle to the sustainable production of crops worldwide. Melatonin (MT) contributes prominently to plant tolerance against abiotic environments. However, the molecular basis of transcriptional regulation underlying melatonin accumulation in tomato under saline–alkali stress is still largely unknown. Herein, we identify SlNAC2, a NAC transcription factor in tomato induced by saline–alkali stress, which suppresses the key melatonin biosynthetic genes SlCOMT2 and SlSNAT, while activating SlCV, a gene linked to reactive oxygen species (ROS) accumulation and programmed cell death. These regulatory effects reduce MT levels and promote excessive ROS production, ultimately altering the plant’s tolerance to saline–alkali stress. Silencing of SlNAC2 through the RNA interference method significantly improves saline–alkali tolerance in tomato, while its constitutive overexpression shows increased susceptibility to saline–alkali stress. Further evidence reveals that under saline–alkali conditions, SlNAC2 directly targets cis-elements of SlCOMT2 and SlSNAT promoters, suppressing their transcription and consequently reducing melatonin levels, whereas simultaneously binding to the SlCV promoter to activate its expression, ultimately leading to ROS accumulation. Moreover, comprehensive protein interaction analyses confirmed that SlNAC2 physically associates with SlDREB2, a DREB-type transcription factor involved in salt stress response. Through its interaction with SlNAC2, SlDREB2 partially attenuates its repression of SlCOMT2 and SlSNAT, thereby increasing melatonin accumulation and ROS scavenging, ultimately enhancing tomato’s resilience to saline–alkali stress conditions. Collectively, our findings reveal a SlNAC2–SlDREB2 regulatory module that finely tunes melatonin synthesis and ROS levels to regulate tomato’s response to saline–alkali stress, providing new strategies for developing stress-resilient tomato varieties.

Oregano ( Origanum vulgare ) is a highly valued aromatic herb for culinary, medicinal, and ornamental purposes. Its commercial value is largely from its essential oil (EO), which is rich in key bioactive terpenoids, such as carvacrol and thymol. Greek oregano ( O. vulgare subsp. hirtum ) subspecies is particularly prized for its high EO content. In this study, we generated a high-quality genome assembly of Greek oregano to investigate its evolutionary trajectory and the genetic basis of terpenoid biosynthesis. The assembly spans 709.74 Mb and is anchored to 15 chromosomes, with a scaffold N50 of 46.36 Mb. Comparative genomic analysis revealed a whole-genome duplication event, estimated at ∼59.93 million years ago, which likely contributed to the diversification of terpenoid biosynthesis pathways within the Lamiaceae family. Using a rapid screening approach, we identified Greek oregano mutants with higher EO content. Integrated genomic and transcriptomic analysis of a high-EO mutant highlighted the importance of α -linolenic acid metabolism/jasmonic acid (JA) biosynthesis pathways in EO production. Exogenous JA treatment led to upregulation of key EO biosynthetic genes and higher EO content. Furthermore, a JA-inducible bHLH transcription factor, OvbHLH13, was identified as a central regulator of terpenoid biosynthesis. Through Y1H, transcriptional activation, and EMSA assays, we demonstrated that OvbHLH13 directly bound to and transactivated the promoter of OvSDR1 , which encodes a critical enzyme in thymol and carvacrol production. Collectively, this genomic resource provides valuable insights into the genetic and regulatory network controlling terpenoid biosynthesis and establishes a critical genomic foundation for molecular breeding of Greek oregano.

Bacterial spot (BS) disease significantly impairs vigor, fruit quality, and yield in peach trees. However, research on this disease remains limited. In this study, peach leaves and fruits were inoculated with the pathogen isolated from infected leaves, triggering a robust accumulation of proanthocyanidins (PA) in both tissues. Further investigation revealed that pathogen inoculation promoted PA accumulation by upregulating PpMYB123, which transactivated the core PA biosynthetic genes PpANR and PpLAR. Notably, the E3 ubiquitin ligase PpPUB23 negatively regulated PpMYB123. However, its transcript levels were significantly suppressed following inoculation, thereby stabilizing PpMYB123 and enhancing PA production. PA conferred dual protection by scavenging excess reactive oxygen species (ROS) and suppressing pathogen growth. Our findings provide molecular evidence for PA-mediated defense against BS disease in peach.

In the context of global warming, elevated temperatures present serious challenges to the growth, quality, and productivity of nonheading Chinese cabbage (NHCC). Understanding the mechanisms underlying thermotolerance in NHCCs is therefore critically important. In this study, we investigated the influence of heat stress (HS) duration and circadian rhythm on gene expression using time-resolved transcriptome sequencing. The results showed that during the early stages of HS, NHCC primarily engaged in physiological processes such as stimulus perception and signal transduction. In contrast, prolonged HS exposure activated antioxidant metabolism, reduced photosynthetic capacity, and accelerated leaf senescence. Weighted gene coexpression network analysis (WGCNA) further revealed a strong link between circadian regulation and HS responses. Notably, our findings demonstrate that the core circadian clock component CIRCADIAN CLOCK ASSOCIATED 1 (BcCCA1) negatively regulated heat tolerance by repressing the transcription of BcHSFA2. Collectively, these results provide new insights into the molecular mechanisms underlying HS responses in NHCCs and highlight the regulatory role of circadian rhythms in plant thermotolerance.

This research examines how the basic leucine zipper (bZIP) transcription factor (TF) influences drought stress responses in tree species, emphasizing its related regulatory pathways, and thus offering a theoretical framework for understanding drought response mechanisms regulated by the bZIP TF family. Specifically, we characterized the functional role of the S subfamily bZIP gene, PtrbZIP12 , from Populus trichocarpa , by developing transgenic poplars that either overexpressed or knocked down PtrbZIP12 . The findings indicated that PtrbZIP12 markedly improved drought tolerance in transgenic plants by facilitating reactive oxygen species scavenging, enhancing proline biosynthesis, and reducing plasma membrane peroxi- dation and cell death. To pinpoint PtrbZIP12 ’s downstream targets, RNA sequencing was performed, followed by chromatin immunoprecipitation-PCR (ChIP-PCR), yeast one-hybrid, and dual-luciferase assays. These analyses confirmed that PtrbZIP12 binds directly to the promoters of PtrDHN (dehydrin) and PtrPOD (peroxidase), leading to the activation of their expression. Transgenic poplars overexpressing (OE) PtrDHN or PtrPOD were subsequently generated, and similar to PtrbZIP12 , their OE conferred enhanced drought tolerance. Moreover, coexpression of PtrbZIP12 with PtrbZIP3 further elevated PtrDHN transcript levels, resulting in improved drought resilience in the PtrbZIP12 transgenic lines. Moreover, phosphorylation was identified as a key factor in boosting PtrbZIP12-mediated transcriptional regulation of PtrPOD and PtrDHN , underscoring the significance of posttranslational modification in plant drought stress responses.

Accurately predicting the performance of trees and crops across diverse and changing climates is essential for matching genotypes to both current and future environments. Yet modelling the complex interplay among genotype, environment, and phenotype in multi-environment trials remains a major challenge. Here, we introduce a unified framework, polygenic environmental interaction (PEI), directly models genotype-by-environment interactions through integrating genotypes and environmental covariates. We implemented an ensemble of 15 estimators spanning parametric, non-parametric, and machine-learning approaches. We then benchmarked our framework against the classical reaction norm (RN) using three genetically distinct populations and three traits with variable genetic architectures. Furthermore, we released an open-source R package, Multiple-environments genomic selection (MMGS), on GitHub. Together, our study offers a flexible and computationally efficient approach for multi-environment genomic prediction, enhancing breeding efficiency, providing deeper insights into modelling the genotype-environment-phenotype continuum.

As an evolutionarily conserved microRNA (miRNA), miR396 regulates plant growth by integrating developmental and environmental signals. In the present study, CsaWPRa4 , a WEB1 ( Weak Chloroplast Movement under Blue Light 1 )/ PMI2 ( Plastid Movement Impaired 2 )- related protein ( WPR ) family member, was predicted to be a novel target gene of CsamiR396 in cucumbers. WPRa4 is a highly conserved protein in plants. Interestingly, bioinformatic analysis showed that WPRa4 acts as a conserved target gene of miR396 in cucumber and its related species in cucurbits, but not in other plants. The miR396 binding site is located within the coding region of the AAK(K/R)AVE motif in WPRa4, and it evolved by synonymous substitutions in cucurbits. Negative regulation of CsaWPRa4 by CsamiR396 was confirmed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR), luciferase assay, gene overexpression, and tobacco ringspot virus (TRSV)-based gene silencing analysis. The subcellular localization assay showed that CsaWPRa4 was localized to both the cell periphery and nuclear periphery. Thereafter, Csawpra4 mutants were generated using CRISPR/Cas9-mediated gene editing. Chloroplast- and flower morphogenesis-related genes were altered, resulting in altered photosynthetic traits and flower morphogenesis in Csawpra4 mutants. In summary, our results showed that WPRa4 evolved as a novel target of miR396 through synonymous substitutions in cucurbits, uncovering the role of synonymous substitutions in genome evolution and providing a new perspective on miRNA–target evolutionary processes in plants.

Clinacanthus nutans is a traditional medicinal plant widely used in Southeast Asia for treating inflammation, viral infections, and cancer. However, its molecular basis remains poorly understood. In this study, the first chromosome-scale genome of C. nutans (731.61 Mbp) was assembled, with 93.76% anchored to 18 pseudochromosomes. Repetitive elements constituted 69.05% of the genome, predominantly long terminal repeat retrotransposons. Phylogenomic and synonymous substitution rate analyses revealed a Lamiales-wide whole-genome duplication event, followed by extensive chromosomal rearrange- ments. Gene family expansion analysis showed that segmental and dispersed duplications were the primary drivers of enzyme-coding genes (EGs) expansion involved in the flavonoid and triterpenoid pathways. Integrated transcriptomic and metabolomic analyses across five organs revealed distinct organ-specific expression and metabolite profiles. Genes exhibited pronounced differential expression between leaves and roots, with enrichment in flavonoid and triterpenoid biosynthetic pathways, highlighting functional divergence and metabolic specialization. Flavonoids were enriched in aerial tissues, whereas triterpenoids accumulated in roots. Weighted gene co-expression network analysis identified key EGs (e.g. CHS, CHI, OSC) and core transcription factors (e.g. MYB, bHLH, WRKY) potentially involved in organ-specific metabolic regulation. These findings suggest a coordinated transcriptional-metabolic regulatory framework underlying the specialized functions of different tissues. This work provides valuable genomic resources and mechanistic insights into the biosynthesis and regulation of bioactive compounds in C. nutans , thereby facilitating future research and molecular breeding of this important ethnomedicinal plant.

Cannabis sativa is a wind-pollinated, predominantly dioecious, and outcrossing crop associated with high levels of genetic variability even within a single cultivar. As such, seed-grown crops are often constrained by variability issues, decreasing production efficiency and product consistency. F ₁ hybrid seed technology offers great potential to address these limitations by generating genetically uniform populations from a cross of two inbred parental lines. In C. sativa, single-seed descent (SSD) is currently the most viable method to produce these homozygous parental lines necessary for F ₁ hybrid seed production. This study exemplifies the potential of SSD coupled with chemically induced sex reversion to produce fully homozygous lines and its subsequent application in creating five F ₁ hybrid accessions. Up to six rounds of SSD were performed in an 18-month period on 16 different lines, highlighting the speed of methodology. Inbreeding through XY males was most successful and offered the greatest advantages of the lines assessed. The F ₁ hybrid lines were statistically more uniform than the inbred or original lines and more vigorous than the inbred lines, with F ₁ lines increasing seed yield between 3.9% and 155% when compared to their midparents indicating the potential to exploit heterosis. Chemotype stability was achieved in some F ₁ hybrid lines, showing that seed-grown cannabinoid crops would be possible in some contexts using F ₁ hybrid methodology, paving the way for the validation of this breeding technique in field settings and highlighting a path toward commercial hybrid seed systems in C. sativa.

Prunus mume ‘Meiren’, a member of the Meiren cultivar group, is a valuable ornamental woody plant prized for its purple flowers and leaves. However, its leaf color exhibits instability during the growth and development and the underlying mechanisms remain unclear. In our study, we conducted genome-wide methylation analysis on leaves at different developmental stages to investigate the role of methylation patterns and allele-specific methylation (ASM) in leaf color change. Results revealed a significant increase in CHH methylation during leaf development, suggesting its responsiveness to environmental factors and dynamic association with color changes. Notably, CG methylation was imbalanced between the ‘Meiren’ haplotype M (HM) and haplotype C (HC), with the HM subgenome showing higher methylation levels, particularly in promoter regions of key anthocyanin-related genes like PmMYB10.5, where ASM negatively correlated with allele-specific expression. Additionally, we identified two alternative splicing variants of PmMYB10.5b, named PmMYB10.5b1 ( PmMYB10.5b △ I24) and PmMYB10.5bP ( PmMYB10.5b △ D10), respectively. Both the InDel mutations altered the R2 domain structure of the MYB protein. Functional assays demonstrated that these variants lost transcriptional activation ability and failed to promote anthocyanin biosynthesis. Instead, they may compete with the PmMYB10.5b for binding to the PmbHLH3, disrupting regulatory complexes in the anthocyanin pathway and exerting inhibitory effects. These results augment our understanding of the epigenetic and genetic factors influencing leaf color change in ‘Meiren’ and provide novel insights into its regulatory mechanisms.

The genus Philodendron exhibits exceptional diversity and ornamental value, but the genetic and evolutionary mechanisms driving its speciation and trait variation remain largely unknown. In this study, we constructed a haplotype-resolved, near-complete genome of Philodendron tatei to investigate its evolutionary origins, resolve its phylogenomic placement within Araceae, reconstruct karyotype evolution, and explore genetic clusters and hybridization patterns within Philodendron cultivars. Additionally, the genetic and regulatory mechanisms underlying leaf color variation, a key horticultural trait, were explored. Phylogenomic analysis placed Philodendron within the Araceae family and provided insights into its karyotype evolution. Comparative genomic analyses identified five major genetic clusters across the genus, highlighting extensive hybridization and allele-specific expression as key contributors to Philodendron ’s diversity. To investigate leaf color variation, variant mining and transcriptome profiling were conducted on samples with diverse pigmentation. Func- tional validation identified PtSGR1 as a critical regulator of pigmentation formation, with differences in promoter activity driving variation in leaf coloration. Overall, this study provides a comprehensive genomic framework for understanding Philodendron evolution and diversity, tracing the significant role of hybridization in shaping its speciation and identify- ing key genetic mechanisms underlying ornamental traits. These insights advance our understanding of plant evolution, contribute to horticultural innovation, and enhance the genetic resources available for studying this ecologically and economically important genus.

Pear ( Pyrus L.) is a fruit tree of global commercial importance. Its genetic relationships, evolutionary history, dissemination routes, and genetic determinants of most agronomic traits remain to be elucidated. We conducted whole-genome resequencing of 495 Pyrus accessions. Phylogenetic and demographic analyses resolved geographic groupings of the accessions, identifying the Yunnan–Guizhou Plateau as the putative dissemination center for cultivated Pyrus pyrifolia and P. bretschneideri. Identification of two evolutionary bottlenecks provides insights into the population dynamics of pear species. Admixture and introgression analyses revealed both intraspecific and interspecific genetic exchanges, substantiating the complex emergence of cultivated populations. Genome-wide association study (GWAS) identified loci associated with nine crucial agronomic traits, together with eight candidate genes. The GWAS, molecular, and biochemical analyses suggested that PbeMADS25, PbeSPP, PbeDHQ-SDH, PbeARF2, PbePPO, PbePIN3, PbeCXE, and PbeMYB38 participate in the regulation of number of stigmas and number of locules, number of stamens, young leaf color, sepal persistence, astringency, acidity, aroma, and fruit skin color, respectively. Overexpression and metabonomic analysis of PbeCXE indicated that it affects the fruit aroma by affecting the balance between ester biosynthesis and substrate consumption. These findings expand our understanding of Pyrus evolution and provide a genomic foundation for genetic improvement of agronomic traits.

Skin color is a crucial quality trait in cucumber fruit, yet the regulatory mechanisms underlying cucumber skin color remain poorly understood. In this study, we characterized a cucumber natural mutant displaying yellow peel, and identified a key gene yellow peel ( CsYP) through map-based cloning. CsYP encodes a rhodanese-like protein with a Rhod domain. A single-base insertion results in premature termination of protein translation, leading to the yellowing pericarp phenotype in the natural mutant. To further investigate the function of CsYP, two knockout lines, yp-1 and yp-2, were generated using CRISPR-Cas9 technology. Phenotypic investigation of yp-1 and yp-2 revealed a significant yellowing of the pericarp starting from 6 days after pollination, consistent with the natural mutant phenotype. Additionally, our study revealed an interaction between CsYP and Cscytb6f, a cytochrome b6-f complex iron–sulfur subunit, suggesting a collaborative role of CsYP and iron–sulfur proteins in regulating cucumber peel color. These findings provide novel insights into the regulatory mechanisms underlying cucumber peel color and broaden our understanding of this important trait.

Plant etiolation, a critical process for seedling emergence, is regulated by ethylene and target of rapamycin (TOR) signaling pathways. However, the cell-type-specific regulation of these pathways remains poorly understood. To address this, we generated a comprehensive single-nucleus RNA transcriptome atlas of etiolated apical hooks and hypocotyls in tomato seedlings treated with the ethylene precursor aminocyclopropane-1-carboxylic acid (ACC), the TOR inhibitor Torin2, or a mock treatment. In total, we obtained high-quality gene expression profiles for 117 929 nuclei across these tissues and treatments. Our analysis identified seven major cell types within each tissue, revealing distinct cellular compositions and transcriptional programs. ACC treatment increased the proportion of epidermal cells in apical hooks, while Torin2 had limited impact on cellular composition. Differential gene expression analysis demonstrated tissue-specific sensitivity to these treatments: apical hooks exhibited extensive ACC-responsive differentially expressed genes, whereas hypocotyls were highly responsive to Torin2. Cellular responsiveness analysis uncovered divergent ethylene/auxin pathway activities, such as ACC-repressed auxin transport in hook endodermis-like cells. Dynamic trajectory analysis indicated both treatments altered cell differentiation, authenticating epidermis as the key cell type for ethylene-mediated etiolated growth. Crucially, we identified JA1 (HD-ZIP I TF) as a negative ethylene regulator enriched in epidermis, and CRISPR knockout ja1 mutants exhibited hypersensitivity to ACC. This study deciphers cell-type-specific ethylene-TOR crosstalk, providing a robust single-cell RNA sequencing framework to dissect signaling networks in crops.

Pathogenic bacteria deploy biofilm as a key virulence factor to cause plant vascular diseases, which are devastating to global agricultural practices. Extracellular DNA (eDNA) constitutes the backbone of bacterial biofilm and is key to biofilm stability, thereby representing as an attractive therapeutic target. Here, we engineered the plant chloroplast-localized Holliday junction (HJ) resolvase MOC1 by replacing its native chloroplast transit peptide with a secretory signal, successfully relocating it to the apoplast. Transgenic tomato and rice expressing secreted MOC1 exhibited robust resistance to bacterial wilt and bacterial blight, respectively, without growth or yield penalties. Additionally, we implemented bacterial pathogen-inducible promoters to achieve precisely spatial and temporal control over the resistance trait. Secreted MOC1 degrades eDNA in situ, disrupts biofilm architecture, and markedly reduces bacterial colonization and systemic spread. Our work presents a novel strategy for controlling vascular diseases by engineering plant HJ resolvases to disrupt biofilms. This approach provides a new blueprint for molecular resistance breeding and disease resistance gene exploration.

Histone modification is an important part of epigenetic research and plays a significant role in maintaining the stability of eukaryotic genomes, regulating gene expression, and chromatin remodeling. Histone methylation is one of the most complex modification forms in epigenetic regulation, which can occur on specific lysine or arginine residues at the tail of histones. Its biological function depends on the degree of methylation (me/me2/me3). Histone methylation involves multiple links, such as ‘writer’, ‘reader’, and ‘eraser’ enzymes, and can activate or inhibit gene transcription by recruiting various downstream effector proteins. As molecular biology techniques have advanced, significant progress has been made in fundamental research on histone methylations in plants, and researchers have gained insights into its complex multilevel regulatory mechanisms. This review systematically summarizes recent advances in the roles of histone methylation in regulating plant dormancy and germination, flowering and senescence, as well as stress responses, and proposes a cross-regulatory model integrating histone methylation with multiple signaling pathways. These insights provide a theoretical foundation for the application of epigenetic breeding strategies in horticultural crops, with the goal of enhancing stress tolerance and yield.

Citrus species are economically and nutritionally vital, with their fruits cultivated globally. Despite the publication of multiple genomes for Citrus, high-quality assemblies that achieve both haplotype resolution and telomere-to-telomere (HR-T2T) continuity remain scarce—pummelo ( Citrus maxima) being a notable example. Compounded by limitations in gene annotation quality, these gaps hinder functional genomic research and genomics-assisted breeding. Here, we report the first high-quality HR–T2T genome assembly of pummelo, generated using PacBio HiFi and Oxford Nanopore sequencing. The two haplotype assemblies presented contig N50 values of 38.58 and 32.57 Mb, completeness scores of 99.36% and 99.66%, and nucleotide accuracies of 99.99994% and 99.99997%, respectively. We developed HapGene, a haplotype-aware annotation pipeline that integrates short-read RNA-Seq and long-read Iso-Seq data to enable unbiased annotation. Benchmarking showed HapGene captured 3% to 10% of genes missed or misannotated by conventional pipelines and reduces false haplotype-specific genes by 4- to 5-fold. Leveraging 380 Gb of newly sequenced and 2792 Gb of public transcriptomic data, we comprehensively annotated protein-coding and non-coding genes across three major Citrus crops (sweet orange, pummelo, and mandarin). This effort revealed 18 757–21 083 alternative splicing events, 1725–1853 resistance gene analogues, and 2392–3757 long intergenic RNAs (lincRNAs). Genomic and transcriptomic characterization of lincRNAs indicated their functional innovation (many associated with stress responses) in Citrus. Additionally, we revealed around one-third of genes exhibited tissue-specific allelic differential expression. Our work provides a critical genomic resource and analytical tool to advance Citrus genomic research, thereby driving progress in functional and evolutionary genomics while laying a robust foundation for precise genomics-assisted breeding.

Papaya is a major tropical fruit crop with notable nutritional and economic value, yet its genetic improvement through modern breeding technologies faces substantial challenges. The traditional tissue culture process is both labor-intensive and time-consuming, causing gene-editing advancements in papaya to lag behind those in other crops. To overcome these obstacles, we developed a tissue culture–independent hairy root system in papaya, which enables efficient gene editing and significantly enhances the application and development of editing tools. This innovative platform allows for the pre-assessment of editing efficiency and supports the establishment of adenine base editor (ABE) and cytosine base editor (CBE) tools in papaya, thereby mitigating the high failure costs associated with the lengthy cycle of conventional genetic transformation. Utilizing this system, we pre-tested sgRNA activity and achieved high editing efficiency of CpWIP3 during stable transformation. Additionally, through promoter screening, we successfully developed ABE and CBE tools, marking the first precise single-nucleotide editing system in papaya. This gene-editing system provides a crucial platform for advancing functional genomics and accelerating precision breeding in papaya.

Chinese jujube ( Ziziphus jujuba Mill., 2 n = 2 x = 24) is a drought-tolerant, nutrient-rich fruit crop. However, its genetic improvement is constrained by protandry, low fruit set, and severe embryo abortion. Interspecies hybridization between Chinese jujube and Indian jujube ( Ziziphus mauritiana Lam., 2 n = 4 x = 48) is further hindered by asynchronous flowering. We developed a dual-regime protocol combining temperature control and strategic heavy pruning to advance the flowering time of Indian jujube (cultivar ‘Niunaidaqingzao’, N) by 2 months, thereby synchronizing its anthesis with that of Chinese jujube (‘Dongzao’, D) and wild Chinese jujube (‘Suanzao’, S). In vitro artificial self-pollination (AS) and in vitro artificial cross-pollination (AC) were conducted to assess pollen tube elongation and ovary expansion. Triple AS (TAS) boosted pollen tube emergence to 59%–87% across the three genotypes, more than doubling in vitro spontaneous self-pollination (SSP) rates and outperforming single AS 1.4 to 2.7 times ( P < 0.05). Ovary-swelling frequencies of TAS reached 68.52% in wild Chinese jujube S and 27.78% in Indian jujube N, indicating 2.85 and 2.14 times increases over SSP and 1.88–4.11 times increases over single AS. In ♀S × ♂D, ♀D × ♂S, and ♀S × ♂N crosses, triple AC (TAC) raised pollen tube emergence to 54%–72% (1.3–2.2 times of single AC) and ovary expansion to 26%–39% (1.4–1.9 times of single AC) ( P < 0.05). These findings provide a practical and efficient strategy for overcoming asynchronous flowering and reproductive barriers of interspecies hybridization in genus Ziziphus, enabling the establishment of interspecies hybrid populations for downstream breeding programs.

Chilli incurs substantial yield losses due to Thrips parvispinus (Karny) infestation, necessitating sustainable resistance breeding strategies. Understanding biochemical basis of resistance will help in exploring the candidate metabolites for indirect selection. LC–MS and GC–MS profiling of two resistant (IIHR-B-HP-79, IIHR 4550) and two susceptible (IIHR 3455, IIHR 4604) chilli accessions were performed. LC–MS profiling revealed Inositol with higher levels in susceptible accession IIHR 3455 (8.74 and 0.33 μ g/g; VIP score: 2 and 2.5 under control and infested conditions respectively), indicating its role as a stress-induced metabolite rather than a marker for resistance. Secondary metabolites contribution to resistance was genotype-specific and may possibly be driven by complex interactions among these metabolites. Untargeted leaf volatile profiling revealed Hex-3(Z)-enyl butyrate as a significant volatile compound in the resistant accessions IIHR 4550 and IIHR-B-HP-79. Its high accumulation across two different species suggests that its production is not strictly species-specific. Validation of Hex-3(Z)-enyl butyrate through bioassays and olfactometer studies demonstrated reduced scraping damage percentage at 8 and 16 μ L -L concentrations in leaf dip bioassays. Four-arm olfactometer studies indicated that Hex-3(Z)-enyl butyrate significantly affected T. parvispinus time spent and entries at 16 μ L -L . Identified metabolites defences can serve as markers for breeding and also can be explored in pest management strategies.