Pucai (蒲菜) (Typha angustifolia L.), within the Typha spp., is a distinctive semiaquatic vegetable. Lignin and chlorophyll are two crucial traits and quality indicators for Pucai. In this study, we assembled a 207.00-Mb high-quality gapless genome of Pucai, telomere-to-telomere (T2T) level with a contig N50 length of 13.73 Mb. The most abundant type of repetitive sequence, comprising 16.98% of the genome, is the long terminal repeat retrotransposons (LTR-RT). A total of 30 telomeres and 15 centromeric regions were predicted. Gene families related to lignin, chlorophyll biosynthesis, and disease resistance were greatly expanded, which played important roles in the adaptation of Pucai to wetlands. The slow evolution of Pucai was indicated by the σ whole-genome duplication (WGD)-associated Ks peaks from different Poales and the low activity of recent LTR-RT in Pucai. Meanwhile, we found a unique WGD event in Typhaceae. A statistical analysis and annotation of genomic variations were conducted in interspecies and intraspecies of Typha. Based on the T2T genome, we constructed lignin and chlorophyll metabolic pathways of Pucai. Subsequently, the candidate structural genes and transcription factors that regulate lignin and chlorophyll biosynthesis were identified. The T2T genomic resources will provide molecular information for lignin and chlorophyll accumulation and help to understand genome evolution in Pucai.

Alfalfa (Medicago sativa L.), a perennial legume forage, has been broadly cultivated owing to a variety of favorable characteristics, including comprehensive ecological adaptability, superior nutritive value and palatability, and nitrogen fixation capacity. The productivity traits of alfalfa, specifically its biomass yield and forage quality, are significantly influenced by a series of determinants, including internal developmental factors and external environmental cues. However, the regulatory mechanisms underlying the fundamental biological problems of alfalfa remain elusive. Here, we conducted a comprehensive review focusing on the genomics of alfalfa, advancements in gene-editing technologies, and the identification of genes that control pivotal agronomic characteristics, including biomass formation, nutritional quality, flowering time, and resistance to various stresses. Moreover, a molecular design roadmap for the ‘ideal alfalfa’ has been proposed and the potential of pangenomes, self-incompatibility mechanisms, de novo domestication, and intelligent breeding strategies to enhance alfalfa's yield, quality, and resilience were further discussed. This review will provide comprehensive information on the basic biology of alfalfa and offer new insights for the cultivation of ideal alfalfa.

Salicylic acid (SA) and jasmonic acid (JA) are the two most important phytohormones in plant immunity. While SA plays pivotal roles in local and systemic acquired resistance (SAR) against biotrophic pathogens, JA, on the other hand, contributes to defense against necrotrophic pathogens, herbivores, and induced systemic resistance (ISR). Over the past 30 years, extensive research has elucidated the biosynthesis, metabolism, physiological functions, and signaling of both SA and JA. Here, we present an overview of signaling pathways of SA and JA and how they interact with each other to fine-tune plant defense responses.

Lignin is a major component of the plant cell wall and has a conserved basic defense function in higher plants, helping the plants cope with pathogen infection. However, the regulatory mechanism of lignin biosynthesis in plants under phytoplasma stress remains unclear. In this study, we reported that peroxidase 51 (ZjPOD51), which is involved in lignin monomer polymerization, was induced by phytoplasma infection and that overexpression of ZjPOD51 in phytoplasma-infected jujube seedlings and Arabidopsis plants significantly increased their defense response against phytoplasma. Yeast one-hybrid (Y1H) and luciferase (LUC) assays showed that ZjPOD51 transcription was directly upregulated by ZjMYB44. Genetic validation demonstrated that ZjMYB44 expression was also induced by phytoplasma infection and contributed to lignin accumulation, which consequently enhanced phytoplasma defense in a ZjPOD51-dependent manner. These results demonstrated that the ZjMYB44-ZjPOD51 module enhanced the jujube defense response against phytoplasma by upregulating lignin biosynthesis. Overall, our study first elucidates how plants regulate lignin to enhance their defense response against phytoplasma and provides clues for jujube resistance breeding.

The tea plant (Camellia sinensis) is a typical crop that accumulates aluminum (Al). Although the physiological mechanisms by which this occurs are well understood, their molecular mechanisms remain elusive. Here, an integrative approach combining quantitative trait locus (QTL) mapping of controlled hybridized populations and comparative transcriptomic analysis using samples treated with different Al concentrations was applied to identify candidate genes associated with Al accumulation in tea plants. Consequently, 41 candidate genes were selected using genome functional annotation of the qAl09 locus in the region of 35 256 594-57 378 817 bp on chromosome 7. Finally, a key gene, CsWRKY17, was identified as encoding a nucleus-localized transcription factor involved in regulating Al accumulation in tea plants, given the finding of a high correlation between its expression level and Al content in leaves. Overexpression of CsWRKY17 in Arabidopsis increased pectin deesterification, sensitivity to Al stress, and Al accumulation in leaves. Expression of the pectin methylesterase gene CsPME6 was found to be highly consistent with CsWRKY17 expression under various Al concentrations. In addition, experiments using a yeast monoclonal, electrophoresis mobility shift assay and dual-luciferase reporter (DLR) system confirmed that CsWRKY17 activated CsPME6 promoter activity. Antisense oligodeoxynucleotide silencing revealed a positive association between CsPME6 expression and Al accumulation in tea shoots. In conclusion, this study suggests that CsWRKY17 promoted the process of pectin deesterification by binding to the CsPME6 promoter, thereby enhancing Al enrichment in tea plants. Our findings lay the foundation for studying the precise mechanisms through which Al enriched in tea leaves.

Parthenocarpy is a desirable trait that enables fruit set in the absence of fertilization. While blueberries typically depend on pollination for optimal yield, certain genotypes can produce seedless fruits through facultative parthenocarpy, eliminating the need for pollination. However, the development of parthenocarpic cultivars has remained limited by the challenge of evaluating large breeding populations. Thus, establishing molecular breeding tools can greatly accelerate genetic gain for this trait. In the present study, we evaluated two blueberry breeding populations for parthenocarpic fruit set and performed genome-wide association studies (GWAS) to identify markers and candidate genes associated with parthenocarpy. We also compared the predictive ability (PA) of three molecular breeding approaches, including (i) genomic selection (GS); (ii) GS de novo GWAS (GSdnGWAS), which incorporates significant GWAS markers into the GS model as prior information; and (iii) in silico marker-assisted selection (MAS), where markers from GWAS were fitted as fixed effects with no additional marker information. GWAS analyses identified 55 marker-trait associations, revealing candidate genes related to phytohormones, cell cycle regulation, and seed development. Predictive analysis showed that GSdnGWAS consistently outperformed GS and MAS, with PAs ranging from 0.21 to 0.36 depending on the population of study and the specific markers utilized. MAS showed PAs comparable to GS in some cases, suggesting it could be a cost-effective alternative to genome-wide sequencing. Together, these findings demonstrate that molecular breeding techniques can be used to improve facultative parthenocarpy, offering new avenues to develop high-yielding blueberry varieties that are less reliant on pollination.

Increasing marker density results in better map coverage and efficiency of genetic analysis. Here, we resequenced a large (N = 235) F1 progeny from two distant peach cultivars, ‘Zhongyou Pan #9’ and ‘September Free’, and constructed two parental maps (1:1 segregations) and one combined map (1:2:1 segregations) with 134 277 SNPs. Markers with the same genotype for all individuals studied were grouped in bins and a unique genotype for each bin was inferred to avoid mapping problems derived from erroneous data. The total genetic distance of the two parental maps was 431.9 and 594.2 cM with a short mean distance, 0.9 cM, between contiguous bins (groups of markers with the same genotype) and high collinearity with the peach genome. The genetics of eight fruit-related traits was analyzed for 2 years, allowing the positions of two major genes, fruit shape (S) and flesh adhesion to the stone (F), to be established, along with nine quantitative trait loci (QTLs) for quantitative traits including fruit soluble solids concentration, titratable acidity, weight, maturity date, and flesh color (yellow to orange). We developed a machine learning-based linear model to assess flesh color, which proved more efficient than physical colorimetric parameters (L, a^*, b^*), detecting consistent QTLs. Based on map position, gene expression patterns, and function, candidate genes were identified. Overall, our results provide two new elements: ultra-high-density maps with resequencing data to enhance mapping resolution and phenotyping strategies based on machine learning models that improve the quality of quantitative measurements to help understand the genetic control of key fruit quality traits.

While breeding for improved immunity is essential to achieve sustainable fruit production, it also requires to account for genotype-by-environment interactions (G × E), which still represent a major challenge. To tackle this issue, we conducted a comprehensive study to identify genetic markers with main and environment-specific effects on pest and disease response in peach (Prunus persica) and apricot (Prunus armeniaca). Leveraging multienvironment trials (MET), we assessed the genetic architecture of resistance and tolerance to seven major pests and diseases through visual scoring of symptoms in naturally infected core collections, repeated within and between years and sites. We applied a series of genome-wide association models (GWAS) to both maximum of symptom severity and kinetic disease progression. These analyses lead to the identification of environment-shared quantitative trait loci (QTLs), environment-specific QTLs, and interactive QTLs with antagonist or differential effects across environments. We mapped 60 high-confidence QTLs encompassing a total of 87 candidate genes involved in both basal and host-specific responses, mostly consisting of the Leucine-Rich Repeat Containing Receptors (LRR-CRs) gene family. The most promising disease resistance candidate genes were found for peach leaf curl on LG4 and for apricot and peach rust on LG2 and LG4. These findings underscore the critical role of G × E in shaping the phenotypic response to biotic pressure, especially for blossom blight. Last, models including dominance effects revealed 123 specific QTLs, emphasizing the significance of non-additive genetic effects, therefore warranting further investigation. These insights will support the development of marker-assisted selection to improve the immunity of Prunus varieties in diverse environmental conditions.

Fleshy fruits are vital to the human diet, providing essential nutrients, such as sugars, organic acids, and dietary fibers. RNA-binding proteins play critical functions in plant development and environment adaption, but their specific contributions to fruit development remain largely unexplored. In this study, we centered on the function of SlRBP1 in tomato fruit and reported an unexpected finding that SlRBP1 controls fruit size by regulating its targets SlFBA7 and SlGPIMT. Here, the fruit-specific silencing of SlRBP1 was achieved by artificial miRNA which subsequently led to a marked reduction of fruit size. Cytological analysis suggested that SlRBP1 silencing decreased cell division and expansion of fruit pericarp. Those key genes involved in cell development were significantly repressed in SlRBP1 knock-down mutants. Furthermore, native RNA immunoprecipitation sequencing deciphered 83 SlRBP1-binding target RNAs in fruit, including two targets that are highly expressed in fruit: SlFBA7 and SlGPIMT, which are involved in developing fruit. Indeed, silencing either SlFBA7 or SlGPIMT resulted in fruit size reduction identical to that seen with SlRBP1 silencing. These results suggest that SlRBP1 modulates fruit size through its targets SlFBA7 and SlGPIMT. Our findings provide novel perspectives on the molecular mechanisms though which RNA-binding proteins control fruit size.

Paeonia plants are famous for their ornamental, medicinal, and oil values. Due to the popularity of seed oil and cut flowers in the market, the mechanisms underlying related traits of Paeonia plants have been fascinating, and the research work on them has increased rapidly in recent years, urging a comprehensive review of their research progress. To unlock the molecular secrets of Paeonia plants, we first summarize the latest advances in their genome research. More importantly, we emphasize the key genes involved in plant growth and development processes, such as bud dormancy, flowering regulation, seed oil formation, flower coloration, stem strength regulation, fragrance emission, as well as plant resistance to stress, including drought, high-temperature, low-temperature, salt, and waterlogging stresses, and biotic stress. In addition, the advances in molecular breeding technology of Paeonia plants are highlighted, such as molecular marker, genetic map, localization of quantitative trait loci, tissue culture, and genetic transformation system. This review covers advances in the past decades and provides valuable insights into the perspectives for the key gene mining and molecular breeding technology of Paeonia plants, which would help breed new Paeonia varieties through molecular breeding technology.

Food legume crops, including common bean, faba bean, mungbean, cowpea, chickpea, and pea, have long served as vital sources of energy, protein, and minerals worldwide, both as grains and vegetables. Advancements in high-throughput phenotyping, next-generation sequencing, transcriptomics, proteomics, and metabolomics have significantly expanded genomic resources for food legumes, ushering research into the panomics era. Despite their nutritional and agronomic importance, food legumes still face constraints in yield potential and genetic improvement due to limited genomic resources, complex inheritance patterns, and insufficient exploration of key traits, such as quality and stress resistance. This highlights the need for continued efforts to comprehensively dissect the phenome, genome, and regulome of these crops. This review summarizes recent advances in technological innovations and multi-omics applications in food legumes research and improvement. Given the critical role of germplasm resources and the challenges in applying phenomics to food legumes—such as complex trait architecture and limited standardized methodologies—we first address these foundational areas. We then discuss recent gene discoveries associated with yield stability, seed composition, and stress tolerance and their potential as breeding targets. Considering the growing role of genetic engineering, we provide an update on gene-editing applications in legumes, particularly CRISPR-based approaches for trait enhancement. We advocate for integrating chemical and biochemical signatures of cells (‘molecular phenomics’) with genetic mapping to accelerate gene discovery. We anticipate that combining panomics approaches with advanced breeding technologies will accelerate genetic gains in food legumes, enhancing their productivity, resilience, and contribution to sustainable global food security.

Plant-metabolite-microbe interactions play essential roles in disease suppression. Most studies focus on the root exudates and rhizosphere microbiota to fight soil-borne pathogens, but it is poorly understood whether the changes in phyllosphere metabolites can actively recruit beneficial microbes to enhance disease resistance. In this study, the differences of phyllosphere microbial communities and key leaf metabolites were systematically explored in resistant and susceptible black currant cultivars related to powdery mildew (PM) by integrating microbiome and metabolomic analyses. The results showed that the diversity and composition of microbiome changed, as highlighted by a reduction in microbial alpha-diversity and beta-diversity of susceptible cultivars. An increasing fungal network complexity and a decreasing bacterial network complexity occurred in resistant cultivar. Bacillus, Burkholderia (bacteria), and Penicillium (fungi) were identified as keystone microorganisms and resistance effectors in resistant cultivar. Metabolites such as salicylic acid, trans-zeatin, and griseofulvin were more abundant in resistant cultivar, which had a positive regulatory effect on the abundance of bacterial and fungal keystones. These findings unravel that resistant cultivar can enrich beneficial microorganisms by adjusting leaf metabolites, thus showing the external disease-resistant response. Moreover, the reduced stomatal number and increased tissue thickness were observed in resistant cultivar, suggesting inherent physical structure also provides a basic defense against PM pathogens. Therefore, resistant black currant cultivar displayed multilevel defense responses of physical structures, metabolites, and microorganisms to PM pathogens. Collectively, our study highlights the potential for utilizing phyllosphere microbiome dynamics and metabolomic adjustments in agricultural practices, plant breeding, and microbiome engineering to develop disease-resistant crops.

Cold stress poses a significant threat to viticulture, particularly under the increasing pressures of climate change. In this study, we identified VaMIEL1, a RING-type E3 ubiquitin ligase from Vitis amurensis, as a negative regulator of cold tolerance. Under normal temperature conditions, VaMIEL1 facilitates the ubiquitination and subsequent proteasomal degradation of the cold-responsive transcription factor VaMYB4a, thereby attenuating its regulatory role in the CBF-COR signaling cascade. However, under cold stress, VaMIEL1 expression is downregulated, leading to the stabilization of VaMYB4a and the activation of CBF-COR signaling. Through a combination of biochemical assays and functional analysis in Arabidopsis thaliana and grapevine calli, we demonstrate that VaMIEL1 overexpression reduces cold tolerance, as evidenced by increased oxidative stress, excessive reactive oxygen species (ROS) accumulation, and downregulated expression of cold-responsive genes. Conversely, silencing of VaMIEL1 enhances cold tolerance by stabilizing VaMYB4a and boosting antioxidant defenses. These findings uncover a previously unrecognized regulatory mechanism by which VaMIEL1 modulates cold tolerance through transcriptional and oxidative stress pathways, offering potential targets for the development of climate-resilient grapevine cultivars and other crops.

The precise timing of flowering in response to environment plays a crucial role in the reproductive processes of plants. The FLOWERING LOCUS T (FT)-FD module is a well-established key node in the photoperiod-mediated pathway. However, the identity of novel partners involved in this network and its regulatory mechanisms remain elusive in most nonmodel species. Here, we found that TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR7 (CmTCP7) functions as a floral repressor in Chrysanthemum morifolium. Its upstream transcriptional regulator AUXIN RESPONSE FACTOR3 (CmARF3) promotes flowering by directly repressing CmTCP7 expression. The expression levels of both genes are short-day inducible. Interestingly, FLOWERING LOCUS T-like3 (CmFTL3) interacts with FD-like1 (CmFDL1), which activates flowering-accelerating gene Chrysanthemum Dendrathema MADS111-like (CmCDM111L). Meanwhile, CmTCP7 interacts with CmFTL3 and CmFDL1, delaying the CmFTL3 and CmFDL1 complex-promoted flowering in chrysanthemum “Jinba.” These findings reveal a novel regulatory module controlling photoperiod-dependent flowering in chrysanthemum.

Tanshinones are valuable compounds found in Salvia miltiorrhiza, and gaining a deeper understanding of their transcriptional regulation mechanisms is a key strategy for increasing their content. Previous research revealed that SmWRKY32 acts as a repressor of tanshinone synthesis. This study identified the SmbHLH65 transcription factor, whose expression was significantly reduced in the SmWRKY32 overexpression transcriptome. Overexpression of SmbHLH65 stimulated tanshinone accumulation, while its silencing resulted in a decrease in tanshinone content. However, SmbHLH65 does not directly target the key enzyme genes involved in tanshinone synthesis. Subsequently, we discovered the SmbHLH65-interacting protein SmbHLH85. SmbHLH85 facilitates tanshinone biosynthesis by directly upregulating SmDXS2 and SmCPS1. Further investigation demonstrated that SmbHLH65 not only promotes the expression of SmbHLH85 but also enhances its binding to the promoters of SmDXS2 and SmCPS1, thereby amplifying the activation of these biosynthetic genes. Additionally, SmWRKY32 directly binds to the SmbHLH65 promoter to suppress its activity. In summary, these findings reveal that the regulatory module SmWRKY32-SmbHLH65/SmbHLH85 controls tanshinone synthesis in S. miltiorrhiza. This study uncovers a novel transcriptional regulatory mechanism, offering fresh insights into the complex network controlling tanshinone biosynthesis.

Euphorbiaceae species are renowned not only for horticultural significance but for their production of numerous bicyclic diterpenes with antitumor and antiviral activities. However, the gene clusters responsible for the biosynthesis of these terpenes remain largely unidentified. We here initiated the construction of a comprehensive procedure for terpene gene clusters in Euphorbiaceae species. A total of 1824 candidate gene clusters with the range of 30-800 kb were identified across seven representative species including Ricinus communis, Hevea brasiliensis, Euphorbia peplus, Jatropha curcas, Manihot esculenta, Vernicia montana, and Vernicia fordii in Euphorbiaceae. The 16 high-confidence terpene gene clusters were ultimately pinpointed in Euphorbiaceae after satisfied the three stringent screening criteria: TPS/CYP pairwise relationship, copathway and coexpression patterns. Notably, the well-known casbene and casbene-derived diterpenoid gene cluster, involved in the biosynthesis of casbene, neocembrene, ingenanes, and jatrophanes, were identified. It was observed that casbene gene clusters were universally presented in Euphorbiaceae species, except M. esculenta. Among the casbene gene cluster, the alcohol dehydrogenase (ADH) was initially appeared, and neocembrene synthase is exclusively present in R. communis while absent in all the other species. These findings represent a significant step toward understanding the genetic basis of terpene biosynthesis in Euphorbiaceae species. Moreover, this knowledge on gene clusters responsible for the biosynthesis of pharmacologically relevant terpenes can serve as a theoretical foundation for future applications.

Mechanical harvesting in the tea industry has become increasingly essential due to its advantages in increasing productivity and reducing labor costs. Leaf droopiness caused a high rate of broken leaves, hindering the mechanized harvesting quality. However, the underlying mechanisms remain unclear. We herein identified a quantitative trait locus, designated as q10.3, along with three lead single nucleotide polymorphisms (SNPs) located near a TPR gene (TETRATRICOPEPTIDE REPEAT), named CsTPR, through performing a genome-wide association study (GWAS) on 130 tea accessions. Integrated analysis of RNA-seq and ATAC-seq confirmed CsTPR as a droopiness-associated candidate gene at the transcriptional level. CsTPR was then proved to negatively regulate brassinosteroid-induced droopiness by using the CsTPR-silencing tea plant. Whole-genome sequencing (WGS) combined with genome walking further indicated that a single-base mutation (T-A) in the promoter of CsTPR. ChIP-seq revealed that this mutation occurred within the binding site, E-box, of CsBES1.2 on the CsTPR promoter. Notably, CsBES1.2 bound the E-box of CsTPR promoter to repress the expression of CsTPR, as demonstrated by chromatin immunoprecipitation quantitative polymerase chain reaction (ChIP-qPCR), electrophoretic mobility shift assays (EMSA), and transient assays. The single-base mutation strengthened the inhibitory effect of CsBES1.2 on the expression of CsTPR via enhancing the binding affinity to the E-box. Altogether, our findings suggest that CsTPR negatively regulates droopiness in tea plants under the transcriptional repression of CsBES1.2 and that a single-base mutation within E-box amplifies the suppression of CsBES1.2 on the expression of CsTPR.

Gray blight is a serious foliar disease that significantly threatens tea plant cultivation. Although dynamic histone methylation was reported in regulating plant immunity, the specific roles of this epigenetic modification in tea plant disease resistance have yet to be fully elucidated. This study demonstrates that the protein arginine methyltransferase CsPRMT5, which catalyzes the symmetric dimethylation of histone H4R3 (H4R3sme2), is involved in the tea plant response to gray blight. Transcription of CsPRMT5 and the level of histone H4R3 methylation in tea were downregulated following infection by the fungal pathogen Pseudopestalotiopsis (Ps). A negative correlation was observed between the resistance of tea plants to Ps and the expression level of CsPRMT5 across various cultivars. Downregulation of CsPRMT5 expression led to reduced H4R3sme2 levels, elevated expression of defense-related genes, and lower reactive oxygen species (ROS) production after Ps infection, thus enhancing pathogen resistance of tea. Furthermore, complementation of Atprmt5 mutant with CsPRMT5 restored the susceptibility to Ps infection in Arabidopsis. Chromatin Immunoprecipitation Sequencing (ChIP-seq)and Chromatin Immunoprecipitation quantitative PCR (ChIP-qPCR) analyses revealed that CsPRMT5 binds to defense-related genes, including CsMAPK3, and regulates their expression through H4R3sme2 modification. Collectively, the results indicate that CsPRMT5 negatively regulates the immune response to pathogens through repressing CsMAPK3 expression in tea plants.

Drought stress limits plant growth, development, and yield in apple (Malus). Strigolactones (SLs) work with abscisic acid (ABA) to improve drought resistance in plants, but how this synergistic mechanism functions remains unclear. Here, we determined that SLs promote drought resistance in apple in an ABSCISIC ACID INSENSITIVE5 (MsABI5)-related manner. During drought stress of a wild apple species (Malus sieversii), SLs enhanced the expression of MsABI5, encoding a major transcription factor involved in ABA signaling. MsABI5 bound to the promoter of the gene encoding delta-1-pyrroline-5-carboxylate synthase (MsP5CS2.2), upregulating its expression and thereby enhancing proline accumulation and drought resistance. In addition, MsABI5 suppressed the expression of MsSMXL1, encoding a major transcriptional repressor involved in SL signaling. MsSMXL1 interacted with MsNAC022 instead of MsABI5 to repress the transactivation activity of MsNAC022. MsNAC022 was upregulated by MsABI5, and MsNAC022 directly promoted MsP5CS2.2 expression to enhance proline accumulation and drought resistance. These findings suggest that MsSMXL1 and MsNAC022 comprise a regulatory node downstream of MsABI5 during drought stress in apple. Together, our findings suggest that in apple, SLs increase drought resistance by activating the MsABI5-MsSMXL1-MsNAC022 cascade.

Lignin deposition in stone cells is a critical factor that limits pear fruit quality, affecting their market value. Calcium ions (Ca ²⁺) play an essential role in lignin biosynthesis during fruit stone cell production. However, the genetic mechanisms underlying the Ca ²⁺ regulated lignin synthesis in stone cell formation are not fully understood. In this study, we identified an NAC transcription factor (TF) PuNAC21, which is repressed by CaCl₂ treatment. PuNAC21 bound directly to the lignin biosynthesis gene peroxidase 42-like (PuPRX42-like) promoter, Ca²⁺ reduced pear fruit stone cell production dependent on PuNAC21 positively regulating PuPRX42-like expression. Furthermore, PuNAC21 directly regulated the expression of PuDof2.5, a TF involved in lignin biosynthesis by binding to PuPRX42-like and caffeoyl-CoA-O-methyltransferase 1(PuCCoAOMT1) promoters. Moreover, PuNAC21 interacted with PuDof2.5 to form a transcriptional regulatory module, lowering the transcription of PuPRX42-like and PuCCoAOMT1 after Ca²⁺ treatment, which contributed to decrease pear stone cells production. Our results revealed Ca²⁺-induced PuNAC21-PuDof2.5-PuPRX42-like/PuCCoAOMT1 regulatory module inhibited lignin biosynthesis, giving important insights into reducing the stone cell content in pears via molecular breeding.

Seasonal nitrogen (N) storage and remobilization are critical for tree growth. Deciduous trees primarily store N in bark; evergreen trees utilize both mature leaves and bark. Citrus is an evergreen species; leaf N storage and remobilization are well studied, but inner bark remains poorly understood. This study used pot experiments with N supply rates (low, moderate and high) to examine seasonal (winter, early, and late spring) N storage and remobilization between mature leaves (developed in autumn) and bark (main stem). Bark contains 15-35 kDa of vegetative storage proteins (VSPs), which are highly abundant and accumulate seasonally, while mature leaves contain 45-55 kDa of VSPs. Proteomic analysis revealed the oxygen-evolving enhancer protein as a key bark VSP, with Rubisco and others predominant in leaves. Under high N supply, the reduction ratio of total N content in bark from winter to early spring was higher than that in mature leaves. Under high N supply, bark arginine decreased significantly in early spring, whereas mature leaf arginine remained unchanged. Under low N supply, the decrease in proline content from winter to late spring was significantly greater in mature leaves than in bark. Thus, under high N, bark supply more arginine in early spring, whereas under low N, leaves supply more proline later. Bioinformatics indicate that ribosomal proteins may be involved in N remobilization in bark under high N and in both bark and leaves under low N. These results demonstrate that bark and mature leaves exhibit different seasonal N remobilization patterns.

Climate change presents significant challenges to agricultural suitability and food security, largely due to the limited adaptability of domesticated crops. However, crop wild relatives maintain greater diversity and are well adapted to various environments. This study evaluates the potential distributional responses of grapevine (Vitis vinifera L.) and its wild relatives (Vitis spp.) to future climate change using the maximum entropy model. We reveal that the annual mean temperature is the primary factor determining the potential distribution of cultivated grapes. By 2080, under the SSP585 scenario, suitable areas for wine and table grapes are predicted to decline by 1.5 million and 1.3 million km ², respectively. The results suggest that grape cultivation, especially for table grapes, is highly vulnerable to future climate change. In contrast, approximately 70% of wild grapes are projected to demonstrate robust adaptability to future conditions. For example, wild grapes from North America, such as Vitis rotundifolia and Vitis labrusca, and from East Asia, such as Vitis heyneana and Vitis davidii, are projected to demonstrate significant adaptability in response to future climate change. These wild grapes are valuable genetic resources for improving the resilience of cultivated grapes through rootstock development and breeding programs to face the climate change. Our results predict the potential future distribution areas of wild grapes and highlight the critical role of their genetic resources in grape breeding for promoting adaptation to climate change.

Clubroot, caused by Plasmodiophora brassicae, poses a serious threat to cruciferous crop production worldwide. Breeding resistant varieties remains the most cost-effective strategy to mitigate yield losses, yet achieving durable, stable, and broad-spectrum resistance continues to be a formidable challenge. Recent advances in genetic and genomic technologies have improved the understanding of complex host-pathogen interactions, leading to the identification of key resistance loci, including dominant resistance genes such as CRa and Crr1, as well as quantitative trait loci. This review discusses the genetic mechanisms governing clubroot resistance and highlights applications in breeding, such as marker-assisted selection and CRISPR/Cas9-based genome editing, which are accelerating the development of resistant germplasm. Furthermore, integrated management strategies, encompassing resistant cultivars, crop rotation, biocontrol agents, and soil amendments, are emphasized as critical components for sustainable disease management. This review summarizes the major resistance genes against clubroot and discusses potential strategies to address the persistent threat posed by the disease.

Controlling branch orientation is a central challenge in tree fruit production, as it impacts light interception, pesticide use, fruit quality, yield, and labor costs. To modify branch orientation, growers use many different management practices, including tying branches to wires or applying growth regulator sprays. However, these practices are often costly and ineffective. In contrast, altering the expression of genes that control branch angles and orientations would permanently optimize tree architecture and reduce management requirements. One gene implicated in branch angle control, LAZY1, has potential for such applications as it is a key modulator of upward branch orientations in response to gravity. Here, we describe the phenotypes of transgenic plum (Prunus domestica) trees containing an antisense vector to silence LAZY1. We found that LAZY1 silencing significantly increased branch and petiole angles. LAZY1-antisense lines also displayed ‘wandering’ or weeping branch trajectories. These phenotypes were not associated with decreases in branch strength or stiffness. We evaluated the utility of LAZY1-antisense trees for use in two planar orchard systems by training them according to super slender axe and espalier methods. We found that the LAZY1-antisense trees had more open canopies and were easier to constrain to the trellis height. This work illustrates the power of manipulating gene expression to optimize plant architecture for specific horticultural applications.

Structural variations (SVs) in repetitive sequences could only be detected within a broad region due to imprecise breakpoints, leading to classification errors and inaccurate trait analysis. Through manual inspection at 4532 variant regions identified by integrating 14 detection pipelines between two tomato genomes, we generated an SV benchmark at base-pair resolution. Evaluation of all pipelines yielded F1-scores below 53.77% with this benchmark, underscoring the urgent need for advanced detection algorithms in plant genomics. Analyzing the alignment features of the repetitive sequences in each region, we summarized four patterns of SV breakpoints and revealed that deviations in breakpoint identification were primarily due to copy misalignment. According to the similarities among copies, we identified 1635 bona fide SVs with precise breakpoints, including substitutions (223), which should be taken as a fundamental SV type, alongside insertions (780), deletions (619), and inversions (13), all showing preferences for SV occurrence within AT-repeat regions of regulatory loci. This precise resolution of complex SVs will foster genome analysis and crop improvement.

The gaseous hormone ethylene controls a variety of physiological processes in horticultural plants, including fruit ripening and elongation, flower development and senescence, and responses to stresses. The functions of ethylene in these processes are intimately linked to its precise biosynthesis, which is finely tuned by a complex network of positive and negative regulators. While significant progress has been made in understanding the roles of positive regulators in ethylene biosynthesis, the negative regulators of ethylene biosynthesis has only recently begun to receive more focus. Ethylene biosynthesis is a simple two-step reaction in land plants, committed by two dedicated enzymes, 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS) and ACC oxidase (ACO). Over the past decade, a growing number of research has identified a wide range of transcriptional, posttranscriptional and epigenetic negative regulators for ACS and/or ACO in horticultural plants, greatly enhancing our understanding of the intricate network that modulates ethylene production. In this review, we provide a comprehensive overview of the negative regulators that mediate ethylene biosynthesis in horticultural plants, with respect to their functions and molecular mechanisms, and their responses to external environmental stimuli or internal growth signals.

Photoperiod-dependent flowering is a critical trait in breeding for flowering time in woody ornamental plants. Circadian clocks are vital for the regulation of photoperiodic flowering in plants, but their molecular regulation pathways in woody perennials remain poorly explored. Here, we identified two circadian clock components LgPSEUDO-RESPONSE REGULATOR 7 (LgPRR7) and LgFLAVIN-BINDING KELCH REPEAT F-BOX 1 (LgFKF1) as key repressors of flowering in Luculia gratissima, a short-day woody ornamental plant with commercial potential. Levels of LgPRR7 and LgFKF1 transcripts exhibited photoperiodic responses and diurnal patterns. Ectopic overexpression of LgPRR7 or LgFKF1 in Arabidopsis thaliana accelerated flowering, whereas silencing LgPRR7 or LgFKF1 in L. gratissima accelerated flowering. Crucially, LgPRR7 directly interacts with LgFKF1, forming a self-reinforcing regulatory module LgPRR7-LgFKF1 to repress flowering in L. gratissima. Furthermore, the observed physical interactions among LgFKF1, LgCONSTANS-LIKE 12 (LgCOL12), and LgREPRESSOR OF ga1-3-LIKE 2 (LgRGL2) implied that they possibly formed a protein complex LgFKF1-LgCOL12-LgRGL2, bridging the circadian clock, photoperiod, and gibberellin signaling pathways to suppress downstream floral integrators. Intriguingly, silencing LgPRR7 and LgFKF1 extended the duration of L. gratissima flowering, a trait of horticultural significance. These results suggest the integration of multilayered environmental and endogenous signals in the regulation of flowering time. The LgPRR7-LgFKF1 module provides novel targets for molecular improvement to manipulate flowering time and duration in L. gratissima and other economically valuable woody ornamental plants. Our results also support the mediation of flowering convergence in short-day plants through the action of circadian clock genes.

Plant growth is inseparable from the presence of mineral nutrients such as nitrogen (N), phosphorus (P), and potassium (K), but the mechanism by which horticultural plants such as tomatoes respond to mineral elements is poorly understood. Here, we collected 28 phenotypic datasets, including 5 agronomic traits and 4 pigment accumulation traits, under full nutrition and nitrogen/phosphorus/potassium-deficiency conditions, most of which showed abundant variation. Phenotyping analysis suggested that the yellowing of leaves under low-nitrogen treatment was caused by an increase in the carotenoid content and a decrease in the chlorophyll b content. A genome-wide association study identified a total of 138 suggestive loci (including 23 significant loci) corresponding to 116 loci, including many reported and new candidate genes related to mineral element response and absorption. Transcriptome analysis of tomato seedlings under full nutrient and N/P/K-deficiency conditions revealed 1108 and 1507 common differentially expressed genes in above-ground and below-ground tissues, respectively, with 103 overlapping genes. Gene Ontology term enrichment analysis revealed that tomato plants resist low nutrient stress by increasing photosynthesis in the above-ground parts and ion transport capacity in the below-ground parts. Through the combined analysis of GWAS and RNA-Seq, we identified 28 mineral element response genes with high confidence, corresponding to 17 loci, which may be closely related to the response and utilization of N, P, and K in tomato. Two candidate genes, auxin-repressed protein (Solyc02g077880), which responds to carotenoid and chlorophyll b accumulation, and guanine nucleotide exchange factor-like protein (Solyc04g005560), which responds to low-phosphorus conditions, were further validated via haplotype analysis. This study provides new insights into the nitrogen, phosphorus, and potassium response mechanisms of tomato and offers valuable genetic resources for future improvements in tomato breeding.

Camellia oleifera, a woody oilseed plant native to China, is highly susceptible to anthracnose, a fungal disease that poses a significant threat to its yield and quality. Mitophagy, a specialized form of autophagy that specifically targets dysfunctional mitochondria, is crucial for cellular homeostasis, stress response, and pathogenesis in fungi. The proteins that potentially participate in mitophagy in Colletotrichum camelliae were identified herein using immunoprecipitation-mass spectrometry (IP-MS) by screening for the potential protein interactors of the core autophagy-related protein, CaAtg8. Among the identified mitochondria-associated proteins, CaSun1 was selected for further investigation. Phenotypic analyses revealed that CaSun1 is a critical regulator of vegetative growth, conidiation, and pathogenicity. CaSun1 localized to the mitochondria, consistent with the conserved function of SUN family proteins. Notably, the findings revealed that CaSun1 was essential for mitophagy and colocalized with CaAtg8 during nitrogen starvation. Functional analyses demonstrated that CaSun1-mediated mitophagy is vital for the growth of invasive hyphae and pathogenicity in C. camelliae. In summary, our findings indicated that CaSun1 mediates mitophagy by facilitating the recruitment of CaAtg8 in C. camelliae, thereby contributing to the establishment of anthracnose. This study provided novel insights into the molecular mechanisms underlying the pathogenesis of fungal infections and identified a potential target for disease control.