The extensive accumulation of genetic, genomic, expression, and breeding data on Prunus species often results in valuable information being lost or difficult to access for breeding purposes. We report a recent effort to increase curation on Prunus data in the Genome Database for Rosaceae (GDR, rosaceae.org) and a case study that explores 25 years of curated data (from 1998 to 2023) to uncover the genetic

Geraniol contributes significantly to the floral scent of herbaceous peony (Paeonia lactiflora) and is abundant in fragrant cultivars. However, the regulatory mechanism of geraniol biosynthesis in herbaceous peony remains unclear. In this study, we identified a transcriptional regulatory complex (PlMYB73-PlMYB70-PlMYB108) that cooperatively regulated geraniol biosynthesis in herbaceous peony. The three

The pear (Pyrus spp.), a perennial fruit tree, is subjected to genetic alterations over decades or even centuries to adapt to complex climatic and cultivation conditions. Genome-wide studies of deleterious mutations remain limited in perennial fruit trees, particularly regarding the effects of domestication on deleterious mutations. In this study, 232 pear accessions were resequenced, and 9,909,773

To produce mature seed, flowering plants must undergo successful male and female gametogenesis and pollination followed by fruit set, growth, and ripening. This sequential process involves complex genetic programming and less understood epigenetic re-programming. Here we report a previously unidentified CHROMOMETHYLASE3-directed epi-control in pollen mother cell (PMC)-to-microspore transition that

Anthocyanins and terpenoids are secondary metabolites with well-documented health benefits. Isopentenyl transferases (IPTs) are key enzymes in cytokinin (CK) biosynthesis. While ADP/ATP-type IPTs and their associated trans-zeatin (tZ)-CKs and iP-CKs are considered to play regulatory roles in growth and development, as well as stress acclimation in plants, tRNA-type IPTs and cis-zeatin CKs (cZ-CKs)

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

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

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

The prostrate growth habit is an important ornamental trait in ground-cover chrysanthemum, offering high aesthetic value, strong lodging resistance, and excellent landscape greening capability. However, the genetic basis underlying this trait in chrysanthemum remains largely unclear. In this study, we utilized the prostrate-type Chrysanthemum yantaiense (tetraploid), the erect-type C. indicum (tetraploid)

Polyploidization has been recognized as a major force in plant evolution. With the continuous progress in sequencing technologies and genome assembly algorithms, high-quality chromosome-level assemblies of polyploid genomes have become increasingly attainable. However, accurately delineating these assemblies into subgenomes remains a challenging task, especially in case where known diploid ancestors

Downy mildew is a major disease that significantly impacts the yield and quality of Brassica rapa. While histone deacetylase family members are implicated in stress responses, their role in regulating downy mildew resistance in B. rapa remains unclear. Herein, we treated the susceptible B. rapa line R32 with Trichostatin A (TSA), a potent histone deacetylase inhibitor. Notably, TSA application significantly

Cell expansion in petals plays a crucial role in flower opening and final size in rose (Rosa hybrida), which largely determines its market value. While cell expansion is known to be closely associated with gibberellins (GAs), the underlying molecular mechanism remains elusive. Here, we measured the levels of GAs during flower opening and demonstrated that GA3 treatment significantly increases petal

Oleanane-type triterpenoid saponins are the primary medicinal components of Eleutherococcus senticosus. During saponin biosynthesis in E. senticosus, various members of the 2,3-oxidosqualene cyclase (OSC) gene family can direct 2,3-oxidosqualene into triterpene saponin and sterol synthesis pathways. However, the precise molecular mechanism underlying this phenomenon remains unclear. We initially screened

Interspecific interactions including plant-plant, plant-microbe, and plant-insect interactions are the important elements to drive the positive plant-soil feedback for maintaining ecosystem stability in biodiversity ecosystems. Yet, the role of diversified foliar pathogens in biodiversity system in influencing the plant-soil feedback (PSF) has often been underestimated. Here, we assessed the effects

Melon (Cucumis melo L.) is a fruit crop in the world, fruit size and fruit shape are major traits for melon quality. Fruit length is a crucial indicator affecting fruit size and shape, but few genes regulating this trait have been identified. Here, we identified the transcription factor CmFUL1 (FRUITFULL) as a candidate for regulating fruit length using genome-wide association analysis (GWAS) and phylogenetic

Cultivated strawberry (Fragaria × ananassa) is a kind of Rosaceae fruit crops grown worldwide. It is popularly consumed for its attractive color, juicy flesh and nutrient content. The rich anthocyanin in strawberry fruits is responsible for its coloration. Anthocyanins are polyphenolic compounds, belonging to the four types of natural plant pigments. As important antioxidant secondary metabolites,

Blueberry (Vaccinium spp. section Cyanococcus) ripening is a complex process involving physiological and molecular changes that affect harvest timing, fruit quality, and market value. This review examines scientific literature on blueberry ripening, aiming to establish a unified phenological framework for lowbush (V. angustifolium), highbush (V. corymbosum, including northern and southern types), and

Crop pests significantly reduce crop yield and threaten global food security. Conventional pest control relies heavily on insecticides, leading to pesticide resistance and ecological concerns. However, crops and their wild relatives exhibit varied levels of pest resistance, suggesting the potential for breeding pest-resistant varieties. This study integrates deep learning (DL)/machine learning (ML)

Investigating the regulatory mechanisms that govern plant growth is crucial for developing high-yield wood varieties. In this context, the KNOX gene family has been identified as a significant regulator of plant growth. Our study focuses on PagKNAT5a, a class II member of the KNOX gene family, which has been found to promote the growth of poplar. Transgenic plants overexpressing PagKNAT5a exhibited

Although extensively studied in various plants, the roles of aquaporin proteins in litchi remain unclear. In this study, low moisture content was observed in the dormant terminal buds of litchi. Transcriptome analysis revealed that two aquaporin genes, PLASMA MEMBRANE INTRINSIC PROTEIN 1;4 (LcPIP1;4) and LcPIP1;5, could be remarkably inhibited by exogenous ethylene (ETH), which also reduced the moisture

This study aimed to predict dry matter partitioning in cucumber fruit (Cucumis sativus L.) by developing a simulation model that integrates photosynthetic characteristics based on leaf age and cropping type. Leaf gas exchange, growth, and environmental data from semi-forcing and forcing cropping types were used to calibrate models including the Farquhar-von Caemmerer-Berry (FvCB) model and other growth-related

One of China's most important resources is flax (Linum usitatissimum L.), an ancient crop with significant nutritional and therapeutic benefits. Despite its importance, existing flax reference genomes remain incomplete, with many unassembled sequences. Here, we report a gapless 482.51 Mb telomere-to-telomere (T2T) flax genome assembly, predicting 46,634 genes, of which 42,805 were functionally annotated

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

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

Large-scale manual measurements of plant architectural traits in tomato growth are laborious and subjective, hindering deeper understanding of temporal variations in gene expression heterogeneity. This study develops a high-throughput approach for characterizing tomato architectural traits at different growth stages and mapping temporal broad-sense heritability using an unmanned ground vehicle-based

Carnation (Dianthus caryophyllus L.) is an important global flower crop, with great ornamental and economic value. It has more than 2000 years of cultivation history and profound cultural heritage, known as mother flower. Now, although carnation is deeply loved by the majority of consumers because of its rich color and various varieties, the original carnation unique clove flavor has disappeared. Furthermore

Leaf senescence, an essential component of the plant life cycle, seriously affects the productivity of numerous commercial crops, with cytokinins serving as crucial regulators in delaying this process. Here, we observed that apple (Malus domestica) leaves exhibiting deficiencies in sorbitol synthesis due to antisense inhibition of ALOSE-6PHOSPHATE REDUCTASE (A6PR) presented an increase in cytokinin

Rapeseed is the second-largest oilseed crop in the world with short domestication and breeding history. This study developed a batch of genomic prediction models for flowering time, oil content and yield components in rapeseed. Using worldwide 404 breeding lines, the optimal prediction model for flowering time, and five quality and yield traits was established by comparison with efficient traditional

Water deficit during flowering can lead to petal wilting, necrosis, and sterility, severely limiting crop fertilization and yield. Therefore, rapid recovery of floral organs after dehydration is essential for angiosperms to achieve their full reproductive potential. Aquaporins (AQPs) are bidirectional membrane channels mediating water transmembrane transport. Plasma membrane intrinsic proteins (PIPs)

Lindera megaphylla, a Lauraceae species, is valued for timber, horticulture, and traditional medicine. Here, a high-quality genome of L. megaphylla was obtained at the chromosome level. A total of 96.77% of genomic sequences were mapped onto 12 chromosomes, with a total length of 1,309.2 megabase (Mb) and an N50 scaffold of 107.75 Mb. Approximately 75.91% of genome consists of repetitive sequences

Plant growth is inseparable from the presence of mineral nutrients such as nitrogen, phosphorus and potassium, 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

Consumers value highly the nutritional content and flavor of fresh fruits, which are influenced by endogenous plant hormones. However, the molecular mechanisms governing the hormonal regulation of essential nutrients such as ascorbic acid (AsA) in fruit are still unclear. This study investigates the regulation of AsA synthesis in kiwifruit by the transcription factor AcABI5a, which is involved in mediating

Nodes are a distinct feature of bamboo plants, categorized into three main types: culm, shoot, and rhizome nodes. However, the latter two are often overlooked due to their underground growth, resulting in a limited understanding of their structure and function. In this study, we examined the structure and mineral elements deposition in the nodes of Moso bamboo (Phyllostachys edulis). Our findings indicate

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

The transition of plants from aquatic to terrestrial environments required effective barriers against water loss and UV damage. The plant cuticle, a hydrophobic barrier covering aerial surfaces, emerged as a critical innovation, yet how its biosynthesis is regulated in specialized structures remains poorly understood. This study identifies two long-chain acyl-CoA synthetases, SlLACS1 and SlLACS2, that

Breeding for improved immunity is essential to achieve sustainable fruit production, yet requiring to account for genotype-by-environment interactions (GxE), 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 (P. persica) and apricot (P. armeniaca)

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 three N supply rates (low, moderate and high) to examine seasonal

Clubroot, caused by Plasmodiophora brassicae (P. 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

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

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 4,532 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

As an important non-cereal food crop grown worldwide, the genetic improvement of potato in tuber yield and quality is largely constrained due to the lacking of a high-quality reference genome and understanding of the regulatory mechanism underlying the formation of superior alleles. Here, a chromosome-scale haplotype-resolved genome assembled from an anther-cultured progeny of ‘Ningshu 15’, a tetraploid

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

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

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

Lignin deposition in stone cells is a critical factor that limits pear fruit quality, affecting their market value. Calcium ions (Ca2+) play an essential role in lignin biosynthesis during fruit stone cell production. However, the genetic mechanisms underlying the Ca2+ regulated lignin synthesis in stone cell formation are not fully understood. In this study, we identified a NAC transcription factor

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

Mechanical harvesting in the tea industry has become increasingly essential due to its advantages in increasing productivity and reducing labor costs. Leaves 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 loci, designated as q10.3, along with three lead SNPs located

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

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

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

Lignin is a major component of the plant cell wall and has a conserved basic defence 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

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

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

Lobed leaves are advantageous for gas exchange, canopy architecture and high-density planting, however, the genetic mechanisms of leaf lobe formation in Brassica crops remains poorly understood. Here, lob10.1, our previously identified major QTL controlling the presence/absence of leaf lobes in B. rapa (AA), was fine-mapped to a confidence interval of 69.8 kb. REDUCED COMPLEXITY ORGAN (BrRCO, BraA10g032440

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

Pucai (蒲菜) (Typha angustifolia L.) within the Typha spp. is a distinctive semi-aquatic 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