Lobularia maritima (sweet alyssum) is a popular ornamental plant that displays a range of flower colors, particularly white and purple. However, the genetic underpinning and evolutionary history of flower colors have remained unknown. To address this, we performed a de novo assembly of a chromosome-level genome for this species and conducted comparative population genomic analyses of both domestic

Acer pentaphyllum Diels (Sapindaceae), a highly threatened maple endemic to the dry-hot valleys of the Yalong River in western Sichuan, China, represents a valuable resource for horticulture and conservation. This study presents the first chromosomal-scale genome assembly of A. pentaphyllum (~626 Mb, 2n = 26), constructed using PacBio HiFi and Hi-C sequencing technologies. Comparative genomic analyses

Sandalwood (Santalum album), a culturally significant and economically valuable horticultural species, is renowned for its heartwood and essential oils enriched with sesquiterpene compounds such as santalol. Despite progress in elucidating the biosynthetic pathway of these valuable metabolites, the transcriptional regulation of this process, particularly under abiotic stress conditions, remains largely

The present research examined the regulatory function of MaEIL4 in the ripening process of banana. The findings demonstrated that MaEIL4 is a transcription factor with activity in the nucleus. The transient modulation of MaEIL4 expression in banana fruit slices has been found to exert a significant impact on maturation, either enhancing or inhibiting its progression, as shown by phenotype and endogenous

Strawberry fruits, known for their excellent taste and potential health benefits, are particularly valued for their rich content of hydrolyzable tannins (HTs). These compounds play key roles in regulating growth and development. However, the molecular mechanisms underlying HT synthesis in plants remains poorly elucidated. In this study, based on a correlation analysis between the transcriptome and

Mung bean (Vigna radiata), an essential annual legume, holds substantial value in global agriculture due to its short growth cycle, low input requirements, and nutritional benefits. Despite extensive domestication, the genetic mechanisms underlying its morphological and physiological evolution remain incompletely understood. In this study, we present a gap-free, telomere-to-telomere genome assembly

Cassava (Manihot esculenta Crantz) is a staple food of 800 million people in the tropical and subtropical regions of the world. Its industrial utilization for bioethanol, animal feed, and starch are still continuously expanding. It was not until the 1970s that significant scientific efforts were undertaken to improve cassava, despite its considerable economic and social significance. Shorten the breeding

Polyphenols represent a significant class of nutrients in apples, contributing to human health and well-being. Among these, procyanidins stand out as the most prevalent polyphenolic compounds in apple fruits. These compounds are abundant in wild apples and generally low in modern apple cultivars. Therefore, it is crucial to identify and recover genetically lost genes that regulate polyphenol accumulation

Taxus L., an important ornamental, economic, and medicinal plant, is renowned for producing paclitaxel (Taxol®), a potent chemotherapeutic agent. The biosynthesis of paclitaxel involves intricate biosynthetic pathways, spanning multiple enzymatic steps. Despite advances, challenges remain in optimizing production methods. Microorganisms, particularly endophytic fungi, show potential in producing paclitaxel

Tea plant is a fluoride (F)-hyperaccumulator, which poses a potential threat to human health via tea consumption. Reducing F accumulation in fresh tea leaves is crucial for enhancing the safety of tea production at its source. This study aims to isolate novel genes responsible for F accumulation or transport in tea plants. We identified an aluminum (Al)-activated malate transporter gene, CsALMT6, which

Proanthocyanidins (PAs), anthocyanins, and flavonols are key flavonoids that play diverse roles in plant physiology and human health. Despite originating from a shared biosynthetic pathway, the regulatory mechanisms of PA biosynthesis and the cooperative regulation of different kinds of flavonoids remain elusive, particularly in flower tissues or organs. Here, we elucidated the regulatory network governing

Pathogens significantly restrict the production of Brassica rapa (Brassica rapa L. ssp. Pekinensis), with climate change and evolving planting patterns exacerbating disease prevalence. Multi-channel rapid diagnostic methods in the field can facilitate the early detection and control of diseases in B. rapa. Here, we established a multi-channel lateral flow biosensor (LFB) combined with a CRISPR/Cas12a

Curcuma alismatifolia is an important ornamental plant of significant economic value, while the floral fragrance has been rarely investigated, leading to a lack of knowledge about the floral scent. By performing metabolomic and transcriptomic analyses, we investigated the variation of 906 volatile organic compounds (VOCs) in florets of eight C. alismatifolia cultivars and four different developmental

High salinity can severely inhibit the growth and development of watermelon (Citrullus lanatus L.). WRKY proteins are believed to mediate the adaptation of plants to abiotic stresses. Here, we identified the ClWRKY61 gene, which positively regulates the tolerance of watermelon to salt stress. Knockout of the ClWRKY61 reduced salt tolerance, while overexpression of the ClWRKY61 enhanced salt tolerance

Brassica rapa includes a variety of important vegetable and oilseed crops, yet it is significantly challenged by clubroot disease. Notably, the majority of genotypes of B. rapa with published genomes exhibit high susceptibility to clubroot disease. The present study presents a high-quality chromosome-level sequence of the genome of the DH40 clubroot-resistant (CR) line, a doubled haploid line derived

Tree and herbaceous peony are considerably important ornamental plants within the genus Paeonia, and hold substantial horticultural value. This review summarizes the progress in research on the senescence mechanisms of tree and herbaceous peony flowers, focusing on the regulation of gene expression, hormonal interactions, and the influence of environmental factors on senescence. Using high-throughput

Commercial value of cucumber is primarily driven by fruit quality. However, breeding goals frequently focus on production constraints caused by biotic and abiotic stresses. As sources of resistances are often present in unadapted germplasm, we sought to provide morphological and genetic information characterizing the diversity of fruit quality traits present in the CucCAP cucumber core collection.

Galloylated flavan-3-ols are key quality and health-related compounds in tea plants of Camellia section Thea. Camellia ptilophylla and Camellia sinensis are two representative species known for their high levels of galloylated flavan-3-ols. Building on our knowledge of galloyl catechin biosynthesis in C. sinensis, we now focus on the biosynthesis of galloylated phenolics in C. ptilophylla, aiming to

The homeostasis of gibberellin (GA) is crucial for the normal development of anthers, but its underlying regulatory mechanisms are not clear. The GA induced v-Myb myeloblastosis viral oncogene homolog (MYB) transcription factor LoMYB65 is involved in anther development. In this study, we screened and identified an interacting protein of LoMYB65, Lilium Oriental Hybrids BEL1-Like Homeodomain6 (LoBLH6)

Bottle gourd (Lagenaria siceraria (Molina) Standl) is a widely distributed Cucurbitaceae species, but gaps and low-quality assemblies have limited its genomic study. To address this, we assembled a nearly complete, high-quality genome of the bottle gourd (Pugua) using PacBio HiFi sequencing and Hi-C correction. The genome, being 298.67 Mb long with a ContigN50 of 28.55 Mb, was identified to possess

Shade-tolerance is a key trait for cultivars in inter/relay-cropped soybeans in maize field. Our previous genome-wide association study (GWAS) results on southern China soybean germplasm revealed that the shade-tolerance was conferred by a complex of genes with multiple alleles. To complete our understanding on shade-tolerance gene system, the GWAS with gene-allele sequences as markers (designated

Mineral nutrients are essential for plant growth and development, playing a critical role in the mutualistic symbiosis between legumes and rhizobia. Legumes have evolved intricate signaling pathways that respond to various mineral nutrients, selectively activating genes involved in nodulation and nutrient uptake during symbiotic nitrogen fixation (SNF). Key minerals, including nitrogen (N), calcium

Most Hydrangea species have inflorescences composed of two types of flowers: decorative flowers with showy sepals, and plain non-decorative flowers. In wild plants of H. macrophylla, the decorative flowers are located at the periphery of the corymb, resulting in the lacecap phenotype. However, after the discovery of the mophead phenotype, in which decorative flowers are borne not only at the periphery

Summary Despite the paramount importance in metal(loid) detoxification by phytochelatin synthase (PCS) genes, no comprehensive analysis of their evolutionary patterns has been carried out in land plants in general and in crops in particular. A phylogenetic large-scale analysis of gene duplication in angiosperms was carried out followed by in vitro recombinant protein assays as well as complementation

Grafting is a propagation method extensively utilized in cucurbits. However, the mechanisms underlying graft healing remain poorly understood. This study employed self-grafted watermelon plants to investigate how rootstock cotyledon affects healing. The complete removal of rootstock cotyledons significantly hindered scion growth, as evidenced by reductions in scion fresh weight and the area of true

Incomplete lineage sorting (ILS) and introgression/hybridization (IH) are prevalent in nature and thus frequently result in discrepancies within phylogenetic tree topologies, leading to misinterpretation of phylogenomic data. Despite the availability of numerous tools for detecting ILS and IH among species, many of these tools lack effective visualization, or are time-consuming, or require prior predetermination

Timed termination of floral meristem (FM) is crucial for proper development of floral organs and fruits. In Solanum lycopersicum, CLAVATA3 (CLV3)-WUSCHEL (WUS) feedback regulation maintains FM homeostasis in early stage of floral buds. It is known that the zinc finger protein SlKNUCKLES (SlKNU) functions to promote FM determinacy by directly repressing the stem cell identity gene SlWUS. However, how

The genus Paris, comprising a series of distinctive medicinal plants, has been utilized globally for its therapeutic properties over centuries. Modern pharmacological studies have demonstrated that secondary metabolites from Paris species exhibit significant pharmacological activities, including anticancer, hemostatic, anti-inflammatory, antimicrobial and other effects. Additionally, the unique morphological

The HAIRY MERISTEM (HAM) gene family encodes Type I and II GRAS domain transcriptional regulators in plants. Type II HAMs, predominantly expressed in meristems and regulated by microRNA171, are essential for maintaining undifferentiated meristems, a role conserved across various species. Conversely, the functions of Type I HAMs have been less characterized. In this study, we investigated the role of

The fading of flower color is caused by changes of anthocyanin content during flower development in many plants, including lilac (Syringa oblata). However, the molecular regulatory mechanism of this phenomenon is still poorly understood. UDP-glucose: flavonoid 3-O-glucosyltransferase (UFGT) has a pivotal role in the formation of stable anthocyanins. Here, SoUFGT1 and three transcription factors, SoMYB44

Genomic prediction for multiple environments can aid the selection of genotypes suited to specific soil and climate conditions. Methodological advances allow effective integration of phenotypic, genomic (additive, non-additive), and large-scale environmental (enviromic) data into multi-environmental genomic prediction models. These models can also account for genotype-by-environment interaction, utilize

Although it is well-established that ethylene and light stimulate the process of chlorophyll degradation in mature apple peels, there is still a need for further exploration of the molecular mechanisms that regulate this process. This study identified MdEIL1 and MdHY5 as promoters of the chlorophyll degradation pathway in apple peels, activated by ethylene and light. Physiological and molecular tests

Wildtype fruit of cultivated strawberry (Fragaria × ananassa) are typically soft and highly perishable when fully ripe. The development of firm-fruited cultivars by phenotypic selection has greatly increased shelf life, decreased post-harvest perishability, and driven the expansion of strawberry production worldwide. Hypotheses for the firm-fruited phenotype include mutations affecting the expression

Potassium (K) availability in plant cells is critical for maintaining plant productivity across many terrestrial ecosystems. Yet, there is no comprehensive assessment of the mechanisms by which plants respond to potassium application in such conditions, despite the global challenge of escalating osmotic stress. Herein, we conducted a meta-analysis using data from 2381 paired observations to investigate

Theanine is a crucial indicator of tea quality, its significance is closely tied to the economic value of tea. There were many reports on the regulation mechanism of theanine synthesis and accumulation, but the mechanism of gibberellin regulates theanine synthesis in tea plants is poorly understood. Previous studies have shown that the content of theanine experiences significant changed in the growth

Peach is one of the most economically valuable fruit trees. Haploid peach trees occur spontaneously at very low frequencies and they are usually highly sterile. Therefore, the haploid with partial fertility is extremely rare germplasm, which is highly valuable to genetic research and breeding programmes. In this study, we investigated the cytological mechanism underlying the fertility of a peach haploid

The fruit softening directly impacts its storage life, transportability, and customer acceptance. Auxin plays a key role during fruit ripening, but the underlying mechanisms of how auxin regulates fruit softening remain unclear. In this study, we investigated the regulatory roles of auxin on berry cell wall degradation during grape (Vitis vinifera L.) softening. During grape berry development, berry

Leaf trichome formation is a very important agronomic trait as it confers resistance to biotic and abiotic stresses, but the causal genes involved in this process in B. juncea remain largely unexplored. In this study, we first characterized the haplotypes of BjB02.GL1 among different inbred lines with leaf trichomes or glabrous leaves. A comparative analysis of the number and density of leaf trichomes

Blackcurrant (Ribes nigrum L., family Grossulariaceae) is a perennial shrub that is widely cultivated for its edible berries. These are rich in antioxidants, vitamin C and anthocyanins, making them a valuable ingredient in the food and beverage industry. However, prolonged periods of drought during the fruiting season lead to drought stress, which has serious ecological and agricultural implications

Golden Camellia refers to a group of species in the genus Camellia that display yellow petals. The secondary metabolites in these petals hold ornamental significance and potential health benefits. However, the biosynthetic mechanisms governing the synthesis of these metabolites in golden petals remain elusive, and the exploitation of their bioactive components is not fully realized. This research involved

Sweet cherry is very appreciated by consumers because of its attractive appearance and taste, which is determined by the balanced sweet-sour flavor. In this work, the genetics of soluble solid content (SSC), titratable acidity (TA), sugars and organic acids was investigated in sweet cherry to facilitate breeding improvement for fruit quality. The fruits of five sweet cherry populations (N = 372), three

Banana breeding is hampered by the very low fertility of domesticated bananas and the lack of knowledge about the genetic determinism of agronomic traits. We analysed a breeding population of 2 723 triploid hybrids resulting from crosses between diploid and tetraploid M. acuminata parents, which was evaluated over three successive crop-cycles for 24 traits relating to yield components and plant, bunch

Grape is an important fruit crop, and its production faces significant threat from diseases, resulting in substantial economic loss. Wild grape relatives are valuable resources for the restoration of disease-resistance loci. However, available resistance loci in wild grape genomes remain largely unexplored. In this study, we assembled two phased genomes, including a high resistant Chinese wild grape

The vector-borne disease Huanglongbing (HLB) causes severe economic losses to citrus production worldwide with no available cure. Herein, we applied virus-induced gene silencing technology to engineer citrus that preferentially attracted and specifically killed Diaphorina citri, the vector associated with HLB. We engineered the infectious citrus tristeza virus (CTV-T36) clone to carry three truncated

Cultivated strawberry (Fragaria x ananassa) is a globally important fruit crop which shows promise as a candidate for various methods of controlled environment production. However, a better understanding of the mechanisms of the regulation of flowering is needed, as more frequent or consistent flowering would be advantageous in controlled production. It is well understood that flowering in F. x ananassa

Tuber dormancy and sprouting are significant for potato cultivation, storage, and processing. Although the substantial role of miRNAs in some biological processes has been recognized, the critical role of miRNA in breaking potato tuber dormancy is not well understood to date. In this investigation, we expand research on miRNA-mediated gene regulation in tuber dormancy release. In this work, 204 known

The genus Brassica includes six species and over 15 types of vegetables that are widely cultivated and consumed globally. This group of vegetables is rich in bioactive compounds, including glucosinolates, vitamins (such as vitamin C, folate, tocopherol, and phylloquinone), carotenoids, phenols, and minerals, which are crucial for enriching diets and maintaining human health. However, the full extent

Next-generation sequencing has fueled significant advancement in plant breeding tools, such as genome-wide association studies (GWAS) and single-nucleotide polymorphism (SNP) analysis. In this dynamic landscape, plant databases housing SNP markers have evolved into hubs facilitating breeding initiatives and genomic research. PrunusMap, accessible at https://prunusmap.eead.csic.es is an open-source

The large diversity of grapevine cultivars includes genotypes more tolerant to water deficit than others. Widely distributed cultivars, like Merlot, are more sensitive to water deprivation than local cultivars like Callet, which are more adapted to water deficit due to their Mediterranean origin. Despite their tolerance, adaptation to water deficit influenced by grafting in rootstocks like 110 Richter

Pre-fertilization hybridization barriers are the main causes of inter-subgeneric hybridization challenges in water lily. However, the mechanism underlying low compatibility between pollen and stigma of water lily remains unclear. This study demonstrates that CBL-interacting protein kinase 6 (CIPK6) responded to the signaling exchange between incompatible pollen and stigma through interactions with

Cold stress seriously affects the plant growth and development. The ubiquitination system plays an important role by degrading and modifying substrates at the protein level. In this study, the U-box type ubiquitin ligase VviPUB19 gene was induced by low temperature (4°C) in grapevine. In Arabidopsis thaliana, the pub19 mutant, a homologous mutation of VviPUB19, exhibited enhanced cold tolerance, and

Black wolfberry (Lycium ruthenicum Murr.) is an important plant for ecological preservation. In addition, its fruits are rich in anthocyanins and have important edible and medicinal value. However, a high quality chromosome-level genome for this species is not yet available, and the regulatory mechanisms involved in the biosynthesis of anthocyanins are unclear. In this study, haploid material was used

GRAS, termed after GAI (gibberellic acid insensitive), RGA (repressor of GA1), and SCR (scarecrow), is a plant-specific transcription factor crucial for plant development and stress response. However, understanding of the functions played by the GRAS members and their target genes in citrus is limited. In this study, we identified a cold stress-responsive GRAS gene from Poncirus trifoliate, designated

The CRISPR-Cas-based gene targeting (GT) method has enabled precise modifications of genomic DNA ranging from single base to several kilobase scales through homologous recombination (HR). In plant somatic cells, canonical nonhomologous end-joining (cNHEJ) is the predominant mechanism for repairing double-stranded breaks (DSBs), thus limiting the HR-mediated GT. In this study, we implemented an approach

Skin color is one of the major traits of fruit appearance quality in pear (Pyrus), which affects the fruit commodity value. Russet skin protects pear fruits from environmental stresses and its formation process is closely linked to lignin accumulation. However, the molecular regulatory networks underlying russet skin formation in pear fruits involve complex secondary metabolic pathways and remain elusive

Flowering Chinese cabbage is a type of leafy vegetable that belongs to the Brassica genus. Originally native to South China, it is now widely cultivated and consumed across the globe, particularly in Asian countries. The recent cultivation and regional expansion of flowering Chinese cabbage provides a valuable opportunity to elucidate the genomic basis underlying environmental adaptation and desired

Cytoplasmic male sterility (CMS) is pivotal in plant breeding and widely employed in various crop hybrids, including pepper. However, the functional validation of the restorer of fertility (Rf) gene in pepper has been lacking until now. This study identifies and characterizes CaRf, a single dominant locus crucial for restoring CMS in the pepper strong recovery inbred line Zhangshugang. The CaRf gene

Coevolution within the plant holobiont extends the capacity of host plants for nutrient acquisition and stress resistance. However, the role of the rhizospheric microbiota in maintaining multinutrient utilization (i.e., multinutrient traits) in the host remains to be elucidated. Multinutrient cycling index (MNC), analogous to the widely used multifunctionality index, provides a straightforward and

Grasses, including turf and forage, cover most of the earth’s surface; predominantly important for land, water, livestock feed, soil and water conservation, as well as carbon sequestration. Improved production and quality of grasses by modern molecular breeding is gaining more research attention. Recent advances in genome-editing technologies are helping to revolutionize plant breeding and also offering

Despite the transformative power of gene editing for crop improvement, its widespread application across species and varieties is limited by the transformation bottleneck that exists for many crops. The genetic transformation of plants is hindered by a general reliance on in vitro regeneration through plant tissue culture. Tissue culture requires empirically-determined conditions and aseptic techniques