Graph pangenome reveals the regulation of malate content in blood-fleshed peach by NAC transcription factors.

Background: Fruit acidity and color are important quality attributes in peaches. Although there are some exceptions, blood-fleshed peaches typically have a sour taste. However, little is known about the genetic variations linking organic acid and color regulation in peaches.

Genome of root celery and population genomic analysis reveal the complex breeding history of celery.

Celery (Apium graveolens L.) is an important vegetable crop in the Apiaceae family. It comprises three botanical varieties: common celery with solid and succulent petioles, celeriac or root celery with enlarged and fleshy hypocotyls and smallage or leaf celery with slender, leafy and usually hollow petioles.

A Linker Histone Acts as a Transcription Factor to Orchestrate Malic Acid Accumulation in Apple in Response to Sorbitol.

High carbohydrate availability promotes malic acid accumulation in fleshy fruits, but the underlying mechanism is not known. Here, we show that antisense repression of ALDOSE-6-PHOSPHATE REDUCTASE in apple (Malus domestica) decreases the concentrations of sorbitol and malate and the transcript levels of several genes involved in vacuolar malate transport, including the aluminum-activated malate transporter (ALMT) gene MdALMT9 (Ma1), the P-ATPase gene MdPH5, the MYB transcription factor gene MdMYB73, and the cold-induced basic helix-loop-helix transcription factor gene MdCIbHLH1, in fruit and leaves. We identified a linker histone H1 variant, MdH1.

Releasing a sugar brake generates sweeter tomato without yield penalty.

In tomato, sugar content is highly correlated with consumer preferences, with most consumers preferring sweeter fruit. However, the sugar content of commercial varieties is generally low, as it is inversely correlated with fruit size, and growers prioritize yield over flavour quality. Here we identified two genes, tomato (Solanum lycopersicum) calcium-dependent protein kinase 27 (SlCDPK27; also known as SlCPK27) and its paralogue SlCDPK26, that control fruit sugar content.

Haplotype-resolved genome assembly and resequencing provide insights into the origin and breeding of modern rose.

Modern rose (Rosa hybrida) is a recently formed interspecific hybrid and has become one of the most important and widely cultivated ornamentals. Here we report the haplotype-resolved chromosome-scale genome assembly of the tetraploid R. hybrida 'Samantha' ('JACmantha') and a genome variation map of 233 Rosa accessions involving various wild species, and old and modern cultivars.

Genome-Wide Association Study of Cuticle and Lipid Droplet Properties of Cucumber ( L.) Fruit.

The fruit surface is a critical first line of defense against environmental stress. Overlaying the fruit epidermis is the cuticle, comprising a matrix of cutin monomers and waxes that provides protection and mechanical support throughout development. The epidermal layer of the cucumber ( L.

Species-specific microsymbiont discrimination mediated by a receptor kinase.

Host range specificity is a prominent feature of the legume-rhizobial symbiosis. and are two closely related species that engage in root nodule symbiosis with legume plants of the genus, but certain species exhibit selectivity in their interactions with the two rhizobial species. We have identified a receptor-like kinase, which can discriminate between the two bacterial species, acting as a genetic barrier against infection by most strains.

Related type 2C protein phosphatases Pic3 and Pic12 negatively regulate immunity in tomato to Pseudomonas syringae.

Type 2C protein phosphatases (PP2Cs) constitute a large family in most plant species, but relatively few of them have been implicated in immunity. To identify and characterize PP2C phosphatases that affect tomato (Solanum lycopersicum) immunity, we generated loss-of-function mutations in 11 PP2C-encoding genes whose expression is altered in response to immune elicitors or pathogens. We report that 2 closely related PP2C phosphatases, PP2C immunity-associated candidate 3 (Pic3) and Pic12, are involved in regulating resistance to the bacterial pathogen Pseudomonas syringae pv.

Molecular basis of one-step methyl anthranilate biosynthesis in grapes, sweet orange, and maize.

Plants synthesize an array of volatile compounds, many of which serve ecological roles in attracting pollinators, deterring herbivores, and communicating with their surroundings. Methyl anthranilate (MeAA) is an anti-herbivory defensive volatile responsible for grape aroma that is emitted by several agriculturally relevant plants, including citrus, grapes, and maize. Unlike maize, which uses a one-step anthranilate methyltransferase (AAMT), grapes have been thought to use a two-step pathway for MeAA biosynthesis.

HortGenome Search Engine, a universal genomic search engine for horticultural crops.

Horticultural crops comprising fruit, vegetable, ornamental, beverage, medicinal and aromatic plants play essential roles in food security and human health, as well as landscaping. With the advances of sequencing technologies, genomes for hundreds of horticultural crops have been deciphered in recent years, providing a basis for understanding gene functions and regulatory networks and for the improvement of horticultural crops. However, these valuable genomic data are scattered in warehouses with various complex searching and displaying strategies, which increases learning and usage costs and makes comparative and functional genomic analyses across different horticultural crops very challenging.

Identification of male-fertility gene and molecular marker development in cultivated garlic ( L.).

Garlic cultivars are predominantly characterized by their sterility and reliance on asexual reproduction, which have traditionally prevented the use of hybrid breeding for cultivar improvement in garlic. Our investigation has revealed a notable exception in the garlic line G398, which demonstrates the ability to produce fertile pollen. Notably, at the seventh stage of anther development, callose degradation in the sterile line G390 was impeded, while G398 exhibited normal callose degradation.

Pattern Recognition of Partial Discharge Faults in Switchgear Using a Back Propagation Neural Network Optimized by an Improved Mantis Search Algorithm.

The dependable functioning of switchgear is essential to maintain the stability of power supply systems. Partial discharge (PD) is a critical phenomenon affecting the insulation of switchgear, potentially leading to equipment failure and accidents. PDs are generally grouped into metal particle discharge, suspended discharge, and creeping discharge.

Genomic and pangenomic analyses provide insights into the population history and genomic diversification of bottle gourd.

Bottle gourd (Lagenaria siceraria (Mol.) Strandl.) is an economically important vegetable crop and one of the earliest domesticated crops.

Complete genome assembly provides a high-quality skeleton for pan-NLRome construction in melon.

Melon (Cucumis melo L.), being under intensive domestication and selective breeding, displays an abundant phenotypic diversity. Wild germplasm with tolerance to stress represents an untapped genetic resource for discovery of disease-resistance genes.

The jet-like chromatin structure defines active secondary metabolism in fungi.

Eukaryotic genomes are spatially organized within the nucleus in a nonrandom manner. However, fungal genome arrangement and its function in development and adaptation remain largely unexplored. Here, we show that the high-order chromosome structure of Fusarium graminearum is sculpted by both H3K27me3 modification and ancient genome rearrangements.

Antibody array-based proteome approach reveals proteins involved in grape seed development.

Grape (Vitis vinifera) is one of the most widely cultivated fruits globally, primarily used for processing and fresh consumption. Seedless grapes are favored by consumers for their convenience, making the study of seedlessness a subject of great interest to scientists. To identify regulators involved in this process in grape, a monoclonal antibody (mAb)-array-based proteomics approach, which contains 21,120 mAbs, was employed for screening proteins/antigens differentially accumulated in grape during development.

A graph-based pan-genome of Brassica oleracea provides new insights into its domestication and morphotype diversification.

The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns of organ development. Here we report a graph-based pan-genome of B. oleracea constructed from high-quality genome assemblies of different morphotypes.

Transcriptional and epigenetic changes during tomato yellow leaf curl virus infection in tomato.

Background: Geminiviruses are DNA plant viruses that cause highly damaging diseases affecting crops worldwide. During the infection, geminiviruses hijack cellular processes, suppress plant defenses, and cause a massive reprogramming of the infected cells leading to major changes in the whole plant homeostasis. The advances in sequencing technologies allow the simultaneous analysis of multiple aspects of viral infection at a large scale, generating new insights into the molecular mechanisms underlying plant-virus interactions.

Identification of QTL associated with resistance to Phytophthora fruit rot in cucumber ( L.).

Phytophthora fruit rot (PFR) caused by the soilborne oomycete pathogen, , can cause severe yield loss in cucumber. With no resistant variety available, genetic resources are needed to develop resistant varieties. The goal of this work was to identify quantitative trait loci (QTL) associated with resistance to PFR using multiple genomic approaches and populations.

Chromosome-level phased genome assembly of "Antonovka" identified candidate apple scab-resistance genes highly homologous to HcrVf2 and HcrVf1 on linkage group 1.

Apple scab, a fungal disease caused by Venturia inaequalis, leads to losses in both yield and fruit quality of apples (Malus domestica Borkh.). Most commercial apple cultivars, including those containing the well-characterized Rvi6-scab-resistance locus on linkage group (LG) 1, are susceptible to scab.