Structural variants (SVs) represent an important yet underexplored component of plant genome diversity. Here we present a graph-based cucumber pangenome constructed from 39 reference-quality genomes, including 27 newly assembled and 12 previously published. The pangenome captures 171,892 high-confidence SVs, which were genotyped across 447 wild and cultivated accessions. Our analyses reveal that, during cucumber domestication, a substantial portion of mildly deleterious SNPs were retained, whereas SVs were consistently purged, highlighting their highly deleterious nature. During geographical expansion, a reduced SV burden and a younger age of SVs compared to SNPs were observed, suggesting stronger purifying selection acting on SVs. Introgressions from wild populations increased SV burden, potentially due to hitchhiking. Notably, incorporating SV burden into genomic prediction models improved prediction accuracy for several agronomically important traits. This study illuminates SV dynamics during cucumber domestication and range expansion and underscores the implications of SVs for future cucumber breeding.

Leaf and fruit size are the crucial fitness characters for plant evolution and the agronomic traits for crop yield and quality improvement in watermelon. However, the underlying genes and molecular mechanisms for regulating fruit size and biomass remain elusive. Here, we identified a Citrullus lanatus UDP-rhamnose (Rha)/UDP-galactose (Gal) transporter ClURGT4, which is localized in the Golgi apparatus and has the dual functions of transporting UDP-Gal and UDP-Rha. Loss-of-function clurgt4 mutants resulted in decreased biomass and reduced Gal, Rha, and galacturonic acid (GalA) in cell wall components. Microscopical analysis showed that ClURGT4 promoted leaf and fruit size by modulating cell expansion. Proteomic analysis revealed that several cell wall metabolism-related proteins were changed in clurgt4 mutants. Moreover, protein glycosylation was changed in the mutants, and several of the differentially glycosylated proteins were related to cell wall metabolism. These findings elucidated that ClURGT4 might control leaf and fruit size by affecting cell wall metabolism and provided a novel case for comprehensively revealing the regulatory network of watermelon biomass.

Tomato (Solanum lycopersicum L.) is a globally important vegetable crop and a key model species for studying reproductive development in other Solanaceae members with edible fleshy fruits, such as eggplant, sweet and hot peppers, and Physalis spp. The morphogenesis and patterning of tomato floral organs fundamentally determine fruit yield and quality. Recent advances in high-throughput sequencing and gene editing have significantly deepened our understanding of the molecular network regulating tomato reproductive development. This process, from the transition of vegetative shoot apical meristem to the inflorescence meristem, forming floral meristems with primordia of sepals, petals, stamens, carpels, and fruits, is precisely coordinated by a genetic network involving homeobox and other types of transcription factors, along with signaling pathways. This review systematically outlines the core regulatory network, with an emphasis on the MADS-domain transcription factor family and its associated ABCDE model. Integrating insights from hormone signaling and mutant phenotypes, we summarize the maintenance of inflorescence meristem identity, the specification of floral meristems, and the morphogenetic patterns and core gene regulatory mechanisms for each floral whorl in tomato. We further extend this framework to the flower-fruit continuum, examining how carpel development, floral meristem termination, and ovule differentiation influence fruit morphology, locule number, pericarp structure, and metabolic traits. Finally, we discuss the integration of floral organ development with molecular design breeding and formulate a forward-looking research agenda that translates floral regulatory mechanisms to breeding strategies for yield, uniformity, and fruit quality. This synthesis provides a theoretical foundation and genetic resources for the genetic improvement of tomato flower architecture and its underlying regulatory mechanisms.

Bacillus species are well-known for plant growth-promoting properties, but how B. altitudinis stimulates cucumber growth is not fully understood. In this study, we evaluated the PGP effect of B. altitudinis JZBQ5 in cucumber and investigated its associated rhizosphere microbial and root transcriptional responses after root-irrigation treatment. In the pot assay, JZBQ5 markedly improved plant height at 10 8 and 10 7 CFU/mL and increased leaf SPAD values at specific concentrations. In the field trials, JZBQ5 significantly increased plant height, root length, plant weight, chlorophyll a, and total chlorophyll content. The average yield per ridge of first-crop cucumbers treated with JZBQ5 increased by 10.83% compared to the control group. Rhizosphere microbiome analysis showed higher bacterial richness after JZBQ5 treatment and a treatment-associated shift in community structure, with Pseudomonadota remaining the dominant phylum. LEfSe and genus-level analyses further showed enrichment of plant-beneficial taxa, including Pseudomonas , Bacillus , Streptomyces , Mesorhizobium , and Bradyrhizobium . Root transcriptome analysis identified 444 differentially expressed genes, including 205 upregulated and 239 downregulated genes, and KEGG enrichment highlighted plant hormone signal transduction, carbon fixation in photosynthetic organisms, alpha-linolenic acid metabolism, and glycolysis/gluconeogenesis. Heatmap and correlation analyses indicated that JZBQ5 reconfigured auxin- and cytokinin-related transcriptional modules and strengthened the association between beneficial rhizosphere bacteria, carbon-fixation genes, chlorophyll accumulation, and growth traits. These findings suggest that JZBQ5 promotes cucumber growth through coordinated rhizosphere microbiome remodeling and host transcriptional regulation, supporting its further development as a biofertilizer for sustainable cucumber production.

Editing the watermelon EPSPS gene using a prime editing platform with visible markers created a non-transgenic glyphosate-resistant line. These robust heterozygous mutants tolerate field-level herbicide doses without growth penalties, serving as ideal parental lines for crop breeding.

Watermelon (Citrullus lanatus), an important member of the Cucurbitaceae family, has become one of the most popular economic crops in the world, and understanding its fruit development and ripening has always been a hot topic. Although DNA methylation is known to play an essential role in fruit ripening, its contribution to watermelon ripening remains unknown. Here, we found a global and conspicuous hypermethylation pattern during watermelon fruit development and ripening, which is opposite to the hypomethylation found in tomato and strawberry. Application of the DNA methylation inhibitor 5-azacytidine (5-Aza) delayed fruit ripening, confirming that the positive role of hypermethylation in this process. The hypermethylation mainly occurred in CHG and CHH types, and gene-body hypermethylation strongly correlated with the expression of genes that related to sugar metabolism and ABA (abscisic acid) response. We also found an overall hypermethylation pattern in domesticated watermelon. ClROS1 (Repressor Of Silencing 1), a gene encoding the DNA demethylase, was under selection; its expression was negatively correlated with DNA methylation levels, suggesting that it contributes to the hypermethylation during ripening. Collectively, our research illuminates the genome-wide DNA methylation dynamics during watermelon ripening and provides an invaluable genetic resource that will greatly benefit the molecular breeding and quality improvement of this important crop.

Strawberry powdery mildew (SPM), caused by Podosphaera aphanis, severely reduces strawberry yield and quality. Due to the pathogen's obligate parasitism, the screening of biocontrol bacteria is challenging, and effective strains remain scarce. In this study, we isolated a novel strain, Bacillus altitudinis DXHS, exhibiting strong control efficacy against SPM. Genomic analysis revealed abundant biosynthetic gene clusters for secondary metabolites in DXHS, including lichenysin, siderophore, and terpenes. Strawberry leaves treated with DXHS showed a 77.05% reduction in SPM incidence versus the infected control, marking the first report, to our knowledge, of B. altitudinis efficacy against SPM. Transcriptomic analysis of strawberry leaves revealed 3,722 upregulated and 1,729 downregulated differentially expressed genes (DEGs) following treatment with the DXHS strain. GO enrichment analysis showed that these DEGs were significantly enriched in biological processes including defense response and the jasmonic acid (JA) signaling pathway. KEGG pathway analysis indicated that the DEGs were enriched in pathways including plant-pathogen interaction, MAPK signaling pathway, and plant hormone signal transduction. Furthermore, GSEA demonstrated a significant enrichment and upregulation of the MAPK signaling pathway. The qPCR validation confirmed significant upregulation of key genes, including MPK3, MPK6, PR1, and ERF1. These results demonstrate that the DXHS strain activates the salicylic acid (SA), JA, and ethylene (ET ) pathways in strawberry leaves, enhancing resistance to SPM. These findings elucidate key aspects of the molecular mechanism underlying the resistance induced by B. altitudinis DXHS against SPM and the application of DXHS strain in the biological control of strawberry diseases.

Pangenomes are increasingly important for harnessing crop genetic diversity, yet their resolution and utility are often limited by insufficient sampling of high-quality genome assemblies. Here we present a population-level watermelon super-pangenome constructed from 138 reference-grade assemblies, including 135 newly generated genomes representing all seven species. This super-pangenome captures approximately 1 million structural variants (SVs), enabling accurate variant genotyping across 914 accessions. Broader sampling within the pangenome provides insights into watermelon genome evolution and the origin of cultivated watermelon. Incorporating SVs into genome-wide association studies improves mapping resolution and reveals a copy number variant upstream of ClFCI1 that regulates flesh color intensity in a dosage-dependent manner. Leveraging this comprehensive variation map, we developed high-accuracy genomic prediction models for 18 agronomic traits. Together, these findings and genomic resources establish a foundation for dissecting complex traits and accelerating precision breeding in watermelon, while offering a valuable model for SV-resolved pangenomics in crops.

Heterosis, characterized by enhanced resistance and yield, has been widely utilized in watermelon breeding. However, our understanding of the regulatory mechanisms underlying male-sterile phenotypes in watermelon remains limited. Here, we determined that the miR159a targets ClMYB33 to regulate anther dehiscence, leading to male sterility in watermelon. Both overexpression of Cl-miR159a (OE-miR159a) and knockout of ClMYB33 (clmyb33) in watermelon suppressed the degradation of septum and stomium tissues, thereby impairing anther dehiscence and preventing successful pollen release. Based on DNA affinity purification sequencing (DAP-seq), RNA-seq, and verified interaction assays, ClPG1 and ClQRT2 were identified as downstream target genes of ClMYB33; both were positively regulated by ClMYB33. Both ClPG1 and ClQRT2 exhibited polygalacturonase (PG) activity in vivo. The knockout of ClQRT2 led to reduced PG activity and a failure in anther dehiscence. Furthermore, the GST-ClQRT2 fusion protein was capable of rescuing the indehiscent anther phenotype observed in both OE-miR159a and clmyb33 plants. Our results reveal a new mechanism by which the miR159a-ClMYB33 module regulates anther dehiscence by mediating PG activity, and provide a new molecular tool to create male sterility in watermelon.

Understanding how crops respond to environmental variation is crucial for biodiversity conservation and food security. Cucurbita pepo (pumpkin, squash, gourd) is one of the first domesticated crop species and exhibits remarkable phenotypic and ecological diversity, making it a powerful system for investigating the genomic basis of adaptation. Here, we constructed a graph-based C. pepo pangenome using nine chromosome-level assemblies and identified 229,431 high-confidence structural variants (SVs) that were genotyped across 206 wild and cultivated accessions. Our results demonstrate that C. pepo underwent parallel domestication, with two deeply diverged gene pools independently giving rise to the pepo and ovifera cultivated lineages, followed by expansion into diverse environments that produced strong signatures of differentiation largely mediated by young adaptive alleles. Single-nucleotide polymorphisms (SNPs) and SVs contribute complementary dimensions of environmental responsiveness. Biogeographical modeling predicts continued range contraction of wild relatives and elevated genetic offset in Eastern North American populations under projected future climates. Populations with higher genetic load harbor fewer adaptive variants and exhibit greater predicted maladaptation, indicating that deleterious mutations constrain adaptive potential. These findings highlight how genomic variants, adaptive diversity, and genetic load together shape environmental adaptation and inform conservation and crop improvement.

Vegetables are crucial to human diet and health. To ensure sustainable vegetable production, regulatory measures are needed to enhance seed germination, plant growth, and resilience to extreme environmental conditions. Nanomaterials (NMs), owing to their high surface area, nanoscale dimensions, and unique photocatalytic properties, exhibit remarkable biological effects, such as promoting germination and growth, as well as improving stress resistance in crops, offering novel solutions to key challenges in vegetable cultivation. This review summarizes the absorption pathways of NMs in plants, specifically through the leaves and roots of vegetables. Their uptake and translocation occur via passive diffusion, active transport, and endocytosis, with key influencing factors including particle size, chemical composition, surface charge, and surface modifications. We further evaluate the advantages of nanofertilizers and nanopesticides, in vegetable production over their traditional counterparts, focusing on improvements in seed germination rates, seedling vigor, biotic and abiotic stress tolerance, and overall yield and quality. Through this review, we aim to offer comprehensive insights into the application of NMs in vegetable crop production.

The regulatory mechanism of brassinolide (BR) signaling in cucurbitaceae crops remains incompletely understood. Previous research demonstrated that the rice genes GW5 and GW5L modulate seed morphology via the BR pathway. However, the conservation of their orthologs in watermelon and their evolutionary trajectory are yet to be elucidated. In this study utilizing the watermelon 97103v2 genome, we identified 15 GW5-LIKE genes. Through structure, phylogenetic tree construction, collinearity, promoter and spatiotemporal expression analysis, we determined that ClGL1 to ClGL3 are the most closely related to GW5 and GW5L. Subsequently, two crucial materials were acquired: the inbred line Jing L6M harboring the homozygous mutant Clgl1, and the near-isogenic line Changhong, a Jing L6M backcross containing the wild-type allele ClGL1. Apart from the disparity in fruit morphology, a clear difference in seed shape was observed between the two. Furthermore, exogenous BR treatment demonstrated that ClGL1 positively regulated the BR signal, aligning with the positive impact of GW5 and GW5L. In conclusion, ClGL1 modulates the morphology of watermelon fruit and seed by enhancing BR signaling, which provides a key gene and theoretical basis for BR signaling evolution and molecular design breeding in Cucurbitaceae.

Fruit size correlates with yield potential and serves as a vital agronomic trait. However, the key regulatory genes controlling fruit size in watermelon (Citrullus lanatus) remain poorly understood. In this study, we identified a NAC transcription factor gene ClNAC100 localized to selective sweep regions that positively regulated plant height and fruit size. CRISPR-Cas9-mediated knockout of ClNAC100 caused dramatic reductions in both plant height and fruit size, concomitant with decreased gibberellin (GA) levels in mutants. Exogenous GA4 application partially rescued the plant height and fruit size of the clnac100 mutant, while it could not restore these traits to wild-type levels. ClNAC100 directly upregulated expansin gene ClEXPA1 and GA biosynthetic genes ClGA3oxs, though DELLA protein interactions attenuated this transcriptional activation. A natural variant (-1087, T/C) of ClNAC100 enabled the Dof transcription factor ClDof4.6 to bind and activate ClNAC100 expression during watermelon domestication. Together, our results demonstrate that ClNAC100 mainly modulates the GA pathway to regulate fruit size and plant height, advancing mechanistic understanding of these agriculturally critical traits.

Pepper (Capsicum annuum L.) is a vegetable crop of significant economic importance, but its yield and quality are severely affected by the combined stress of low temperature and low light (LL), particularly in greenhouse environments. Despite this, the physiological and molecular mechanisms underlying pepper’s response to LL stress remain poorly understood. In this study, we conducted physiological and transcriptomic analyses on two pepper genotypes: Y2, a LL-sensitive genotype, and Y425, a LL-tolerant genotype. These genotypes were subjected to LL stress conditions (10 °C/5°C, 100 µmol m⁻²s⁻¹) and control (CK) conditions (28 °C/18°C, 300 µmol m⁻²s⁻¹). Three days after treatment, the phenotypes of the two pepper genotypes began to show clear distinctions, with Y425 seedlings exhibiting greater root length, shoot fresh weight, and root fresh weight compared to Y2. Additionally, comparative transcriptome analysis of leaf samples from both genotypes identified a total of 13,190 differentially expressed genes (DEGs). Gene Ontology (GO) enrichment analysis revealed that genes associated with photosynthesis, osmotic stress response, reactive oxygen species response, and other GO terms potentially contribute to LL tolerance. Moreover, three key pathways involved in the response to LL stress were identified: photosynthesis-antenna proteins, zeatin biosynthesis, and circadian rhythm pathways. The key DEGs in these pathways were expressed at higher levels in Y425 as compared with Y2. Furthermore, physiological indicators such as chlorophyll fluorescence parameters, chlorophyll content, osmoregulatory substances, and antioxidant enzyme activities decreased under LL stress; however, the reduction was significantly greater in Y2 compared to Y425, further validating the molecular findings from the transcriptome analysis. This study identified significant physiological and transcriptomic differences in two pepper genotypes under LL stress. It highlighted key pathways and provide novel insights into the molecular and physiological mechanisms of pepper’s LL tolerance. These results emphasize the importance of optimizing greenhouse conditions for better crop productivity.

Oriental melon, a climacteric fruit prized for its superior quality, faces limited shelf life. Although knockout NON-RIPENING (CmNOR) prolongs storage duration at the expense of quality loss, the potential of its direct agricultural application to reconcile this conflict remains uninvestigated. Through crossing homozygotes Cmnor and wild-type (WT) plants, we created CmNOR/Cmnor heterozygotes. These heterozygotes exhibited a 6-day ripening delay accompanied by reduced sucrose and β-carotene levels, yet ultimately attained WT quality parameters. Exogenous ethylene treatment accelerated fruit softening but failed to restore key quality parameters in both heterozygotes and homozygotes to WT levels. Transcriptomic and quantitative polymerase chain reaction (qPCR) analysis revealed that homozygotes displayed >10-fold expression differences versus WT in quality-associated genes (e.g. involved in carotenoid biosynthesis and sucrose metabolism). These expression disparities diminished to approximately 2-fold in heterozygotes. Furthermore, heterozygotes extended shelf life by 3-5 days during storage at 20°C while maintaining fruit quality. Storage-phase differential genes clustered in water regulation and cell wall modification pathways, with heterozygous-WT expression disparities gradually decreasing over time. The CmNOR dosage effect dynamically modulates interconnected quality and preservation networks, proposing an editing-based solution to overcome the storability-quality dichotomy in climacteric fruits.

The regulation of non-climacteric fruit ripening by the transcription factor NON-RIPENING (NOR) is poorly understood. Here, we identified that the NOR homolog in the non-climacteric fruit watermelon (Citrullus lanatus) was located within the selective sweep and sweetness quantitative trait locus that was selected during domestication from landraces to cultivars. ClNOR knockout substantially delayed fruit ripening, and the fruits of the knockout plants had lower abscisic acid (ABA) levels, lighter colored flesh, and were less sweet compared to wild type. Transcriptome analysis and DNA affinity purification sequencing revealed that ClNOR targeted the Basic Leucine Zipper gene ClbZIP1, which links ClNOR to genes that do not have a ClNOR-binding motif in their promoters, such as the ABA biosynthesis gene, 9-cis-epoxycarotenoid dioxygenase ClNCED1 and the chromoplast phosphate transporter gene ClPHT4;2. The double mutant Clnor Clbzip1 exhibited delayed fruit ripening, lower ABA level, and lighter colored flesh. Its delayed ripening phenotype was stronger than that of the Clbzip1 single mutant. Additionally, the ClNORT,T haplotype in cultivated watermelon resulted in higher ClbZIP1 expression, but ClNORC,T from landraces and ClNORC,G from ancestral watermelon did not. Heterologous ClNORT,T expression rescued the delayed ripening phenotype of the Slnor knockout in tomato (Solanum lycopersicum). This natural variant (564T/C) of ClNOR promoted fruit ripening by enhancing target genes transcription. Overall, these findings will help elucidate the evolutionary mechanisms of nonclimacteric fruit ripening.

The external appearance of fruit commodities is an essential trait that has profound effects on consumer preferences. A natural melon variety, characterized by an uneven and patchy arrangement of dark green streaks and spots on the white-skinned rind, resembles shooting stars streaking across the sky; thus, this variety is called "Shooting Star" (SS). To investigate the mechanism underlying the SS melon rind pattern, we initially discovered that the variegated dark green color results from chlorophyll accumulation on the white skin. We then constructed a segregation population by crossing a SS inbred line with a white rind (WR) inbred line and used bulk segregant analysis (BSA) revealed that the SS phenotype is controlled by a single dominant gene, CmAPRR2, which has been previously confirmed to determine dark green coloration. Further genomic analysis revealed a hAT-like transposable element (TE) inserted in CmAPRR2. This TE in CmAPRR2 is recurrently excised from rind tissues, activating the expression of CmAPRR2. This activation promotes the accumulation of chlorophyll, leading to the variegated dark green color on the rind, and ultimately resulting in the SS rind phenotype. Therefore, we propose that the SS phenotype results from the recurrent excision of the hAT-like TE in CmAPRR2.

Gibberellins (GAs), enzymes that play a significant role in plant growth and development, and their levels in plants could be regulated by gibberellin-oxidases (GAoxs). As important fruit trees and ornamental plants, the study of the mechanism of plant architecture formation of the Prunus genus is crucial. Here, 85 GAox genes were identified from P. mume, P. armeniaca, P. salicina, and P. persica, and they were classified into six subgroups. Conserved motif and gene structure analysis showed that GAoxs were conserved in the four Prunus species. Collinearity analysis revealed two fragment replication events of PmGAoxs in the P. mume genome. Promoter cis-elements analysis revealed 24 PmGAoxs contained hormone-responsive elements and development regulatory elements. The expression profile indicated that PmGAoxs have tissue expression specificity, and GA levels during the dormancy stage of flower buds were controlled by certain PmGAoxs. After being treated with IAA or GA3, the transcription level of PmGA2ox8 in stems was significantly increased and showed a differential expression level between upright and weeping stems. GUS activity driven by PmGA2ox8 promoter was detected in roots, stems, leaves, and flower organs of Arabidopsis. PmGA2ox8 overexpression in Arabidopsis leads to dwarfing phenotype, increased number of rosette leaves but decreased leaf area, and delayed flowering. Our results showed that GAoxs were conserved in Prunus species, and PmGA2ox8 played an essential role in regulating plant height.