Target leaf spot (TLS), caused by Corynespora cassiicola, is a prevalent leaf disease that significantly impacts cucumber yield and quality. Breeding disease-resistant cucumber varieties is a key strategy for managing this disease, and identifying critical resistance genes is essential for genetic improvement. In this study, we identified a highly susceptible mutant to TLS in the Tnt1 retrotransposon mutant library. Bulked segregation analysis sequencing (BSA-seq) further pinpointed a candidate gene for TLS resistance, encoding the Mildew Resistance Locus O (MLO) protein, CsMLO4. Expression analysis revealed that CsMLO4 is strongly induced by C. cassiicola infection. Functional analyses revealed that loss of function and silencing of CsMLO4 attenuated resistance to TLS and exhibited reduced reactive oxygen species (ROS) accumulation, while transient overexpression of CsMLO4 enhanced both disease resistance and ROS levels. These findings suggest that CsMLO4 mediates cucumber defense against C. cassiicola by modulating ROS levels. Additionally, transcriptome analysis identified multiple disease-resistance-related pathways affected by the loss of function of CsMLO4. Overexpression of CsMYB, a potential candidate gene regulated by CsMLO4, showed enhanced resistance to C. cassiicola. This study expands insights into the functional role of MLO family beyond their association with powdery mildew resistance and offers new perspectives on the mechanisms underlying TLS resistance in cucumber.

Stevia rebaudiana, a member of the Asteraceae family, is a sugar-yielding plant abundant in stevia glycosides (SGs), which are extensively applied in sweeteners and pharmaceuticals. Although DNA methylation has been implicated in the regulation of specialized metabolite synthesis, its specific involvement in SG metabolism remains insufficiently elucidated. In this study, a chromosome-level genome assembly of S. rebaudiana was generated, including 1436 Mb across 11 chromosomes. DNA methylation profiling indicated that the expression of UDP-glycosyltransferases may be regulated by CG methylation within gene bodies across distinct tissues of S. rebaudiana. In conclusion, this study not only delivers a high-quality reference genome for S. rebaudiana but also provides novel perspectives on the potential regulatory mechanisms by which DNA methylation influences SG biosynthesis.

Cut flowers are favored globally for their ornamental value, but their commercial value is limited by their short vase life, which depends closely on the postharvest preservation technology of cut flowers. Currently, complex types of preservatives and a variety of preservation methods have been used, but there is a lack of summary and comparison of them. In this study, 45 publications were synthesized and analyzed through meta-analysis and machine learning. The meta-analysis results showed that: (i) pulse treatments demonstrated superior vase life extension over conventional vase solution treatments by acutely enhancing antioxidant enzyme activity and suppressing ethylene biosynthesis, but their transient nature necessitated subsequent vase solution treatment maintenance for optimal floral appearance. (ii) As unique preservatives, nanomaterials had advantages in water balance and antimicrobial protection, which required synergistic integration with other preservatives to further enhance antioxidant capacity and supply nutrient. (iii) Plant species specificity needed to be taken into account when choosing the preservative types for vase solution treatment. The model prediction results of machine learning revealed that identical preservatives exhibited distinct differences when applied as pulse treatments versus vase solution treatments, indicating pulse treatment could amplify the preservation effect of preservatives. Based on the above results, an optimized implementation protocol was proposed: initial pulse treatment with nanomaterials, then species-specific preservatives addressed as supplement vase solutions treatment. Our verification experiments further validated that the optimized preservation protocol was effective in cut roses (Rosa hybrida L. cv. Carola). The findings provided mechanistic guidance for optimizing preservative combinations, and a theoretical foundation and direction for future research.

Grapevine (Vitis vinifera) is economically important for fresh consumption, winemaking, and drying. The circadian systems of flowering and fruit development are crucial for viticulture and yield formation. However, the genetic basis of continuous flowering and bearing has been rarely elucidated. Here, we integrate pan-genomics, comparative genomics, single-cell transcriptomics, and bulk transcriptomics to investigate the continuous flowering and bearing trait (CFB) in the ‘Julian’ grape, which bears fruits at different development stages from flower to mature berries simultaneously. Pan-genomics and comparative genomics discovered 558 unique structural variations (SVs) and eight genes enriched in flowering pathways exclusively in Julian, based on the newly generated haplotype-resolved near telomere-to-telomere (T2T) genome of ‘Julian’ and 15 previously published genomes of grapevine, which bears fruits in the same developmental stage (i.e., seasonal flowering and bearing, SFB). Single-cell transcriptomes of flowering buds for CFB ‘Julian’ and SFB ‘Muscat Hamburg’ detected seven distinct cell types, which provide detailed cell-type-specific gene expression profiles for both cultivars, with differential gene expression (DEG) insights highlighting growth, metabolism, and hormonal regulation pathways in ‘Julian’. Integrating SVs and DEG data, we pinpoint 37 candidate genes potentially associated with CFB, including Auxin/IAA, Cytochrome P450, Vicilin-like antimicrobial peptides (AMP) and respiratory burst oxidase homolog protein B (RBOH) related genes. This study provides insights into the genetic basis of CFB in grapevine, facilitating grapevine breeding with continuous flowering and bearing.

The Asteraceae family, one of the largest angiosperm families, is rich in terpenoid secondary metabolites with significant medicinal value. Asteraceae plants have evolved a diverse array of terpenoid biosynthesis pathways, reflecting their adaptive significance and complex regulatory mechanisms. However, the evolutionary patterns and transcriptional regulatory mechanisms governing these biosynthetic processes remain unclear. This study investigates the evolution and transcriptional regulation of terpenoid biosynthesis genes in Asteraceae. Comparative genomic analysis of 19 Asteraceae and six out-group species revealed that Asteraceae species diverged ~74.03 million years ago and were distinctly divided into three subfamilies. A total of 1714 terpene synthase (TPS) genes were identified, predominantly in the TPS-a and TPS-b subfamilies. Caryophyllene-type sesquiterpene biosynthetic gene clusters (BGCs) were detected in 10 species, with their formation due to whole-genome duplication (WGD) and tandem duplication. By integrating weighted gene coexpression network analysis (WGCNA) and machine learning methods, key transcription factors regulating caryophyllene synthase (CPS) in Carthamus tinctorius were identified. A multilayered gene regulatory network was constructed to identify potential regulatory factors involved in TPS gene regulation under light stress. By exploring the evolutionary patterns and potential regulatory relationships involved in terpenoid biosynthesis in Asteraceae, this study provides important insights into TPS gene evolution. In addition, the findings also offer guidance for optimizing genetic engineering strategies in terpenoid-based drug development.

Activating chloroplast immunity to enhance host resistance offers a novel and sustainable approach for the effective control of kiwifruit bacterial canker. Chloroplasts serve as a central hub for ROS, SA, and Ca²⁺ signaling. As a chloroplast-localized protein, CaS participates in Ca²⁺-signaling pathways. However, the mechanisms underlying CaS-mediated immune regulation and whether to be attacked by pathogens remain unclear. Here, we created AcCaS-overexpressing transgenic plants, then we found that AcCaS activates chloroplast reactive oxygen species (ROS) bursts and enhances resistance against Pseudomonas syringae pv. actinidiae (Psa). Mutational analysis revealed that the chloroplast transit peptide (cTP) of AcCaS is essential for its immune function, and deletion of cTP abolished ROS production and disease resistance. Yeast two-hybrid reveals that Psa employs the effector HopAU1 targets AcCaS in kiwifruit. Luciferase complementation imaging, and microscale thermophoresis assays identified Asn-121 of AcCaS as the critical residue mediating both HopAU1 binding and Ca²⁺ sensing. Strikingly, molecular modeling and competitive binding experiments showed that HopAU1 directly occupies the Ca²⁺-binding site at Asn-121, thereby blocking calcium signaling and suppressing chloroplast immunity. In summary, this study uncovers that AcCaS enhances resistance against Psa by activating chloroplast ROS and binding with Ca²⁺. The Asn-121 residue plays a pivotal role in Ca²⁺-binding and HopAU1-mediated immune suppression, as mutations at this site abolish both activities. These findings revealed the battle of chloroplast Ca² signaling in plant-pathogen conflicts and provide a mechanistic basis for engineering AcCaS-centered resistance in kiwifruit.

Wucai (Brassica rapa), a widely cultivated non-heading Chinese cabbage in autumn and winter in China, has been limited in its genetic and genomic analyses due to the lack of a reference genome. Here, we have assembled a high-quality chromosome-level genome assembly of wucai, which is 480.57 Mb in length, with a scaffold N50 of 46.53 Mb and a contig N50 of 4.45 Mb. We annotated 42 634 protein-coding genes in the B. rapa W7-2 genome and 55.08% of repetitive sequences. Additionally, we performed DNA methylome analysis to investigate the characteristic yellowing response of wucai inner leaves to low temperature. CHH methylation levels increased under low-temperature conditions, while a slight decrease was observed under normal temperatures with more hypo-differentially methylated regions. The expression levels of DNA methyltransferases BrCMT2 and BrDRM2 were significantly up-regulated under low-temperature conditions but down-regulated at normal temperature. Furthermore, chlorophyll metabolism genes, BrHemA, BrHemL, BrHemD, BrCLH2, BrCHLP, BrSGR, and BrPPD, were identified as differentially expressed, which exhibited elevated CHH methylation levels in their promoter regions across three stages. Leaves of Nicotiana benthamiana transiently overexpressing BrCLH2.1 exhibited a slight degreening phenotype compared to wild type. The application of a DNA methylation inhibitor into the inner leaves of W7-2 induced obvious bleaching, and the total chlorophyll content decreased significantly. In conclusion, the genome data of W7-2 provide a valuable resource for functional gene research and genetic breeding of non-heading Chinese cabbage.

Glucosinolates (GSLs) are sulfur-containing metabolites in Brassica species with dual roles in plant defense and human health. While glucoraphanin (GRA) offers anticancer benefits, progoitrin (PRO) poses risks due to goitrogenic effects. This study aimed to dissect the genetic basis of GRA, gluconapin (GNA), and PRO accumulation in florets of Brassica oleracea by integrating linkage mapping and quantitative trait locus (QTL) analysis using two F₂ populations (JB-F₂ and GJ-F₂) derived from crosses between broccoli, Chinese kale, and purple cauliflower. High-density linkage maps were constructed using a 10 K SNP array, and GSL profiles were quantified via high-performance liquid chromatography. QTL mapping identified 23 significant loci across both populations, with major-effect QTL clusters on chromosomes C3 and C9. Notably, epistatic analysis revealed strong interactions between major QTLs, particularly between loci on chromosomes C3 and C9, further emphasizing their central role in regulating GSL biosynthesis. Functional analysis prioritized BolC9t53177H (homologous to AOP2) and BolC3t13531H (homologous to GSL-OH) as key genes governing GRA-to-GNA and GNA-to-PRO conversions, respectively. Sequence variations in these genes explained parental GSL profiles: A 2-bp deletion causing a frameshift mutation in BolC9t53177H disrupted GRA metabolism in broccoli (B58-6), while defective BolC3t13531H in Chinese kale (J1402) abolished PRO synthesis. KASP markers developed for these loci enabled efficient genotyping of 104 B. oleracea accessions, revealing significant associations with GSL content. This study provides genetic insights and molecular tools to optimize GSL composition, facilitating the breeding of high-GRA/low-PRO Brassica varieties with enhanced nutritional value.

Nocturnal starch remobilization is critical for plant carbon allocation and stress adaptation. While β-amylase 3 (BAM3) serves as the primary catalyst for starch degradation at night, its regulation mechanisms under stress remain to be fully characterized. The chloroplast vesiculation (CV) protein is crucial for maintaining chloroplast homeostasis during stress conditions, though its potential involvement in starch metabolic processes remains unexplored. Herein, we show that low night temperature (LNT) stress induces starch accumulation in tomato leaves, with SlCV overexpression exacerbating this phenotype and compromising LNT tolerance, whereas SlCV silencing promotes starch catabolism. RNA-seq and metabolome analyses detected lower levels of starch metabolites and amylase activity in SlCV overexpression plants. Strikingly, we have confirmed the physical interaction between SlCV and SlBAM3, and SlCV overexpression significantly accelerated the degradation of SlBAM3 under LNT stress, while SlCV knockout enhanced the stability of SlBAM3. Genetic validation confirmed that SlBAM3-silenced plants accumulate excessive starch and exhibit LNT-sensitive phenotypes, and SlBAM3 overexpression enhances cold tolerance. Furthermore, SlBAM3 complementation rescues the starch overaccumulation and LNT hypersensitivity of SlCV overexpression plants. These results elucidate the regulatory mechanism of starch metabolism mediated by SlCV and associated with SlBAM3 protein stability, providing novel insights into the starch metabolic pathway under cold stress.

Senescence is a complex biological process coordinately regulated by multiple genes at the molecular level. Deciphering its regulatory mechanisms holds significant potential for enhancing crop yield and stress resistance. However, the study on identification of senescence-related genes in watermelon has been limited by low genetic diversity. In this study, we identified an early-senescence watermelon inbred line, WM103, which displayed a pale green phenotype at the seedling stage that transitions to yellow at maturity. Genetic analysis indicated the early-senescence phenotype was controlled by a single recessive gene. Combined by BSA-seq and linkage analysis in a large F₂ population, we identified Cla97C10G186360 as the candidate gene, which encoded a BALANCE OF CHLOROPHYLL METABOLISM (ClBCM) protein. Further functional validation through virus-induced gene silencing and CRISPR/Cas9-mediated knockout confirmed that the down-regulation and loss of function of ClBCM can accelerate senescence. RNA-seq analysis revealed that the ClBCM was involved in the chlorophyll metabolism pathway, and these chlorophyll degradation-related genes were significantly up-regulated in WM103. Molecular interaction assays revealed a direct physical interaction between ClBCM and ClSGR. Furthermore, we found WRKY family transcription factors were significantly enriched in differentially expressed genes. In vivo and in vitro experiments showed ClWRKY53 directly bound to the ClBCM promoter and suppressed its transcription, thereby promoting chlorophyll degradation and senescence. These findings provide novel insights into the molecular regulation of senescence in watermelon and establish a theoretical framework for genetic improvement of fruit yield and stress tolerance in cucurbit crops.

Anthocyanins play diverse roles in plants, including attracting pollinators and protecting cells from oxidative damage. In zoysiagrass, a warm season turfgrass, their accumulation in seed heads and stolons can decrease the aesthetic appeal. In this study, a high-density genetic map with ~8000 single nucleotide polymorphism (SNP) markers organized into 20 linkage groups was generated in a Zoysia japonica acc. Meyer ×  Zoysia matrella acc. PI 231146 F₂ population. Using this genetic map, a large-effect quantitative trait locus (QTL) for anthocyanin variation in stolons and seed heads was mapped to chromosome 12 (PP locus). Variant analysis of a candidate gene for PP, Zjn_sc00004.1.g07010.1.sm.mk, which encodes an MYC-bHLH transcription factor that regulates anthocyanin biosynthesis, revealed a SNP at an exon-intron boundary in Meyer that led to intron retention. Interestingly, an F₁ population derived from the same parents segregated for seed head color but uniformly displayed purple stolons. Seed head color in the F₁ population comapped with the PP locus which, combined with genotypic and yeast two-hybrid analyses, revealed that a SNP in PI 231146 leading to an Ala163Ser substitution in the MYB-interacting N-terminal domain of the same MYC-bHLH transcription factor was likely causal. The Ala163Ser substitution affected interaction of MYC-bHLH with MYB in an MYB-dependent manner. The identified mutations can be exploited to develop cultivars with green seed heads and stolons. The high-marker-density interspecific Z. japonica ×  Z. matrella F₂ genetic map also provides a robust tool for identifying genomic regions and genes of agronomic interest that differentiate the two species.

As a bridge between human health and plant nutrition, Selenium (Se) phytofortification represents a promising strategy for achieving a safe and effective dietary Se supplementation. Due to chemical similarities, Se absorption, transformation, and storage in crops primarily follow the sulfur metabolic pathway. Se enhances horticultural crop resilience against abiotic and biotic stresses by: (i) boosting antioxidant capacity, (ii) inducing hormonal cascades, (iii) promoting the accumulation of key metabolites (e.g. amino acids, flavonoids), (iv) strengthening cellular functions, and (v) harnessing plant-microbiome interactions. In horticultural crops, most Se exists in organic forms, such as selenoamino acids, selenoproteins, selenium-polysaccharides, and selenium-polyphenols, which contribute to unique quality traits. Additionally, Se regulates the synthesis of core nutrients, including amino acids, flavonoids, phenolic compounds, soluble sugars, mineral elements, alkaloids, and volatile compounds. It also extends postharvest shelf life by delaying senescence and deterioration. Current phytofortification strategies focus on enhancing bioavailable Se in edible parts through agronomic interventions and plant breeding. Artificial Se fertilization is the most common agronomic approach, classified by the application method (soil fertilization, foliar spraying, hydroponic supplementation, and seed soaking) and fertilizer type (inorganic, organic, nano-Se, and biosynthesized fertilizers). Optimizing plant species, fertilization methods, dosage, timing, and elemental synergies maximize phytofortification efficiency.

Grapevine cultivars are vegetatively propagated to maintain their varietal characteristics. However, long periods of cultivar multiplication result in the accumulation of spontaneous somatic mutations that can differ among clonal lines. Here, we explored this intravarietal genetic diversity to trace back the origin and dissemination history of ‘Tempranillo Tinto’, the third most cultivated wine grape variety worldwide. A stringent somatic variant calling over whole-genome resequencing data of 35 ‘Tempranillo Tinto’ grapevines from seven Iberian winemaking regions revealed 158 somatic single nucleotide variants (SNVs) shared by some of the plants. Among them, 56 highly informative SNVs were used to custom-design a high-throughput intravarietal genotyping assay, which was validated and used to analyze 185 vines representing a broader geographic distribution. Phylogenetic analyses revealed three major clonal lineages in ‘Tempranillo Tinto’ that grouped the samples according to their geographic origin. By inferring the ancestral SNV alleles in ‘Tempranillo Tinto’ from whole-genome resequencing data of its parents, we determined the Ebro River Valley in Northeast Spain as the most likely birthplace of the cultivar. Derived alleles revealed one major historical human-mediated westward dissemination route from this original site towards the winemaking regions following the Duero River Valley and then, to the South in Portugal. Clonal lineages also revealed the polyphyletic nature of somatic variant traits of interest for grape and wine quality production under climate change conditions. Our findings elucidate the origin and historical dispersal of ‘Tempranillo Tinto’ and underscore genomic strategies for advancing clonal improvement to ensure the sustainability of valuable traditional grapevine cultivars.

DNA methylation is a critical epigenetic regulator in plant development, yet its role in grape berry ripening remains poorly understood. Here, we profiled the genome-wide DNA methylation landscapes of two cultivars, ‘Wink’ and ‘Cabernet Sauvignon’, across developmental stages and tissues (skin and pulp tissues), revealing widespread DNA hypermethylation during ripening. We observed a progressive increase in global DNA methylation, particularly in the CHH context, across transposable elements, gene bodies, and adjacent regions during ripening. This hypermethylation was conserved across both varieties and was pronounced in both skin and pulp tissues. Differentially methylated regions (DMRs) revealed tissue-specific methylation patterns, with skin and pulp exhibiting distinct hypermethylation dynamics. Further analysis demonstrated that these tissue-specific hypermethylation dynamics are partially attributable to pre-existing methylation differences between skin and pulp at earlier developmental stages. Functional analysis demonstrated that DNA methylation inhibitors (zebularine and RG108) delayed berry ripening in vitro, underscoring the critical role of methylation in this process. Furthermore, RNA-seq analysis identified tissue-specific gene expression changes associated with differential methylation, particularly in metabolic pathways such as anthocyanin biosynthesis, fructose metabolism, and glycolysis. Notably, tissue-specific hypermethylation of genes involved in anthocyanin metabolism correlated with their expression patterns, suggesting a regulatory role for DNA methylation in metabolite accumulation during ripening. Collectively, these findings underscore DNA methylation as a critical regulatory layer that orchestrates tissue-specific gene expression with metabolic shifts during grape maturation, thereby advancing our understanding of epigenetic control in fruit development.

Since its inaugural release in 2022, The Vegetables Information Resources (TVIR) has been a cornerstone for genomics and genetic breeding studies within the vegetable research community. With advancements in sequencing technologies leading to an influx of new genome sequences, TVIR has been upgraded to version 2.0 (http://tvir2.bio2db.com/), expanding from 59 to 84 vegetable species and introducing new functional modules to accelerate research. This upgrade incorporates a CRISPR/Cas9 resource module, which integrates four specialized tools: CasFinder, CasOT, Crisflash, and CRISPRCasFinder, to facilitate gene editing research. The database further features dynamic synteny analysis with an interactive interface, enabling users to visualize genomic relationships between species. Additionally, two novel bioinformatics tools Hmmsearch and CRISPRCasViewer are integrated to enhance comparative and functional genomic analyses. TVIR 2.0 retains all TVIR 1.0 features while updating resistance gene identification, expanding from 3 to 8 types, and transcription factor datasets, now including 237 431 TFs, an increase from 172 493.The database integrates comprehensive genomic, transcriptomic, and functional annotation data, providing freely accessible resources for vegetable breeding and gene editing.

Improving gene editing efficiency has been a prominent research focus with the increasing application of CRISPR/Cas9 in crop genetic enhancement. In this study, we demonstrated that increasing exogenous auxin levels during in vitro tissue culture significantly enhances gene editing efficiency, leading to a higher frequency of functionally edited T₀ plants. While higher auxin levels promoted callus growth, it also delayed shoot initiation and slightly decreased shoot regeneration. Subsequent RNA-Seq analysis revealed significant alterations in the expression of plant developmental regulatory genes and chromatin remodeling genes at two plant regeneration stages. Further analysis using nuclei staining and Transposase-Accessible Chromatin using sequencing showed that excessive auxin resulted in a more relaxed chromatin structure in callus cells, thus enhancing the genomic DNA accessibility to Cas9. Additionally, the prolonged growth period of dedifferentiated callus cells and the delay in shoot initiation likely provided additional time for Cas9 to exert its function, explaining the improved gene editing efficiency due to excessive auxin application. To mitigate the inhibitory effects of excessive auxin on shoot regeneration, a ‘two-phase’ culture strategy was developed and validated using tomatoes, in which the explants were first cultured in media containing excessive auxin to promote calli growth and gene editing, then transferred to the media with lower auxin concentrations to promote the following shoots regeneration. Overall, our research has revealed novel aspects of auxin function in gene editing, offering new insights and a theoretical basis for future studies. Furthermore, the proposed culture method could accelerate the application of gene editing across various plant species.

Plants often experience aluminum (Al) toxicity in acidic soils, where the transcription factor SENSITIVE TO PROTON RHIZOTOXICITY1 (STOP1) plays a pivotal role in regulating transcriptional responses to Al stress. While posttranscriptional regulation of STOP1 under Al toxicity has been extensively studied, the mechanisms linking Al stress signals to STOP1 protein stability remain unclear. In this study, we employed multiscale pH imaging and noninvasive microtest (NMT) techniques to demonstrate that Al stress induces cytosolic acidification in the root apex of tomato (Solanum lycopersicum), which promotes the accumulation of SlSTOP1. This finding suggests that cytosolic acidification serves as a critical intermediate connecting Al stress to SlSTOP1 stabilization. Comparative transcriptomic analysis revealed that a significant subset of Al-responsive genes, including the known Al-resistance gene SlHAK5, are coregulated by both Al stress and low pH. Further functional characterization showed that SlHAK5 not only contributes to Al resistance but also plays a key role in maintaining cytosolic pH homeostasis under Al stress. In Slhak5 mutants, the expression of Al-induced genes was dysregulated, concomitant with attenuated cytosolic acidification. Correspondingly, SlSTOP1 accumulation was significantly reduced in Slhak5 mutants compared to wild-type (AC) plants under Al stress, indicating that SlSTOP1-mediated SlHAK5 expression feedback regulates cytosolic acidification. Additionally, Slhak5 mutants exhibited heightened sensitivity to proton stress. Collectively, our findings uncover a novel regulatory circuit involving SlSTOP1 and SlHAK5, which modulates SlSTOP1 stability through cytosolic acidification, thereby enhancing plant adaptation to proton and Al toxicity.

Vegetable and grain soybeans are typically distinguished by harvest time and pod size, yet their nutritional differences are often overlooked in breeding programs. This study compared 10 varieties each of vegetable and grain soybeans to find key nutritional markers distinguishing them. Results showed that vegetable soybeans have higher concentrations of sucrose, total soluble sugar, and crude protein, along with lower concentrations of crude oil and total fatty acid. Specifically, vegetable soybeans contain a relatively higher amount of unsaturated fatty acids, particularly oleic acid, at green edible stages. Principal component analysis of 12 nutritional components revealed clear distinctions between vegetable and grain soybeans. Additionally, machine learning algorithms identified sucrose as the most critical nutritional marker for distinguishing these two types. Dynamic RNA-seq analysis combined with weighted gene co-expression network analysis identified a sucrose-related module, highlighting GmSPS17 as a predominant sucrose phosphate synthase encoding gene involved in sucrose accumulation in soybean seeds. Furthermore, we identified GmZF-HD1 as an upstream transcription factor regulating GmSPS17. Yeast one-hybrid, luciferase, and electrophoretic mobility shift assays confirmed that GmZF-HD1 directly activates GmSPS17 transcription. Overexpression experiments in hairy roots validated that GmZF-HD1 enhances GmSPS17 expression, thereby increasing sucrose accumulation. In summary, this study establishes sucrose as a key nutritional marker for distinguishing vegetable soybeans from grain soybeans and elucidates the GmZF-HD1-GmSPS17 regulatory pathway, providing valuable insights into sugar accumulation mechanisms and offering guidance for breeding high-sugar vegetable soybean varieties.

Capsicum chinense (habanero pepper) exhibits substantial variation in fruit pungency, color, and flavor due to its rich secondary metabolite composition, including capsaicinoids, carotenoids, and volatile organic compounds (VOCs). To dissect the genetic and regulatory basis of these traits, we conducted an integrative analysis across 244 diverse accessions using metabolite profiling, genome-wide association studies (GWAS), and transcriptome-wide association studies (TWAS). GWAS identified 507 SNPs for capsaicinoids, 304 for carotenoids, and 1176 for VOCs, while TWAS linked gene expression to metabolite levels, highlighting biosynthetic and regulatory genes in phenylpropanoid, fatty acid, and terpenoid pathways. Segmental RNA sequencing across fruit tissues of contrasting accessions revealed 7034 differentially expressed genes, including MYB31, 3-ketoacyl-CoA synthase, phytoene synthase, and ABC transporters. Notably, AP2 transcription factors and Pentatrichopeptide repeat (PPR) emerged as central regulators, co-expressed with carotenoid and VOC biosynthetic genes. High-resolution spatial transcriptomics (Stereo-seq) identified 74 genes with tissue-specific expression that overlap with GWAS and TWAS loci, reinforcing their regulatory relevance. To validate these candidates, we employed CRISPR/Cas9 to knock out AP2 and PPR genes in tomato. Widely targeted metabolomics and carotenoid profiling revealed major metabolic shifts: AP2 mutants accumulated higher levels of β-carotene and lycopene. In contrast, PPR mutants altered xanthophyll ester and apocarotenoid levels, supporting their roles in carotenoid flux and remodeling. This study provides the first integrative GWAS-TWAS-spatial transcriptomics in C. chinense, revealing key regulators of fruit quality traits. These findings lay the groundwork for precision breeding and metabolic engineering to enhance nutritional and sensory attributes in peppers.

HKT proteins are the conserved voltage-gated ion channel proteins that act on the transmembrane transport of positive ions, but the evolutionary history of the HKT gene family is not clear. To create comparative HKT resources, we collected 134 HKT sequences in different phylogenetic lineages ranging from algae to angiosperms, encompassing fifty distinct taxonomic species. The evolutionary history of the HKT gene family was revisited through phylogenetic reconstruction. Phylogenetic reconstruction and comparative genomic analysis suggested that the HKT gene family originated from land plants and had a large number of tandem duplications. The evolution of HKT genes was mostly linear in non-seed plants. The genome duplication event was a potential factor in the change of the HKT gene copies in seed plants. In eudicots, the contraction event of HKT genes occurred every time the plant underwent a whole-genome duplication event after the ancient triplication. Amino acid sequence variations in the HKT transporters of TrkH domain influence their tertiary protein structure. Meanwhile, six HKT genes, represented by the Vitis vinifera, exhibit tissue-specific expression patterns and respond differentially to salt and drought stress. Frequent gene and genome duplications contributed significantly to the expansion/contraction of the HKT gene family. Our findings regarding the origin and evolution of HKT offer unique backgrounds and new insight into the functional evolution of this gene family.

Wild species have been extensively used as a reservoir of genetic variability in plant breeding. Both blueberries and cranberries are crops from the highly diverse Vaccinium genus that have benefited from interspecific hybridizations throughout their domestication history. In this review, we compiled all documented interspecific hybridizations performed for blueberry and cranberry aiming to guide future breeding efforts. We report the traits of interest, success and failure of crosses, and give the taxonomic sections of the species involved. Out of the 500 species listed in Vaccinium, only 42 have been tested for hybridization so far. Successful crosses with fertile progenies have been reported across distantly related sections. Considering the polyphyletic nature of Vaccinium, the definition of crop wild relatives for these crops could be expanded to incorporate other genera. This review highlights the enormous potential of the wild gene pools for breeding of Vaccinium berry crops, and the need to characterize these species and establish germplasm collections to face the agricultural challenges ahead.

The shikimate pathway is critical for the biosynthesis of aromatic amino acids and a diverse array of secondary metabolites in plants, including anthocyanins. Erythrose-4-phosphate (E4P) serves as a crucial precursor in the shikimate pathway. Transaldolase (TA) and transketolase (TK) are two pivotal enzymes involved in E4P synthesis in plants through the oxidative pentose phosphate pathway (OPPP) and Calvin cycle pathways. During the coloring stage of flowers, a large number of anthocyanins accumulate. However, the source of E4P required for anthocyanin accumulation is still unknown. In this study, we characterized the TA and TK family members in petunia (Petunia hybrida), an important ornamental plant. Virus-induced gene silencing (VIGS) and RNAi techniques indicated that PhTA1 or PhTA2 silencing did not lead to visible phenotype change in petunia, while cosilencing of PhTK1-TK2 resulted in significantly lighter colors in flowers and leaves. The levels of anthocyanins, chlorophyll, E4P, flavonoids, and three aromatic amino acids all significantly decreased in PhTK1-TK2-silenced plants compared with the control. Additionally, cosilencing of PhTK1 and PhTK2 disrupted the flavonoid metabolome profile in petunia flowers. In summary, PhTK1 and PhTK2 provide the primary E4P source for anthocyanin biosynthesis.