Potato breeding faces challenges due to clonal propagation and complex polyploid genetics, limiting the rate of genetic gain. Predictive breeding integrating genomic and high-throughput phenotypic data offers potential to enhance selection accuracy. Here we evaluated multiple regression models combining genomic single-nucleotide polymorphism (SNP) data and unmanned aerial vehicle-derived image-based traits across diverse potato clones and cultivars to predict key agronomic traits. Combining genomic and phenomic data significantly improved prediction accuracy for total tuber yield compared with using either data source alone, with phenomic data contributing complementary environmental information. Prediction accuracy varied by trait, with genomic data better predicting starch content and phenomic data excelling for tuber yield-related traits. Our findings demonstrate that integrating genomic and phenomic information can enhance predictive breeding strategies, potentially accelerating genetic gain and optimizing resource use in potato breeding programs.

Plants have evolved a structurally diverse chemical repertoire to mediate various environmental interactions. Yet, little is known about the chemical complexity and metabolic pathways across many plant genera. Acylsugars are a class of specialized metabolite widely distributed across the Solanaceae that play a role in deterring herbivores, insects, and fungal pathogens. Although acylsugars have been extensively characterized from leaf glandular trichomes, they have also been detected in other organs. Nevertheless, the biosynthesis, structures, and function of acylsugars outside of leaf trichomes remain unknown. Here, we performed organ-specific metabolomics across 28 Physalis species, an emerging model and crop genus closely related to important Solanum crops. Automated feature extraction revealed thousands of mass spectral features across the different species and organs. Acylsugar mass spectral features were manually annotated from surface extracts, revealing at least 323 unique acylsugars, substantially expanding the known acylsugar diversity in the Physalis genus. Some, but not all, species in the Physalis genus accumulated acylsugars on the fruit surface, and acylsugars were as abundant or sometimes more abundant in fruits than in leaves or calyces. Hierarchical clustering and phylogenetic tests indicated that species with similar acylsugar profiles did not cluster taxonomically. To determine the biochemical mechanism underlying acylsugar structural diversity, we characterized the first step of acylsugar biosynthesis, catalyzed by an acylsugar acyltransferase. Three Physalis ASAT1 homologs displayed broad substrate preferences, which may partially explain the differences in acylsugar profiles. The diverse fruit-localized acylsugars across the Physalis genus can inform engineering strategies for increased crop resilience.

Structural variations that generate novel alleles are fundamental drivers of phenotypic diversity. In crape myrtle (Lagerstroemia indica), an important summer-flowering woody species, the purple leaf trait is prized for its visual appeal and stress resistance, representing a key breeding objective. Although anthocyanin accumulation underlies purple leaf formation, its key genetic locus has remained unclear. Here, we constructed five segregated populations of crape myrtle and confirmed that the purple leaf trait is a single-gene dominant trait. Combining bulked segregant analysis with metabolomics and RNA-seq led to the identification of LiBBX16, a B-box zinc-finger transcription factor. This gene has two alleles in purple-leafed (LiBBX16p and LiBBX16a) and green-leafed (LiBBX16g and LiBBX16a) plants. LiBBX16p contains a unique 32-bp deletion causing a frameshift, premature termination, and nucleo-cytoplasmic localization. An InDel marker derived from this deletion effectively distinguished purple-leafed from green-leafed plants and identified that all plants homozygous for LiBBX16p are seedling lethal. Heterologous expression of LiBBX16p in Arabidopsis resulted in purple leaves and stems, with anthocyanin content ~9.5-fold higher than in controls. Conversely, silencing LiBBX16 in purple-leafed L. indica reduced anthocyanin content, turning leaves green. We further found that the 32-bp deletion enhances LiBBX16’s activation of anthocyanin synthesis-related genes, particularly LiF3GT and LiMYB75. Mechanistically, unlike LiBBX16g, which directly binds DNA, LiBBX16p likely acts as a coactivator recruited via protein–protein interactions. Overall, our results identified a neomorphic LiBBX16 allele that coregulates anthocyanin accumulation and seedling development, providing valuable insights into purple leaf formation and a target gene for molecular breeding.

Ultraviolet-B (UV-B, 280–315 nm) radiation acts as a key environmental signal that regulates plant development and acclimation responses. The UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8) plays a central role in perceiving and transducing these signals. In the absence of UV-B, UVR8 exists predominantly as a homodimer in the cytoplasm. Upon UV-B absorption, UVR8 dissociates into active monomers that translocate to the nucleus, where they initiate downstream signaling via interactions with core regulatory components. In this review, we systematically elaborate on the UVR8-mediated UV-B signal transduction cascade and the origin and diversification of UVR8, with a focus on the regulatory effects of UV-B on the nutritional quality, stress resilience, and reproductive traits of horticultural plants. We further propose future directions for the genetic improvement of horticultural crops and the development of light-environment manipulation technologies based on the UVR8 signaling network. This review aims to provide a theoretical reference for enhancing the economic value of horticultural products and advancing green, efficient horticultural production.

Fruit firmness is a critical quality trait primarily governed by the structure and composition of the cell wall. While extensive research has focused on firmness dynamics during fruit ripening, the regulatory mechanisms governing its establishment during early fruit development remain poorly understood. Previous studies have demonstrated that VASCULAR SPECIFICITY FACTOR 1 (VSF-1), a member of the bZIP family, is activated in vitro by the key fruit softening regulator LOB1, suggesting its potential role in the regulation of fruit firmness. In this study, we generated both CRISPR-Cas9-mediated knockout and overexpression lines in tomato; functional analysis revealed that the loss of VSF-1 function reduced fruit firmness, whereas its overexpression enhanced it, thereby establishing VSF-1 as a positive regulator of firmness. By integrating transcriptomic and DNA affinity purification sequencing profiling, we delineated the VSF-1-controlled gene regulatory network associated with cell wall remodeling and identified the β-galactosidase gene, TBG6, as a direct target. Our findings uncover a novel role for VSF-1 in the transcriptional regulation of tomato fruit texture, underscore the functional diversification within the Solanaceae bZIP subfamily I, and provide new insights into the genetic improvement of fruit quality.

Citric acid and anthocyanins are key metabolites that determine fruit flavor and coloration. Although the accumulation mechanisms of citric acid and anthocyanins are known in citrus, little is known about the cross-regulatory mechanism between the two important metabolites. In this study, we identified a purple wampee (Clausena lansium) that exhibits simultaneous accumulation of citric acid and anthocyanins in fruit. Functional analyses confirmed that the ClPH4 positively regulate citric acid accumulation; however, the homologous gene of Ruby1, the activator of anthocyanin biosynthesis, has lost the capacity to induce anthocyanin accumulation in the purple wampee. We subsequently identified a PH4-Like based on gene family and expression analyses. Stable overexpression of ClPH4-Like in citrus, along with transient silencing in purple wampee pulp, demonstrated that it can simultaneously induce both anthocyanin and citric acid accumulation. Moreover, PH4-Like is specifically and highly expressed in purple wampee, consistent with the observation that its promoter activity is much higher in purple wampee than in other citrus species. Biochemical assays showed that PH4-Like binds to the promoters of Flavonoid 3′-Hydroxylase (F3′H), Dihydroflavonol 4-reductase (DFR), Anthocyanidin synthase (ANS) and the proton pump genes PH5 and VHA-a2, the key genes in the anthocyanin and citric acid accumulation. Together, our findings uncover a key gene that coordinately regulates citric acid and anthocyanin accumulation, providing insight into the genetic events involved in the diversification of fruit color and taste in Aurantioideae, and offering valuable targets for simultaneous improvement of fruit quality.

DNA methylation plays a central role in the regulation of gene expression. In plants, methylation occurs in the CG, CHG, and CHH contexts, via distinct DNA methyltransferases including MET1, CMT3, and the RNA-directed DNA methylation (RdDM) pathway via DRM2. In interspecific hybrids, these epigenetic mechanisms are confronted to a mixed small RNA population and two subgenomes harbouring specific methylation patterns, therefore generating unique expression profiles. The aim of this work was to understand these regulations by analysing gene expression, DNA methylation, and small RNA s in a citrus hybrid resulting from the cross between Citrus reticulata (mandarin) and Citrus australasica (finger lime). Haplotype -resolved subgenomes assembly identified hundreds of allele -specifically expressed genes. A symmetric reprogramming of methylation was obser ved, in particular an increase in CHH in C. australasica haplotype. Surprisingly, CHH methylation, usually associated with gene silencing, was correlated here with increased expression, but also 24 nt small RNA populations at their promoter regions. Similar analyses of the parental lines and other Citrus species suggest the correlation between CHH methylation- enriched promoter and high expression level is not due to the hybridization, but seem to be generally true for all citrus. These obser vations suggest that, in citrus fruit, RdDM is associated with higher transcriptional activity. This work also provides a full pipeline to analyse the expression profiles and DNA methylation in complex hybrids, which could be crucial for anticipating varieties resistant to diseases and the current threats affecting citriculture, such as the Huanglongbing disease.

Trichomes, specialized epidermal cells on plant leaves, contribute to resistance against both abiotic and biotic stress. Wucai, an important leafy vegetable in China, is predominantly characterized by low trichome density or even hairlessness in commercial cultivars. However, the genetic and molecular mechanisms underlying trichome loss remain largely unknown. In this study, we investigate the genetic basis of trichome loss using a high-trichome-density wucai inbred line, W7-1, and a low-trichome-density cultivar, W7-2. Through a combination of bulked segregant analysis sequencing and map-based cloning, we identified the homolog of the Arabidopsis CPR5 (Constitutive Pathogen Response 5) gene located on chromosome A06 as the candidate locus. A 3365-bp transposon insertion in the promoter of W7-2 disrupts its transcriptional activity, leading to reduced expression of BcCPR5 and impaired trichome formation. Further analysis showed that BcCPR5 expression is positively regulated by BcWRKY44 through a W-box cis-element in the promoter. In W7-2, this transposon insertion physically separates the W-box from the transcription start site. Population genetic analysis revealed that the insertion is prevalent among low-trichome-density or hairless cultivated varieties, reflecting selection during domestication and breeding. Collectively, our findings partially uncover the genetic mechanism underlying trichome loss in wucai and establish a novel BcWRKY44–BcCPR5 regulatory module controlling trichome formation.

The triterpenoid-rich Panax spp. possess notable allelopathic capabilities, yet current knowledge lacks comprehensive understanding of the biological mechanisms underlying these inhibitory effects. Here, we show that zingibroside R1 (ZR1), a newly identified allelochemical from Panax spp., inhibits the adventitious root growth in ginseng and primary root elongation in Arabidopsis. Mechanistic analyses revealed that ZR1 disrupts auxin transport, as evidenced by monitoring DR5::GFP and PINs markers. The effect of ZR1 on auxin transport was further elucidated through synergistic effects observed with the auxin transport inhibitor NPA and in the auxin transport mutants aux1 and pin2. Additionally, ZR1 downregulates key root development regulators, including stem cell maintenance regulators PLT1/2, WOX5, SHR, and SCR. Transcriptomic and biochemical data indicate that ZR1 triggers an ROS response in plants, which disrupts ROS scavenging-via altered peroxidase activities and reduced glutathione/oxidized glutathione balance-thereby impairing detoxification function and resulting in root shortening by regulation of auxin distribution and stem cell gene expression. Our results establish a mechanistic framework for understanding how ginsenosides mediate allelopathic effects on root development.

Epimedium sagittatum is an important medicinal plant whose main bioactive flavonol glycosides, such as epimedin C and icariin, are derived from kaempferol. However, the spatial distribution of these compounds within the plant and the genetic basis for their structural diversity remain unclear. Here, we employed MALDI-TOF mass spectrometry imaging to visualize the distribution of epimedin C and icariin in E. sagittatum leaves, revealing their predominant accumulation in nonleaf vein mesophyll part. Integrated metabolomic and transcriptomic analyses of leaves, petioles, and rhizomes highlighted glycosylation as a key contributor to kaempferol derivative diversity. We identified five candidate UDP-glycosyltransferase genes, among which UGT72B113 exhibited remarkable functional versatility. In vitro enzymatic assays demonstrated that UGT72B113 accepts multiple kaempferol-type aglycones and various sugar donors, catalyzing the formation of monoglycosylate, diglycosylate, and even triglycosylated products from a single substrate. Our findings reveal that UGT72B113 is involved in generating flavonol glycoside diversity in E. sagittatum via its broad substrate promiscuity, multi-glycosylation capability, and sugar donor flexibility. This study provides new insights into the spatial regulation of flavonol accumulation and the enzymatic mechanisms underlying phytochemical diversity in medicinal plant.

Monoterpenoids contribute to grape and wine varietal aroma as free volatiles and glycosidically bound precursors. While glycosylated forms largely determine postharvest aroma potential, the genes controlling their accumulation remain largely unidentified. Here, we compared free and glycosylated monoterpenoids and the accompanying transcriptome between the green-skinned ‘Ruiduxiang yu’ (RDXY) and the pink-skinned ‘Ruiduhong yu’ (RDHY), two siblings derived from the same cross. RDHY berries accumulated higher levels of glycosylated monoterpenoids during ripening, whereas RDXY berries were enriched in the free forms. Integrated metabolome–transcriptome analysis revealed a tight correlation between glycosylated monoterpenoid content and the expression of five glycosyltransferase (GT) genes (VviGTs) and the transcription factor VviMYB174. Besides the previously characterized VviGT14 and VviGT7, enzyme activity assay and transient overexpression experiments in tobacco leaves, grape leaves, and grape berries demonstrated that VviGT22, VviGT37, and VviGT74 also possess monoterpenol glycosylation activity. Yeast one-hybrid assays, combined with overexpression and silencing analyses, confirmed that VviMYB174 directly upregulates these three GT genes in RDHY, thereby promoting glycosylated monoterpenoid accumulation. Sequence alignment revealed that only VviGT74 exhibited different promoter sequence divergence between the two cultivars, notably, the VviGT74 promoter from RDXY failed to bind VviMYB174, which correlated with its reduced expression in RDXY berries. These findings provide new targets for manipulating the glycosylated aroma precursor pool and advance the molecular understanding of monoterpenoid metabolism in grapevine.

Collapsed (haploid) genome assemblies omit large portions of genetic information, especially in heterozygous, clonally propagated crops such as pineapple. Here, we assembled a telomere-to-telomere, haplotype-resolved genome for a key pre-Colombian cultivar of pineapple (Ananas comosus) ‘Smooth Cayenne’ (F180) using PacBio HiFi and Hi-C data. The two 25-chromosome haplotypes span 858 Mb (N50 ≈ 16.8 Mb) and are > 99% complete, each resolving all centromeres and 22 of 25 telomeres. Comparison of the phased chromosomes reveals 1.5 million single nucleotide polymorphisms and 1953 large structural variants (74 inversions, 750 translocations, and 1129 segmental duplications). This assembly reveals that inversions have profoundly impacted the ‘Smooth Cayenne’ genome, reshaping ~ 3%–4% of the total sequence. Structural context dictates the genetic impact of these large inversions, as shown in recombination landscape analysis of 374 F₁ seedlings, wherein a 1.3-Mb paracentric inversion on chromosome 20 forms a strict recombination coldspot, whereas a 6-Mb pericentric inversion on chromosome 24 still permits gene flow likely via short double crossovers, albeit at lower rates than the rest of the chromosome. Re-anchoring the 11 879 DArTseq markers from the F₁ seedlings to the phased reference assembly removes the dense network of spurious interchromosomal linkage seen in the collapsed F153 ‘Smooth Cayenne’ genome, likely providing markedly cleaner baselines for genome-wide association studies and genomic prediction. These results establish the new F180 assembly as a very high-quality reference, illustrate how undetected inversions can silently constrain genetic gain, and demonstrate the broader value of phased genomes for dissecting heterozygosity, structural variation, and meiotic behaviour in perennial crops.

Fruit shape is a critical determinant of market value in wax gourd (Benincasa hispida), yet its genetic and mechanistic basis remains largely unknown. Here, we identify BhSUN, which encodes an IQ67-domain (IQD) family protein, as a major regulator of fruit shape through quantitative trait locus mapping in a recombinant inbred line population. BhSUN harbors two nonsynonymous single-nucleotide polymorphisms that define haplotypes strongly associated with long cylindrical (BhSUN_CC–TT) vs. spherical (BhSUN_GG–GG) fruits. Near-isogenic line analysis, F₂ segregation, marker-assisted selection, and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated knockout consistently demonstrate that loss of BhSUN function causes a transition from long cylindrical to spherical fruits. Histological analyses reveal that BhSUN controls fruit morphology by coordinating oriented cell division and cell expansion. Protein interaction assays show that BhSUN protein interacts with calcium-bound calmodulin (CaM), CaM-like proteins, and the microtubule (MT)-associated protein MAP65-1, thereby linking calcium signaling to MT organization. Concurrently, phytohormone analysis revealed changes in auxin, cytokinin, and gibberellin pathways during BhSUN-mediated fruit shape regulation. Our findings identify BhSUN as a key regulator that integrates calcium signaling, MT dynamics, and hormone metabolism to direct directional fruit morphogenesis.

Potato (Solanum tuberosum L.) is a globally important staple crop. Improving its nutritional quality without compromising yield-a classic manifestation of the growth–defense trade-off-remains a major challenge in modern agriculture. Traditional breeding in potato is hindered by its highly heterozygous genome and tetrasomic inheritance, making it difficult and time-consuming to introduce and fix new traits. To address this, we applied a gene-editing approach to enhance vitamin C (Vc) content in tubers by mutating the upstream open reading frames of two potato GDP-L-galactose phosphorylase genes. New variants, with significantly elevated Vc levels, well-balanced nutrient profiles, and maintained yield, were created. The nutritionally enriched tubers retained high Vc content after culinary processing and exhibited substantially increased antioxidant activity. Importantly, we also found that excessive Vc enrichment can disrupt auxin activity, leading to developmental arrest and yield penalties. Thus, our study not only provides an effective strategy for multitrait improvement in potato, but also offers broader insights into the physiological mechanisms governing the balance between yield and nutritional quality in horticultural crops.

Astragali Radix, the dried root of Astragalus mongholicus, is a prominent traditional Chinese medicinal material, with isoflavonoids serving as its primary bioactive components. Light serves as a pivotal environmental cue modulating isoflavonoid biosynthesis, its regulatory influence on A. mongholicus remains poorly understood, and the underlying biosynthetic pathways have yet to be fully elucidated. This study investigated the impacts of different light on isoflavonoid accumulation through integrated transcriptome and metabolome analyses. Compared to white light, red and blue light treatments significantly altered the expression of 93 genes within the isoflavonoid biosynthetic pathway, 52 of which were up-regulated. Metabolomic analysis revealed 35 differential isoflavonoid metabolites, with 23 compounds, including the primary medicinal components calycosin (CA) and formononetin (FO), showing increased accumulation. Notably, blue light exhibited a significantly stronger promoting effect on CA and FO accumulation than red light. Through integrated multi-omics analysis, we revealed the molecular network underlying this light quality–specific regulation. Correlation analysis revealed that multiple structural genes were significantly positively correlated with these key active components, among which AmCHR, AmCHS, AmCHI, and AmIFS were identified as core regulatory genes. The biochemical roles of candidate genes AmCHR, AmCHS, AmCHI, and AmIFS were validated via in vitro enzymatic assays. Furthermore, utilizing a newly established nonsterile hairy root transformation system, functional validation through overexpression and RNA interference experiments demonstrated that these candidate genes positively regulate the accumulation of key isoflavonoids, including CA, calycosin-7-O-β-D-glucoside, FO, and ononin. These findings were further corroborated by transient gene silencing using antisense oligodeoxynucleotides. This study elucidates the regulatory network of light-induced isoflavonoid biosynthesis in A. mongholicus and provides essential genetic resources for the metabolic engineering and sustainable production of these medicinal compounds.

Pak choi (Brassica rapa subsp. chinensis, AA genome) is a widely cultivated leafy vegetable that comes in green and purple varieties. The enrichment of anthocyanins enhances its nutritional value, making it highly preferred by consumers. However, the genes responsible for the purple phenotype in pak choi remain mostly unknown. Here, we assembled a near-complete telomere-to-telomere genome of the ‘ZBC’ variety using PacBio HiFi, HiC, and Illumina sequencing technologies. The assembled genome is 420.97 Mb and contains 51 387 genes. Through genomic variation and evolutionary analysis, we identified an introgressed fragment of 854.53 kb on chromosome A03, which originates from B. carinata. The BSA-seq and fine-mapping of the purple trait revealed that the target region overlaps with the 854.53-kb introgressed fragment by 390 kb. Functional annotation of the 390-kb interval revealed 48 genes, including BraA03G007112, an MYB114-like transcription factor named BraMYB114. It positively regulates anthocyanin biosynthesis by activating BraDFR.A09 and BraANS.A01 genes, as shown by transcriptomic, metabolomic, and quantitative real-time PCR analyses. Our research is the first to demonstrate that the BrMYB114 gene, carried by an introgressed fragment, positively regulates anthocyanin synthesis in B. rapa. These findings advance our understanding of the B. rapa genome, introduce approaches for investigating key trait genes in introgression lines, and provide valuable targets for developing anthocyanin-rich vegetables.

Horticultural plants play a vital role in agricultural production and daily life. Post-translational modifications are essential for regulating various cellular processes, but the functions of SUMOylation, an increasingly significant post-translational modification, remain to be thoroughly explored in horticultural plants. In this review, we summarize the current research advancements regarding protein SUMOylation in horticultural plants and offer perspectives for future investigations. We begin by introducing the SUMOylation system in horticultural plants. Subsequently, we focus on the roles of SUMOylation in development and stress responses in horticultural plants, with association of plant hormones in these processes. Following this discussion, we outline potential techniques for detecting SUMOylation substrates in horticultural species. Finally, we present prospective directions for future research in this field. This work aims to enhance our understanding of functional implications of SUMOylation while providing novel insights into strategies for improving yield, quality, and resistance in horticultural crops.

Terpene synthases (TPSs) are key drivers of terpenoid diversity in plants, yet the diversity and mechanisms driving their diversification in gymnosperms remain poorly understood. Through comparative genomic analyses of 16 representative land plant species, we demonstrate that tandem duplication (TD) plays an important role in the expansion of gymnosperm-specific TPS-d subfamily. These TD-generated TPS-d genes exhibit elevated sequence variability and markedly increased tissue specificity (τ) compared with conserved primary-metabolic TPS-c and TPS-e/f genes, indicating rapid functional and regulatory divergence following duplication. Together, our results propose a comprehensive evolutionary framework that illustrates how TD, sequence divergence, and expression diversification collectively shape TPS-d gene evolution in gymnosperms, providing new insights into lineage-specific terpenoid profiles and ecological adaptation in gymnosperms.

Soluble solids content (SSC) is a major determinant of flavor quality in melon fruit; however, the key genes regulating this trait remain poorly characterized. To elucidate the molecular basis of SSC variation, we performed genome-wide association studies (GWAS) using a diverse panel of 200 melon accessions, which detected 79 significant single nucleotide polymorphisms associated with SSC. Linkage disequilibrium decay analysis annotated 86 candidate genes within the associated genomic regions. To prioritize functionally relevant candidates, we further integrated transcriptome data from two genotypes with contrasting SSC levels, ‘San Ye Hua sugua’ (SYH; low SSC) and ‘Bai Sha Mi’ (BSM; high SSC). Comparative transcriptomic analysis revealed 18 candidate genes that were both GWAS-associated and differentially expressed between the two genotypes. Subsequent qRT-PCR validation confirmed concordant expression patterns for 14 of these candidates. Haplotype analysis demonstrated that natural variation at these loci was significantly correlated with SSC phenotypic variation across the population. Physicochemical component analysis revealed sucrose as the major driver of SSC accumulation. Five key candidate genes (MELO3C024714.2, MELO3C026992.2, MELO3C012177.2, MELO3C007562.2, and MELO3C007563.2) showed differential expression within the lipid metabolism-glyoxylate cycle-gluconeogenesis pathway, implicating their synergistic involvement in energy metabolism and cellular homeostasis. In conclusion, our multiomics approach identifies a robust set of candidate genes modulating melon SSC, providing mechanistic insights into fruit flavor formation and offering valuable genetic targets for marker-assisted or genomics-informed breeding of high-quality melons.

Understanding how plants adapt to extreme cold and ripen fruit is a key question in plant biology. Lonicera caerulea (blue honeysuckle), a cold-tolerant berry species native to the northern temperate zone, is valued as a ‘noble fruit’ for its rich nutrient profile and serves as an ideal model for studies due to its unique ability to thrive in low temperatures and ripen fruit during early spring. Here, we generated a chromosome-level genome assembly for wild L. caerulea from the Changbai Mountain region. We integrated it with transcriptomic and metabolomic analyses to explore its molecular cold adaptation mechanisms. We found that L. caerulea achieves cold tolerance and fruit ripening through dynamic regulation of two important metabolic pathways. Under cold stress, the LcODO1/LcMYB15–LcSLAS module promotes iridoid accumulation, while the LcbHLH62/LcMYB3R5–LcF3GT module enhances anthocyanin biosynthesis, jointly increasing plant cold resistance. During fruit maturation, metabolite profiles show dynamic reprogramming: anthocyanin levels rise in both pulp and peel, while the content of bitter iridoids markedly decreases in the pulp. This work provides a comprehensive genomic framework for understanding cold adaptation mechanisms, offering valuable gene resources and a theoretical foundation for improving cold resistance and fruit quality in breeding programs.

Glomerella leaf spot (GLS), incited by Colletotrichum gloeosporioides, poses a significant threat to apple (Malus domestica) production. microRNA s (miRNA s) are critical regulators of plant–pathogen crosstalk. However, the underlying mechanism through which miR482 regulates apple resistance to GLS remains unclear. Here, we show that overexpression of miR482c com-promises resistance against C. gloeosporioides, while silencing miR482c confers resistance to C. gloeosporioides. 5′ RACE assays in apple and co-expression assays in Nicotiana benthamiana confirmed that miR482c targets and cleaves the MdCCR4 mRNA. Subsequent research revealed that overexpression of MdCCR4 significantly enhances apple resistance to C. gloeosporioides. Notably, MdCCR4 physically interacts with the thaumatin-like protein MdTLP1b, which also positively regulates resistance to C. gloeosporioides. Additionally, MdERF1B was identified as an upstream regulator of miR482c through bioinformatics and Y1H screening, and was further confirmed to negatively regulate miR482c transcription by directly binding to its promoter. Meanwhile, MdERF1B overexpression enhances resistance to C. gloeosporioides, while silencing MdERF1B compromises resistance to C. gloeosporioides. Collectively, our findings indicate that the MdERF1B-miR482c-MdCCR4-MdTLP1b regulatory network is pivotal for apple defense against C. gloeosporioides, highlighting promising candidates for the genetic improvement of disease resistance.

Lodging remains a significant agronomic challenge that limits the yield potential of Brassica napus globally, making the elucidation of its molecular basis critical for breeding new germplasm. Lignocellulose components (including lignin, cellulose, and hemicellulose) play an essential role in the mechanical strength of the stem, and they are regarded as the key determinants of lodging. In a doubled haploid (DH) population, 61 consensus quantitative trait loci (QTLs) associated with the lignocellulose content in the stem were identified through QTL analysis. Integrating QTL mapping with transcriptomic data revealed 1035 candidate genes potentially involved in stem lignocellulose biosynthesis, of which 52 high-confidence candidates were selected. Among them, BnaC01.MYB85, BnaA04.WRKY12, and BnaC03.ASMT exhibited stem-specific expression. A stem-specific lignocellulose biosynthetic pathway characterized by the coordinated expression of these high-confidence genes was delineated. Haplotype analysis in a natural population showed that BnaC03.ASMT segregated into two major haplotypes, with hap01 exhibiting a significantly higher hemicellulose content (HC) than hap02. These findings provide novel insights into the genetic regulation of lodging resistance and offer a valuable foundation for breeding B. napus cultivars with higher stem strength and lodging tolerance.

Extremely low light (ELL) is widely applied as a strategy to enhance adventitious shoot (AS) regeneration in woody plants. However, how ELL acts as an environmental signal to reprogram regenerative competence remains unclear. Here, we show that ELL for 14 days (ELL₁₄) markedly promotes AS regeneration across multiple genotypes of Robinia pseudoacacia. Transcriptomic and functional enrichment analyses revealed that auxin biosynthesis, transport, and signaling constitute the core pathways activated under ELL₁₄. Consistently, auxin levels increased, and the inhibition of biosynthesis or transport largely abolished the regeneration-promoting effect. Integrative weighted gene co-expression network analysis and regulatory analyses identified RpPHYA as a key integrator of ELL-responsive networks. Under ELL₁₄, the RpPHYA-associated module promotes auxin biosynthesis by upregulating RpAMI1 and coordinates auxin transport through RpPIN1 via transcriptional regulation and RpROS1-mediated CHG demethylation, forming a dual regulatory mechanism. In contrast, under normal light, RpHYH antagonizes this regulatory program, thereby restricting regenerative capacity. Overexpression of RpPHYA, RpAMI1, RpPIN1, and RpROS1 significantly enhanced AS regeneration, functionally validating this ELL₁₄-induced module. Collectively, our findings demonstrate that ELL functions as an environmental signal that promotes AS regeneration in R. pseudoacacia through coordinated transcriptional and DNA demethylation of auxin transport, providing mechanistic insights for improving regeneration in woody plants.

Callicarpa nudiflora is a medicinal plant rich in phenylethanoid glycosides (PhGs), particularly verbascoside, but the genetic basis of PhG biosynthesis and natural variation in its content remain largely unexplored. Here, we assembled a chromosome-level genome of C. nudiflora (511 Mb, contig N50 = 12.78 Mb) with 39 317 annotated protein-coding genes and 99.5% Benchmarking Universal Single-Copy Orthologs completeness and quantified its bioactive compounds and gene expression across multiple tissues. Using the dataset, we elucidated the complete biosynthetic pathway of verbascoside and demonstrated multiple paralogous enzymes catalyzing one step, a functional redundancy that may contribute to the high verbascoside accumulation observed in this species. Population genomic analysis, together with quantification of verbascoside content of 95 samples grown in a common garden over three consecutive years, revealed that Southcentral Hainan was identified as the genetic diversity center and exhibited the highest content of verbascoside. Selective sweep analysis comparing high-and low-content individuals identified CnUGT79G7, a key glycosyltransferase in the verbascoside pathway, as being under positive selection. Two major haplotypes of CnUGT79G7 were identified: Hap1, a high-expression haplotype prevalent in the top-geoherb region (77% frequency), and Hap2, a low-expression haplotype fixed in other populations. Although the two haplotypes encode proteins with similar catalytic activity, Hap1 is associated with significantly higher CnUGT79G7 expression and elevated verbascoside content, suggesting that cis-regulatory variation underlies chemotypic differentiation. Collectively, this work identifies key molecular components for verbascoside biosynthesis, establishes a genomic and metabolic framework for understanding top-geoherb, and provides valuable resources for the conservation and molecular breeding of medicinal plants.

Anthocyanin is responsible for the colored hues of fruit and plays a key role in determining consumer preference and marketability. Anthocyanin accumulation exhibits remarkable diversity among fruit species and cultivars, providing invaluable genetic resources for trait improvement. This review summarizes the multifaceted mechanisms underlying the differential anthocyanin accumulation in fruit between species and cultivars. There are diverse control mechanisms governing anthocyanin accumulation, including mutations in genes involved in biosynthesis, transport, and transcriptional regulation, as well as multilayered regulation through epigenetic, post-transcriptional, and post-translational processes. The discovery of these genetic variants affecting anthocyanin accumulation, along with an understanding of the underlying molecular mechanisms, provides potential targets for fruit color modification through molecular breeding or biotechnological approaches.

With the expansion of modern horticultural production systems, anthocyanins have attracted increasing attention for their dual role in imparting vibrant coloration and delivering health-promoting benefits. Prehar vest temperature management, particularly controlled low-temperature exposure, has emerged as an effective strateg y to enhance anthocyanin accumulation in horticultural crops. Despite extensive molecular insights, decision-driven temperature management (DDTM) frameworks that integrate species-, genotype-, and operational parameter-specific strategies for plant factor y applications remain lacking. This review addresses this gap by proposing a DDTM-based framework that links molecular regulation to operational protocols for precise anthocyanin enrichment. Evidence is synthesized across diverse horticultural crops representing major production families, including Brassicaceae, Solanaceae, Rosaceae, and other representative horticultural groups, which were selected for their economic importance, high anthocyanin potential, and relevance to human health. Species-and genotype-dependent responses are highlighted, and key operational parameters, including temperature range, exposure duration, and prehar vest timing, are analyzed to balance pigmentation intensity, biomass production, and energ y efficiency. Plant factories are emphasized as enabling platforms for short-term end-of-cycle cooling and diurnal temperature modulation, which can be integrated with light spectrum management to optimize anthocyanin accumulation while maintaining yield stability. By organizing current knowledge into practical, decision-oriented temperature strategies, this review provides a framework to improve the nutritional quality, compositional consistency, and functional value of anthocyanin-rich crops, supporting horticulture-driven quality assurance and resilient controlled-environment production systems.

A sustainable approach to address climate change and increasing water demand in agriculture is breeding for plant functional traits that conserve water and enhance climate resilience. Stomata regulate plant–water relations and are promising targets for crop improvement. Here, we investigate the variation in stomatal density (SD) in a diverse apple population (Malus domestica Borkh.) consisting of 269 accessions. Genome-wide association studies identified robust associations with SD on chromosomes 2, 9, and 10 (classified as SNPs with a P-value higher than adjusted Bonferroni threshold of −log₁₀(P) > 8.78 that were consistently identified across datasets). On chromosome 9, a candidate gene that negatively regulates stomatal development, EPIDERMAL PATTERNING FACTOR 1 (EPF1), was identified inside a genomic region of 241 kb determined by six robust associations. On chromosome 10, a positive regulator candidate gene, EPIDERMAL PATTERNING FACTOR LIKE 9 (STOMAGEN), was identified 1680 kb from the robust association. Identification of positive (STOMAGEN) and negative (EPF1) regulators of SD suggest potential antagonistic roles at the population scale in determining SD. On chromosome 2, a gene co-expression analysis identified a gene cluster containing both EPF1 and STOMAGEN together with a novel candidate gene, CYTOCHROME P450 (CYP77A4), that was located 544 kb from the robust association. The percentage of SD phenotypic variance explained by each robust association was between 7% and 10%. These findings provide a foundation for understanding SD variation at the population scale and opportunities to modulate SD by genomics-assisted breeding strategies.

Begonia semperflorens is an important ornamental plant worldwide, but its practical application is severely limited by low temperature sensitivity. However, the molecular regulatory mechanisms underlying low temperature-induced anthocyanin biosynthesis remain unclear. In this study, we assembled a high-quality chromosome-level B. semperflorens genome. Through genomic and MYB gene family analysis, we identified a key transcription factor BsTT2, which directly binds to the BsDFR promoter and enhances its activity, thereby driving anthocyanin accumulation in B. semperflorens. Furthermore, using BsTT2 as bait, we identified its interacting protein BsAlfin2. Under low temperature-induced reactive oxygen species (ROS) signaling, BsAlfin2 undergoes nuclear translocation and forms a complex with BsTT2, synergistically enhancing the activation of the BsDFR promoter and significantly improving anthocyanin production efficiency. Based on these results, we propose a previously uncharacterized BsAlfin2/BsTT2-BsDFR regulatory module, which reveals a molecular links low-temperature ROS signaling to anthocyanin biosynthesis in B. semperflorens. In summary, this study not only provides chromosome-level genomic resources for B. semperflorens research but also elucidates a key molecular module in low temperature-induced anthocyanin biosynthesis regulatory pathway, laying a theoretical and data foundation for future studies on leaf color improvement and stress resistance breeding in Begonia.