Passion fruit (Passiflora spp.) is a highly valued tropical fruit crop due to its unique sensory attributes, high nutritional value, and therapeutic properties. Enhancing yield stability, stress adaptation, and cultivar quality remains a key priority in passion fruit breeding programs. With more than 500 species, the wide genetic variability of Passiflora makes it a valuable resource for breeding. However, passion fruit breeding is constrained by the complex inheritance of key traits, high heterozygosity and relatively long breeding cycles. In this context, the integration of advanced genomic tools and AI-assisted breeding presents transformative opportunities to accelerate and enhance the precision of cultivar development. This review synthesizes current breeding strategies and discusses their application in Passiflora, highlighting innovations such as genomic selection, speed breeding, and CRISPR-based gene editing. Furthermore, we explore future avenues to improve breeding efficiency, develop climate-resilient and high-quality cultivars, and ultimately support the sustainability and profitability of the passion fruit industry.
Chili pepper (Capsicum spp.) faces severe yield and quality challenges due to increasing heat stress (HS) associated with climate change. This review synthesizes the physiological, biochemical, and molecular mechanisms underpinning heat tolerance, establishing a coherent roadmap from stress perception to climate-resilient cultivar development. We begin by delineating the phenotypic bottlenecks induced by elevated temperatures (> 32 °C), which include impaired germination, suppressed photosynthesis, and particularly, reproductive failure. At the molecular level, we describe a core regulatory network centered on heat shock factors (e.g., HSFA1a) and proteins (HSPs), which orchestrate downstream responses involving antioxidants, osmolytes, and epigenetic modifications for stress memory. To harness this mechanistic knowledge for breeding, we highlight the untapped potential within landraces and wild relatives, which serve as invaluable reservoirs of natural genetic variation for thermotolerance. Finally, we propose a convergent breeding framework that synergistically integrates genomics-assisted selection, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas9-mediated genome editing, cytoplasmic male sterility (CMS), and high-throughput phenotyping to accelerate the development of heat-resilient varieties. By bridging fundamental research with advanced breeding technologies, this synthesis provides a comprehensive blueprint for safeguarding pepper production against the escalating threats of global warming.
Branching is a fundamental determinant of plant architecture and a key agronomic trait. Shoot branching originates from axillary meristems and is tightly regulated by a complex network of genetic, hormonal, and environmental cues. Cytokinin (CTK) promotes apple branching by regulating axillary bud outgrowth. However, the underlying genetic and molecular mechanisms remain unclear. Here, we identified 34 members of the MdSBP transcription factor family through genome-wide analysis. Phylogenetic analysis revealed that MdSBP24 (designated as MdSPL9) is closely related to the known branching regulators AtSPL9/15 in Arabidopsis and OsSBP14 in rice. Gene expression and promoter activity assays showed that MdSPL9 is downregulated by CTK. MdSPL9-RNAi apple plants exhibited increased branching, whereas overexpression of MdSPL9 in the Arabidopsis spl9 mutant reduced branch number and rosette leaf formation, indicating a role in inhibiting branching and axillary meristem formation. MdSPL9 directly activated MdTCP12 and MdTCP18 (TB1/BRC1-like genes), which were also significantly downregulated by CTK. Moreover, MdSPL9 physically interacted through its N-terminal region with the transcriptional repressor MdWUS2, which is activated by CTK and promotes branching. This interaction occurred independently of the C-terminal EAR motif in MdWUS2. Transient assays showed that MdWUS2 suppressed MdSPL9-mediated transcriptional activation of MdTCP12/18 in an EAR motif-dependent manner. Collectively, our findings reveal a CTK-regulated transcriptional module in which MdWUS2 antagonizes MdSPL9 activity, thereby modulating the expression of MdTCP12/18 to control apple branching. This study provides novel insights into the hormonal regulation of axillary bud outgrowth and potential molecular targets for optimizing apple tree architecture.
Plant genomics underpins a foundation for understanding evolution, gene regulation, and fundamental biological processes, subsequently supporting both the conservation and innovative utilization of plant germplasm resources. The Lythraceae family encompasses numerous species of economic and ecological significance, and are valued for their edible, medicinal, and ornamental properties. The family-wide distribution, spanning extreme intertidal zones, semi-deserts and tropical forests, positions Lythraceae as an exemplary model for investigating the genomic mechanisms underlying ecological adaptation. Recent advances in chromosome-level genomes, pan-genomics, genetic mapping, multi-omics integration, and large-scale phenotyping have greatly accelerated research in plant evolution and breeding. Nevertheless, despite the growing genomic and trait-focused studies in Lythraceae, a comprehensive conceptual synthesis linking evolutionary events, structural variation (SV), regulatory networks, and future research directions remain absent. In this review, we present an overview of genomic resources and introduce a unified framework linking whole-genome duplications, lineage-specific SVs, and their functional impacts on species diversification. We also synthesize recent advances in genome evolution, phylogenetic relationships, biotechnology, and molecular mechanisms controlling growth, development, and stress responses. In addition, we address challenges associated with genetic transformation of woody Lythraceae species and discuss strategies to enhance molecular breeding. This review provides a forward-looking perspective on Lythraceae genomics and identifies key scientific questions that will steer future research in evolutionary biology, functional genomics, and crop improvement.
Ethylene promotes fruit senescence, whereas salicylic acid (SA) has been extensively characterized for its antagonistic effects on this process. However, the molecular link between SA signaling and ethylene response factor remains unclear. Here, PpERF113, an ethylene response factor gene whose expression was significantly down-regulated by SA, was identified from transcriptomic analysis of SA-treated sand pear (Pyrus pyrifolia). Overexpression of PpERF113 accelerated the senescence of sand pear fruit, calli and tomato fruit. SA delayed the senescence process caused by PpERF113. Yeast two-hybrid and luciferase assays demonstrated interactions between PpERF113 and PpbZIP1, PpEIN3. Silencing PpERF113 or PpbZIP1 delayed senescence, and dual silencing enhanced this effect, especially under SA treatment. Additionally, PpERF113 directly activated PpACO11, a gene involved in ethylene biosynthesis. In conclusion, the PpERF113-PpbZIP1 complex responds to salicylic acid, with PpERF113 controlling sand pear fruit senescence by regulating PpACO11 expression.
Anthocyanins and proanthocyanidins are flavonoid compounds that exhibit antioxidant activity and play essential roles in fruit pigmentation. However, the synergistic regulatory mechanisms underlying their biosynthesis remain poorly understood. In this study, we identified a transcription factor, AcbHLH137, which showed a strong correlation with flavonoid level. Overexpression of AcbHLH137 significantly elevated the anthocyanin level in transgenic kiwifruit plants and calli. Yeast one-hybrid (Y1H), dual-luciferase (LUC), and electrophoretic mobility shift assays (EMSA) demonstrated that AcbHLH137 could directly bind to the promoters of structural genes AcCHI, AcDFR and AcUFGT, and activate their transcription, while repressing the proanthocyanidin biosynthesis gene AcLAR. Moreover, AcbHLH137 interacts with AcMYB12, a positive regulator of AcDFR, AcF3GT1, and AcLAR, to form a functional complex that coordinates the biosynthesis of anthocyanins and proanthocyanidins. The AcMYB12-AcbHLH137 complex synergistically enhances AcDFR expression while antagonistically modulating AcLAR transcription. Our findings reveal the critical role of the AcMYB12-AcbHLH137 module in fine-tuning the balance between anthocyanin and proanthocyanidin accumulation during fruit development, providing new insights into strategies for improving fruit quality.
Plant transpiration and photosynthesis are primarily driven by light, and regulating light to improve crop water use efficiency (WUE) and yield has become a research focus in protected horticulture. However, the responses of the coordination between transpiration and photosynthesis to light changes remain underexplored, particularly across different time scales (hourly, daily, and the entire growth cycle). To elucidate the physiological mechanisms by which the coordination between transpiration and photosynthesis enhances WUE and yield, we investigated the dynamic responses across different time scales of the transpiration and photosynthetic systems in tomato and their coordination under varying light intensities, durations, and supplementation periods. Our results showed that transpiration and photosynthetic systems exhibited optimal coordination under 200 W · m−2 supplemental light, a 16-hour duration, and light supplementation around sunset, effectively enhancing WUE and yield. Regarding water transport, predawn and midday leaf water potential, hydraulic conductance, and hydraulic anatomical traits were significantly increased, thereby improving the water transport capacity of the whole plant. In the photosynthetic system, carboxylation rate, electron transport rate, maximum net photosynthetic rate, and initial quantum efficiency were enhanced, while CO2 diffusion resistance in stomata and mesophyll was reduced. Importantly, structural equation modeling analysis revealed that the coordination between water transport and photosynthesis was strengthened, enabling plants to optimize photosynthetic efficiency per unit of water loss. Enhancing this coordination is therefore critical for improving WUE and yield more rapidly and cost-effectively. This study aligns with the future trend of high-efficiency development in protected and smart horticulture.
Reactive oxygen species (ROS) are essential signaling molecules that induce oxidative damage to various cellular organelles in plants. However, the regulatory mechanisms underlying the ROS-mediated petal senescence are not fully understood. Here, the effects of eight up-regulated WRKY transcription factors on petal senescence of petunia were examined through virus-induced gene silencing (VIGS). Of them, down-regulation of PhWRKY41, a putative member of subgroup IIIa, resulted in the most pronounced acceleration of flower senescence and increase in the transcription of senescence-associated marker PhSAG12. PhWRKY41 was therefore selected for further functional characterization. Through stable genetic transformation, transgenic petunia plants overexpressing PhWRKY41 exhibited a delay of 2.0–2.3 days in petal senescence compared with wild type (WT). Conversely, RNAi silencing of PhWRKY41 accelerated petal senescence by 1.5–2.1 days. Decreased and increased levels of hydrogen peroxide (H2O2) were detected in transgenic plants with PhWRKY41 overexpression and RNAi silencing, respectively. PhWRKY41 was significantly responsive to H2O2 signals, and exogenous H2O2 treatment substantially mitigated flower lifespan variation among WT and transgenic petunia plants. Promoter binding assays revealed that PhWRKY41 specifically activated the transcription of alternative oxidase 3 (PhAOX3), which is a repressor of ROS production. Further data verified that silencing of PhAOX3 decreased the longevity of petunia flowers with elevated H2O2 content. In terms of transcriptional changes, expression trends of PhWRKY41 and PhAOX3 were opposite to that of PhSAG12 in the overexpression and silencing assays. Our findings indicate that PhWRKY41 functions as a negative modulator of flower senescence by eliminating ROS-mediated damage.
Angiosperms synthesize diverse volatile organic compounds (VOCs) that facilitate ecological interactions and provide valuable resources for human applications. The primary biochemical pathways responsible for floral scent biosynthesis involve terpenes, phenylpropanoids, and fatty acid derivatives. These volatile compounds are regulated through complex multigene networks subject to extensive pre-transcriptional process. Despite decades of research, fundamental questions persist about the evolutionary origins and regulatory mechanisms of these pathways, largely due to methodological limitations and species-specific biases in current studies. Transcriptional regulation of VOC biosynthesis occurs through both direct gene expression and upstream regulatory mechanisms, wherein transcription factors (TFs) modulate volatile compound production by activating or repressing target gene transcription. However, current models of TF-mediated regulation are largely based on a limited number of model species, raising questions about their universal applicability. Recent comparative genomic studies across multiple plant species have identified novel genes that fundamentally reshape our understanding of volatile biosynthetic pathways though, these findings often contradict earlier biochemical models and highlight the inadequacy of single-species approaches. This review evaluates the current state of knowledge, identifies major methodological limitations, and assesses conflicting evidence in the field. We argue that the field's reliance on candidate gene approaches and limited phylogenetic sampling has created significant blind spots in our understanding of VOC evolution and regulation. Substantial knowledge gaps persist regarding regulatory network architecture, candidate gene functionality, and epigenetic control mechanisms, partly due to the field's failure to adopt systems-level approaches and integrate ecological context into molecular studies.
Stone cells can negatively affect the quality of pear fruit, particularly in the core area. Their formation primarily results from cell wall lignification. However, the genes, proteins, and metabolites related to stone cell development have not been comprehensively characterized. To better understand this process, we conducted transcriptomic, proteomic, and metabolomic analyses on different fruit parts during ‘Cuiguan’ fruit development. In this study, we identified 3 479 differentially expressed genes (DEGs), 656 differentially expressed proteins (DEPs), and 187 differentially abundant metabolites (DAMs) between the stone cell-rich area (SR) and the stone cell-less area (SL) of pear fruit. Comprehensive multi-omics analyses indicated that phenylpropanoid biosynthesis pathway was more active near the fruit core, which promoted the formation of lignin precursor compounds and stones cell through the upregulation of lignin biosynthesis genes and proteins. Furthermore, we isolated PbWRKY43, which is the homologous gene of Arabidopsis AtWRKY43. Overexpression of PbWRKY43 in pear fruit, Arabidopsis, and tobacco leaves resulted in increasing lignin and stone cell contents, thickening secondary cell walls, and enhancing the expressions of lignin biosynthesis genes. Mechanistically, PbWRKY43 significantly upregulated the expressions of PbC3H1 and PbCCoAOMT1 by interacting with W-box elements within their promoter regions. These findings suggest that PbWRKY43 may serve as a positive regulatory factor in stone cell formation around the pear fruit core. This study provides a foundation for future investigations into stone cell development and multi-omics analyses in fruit trees.
Purple–hued foliage is a highly valued ornamental trait in the commercial cultivation of the woody ornamental Prunus mume ‘Meiren’. Glutathione S–transferase (GST) genes are known mediators of anthocyanin accumulation, yet their functional roles in ‘Meiren’ leaf coloration remain unexplored. Here, we systematically identified 88 PmMGST genes, which were classified into eight distinct subfamilies within a large–scale phylogenetic clustering. Gene family analysis revealed conserved exon–intron structures and motif compositions within phylogenetic clades. Duplication and synteny analyses indicated that the expansion of this family was primarily driven by tandem duplication events on chromosomes 3a/b and 6a/b. Moreover, we identified abundant MYB/Myb–binding sites on the PmMGST promoters, suggesting potential regulatory interactions with MYB transcription factors. Expression profiling demonstrated that PmGST17/21/51 were significantly upregulated across development stages accompanied by varying leaf colors. Functional investigations revealed that the overexpression of PmGST21/51 induced purple coloration or deepening in transgenic ‘Meiren’, concomitant with increased anthocyanin accumulation, and elevated transcript levels of anthocyanin synthase genes. PmMYB10.5b, the key regulator of purple–leaf trait formation, directly bounded to PmGST21/51 promoters, establishing a MYB10.5b–GST21/51 regulatory module involved in leaf coloration. Collectively, these results identify PmGST21 and PmGST51 as positive regulators of anthocyanin accumulation and provide foundational insights into the PmGST family in ‘Meiren’. This study offers a novel perspective on anthocyanin regulation in purple-leaved P. mume and contributes to the genetic improvement of foliage color in woody ornamentals.
Ponkan (Citrus reticulata Blanco), renowned for its sensory quality and ease of peeling, is a widely cultivated mandarin in China. However, like most commercial citrus cultivars, it is susceptible to citrus canker and Huanglongbing (HLB). Polyploid breeding may be a useful way to identify resistant or tolerant varieties. In this study, we obtained 1 060 seeds from six pollination combinations using ‘Xinnv’ ponkan and its bud mutation ‘Zaomi’ as parents. Among these, 876 seeds were classified as normal and 184 as small. Twenty-four tetraploids and one chimera were identified from progeny populations by flow cytometry. The polyploid frequency varied among combinations, with the highest rate (7.89%) observed in small seeds from open-pollinated ‘Zaomi’, compared to 1.55% to 4.76% in other groups. Morphological and microscopic analyses revealed that tetraploid progeny displayed increased leaf thickness, epidermal cells, and stomatal apparatus, whereas stomatal density was reduced compared with diploid lines. In vitro and in vivo evaluations for citrus canker tolerance demonstrated that lines #007, #315, and #369 exhibited reduced lesion area, lesion density, and Xanthomonas citri subsp. Citri content at 7 days post-inoculation relative to the diploid control ‘Zaomi’. Regarding HLB evaluation, tetraploid line #331 exhibited a lower titer of Candidatus Liberibacter asiaticus than the diploid control and maintained superior growth at 6 months post-inoculation, evidenced by a 96.3% increase in leaf area and a 48% increase in SPAD value. These novel tetraploid ponkan germplasms possess enhanced disease tolerance and represent valuable resources for future citrus breeding programs.
The enhancement of fruit quality in pepper (Capsicum annuum L.) is a core objective in modern breeding programs. However, the metabolic pathways and genetic mechanisms underlying two critical classes of quality-related metabolite classes, carotenoids and volatile compounds, remain insufficiently understood. In this study, a yellow-fruited pepper (yfp) mutant was identified through a natural mutation in the red pepper variety 'Zhangshugang'. LC-MS/MS and HS-SPME/GC-MS analyses revealed alterations in the metabolic fluxes of carotenoids and volatile compounds in 'yfp' compared to 'Zhangshugang'. The 'yfp' phenotype was controlled by the Capsicum annuum capsanthin/capsorubin synthase (CaCCS) gene on chromosome 6, in which a 6.9 kb Ty1-copia long terminal repeat-retrotransposon (LTR-RT) was inserted at position +1 109bp in the 5’ coding sequence (CDS). This element contains two identical 1,094 bp LTRs flanked by 5 bp target site duplications (TSD: 5’-CGTAG-3’), initiating with “TG” and terminating with “CA”. Integration of the retrotransposon CaRE-1 altered the conserved domain and protein conformation of CaCCS. Virus-induced gene silencing (VIGS) demonstrated that CaCCS regulates carotenoid accumulation and reduces α-ionone and geranylacetone levels. Weighted gene co-expression network analysis (WGCNA) showed that CaCCS is highly coexpressed with transcription factors from WRKY, NAC, MYB, MADS-MIKC, C2H2, bHLH, and AP2/ERF families, which are associated with carotenoid, fatty acid, amino acid, and terpenoid biosynthesis. Dual-luciferase assay, yeast one-hybrid assays, and electrophoretic mobility shift assay (EMSA) confirmed that CaNAC18 directly binds the CaCCS promoter. Silencing CaNAC18 increased chlorophyll and carotenoid accumulation, delayed degreening and fruit ripening, and affected α-ionone and geranylacetone biosynthesis. Collectively, this study identifies the CaNAC18–CaCCS regulatory module as central to carotenoid accumulation and volatile biosynthesis in pepper, providing insights into fruit quality formation and genetic resources for quality-oriented breeding programs.
Tea (Camellia sinensis), a highly valued perennial crop, faces severe threats from fungal pathogens that negatively affect both yield and quality. Climate change, manifesting as extreme weather and seasonal shifts, intensifies these disease pressures by altering pathogen dynamics and host resistance. Specifically, temperature fluctuations directly regulate fungal life cycles, including spore germination and growth, while simultaneously reprogramming tea plant immunity through changes in defensive enzymes and specialized metabolites. These dual effects collectively shift infection thresholds, modify epidemic patterns, and redistribute pathogen ranges. Addressing this complexity requires a multidisciplinary approach that integrates molecular biology, ecology, and epidemiology. Moving forward, the development of climate-resilient strategies, such as breeding resistant cultivars, refining adaptive management practices, and improving biologically based disease management strategies, is essential to ensure the sustainable future of global tea production.
Global crop productivity is increasingly threatened by climate change, with drought stress (DS) a severe and escalating challenge to food security. Therefore, developing resilient crops is crucial for sustainable agriculture. Recent research has transitioned from examining general responses, such as hormonal imbalances, photosynthetic inhibition, and oxidative damage, to elucidating the intricate adaptive mechanisms, including signal transduction pathways and stress-responsive gene networks. Advances in omics technologies have significantly enhanced our understanding of plant responses to DS. Techniques such as genomics, transcriptomics, proteomics, and metabolomics have facilitated the dissection of drought-responsive genes, metabolic pathways, and regulatory networks, thereby contributing to the development of drought-resilient crops. This review synthesizes recent advancements in omics to provide a comprehensive analysis of the DS tolerance mechanisms in plants. It also explores the emerging potential of single-cell omics and artificial intelligence in deciphering the complex plant responses to DS. Finally, it evaluates the challenges associated with omics and outlines strategies to translate omics insights into the development of drought-resilient crops, ultimately enhancing crop productivity and food security.
Sea buckthorn (Hippophae rhamnoides L.) is a perennial woody oil and horticultural crop from the Elaeagnaceae family with high nutritional and economic value. The novel cultivar 'Gaoyou No.1' (PVR No. 20190345) exhibits superior seed oil yield and quality. However, the lack of a high-quality reference genome for this cultivar has greatly hindered molecular studies on the accumulation of unsaturated fatty acids (FAs) and triacylglycerols (TAGs) in its seed oil. Here, we report a chromosome-level genome assembly of 'Gaoyou No.1', with a final size of 1.27 Gb and a scaffold N50 of 99.72 Mb, alongside 26 429 annotated protein-coding genes. Repetitive sequences accounted for 72.35% of the genome. Comparative genomic analysis dated the divergence of H. rhamnoides from Juglans regia to approximately 107.5 million years ago. We identified 14 298 structural variations (SVs) in 'Gaoyou No.1' compared with a common cultivated sea buckthorn accession. Through whole-transcriptome profiling, 49 and 55 enzymatic genes involved in the FA and TAG biosynthesis pathways were identified, respectively; 21 of these genes harbored SVs, in which the copy number variations of SAD_0.613 and LPCAT_ 16.398 enhanced their expression via a gene dosage effect, and further promoted the oil biosynthesis in 'Gaoyou No.1'. Furthermore, 90 lncRNA–mRNA pairs, 88 miRNA–mRNA pairs, and 42 lncRNA–miRNA–mRNA regulatory modules were predicted. The interactions within 12 key modules, such as lncRNA051245–miRn43–FAD2 and lncRNA111000–miRn275–LPAT were experimentally verified. We propose that these SVs and regulatory modules collectively contribute to the improved seed oil yield and quality of 'Gaoyou No.1', providing promising targets for genetic improvement. Our research yields novel insights into the molecular mechanisms underlying high FA and TAG accumulation in sea buckthorn, while also furnishing valuable genomic resources for evolutionary research in Elaeagnaceae and molecular breeding development.
Melon (Cucumis melo L.) is an economically important horticultural crop grown globally for its edible fruits, where fruit morphological characteristics directly determine crop productivity and fruit quality. Deciphering the genetic regulators of melon fruits quality, alongside the rapid development of genome-editing technology, has greatly advanced the genetic improvement of melon fruit quality. This review comprehensively provides an overview of the molecular mechanisms governing critical fruit quality attributes including sugar accumulation and phytohormone signaling pathways, as well as the genetic determinants of fruit size, with a focus on key functional enzymes, hormones crosstalk, and regulatory transcription factors. Furthermore, this review explores cutting-edge technological innovations that facilitate targeted melon breeding and trait improvement, such as high-resolution quantitative trait locus (QTL) mapping, precision CRISPR/Cas9 genome editing, Targeting Induced Local Lesions in Genomes (TILLING) platforms, and intelligent information systems for optimized trait selection, all of which contribute to improve fruit quality and prolonged shelf life. The combination of conventional breeding strategies with advanced molecular tools and computational phenotyping systems provides strategic directions for melon cultivar breeding and development. Moreover, this review highlights emerging non-destructive phenotyping technologies that incorporate hyperspectral imaging, machine learning analytics, and 3D hyperspectral morphological modeling as powerful transformative tools for precise, high-throughput fruit maturity phenotyping. Collectively, this review seeks to advance mechanistic insights into melon fruit development and quality regulation, enable efficient and sustainable utilization of melon genetic resources, and establish robust valorization strategies to enhance melon productivity and fruit quality stability under fluctuating environmental scenarios.
