Editorial: Advances in phenomics, metabolomics, and genomics for precision breeding of ornamental horticultural crops
Peony represents one of the world's most valuable ornamental crops, prized for its aesthetic appeal and expanding commercial significance. However, conventional propagation methods remain slow and inefficient, limiting the rapid dissemination of elite cultivars and the implementation of precision breeding strategies. Somatic embryogenesis (SE) has emerged as a promising solution, offering opportunities for large-scale propagation and genetic transformation. Recent advances in peony biotechnology have clarified several factors influencing SE efficiency (Elhiti et al., 2013). Among these, genotype remains the most decisive determinant of successful embryogenic induction. Significant variation exists among cultivars, with many commercially important genotypes exhibiting strong recalcitrance to tissue culture. Explant selection also plays a critical role, as developmental stage and tissue origin directly influence embryogenic competence (Jia et al., 2022). Furthermore, optimized combinations of plant growth regulators and carefully controlled culture conditions are essential for successful embryo formation and regeneration. Despite encouraging progress, major bottlenecks continue to hinder widespread adoption of SE-based systems. Browning, caused primarily by the oxidation of phenolic compounds, remains a persistent obstacle, often leading to tissue necrosis and culture failure. Hyperhydricity, characterized by abnormal water accumulation and malformed tissues, further reduces regeneration quality. These physiological disorders substantially limit commercial-scale applications. Parallel advances in genetic transformation technologies have expanded opportunities for functional genomics in peony. Stable transformation systems utilizing Agrobacterium-mediated approaches have demonstrated feasibility, while transient expression techniques, including Agrobacterium infiltration and virus-induced gene silencing (VIGS), have accelerated gene function studies. Nevertheless, transformation efficiency remains low, regeneration systems are often incomplete, and genotype dependency continues to restrict applicability. Future progress will likely depend on combining optimized tissue culture systems with next-generation gene editing technologies. Such integration could enable precise trait modification while overcoming limitations associated with traditional breeding, ultimately supporting the development of novel peony cultivars with improved ornamental value, disease resistance, and production efficiency.Paeonia sp. (peony) represents one of the world's most valuable ornamental crops, prized for its aesthetic appeal, extended vase life, and expanding commercial significance in horticulture and nutraceutical markets. However, conventional propagation by division remains slow, labor-intensive, and constrained by seasonal cycles, limiting the rapid dissemination of elite cultivars and the implementation of precision breeding strategies. Somatic embryogenesis SE has emerged as a promising biotechnological solution, offering opportunities for large-scale clonal propagation, cryopreservation, and genetic transformation with high genetic fidelity. The article by Fu et al. (2026), evaluated the current state of SE and genetic transformation in Paeonia, a traditional ornamental flower and economically important crop that requires efficient propagation and targeted breeding for industrial scalability. They have assessed the key determinants of SE efficiency, including the decisive role of genotype, explant developmental stage and origin, plant growth regulator combinations, and controlled culture conditions, and identified genotype-dependent recalcitrance as the primary constraint. The authors have also analyzed critical bottlenecks limiting commercial SE application, with particular emphasis on browning caused by phenolic oxidation and hyperhydricity, and discussed physiological and molecular factors underlying these disorders. In addition, they have reviewed advances in Paeonia transformation systems, evaluating both stable Agrobacterium-mediated methods and transient approaches such as Agrobacterium infiltration and virus-induced gene silencing VIGS for functional genomics. Based on this evaluation, the authors conclude that despite progress, low regeneration efficiency, incomplete transformation pipelines, and broad genotype dependence persist, and they propose that integrating optimized tissue culture systems with emerging gene editing technologies will be essential to overcome these barriers and develop new Paeonia cultivars with improved industrial and market potential.Recent advances in peony biotechnology have clarified several determinants of SE efficiency. Genotype remains the most decisive factor: substantial variation in embryogenic competence exists among Paeonia ostii, P. suffruticosa, and P. lactiflora cultivars, with many commercially important genotypes exhibiting strong recalcitrance to tissue culture. Transcriptomic studies in tree peony 'Fengdan' confirm that embryogenic potential is genotypedependent and linked to differential expression of SE-related genes such as SERK, WUS, CUC, and LEC. Explant selection also plays a critical role: developmental stage and tissue origin directly influence competence. Cotyledons and immature zygotic embryos show higher embryogenic response than mature vegetative tissues, while single-node and leaf explants require optimized pretreatments to achieve organogenesis. Plant growth regulators PGRs and culture conditions must be precisely balanced. Combinations of auxins 2,4-D, NAA, IBA with cytokinins BA, TDZ, CPPU are critical for induction and proliferation, and auxin:cytokinin ratios regulate embryogenic transition through ARF, ARR-B, and PIN pathways. Light quality, vernalization, and etiolation pretreatments further enhance regeneration while modulating oxidative metabolism.Nevertheless, transformation efficiency remains low, regeneration systems are often incomplete, and strong genotype dependency continues to restrict broad applicability. Future progress will likely depend on integrating optimized SE-based tissue culture platforms with nextgeneration gene editing technologies such as CRISPR/Cas. Coupling precise hormonal and light regulation with embryogenic marker-guided selection could overcome bottlenecks of browning and hyperhydricity, while tissue culture-free transformation methods reduce genotype constraints. Such integration could enable precise trait modification for ornamental value, disease resistance, and production efficiency, ultimately supporting development of novel peony cultivars with improved commercial traits.While genetic improvement remains a central focus of crop research, sustainable production also depends heavily on understanding plant-soil interactions (Xie et al., 2023). The long-term cultivation challenges observed in Paeonia suffruticosa 'Luoyang Hong' provide a compelling example of how rhizosphere ecology influences crop performance. Continuous cropping systems frequently suffer from replanting problems characterized by declining plant vigor and productivity. Through an innovative multi-omics approach integrating metagenomics and metabolomics, researchers investigated rhizosphere dynamics across a 30-year cultivation chronosequence. The findings reveal a complex pattern of ecological succession. During early cultivation stages, beneficial microbial populations dominate the rhizosphere environment. However, these beneficial communities decline significantly after approximately two decades of continuous cultivation. Subsequently, microbial communities shift toward taxa associated with organic matter degradation, indicating ecosystem imbalance (Xue et al., 2014). Although partial recovery of beneficial microbes occurs after extended cultivation periods, overall degradation persists. Simultaneously, researchers identified several metabolites potentially associated with replanting disorders, including succinic acid, trans-ferulic acid, vanillic acid, and specific peptide compounds. Strong correlations between differential metabolites and microbial taxa underscore the intricate interactions governing rhizosphere function. These results emphasize that crop productivity cannot be understood solely through plant genetics (Zhang et al., 2023). The rhizosphere represents a dynamic biological system where plants, microbes, and metabolites interact continuously. Future management strategies aimed at mitigating replanting problems may benefit from microbiome engineering, soil amendment technologies, and targeted manipulation of rhizosphere metabolic networks.Soil salinization is a growing global constraint on agriculture, with over 900 million hectares of land affected worldwide. It acts as a major abiotic stress that limits plant growth by triggering three interrelated types of damage: osmotic stress, ionic stress, and oxidative stress. Osmotic stress reduces water uptake, ionic stress causes toxic accumulation of Na + and Cl -and disrupts nutrient balance, and oxidative stress generates reactive oxygen species that damage membranes, proteins, and DNA. Together, these effects impair metabolism, inhibit photosynthesis, reduce biomass, cause leaf chlorosis, and can lead to plant death (Dehnavi et al., 2023). Plant salt tolerance is therefore a complex, multigenic adaptive trait. Common adaptive strategies include osmotic adjustment with compatible solutes, ion compartmentalization into vacuoles to reduce cytosolic toxicity, and activation of antioxidant defense systems to control oxidative damage. Most salt tolerance research to date has focused on staple crops, forages, and vegetables. Ornamental flowering plants have received comparatively little attention, despite their economic and cultural value. Herbaceous peony Paeonia lactiflora Pall. is one such case. With a cultivation history of more than 4,000 years in China, it is valued for large, colorful flowers, strong adaptability, and high landscaping and cut-flower market value. It also has medicinal importance because its main bioactive compound, paeoniflorin, shows antioxidant, anti-inflammatory, and anticancer activities. However, soil salinity strongly limits large-scale cultivation and landscape use of peony because salt stress reduces growth, development, and ornamental quality (Jiang et al., 2018). Understanding how peony responds physiologically to salt and evaluating available germplasm are thus critical for expanding its cultivation into salineaffected areas. Existing salt tolerance evaluation methods in plants rely heavily on physiological and biochemical indicators. Studies in other species have used traits such as the K + /Na + ratio, malondialdehyde MDA, membrane stability index MSI, superoxide dismutase SOD, proline content, leaf area, relative electrical conductivity, chlorophyll fluorescence parameters like Fv/Fm, and SPAD values. These indicators are informative but often require destructive sampling, specialized equipment, and time-consuming laboratory assays. This makes them impractical for rapid, large-scale screening of many ornamental cultivars (Weng et al., 2021). Cluster analysis and stepwise regression have been used to group germplasm and identify the most predictive traits, but in peony and related ornamentals, pre-stress morphological indicators have not been systematically validated for salt tolerance. Morphological traits may be valuable proxies because they can reflect underlying physiological adaptation. For example, thicker leaves can store more water and provide greater tissue volume for ion dilution, reducing ion toxicity. Larger stem diameter may indicate stronger vascular capacity and structural stability under osmotic stress. In ornamentals, these traits also directly influence plant vigor and visual quality. Thus, easily measured morphological characters could enable fast preliminary screening before stress is applied, which would be a major practical advantage for breeders and nursery producers.The study by Lu et al. (2026), has addressed the impact of soil salinization on herbaceous peony (P. lactiflora), a widely cultivated ornamental flower in China, by screening for relative salt tolerance among 20 cultivars. They have evaluated salt response using a severe stress regime of 400 mM NaCl applied five times over 15 days, with a non-saline control for phenotypic reference, and measured seven pre-treatment morphological indices alongside post-treatment phenotypic and physiological traits. Based on phenotypic scoring and cluster analysis, the authors have identified 'Red Charm', 'Bartzella', and 'Sarah Bernhardt' as the most salt-tolerant cultivars under severe stress. They have further determined, through correlation and stepwise regression analyses, that leaf thickness and stem diameter are potential preliminary morphological indicators for rapid salt tolerance assessment, with higher values associated with greater tolerance. Physiologically, the authors have shown that tolerant cultivars maintained higher antioxidant enzyme activities and exhibited significantly lower relative electrolyte leakage and MDA content than sensitive cultivars, while Fv/Fm declined markedly with decreasing salt tolerance. Overall, the authors provide exploratory evidence that specific morphological and photosynthetic parameters can support rapid screening of salt-tolerant herbaceous peony germplasm.While ornamental crops highlight the importance of aesthetic traits, food crops underscore the necessity of improving productivity and food security. Potato remains one of the world's most important staple crops, contributing significantly to global nutrition and economic development. Understanding the molecular mechanisms regulating tuber formation is therefore of considerable agricultural importance. Hamm et al. (2026) reviewed the big-bracted Benthamidia dogwood clade within Cornus of family Cornaceae, Cornales, a lineage of small-to medium-sized deciduous trees valued for their showy spring floral bract display and phylogenetic importance as one of the earliest diverging asterid groups. They have evaluated three economically significant North American ornamental species, such as flowering dogwood C. florida, kousa dogwood C. kousa, and Pacific dogwood C. nuttallii, along with the more than 130 cultivars developed from them, and identified that persistent research gaps continue to limit both fundamental investigations and commercial breeding progress. The authors have synthesized current knowledge on the phylogenetic relationships and biogeographic history that shape species diversification, the key aspects of plant biology together with the major insect pests and pathogens that constrain landscape performance and commercialization, and the historical propagation methods that have underpinned nursery production. They have also examined the status of genetic and genomic resources, including marker systems, transcriptomic datasets, and reference genomes, and how these tools have been applied to characterize diversity, trace pedigrees, and inform selection. Across these themes, the authors have highlighted critical bottlenecks, articulated priority research gaps, and proposed future directions needed to advance basic research and enable more efficient breeding of big-bracted ornamental dogwoods.Advances in genomic technologies offer promising opportunities to address these issues through marker-assisted selection and genomic breeding approaches. Expanding genomic databases and developing high-resolution genetic maps will be essential for accelerating cultivar development and enhancing disease resistance. The dogwood case highlights an important lesson applicable across ornamental breeding programs: successful