Advances in Phenomics, Metabolomics, and Genomics for Precision Breeding of Ornamental Horticultural Crops

Precision breeding has revolutionized the field of crop improvement, with ornamental plants benefitting significantly from technological advances. The integration of phenomics, metabolomics, and genomics provides a comprehensive approach to breeding that can enhance traits like flower color, fragrance, disease resistance, and stress tolerance in ornamental crops. Phenomics has rapidly evolved with the advent of high-throughput technologies that enable the rapid measurement of plant traits in real time. Advances in remote sensing technologies (e.g., UAVs, drones, and satellites), image analysis, and sensor-based systems allow for detailed monitoring of growth, flower development, leaf morphology, and stress responses in ornamental crops. For example, recent studies have demonstrated the use of hyperspectral imaging and infrared thermography to detect early signs of disease and drought stress in ornamental plants, which has gained popularity among breeders. These technologies enable breeders to assess a large number of plants rapidly and non-invasively, providing accurate phenotypic data that can be integrated with genomic information for more targeted breeding efforts.

Metabolomics is a powerful tool for understanding the biochemical processes that underlie plant traits, particularly those related to floral scents, pigments, and secondary metabolites that define ornamental crops. Metabolic profiling, achieved through mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy provide insights into the complex biosynthetic pathways that contribute to fragrance and color in ornamental plants. Recent research has demonstrated how the application of metabolomics can aid in breeding ornamental plants with enhanced fragrance. For instance, the identification of key volatile organic compounds (VOCs) and their metabolic pathways in ornamentals has led to targeted breeding efforts aimed at enhancing scent production. Similarly, metabolomics helps unravel the biosynthesis of anthocyanins in ornamentals, such as roses, chrysanthemums, cyclamen, gerbera, and petunias, enabling breeders to optimize color stability and intensity. Furthermore, metabolomics is crucial for studying plant resilience, especially in relation to abiotic stresses, such as drought and salinity. By analyzing metabolite profiles under stress conditions, breeders can identify metabolites that confer stress tolerance and use them as biomarkers for selecting resilient cultivars. The identification of key metabolites and pathways involved in desirable ornamental traits will enable the breeding of plants with enhanced color, scent, and stress resilience, leading to superior varieties with improved marketability and longevity.

Plant genotyping has progressed from the use of basic molecular markers, such as microsatellites (SSRs), SRAP (Sequence-Related Amplified Polymorphism), SCoT (Start Codon Targeted Polymorphism), RAPD (Random Amplified Polymorphic DNA), and CDDP (Codominant Diversity-Associated PCR), to more advanced techniques, including high-throughput sequencing technologies, such as next-generation sequencing (NGS), which has revolutionized genomics and its application in ornamental crops. In recent years, advancements in ornamental plant genomics have incorporated a variety of molecular markers, including the ones which provide higher levels of genetic resolution and diversity detection. Furthermore, the application of microarray technologies in genotyping has revolutionized the field, enabling the simultaneous analysis of thousands of genetic markers. Recent studies have demonstrated that integrating these modern molecular tools enhances genetic mapping, marker-assisted breeding, and the understanding of trait associations in ornamental plants, accelerating their improvement and conservation.

Please note: descriptive studies that report responses of growth, yield, or quality to treatments will not be considered if they do not progress the molecular, genetic, or physiological understanding of these responses.

Recent developments in these fields are paving the way for the next generation of ornamental crops with more consistent, predictable, and desirable traits. This research topic aims to synthesize the latest research on how advances in these three disciplines are being applied to the precision breeding of ornamental plants. Regarding metabolomics, the manuscripts should aim to describe the application of MS to provide insights into the complex biosynthetic pathways that contribute to fragrance (volatile profile) and color (pigment metabolites) in ornamental plants and responses to environmental stresses (osmoprotectants or defense compounds).

We welcome Original Research, Review and Methods contributions on current knowledge and approaches facilitating plant breeding under (but not limited to) the following categories:

• Validation of phenotypic data with genetic markers to enhance breeding precision.

• Identifying metabolomic biomarkers for stress tolerance, such as antioxidants, osmolytes, and hormones involved in stress responses;

• Integration of metabolomic data with genomic and phenomic data to identify genes involved in metabolite production and regulation;

• Molecular marker development and use for plant genotyping;

• Plant genotyping based on traditional molecular markers and marker-assisted selection based on QTLs or functional genes;

• PCR-based plant genotyping: theoretical and practical applications;

• Microarray technologies for whole-genome analysis in ornamental plants;

• Bioinformatics techniques, software, and database to analyze NGS data.

Article types and fees

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Data Report
• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• ... View all formats

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Article types

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Data Report
• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Policy and Practice Reviews
• Review
• Systematic Review
• Technology and Code

Keywords: precision breeding, ornamental plant genomics, phenomics technologies, metabolomics floral traits, molecular markers

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.