Plant Gene and Trait 2025, Vol.16, No.5, 215-224 http://genbreedpublisher.com/index.php/pgt 219 6 Integrative Breeding Approaches 6.1 Combining ornamental and edible trait improvement in breeding programs The ornamental value of lotus mainly lies in its color, shape and flowering period, while its edible value mainly depends on the yield, nutrition and taste of its roots and stems. Modern breeding, through phenotypic screening combined with molecular marker-assisted selection (MAS), can simultaneously improve ornamental and edible traits. For instance, by using QTL mapping and genome selection techniques, researchers have identified key genes that affect flower color (such as genes related to yellow flower color) and rhizome yield, providing tools and theoretical support for the improvement of dual traits (Zhu et al., 2019; Lin et al., 2020; Huang et al., 2021; Li et al., 2021). In addition, the screening of early-flowering varieties and the analysis of nutritional traits have also provided practical experience for breeding that takes into account both ornamental and edible values (Jiang et al., 2023; Yang et al., 2024). 6.2 Trade-offs and strategies to optimize dual-purpose cultivars In actual breeding, there is often a conflict between ornamental and edible traits. Some highly ornamental varieties perform poorly in terms of root and stem yield or quality. To solve this problem, breeders adopted methods such as multi-parent hybridization, backcrossing and population improvement, combined with phenotypic and molecular data, to screen out materials that have both excellent flower shapes and high-yield roots and stems (Lin et al., 2019; Huang et al., 2021; Jiang et al., 2023). Meanwhile, regulating the expression of genes related to flowering period and root and stem development can reduce the negative correlation between traits, thereby achieving synergistic improvement (Lin et al., 2020; Hu et al., 2024). In addition, based on large-scale evaluation of germplasm resources and trait association analysis, researchers established trait trade-off and optimization models, providing a reference for the breeding of dual-use varieties (Li et al., 2021; Sun et al., 2025). 6.3 Multi-omics approaches for balancing aesthetics and nutrition Multi-omics integration provides a new idea for lotus to balance ornamental and edible values. Through the combined analysis of the genome, transcriptome and metabolome, the molecular basis of flower color, nutritional components (such as flavonoids, starch) and their regulatory networks can be revealed (Figure 2) (Zhu et al., 2019; Li et al., 2021; Yu et al., 2025). For instance, transcriptome and metabolome analyses revealed that certain specific transcription factors regulate the synthesis of anthocyanins and nutrients, providing potential targets for molecular design breeding (Zhu et al., 2019; Yu et al., 2025). In addition, the in-depth mining of genomic databases and functional genes has also promoted the development of molecular markers and the application of precision breeding (Li et al., 2021; Sun et al., 2025). 7 Case Study: Breeding Program of Nelumbo nucifera 7.1 Breeding objectives and trait prioritization Lotus is an important aquatic plant, which not only has ornamental value but also edible value. When breeding, it is necessary to strike a balance between ornamental traits such as flower shape, color and plant type and edible qualities such as tuber yield, quality and nutritional components. Recent studies, through genetic diversity analysis, population genomics and trait association research, have clearly identified flower shape, flower color, flower diameter, tuber size, starch content and stress resistance as key traits for improvement. Different types of lotus (flower lotus, seed lotus, lotus root lotus) have significant differences in ornamental and edible traits. Trait weights need to be allocated according to the target during breeding (Li et al., 2020; Kumar et al., 2024; Kumar et al., 2025). 7.2 Methods: hybridization, marker-assisted selection, field evaluation There are various breeding methods for lotus. Traditional hybridization involves crossing different types of lotus to obtain offspring with complementary traits. Molecular marker-assisted selection (MAS) and genome-wide association study (GWAS) have been widely used for trait localization and screening of superior genes. For instance, based on high-density SNP genetic mapping and QTL mapping, researchers identified genetic loci related to tuber yield and flower shape. These achievements provided tools for early selection and precision breeding (Lin et al., 2020; Huang et al., 2021; Hu et al., 2024). In addition, field assays combined with
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