Plant Gene and Trait 2025, Vol.16, No.5, 215-224 http://genbreedpublisher.com/index.php/pgt 221 7.3 Outcomes: cultivars with enhanced ornamental appeal and edible quality Through these integrated methods, breeders have developed a number of new lotus varieties that are both ornamental and edible. Some new varieties performed better in ornamental traits such as flower diameter, flower color and number of petals. Meanwhile, the yield, starch content and nutritional quality of tubers were also improved (Li et al., 2020; Huang et al., 2021; Kumar et al., 2024; Kumar et al., 2025). The application of molecular breeding methods has accelerated the aggregation of superior genes and enhanced the efficiency of breeding. Some studies have also attempted to use methods such as gene transformation to further expand the possibility of improving the traits of lotus (Verma et al., 2025). 8 Challenges and Research Gaps 8.1 Long breeding cycles and trait complexity Lotus is a perennial aquatic plant with a rather complex genetic background and a wide variety of traits. Its ornamental traits (such as flower color, flower shape, and plant type) and edible qualities (such as root and stem yield and nutritional components) are usually regulated by multiple genes. There are also genetic correlations and environmental interactions among different traits, which prolongs the traditional breeding cycle and makes it difficult to concentrate superior traits in one variety. In addition, the genetic mechanisms of some traits (such as flower color and plant type) have not been fully understood, which also increases the difficulty of molecular breeding and precise improvement (Zhu et al., 2019; Lin et al., 2020; Qi et al., 2022; Hu et al., 2024). 8.2 Limited genomic resources compared to other crops Although the genome sequencing and database construction of lotus have made progress in recent years, compared with major food crops, its genomic resources are still not rich enough. High-quality genome assembly, functional gene annotation and molecular marker development are all relatively limited. This to some extent restricts the application of modern breeding methods such as GWAS, QTL mapping and MAS. Meanwhile, the existing genomic databases and germplasm resource banks have insufficient coverage and diversity, which poses obstacles to the analysis of complex traits and the mining of excellent genes (Gui et al., 2018; Li et al., 2021; Qi et al., 2022). 8.3 Consumer-driven demand versus ecological adaptability The market demand for lotus is becoming increasingly diverse. It is not only required that the flower colors and shapes be rich, but also that the roots and stems be high-yielding and have high nutritional value. However, if one overly pursues a certain trait, such as only focusing on yield or flower color, it may lead to problems like a decline in genetic diversity, weakened stress resistance, and even affect the ecological adaptability of plants. Moreover, some excellent traits do not behave stably in different environments. How to meet consumer demands while ensuring the ecological adaptability and sustainable utilization of varieties is a key issue that needs to be addressed in current lotus breeding (Huang et al., 2018; Lin et al., 2019; Mekbib et al., 2020; Gowthami et al., 2021; Kumar et al., 2024). 9 Future Perspectives 9.1 Application of synthetic biology and metabolic engineering With the progress of research on the genome and molecular biology of lotus, synthetic biology and metabolic engineering have brought new opportunities for the improvement of lotus. By regulating key metabolic pathways (such as flavonoids and anthocyanins), the flower color, nutritional components and medicinal active substances can be specifically changed, thereby taking into account both ornamental and edible values. For instance, studies on transcription factor families have revealed their roles in regulating flavonoid synthesis, which provides a theoretical basis for enhancing the accumulation of functional components in specific tissues and lays the foundation for molecular breeding and resource utilization (Zhu et al., 2019; Sun et al., 2025; Yu et al., 2025). In addition, based on high-density genetic mapping and QTL mapping, combined with technologies such as gene editing, it is expected to accelerate the breeding of new varieties of lotus (Liu et al., 2016; Huang et al., 2021). 9.2 Integration of lotus breeding into sustainable agriculture and urban landscaping Lotus not only have ornamental value but also edible and ecological value, thus having unique advantages in
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