Plant Gene and Trait 2025, Vol.16, No.5, 215-224 http://genbreedpublisher.com/index.php/pgt 217 expression of related genes. Combined analysis of transcriptome and metabolome can screen out superior germplasm (Pott et al., 2021; Zhu et al., 2022). Lotus seeds also contain active substances such as polyphenols and flavonoids, which enhance their health value (Lin et al., 2019; Qi et al., 2022). The improvement process of high-quality seeds can be accelerated by using molecular markers and genomic selection (Li et al., 2021; Sun et al., 2025). 3.3 Breeding for stress tolerance to improve edible productivity Adverse stress conditions (such as salinity, drought and diseases) can seriously affect the yield and quality of lotus. The exploration and verification of genes related to stress resistance have provided a theoretical basis for breeding new varieties with high yield, high quality and strong adaptability (Qi et al., 2022; Sun et al., 2025). Through molecular marker-assisted selection and genome-wide association analysis, stress resistance and edible quality traits can be combined to achieve multi-trait improvement (Li et al., 2021; Sun et al., 2025). Improving stress resistance can also help lotus plants grow on marginal land, thereby increasing food security (Escaray et al., 2014; Qi et al., 2022). 4 Conventional Breeding Approaches 4.1 Germplasm collection and phenotypic selection Lotus is an important aquatic plant that has both ornamental and edible value. The collection of germplasm resources and the assessment of phenotypic traits are the basis of conventional breeding. The collection and genetic diversity analysis of lotus germplasm from different regions revealed significant differences in lotus in terms of plant height, leaf shape, flower color, flowering period and tuber yield, which provided a rich genetic basis for subsequent trait improvement and new variety breeding (Lin et al., 2019). Phenotypic selection mainly relies on field investigation and evaluation of target traits (such as flower color, flower shape, tuber size, nutritional components, etc.), and combines multi-environment experiments to screen out superior individual plants or strains (Jiang et al., 2023; Kumar et al., 2024). 4.2 Hybridization and clonal propagation Hybrid breeding is a commonly used method for lotus. Through artificial pollination, the superior traits of different varieties can be combined to obtain new types that are both aesthetically pleasing and highly productive. For example, hybridization of tuber type and floral type can yield offspring with rich flower colors and high tuber yield (Liu et al., 2016). Lotus has a strong asexual reproductive ability. Therefore, methods such as tuber segmentation and tissue culture are often used for the rapid propagation of superior varieties and can also maintain the stability of traits (Lin et al., 2019; Jiang et al., 2023). 4.3 Successes and limitations in traditional breeding Traditional breeding has achieved many results, developing many varieties with diverse flower colors, controllable flowering periods and high-yield tubers, meeting the dual demands of ornamental and edible (Lin et al., 2019; Jiang et al., 2023). However, it also has limitations: first, the breeding cycle is too long and the efficiency of trait aggregation is low; second, phenotypic selection is influenced by subjective factors and the environment, making it difficult to precisely improve complex traits. Thirdly, the genetic basis is unclear, making it difficult to achieve precise improvement at the molecular level (Liu et al., 2016; Lin et al., 2019; Kumar et al., 2024). Therefore, it is necessary to combine conventional breeding with modern technologies such as molecular marker-assisted selection to enhance the efficiency and innovation of lotus breeding. 5 Molecular and Genomic Breeding Tools 5.1 Development of molecular markers for ornamental and edible traits The research on molecular markers of lotus has developed rapidly. Commonly used markers such as SSR, SNP and InDel accelerate trait localization and molecular-assisted selection. Through whole-genome resequencing and transcriptome analysis, researchers have identified millions of SNPs and a large number of SSR/InDel markers. These markers have been widely used in the research and breeding of important traits such as flower color, flower shape, seed starch content and rhizome quality (Lin et al., 2019; Li et al., 2021; Qi et al., 2022). For example, the genetic map constructed with high-density SNP markers has greatly improved the accuracy of agronomic trait localization of lotus (Hu et al., 2015; Liu et al., 2016).
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