Medicinal Plant Research 2025, Vol.15, No.3, 142-150 http://hortherbpublisher.com/index.php/mpr 146 4.3 Diversity of genes related to medicinal compounds Astragalus has been discovered to harbor a complex profile of bioactive compounds with more than 200 compounds being reported, including saponins, flavonoids, and polysaccharides (Dong et al., 2024). Functional genes and regulatory factors involved in the biosynthesis of compounds have begun to be uncovered by recent studies. Gene diversity is used to reflect differential medicinal quality and efficacy between species and germplasms, enabling targeted breeding for greater bioactivity content (Dong et al., 2024). 4.4 Genetic basis of stress-resistance traits and adaptive evolution Genetic studies indicate Astragalus has a great adaptability to changing and usually stressful conditions, and a high level of genetic diversity within the species to enable resistance and possible evolution (Szabo et al., 2021). Self-compatibility breeding mechanism and insect pollination have helped this adaptability. Genetic differentiation of the populations was demonstrated to be rather low by molecular marker surveys, showing intensive gene flow and high adaptive ability (Zhang, 2024). These findings provide a genetic account of the generation of climatic and stress-tolerant lines. 5 Genetic Basis of Trait Diversity 5.1 Impact of gene loss and copy number variation on medicinal traits Gene loss and copy number variation (CNV) are the major contributors to trait diversity in medicinal plants. These genomic changes can result in gene dosage and presence alterations in biosynthetic pathways and directly impact the content and quality of pharmacologically active metabolites. In medicinal plants, CNVs have been linked to metabolite content diversity and adaptation and affect breeding efficiency and selection of elite genotypes for target traits (Chen et al., 2020). 5.2 Regulation of pharmacologically active compounds by snps and structural variations Single nucleotide polymorphisms (SNPs) and structural variations (SVs) play a role in biosynthesis and accumulation regulation of the active compounds. SNPs can influence gene expression or enzyme activity, while SVs such as insertions, deletions, and inversions have the potential to disrupt or enrich biosynthetic gene clusters. These variations cause metabolite profile diversity and are very important to clarify the molecular mechanism of trait diversity in medicinal plants (Cao et al., 2024). 5.3 Associations of phenotypic diversity with metabolomics and transcriptomics The integration of metabolomic and transcriptomic information and genetic analysis enables detection of genes and pathways responsible for phenotypic variation. Multi-omics approach reveals the mechanisms by which genetic diversity is converted to variation in metabolite accumulation and expression of traits and facilitates the selection of superior germplasms and improvement of medicinal quality (Chen et al., 2020). 5.4 Complex regulatory networks of traits revealed by pan-genomics Pan-genomic studies uncover the complexity of regulatory networks behind significant traits. By comparing the core and dispensable genomes, gene families, regulatory elements, and network modules driving trait diversity, adaptation, and the biosynthesis of medicinal compounds can be identified. These systems-level understandings are vital for metabolic engineering and precision breeding (Cao et al., 2024). 5.5 Case studies: genetic mechanisms underlying polysaccharide content, flavonoid accumulation, and stress-resistance differences Medicinal plant case studies indicate that some genetic markers are associated with multiple traits, including polysaccharide content, flavonoid accumulation, and stress tolerance. Marker-trait association mapping with SSRs and other types of markers have identified genomic regions controlling these traits, allowing marker-assisted breeding and selection for improved medicinal quality and resilience (Rahimi et al., 2023). 6 The Value of Pan-genomics in Astragalus Breeding and Application 6.1 Discovery of elite germplasm and development of molecular markers Pan-genome analysis facilitates the complete characterization of genetic diversity in Astragalus and contributes to
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