1 Introduction

Astragalus membranaceus, or Huangqi, is one of the most prized traditional Chinese medicinal (TCM) plants that are widely utilized across Asia for more than a thousand years for the purpose of immune enhancement, replenishment of vital energy, and promotion of longevity. Its root accumulates a complex mixture of bioactive molecules such as polysaccharides, flavonoids, and saponins that attribute its pharmacological effects including immunomodulatory, antioxidant, anti-inflammatory, and cardiovascular protective activities. A. membranaceus is also of considerable economic significance as an expensive herbal product in global TCM and nutraceutical trade. As enhanced global interest in TCM grows, Astragalus production and genetic improvement become top agendas in agriculture and pharmaceutical use (Ren et al., 2023).

Though of medicinal and economic importance, Astragalus is of high germplasm complexity and trait variability, ranging from variation in ecological fitness and stress resistance to metabolite profile differences. Conventional research has mainly focused on phytochemical characterization, screening for pharmacological activity, and cultivation. However, the genetic basis for such biochemical and phenotypic variability has not been well comprehended. Present genomic studies are also limited in scope and aimed at a few reference genomes or transcriptomes which are insufficient to reflect the entire scope of genetic variation among various populations of Astragalus (Salehi et al., 2020). Lack of such a broad variety of genomic resources limits identification of key functional genes, revealing molecular mechanisms that regulate medicinal properties and enhancing genetic diversity in breeding schemes (Salehi et al., 2020).

Over the past decade, the pan-genome platform, including the core and accessory gene set of a species, has also emerged as an analytical tool of immense utility for defining the entire genetic repertoire and structural variation of a species. Pan-genome analyses of rice, maize, and soybean crops have unraveled extensive-scale genetic diversity linked with agronomic quality, stress resistance, and metabolite diversity. Alternatively, in pharmaceutical factories, pan-genomics is increasingly utilized to investigate genetic diversity underlying secondary metabolite biosynthesis and adaptive adaptation. By integrating multi-omics data into advanced bioinformatics tools, pan-genomics reveals unprecedented opportunities to research the molecular foundation of difference in traits, unveiling novel understandings of plant biology and functional breeding (Liu et al., 2025).

This Study gives an overall overview of advances in the genomics of Astragalus and the emerging application of pan-genomics to account for trait diversity. It condenses existing developments in genome sequencing and functional annotation, highlights the theoretical foundations and principles of pan-genomic analysis, and outlines how pan-genome research reveals structural variations, metabolic gene diversity, and adaptation traits in Astragalus. Particular emphasis is given to the genetic basis of variation in traits, and examples are taken from polysaccharide composition, flavonoid accumulation, and stress resistance. The study also mentions the possible advantages of pan-genomics to breeding, germplasm utilization, and precision herbal medicine formulation. Through the adoption of information of multi-omics and computation techniques, the study shows the significance of Astragalus pan-genome research in Medicinal plant improvement and promotion of modernization of traditional Chinese medicine.

2 Advances in Astragalus Genomic Research: A Review

2.1 Overview of Astragalus genome sequencing and annotation

Recent years have seen impressive progress in the genomics of Astragalus membranaceus and its closest relatives. High-quality chromosome-scale genome assemblies were achieved with the latest sequencing technologies such as PacBio long reads and Hi-C scaffolding. For example, recently available was a 1.43 Gb genome with 98% of assembly anchored onto nine pseudochromosomes and nearly 30 000 protein-coding genes, offering a solid platform for comparative and functional studies (Fan et al., 2024) (Figure 1). Similarly, a reference-quality genome of Astragalus mongholicus detected 27 868 protein-coding genes and reported the gene families for secondary metabolite biosynthesis to be enriched (Chen et al., 2022). Transcriptome sequencing guided by reference genomes as well as without reference genomes has also made it possible to identify full-length transcripts and isoforms to enhance gene annotation and transcript variant discovery (Li et al., 2017; Kang et al., 2024).

2.2 Genes and metabolic pathways related to medicinal compounds

Genomic and transcriptomic studies have revealed key genes and pathways for the biosynthesis of the primary medicinal ingredients of Astragalus, such as triterpenoid saponins (astragalosides), flavonoids (e.g., calycosin), and isoflavonoids. Studies have shown that pathways involve dozens of genes and transcription factors (e.g., MYBs, bHLHs, AP2-EREBPs), with gene family expansion through tandem duplication. For instance, the phenylalanine ammonia-lyase (PAL) gene cluster has high expression in roots and is a key player in the biosynthesis of phenylpropanoid and flavonoids (Liang et al., 2020). Differentially expressed during development and tissues related to the accumulation of bioactive compounds and provides targets for breeding and metabolic engineering (Li et al., 2024; Li et al., 2025).

2.3 Comparative applications of genomic research in medicinal plants

Comparative genomics of Astragalus and medicinal plants has revealed evolutionary trends, e.g., the absence of recent whole-genome duplication in Astragalus mongholicus and long terminal repeat retrotransposon activity in genome growth (Bagheri et al., 2022). Studies of chloroplast and mitochondrial genomes have contributed to phylogenetic resolution, species definition, and building molecular markers (Lei et al., 2016; Liu et al., 2020; Tian et al., 2021). These resources allow the study of medicinal property trait diversity, adaptation, and molecular basis of medicinal properties to conserve and improve medicinal plant germplasm (Bagheri et al., 2022; Moghaddam et al., 2023; Li et al., 2024) (Figure 2).

3 Advances in Pan-genome Construction: Sequencing, Assembly, and Alignment

3.1 Concept of the pan-genome

Pan-genome is the totality of the genes of a species, comprising the core genome (genes shared by all individuals) and accessory or dispensable genome (genes present in some but not all individuals). The term encompasses genetic variation as well as structural variation and helps to explain adaptation and diversity of traits (Jayakodi et al., 2021).

3.2 Technical approaches for pan-genome construction

Pan-genome assembly typically involves sequencing several samples through the use of high-throughput techniques. Short-read and long-read sequencing are utilized, but long-read platforms such as PacBio and Oxford Nanopore now enable more contiguous and completed assemblies, especially in repeat or complex regions (Jayakodi et al., 2021). Assembly methods include de novo assembly of every genome and subsequent whole-genome alignment for identifying common and specific sequences (Zhang et al., 2022). Reference-assisted scaffolding tools, such as RaGOO, can even facilitate assembly contiguity and identify structural variants (Alonge et al., 2019). Assembly quality and depth of sequencing are also crucial as they directly affect the gene presence/absence calling accuracy and also the structure of the pan-genome.

3.3 Analytical methods and bioinformatics tools

A few of the bioinformatics tools to be used for pan-genome analysis include whole-genome aligners (progressiveMauve, Mugsy, progressiveCactus) for multiple genome alignment and locally collinear block detection (Alonge et al., 2019). Compressed hybrid-indexing methods (DHPGIndex) enable large-scale and rapid sequence alignment of big pan-genome datasets (Maarala et al., 2021). Gene clustering and orthology finding tools (OrthoMCL) are utilized for classifying core and dispensable genes. The tools and techniques employed, together with sequencing depth and assembly method, can impose a substantial effect on the ultimate pan-genome and its biological significance (Jayakodi et al., 2021).

4 Construction and Application Progress of the Astragalus Pan-genome

4.1 Germplasm resources and genetic diversity of Astragalus

Astragalus has abundant germplasm resources and high genetic diversity, and over 2 500-3 000 species are available in the world with great variation among wild and cultivated populations. With SSR, ISSR, and RAPD markers, studies have detected abundant genetic diversity within and among populations, and most of the genetic variation being between populations but not within them. Core collections produced through molecular markers preserve the majority of allelic diversity and population structure and are a good investment for breeding and conservation (Dong et al., 2024). Genetic diversity in Astragalus plays significant roles in germplasm identification, conservation of resources, and the production of novel varieties with target traits (Liu et al., 2016; Dong, 2024).

4.2 Gene structural variations revealed by the pan-genome

Pan-genomic and genomic comparative analyses portrayed the structural divergence in Astragalus as utmost, including chromosomal reorganization, inversions, and repeat-mediated recombination events particularly plastid genomes (Moghaddam et al., 2023). Structural variation and hypervariable loci like a 13-kb inversion within the IR region have been shown to cause genome evolution and diversity. Structural variation is an important molecular markers for phylogeny and species identification studies (Moghaddam et al., 2023).

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 the identification of high-performing germplasm with high-quality traits. Pan-genomics facilitates the cataloging of variable and core genes, which are of good use in the development of high-resolution molecular markers such as SSRs. The markers are vital during variety registration, germplasm characterization, and marker-assisted selection in breeding programs (Hur et al., 2021; Moghaddam et al., 2023). These materials assist in accelerating selection and protection of improved Astragalus lines.

6.2 Improvement of medicinal components and quality consistency control

The pan-genome provides an accurate map of gene families and structural variations engaged in the biosynthesis of key bioactive molecules like triterpenoids and flavonoids. This data enables specific breeding and genetic enhancement to generate high bioactive content and consistent quality. With the knowledge of the genetic determinants of metabolic pathways, breeders can select lines for uniform and high levels of pharmacologically active metabolites that facilitate the standardization of traditional Chinese medicine products (Chen et al., 2022; Shi et al., 2022).

6.3 Enhancement of stress-resistance traits and ecological adaptability

Pan-genomic studies-uncovered variable genes are usually enriched in biotic and abiotic stress-resistance functions. The results are beneficial for breeding Astragalus cultivars with increased environmental stress and pathogen tolerance. Pan-genomic information coupled with phenotypic and ecological information facilitate the development of cultivars for varied and changing environments to meet sustainable production (Bayer et al., 2020; Chang et al., 2021).

6.4 Pan-genome-enabled precision development of traditional chinese medicine

Pan-genomics also offers a new reference platform for precision breeding and modernization of traditional Chinese medicine. By linking structural and sequence variation to phenotypic traits and medicinal quality, pan-genome resources enable the rational design of Astragalus cultivars for target therapeutic uses. Integration of pan-genomic data with metabolomics and transcriptomics also enables precision development and quality control of herbal medicines (Jayakodi et al., 2021).

7 Interdisciplinary Integration and Application Expansion of Pan-genomics in Astragalus

7.1 Integration of pan-genomics with multi-omic

Integrating pan-genomics with multi-omics approaches—i.e., metabolomics, epigenomics, and transcriptomics-allows for a comprehensive understanding of genetic diversity, gene regulation, and metabolic networks. Integration unveils novel aspects of genome complexity, relates genetic diversity to phenotypic traits, and facilitates the identification of regulatory elements and metabolic pathways in medicinal quality and adaptation. Multi-omics approaches like these are increasingly important for deciphering the functional effects of pan-genomic variation in plants and other species.

7.2 Combination with systems biology and network pharmacology

Pan-genomics coupled with systems biology and network pharmacology allows one to reconstruct gene regulatory and metabolic networks. It is by virtue of this inter-disciplinary approach that one can model intricate biological processes, predict the function of genes, and unveil significant nodes of pharmacological routes. Such information is significant for understanding the all-encompassing influence of genetic variance on crop traits and for rational drug design and discovery (Reghu et al., 2024).

7.3 Applications of big data and artificial intelligence in gene function analysis

The genomic flood requires advanced computational strategies. Artificial intelligence (AI) and big data analytics and machine learning models are increasingly utilized currently to pan-genomic datasets in predicting gene function, genome mining, and discovery of new biosynthetic gene clusters. These enhance functional annotation in terms of speed and accuracy and accelerate identification of genes linked to important traits and medicinal attributes (Kloosterman et al., 2020; Liu et al., 2022).

7.4 Clinical translation and industrial potential

Pan-genomics integration with multi-omics and computational technologies expands Astragalus' utility in the clinic and industries. Pan-genomic resources make it easier to prepare standardized high-quality medicinal products, precision breeding, and genetic discovery to therapeutic translation. Such technologies also speed up the industrialization of traditional Chinese medicine by providing a scientific foundation for quality control, efficacy evaluation, and discovery of new therapeutic drugs (Reghu et al., 2024).

8 Concluding Remarks

The new breakthroughs in genomic and pan-genomic research have significantly enriched our understanding of Astragalus membranaceus. High-quality genome assemblies, functional annotations, and comparative genomic analysis have made it possible to characterize genes that contribute to medicinally useful metabolites, including polysaccharides, flavonoids, and saponins. Construction of a pan-genome scaffold has also revealed core and variable gene collections, structural variation, and lineage-specific genes accountable for the species' incredible phenotypic and metabolic diversity. These results constitute an initial step in connecting genomic variety to functional qualities within this medicinally valuable genus.

The Astragalus pan-genome is emerging as an extremely useful tool to untangle the genetic determinants of trait variability. By integrating gene presence/absence variation, copy number variation, SNP, and large-scale structural rearrangement analyses, researchers are beginning to untangle the molecular determinants of variations in accumulation of bioactive compounds, stress tolerance, and adaptive evolution. These results not only reveal more on trait plasticity in Astragalus, but also provide outstanding genetic material to support directed breeding and improvement in quality.

Future research will include the coupling of pan-genomics with multi-omics platforms like transcriptomics, metabolomics, and epigenomics to attain a deeper understanding of regulatory networks for Astragalus trait diversity. Big data analysis, machine learning, and network pharmacology will enable functional genes and pathways of pharmacological efficacy to be discovered. Finally, combination of clinical data and precision breeding techniques can transcend the divide between genomic advances and practical use, enabling standardized cultivation, increased consistency of herbal quality, and rationale production of new herbal remedies. Finally, research of the Astragalus pan-genome will not only enable genetic improvement of this critical medicinal plant but also drive overall modernization and world acceptance of traditional Chinese medicine.

Acknowledgments

The authors extend heartfelt gratitude to the research team for their dedicated support and active collaboration throughout data collection and literature organization, whose contributions have laid a solid foundation for the successful completion of this study. The authors also acknowledge the invaluable feedback and constructive suggestions provided by the two anonymous reviewers during the review process, which played a crucial role in enhancing and refining the quality of this paper.

Conflict of Interest Disclosure

The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

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