Construction of a Core Collection of Notopterygii Rhizoma et Radix Based on Molecular Phylogeography

Background As both an endangered medicinal species (China's Category III protected plant) and an authentic traditional Chinese medicine, Notopterygium incisum Ting ex H. T. Chang and N. franchetii Boiss . require urgent conservation of their germplasm resources. While core collections offer an efficient solution for preserving genetic diversity, no such resource currently exists for these species despite their ecological and pharmacological importance. Methods In this study, three chloroplast DNA regions ( rbcL , matK , and trnS - trnG ) and the nuclear ribosomal ITS sequence were employed as molecular markers to conduct phylogeographic analyses of N. incisum and N. franchetii , and their core collections were constructed through stratified sampling of evolutionary significant haplotypes. Results Network analyses revealed complete cpDNA differentiation between species (12 vs. 10 haplotypes separated by ≥5 mutations), while ITS data showed limited historical introgression. Wild populations exhibited strong genetic structure ( G _ST : 0.673-0.713) with ancestral haplotypes (cpDNA Hap_2/Hap_13; ITS Hap_3-Hap_4/Hap_23), whereas cultivated accessions showed 3.2× higher haplotype diversity but reduced differentiation ( G _ST : 0.077-0.094). Demographic tests (Tajima's D = -1.39 to -2.15, P<0.01) and growth indices (G=856-2901) confirmed post-glacial expansions. Conclusion Using integrated cpDNA and ITS markers, we established optimized core collections for both species ( N. incisum : 50-103 accessions; N. franchetii : 30-40 accessions) that effectively preserved genetic diversity. The dual-marker approach resolved cultivated populations' paradoxical genetic patterns (higher diversity but lower differentiation) and provides a conservation model for medicinal plants facing anthropogenic pressures.