Comprehensive Evaluation of Nanhaia speciosa Germplasm Resources Using Agronomic Traits, Molecular Markers, and Metabolomics

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Nanhaia speciosa is a valuable industrial crop known for its significant edible and medicinal properties, attributed to its abundance of secondary metabolites. This study aims to elucidate the genetic relationships among N. speciosa, enhance species identification accuracy, and select genetically stable, high-quality germplasms of N. speciosa. To achieve this, we conducted chloroplast gene amplification and sequencing, alongside an analysis of the agronomic traits of 19 N. speciosa germplasms. Additionally, non-targeted metabolomic profiling using UPLC-Q-Orbitrap/MS and chemometric methods was employed to assess their metabolic diversity and genetic relationships. The results revealed notable differences in DNA barcodes and secondary structures across the germplasms, with the atpF-atpH sequence successfully distinguishing all 19 germplasms into distinct varieties. Multivariate statistical analyses, including principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and hierarchical clustering, identified 12 key marker metabolites that effectively differentiated the germplasms, consistent with the observed phenotypic diversity. A clustering analysis integrating genetic, phenotypic, and metabolomic data further validated the utility of DNA barcoding for species identification. The results of the comprehensive analysis showed that NDL-2 and NDL-18 exhibited relatively good edible and medicinal properties, while NDL-1 and NDL-19 exhibited relatively poor edible and medicinal properties. This study provides crucial insights for the breeding and genetic improvement of N. speciosa and related species, offering a valuable reference for the identification, conservation, and utilization of germplasm resources within the N. speciosa.