Germplasm evaluation and differentiation in Polygonatum kingianum via chloroplast genome resources

Polygonatum kingianum (PK) is an important medicinal crop with diverse germplasm that is difficult to distinguish morphologically, particularly at early developmental stages. Misidentification can lead to inappropriate regional cultivation and yield losses when germplasm is introduced into unsuitable environments. Although chloroplast (cp) genomes provide abundant sequence information, variation among PK germplasm groups has not been systematically translated into practical markers for authentication.

Here, 39 cp genomes representing seven PK germplasm groups and five related Polygonatum species were comparatively analyzed to characterize genomic variation and develop PCR-based markers.

Rather than extensive structural divergence, the genomes exhibited localized sequence variation. In an expanded dataset of 118 PK cp genomes, 1,247 single-nucleotide polymorphisms (SNPs) and 263 indels were identified, with higher variant densities in the single-copy regions than in the inverted repeats. Integration of comparative alignments, nucleotide-diversity profiles, and locus-specific differences identified five regions: ycf2, clpP, rps7-trnV, atpF-atpH, and ycf4-cemA for marker development. Six primer pairs showed 100% amplification and sequencing success in the tested samples and collectively distinguished the tested PK germplasm groups and related Polygonatum species. Phylogenomic analyses further resolved PK as a distinct lineage within sect. Verticillata and revealed cp differentiation among PK germplasm.

These findings show that cp genomic variation provides additional molecular resources for PK germplasm authentication and characterization and may support the evaluation and utilization of medicinal crop genetic resources.