Integrated application of CBDP, iPBS, and SCoT markers with DNA barcoding enables effective classification of Chinese prickly ash (Huajiao)

A combined molecular framework classified 109 accessions of Chinese prickly ash germplasm and identified close relationships between several ambiguously named local varieties and Zanthoxylum simulans, according to peer-reviewed research in BMC Plant Biology. The study examined key species in the genus Zanthoxylum and related outgroups using three dominant molecular marker systems—CBDP, iPBS and SCoT—together with two DNA barcodes, ITS2 and trnH-psbA. Chinese prickly ash, or Huajiao, refers to the edible-pericarp species within Zanthoxylum.

These plants are cultivated as medicinal and aromatic crops, but their classification has been impeded by ambiguous taxonomy, inconsistent nomenclature and genetic admixture, particularly between Z. bungeanum and Z. simulans. The research set out to clarify relationships among the sampled germplasm by integrating several classes of molecular marker rather than relying on a single identification system. Amplification with 36 selected primers produced 841 polymorphic bands across the assessed material.

The retained primers had a percentage of polymorphic bands, or PPB, of 100%. Among the three dominant marker systems, iPBS delivered the highest level of informativeness, exceeding CBDP and SCoT. Mantel tests also found significant pairwise correlations among all three systems, supporting the consistency of their combined genetic signals.

Cluster analysis and population-structure analysis divided the accessions into two principal genetic groups. Cluster I was dominated by Z. bungeanum, Z. simulans and Z. piasezkii, while Cluster II was dominated by Z. armatum, Z. schinifolium and Z. acanthopodium. These divisions were based on the 109 accessions included in the study and characterize the genetic patterns detected by the selected markers.

The two DNA barcodes supplied complementary taxonomic information. ITS2 supported Z. armatum as a monophyletic clade, indicating that the sampled accessions assigned to that species grouped into a distinct branch in the barcode analysis. In contrast, trnH-psbA exposed geographic substructure within Z. armatum corresponding to populations from Yunnan, the Shaanxi–Hubei region and Sichuan.

The most direct resolution of persistent classification uncertainty came from integrating the dominant-marker results with ITS2 data. Together, these datasets placed the local varieties “Choujiao,” “Qiujiao,” “Fuguhuajiao,” “Goujiao” and “Bayuejiao,” as well as the Shandong germplasm, closely related to Z. simulans. The study therefore establishes a coherent molecular system for identifying and classifying the Chinese prickly ash germplasm represented in the sample.

Its practical scope is resource standardization: the framework provides a way to distinguish accessions whose conventional names and classifications had been inconsistent. The results concern the relationships detected among the 109 evaluated accessions through the specified marker systems and do not by themselves establish the full taxonomic or genetic boundaries of every Zanthoxylum population. By demonstrating that iPBS, CBDP and SCoT markers capture related but complementary variation, and that DNA barcoding can resolve both broader relationships and geographic structure, the research provides an integrated molecular basis for Chinese prickly ash germplasm identification.

The principal reported outcome is a practical classification framework for the assessed material, with the closest affinities of five ambiguously named varieties and Shandong germplasm supported by combined marker and ITS2 evidence.

Subject of Research: Molecular classification and genetic relationships among 109 Chinese prickly ash germplasm accessions

Article Title: Integrated application of CBDP, iPBS, and SCoT markers with DNA barcoding enables effective classification of Chinese prickly ash (Huajiao)

Article References: Liang, S., Feng, Z., Yu, G., Li, Z., Liu, Y., & Liu, Y. (2026). Integrated application of CBDP, iPBS, and SCoT markers with DNA barcoding enables effective classification of Chinese prickly ash (Huajiao). BMC Plant Biology. https://doi.org/10.1186/s12870-026-09978-6

Image Credits: AI Generated

DOI: 10.1186/s12870-026-09978-6

Keywords: Chinese prickly ash, Zanthoxylum, DNA barcoding, iPBS markers, SCoT markers, CBDP markers, taxonomy, genetic diversity, germplasm identification, ITS2, Integrated, application