Development of specific molecular markers for medicinal peony (Paeonia lactiflora) with double flower

In China, medicinal Paeonia lactiflora with double flowers (DFs) does not produce seeds, yet it possesses significantly higher paeoniflorin content compared with its single-flowered counterpart. The propagation of medicinal P. lactiflora with DFs relies solely on rhizomes. However, due to economic motivations, the rhizomes of medicinal P. lactiflora with single flowers (SFs) are often mixed with those of medicinal P. lactiflora with DFs. This practice results in a mixed population and a subsequent decline in quality. To ensure the quality of medicinal P. lactiflora with DFs, it is essential to develop specific molecular markers for its identification and breeding. The genetic diversity of 30 populations from six species in sect. Paeonia was studied using inter-simple sequence repeat (ISSR) analysis. Specific bands in medicinal P. lactiflora with DFs and medicinal P. lactiflora with SFs were cloned and utilized as distinctive molecular markers for their identification. A total of 244 polymorphic bands were identified from 18 primers. Among these primers, UBC844 displayed the highest genetic diversity (N_e = 1.37, h = 0.23, I = 0.36). Based on the UPGMA and PCA analyses, all species were classified into three clusters. Medicinal P. lactiflora with SFs showed closer proximity to the wild-type species of Paeonia, while it was further apart from medicinal P. lactiflora with DFs. The specific band amplified by UBC836-3 (~431 bp) was exclusive to medicinal P. lactiflora with DFs, while the band amplified by UBC842-7 (~341 bp) was specific to medicinal P. lactiflora with SFs. There are significant genomic disparities between medicinal P. lactiflora with SFs and DFs. Consequently, stable and specific sequence characterized amplified region markers (UBC836-3 and UBC842-7) have been established to effectively differentiate between the two types. This development will substantially enhance the quality and efficiency of medicinal P. lactiflora, thus supporting the growth of the industry. By utilizing these specific molecular markers, breeding experts can select parent plants and shorten the cultivation cycle for new medicinal peony varieties.