Genetic polymorphism of Japanese cultivated Rheum species in the internal transcribed spacer region of nuclear ribosomal DNA

• Published in: Journal of natural medicines 2019-06, Vol.73 (3), p.541-554
• Main Authors: Asanuma, Mai, Zhu, Shu, Okura, Naoki, Cai, Shao-Qing, Yoshimatsu, Kayo, Komatsu, Katsuko
• Format: Article
• Language: English
• Subjects: Base Sequence; Biomedical and Life Sciences; Biomedicine; China; Cloning; Cloning, Molecular; Complementary & Alternative Medicine; DNA, Plant - genetics; DNA, Ribosomal Spacer - genetics; Flowers & plants; Genotype; Genotype & phenotype; Japan; Medicinal Chemistry; Medicine, Chinese Traditional; Organic chemicals; Original Paper; Pharmacology/Toxicology; Pharmacy; Phytochemicals; Plant Sciences; Plants, Medicinal - genetics; Polymorphism; Polymorphism, Genetic - genetics; Rheum - chemistry; Rheum - genetics; Ribosomal DNA; Sequence Analysis, DNA
• ISSN: 1340-3443; 1861-0293
• DOI: 10.1007/s11418-019-01298-4

In order to develop new domestic production of Rhei Rhizoma (RR) from Rheum specimens cultivated in the Sugadaira Medicinal Plant Cultivation Test Field (SMPCF), the ITS sequences of 12 SMPCF specimens and Chinese Rheum specimens of four species, as well as RR samples produced in North Korea, China and Japan, were determined by subcloning and their sequences were compared. As the ITS sequences of 10 SMPCF specimens showed significant intra-individual polymorphism, identification of pseudogenes was conducted by detecting the three motifs of the 5.8S sequence and the stability of the 5.8S secondary structure. Approximately 46% of sequences obtained from the SMPCF specimens were putative pseudogenes. The maximum likelihood tree based on ITS sequences showed three main groups—the outer group and inner clusters I and II; clones from 10 SMPCF specimens including putative pseudogenes belonged to the outer group. Cluster I was composed of two clades, one including clones from R. officinale specimens and R. palmatum -derived samples with mat K genotype Rp9, and another including clones from R. coreanum -derived samples. Cluster II consisted of three clades, one including clones from R. palmatum specimens with genotype Rp5, another including clones mainly from R. tanguticum specimens with genotype Rt4, and the third including clones from R. palmatum or R. tanguticum specimens with various mat K genotypes. Clones from SMPCF specimen RC5 showed a close relationship with those from R. tanguticum specimens with mat K genotype Rt4, whereas those from specimen RC9 related to R. coreanum -derived samples. As a result, specimens RC5 and RC9 were considered as candidates for the development of domestic RR.