Development and application of chloroplast molecular markers in Panax notoginseng.
10.19540/j.cnki.cjcmm.20200104.105
- Author:
Jia-Ling SUN
1
;
Yan HAN
1
;
Xiu-Ming CUI
2
;
Yuan LIU
2
Author Information
1. Kunming University of Science and Technology Faculty of Life Science and Technology Kunming 650500, China.
2. Kunming University of Science and Technology Faculty of Life Science and Technology Kunming 650500, China Yunnan Provincial Key Laboratory of Panax notoginseng Kunming 650500, China Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine Kunming 650500, China Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug Kunming 650500, China.
- Publication Type:Journal Article
- Keywords:
Panax notoginseng;
cpIndel;
cpSNP;
cpSSR
- MeSH:
DNA, Chloroplast/genetics*;
Genetic Markers;
Genetics, Population;
INDEL Mutation;
Panax notoginseng/genetics*;
Polymorphism, Single Nucleotide;
Sequence Alignment
- From:
China Journal of Chinese Materia Medica
2020;45(6):1342-1349
- CountryChina
- Language:Chinese
-
Abstract:
The molecular markers(cpSSR, cpSNP and cpIndel) were developed based on the whole genome sequence of Panax notoginseng chloroplast genome, which provide a powerful tool for the evaluation and analysis of the future P. notoginseng germplasm resources. The 89 P. notoginseng samples from 9 groups were used for the experiment, and the data for the study were derived from NCBI and the GenBank numbers were: KJ566590, KP036468, KR021381 and KT001509. Through sequence alignment, 30 polymorphic sites(SNP and Indel) were identified, including 16 cpSNP and 14 cpIndel; cpSNP and cpIndel accounted for far more than the gene region in the intergenic region. The developed cpSSR reached 87-89, the repeat unit was mainly composed of trinucleotide, accounting for 70%-71%, and the dinucleotide was the least, accounting for 7%. Eighteen cpDNA molecular markers were developed, including 7 cpSSR primers, 6 cpIndel primers, and 5 cpSNP primers. The MatK gene and ycf1 primers were chosen as control. According to the results of DNA gel electrophoresis, cpSSR-5, pgcpir019 and pncp08 can be used to distinguish different cultivated populations of P. notoginseng. Among them, cpSSR-5 and pgcpir019 can also be used to distinguish the inter-species resources of ginseng by comprehensive sequence length, population π value and average nucleotide difference. However, pncp08 can only be used to distinguish different populations of P. notoginseng. In addition, the effect of distinguishing the groups of P. notoginseng, which the primer pncp-M(based on the MatK gene) is weaker than the cpSSR-5, pgcpir019 and pncp08.
