Screening of specific DNA barcode, identification of germplasm resources, and analysis of genetic diversity of Atractylodes chinenesis
10.16438/j.0513-4870.2022-1118
- VernacularTitle:北苍术特异性DNA条形码筛选、种质资源鉴定及遗传多样性分析
- Author:
Guang-yao YIN
1
;
Lin YUAN
2
;
Xin WANG
1
;
Zhi-fei ZHANG
1
;
Ying CHEN
1
;
Shan-hu LIU
1
;
Jin-hui MAN
1
;
Yue SHI
1
;
Yu-ying HUANG
1
;
Xiao-qin ZHANG
1
;
Xiao-hui WANG
3
;
Sheng-li WEI
1
,
4
Author Information
1. School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
2. National Medical Products Administration, Beijing 100037, China
3. Modern Research Center for Traditional Chinese Medicine, Beijing Institute of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 102488, China
4. Engineering Research Center of Good Agricultural Practice for Chinese Crude Drugs of Ministry of Education, Beijing 100102, China
- Publication Type:Research Article
- Keywords:
italic>Atractylodes chinensis;
chloroplast genome;
DNA barcode;
haplotype;
genetic diversity
- From:
Acta Pharmaceutica Sinica
2023;58(6):1693-1704
- CountryChina
- Language:Chinese
-
Abstract:
italic>Atractylodes chinensis has important medicinal and economic values. In this study, the chloroplast genome sequences of four A. chinensis samples from different producing areas were sequenced using the Illumina platform. The specific DNA barcodes were screened and the germplasm resources of A. chinensis samples from different producing areas and the genetic diversity of the population were analyzed basing on the specific barcodes. The whole chloroplast genomes of the four A. chinensis samples had a typical cyclic tetrad structure, with 112 genes annotated. The comparative genomics results indicated that ccsA and trnC-GCA_petN were potential specific DNA barcodes for intraspecific identification of A. chinensis. Polymerase chain reaction (PCR) analysis of ccsA and trnC-GCA_petN was performed on 256 samples from 14 areas in 9 provinces, and the amplification efficiency was 100%. Sequence analysis showed that ccsA and trnC-GCA_petN had 11 and 22 variant positions, which could identify 16 and 22 haplotypes, respectively. The combined sequence analysis identified 39 haplotypes, named Hap1-Hap39, of which the most abundant and widely distributed genotype was Hap9. Haplotype diversity (Hd) = 0.896 and nucleotide diversity (Pi) = 0.002 22 indicated high genetic diversity at the species level in A. chinensis. The genetic distances of the haplotypes were 0.000 00-0.004 88, indicating that there were small genetic differences among the haplotypes. The results of phylogenetic tree analysis showed that 39 haplotypes had very close genetic relationship, and formed two obvious branches with other groups of the same genus except Atractylodes macrocephala. This study plays an important role in the identification of the origin of A. chinensis and the protection and breeding of germplasm resources.
