Development of EST Intron-Targeting SNP Markers for Panax ginseng and Their Application to Cultivar Authentication.
Panax ginseng is one of the most valuable medicinal plants in the Orient. The low level of genetic variation has limited the application of molecular markers for cultivar authentication and marker-assisted selection in cultivated ginseng. To exploit DNA polymorphism within ginseng cultivars, ginseng expressed sequence tags (ESTs) were searched against the potential intron polymorphism (PIP) database to predict the positions of introns. Intron-flanking primers were then designed in conserved exon regions and used to amplify across the more variable introns. Sequencing results showed that single nucleotide polymorphisms (SNPs), as well as indels, were detected in four EST-derived introns, and SNP markers specific to "Gopoong" and "K-1" were first reported in this study. Based on cultivar-specific SNP sites, allele-specific polymerase chain reaction (PCR) was conducted and proved to be effective for the authentication of ginseng cultivars. Additionally, the combination of a simple NaOH-Tris DNA isolation method and real-time allele-specific PCR assay enabled the high throughput selection of cultivars from ginseng fields. The established real-time allele-specific PCR assay should be applied to molecular authentication and marker assisted selection of P. ginseng cultivars, and the EST intron-targeting strategy will provide a potential approach for marker development in species without whole genomic DNA sequence information.
School of Life Sciences, Yantai University, Yantai 264005, China. wht1211@gmail.com.
Hongtao
H
Wang
School of Pharmacy, Yantai University, Yantai 264005, China. lsyq_003@163.com.
Guisheng
G
Li
Korean Ginseng Center for Most Valuable Products &amp; Ginseng Genetic Resource Bank, Kyung Hee University, Yongin, Gyunggi-do 446-701, Korea. cosmolife@khu.ac.kr.
Woo-Saeng
WS
Kwon
Korean Ginseng Center for Most Valuable Products &amp; Ginseng Genetic Resource Bank, Kyung Hee University, Yongin, Gyunggi-do 446-701, Korea. dcyang@khu.ac.kr.
Deok-Chun
DC
Yang
D000483:Alleles; D001483:Base Sequence; D058893:DNA Barcoding, Taxonomic; D018744:DNA, Plant; D020224:Expressed Sequence Tags; D017343:Genes, Plant; D005819:Genetic Markers; D007438:Introns; D005894:Panax / Q000145:classification* / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
D018744:DNA, Plant; D005819:Genetic Markers
Panax ginseng; SNP; cultivar authentication; intron-targeting; real-time allele-specific PCR