EST-SSR Marker Sets for Practical Authentication of All Nine Registered Ginseng Cultivars in Korea

Abstract

Panax ginseng has been cultivated for centuries, and nine commercial cultivars have been registered in Korea. However, these nine elite cultivars are grown in less than 10% of ginseng fields, and there is no clear authentication system for each cultivar even though their values are higher than those of local landraces. Here, we have developed 19 microsatellite markers using expressed gene sequences and established an authentication system for all nine cultivars. Five cultivars, ‘Chunpoong’, ‘Sunpoong’, ‘Gumpoong’, ‘Sunun’, and ‘Sunone’, can each be identified by one cultivar-unique allele, gm47n-a, gm47n-c, gm104-a, gm184-a (or gm129-a), and gm175-c, respectively. ‘Yunpoong’ can be identified by the co-appearance of gm47n-b and gm129-c. ‘Sunhyang’ can be distinguished from the other eight cultivars by the co-appearance of gm47n-b, gm129-b, and gm175-a. The two other cultivars, ‘Gopoong’ and ‘Cheongsun’, can be identified by their specific combinations of five marker alleles. This marker set was successfully utilized to identify the cultivars among 70 ginseng individuals and to select true F1 hybrid plants between two cultivars. We further analyzed the homogeneity of each cultivar and phylogenetic relationships among cultivars using these markers. This marker system will be useful to the seed industry and for breeding of ginseng.

High-Throughput Development of Polymorphic Simple Sequence Repeat Markers Using Two Whole Genome Sequence Data in Peucedanum japonicum

“…Therefore, many efforts were conducted to develop SSR markers by construction and sequencing of SSR-rich genomic libraries for the minor crops and by utilization of EST sequence (Choi et al 2011;Kim 2012;Izzah et al 2014). However, previous researches required the time consuming wet experiments to find polymorphic SSR markers due to low polymorphism rate (with less than 5 % of success rate) from the SSR candidates because they utilized sequence harboring the SSR motif from one genotype (Choi et al 2011;Kim 2012;Izzah et al 2014). In this study, we explored two WGSs to discover polymorphic SSR markers for the valuable resource plants P. japonicum as leafy vegetable and functional foods.…”

“…Next-generation sequencing (NGS) technology is widely used because of its high-throughput productivity (Varshney et al 2009;Choi et al 2011;Kim 2012). Recently, we developed a high-throughput method to assemble complete sequences of chloroplast genome and nuclear ribosomal DNA (nrDNA) simultaneously using low coverage WGS data, coined as de novo assembly using low coverage WGS (dnaLCW) (Kim et al 2015b).…”

A simple real-time polymerase chain reaction (PCR)-based assay for authentication of the Chinese Panax ginseng cultivar Damaya from a local ginseng population

“…Recently, different types of molecular markers have been developed to authenticate P. ginseng cultivars, namely, RAPD (random amplified polymorphic DNA) (Shao et al, 2004;Reunova et al, 2010), ISSR (inter simple sequence repeat) (In et al, 2005;Xu et al, 2010;Li et al, 2011), PCR-RFLP (restriction fragment length polymorphism) (Kim et al, 2007), AFLP (amplified fragment length polymorphism) (Ma et al, 2000;Reunova et al, 2010), and SSR (simple sequence repeat) (Choi et al, 2011;Kim et al, 2012;Li et al, 2013). However, these methods are not suitable for the selection of cultivars from large number of samples, as the fragment profiles of RAPD and ISSR are easily affected by minor change in PCR conditions.…”

Authentication of Golden-Berry P. ginseng Cultivar ‘Gumpoong’ from a Landrace ‘Hwangsook’ Based on Pooling Method Using Chloroplast-Derived Markers

“…Molecular markers have been widely used for various applications including physical and genetic mapping of genome, identifying traits, genetic diversity and evolutionary analysis (Kumar et al 2009). In ginseng, very few studies have used molecular markers such as RAPD (In et al 2005), AFLP (Ha et al 2002), SSR (Choi et al 2011;Kim et al 2012) and SNP (Wang et al 2010;Sun et al 2011) for differentiating ginseng species and cultivars. Most of the ginseng landraces have reddish color berry (red berry) except HS, which has golden color berry (golden berry).…”