Development of Reproducible EST-derived SSR Markers and Assessment of Genetic Diversity in Panax ginseng Cultivars and Related Species

Abstract

Little is known about the genetics or genomics of Panax ginseng. In this study, we developed 70 expressed sequence tag-derived polymorphic simple sequence repeat markers by trials of 140 primer pairs. All of the 70 markers showed reproducible polymorphism among four Panax speciesand 19 of them were polymorphic in six P. ginseng cultivars. These markers segregated 1:2:1 manner of Mendelian inheritance in an F2 population of a cross between two P. ginseng cultivars, ‘Yunpoong’ and ‘Chunpoong’, indicating that these are reproducible and inheritable mappable markers. A phylogenetic analysis using the genotype data showed three distinctive groups: a P. ginseng-P. japonicus clade, P. notoginseng and P. quinquefolius, with similarity coefficients of 0.70. P. japonicus was intermingled with P. ginseng cultivars, indicating that both species have similar genetic backgrounds. P. ginseng cultivars were subdivided into three minor groups: an independent cultivar ‘Chunpoong’, a subgroup with three accessions including two cultivars, ‘Gumpoong’ and ‘Yunpoong’ and one landrace ‘Hwangsook’ and another subgroup with two accessions including one cultivar, ‘Gopoong’ and one landrace ‘Jakyung’. Each primer pair produced 1 to 4 bands, indicating that the ginseng genome has a highly replicated paleopolyploid genome structure.

Identification of Korean Ginseng (Panax ginseng) Cultivars Using Simple Sequence Repeat Markers

“…The traditional ginseng classification was based on morphology, so we generated molecular data to establish the Panax species lineage. Some researchers have published molecular markers for the identification of Panax species (Choi et al 2011;Bang et al 2012). But there is no report on the DNA fragment analysis method.…”

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.…”