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

Abstract

This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.Plant Breed. Biotech. 2016 (February) ABSTRACT Panax ginseng has been one of the most important herbal medicines used in Eastern Asia. Recently, various molecular markers have been developed to authenticate Panax species, but these markers cannot differentiate the exact varieties or variants of Korean ginseng cultivars. In this study, six cultivars of Korean ginseng (Chunpoong, Yunpoong, Gopoong, Gumpoong, Jakyung, and Hwangsook), P. quinquefolius, and P. notoginseng were differentiated by simple sequence repeat (SSR) marker development. Specific primer sets were designed for the 54 candidate sequences containing SSRs that were predicted. Finally, eight polymorphic SSR loci were developed. DNA fragment analysis was performed using fluorescence-labelled primers for the amplicons. Reproducibility tests were carried out using multiple samples of Korean ginseng cultivars and Panax species. Eight primer sets (PgSSR07, PgSSR08, PgSSR09, PgSSR17, PgSSR37, PgSSR40, PgSSR51, and PgSSR53) showing polymorphism were used for phylogenetic relationship analysis. Consequently, six Korean ginseng cultivars (Chunpoong, Yunpoong, Gopoong, Gumpoong, Jakyung, and Hwangsook), P. quinquefolius, and P. notoginseng could be identified using the combination of SSR markers discovered.

De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

“…The leading was dinucleotide, tri-nucleotide, tetra-nucleotide repeat motif in P. vietnamensis with AG/TC (90.06%), CCG/GGC (22.65%), ACTG/TGAC (19.30%), respectively. Which con rmed the study of Um et al [49] on P. ginseng, but tri-nucleotide repeat motif was different in P. vietnamensis than other plants, such as Myricarubra [27], Salix, Populus and Eucalyptus [29]. The CG/CG motif (0.17%) was irregularly detected in P. vietnamensis, as also observed by Wu et al [44], which con rmed that the repeat motif CG/CG is not common in numerous dicotyledon plants [63][64][65][66].…”

“…fuscidiscus with 2,918 containing more than one SSR. In the previous studies of Um et al [49] on P. ginseng and Zhang et al [2] on P. vietnamensis var. fuscidiscus in EST-SSRs di-nucleotide repeats (60.1% and 52.25%, respectively) were the most abundant type.…”

“…To date, many researchers have studied the molecular markers for the genetic analysis of Panax species i.e. P. ginseng [40][41][42]46,48,49], P. notoginseng [45]. However, due to unavailability of reference genome for P. vietnamensis, using Illumina HiSeq™ 4000 the produced reads were assembled through the de novo assembler Trinity.…”

“…fuscidiscus and P. ginseng in the National Center for Biotechnology Information (NCBI) database are available (August 2019), while no ESTs are available in GenBank for P. vietnamensis. Previous studies investigated the genetic variation and veri ed the taxonomic status of the Panax species at the molecular level [40][41][42][43][44][45][46][47][48][49]. However, few researchers studied the P. vietnamensis in Vietnam [50][51][52].…”

Whole genome re-sequencing and development of SSR markers in oriental melon

“…이러한 부분을 보안하기 위해서는 추가적인 SSR 및 Indel 마커를 개발하거나, SNP 후보군들을 이용하여 유전자 지도의 부족한 부분을 채워줄 새로운 마커를 개발하는 것이 도움이 될 것이라 생각한다. SSR 마커의 경우 유전체 상에서 반복서열의 횟수에 따라 다형성을 보이며 근연 종 내에서 마 커의 호환성을 갖는다고 알려져 있다(Um et al 2016). 따라서 본 연구에서 개발된 299 개의 SSR 마커는 '향서 1 호'와 '단 타 PR' 참외 이외의 참외 계통에도 적용할 수 있을 것이라 판 단되며, 새로운 참외 품종을 개발하기 위한 분자 마커로서 기여할 것으로 기대된다.…”