Characterization of polymorphic microsatellite loci in cultivated and wildPanax ginseng

Jo, Beom Ho; Suh, Dong Sang; Cho, Eun Min; Kim, Joonki; Ryu, Gi-Hyung; Chung, Ki Wha

doi:10.1007/bf03191145

Cited by 22 publications

(16 citation statements)

References 15 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Recently, researchers reported the development of ginseng SSR markers and genetic analysis among national collection species (Park et al 2009), genetic diversity analysis between wood-cultivated ginseng and fieldcultivated ginseng (Jo et al 2009), as well as identification of P. ginseng and P. notoginseng (Ahn et al 2009). Besides, many researchers have tried to identify ginseng species and varieties using SSR markers Ma et al 2007;Nguyen et al 2010;Bang et al 2011aBang et al , 2011b.…”

Section: Introductionmentioning

confidence: 99%

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

Um¹,

Mitsugi²,

Kim³

et al. 2016

Plant Breed. Biotech

View full text Add to dashboard Cite

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.

show abstract

Section: Introductionmentioning

confidence: 99%

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

Um¹,

Mitsugi²,

Kim³

et al. 2016

Plant Breed. Biotech

View full text Add to dashboard Cite

show abstract

“…This is likely also the situation for American ginseng, as implied in a previous study [27]. This might explain why intensive efforts to authenticate cultivated and wild forms by a variety of DNA markers at the intraspecific level have met with limited success [28][29][30][31]. Our results indicate that the 2 forms of ginseng are nonetheless epigenetically distinct if grown under different habitats.…”

Section: Resultsmentioning

confidence: 54%

Habitat-induced reciprocal transformation in the root phenotype of Oriental ginseng is associated with alteration in DNA methylation

Ngezahayo

Wang

et al. 2011

Chin. Sci. Bull.

View full text Add to dashboard Cite

Oriental ginseng is an important medicinal plant that grows in 2 major forms or ecotypes, wild and domesticated. Each form differs conspicuously in root phenotype, but can be converted from one type to another by habitat. Here we show that the habitat-induced transformation of ginseng root phenotype was accompanied by alteration in cytosine methylation at a large number of 5′-CCGG-3′ sites detected by the methylation-sensitive polymorphism (MSAP) marker. The collective CG and CHG methylation levels of all 4 landraces of the domesticated form were significantly lower than those of the wild form. Interestingly, artificially transplanted ginseng plants recreated in both directions the methylation levels (at least in CHG) of their natural counterparts. The methylation differences between the 2 ginseng ecotypes were validated at 2 isolated MSAP loci bearing homology to a 5S rRNA gene or a copia retrotransposon. Our results implicate a link between epigenetic variation and habitat-induced phenotypic flexibility in Oriental ginseng. cytosine methylation, epigenetics, habitat, Oriental ginseng, phenotypic flexibility Citation: Ngezahayo F, Wang X L, Yu X M, et al. Habitat-induced reciprocal transformation in the root phenotype of Oriental ginseng is associated with alteration in DNA methylation.

show abstract

“…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.…”

Section: Discussionmentioning

confidence: 99%

“…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].…”

Section: Introductionmentioning

confidence: 99%

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

Shah

Pham

et al. 2020

Preprint

View full text Add to dashboard Cite

Abstract Background: Understanding the genetic diversity in endangered species that occur in forest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers. Results: In this study, we employed Illumina HiSeqTM 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7,774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances. Conclusion: Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.

show abstract

Characterization of polymorphic microsatellite loci in cultivated and wildPanax ginseng

Cited by 22 publications

References 15 publications

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

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

Habitat-induced reciprocal transformation in the root phenotype of Oriental ginseng is associated with alteration in DNA methylation

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

Contact Info

Product

Resources

About