Molecular Genetic Diversity and Population Structure of Ginseng Germplasm in RDA-Genebank: Implications for Breeding and Conservation

Lee, Kyung Jun; Lee, Jung-Ro; Raveendar, Sebastin; Cho, Gyu-Taek; Hyun, Do Yoon

doi:10.3390/agronomy10010068

Cited by 22 publications

(13 citation statements)

References 51 publications

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“…Preserving the biological and genetic diversity from wild plant species were considered as an essential and effective way of conservation and sustainable use of medicinal plants ( Hamilton, 2008 ; Chen et al, 2016 ; Vining et al, 2020 ). Therefore, it is important to characterize genetic diversity and population structure of targeted species and its relatives, especially threatened ones ( Lee et al, 2018 , 2020 ). The genetic diversity in three studied species are relatively high compare to other medicinal herbs, for example, Coptis species ( Wang et al, 2020 ), Valeriana officinalis ( Boczkowska et al, 2020 ), Aconitum austrokoreense ( Lee et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Conservation Genomics of Wild Red Sage (Salvia miltiorrhiza) and Its Endangered Relatives in China: Population Structure and Interspecific Relationships Revealed From 2b-RAD Data

et al. 2021

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Red sage (Salvia miltiorrhiza) is a widely used medicinal plant for treatment of cardiovascular and cerebrovascular diseases. Because of excessive excavation by huge market demand and habitat loss by human activities, the wild population resources of S. miltiorrhiza have reduced drastically in recent years. Meanwhile, population status of two closely related species S. bowleyana and S. paramiltiorrhiza were in a trend of decreasing due to their potential replacement of S. miltiorrhiza. Particularly, S. paramiltiorrhiza was threatened and endemic to a small region in eastern China. However, to date there has been no conservation genetic research reported for wild S. miltiorrhiza population and its endangered relatives. Assess the wild germplasm diversity for S. miltiorrhiza and its related species would provide fundamental genetic background for cultivation and molecular breeding of this medicinally important species. In the present study, we investigated the genetic diversity, population structure, and intra/inter-specific differentiation of S. miltiorrhiza and above two relatives using 2b-RAD genome-wide genotyping method. By investigating 81 individuals of S. miltiorrhiza, 55 individuals of S. bowleyana and 15 individuals of S. paramiltiorrhiza from 23 locations in China, we obtained 23,928 SNPs in total. A comparatively high genetic diversity was observed in S. miltiorrhiza (π = 0.0788, He = 0.0783 ± 0.0007). The observed and expected heterozygosity in populations of these three species ranged from 0.0297 to 0.1481 and 0.0251 to 0.831, respectively. Two major lineage groups were detected in the examined S. miltiorrhiza populations. The results indicated that Dabie Mountain as a genetic diversity center of S. miltiorrhiza and possible complex inter-specific genetic exchange/hybridization occurred between S. miltiorrhiza and the two relatives. We suggest that strategic conservation and germplasm preservation should be considered not only for wild populations of S. miltiorrhiza, but also for its related S. bowleyana and S. paramiltiorrhiza.

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Section: Discussionmentioning

confidence: 99%

Conservation Genomics of Wild Red Sage (Salvia miltiorrhiza) and Its Endangered Relatives in China: Population Structure and Interspecific Relationships Revealed From 2b-RAD Data

et al. 2021

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“…The population structure was evaluated with a DAPC using the adegenet package for R software [69,70] according to Lee et al [33]. Bayesian-based clustering was performed using STRUCTURE v.2.3.4 [71], testing 3 independent runs with K from 1 to 11.…”

Section: Population Structure and Genetic Diversitymentioning

confidence: 99%

“…In the study of potato, random amplified polymorphic DNA (RAPD) [20][21][22], inter-retrotransposon amplified polymorphism (IRAP) [23], inter-simple sequence repeats (ISSRs) [24], amplified fragment length polymorphism (AFLP) [25][26][27], and simple sequence repeats (SSRs) [19,[25][26][27][28][29] have been used for the estimation of genetic diversity and genetic relationships. Among DNA markers, SSRs have been used successfully in polyploid species such as Brassica napus [30,31], Arachis [32], ginseng [33], tea [34], sweet potato [19], and potato species [28,35]. SSR markers have been preferred due to their co-dominance, random genome distribution, high level of polymorphism, simplicity of use, high clarity and reproducibility, low operational cost, hyper-variability, amenability to automation, ease of multiplexing, and use with low quality DNA [19,26,28,35].…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Population Structure of Potato Germplasm in RDA-Genebank: Utilization for Breeding and Conservation

Lee

Raveendar

Cho

et al. 2021

Plants

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Potato (Solanum tuberosum L.) is an important staple food and economic crop in many countries. It is of critical importance to understand the genetic diversity and population structure for effective collection, conservation, and utilization of potato germplasm. Thus, the objective of the present study was to investigate the genetic diversity and population structure of potato germplasm conserved in the National Agrobiodiversity Center (NAC) of South Korea to provide basic data for future preservation and breeding of potato genetic resources. A total of 24 simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 482 potato accessions. A total of 257 alleles were detected, with an average of 10.71 alleles per locus. Analysis of molecular variance showed that 97% of allelic diversity was attributed to individual accessions within the population, while only 3% was distributed among populations. Results of genetic structure analysis based on STRUCTURE and discriminant analysis of principal components revealed that 482 potato accessions could be divided into two main subpopulations. Accessions of subpopulation 1 mainly belonged to cultivars and breeding lines. Accessions of subpopulations 2 basically corresponded to wild relatives of potatoes. Results of this study provide useful information for potato improvement and conservation programs, although further studies are needed for a more accurate evaluation of genetic diversity and phenotypic traits of potatoes.

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“…Using SSR markers approach, 94.0%, 5.5% and 0.5% of 1109 accessions of Ginseng (Panax ginseng C.A. Meyer) in South Korea were landraces, breeding and cultivars lines, respectively, that were revealed from 56 different alleles from 12 clusters and indicated that average gene diversity was 0.49 (Lee et al, 2020). RAPD-PCR was utilized for investigating the genetic diversity of North American ginseng (P. quinquefolius L.) population in Ontario (Canada).…”

Section: Genetic Diversity Analysis Of Panaxmentioning

confidence: 99%

Molecular markers for analysis of plant genetic diversity

Nam¹,

Hang²,

Linh³

et al. 2021

Vietnam J. Biotechnol.

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Genetic diversity plays an important role in diversity conservation at multiple levels and supports to monitor and assess genetic variation. In plants, genetic diversity provides the ability to adapt and respond to environmental conditions that helps plants to survive through changing environments. Genetic diversity analyses based on molecular genetic markers are effective tools for conservation and reintroduction of rare and endangered species. In recent years, the development of various chemical and molecular techniques for studying genetic diversity has received great attention. While biochemical markers are primarily used in the diagnosis of pathogens, DNA markers have been developed and widely applied for identification of species and population based on the genotype of an organism that is more stable and not easily affected by the environmental factors. PCR-based molecular marker tools, such as restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPD), simple sequence repeats (SSRs) are used for analysing the difference in the targeted DNA sequences. With the rapid and robust development of genomic sequencing technology it is now possible to obtain and analyse DNA sequences of the whole genome of studied organisms. However, each type of DNA markers has different principles, as well as the pros and cons of specificity. In this article, we review methods and point out DNA markers, which are considered as reliable and widely used tools for the detection of genetic variation. In addition, we present the application of DNA marker in analysing genetic diversity of wild, domestic and medicinal plants, as well as some perspectives on the future of DNA marker’s application in the analysis of genetic diversity.

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Molecular Genetic Diversity and Population Structure of Ginseng Germplasm in RDA-Genebank: Implications for Breeding and Conservation

Cited by 22 publications

References 51 publications

Conservation Genomics of Wild Red Sage (Salvia miltiorrhiza) and Its Endangered Relatives in China: Population Structure and Interspecific Relationships Revealed From 2b-RAD Data

Conservation Genomics of Wild Red Sage (Salvia miltiorrhiza) and Its Endangered Relatives in China: Population Structure and Interspecific Relationships Revealed From 2b-RAD Data

Genetic Diversity and Population Structure of Potato Germplasm in RDA-Genebank: Utilization for Breeding and Conservation

Molecular markers for analysis of plant genetic diversity

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