Development of Genome-Wide SSR Markers from Angelica gigas Nakai Using Next Generation Sequencing

Gil, Jinsu; Um, Yurry; Kim, Serim; Kim, Ok-Tae; Koo, Sung Cheol; Reddy, Chinreddy Subramanyam; Kim, Seong-Cheol; Hong, Chang Pyo; Park, Sin‐Gi; Kim, Ho Bang; Lee, Dong Hoon; Jeong, Byung‐Hoon; Chung, Jong‐Wook; Lee, Yi

doi:10.3390/genes8100238

Cited by 20 publications

(11 citation statements)

References 33 publications

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“…Forty‐eight polymorphic SSR loci with at least a 4‐bp motif containing a minimum of four repeats were selected by the comparison of the specific SSR loci of the four sequenced individuals using CLC Main Workbench (version 6.8.4, QIAGEN) according to Gil et al. (). SSR primers were designed using Primer3 (Untergasser et al., ) using the following conditions: length 18–26 bp, GC content 50–70%, and melting temperature 55–62°C.…”

Section: Methods and Resultsmentioning

confidence: 99%

Development of 18 microsatellite markers for Atractylodes japonica

Jeong

Chung

et al. 2020

Appl Plant Sci

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Premise Atractylodes japonica (Asteraceae) is endemic to East Asia, where its rhizomes are used in traditional medicine. To investigate the genetic diversity of this species, we developed polymorphic microsatellite markers. Methods and Results We obtained a total of 175,825 simple sequence repeat (SSR) loci using the Illumina HiSeq 2500 system. Eighteen polymorphic SSR primer pairs were selected to determine heterozygosity levels and allele numbers in 80 individuals from four A. japonica populations. The levels of observed and expected heterozygosity ranged from 0.000 to 1.000 and from 0.133 to 0.892, respectively. Cross‐amplification in the related species A. macrocephala and A. lancea was successful in 15 and 14 of the 18 markers, respectively. Conclusions These microsatellite markers will be useful for future studies involving A. japonica population genetics and breeding.

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Section: Methods and Resultsmentioning

confidence: 99%

Development of 18 microsatellite markers for Atractylodes japonica

Jeong

Chung

et al. 2020

Appl Plant Sci

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“…In previous studies, SSR markers have been widely used for genetic analyses of date palm 22 , barley 23 , angelica gigas 24 and maize 14 , 25 . In this study, 40 core SSR markers with proven performance for maize genotype identification 26 were used to genetically analyze 200 waxy maize accessions.…”

Section: Discussionmentioning

confidence: 99%

Sequence polymorphism of the waxy gene in waxy maize accessions and characterization of a new waxy allele

Luo

Shi

Yang

et al. 2020

Sci Rep

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Waxy maize has many excellent characteristics in terms of its nutritional and economic value. In recent decades, the waxy maize germplasm has increased dramatically as a result of different selection methods. We collected 200 waxy maize inbred accessions from different origins to study their genetic diversity and phylogenetic relationships, and to identify new waxy mutations. A simple sequence repeat (SSR) analysis revealed wide genetic diversity among the 200 waxy maize accessions. The maize accessions were clustered into three groups. We sequenced the waxy gene from the first to the 14th exon. Nucleotide variation analysis of 167 waxy maize and 14 flint maize lines revealed some nucleotide differences in the waxy gene among different waxy maize groups, and much narrower nucleotide diversity in waxy maize than in flint maize. In a phylogenetic analysis, waxy maize carrying the same mutation allele clustered together, and waxy maize carrying different mutation alleles distributed in different groups; waxy maize was intermixed with flint maize in each branch, and wx-D7 waxy maize separated significantly from waxy maize lines carrying wx-D10, wx-124 and wx-hAT mutant alleles. The wx-hAT was a new waxy mutation identified in this study. It consisted of a 2286-bp transposon inserted into the middle of exon three of the waxy gene. A PCR marker specific for the wx-hAT allele was developed. These results will be useful for the utilization and preservation of the waxy maize germplasm, and the PCR marker has potential uses in waxy maize breeding programs.

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“…Constraints associated with medicinal plant studies include the complexity of plant secondary metabolism, which is often unique to the species, and the lack of genomic information. Genome sequences have been provided for some species [ 83 , 84 ], but as the basis for secondary metabolism studies, transcriptomic analysis is of growing importance ( Figure 1 ) [ 85 ]. RNA sequencing-based transcriptomic data are now available for medicinal plants such as Dendrobium officinale [ 86 ], Dioscorea nipponica [ 87 ], Ephedra sinica [ 88 ], L. japonica [ 89 ], and Polygonum minus [ 90 ].…”

Section: Application Of Proteomics To Indigenous Plantsmentioning

confidence: 99%

Proteomic Contributions to Medicinal Plant Research: From Plant Metabolism to Pharmacological Action

2017

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Herbal medicine is a clinical practice of utilizing medicinal plant derivatives for therapeutic purposes. It has an enduring history worldwide and plays a significant role in the fight against various diseases. Herbal drug combinations often exhibit synergistic therapeutic action compared with single-constituent dosage, and can also enhance the cytotoxicity induced by chemotherapeutic drugs. To explore the mechanism underlying the pharmacological action of herbs, proteomic approaches have been applied to the physiology of medicinal plants and its effects on animals. This review article focuses on the existing proteomics-based medicinal plant research and discusses the following topics: (i) plant metabolic pathways that synthesize an array of bioactive compounds; (ii) pharmacological action of plants tested using in vivo and in vitro studies; and (iii) the application of proteomic approaches to indigenous plants with scarce sequence information. The accumulation of proteomic information in a biological or medicinal context may help in formulating the effective use of medicinal plants.

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Development of Genome-Wide SSR Markers from Angelica gigas Nakai Using Next Generation Sequencing

Cited by 20 publications

References 33 publications

Development of 18 microsatellite markers for Atractylodes japonica

Development of 18 microsatellite markers for Atractylodes japonica

Sequence polymorphism of the waxy gene in waxy maize accessions and characterization of a new waxy allele

Proteomic Contributions to Medicinal Plant Research: From Plant Metabolism to Pharmacological Action

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