3 Biotech

, 8:220 | Cite as

Development of cleaved amplified polymorphic sequence (CAPS) and high-resolution melting (HRM) markers from the chloroplast genome of Glycyrrhiza species

  • Ick-Hyun Jo
  • Jwakyung Sung
  • Chi-Eun Hong
  • Sebastin Raveendar
  • Kyong-Hwan Bang
  • Jong-Wook Chung
Original Article
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Abstract

Licorice (Glycyrrhiza glabra) is an important medicinal crop often used as health foods or medicine worldwide. The molecular genetics of licorice is under scarce owing to lack of molecular markers. Here, we have developed cleaved amplified polymorphic sequence (CAPS) and high-resolution melting (HRM) markers based on single nucleotide polymorphisms (SNP) by comparing the chloroplast genomes of two Glycyrrhiza species (G. glabra and G. lepidota). The CAPS and HRM markers were tested for diversity analysis with 24 Glycyrrhiza accessions. The restriction profiles generated with CAPS markers classified the accessions (2–4 genotypes) and melting curves (2–3) were obtained from the HRM markers. The number of alleles and major allele frequency were 2−6 and 0.31–0.92, respectively. The genetic distance and polymorphism information content values were 0.16–0.76 and 0.15–0.72, respectively. The phylogenetic relationships among the 24 accessions were estimated using a dendrogram, which classified them into four clades. Except clade III, the remaining three clades included the same species, confirming interspecies genetic correlation. These 18 CAPS and HRM markers might be helpful for genetic diversity assessment and rapid identification of licorice species.

Keywords

Licorice Genetic diversity SNP CAPS HRM 

Abbreviations

SNP

Single nucleotide polymorphism

CAPS

Cleaved amplified polymorphic sequence

HRM

High-resolution melting

INDEL

Insertion and deletion

GD

Genetic distance

PIC

Polymorphism information content

NA

Number of alleles

MAF

Major allele frequency

SSR

Simple sequence repeats

Notes

Author contributions

I-HJ and JS participated in the study design, coordinated the experiment, and drafted the manuscript; C-EH, SR, and K-HB performed the experiments; J-WC participated in the study design, collected samples, analyzed genetic diversity, and coordinated the draft of the manuscript. All authors critically read and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Ick-Hyun Jo
    • 1
  • Jwakyung Sung
    • 2
  • Chi-Eun Hong
    • 1
  • Sebastin Raveendar
    • 3
  • Kyong-Hwan Bang
    • 1
  • Jong-Wook Chung
    • 4
  1. 1.Department of Herbal Crop ResearchNational Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA)EumseongRepublic of Korea
  2. 2.Soil and Fertilizer DivisionNational Institute of Agricultural Science (NIAS), Rural Development Administration (RDA)WanjuRepublic of Korea
  3. 3.National Agrobiodiversity Center, National Institute of Agricultural Sciences (NIAS), Rural Development Administration (RDA)JeonjuRepublic of Korea
  4. 4.Department of Industrial Plant Science and TechnologyChungbuk National UniversityCheongjuRepublic of Korea

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