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

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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.

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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

N A :

Number of alleles

M AF :

Major allele frequency

SSR:

Simple sequence repeats

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Author information

Author notes

  1. Ick-Hyun Jo and Jwakyung Sung contributed equally to this work.

Authors and Affiliations

  1. Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Eumseong, 27709, Republic of Korea

    Ick-Hyun Jo, Chi-Eun Hong & Kyong-Hwan Bang

  2. Soil and Fertilizer Division, National Institute of Agricultural Science (NIAS), Rural Development Administration (RDA), Wanju, 55365, Republic of Korea

    Jwakyung Sung

  3. National Agrobiodiversity Center, National Institute of Agricultural Sciences (NIAS), Rural Development Administration (RDA), Jeonju, 54874, Republic of Korea

    Sebastin Raveendar

  4. Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, 28644, Republic of Korea

    Jong-Wook Chung

Authors
  1. Ick-Hyun Jo
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  2. Jwakyung Sung
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  3. Chi-Eun Hong
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  4. Sebastin Raveendar
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  5. Kyong-Hwan Bang
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  6. Jong-Wook Chung
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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.

Corresponding author

Correspondence to Jong-Wook Chung.

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Jo, IH., Sung, J., Hong, CE. et al. Development of cleaved amplified polymorphic sequence (CAPS) and high-resolution melting (HRM) markers from the chloroplast genome of Glycyrrhiza species. 3 Biotech 8, 220 (2018). https://doi.org/10.1007/s13205-018-1245-8

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