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Development of genome-wide simple sequence repeat markers in Codonopsis lanceolata using next-generation sequencing

Abstract

Codonopsis lanceolata is an herbaceous perennial plant predominantly cultivated in East Asia and used for medicinal purposes. However, genetic information of C. lanceolata is lacking. Therefore, we sequenced genomic DNA using next-generation sequencing (NGS) and searched for simple sequence repeats (SSRs) to develop molecular markers in C. lanceolata. A total of 250,455 SSRs were identified, and di-nucleotides and tri-nucleotides accounted for the majority of all the SSRs. Among these SSRs, we designed 26,334 primer sets from di- to octa-nucleotide motifs. We used an in silico approach to investigate 2626 SSRs (tri- to penta-nucleotide motifs) and found 573 SSRs showing polymorphism. Of the 573 SSRs showing polymorphism in silico, we randomly selected 39 SSRs and verified polymorphism in 16 C. lanceolata accessions. The number of alleles ranged from 2 to 13, and the mean polymorphic information content value was 0.54. Therefore, we successfully designed 39 SSR markers for use in breeding and genetic studies of C. lanceolata.

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Data availability

Sequencing reads have been deposited in the National Agricultural Biotechnology Information Center (NABIC) Sequence Read Archive (BioProject ID: NN-7251, NN-7252, NN-7253, NN-7254, NN-7255, and NN-7256). Primer sequences have been deposited in the National Center for Biotechnology Information’s GenBank database; accession numbers are listed in Table 3.

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Acknowledgements

This work was carried out with the support of "Cooperative Research Program for Agriculture Science & Technology Development (Project No. PJ01588301)" Rural Development Administration, Republic of Korea.

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Authors

Contributions

SCK, OTK, S-CK, HBK, YL: conceived and designed the experiments, SK, JG, YU: performed the experiments, NJ, CPH, S-GP, YL: analyzed the data, DHL, B-HJ: contributed reagents/materials/analysis tools, SK, NJ, YL: wrote the paper.

Corresponding author

Correspondence to Yi Lee.

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The authors declare no conflict of interest. The founding sponsors had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

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Communicated by Inhwa Yeam.

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Cite this article

Kim, S., Jo, N., Gil, J. et al. Development of genome-wide simple sequence repeat markers in Codonopsis lanceolata using next-generation sequencing. Hortic. Environ. Biotechnol. 62, 985–993 (2021). https://doi.org/10.1007/s13580-021-00389-0

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Keywords

  • Codonopsis lanceolata
  • Marker
  • Medicinal plant
  • Next-generation sequencing
  • Simple sequence repeat