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

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...

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Published in:Horticulture, environment and biotechnology 2021, Environment, and Biotechnology, 62(6), , pp.985-994
Main Authors: Kim, Serim, Jo, Namsu, Gil, Jinsu, Koo, Sung Cheol, Um, Yurry, Hong, Chang Pyo, Park, Sin-Gi, Kim, Ok Tae, Kim, Seong-Cheol, Kim, Ho Bang, Lee, Dong Hoon, Jeong, Byung-Hoon, Lee, Yi
Format: Article
Language:English
Subjects:
Agriculture
Biomedical and Life Sciences
Codonopsis lanceolata
DNA sequencing
Life Sciences
Markers
Medicinal plants
Next-generation sequencing
Nucleotide sequence
Nucleotides
Plant Breeding/Biotechnology
Plant Ecology
Plant Physiology
Polymorphism
Research Report
Simple sequence repeats
농학
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Summary: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 .
ISSN:2211-3452
2211-3460
DOI:10.1007/s13580-021-00389-0