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

• DOI: 10.1007/s13580-021-00389-0
• Publication Date: 2021-10-11T09:21:36Z
• Authors: Serim Kim; Namsu Jo; Jinsu Gil; Sung Cheol Koo; Yurry Um; Chang Pyo Hong; Sin-Gi Park; Ok Tae Kim; Seong-Cheol Kim; Ho Bang Kim; Dong Hoon Lee; Byung-Hoon Jeong; Yi Lee
• Keywords: Primer (cosmetics)

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.