Simple sequence repeat marker development fromCodonopsis lanceolataand genetic relation analysis

Abstract

This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.Abstract In this study, we developed 15 novel polymorphic simple sequence repeat (SSR) markers by SSR-enriched genomic library construction from Codonopsis lanceolata.We obtained a total of 226 non-redundant contig sequences from the assembly process and designed primer sets. These markers were applied to 53 accessions representing the cultivated C. lanceolata in South Korea. Fifteen markers were sufficiently polymorphic, and were used to analyze the genetic relationships between the cultivated C. lanceolata. One hundred three alleles of the 15 SSR markers ranged from 3 to 19 alleles at each locus, with an average of 6.87. By cluster analysis, we detected clear genetic differences in most of the accessions, with genetic distance varying from 0.73 to 0.93. Phylogenic analysis indicated that the accessions that were collected from the same area were distributed evenly in the phylogenetic tree. These results indicate that there is no correlative genetic relationship between geographic areas. These markers will be useful in differentiating C. lanceolata genetic resources and in selecting suitable lines for a systemic breeding program.

Development of genomic simple sequence repeat markers for Glycyrrhiza lepidota and cross-amplification of other Glycyrrhiza species

“…The mean PIC value of the SSR markers developed in the present study using wild ( G. lepidota and G. echinata ) and cultivated ( G. uralensis and G. glabra ) licorice accessions was 0.730, which is higher than that reported for other medicinal plants: 0.314 for Zingiber officinale (Pandotra et al, 2013), 0.57 for Codonopsis lanceolata (Kim et al, 2016), and 0.272 for Festuca arundinacea (Tehrani et al, 2009). These results showed that the SSR markers developed in the present study have a higher diversity than those developed for other species.…”

The application of DNA molecular markers in the study of Codonopsis species genetic variation, a review

“…For the first time, ten microsatellite polymorphic loci were developed for C. pilosula, and the polymorphism of each locus was evaluated, using 27 individuals from four geographically distant populations of the 33 primers pairs, a total of 14 effectively amplified the target regions and 10 displayed polymorphic banding patterns (49). The PCR-based microsatellite amplification enables to create a distinctive pattern and a particular description for an individual, because of that it was used to identify and authenticate plants showing inter-specific variation (50).…”

“…According to reports, it was indicated that C. pilosula transcriptome SSR is commonly used in China, as a total of 7327 SSRs were searched in the transcription group of C. pilosula, and by comparing the current frequency of C. pilosula SSR with other medicinal plants, C. pilosula frequency was lower than that of Salvia miltiorrhiza and higher than that of Ginseng (5). SSR markers were effectively identified and implemented to explore the genetic variation and the construction of the population in C. tangshen and C. pilosula (50). This technique was also used to study genomic variability in C. lanceolate (20).…”

“…SSR, EST-SSR, or SNP markers were suggested to be used to develop comprehensive genomics from plants without requiring genome reference (50). Consequently, DNA as a molecular marker has several benefits over classic phenotypic markers because the genetic structure is unique to each organism and is not influenced by time, physiological as well as ecological factors (20).…”

Characterization of Codonopsis pilosula subsp. tangshen plastome and comparative analysis of Codonopsis species

“…The application of DNA molecular markers in studying the genetic variation in Codonopsis has been reported [ 11 ] and showed that Codonopsis species were difficult to classify and discriminate using conventional markers. Previous studies have used nuclear internal transcribed spacer (nrITS) [ 12 ], microsatellite polymorphic loci [ 13 ], simple sequence repeats (SSRs) [ 14 ], inter simple sequence repeats (ISSR), random amplified polymorphic DNA (RAPD) [ 15 ], amplified fragment length polymorphism (AFLP), sequencing-based markers (SNP) to discriminate Codonopsis species. In particular, Hwang et al used the genetic information from the plastomes of Codonopsis lanceolata and Platycodon grandiflorus for molecular marker development.…”