Research Article

SSR Molecular Markers Development Based on Whole Genome Sequences in Glycyrrhiza uralensis Fisch.  

Haixian Zhan , Yingli Wang , Chenhui Du , Dan Zhang , Rui Li , Mengru Yang , Shuosheng Zhang
School of Chinese Materia Medica and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong, 030619, China
Author    Correspondence author
Medicinal Plant Research, 2020, Vol. 10, No. 4   doi: 10.5376/mpr.2020.10.0004
Received: 26 May, 2020    Accepted: 11 Jun., 2020    Published: 30 Jun., 2020
© 2020 BioPublisher Publishing Platform
This article was first published in Molecular Plant Breeding in Chinese, and here was authorized to translate and publish the paper in English under the terms of Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

Zhan H.X., Wang Y.L., Du C.H., Zhang D., Li R., Yang M.R., and Zhang S.S., 2020, SSR molecular markers development based on whole genome sequences in Glycyrrhiza uralensis Fisch., Medicinal Plant Research, 10(4): 1-8 (doi: 10.5376/mpr.2020.10.0004)

Abstract

It is different in terms of active ingredients from various sources and origins on Glycyrrhiza Linn.. The development of specific molecular markers is of great significance for identification of germplasm resources. In the study, simple sequence repeat (SSR) motifs were analyzed based on the whole genome data in Glycyrrhiza uralensis Fisch.. SSRs were identified with MISA tool in all scaffold sequences. Suitable SSRs were used to design primers by using Primer3-2.4.0 software and 100 pairs of SSR primers were randomly utilized for the validity of molecular markers. The results showed 193 207 SSRs were detected from the whole genome sequence of G. uralensis distributed in 9 250 scaffolds. Of these, mono-nucleotide repeat SSRs was the main type, accounting for 60.73%, followed by dinucleotide (26.11%) and trinucleotide repeat (10.95%). Of the 284 repeat motifs, A/T (58.28%), AG/CT (10.48%), AT/AT (10.48%), AC/GT (5.12%) and AAT/ATT (3.57%) were the main repeat base. In addition, SSR primers for 140294 SSRs were designed using Primer3-2.4.0 software. We eventually developed 701 302 pairs of SSR markers in G. uralensis. Subsequently, 100 pairs of SSR primers were randomly selected for the further verifying. PCR results indicated that 63 of them (63%) had amplified the target bands, and 12 pairs of primers could generate polymorphic bands in seven samples. A large number of SSR markers developed will be used for identification of Glycyrrhiza germplasm resources and future molecular marker assisted breeding.

Keywords
Glycyrrhiza uralensis Fisch.; Genome; Repetitive sequence; SSR marker; Development
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