EST-SSR markers development and application in an important medicinal plant, Schisandra chinensis (Schisandraceae)

Abstract

Schisandra chinensis, classed as a climbing woody vine, is representative of the Schisandraceae family regarded as a significant plant in Chinese herbal medicine. However, the application of molecular breeding is constrained by the fact that the number of genetic markers is small for this species. In this study, transcriptome sequencing of S. chinensis was performed using the Illumina HiSeq platform to construct a library of expressed sequence tag-simple sequence repeat (EST-SSR) markers. A total of 59,786 unigenes were obtained on the basis of 8.57 Gbp clean data. A total of 3460 putative SSR sites were detected with a frequency of 5.79%. The predominant type of repeat markers was dinucleotide (64.54%), followed by trinucleotide (23.87%), hexanucleotide (0.90%), tetranucleotide (0.12%) and pentanucleotide (0.40%). Besides, 50 pairs of EST-SSR primers were randomly selected for verification, among which 14 pairs (28%) showed polymorphism in 42 different types of S. chinensis accessions. The mean values of Na, Ne, PIC, Ho, He and SI were 2.71, 1.7642, 0.4295, 0.6016, 0.3934 and 0.6078, respectively. All of the 42 accessions were successfully identified and formed four major clusters, indicating that the EST-SSR markers are applicable for genetic diversity analysis and identification in S. chinensis. According to the result, the transcriptome data are an effective resource for developing SSR markers. These markers can provide a basis for the identification of S. chinensis accessions, genetic diversity analysis, the conservation and construction of genetic linkage maps as part of selective breeding and the conservation efforts for this valuable plant.