Development of EST-SSR markers and their application in the analysis of the genetic diversity of Sophora japonica Linn

Abstract

We developed and identified a new set of polymorphic EST-SSR markers in Sophora japonica Linn. and analyzed their genetic diversity. Sophora japonica is a native species in China with ornamental and medicinal value. To explore the genetic diversity and the genetic differentiation of this species, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed based on de novo transcriptome sequencing. In total 35,844 unigenes were obtained with an average length of 923 bp. 7,520 potential EST-SSRs were identified from 6,084 unigenes, of which there was one SSR per 4.40 kb. The dinucleotide repeats were the most common SSRs. Based on the SSR-containing sequence, 30 superior EST-SSRs were developed from 100 primer pairs and further used to characterize the genetic diversity and genetic differentiation of S. japonica in five populations. The results showed that the genetic diversity of the five groups was high, but the frequency of gene exchange between the groups was not. The analysis of molecular variance (AMOVA) showed that the genetic variation within individuals was 86.10%, which means the individual variation was the more significant in selective breeding of S. japonica. Nei’s genetic identity and genetic distance analyses yielded a high genetic identity value of 0.896 and mean genetic distance of 0.1095 suggesting high similarities among the five tested S. japonica populations. Based on genetic distance, S. japonica populations were classified into two groups. The findings of this study provide insights into the genetic information of S. japonica and will guide the development of conservation and management strategies for existing S. japonica germplasm.