Development of EST-SSR markers and their application in the analysis of the genetic diversity of Sophora japonica Linn
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ORIGINAL ARTICLE
Development of EST‑SSR markers and their application in the analysis of the genetic diversity of Sophora japonica Linn Yizeng Lu2 · Cuiping Zhang1 · Xueyun Li1 · Yan Liang3 · Yinhua Wang3 · Wei Li1 Received: 29 November 2019 / Accepted: 30 April 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Key message We developed and identified a new set of polymorphic EST-SSR markers in Sophora japonica Linn. and analyzed their genetic diversity. Abstract 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. Keywords Sophora japonica · Illumina sequencing · EST-SSRs · Genetic diversity · Population structure
Introduction Communicated by J. Carlson. Yizeng Lu and Cuiping Zhang authors contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00468-020-01985-w) contains supplementary material, which is available to authorized users.
Sophora japonica Linn. is a deciduous tree species in genus Sophora, which belongs to subfamily Papilionoideae in the family Leguminosae S. japonica originated in China and is distributed in Japan, Vietnam, Korea, and widely cultivated in Europe and North America (Sciences 1990). At present, more than 25 varieties and cultivars of S. japonica
* Wei Li [email protected]
Yinhua Wang [email protected]
Yizeng Lu [email protected]
1
Cuiping Zhang [email protected]
College of Landscape Architecture and Forestry, Qingdao Agricultural University, Shandong Province, Qingdao 266109, China
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