Skip to main content
SpringerLink
Log in

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

  • Original Article
  • Published:
Trees Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Abdelhady MIS, Kamal AM, Othman SM et al (2015) Total polyphenolic content, antioxidant, cytotoxic, antidiabetic activities, and polyphenolic compounds of Sophora japonica grown in Egypt. Med Chem Res 24:482–495

    Article  CAS  Google Scholar 

  • Benbouza H, Jacquemin JM, Baudoin JP, Mergeai G (2006) Optimization of a reliable, fast, cheap and sensitive silver staining method to detect SSR markers in polyacrylamide gels. Biotechnol Agron Soc 10:77–81

    CAS  Google Scholar 

  • Biswas MK, Chai LJ, Mayer CU et al (2012) Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus. Mol Biol Rep 39:5373–5386

    Article  CAS  PubMed  Google Scholar 

  • Cai QF, Li B, Lin FR et al (2018) De novo sequencing and assembly analysis of transcriptome in Pinus bungeana Zucc. ex Endl. Forests 9:156

    Article  Google Scholar 

  • Chen HL, Liu LP, Wang LX et al (2015a) Development and validation of EST-SSR Markers from the transcriptome of Adzuki bean (Vigna angularis). PLoS ONE 10:e0131939

    Article  PubMed  PubMed Central  Google Scholar 

  • Chen HL, Wang LX, Liu XY et al (2017) De novo transcriptomic analysis of cowpea (Vigna unguiculata.) for genic SSR marker development. BMC Genet 18:65.

  • Chen HL, Wang LX, Wang SH et al (2015b) Transcriptome Sequencing of Mung Bean (Vigna radiate L.) Genes and the Identification of EST-SSR Markers. PLoS One 10:e0120273

  • Chen LY, Cao YN, Yuan N et al (2015c) Characterization of transcriptome and development of novel EST-SSR makers based on next-generation sequencing technology in Neolitsea sericea (Lauraceae) endemic to East Asian land-bridge islands. Mol Breed 35:187

    Article  CAS  Google Scholar 

  • Choudhary S, Sethy NK, Shokeen B, Bhatia S (2009) Development of chickpea EST-SSR markers and analysis of allelic variation across related species. TAG 118:591–608

    Article  CAS  PubMed  Google Scholar 

  • Conesa A, Gotz S, Garcia-Gomez JM et al (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676

    Article  CAS  PubMed  Google Scholar 

  • Dumolin S, Demesure B, Petit RJ (1995) Inheritance of chloroplast and mitochondrial genomes in pedunculate oak investigated with an efficient PCR method. TAG 91:1253–1256

    Article  CAS  PubMed  Google Scholar 

  • Dutta S, Kumawat G, Singh BP et al (2011) Development of genic-SSR markers by deep transcriptome sequencing in pigeon pea [Cajanus cajan]. BMC Plant Biol 11:10–17

    Article  Google Scholar 

  • Editorial board of Chinese flora of the Chinese Academy of Sciences (1990) Chinese flora forty-second volume second, Leguminosae

  • Editorial board of Kunming Institute of Botany (2006) Chinese Academy of Sciences. Flora of Yunnan

  • Evanno GS, Regnaut SJ, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Ferrer MM, Eguiarte LE, Montana C (2004) Genetic structure and outcrossing rates in Flourensia cernua (Asteraceae) growing at different densities in the South-western Chihuahuan Desert. Ann Bot 94:419–426

    Article  PubMed  PubMed Central  Google Scholar 

  • Forest F, Grenyer R, Rouget M et al (2007) Preserving the evolutionary potential of floras in biodiversity hotspots. Nature 445:757–760

    Article  CAS  PubMed  Google Scholar 

  • Gadissa F, Tesfaye K, Dagne K, Geleta M (2018) Genetic diversity and population structure analyses of Plectranthus edulis (Vatke) Agnew collections from diverse agro-ecologies in Ethiopia using newly developed EST-SSRs marker system. BMC Genet

  • Gambino G, Perrone I, Gribaudo I (2010) A Rapid and effective method for RNA extraction from different tissues of grapevine and other woody plants. Phytochem Anal 19:520–525

    Article  Google Scholar 

  • Ge J (2011) Study on Genistein Preparation from Sophoricoside in Sophora japonica by Schizophyllum commune. Master’s thesis Huazhong U Sci Tec

  • Ge Y, Tan L, Wu B et al (2019) Transcriptome sequencing of different avocado ecotypes: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers. Forests 10:411

    Article  Google Scholar 

  • Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hamrick JL, Godt MJW (1990) Allozyme diversity in plant species. Plant Popul Genet Breeding Genet Resour 43–63

  • Heenan P, Mitchell C, Houliston G (2018) Genetic variation and hybridisation among eight species of kowhai (Sophora: Fabaceae) from New Zealand revealed by microsatellite markers. Genes 9:11

    Article  Google Scholar 

  • Jia XP, Deng YM, Sun XB et al (2016) De novo assembly of the transcriptome of Neottopteris nidususing Illumina paired-end sequencing and development of EST-SSR markers. Mol Breed 36:94

    Article  Google Scholar 

  • Kalionwski ST (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16

  • Lee HY, Ro NY, Jeong HJ et al (2016) Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm. BMC Genet 17:142

    Article  PubMed  PubMed Central  Google Scholar 

  • Li W, Zhang CP, Jiang XQ et al (2018a) De novo transcriptomic analysis and development of EST–SSRs for Styrax japonicus. Forests 9

  • Li X, Li M, Hou L et al (2018) De novo transcriptome assembly and population genetic analyses for an endangered chinese endemic acer miaotaiense (Aceraceae). Genes 9:378

    Article  PubMed Central  Google Scholar 

  • Liu FM, Hong Z, Yang Z-J et al (2019a) De novo transcriptome analysis of Dalbergia odorifera and transferability of SSR markers developed from the transcriptome. Forests 10

  • Liu FM, Hong Z, Yang ZJ et al (2019) De novo transcriptome analysis of Dalbergia odorifera and transferability of SSR markers developed from the transcriptome. Forests 10:98

    Article  Google Scholar 

  • Liu GL, Liang HY, Liu XY (2003) Study on photosynthesis characteristic of Sophora japonica L. J Agric U HeB 26:68–70

    CAS  Google Scholar 

  • Ma S, Dong W, Lyu T, Lyu Y (2019) An RNA sequencing transcriptome analysis and development of EST-SSR markers in Chinese Hawthorn through Illumina sequencing. Forests 10

  • Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200

    Article  CAS  PubMed  Google Scholar 

  • Nybom H (2004) Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Mol Ecol 13:1143–1155

    Article  CAS  PubMed  Google Scholar 

  • Pablo FC, Douglas AS, Yang LM et al (2010) Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L). BMC Genom 11:569

    Article  Google Scholar 

  • Peakall R, Smouse PE (2005) GenAIEx 6: genetic analysis in excel. Population genetic software for teaching and research. Mol Ecol Resour 6:288–295

    Article  Google Scholar 

  • Peakall R, Smouse PE (2012) GenAlEx6.5. Bioinformatics 28:2537–2539

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Powell W, Morgante M, Andre C et al (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238

    Article  CAS  Google Scholar 

  • Rohlf FJ (1998) NTSYS-pc: numerical taxonomy and multivariate analysis system, version 2. 10e. NewYork: Exeter Software, Setauket

  • Sun RX, Zhang CH, Zheng YQ et al (2016) Molecular identification and genetic variation of varieties of Styphnolobium japonicum (Fabaceae) using SRAP markers. Genetics Mol Res 15 (2)

  • Schaal BA, Hayworth DA, Olsen KM et al (1998) Phylogeographic studies in plants: problems and prospects. Mol Ecol 7:465–474

    Article  Google Scholar 

  • Shu WJ, Jm T, Chen ZY et al (2019) Analysis of genetic diversity and population structure in Sophora japonica Linn. in China with newly developed SSR markers. Plant Mol Biol Rep 37:87–97

    Article  CAS  Google Scholar 

  • Slatkin (1987) Gene flow and the geographic structure of natural populations. Science 236:787–792

    Article  CAS  PubMed  Google Scholar 

  • Song W (2013) Study on genetic diversity of the ancient Sophora japonica. By SRAP analysis. Master’s thesis ShanD Agr U

  • Souframanien J, Sreenivasulu RK, Manoj P (2015) De novo assembly, characterization of immature seed transcriptome and development of genic-SSR markers in black gram [Vigna mungo]. PLoS ONE 10:e0128748

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Squirrell J, Hollingsworth PM, Woodhead ML et al (2003) How much effort is required to isolate nuclear microsatellites from plants? Mol Ecol 12:1339–1348

    Article  CAS  PubMed  Google Scholar 

  • Tang JM, Zhou R, Shi YC et al (2017) Optimization of ISSR-PCR reaction system and primer screening of Sophora japonica cv.jinhuai. Lishizhen. Med Mate Med Res 2747–2749

  • Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23(1):48–55

    Article  CAS  PubMed  Google Scholar 

  • Vatanparast M, Shetty P, Chopra R et al (2016) Transcriptome sequencing and marker development in winged bean (Psophocarpus tetragonolobus; Leguminosae). Sci Rep 6:29070

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang L, Kim KD, Gao D et al (2016) Analysis of simple sequence repeats in rice bean(Vigna umbellata) using an SSR-enriched library. Corp J: 40–47

  • Wang LX, Chen HL, Bai P et al (2015) The transferability and polymorphism of mung bean SSR markers in rice bean germplasm. Mol Breed 35:77

    Article  Google Scholar 

  • Wang Y, Zhou T, Li D et al (2019) The genetic diversity and population structure of Sophora alopecuroides (Faboideae) as determined by microsatellite markers developed from transcriptome. PLoS ONE 14(12):e0226100

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • White TL, Adams WT Neale DB (2014) Forest genetics. Forest genet

  • Xing W, Liao JY, Cai MM et al (2017) De novo assembly of transcriptome from Rhododendron latoucheae Franch using Illumina sequencing and development of new EST-SSR markers for genetic diversity analysis in Rhododendron. Tree Genet Genom 13:53

    Article  Google Scholar 

  • Yates SA, Swain MT, Hegarty MJ, Chernukin I (2014) De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification. BMC Genomics 15

  • Yeh FC, Yang RC, Boyle TBJ (1999) PopGene32, Microsoft Windows-based freeware for population genetic analysis, version 1.32. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton, Alberta, Canada

  • Ye J (2006) WEGO: a web tool for plotting GO annotations. 34:W293–W297.

  • Yoichi W, Sakaguchi S, Ueno S et al (2016) Development and characterization of EST log SR markers for the genus Rhododendron section Brachycalyx (Ericaceae). Plant Spec Biol. https://doi.org/10.1111/1442-1984.12155

    Article  Google Scholar 

  • Yoon HJ, Seo C-R, Kim M et al (2013) Dichloromethane extracts of Sophora japonica L. stimulate osteoblast differentiation in mesenchymal stem cells. Nutr Res 33:1053–1062

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y, Zhang X, Wang YH et al (2017) De novo assembly of transcriptome and development of novel EST-SSR markers in Rhododendron rex Lévl. through Illumina sequencing. Front Plant Sci 8:1664

  • Zhao Y (2012) Study on taxonomy and reproduction characteristics of Sophora japonica. Master’s thesis. ShanD Norm U

  • Zhou F, Wang J, Yang N (2015) Growth responses, antioxidant enzyme activities and lead accumulation of Sophora japonica and Platycladus orientalis seedlings under Pb and water stress. Plant Growth Regul 75:383–389

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This research was funded by “Collection, Preservation and Accurate Identification of Germplasm Resources of Precious Timber Tree Species” of the Shandong Provincial Agricultural Elite Varieties Project (2019LZGC01804). The authors thank the National Forest Genetic Resources Platform (NFGRP) for providing the Sophora japonica resources.

Author information

Author notes

  1. Yizeng Lu and Cuiping Zhang authors contributed equally to this work.

Authors and Affiliations

  1. College of Landscape Architecture and Forestry, Qingdao Agricultural University, Shandong Province, Qingdao, 266109, China

    Cuiping Zhang, Xueyun Li & Wei Li

  2. Shandong Provincial Center of Forest Tree Germplasm Resources, Shandong Province, Jinan, 250102, China

    Yizeng Lu

  3. Shandong Academy of Forest, Shandong Province, Jinan, 250102, China

    Yan Liang & Yinhua Wang

Authors
  1. Yizeng Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Cuiping Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xueyun Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yan Liang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yinhua Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Wei Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Wei Li.

Ethics declarations

Conflict of interest

The authors declare that they do not have any conflicts of interest.

Additional information

Communicated by J. Carlson.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Lu, Y., Zhang, C., Li, X. et al. Development of EST-SSR markers and their application in the analysis of the genetic diversity of Sophora japonica Linn. Trees 34, 1147–1156 (2020). https://doi.org/10.1007/s00468-020-01985-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00468-020-01985-w

Keywords

Search

Navigation