Skip to main content
SpringerLink
Log in

Development of Simple Sequence Repeat Markers from Functional Genes and Establishment of Molecular Identity for Tree Peony

  • Original Article
  • Published:
Journal of Plant Biochemistry and Biotechnology Aims and scope Submit manuscript

Abstract

Gene-derived simple sequence repeats (genic SSRs), also known as functional markers, are generally superior to random markers because they are located in genes and therefore may affect gene expression or function. However, extremely limited genic SSRs are available for tree peony. We used the functional gene sequences available from Paeonia to develop genic SSRs. A total of 132 SSR loci were identified from 35 cDNA sequences, of which trinucleotide (58, 43.9%) and hexanucleotide repeat (37, 28.0%) were dominant. Moreover, 121 primer pairs were successfully designed and synthesized, of which 49 primer pairs (40.5%) provided efficient and reliable amplification. By screening 16 tree peony varieties, we developed eight polymorphic genic SSRs with 37 alleles, ranging from 2 to 11 for each marker. Transferability analysis indicated that 100% of the genic SSRs could be amplified in eight other Paeonia samples. Based on eight polymorphic genic SSRs and 12 polymorphic EST-SSRs developed by predecessors, the molecular identity of 190 tree peony cultivars was constructed by capillary electrophoresis. The results showed that 146 alleles and 338 genotypes were detected, with 2–13 alleles and 3–36 genotypes for each marker. All cultivars were completely identified and exhibited unique DNA identity. In addition, the identification efficiency of different primers combinations was analyzed, and 190 germplasms were identified using 6 core primers. This study provides valuable genic SSR resources for marker-assisted selection breeding of the genus Paeonia. The DNA identity of cultivars is of great significance for the protection, utilization and management of tree peony resources.

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

Similar content being viewed by others

Abbreviations

MAS:

Marker-assisted selection

SSR:

Simple sequence repeat

RFLP:

Restriction fragment length polymorphism

AFLP:

Amplified fragment length polymorphism

RAPD:

Random amplified polymorphic DNA

ISSR:

Inter-simple sequence repeat

SRAP:

Sequence-related amplified polymorphism

CDDP:

Conserved DNA-derived polymorphism

SNP:

Single nucleotide polymorphism

PCR:

Polymerase chain reaction

EST:

Expressed sequence tag

QTL:

Quantitative trait loci

cDNA:

Complementary DNA

References

  • Andreas H, Maria B, Kornel B, Dieter K, Silvia F (2011) Microsatellite markers in the tree peony, Paeonia suffruticosa (Paeoniaceae.). Am J Bot 97(6):e42–e44

    Google Scholar 

  • Button P (2008) International union for the protection of new varieties of plants (UPOV) recommendations on varieties denominations. Acta Hortic 799:191–200

    Article  Google Scholar 

  • Chan YM, Twyford AD, Tnah LH, Lee CT (2015) Characterisation of EST-SSR markers for begonia maxwelliana (begoniaceae) and cross-amplification in 23 species from 7 asian sections. Sci Hortic 190:70–74

    Article  CAS  Google Scholar 

  • Chandra A, Grisham MP, Pan YB, Mcintyre CL (2014) Allelic divergence and cultivar-specific SSR alleles revealed by capillary electrophoresis using fluorescence-labeled ssr markers in sugarcane. Genome 57(6):363–372

    Article  CAS  PubMed  Google Scholar 

  • Chen XB, Xie YH, Sun XM (2015) Development and characterization of polymorphic genic-SSR markers in Larix kaempferi. Molecules 20(4):6060–6067

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cheng FY (2007) Advances in the breeding of tree peonies and a cultivar system for the cultivar group. Int J Plant Breed 1(2):89–104

    Google Scholar 

  • Du QZ, Zhang DQ, Li BL (2012) Development of 15 novel microsatellite markers from cellulose synthase genes in Populus tomentosa (salicaceae). Am J Bot 99(2):e46–e48

    Article  PubMed  Google Scholar 

  • Du QZ, Pan W, Xu B, Li BL, Zhang DQ (2013) Polymorphic simple sequence repeat (SSR) loci within cellulose synthase (PtoCesA) genes are associated with growth and wood properties in Populus tomentosa. New Phytol 197(3):763–776

    Article  CAS  PubMed  Google Scholar 

  • Gai SP, Zhang YX, Mu P, Liu CY, Liu S, Dong L, Zheng GS (2012) Transcriptome analysis of tree peony during chilling requirement fulfillment: assembling, annotation and markers discovering. Gene 497(2):256–262

    Article  CAS  PubMed  Google Scholar 

  • Gao YF, Liu Z, Wang K, Wang DJ, Gong X, Liu LJ (2015) Establishment of molecular ID for some apple germplasm resources. Scientia Agricultura Sinica 48(19):3887–3898

    CAS  Google Scholar 

  • Guo LL, Li MY, Guo DL, Ma HL, Zhang LX, Hou XG (2018) Genetic diversity assessment and cluster analysis of phenotypic traits of Paeonia suffruticosa cultivar groups based on SSR marker. Acta Agric Shanghai 34(2):43–49

    Google Scholar 

  • Qi G, Wang JX, Su LZ, Lv W, Sun YH, Li Y (2017) Development and Evaluation of a novel set of EST-SSR markers based on transcriptome sequences of black locust (Robinia pseudoacacia L). Genes 1:1

    Google Scholar 

  • He D, Wu FF, Zhang JR, Xie DB, Li XK, Liu YP, Jia Y, He SL (2019) Analysis of SSR information in transcriptome and development of molecu- lar markers in Paeonia suffruticosa. Jiangsu J Agric Sci 35(6):1428–1433

    Google Scholar 

  • Hou XG, Yin WL, Li JJ, Wang HF (2006) Phylogenetic relationship of dwarf tree peony cultivars by AFLP analysis. J Beijing For Univ 28(5):77–81

    Google Scholar 

  • Homolka A, Berenyi M, Burg K et al (2010) Microsatellite markers in the tree peony, Paeonia suffruticosa (Paeoniaceae). Am J Bot 97(6):e42–e44

    Article  CAS  PubMed  Google Scholar 

  • Li C, Yang YY, Zhang KZ, Li SS, Shang HY, Wu J (2019) Selection of tea cultivars and establishment of SSR molecular identification for tree peony. Mol Plant Breed 17(20):6724–6735

    Google Scholar 

  • Li H, Li D, Chen A,Tang H, Huang S (2016) Characterization of the kenaf (Hibiscus cannabinus) global transcriptome using illumina paired-end sequencing and development of EST-SSR markers. Plos One 11(3).

  • Li YC, Korol AB, Fahima T (2004) Microsatellites within genes: structure, function, and evolution. Mol Biol Evol 21(6):99–1007

    Article  Google Scholar 

  • Li YH, Yu XL, Ma HP, Gao K, Liu MX (2020) Analysis on genetic diversity of ISSR from different Paeonia suffruticosa Cultivars. Biotechnol Bull 36(04):78–83

    Google Scholar 

  • Liu HB, You YN, Zhu ZX, Zheng XF, Huang JB, Hu ZL, Diao Y (2015) Leaf transcriptome analysis and development of SSR markers in water chestnut (eleocharis dulcis). Genet Mol Res 14(3):8314–8325

    Article  CAS  PubMed  Google Scholar 

  • Luan MB, Chen BF, Zou ZZ, Zhu JJ, Wang XF, Xu Y, Sun ZM, Chen JH (2015) Molecular identity of ramie germplasms using simple sequence repeat markers. Genet Mol Res 14(1):2302–2311

    Article  CAS  PubMed  Google Scholar 

  • Manosh B, Ujjal N, Jewel H, Mita B, Sathishkumar N, Abdul KM, Kim HT, Park JI, Kang JG, Nou IS (2018) Exploration and exploitation of novel ssr markers for candidate transcription factor genes in lilium species. Genes 9(2):97

    Article  Google Scholar 

  • Shi QQ, Wang Y, Zhou L, Huang GW (2012) Optimization of SRAP-PCR system and selection of primers for Paeonia suffruticosa Andr.based on capillary electrophoresis. Acta Agric Univ Jiangxiensis (Nat Sci Ed) 34(1): 158–164

  • Souframanien J, Reddy KS (2015) De novo assembly, characterization of immature seed transcriptome and development of genic-SSR markers in black gram [Vigna mungo (L) Hepper]. PLoS ONE 10(6):e0128748

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang HL, Yan AL, Sun L, Zhang GJ, Wang XY, Xu HY (2016) Molecular ID establishment of 13 chinese newly-developed grape cultivars. Biotechnol Bull 32(4):137–142

    Google Scholar 

  • Wang JX, Xia T, Zhang JM, Zhou SL (2009) Isolation and characterization of fourteen microsatellites from a tree peony (Paeonia suffruticosa). Conserv Genet 10(4):1029–1031

    Article  CAS  Google Scholar 

  • Wang LY (1998) Chinese tree peony. China Forestry Publishing House, Beijing

    Google Scholar 

  • Wang XM (2011) Inter-simple sequence repeats (ISSR) molecular fingerprinting markers for authenticating the genuine species of rhubarb. J Med Plants Res 5(5):758–764

    CAS  Google Scholar 

  • Wu J, Cai CF, Cheng FY, Cui HL, Zhou H (2014) Characterisation and development of EST-SSR markers in tree peony using transcriptome sequences. Mol Breed 34(4):1853–1866

    Article  CAS  Google Scholar 

  • Wu J, Cheng FY, Zhong Y, Jie X (2016) Association mapping for floral traits in cultivated paeonia rockii based on SSR markers. Mol Genet Genom 292(1):1–14

    Google Scholar 

  • Wu JZ, Zhao Q, Wu GW, Zhang SQ, Jiang TB (2017) Development of novel SSR markers for flax (linum usitatissimum l) using reduced-representation genome sequencing. Front Plant Sci 7:1

    Article  Google Scholar 

  • Xu LF, Ge L, Yuan SX, Ren JF, Yuan YY, Li YN, Liu C, Ming J (2014) Using the fluorescent labeled SSR markers to establish molecular identity of lily germplasms. Acta Hortic Sinica 41(10):2055–2064

    CAS  Google Scholar 

  • Xu X, Zhou C, Zhang Y, Zhang W, Gan X, Zhang HX, Guo Y, Gan SM (2018) A novel set of 223 EST-SSR markers in casuarina l ex adans: polymorphisms, cross-species transferability, and utility for commercial clone genotyping. Tree Genetics and Genomes 14(2):30

    Article  Google Scholar 

  • Yan ZZ, Wu F, Luo K, Zhao YF, Yan Q, Zhang YF, Wang YR, Zhang JY (2017) Cross-species transferability of EST-SSR markers developed from the transcriptome of melilotus and their application to population genetics research. Sci Rep 7(8):1

    Google Scholar 

  • Yang ZG, Zhu D, Luo B (2015) Construction of fingerprint and analysis of genetic diversity with EST-SSR markers for thirty-seven peony cultivars in Shandong. Northern Hortic 7:77–81

    Article  Google Scholar 

  • Yeh FC, Yang RC, Boyle TBJ, Ye ZH, Mao JX (1999) Popgene version 1.32, the user-friendly shareware for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton, USA

  • Yin Y, Zhao JH, An W, Li YL, He J, Cao YL (2018) Establishment of molecular identity for wolfberry cultivars based on SSR markers. Biotechnol Bull 34(9):195–201

    Google Scholar 

  • Yu HP, Cheng FY, Zhong Y, Cai CF, Wu J, Cui HL (2013) Development of simple sequence repeat (SSR) markers from Paeonia ostii to study the genetic relationships among tree peonies (Paeoniaceae). Sci Hortic 164:58–64

    Article  CAS  Google Scholar 

  • Yuan JH, Cheng FY, Zhou SL (2010) Hybrid origin of Paeonia × yananensis revealed by microsatellite markers, chloroplast gene se-quences, and morphological characteristics. Int J Plant Sci 171:409–420

    Article  CAS  Google Scholar 

  • Zhai LJ (2018) Study on the genetic diversity and evolutionary relationship of wild tree peony in the subsect vaginate. Northwest A&F University, Xianyang

    Google Scholar 

  • Zhai LJ, Shi QQ, Li X, Luo XY, Niu LX, Zhang YL (2019) Genetic diversity analysis of peony in yanan wanhua mountain based on phenotype traits and CDDP molecular marker. Jiangsu Agric Sci 47(2):95–101

    Google Scholar 

  • Zhang QY, Yu R, Xie LH, Mahbubur RM, Aruna K, Niu LX, Zhang YL (2018) Fatty acid and associated gene expression analyses of three tree peony species reveal key genes for α-linolenic acid synthesis in Seeds. Front Plant Sci 9:1

    Google Scholar 

  • Zhang X (2011) Research about RAPD of genetic relationship and genetic diversity for partial peony in Peng zhou area. Sichuan Agricultural University, Sichuan

    Google Scholar 

  • Zhong Y, Cheng FY, Wu J (2016) The study advances on functional genes in tree peony (Paeonia sect: Moutan). Mol Plant Breed 9:2353–2364

    Google Scholar 

Download references

Acknowledgements

This work was supported by the National Natural Science Foundation of China (No. 31800602) and the Outstanding Talent Project of the Organizational Department of the Beijing Municipal Committee (2017000020124G120), and the Project of Construction of Innovative Teams and Teacher Career Development for Universities and Colleges Under Beijing Municipality (IDHT20180509).

Author information

Authors and Affiliations

  1. Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing University of Agriculture, Beijing, 102206, People’s Republic of China

    Jing Wu

  2. College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People’s Republic of China

    Cheng Li, Jing Wu, Yunyao Yang & Kezhong Zhang

  3. Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, People’s Republic of China

    Jing Wu & Kezhong Zhang

  4. Luoyang Suitangcheng Heritage Bontanical Garden, Luoyang, 471000, Henan, People’s Republic of China

    Qingdao Li

Authors
  1. Cheng Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jing Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Qingdao Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yunyao Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kezhong Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Jing Wu and Kezhong Zhang conceived and designed the study. Cheng Li and Yunyao Yang performed the experiments. Qingdao Li provided experimental materials of Paeonia for this study. Cheng Li and Jing Wu wrote the paper, reviewed and edited the manuscript. All authors read and approved the manuscript.

Corresponding authors

Correspondence to Jing Wu or Kezhong Zhang.

Ethics declarations

Conflict of interest

All the authors declare that they have no conflict of interest.

Additional information

Publisher's Note

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

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Li, C., Wu, J., Li, Q. et al. Development of Simple Sequence Repeat Markers from Functional Genes and Establishment of Molecular Identity for Tree Peony. J. Plant Biochem. Biotechnol. 31, 22–36 (2022). https://doi.org/10.1007/s13562-021-00651-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13562-021-00651-7

Keywords

Search

Navigation