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Characterisation and development of EST-SSR markers in tree peony using transcriptome sequences

Abstract

Tree peony is a well-known ornamental and medicinal plant in China, as well as a new crop that has been recently demonstrated to exhibit a great potential for edible oil production. However, only limited molecular markers are currently available in this species, which hinders its genetic and breeding studies. The objective of this study was to develop expressed sequence tag (EST)-simple sequence repeat (SSR) markers based on transcriptome sequences in tree peony. A total of 4,373 EST-SSRs were identified from 3,787 unigene sequences with an average of one SSR per 9.24 kb. Di-nucleotide repeats (46.26 %) were the most abundant type followed by tri-, hexa-, tetra-, and penta-nucleotide repeats. Moreover, 788 primer pairs were synthesised, out of which 373 primer pairs (47.3 %) produced successful amplifications, and 149 primer pairs (39.9 %) were polymorphic in both parents of one mapping population. The 30 polymorphic EST-SSR markers were randomly selected to assess polymorphism further in 36 tree peony accessions, in which the polymorphism information content values ranged from 0.36 to 0.85 with a mean of 0.69, thereby indicating a high level of informativeness. Transferability studies indicated that 95.3 % EST-SSR markers were transferable to nine other Paeonia species, thereby expanding their utility. In addition, as a demonstration of utility, a genetic relationship study was performed in 56 accessions. Cluster analysis using the neighbour-joining tree method demonstrated that major clusters corresponded to known pedigree trees. Thus, these newly developed markers will be valuable in facilitating marker-assisted selection breeding in tree peony and its related species.

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References

  • Agarwal M, Shrivastava N, Padh H (2008) Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep 27:617–631

    CAS  PubMed  Google Scholar 

  • Aggarwal RK, Hendre PS, Varshney RK, Bhat PR, Singh L, Krishnakumar V (2007) Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theor Appl Genet 114(2):359–372

    CAS  PubMed  Google Scholar 

  • Agrama HA, Eizenga GC, Yan W (2007) Association mapping of yield and its components in rice cultivars. Mol Breed 19(4):341–356

    Google Scholar 

  • Bostein D, White RL, Sholnick M, David RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphism. Am J Hum Genet 32:314–331

    Google Scholar 

  • Bouck AMY, Vision T (2007) The molecular ecologist’s guide to expressed sequence tags. Mol Ecol 16(5):907–924

    CAS  PubMed  Google Scholar 

  • Bushman BS, Larson SR, Tuna M et al (2011) Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability. Theo Appl Genet 123(1):119–129

    Google Scholar 

  • Chen M, Wu J, Wang L et al (2014) Development of mapped simple sequence repeat markers from common bean (Phaseolus vulgaris L.) based on genome sequences of a Chinese landrace and diversity evaluation. Mol Breed 33:489–496

    CAS  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 

  • Chung JW, Kim TS, Sundan S et al (2014) New cDNA-SSR markers in the narrow-leaved vetch (Vicia sativa subsp. nigra) using 454 pyrosequencing. Mol Breed 33:749–754

    CAS  Google Scholar 

  • Cordeiro GM, Casu R, McIntyre CL, Manners JM, Henry RJ (2001) Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to Erianthus and Sorghum. Plant Sci 160:1115–1123

    CAS  PubMed  Google Scholar 

  • Dutta S, Kumawat G, Singh BP et al (2011) Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]. BMC Plant Biol 11(1):17

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ellis J, Burke J (2007) EST-SSRs as a resource for population genetic analyses. Heredity 99(2):125–132

    CAS  PubMed  Google Scholar 

  • Eujayl I, Sledge MK, Wang L et al (2004) Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp. Theor Appl Genet 108(3):414–422

    CAS  PubMed  Google Scholar 

  • Feng SP, Li WG, Huang HS, Wang JY, Wu YT (2009) Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis). Mol Breed 23(1):85–97

    CAS  Google Scholar 

  • Gai SP, Zhang YX, Mu P et al (2012) Transcriptome analysis of tree peony during chilling requirement fulfillment: assembling, annotation and markers discovering. Gene 497(2):256–262

    CAS  PubMed  Google Scholar 

  • Gao Z, Wu J, Wang L et al (2013) Rapid microsatellite development for tree peony and its implications. BMC Genomics 14(1):886

    PubMed Central  PubMed  Google Scholar 

  • Gilmore B, Bassil N, Nyberg A et al (2013) Microsatellite marker development in peony using next generation sequencing. J Am Soc Hortic Sci 138(1):64–74

    CAS  Google Scholar 

  • Gong L, Deng Z (2010) EST-SSR markers for gerbera (Gerbera hybrida). Mol Breed 26(1):125–132

    CAS  Google Scholar 

  • Gupta SK, Bansal R, Gopalakrishna T (2014) Development and characterization of genic SSR markers for mungbean (Vigna radiata (L.) Wilczek). Euphytica 195(2):245–258

    CAS  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Hou XG, Guo DL, Cheng SP, Zhang JY (2011a) Development of thirty new polymorphic microsatellite primers for Paeonia suffruticosa. Biol Plant 55(4):708–710

    CAS  Google Scholar 

  • Hou XG, Guo DL, Wang J (2011b) Development and characterization of EST-SSR markers in Paeonia suffruticosa (Paeoniaceae). Am J Bot 11:e303–e305

    Google Scholar 

  • Iorizzo M, Senalik DA, Grzebelus D et al (2011) De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity. BMC Genomics 12:389

    CAS  PubMed Central  PubMed  Google Scholar 

  • Jena SN, Srivastava A, Rai KM et al (2012) Development and characterization of genomic and expressed SSRs for levant cotton (Gossypium herbaceum L.). Theor Appl Genet 124(3):565–576

    CAS  PubMed  Google Scholar 

  • Kale SM, Pardeshi VC, Kadoo NY et al (2012) Development of genomic simple sequence repeat markers for linseed using next-generation sequencing technology. Mol Breed 30:597–606

    CAS  Google Scholar 

  • Kumpatla SP, Mukhopadhyay S (2005) Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome 48:985–998

    CAS  PubMed  Google Scholar 

  • Li L, Cheng F, Zhang Q (2011) Microsatellite markers for the Chinese herbaceous peony Paeonia lactiflora (Paeoniaceae). Am J Bot 98(2):e16–e18

    CAS  PubMed  Google Scholar 

  • Li K, Zhou N, Li HY (2012a) Composition and function research of peony flowers and peony seeds. Food Res Dev 33(3):228–230

    Google Scholar 

  • Li DJ, Deng Z, Qin B, Liu XH, Men ZH (2012b) De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). BMC Genomics 13(1):192

    CAS  PubMed Central  PubMed  Google Scholar 

  • Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21(9):2128–2129

    CAS  PubMed  Google Scholar 

  • Liu Z, Chen T, Ma L et al (2013a) Global transcriptome sequencing using the Illumina platform and the development of EST-SSR markers in autotetraploid alfalfa. PLoS One 8(12):e83549

    PubMed Central  PubMed  Google Scholar 

  • Liu L, Huang Y, Punnuri S, Samuels T, Wu Y, Mahalingam R (2013b) Development and integration of EST-SSR markers into an established linkage map in switchgrass. Mol Breed 32(4):923–931

    CAS  Google Scholar 

  • Luro FL, Costantino G, Terol J et al (2008) Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping. BMC Genomics 9:287

    PubMed Central  PubMed  Google Scholar 

  • Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30(2):194–200

    CAS  PubMed  Google Scholar 

  • Ong WD, Voo CLY, Kumar SV (2011) Development of ESTs and data mining of pineapple EST-SSRs. Mol Biol Rep 39(5):5889–5896

    PubMed  Google Scholar 

  • Pan L, Xia Q, Quan Z, Liu H, Ke W, Ding Y (2010) Development of novel EST-SSRs from sacred lotus (Nelumbo nucifera Gaertn) and their utilization for the genetic diversity analysis of N. nucifera. J Hered 101(1):71–82

    CAS  PubMed  Google Scholar 

  • Paux E, Sourdille P, Mackay I, Feuillet C (2012) Sequence-based marker development in wheat: advances and applications to breeding. Biotechnol Adv 30(5):1071–1088

    CAS  PubMed  Google Scholar 

  • Qiu LJ, Yang C, Tian B, Yang JB, Liu AH (2010) Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.). BMC Plant Biol 10:278

    CAS  PubMed Central  PubMed  Google Scholar 

  • Scott KD, Eggler P, Seaton G et al (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726

    CAS  Google Scholar 

  • Sharma RK, Bhardwaj P, Negi R, Mohapatra T, Ahuja PS (2009) Identification, characterization and utilization of unigene derived microsatellite markers in tea (Camellia sinensis L.). BMC Plant Biol 9:53

    PubMed Central  PubMed  Google Scholar 

  • Shu QY, Wischnitzki E, Liu ZA et al (2009) Functional annotation of expressed sequence tags as a tool to understand the molecular mechanism controlling flower bud development in tree peony. Physiol Plant 135(4):436–449

    CAS  PubMed  Google Scholar 

  • Stern FC (1946) A study of the genus Paeonia. Royal Horticulture Society, London

    Google Scholar 

  • Sun J, Yuan J, Wang B et al (2011) Development and characterization of 10 microsatellite loci in Paeonia lactiflora (Paeoniaceae). Am J Bot 98(9):e242–e243

    CAS  PubMed  Google Scholar 

  • Tan C, Wu Y, Taliaferro CM, Anderson MP, Tauer C, Samuels T (2012) Development of simple sequence repeat markers for bermudagrass from its expressed sequence tag sequences and preexisting sorghum SSR markers. Mol Breed 29(1):23–30

    CAS  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(8):1441–1452

    CAS  PubMed Central  PubMed  Google Scholar 

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

    CAS  PubMed  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

    CAS  Google Scholar 

  • Wang Z, Li J, Luo Z et al (2011) Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas). BMC Plant Biol 11(1):139

    CAS  PubMed Central  PubMed  Google Scholar 

  • Wang Z, Yan H, Fu X, Li X, Gao H (2013) Development of simple sequence repeat markers and diversity analysis in alfalfa (Medicago sativa L.). Mol Biol Rep 40(4):3291–3298

    CAS  PubMed  Google Scholar 

  • Wister JC (1995) The Peonies. American Peony Society, Hopkins

    Google Scholar 

  • Yeh FC, Yang RC, Boyle T et al (1999) POPGENE, version 1.32: the user friendly software for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton, AB, Canada

  • 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

    CAS  Google Scholar 

  • Yuan JH, Cheng FY, Zhou SL (2010) Hybrid origin of Paeonia × yananensis revealed by microsatellite markers, chloroplast gene sequences, and morphological characteristic. Int J Plant Sci 171(4):409–420

    CAS  Google Scholar 

  • Yuan JH, Cheng FY, Zhou SL (2012) Genetic structure of the tree Peony (Paeonia rockii) and the Qinling mountains as a geographic barrier driving the fragmentation of a large population. PLoS One 7(4):e34955

    CAS  PubMed Central  PubMed  Google Scholar 

  • Yuan JH, Cornille A, Giraud T, Cheng FY, Hu YH (2014) Independent domestications of cultivated tree peonies from different wild peony species. Mol Ecol 23(1):82–95

    PubMed  Google Scholar 

  • Zeng SH, Xiao G, Guo J et al (2010) Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim. BMC Genomics 11:94–105

    PubMed Central  PubMed  Google Scholar 

  • Zhai L, Xu L, Wang Y et al (2014) Novel and useful genic-SSR markers from de novo transcriptome sequencing of radish (Raphanus sativus L.). Mol Breed 33:749–754

    Google Scholar 

  • Zhang JM, Liu J, Sun HL, Yu J, Wang JX, Zhou SL (2011) Nuclear and chloroplast SSR markers in Paeonia delavayi (Paeoniaceae) and cross-species amplification in P. ludlowii. Am J Bot 98(12):e346–e348

    CAS  PubMed  Google Scholar 

  • Zhang JJ, Shu QY, Liu ZA, Ren HX, Wang LS, De Keyser E (2012) Two EST-derived marker systems for cultivar identification in tree peony. Plant Cell Rep 31(2):299–310

    CAS  PubMed  Google Scholar 

  • Zhang MY, Fan L, Liu QZ et al (2014) A novel set of EST-derived SSR markers for pear and cross-species transferability in Rosaceae. Plant Mol Biol Rep 32:290–302

    Google Scholar 

  • Zhao X, Zhou ZQ, Lin QB, Pan KY, Li MY (2008) Phylogenetic analysis of Paeonia sect. Moutan (Paeoniaceae) based on multiple DNA fragments and morphological data. Acta Phytotax Sin 46(4):563–572

    Google Scholar 

  • Zhou HM, Ma JQ, Miao CY et al (2009) Physicochemical indexes and fatty acid composition of peony seed oil. China Oils Fats 34(7):72–74

    CAS  Google Scholar 

  • Zhou H, Cheng FY, Wang R, Zhong Y, He CY (2013) Transcriptome comparison reveals key candidate genes responsible for the unusual reblooming trait in tree peonies. PLoS One 8(11):e79996

    PubMed Central  PubMed  Google Scholar 

  • Zhou CP, He XD, Li FG et al (2014) Development of 240 novel EST-SSRs in Eucalyptus L’Hérit. Mol Breed 33(1):221–225

    Google Scholar 

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Acknowledgments

We deeply thank Gaixiu Liu for her help during the sample collection. This study was funded by the National High Technology Research and Development Program of China (863 Program, 2011AA100207) and the National Science and Technology Support Program of China (2012BAD01B07).

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Correspondence to Fangyun Cheng.

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Wu, J., Cai, C., Cheng, F. et al. Characterisation and development of EST-SSR markers in tree peony using transcriptome sequences. Mol Breeding 34, 1853–1866 (2014). https://doi.org/10.1007/s11032-014-0144-x

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  • DOI: https://doi.org/10.1007/s11032-014-0144-x

Keywords

  • Paeonia suffruticosa
  • Simple sequence repeats (SSRs)
  • Transcriptome sequences
  • Polymorphism
  • Transferability
  • Genetic relationships