Skip to main content
SpringerLink
Log in

Development of transcript-associated microsatellite markers for diversity and linkage mapping studies in hop (Humulus lupulus L.)

  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

Data mining of gene sequences available from various projects dealing with the development of expressed sequence tags (ESTs) can contribute to the discovery of new microsatellite markers. Our aim was to develop new microsatellite markers in hop isolated from an enriched cDNA library and from coding GenBank sequences and to test their suitability in hop diversity studies and for construction of a linkage map. In a set of 614 coding GenBank sequences, 72 containing microsatellites were found (11.7%); the most frequent were trinucleotide repeats (54.0%) followed by dinucleotide repeats (34.5%). Additionally, 11 sequences containing microsatellites were isolated from an enriched cDNA library. A total of 34 primer pairs were designed, 29 based on GenBank sequences and five on sequences from the cDNA enriched library. Twenty-seven (79.4%) coding microsatellites were successfully amplified and used in diversity and linkage mapping studies. Eleven primer pairs amplified 12 coding microsatellite loci suitable for mapping and were placed on female and male linkage maps. We were able to extend previous simple sequence repeat (SSR) female, male and integral maps by 38.8, 25.8 and 40.0 cM, respectively. In the diversity study, 36 diverse hop genotypes were analyzed. Twenty-four coding microsatellites were polymorphic, 17 showing co-dominant behavior and 7 primer pairs amplifying three or more bands in some hop genotypes. Altogether, 143 microsatellite DNA fragments were amplified and they revealed a clear separation of hop genotypes according to geographical region, use or breeding history. In addition, a discussion and comparison of results with other plant coding/EST SSR studies is presented. Our results showed that these microsatellite markers can enhance hop diversity and linkage mapping studies and are a comparable marker system to non-coding SSRs.

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

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    PubMed  CAS  Google Scholar 

  • Asp T, Frei UK, Didion T, Nielsen KK, Lübberstedt T (2007) Frequency, type, and distribution of EST-SSRs from three genotypes of Lolium perenne, and their conservation across orthologous sequences of Festuca arundinacea, Brachypodium distachyon, and Oryza sativa. BMC Plant Biol 7:36

    Article  PubMed  Google Scholar 

  • Ayers NM, McClung AM, Larkin PD, Bligh HFJ, Jones CA, Park WD (1997) Microsatellite and single nucleotide polymorphism differentiate apparent amylose classes in an extended pedigree of US rice germplasm. Theor Appl Genet 94:381–773

    Google Scholar 

  • Barrett B, Grifiths A, Schreiber M, Ellison N, Mercer C, Bouton J, Ong B, Forster J, Sawbridge T, Spangenberg G, Bryan G, Woodfield D (2004) A microsatellite map of clover. Theor Appl Genet 109:596–608

    PubMed  CAS  Google Scholar 

  • Bassil NV, Gilmore B, Oliphant JM, Hummer KE, Henning JA (2008) Genic SSRs for European and North American hop (Humulus lupulus L.). Genet Resour Crop Evol 55:959–969

    Article  Google Scholar 

  • Brady JL, Scott NS, Thomas MR (1996) DNA typing of hops (Humulus lupulus) through application of RAPD and microsatellite marker sequences converted to sequence tagged sites (STS). Euphytica 91:277–284

    Article  CAS  Google Scholar 

  • Caruso M, Federici CT, Roose ML (2008) EST-SSR markers for asparagus genetic diversity evaluation and cultivar identification. Mol Breed 21:195–204

    Article  CAS  Google Scholar 

  • Cerenak A, Satovic Z, Javornik B (2006) Genetic mapping of hop (Humulus lupulus L.) applied to the detection of QTLs for alpha-acid content. Genome 49:485–494

    Article  PubMed  CAS  Google Scholar 

  • Chadwick LR, Pauli GF, Farnsworth NR (2006) The pharmacognosy of Humulus lupulus L. (hops) with an emphasis on estrogenic properties. Phytomedicine 13:119–131

    Article  PubMed  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. Theor Appl Genet 118:591–608

    Article  PubMed  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

    Article  PubMed  CAS  Google Scholar 

  • Decroocq V, Fave MG, Hagen L, Bordenave L, Decroocq S (2003) Development and transferability of apricot and grape EST microsatellite markers across taxa. Theor Appl Genet 106:912–922

    PubMed  CAS  Google Scholar 

  • Eujayl I, Sorrells ME, Baum M, Wolters P, Powell W (2002) Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theor Appl Genet 104:399–407

    Article  PubMed  CAS  Google Scholar 

  • Eujayl I, Sledge MK, Wang L, May GD, Chekhovskiy K, Zwonitzer JC, Milan MAR (2004) Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp. Theor Appl Genet 108:414–422

    Article  PubMed  CAS  Google Scholar 

  • Fraser LG, Harvey CF, Crowhurst RN, De Silva HN (2004) EST-derived microsatellites from Actinidia species and their potential for mapping. Theor Appl Genet 108:1010–1016

    Article  PubMed  CAS  Google Scholar 

  • Gonzalez-Ibeas D, Blanca J, Roig C, González-To M, Picó B, Truniger V, Gómez P, Deleu W, Caño-Delgado A, Arús P, Nuez F, Garcia-Mas J, Puigdomènech P, Aranda MA (2007) MELOGEN: an EST database for melon functional genomics. BMC Genomics 8:306

    Article  PubMed  Google Scholar 

  • Grattapaglia D, Sederoff R (1994) Genetic linkage mapping in Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross mapping strategy and RAPD markers. Genet 137:1121–1137

    CAS  Google Scholar 

  • Hadonou AM, Walden R, Darby P (2004) Isolation and characterization of polymorphic microsatellites for assessment of genetic variation of hops (Humulus lupulus L.). Mol Ecol Notes 4:280–282

    Article  CAS  Google Scholar 

  • Hisano H, Sato S, Isobe S, Sasamoto S, Wada T, Matsuno A, Fujishiro T, Yamada M, Nakayama S, Nakamura Y, Watanabe S, Harada K, Tabata S (2007) Characterization of the soybean genome using EST-derived microsatellite markers. DNA Res 14:271–281

    Article  PubMed  CAS  Google Scholar 

  • Jakse J, Javornik B (2001) High throughput isolation of microsatellites in hop (Humulus lupulus L.). Plant Mol Biol Rep 19:217–226

    Article  CAS  Google Scholar 

  • Jakse J, Bandelj D, Javornik B (2002) Eleven new microsatellites for hop (Humulus lupulus L.). Mol Ecol Notes 2:544–546

    Article  CAS  Google Scholar 

  • Jakse J, Satovic Z, Javornik B (2004) Microsatellite variability among wild and cultivated hops (Humulus lupulus L.). Genome 47:889–899

    Article  PubMed  CAS  Google Scholar 

  • Jakse J, Luthar Z, Javornik B (2008) New polymorphic dinucleotide and trinucleotide microsatellite loci for hop Humulus lupulus L. Mol Ecol Notes 8:769–772

    CAS  Google Scholar 

  • Jayamani P, Negrão S, Brites C, Oliveira MM (2007) Potential of Waxy gene microsatellite and single-nucleotide polymorphisms to develop japonica varieties with desired amylose levels in rice (Oryza sativa L.). J Cereal Sci 46:178–186

    Article  CAS  Google Scholar 

  • Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1006–1099

    Article  Google Scholar 

  • Khlestkina EK, Than MHM, Pestsova EG, Roder MS, Malyshev SV, Korzun V, Borner A (2004) Mapping of 99 new microsatellite-derived loci in rye (Secale cerale L.) including 39 expressed sequence tags. Theor Appl Genet 190:725–732

    Article  Google Scholar 

  • Kump B, Javornik B (1996) Evaluation of genetic variability among common buckwheat (Fagopyrum esculentum Moench) populations by RAPD markers. Plant Sci 114:149–158

    Article  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

    Article  PubMed  CAS  Google Scholar 

  • Ky CL, Barre P, Lorieux M, Trouslot P, Akaffou S, Louarn J, Charrier A, Hamon S, Noirot M (2000) Interspecific genetic linkage map segregation distortion and genetic conversion in coffee (Coffea sp.). Theor Appl Genet 101:669–676

    Article  CAS  Google Scholar 

  • Lewers KS, Bassil NV, Styan SMN, Hokanson SC (2005) Strawberry GenBank-derived and genomic simple sequence repeat (SSR) markers and their utility with strawberry, blackberry, and red and black raspberry. J Am Soc Hort Sci 130:102–115

    CAS  Google Scholar 

  • Lewers KS, Saski CA, Cuthbertson BJ, Henry DC, Staton ME, Main DS, Dhanaraj AL, Rowland LJ, Tomkins JP (2008) A blackberry (Rubus L.) expressed sequence tag library for the development of simple sequence repeat markers. BMC Plant Biol 8:69

    Article  PubMed  Google Scholar 

  • Li Y-C, Korol AB, Fahima T, Nevo E (2004) Microsatellites within genes: Structure, function, and evolution. Mol Biol Evol 21:991–1007

    Article  PubMed  CAS  Google Scholar 

  • Matoušek J, Novák P, Patzak J, Břiza J, Krofta K (2002) Analysis of true chalcone synthase from Humulus lupulus L. and biotechnology aspects of medicinal hops. Rostl Výroba 48:7–14

    Google Scholar 

  • Matoušek J, Vrba L, Novák P, Patzak J, De Keukeleire J, Škopek J, Heyerick A, Roldan-Ruiz I, De Keukeleire D (2005) Cloning and molecular analysis of the regulatory factor HlMyb1 in hop (Humulus lupulus L.) and the potential of hop to produce bioactive prenylated flavonoids. J Agric Food Chem 53:4793–4798

    Article  PubMed  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Murakami A, Darby P, Javornik B, Pais MSS, Seigner E, Lutz A, Svoboda P (2006) Molecular phylogeny of wild hops, Humulus lupulus L. Heredity 97:66–74

    Article  PubMed  CAS  Google Scholar 

  • Nagel J, Culley LK, Lu Y, Liu E, Matthews PD, Stevens JF, Page JE (2008) EST analysis of hop glandular trichomes identifies an O-methyltransferase that catalyzes the biosynthesis of xanthohumol. Plant Cell 20:186–200

    Article  PubMed  CAS  Google Scholar 

  • Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonuclease. Proc Natl Acad Sci USA 76:5269–5273

    Article  PubMed  CAS  Google Scholar 

  • Newcomb RD, Crowhurst RN, Gleave AP, Rikkerink EHA, Allan AC, Beuning LL, Bowen JH, Gera E, Jamieson KR, Janssen BJ, Laing WA, McArtney S, Nain B, Ross GS, Snowden KC, Souleyre EJF, Walton EF, Yauk Y-K (2006) Analyses of expressed sequence tags from apple. Plant Physiol 141:147–166

    Article  PubMed  Google Scholar 

  • Okada Y, Sano Y, Kaneko T, Abe I, Noguchi H, Ito K (2004) Enzymatic reactions by five chalcone synthase homologs from hop (Humulus lupulus L.). Biosci Biotechnol Biochem 68:1142–1145

    Article  PubMed  CAS  Google Scholar 

  • Rohlf JF (1998) NTSYS: numerical taxonomy and multivariate analysis system, version 2.02. Exeter Software, Setauket

    Google Scholar 

  • Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Meth Mol Biol 132:265–386

    Google Scholar 

  • Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments—a poor man’s approach to genotyping for research and high-throughput diagnostics. Nat Biotechnol 18:233–234

    Article  PubMed  CAS  Google Scholar 

  • Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:697–712

    Article  Google Scholar 

  • Seefelder S, Ermaier H, Schweizer G, Seigner E (2000a) Genetic diversity and phylogenetic relationships among accessions of hop, Humulus lupulus, as determined by amplified fragment length polymorphism fingerprinting compared with pedigree data. Plant Breed 119:257–263

    Article  CAS  Google Scholar 

  • Seefelder S, Ehrmaier H, Schweizer G, Seigner E (2000b) Male and female genetic linkage map of hops, Humulus lupulus. Plant Breed 119:249–255

    Article  CAS  Google Scholar 

  • Singh R, Zaki NM, Ting N-C, Rosli R, Tan S-G, Low E-TL, Ithnin M, Cheah S-C (2008) Exploiting an oil palm EST database for the development of gene-derived SSR markers and their exploitation for assessment of genetic diversity. Biologia 63:227–235

    Article  CAS  Google Scholar 

  • Small E (1978) Numerical and nomenclatural analysis of morpho-geographic taxa of Humulus. Syst Bot 3:37–76

    Article  Google Scholar 

  • Stajner N, Jakse J, Kozjak P, Javornik B (2005) The isolation and characterisation of microsatellites in hop (Humulus lupulus L.). Plant Sci 168:213–221

    Article  CAS  Google Scholar 

  • Stajner N, Satovic Z, Cerenak A, Javornik B (2008) Genetic structure and differentiation in hop (Humulus lupulus L.) as inferred from microsatellites. Euphytica 161:301–311

    Article  CAS  Google Scholar 

  • Sustar-Vozlic J, Javornik B (1999) Genetic relationships in cultivars of hop, Humulus lupulus L., determined by RAPD analysis. Plant Breed 118:175–181

    Article  Google Scholar 

  • Thiel T, Michalek W, Varshney R, Graner A (2004) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422

    Google Scholar 

  • Van Ooijen JW, Voorrips RE (2001) JoinMap® version 3.0: software for the calculation of genetic linkage maps. Plant Research International, Wageningen

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78

    Article  PubMed  CAS  Google Scholar 

  • Wang G, Tian L, Aziz N, Broun P, Dai X, He J, King A, Zhao PX, Dixon RA (2008) Terpene biosynthesis in glandular trichomes of hop. Plant Physiol 148:1254–1266

    Article  PubMed  CAS  Google Scholar 

  • Yasodha R, Sumathi R, Chezhian P, Kavitha S, Ghosh M (2008) Eucalyptus microsatellites mined in silico: survey and evaluation. J Genet 87:21–25

    Article  PubMed  CAS  Google Scholar 

  • Yi G, Lee JM, Lee S, Choi D, Kim BD (2006) Exploitation of pepper EST-SSRs and an SSR-based linkage map. Theor Appl Genet 114:113–130

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This study was funded by the Slovenian Research Agency, contract no. P4-0077, and by the Proteus bilateral France–Slovenia programme, contract no. BI-FR/08-09-PROTEUS-006.

Author information

Authors and Affiliations

  1. Agronomy Department, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia

    Jernej Jakse, Natasa Stajner, Zlata Luthar & Branka Javornik

  2. Université de Strasbourg, 4 rue Blaise Pascal, CS 90032, 67081, Strasbourg Cedex, France

    Jean-Marc Jeltsch

Authors
  1. Jernej Jakse
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Natasa Stajner
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Zlata Luthar
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jean-Marc Jeltsch
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Branka Javornik
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Branka Javornik.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 124 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Jakse, J., Stajner, N., Luthar, Z. et al. Development of transcript-associated microsatellite markers for diversity and linkage mapping studies in hop (Humulus lupulus L.). Mol Breeding 28, 227–239 (2011). https://doi.org/10.1007/s11032-010-9476-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11032-010-9476-3

Keywords

Search

Navigation