Skip to main content
SpringerLink
Log in

Generation and exploitation of EST-derived SSR markers for assaying molecular diversity in durum wheat populations

  • Regular Article
  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

Durum wheat [Triticum turgidum L. subsp. turgidum convar. durum (Desf.) MK] is an important cereal crop economically and nutritionally in the Central Asia and Caucasian, West Asia, and North Africa (CWANA) regions. Durum landraces and improved lines are largely grown in this region. Its genetic diversity has been studied using different molecular markers. The increasing availability of expressed sequence tags (ESTs) in wheat (Triticum aestivum) and related cereals provides a valuable resource of non-anonymous DNA markers to study durum diversity. In this study, a set of 517,319 Triticum aestivum EST sequences was employed for the identification of wheat simple sequence repeats called microsatellites (W-eSSRs) with the help of a PERL5 script called MISA. In comparison, barley microsatellites (B-eSSRs) have been used to exploit their transferability to durum wheat. Newly developed W-eSSR markers were probed on the 115 recombinant inbred lines (RIL) of the International Triticeae Mapping Initiative (ITMI) population (Opata 85 × Synthetic 7984). The polymorphic eSSRs were mapped. To examine the potential of the two types of eSSRs markers, 12 W-eSSR markers and 13 B-eSSR markers were used to fingerprint 153 wheat genotypes. Our results indicate that: (1) B-eSSRs show a high level of transferability to wheat, (2) the developed W-eSSRs are significantly polymorphic than those derived from genomic regions, (3) new W-eSSRs were identified and integrated in the ITMI genetic linkage map and, (4) B-eSSR and W-eSSRs are providing additional markers for comparative mapping following gene introgressions from wild species and carrying out evolutionary studies.

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.

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrels ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181–186

    Article  PubMed  CAS  Google Scholar 

  • Autrique E, Nachit M, Monneveux P, Tanksley SD, Sorrels ME (1996) Genetic diversity in durum wheat based on RFLPs, Morphophysiological Traits, and Coefficient of Parentage. Crop Sci 36:735–742

    Article  Google Scholar 

  • Blumler MA (1998) Introgression of durum wheat into wild emmer and the agricultural question. In: Damania AB, Valkoun J, Wilcox G, Qualset CO (eds) The origin of agriculture and crop domestication. ICARDA, Aleppo, Syria. pp 252–268

    Google Scholar 

  • Chabane K, Valkoun J (2001) Molecular characterization of wild and cultivated tetraploid wheat of the Near East Origin. Proceeedings of the 4th international triticeae symposium September 10–12, 2001, Cordoba, Spain, pp 211–214

  • Chabane K, Ablett GA, Cordeiro GM, Valkoun J, Henry RJ (2005) EST versus genomic derived microsatellite markers for genotyping wild and cultivated barley. Genet Resour Crop Evol 52:903–909

    Article  CAS  Google Scholar 

  • Chabane K, Abdalla O, Sayed H, Valkoun J (2007) Assessment of EST-microsatellites markers for discrimination and genetic diversity in bread and durum wheat landraces from Afghanistan. Genet Resour Crop Evol 54:1073–1080

    Article  CAS  Google Scholar 

  • Cho YG, Ishii T, Temmykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and Genebank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713–722

    Article  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Dubcovsky J, Dvorak J (2007) Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316:1862–1866

    Article  PubMed  CAS  Google Scholar 

  • Eujayl I, Sorrels ME, Baum M, Wolters P, Powel W (2001) Isolation of EST-derived microsatellites markers for genotyping the A and B genomes of wheat. Theor Appl Genet 104:399–407

    Article  Google Scholar 

  • Gao LF, Jing RJ, Huo NX, Li Y, Li XP, Zhou RH, Chang XP, Tang JF, Ma ZY, Jia JZ (2004) One hundred and one new microsatellite loci derived from ESTs (EST-SSRs) in bread wheat. Theor Appl Genet 108:1392–1400

    Article  PubMed  CAS  Google Scholar 

  • Giancola S, Heather I, Mckhman AB, Camilleri C, Durand S, Libeau P, Roux F, Reboud X, Ivo G, Brunel D (2006) Utilization of the three high-throughout SNP genotyping methods, the GOOD assay, Amplifluor and TaqMan, in diploid and polyploidy plants. Theor Appl Genet 112:115–1124

    Article  CAS  Google Scholar 

  • Graner A, Dehmer KJ, Thiel T, Börner A (2004) Plant genetic resources: benefits and implications of using molecular markers. In: Carmen de Vicente M (ed) Issues in Genetic Resources No. 11. IPGRI, Rome, Italy, pp 26–32

    Google Scholar 

  • Grimaldi MC, Crouau-Roy B (1997) Microsatellite allelic homoplasy due to variable flanking sequences. J Mol Evol 44:336–340

    Article  PubMed  CAS  Google Scholar 

  • Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–185

    Article  CAS  Google Scholar 

  • Gupta PK, Varshney RK, Prasad M (2002) Molecular markers: principles and methodology. In: Jain SM, Ahloowalia BS, Brar DS (eds) Molecular techniques in crop improvement. Kluwer Academic Publishers, The Netherlands, pp 9–54

    Google Scholar 

  • Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N, Balayan HS (2003) Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Genet Genomics 270:315–323

    Article  PubMed  CAS  Google Scholar 

  • Hackauf B, Wehling P (2002) Identification of microsatellite polymorphisms in an expressed portion of the rye genome. Plant Breed 121:17–25

    Article  CAS  Google Scholar 

  • Hayden MJ, Kuchel H, Chalmers KJ (2004) Sequence tagged microsatellites for the Xgwm533 locus provide new diagnostic markers to select for the presence of stem rust resistance gene Sr2 in bread wheat (Triticum aestivum L.). Theor Appl Genet 109:1641–1647

    Article  PubMed  CAS  Google Scholar 

  • Heun M, Schäfer-Pregl R, Klawan D, Castagna R, Accerbi M, Borghi B, Salamani F (1997) Site of einkorn wheat domestication identified by DNA fingerprinting. Science 278:1312–1314

    Article  CAS  Google Scholar 

  • Holton TA, Christopher JT, McClure L, Harker N, Henry RJ (2002) Identification and mapping of polymorphic SSR markers from expressed gene sequences of barley and wheat. Mol Breed 9:63–71

    Article  CAS  Google Scholar 

  • Kantety RV, La Rota M, Matthews DE, Sorrels M (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48:501–510

    Article  PubMed  CAS  Google Scholar 

  • Kota R, Varshney RK, Thiel T, Dehmer KJ, Graner A (2001) Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.). Hereditas 135:145–151

    Article  PubMed  CAS  Google Scholar 

  • Khlestkina E, Varshney RK, Röder M, Graner A, Bömer A (2006) Comparative assessment of genetic diversity in cultivated barley collected at different periods of the last century in Austria, Albania and India by using genomic and genic SSR markers. Plant Genet Resour 4(2):125–133

    CAS  Google Scholar 

  • Leigh P, Lea V, Wolters P, Powell W, Donini P (2003) Assessment of EST- and genomic microsatellite markers for variety discrimination and genetic diversity studies in wheat. Euphytica 133:359–366

    Article  CAS  Google Scholar 

  • Maccaferi M, Sanguineti MC, Natoli J, Ortega JLA, Ben Salem M, Bort J, Chenenaoui C, De Ambrogio E, Del Moral LG, De Montis A, Ahmed A, Maalouf F, Machlab H, Moragues M, Motawaj J, Nachit M, Nesrallah N, Ouabbou H, Royo C, Tuberosa R (2006) A panel of elite accessions of durum wheat (Triticum durum Desf.) suitable for association mapping studies. Plant Genet Resour 4(1):79–85

    Google Scholar 

  • Metzgar D, Bytof J, Wills C (2000) Selection against frame shift mutations limits microsatellite expansion in coding DNA. Genome Res 10:72–80

    PubMed  CAS  Google Scholar 

  • Nachit M, Elouafi I, Pagnotta MA, El Saleh A, Iacono E, Labhilili M, Asbati A, Azrak M, Hazzam H, Benscher D, Khairallah M, Ribaut JM, Tanzarella OA, Porceddu E (2001) Molecular linkage map for an intraspecific recombinant inbred population of durum wheat (Triticum turgidum L. var . durum). Theor Appl Genet 102:177–186

    Article  CAS  Google Scholar 

  • Nei M (1978) Estimation of average heterozygosity and genetic distance from small number of individuals. Genetics 89:583–590

    PubMed  CAS  Google Scholar 

  • Nelson JC, Sorrells ME, Van Deynze AE, Lu YH, Atkinson M (1995) Molecular mapping of wheat: major genes and rearrangements in homoeologous groups 4, 5, and 7. Genetics 141:721–731

    PubMed  CAS  Google Scholar 

  • Nicot N, Chiquet V, Gandon B, Amilhat L, Legeai F, Leroy F, Bernard M, Sourdille P (2004) Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs). Theor Appl Genet 109:800–805

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Perry DJ (2004) Identification of Canadian durum wheat varieties using a single PCR. Theor Appl Genet 109:55–61

    Article  PubMed  CAS  Google Scholar 

  • Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238

    Article  CAS  Google Scholar 

  • Prasad M, Varshney RK, Roy JK, Balyan HS, Gupta PK (2000) The use of microsatellites for detecting DNA polymorphism genotype identification and genetic diversity in wheat. Theor Appl Genet 100:584–592

    CAS  Google Scholar 

  • Rafalski A (2002) Application of single nucleotide polymorphism in crop genetics. Curr Opin Plant Biol 5:94–100

    Article  PubMed  CAS  Google Scholar 

  • Röder MS, Korzun V, Wendehake K, Plaske J, Tixier M, Leroy P, Ganal M (1998) A microsatellite map of wheat. Genetics 149:2007–2023

    PubMed  Google Scholar 

  • Röder MS, Wendehake K, Korzun V, Bredemijer G, Laborie D, Bertrand L, Issac P, Rendell S, Jackson J, Cooke RJ, Vosman B, Ganal MW (2002) Construction and analysis of a microsatellite-based database of European wheat varieties. Theor Appl Genet 106:67–73

    PubMed  Google Scholar 

  • Russell JR, Fuller JD, Macaulay M, Hatz BG, Jahoor A, Powell W, Waugh R (1997a) Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor Appl Genet 95:714–722

    Article  CAS  Google Scholar 

  • Russell JR, Fuller JD, Young G, Thomas B, Taramino G, Macaulay M, Waugh R, Powell W (1997b) Discriminating between barley genotypes using microsatellite markers. Genome 40:442–450

    Article  PubMed  CAS  Google Scholar 

  • Salamiani F, Ozkan H, Brandolini A, Schäfer-Pregl R, Martin W (2002) Genetics and geography of wild cereal domestication in the Near East. Nat Rev Genet 3:429–441

    Google Scholar 

  • Sasanuma T, Chabane K, Endo TR, Valkoun J (2004) Characterization of genetic variation in and phylogenetic relationships among diploid Aegilops species by AFLP: incongruity of chloroplast and nuclear data. Theor Appl Genet 108:612–618

    Article  PubMed  CAS  Google Scholar 

  • Scott KD, Eggler P, Seaton G, Rossetto EM, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726

    Article  CAS  Google Scholar 

  • Sourdille P, Tavaud M, Charmet G, Bernard M (2001) Transferability of wheat microsatellites to diploid Triticeae species carrying the A, B and D genomes. Theor Appl Genet 103:346–352

    Article  CAS  Google Scholar 

  • Swarup K, Parida K, Anand Raj Kumar K, Dalal V, Singh NK, Mohapatra T (2006) Unigene derived microsatellite markers for the cereal genomes. Theor Appl Genet 112:808–817

    Article  CAS  Google Scholar 

  • Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422

    PubMed  CAS  Google Scholar 

  • Yu J-K, Dake TM, Singh S, Benscher D, Li WL, Gill B, Sorrells ME (2004a) Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat. Genome 47:805–818

    Article  PubMed  CAS  Google Scholar 

  • Yu JK, La Rota M, Kantety RV, Sorrells ME (2004b) EST derived SSR markers for comparative mapping in wheat and rice. Mol Genet Genomics 271:742–751

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Varshney RK, Sigmund R, Bömer A, Korzun V, Stein N, Sorrels ME, Langridge P, Graner A (2005b) Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Sci 168:195–202

    Article  CAS  Google Scholar 

  • Varshney RK, Grosse I, Hähnel U, Siefken R, Prasad M, Stein N, Langridge P, Altschmied L, Graner A (2006) Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome. Theor Appl Genet 113:239–250

    Article  PubMed  CAS  Google Scholar 

  • Vogel JP, Gu YQ, Twigg P, Lazo GR, Chingcuanco DL, Hayden DM, Donze T, Vivia-Lindsay A, Stamova B, Coleman-Derr D (2006) EST sequencing and phylogenetic analysis of the model grass brachypodium distachyon. Theor Appl Genet 113: 186–195

    Article  PubMed  CAS  Google Scholar 

  • Woodhead M, Russell J, Squirrell J, Hollingsworth PM, Mackenzie K, Gibby M, Powell W (2004) Comparative analysis of population genetic structure in Athyrium distentifolium (Pteridophyta) using AFLPs and SSRs from anonymous and transcribed gene regions. Mol Ecol 14:1681–1695

    Article  CAS  Google Scholar 

  • Zhang LY, Bernard M, Leroy P, Feuillet C (2005) High transferability of bread wheat EST-derived SSRs to other cereals. Theor Appl Genet 111:677–687

    Article  PubMed  CAS  Google Scholar 

  • Zhang P, Dreisigacker S, Buerkert A, Alkhanjari S, Melchinger AE, Warburton ML (2006) Genetic diversity and relationships of wheat landraces from oman investigated with SSR markers. Genet Resour Crop Evol 53:1351–1360

    Article  Google Scholar 

Download references

Acknowledgements

The authors’ research was supported by grants to ICARDA from the German Federal Ministry of Economic Cooperation and Development (BMZ, Bonn, Germany) under the project “Exploration of Genetic Resources Collections at ICARDA for Adaptation to Climate Change: Identification and Utilization of Sources of Stress Tolerance”. We thank Dr. W. Choumane (Teschrine University, Lattakia, Syria), Dr. M. Nachit (durum wheat breeder, ICARDA) and Dr. K. Amar (durum wheat breeder, CIMMYT) for their comments and reviewing the manuscript; and Dr. J. Rayan and Mr. A. Varadachary for editing the paper.

Author information

Authors and Affiliations

  1. International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5466, Aleppo, Syria

    Kamel Chabane & J. Valkoun

  2. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, AP, India

    R. K. Varshney

  3. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corensstrasse 3, 06466, Gatersleben, Germany

    A. Graner

Authors
  1. Kamel Chabane
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. R. K. Varshney
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. A. Graner
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. J. Valkoun
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Kamel Chabane.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Chabane, K., Varshney, R.K., Graner, A. et al. Generation and exploitation of EST-derived SSR markers for assaying molecular diversity in durum wheat populations. Genet Resour Crop Evol 55, 869–881 (2008). https://doi.org/10.1007/s10722-007-9292-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-007-9292-8

Keywords

Search

Navigation