Genetic Resources and Crop Evolution

, Volume 55, Issue 6, pp 869–881 | Cite as

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

  • Kamel Chabane
  • R. K. Varshney
  • A. Graner
  • J. Valkoun
Regular Article


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.


B-eSSRs ESTs Genetic diversity Genetic linkage mapping Polymorphism Information Content (PIC) W-eSSRs 



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.


  1. Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrels ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181–186PubMedCrossRefGoogle Scholar
  2. 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 36:735–742CrossRefGoogle Scholar
  3. 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 252–268Google Scholar
  4. 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 211–214Google Scholar
  5. 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 52:903–909CrossRefGoogle Scholar
  6. 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 54:1073–1080CrossRefGoogle Scholar
  7. 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 100:713–722CrossRefGoogle Scholar
  8. 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 160:1115–1123PubMedCrossRefGoogle Scholar
  9. Dubcovsky J, Dvorak J (2007) Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316:1862–1866PubMedCrossRefGoogle Scholar
  10. 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 104:399–407CrossRefGoogle Scholar
  11. 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 108:1392–1400PubMedCrossRefGoogle Scholar
  12. 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 112:115–1124CrossRefGoogle Scholar
  13. 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 26–32Google Scholar
  14. Grimaldi MC, Crouau-Roy B (1997) Microsatellite allelic homoplasy due to variable flanking sequences. J Mol Evol 44:336–340PubMedCrossRefGoogle Scholar
  15. Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–185CrossRefGoogle Scholar
  16. 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 9–54Google Scholar
  17. 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 270:315–323PubMedCrossRefGoogle Scholar
  18. Hackauf B, Wehling P (2002) Identification of microsatellite polymorphisms in an expressed portion of the rye genome. Plant Breed 121:17–25CrossRefGoogle Scholar
  19. 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 109:1641–1647PubMedCrossRefGoogle Scholar
  20. 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 278:1312–1314CrossRefGoogle Scholar
  21. 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 9:63–71CrossRefGoogle Scholar
  22. 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 48:501–510PubMedCrossRefGoogle Scholar
  23. 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 135:145–151PubMedCrossRefGoogle Scholar
  24. 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):125–133Google Scholar
  25. 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 133:359–366CrossRefGoogle Scholar
  26. 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):79–85Google Scholar
  27. Metzgar D, Bytof J, Wills C (2000) Selection against frame shift mutations limits microsatellite expansion in coding DNA. Genome Res 10:72–80PubMedGoogle Scholar
  28. 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 102:177–186CrossRefGoogle Scholar
  29. Nei M (1978) Estimation of average heterozygosity and genetic distance from small number of individuals. Genetics 89:583–590PubMedGoogle Scholar
  30. 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 141:721–731PubMedGoogle Scholar
  31. 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 109:800–805PubMedCrossRefGoogle Scholar
  32. Nybom H (2004) Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Mol Ecol 13:1143–1155PubMedCrossRefGoogle Scholar
  33. Perry DJ (2004) Identification of Canadian durum wheat varieties using a single PCR. Theor Appl Genet 109:55–61PubMedCrossRefGoogle Scholar
  34. 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 2:225–238CrossRefGoogle Scholar
  35. 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 100:584–592Google Scholar
  36. Rafalski A (2002) Application of single nucleotide polymorphism in crop genetics. Curr Opin Plant Biol 5:94–100PubMedCrossRefGoogle Scholar
  37. Röder MS, Korzun V, Wendehake K, Plaske J, Tixier M, Leroy P, Ganal M (1998) A microsatellite map of wheat. Genetics 149:2007–2023PubMedGoogle Scholar
  38. 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 106:67–73PubMedGoogle Scholar
  39. 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 95:714–722CrossRefGoogle Scholar
  40. 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 40:442–450PubMedCrossRefGoogle Scholar
  41. 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 3:429–441Google Scholar
  42. 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 108:612–618PubMedCrossRefGoogle Scholar
  43. 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 100:723–726CrossRefGoogle Scholar
  44. 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 103:346–352CrossRefGoogle Scholar
  45. 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 112:808–817CrossRefGoogle Scholar
  46. 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 106:411–422PubMedGoogle Scholar
  47. 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 47:805–818PubMedCrossRefGoogle Scholar
  48. Yu JK, La Rota M, Kantety RV, Sorrells ME (2004b) EST derived SSR markers for comparative mapping in wheat and rice. Mol Genet Genomics 271:742–751PubMedCrossRefGoogle Scholar
  49. Varshney RK, Graner A, Sorrells ME (2005a) Genic microsatellite markers: features and applications. Trends Biotechnol 23:48–55PubMedCrossRefGoogle Scholar
  50. 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 168:195–202CrossRefGoogle Scholar
  51. 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 113:239–250PubMedCrossRefGoogle Scholar
  52. 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: 186–195PubMedCrossRefGoogle Scholar
  53. 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 14:1681–1695CrossRefGoogle Scholar
  54. Zhang LY, Bernard M, Leroy P, Feuillet C (2005) High transferability of bread wheat EST-derived SSRs to other cereals. Theor Appl Genet 111:677–687PubMedCrossRefGoogle Scholar
  55. 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 53:1351–1360CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Kamel Chabane
    • 1
  • R. K. Varshney
    • 2
  • A. Graner
    • 3
  • J. Valkoun
    • 1
  1. 1.International Center for Agricultural Research in the Dry Areas (ICARDA)AleppoSyria
  2. 2.International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)PatancheruIndia
  3. 3.Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany

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