Advertisement

Theoretical and Applied Genetics

, Volume 93, Issue 5–6, pp 869–876 | Cite as

Development of simple sequence repeat DNA markers and their integration into a barley linkage map

  • Z. -W. Liu
  • R. M. Biyashev
  • M. A. Saghai Maroof
Article

Abstract

Simple sequence repeats (SSRs), or microsatellites, are a new class of PCR-based DNA markers for genetic mapping. The objectives of the present study were to develop SSR markers for barley and to integrate them into an existing barley linkage map. DNA sequences containing SSRs were isolated from a barley genomic library and from public databases. It is estimated that the barley genome contains one (GA)n repeat every 330 kb and one (CA)n repeat every 620 kb. A total of 45 SSRs were identified and mapped to seven barley chromosomes using doubled-haploid lines and/or wheat-barley addition-line assays. Segregation analysis for 39 of these SSRs identified 40 loci. These 40 markers were placed on a barley linkage map with respect to 160 restriction fragment length polymorphism (RFLP) and other markers. The results of this study demonstrate the value of SSRs as markers in genetic studies and breeding research in barley.

Key words

Microsatellites Hordeum vulgare Molecular marker Linkage map 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Akkaya MS, Bhagwat AA, Cregan PB (1992) Length polymorphisms of simple sequence repeat DNA in soybean. Genetics 132:1132–1139Google Scholar
  2. Akkaya MS, Shoemaker RC, Specht JE, Bhagwat AA, Cregan PB (1995) Integration of simple sequence repeat DNA markers into a soybean linkage map. Crop Sci 35:1439–1445Google Scholar
  3. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218Google Scholar
  4. Becker J, Heun M (1995) Barley microsatellites: allele variation and mapping. Plant Mol Biol 27:835–845PubMedGoogle Scholar
  5. Bell CJ, Ecker JR (1994) Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics 19:137–144Google Scholar
  6. Bronson CR, Taga M, Yoder OC (1990) Genetic control and distorted segregation of T-toxin production in field isolates of Cochliobolus heterotrophus. Phytopathology 80:819–823Google Scholar
  7. Brummer EC, Bouton JH, Kochert G (1993) Development of an RFLP map in diploid alfalfa. Theor Appl Genet 86:329–332Google Scholar
  8. Cregan PB, Akkaya MS, Bhagwat AA, Lavi U, Rongwen J (1994) Length polymorphisms of simply sequence repeat (SSR) DNA as molecular markers in plants. In: Gresshoff PM (ed) Plant Genome Analysis. CRC Press, Boca Raton, Florida, pp 47–56Google Scholar
  9. Graner A, Siedler H, Jahoor A, Herrmann RG, Wenzel G (1990) Assessment of the degree and type of restriction fragment length polymorphism in barley (Hordeum vulgare). Theor Appl Genet 80:826–832Google Scholar
  10. Graner A, Jahoor A, Schondelmaier J, Siedler H, Pillen K, Fischbeck G, Wenzel G, Herrmann RG (1991) Construction of an RFLP map of barley. Theor Appl Genet 83:250–256Google Scholar
  11. Heun M, Kennedy AE, Anderson JA, Lapitan NLV, Sorrels ME, Tanksley SD (1991) Construction of a restriction fragment length polymorphism map for barley (Hordeum vulgare). Genome 34:437–447Google Scholar
  12. Islam AKMR, Shepherd KW, Sparrow DHB (1981) Isolation and characterization of euplasmic wheat-barley chromosome addition lines. Heredity 46:161–174Google Scholar
  13. Kandpal RP, Kandpal G, Weissman SM (1994) Construction of libraries enriched for sequence repeats and jumping clones, and hybridization selection for region-specific markers. Proc Natl Acad Sci USA 91:88–92Google Scholar
  14. Kleinhofs A, Kilian A (1994) RFLP maps of barley. In: Phillips RL, Vasil IK (eds) Advances in cellular and molecular biology of plants, vol 1: DNA-based markers in plants. Klumer Academic Publishers, the Netherlands, pp 163–198Google Scholar
  15. Kleinhofs A, Kilian A, Saghai Maroof MA, Biyashev RM, Hayes P, Chen FQ, Lapitan N, Fenwick A, Blake TK, Kanazin V, Ananiev E, Dahleen L, Kudrna D, Bollinger J, Knapp SJ, Liu B, Sorrells M, Heun M, Franckowiak JD, Hoffman D, Skadsen R, Steffenson BJ (1993) A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome. Theor Appl Genet 86:705–712Google Scholar
  16. Lagercrantz U, Ellegren H, Andersson L (1993) The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res 21:1111–1115Google Scholar
  17. Lander ES, Green P, Abrahamson J, Barlow A, Daly M, Lincoln S, Newburg L (1987) Mapmaker: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genetics 1:174–181Google Scholar
  18. Liu, Z-W, Jarret RL, Kresovich S, Duncan RR (1995) Characterization and analysis of simple sequence repeat (SSR) loci in seashore paspalum (Paspalum vaginatum Swartz). Theor Appl Genet 91:47–52Google Scholar
  19. Maughan PJ, Saghai Maroof MA, Buss GR (1995) Microsatellite and amplified sequence length polymorphisms in cultivated and wild soybean. Genome 38:715–723Google Scholar
  20. Mongante M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J 3:175–182CrossRefPubMedGoogle Scholar
  21. Morgante M, Rafalski A, Bidle P, Tingey S, Oliveri AM (1994) Genetic mapping and variability of seven soybean simple sequence repeat loci. Genome 37:763–769Google Scholar
  22. Ostrander EA, Jong PM, Rine J, Duyk G (1992) Construction of small-insert genomic DNA libraries highly enriched for microsatellite repeat sequences. Proc Natl Acad Sci USA 89:3419–3423Google Scholar
  23. Röder MS, Plaschke J, Konig SU, Borner A, Sorrells ME, Tanksley SD, Ganal MW (1995) Abundance, variability and chromosomal location of microsatellites in wheat. Mol Gen Genet 246:327–333PubMedGoogle Scholar
  24. Rongwen J, Akkaya MS, Bhagwat AA, Lavi U, Cregan PB (1995) The use of microsatellite DNA markers for soybean genotype identification. Theor Appl Genet 90:43–48Google Scholar
  25. Saghai Maroof MA, Soliman KM, Jorgenson RA, Allard RW (1984) Ribosomal DNA spacer length polymorphism in barley: Mendelian inheritance, chromosomal location and population dynamics. Proc Natl Acad Sci USA 81:8014–8018PubMedGoogle Scholar
  26. Saghai Maroof MA, Biyashev RB, Yang GP, Zhang Q, Allard RW (1994) Extraordinarily polymorphic microsatellite DNA in barley: species diversity, chromosomal locations, and population dynamics. Proc Natl Acad Sci USA 91:5466–5470PubMedGoogle Scholar
  27. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, New YorkGoogle Scholar
  28. Senior ML, Heun M (1993) Mapping maize microsatellites and polymerase chain reaction confirmation of the targeted repeats using a CT primer. Genome 36:884–889Google Scholar
  29. Suiter KA, Wendel JF, Case JS (1983) LINKAGE-1: a PASCAL computer program for the detection and analysis of genetic linkage. J Hered. 74:203–204Google Scholar
  30. Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471PubMedGoogle Scholar
  31. Walther-Larsen H, Brandt J, Collinge DB, Thordal-Christensen H (1993) A pathogen-induced gene of barley encodes a HSP90 homologue showing striking similarity to vertebrate forms resident in the endoplasmic reticulum. Plant Mol biol 21:1097–1108Google Scholar
  32. Wang Z, Weber JL, Zhong G, Tanksley SD (1994) Survey of plant short tandem DNA repeats. Theor Appl Genet 88:1–6Google Scholar
  33. Weber JL (1990) Human DNA polymorphisms based on length variations in simple-sequence tandem repeats. In: Davies KE, Tilghman SM (eds) Genome analysis, vol 1: genetic and physical mapping, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, pp 159–181Google Scholar
  34. Wu KS, Tanksley SD (1993) Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet 241:225–235PubMedGoogle Scholar
  35. Yang GP, Saghai Maroof MA, Xu CG, Zhang Q, Biyashev RB (1994) Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice. Mol Gen Genet 245:187–194PubMedGoogle Scholar
  36. Yu YG, Saghai Maroof MA, Buss GR, Maughan PJ, Tolin SA (1994) RFLP and microsatellite mapping of a gene for soybean mosaic virus resistance. Phytopathology 84:60–64Google Scholar
  37. Zhang Q, Gao YJ, Yang SH, Ragab R, Saghai Maroof MA, Li ZB (1994) A diallel analysis of heterosis in elite hybrid rice based on RFLPs and microsatellites. Theor Appl Genet 89:185–192Google Scholar
  38. Zhao X, Kochert G (1993). Phylogenetic distribution and genetic mapping of a (GGC)n microsatellite from rice (Oryza sativa L.). Plant Mol Biol 21:607–614Google Scholar

Copyright information

© Springer-Verlag 1996

Authors and Affiliations

  • Z. -W. Liu
    • 1
  • R. M. Biyashev
    • 1
  • M. A. Saghai Maroof
    • 1
  1. 1.Department of Crop and Soil Environmental SciencesVirginia Polytechnic Institute and State UniversityBlacksburgUSA

Personalised recommendations