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Genetics. Dec 2000; 156(4): 1997–2005.
PMCID: PMC1461369

A simple sequence repeat-based linkage map of barley.


A total of 568 new simple sequence repeat (SSR)-based markers for barley have been developed from a combination of database sequences and small insert genomic libraries enriched for a range of short simple sequence repeats. Analysis of the SSRs on 16 barley cultivars revealed variable levels of informativeness but no obvious correlation was found with SSR repeat length, motif type, or map position. Of the 568 SSRs developed, 242 were genetically mapped, 216 with 37 previously published SSRs in a single doubled-haploid population derived from the F(1) of an interspecific cross between the cultivar Lina and Hordeum spontaneum Canada Park and 26 SSRs in two other mapping populations. A total of 27 SSRs amplified multiple loci. Centromeric clustering of markers was observed in the main mapping population; however, the clustering severity was reduced in intraspecific crosses, supporting the notion that the observed marker distribution was largely a genetical effect. The mapped SSRs provide a framework for rapidly assigning chromosomal designations and polarity in future mapping programs in barley and a convenient alternative to RFLP for aligning information derived from different populations. A list of the 242 primer pairs that amplify mapped SSRs from total barley genomic DNA is presented.

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Selected References

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  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389–3402. [PMC free article] [PubMed]
  • Areshchenkova T, Ganal MW. Long tomato microsatellites are predominantly associated with centromeric regions. Genome. 1999 Jun;42(3):536–544. [PubMed]
  • Becker J, Heun M. Barley microsatellites: allele variation and mapping. Plant Mol Biol. 1995 Feb;27(4):835–845. [PubMed]
  • Bennett MD, Smith JB. Nuclear dna amounts in angiosperms. Philos Trans R Soc Lond B Biol Sci. 1976 May 27;274(933):227–274. [PubMed]
  • Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R. Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics. 2000 Oct;156(2):847–854. [PMC free article] [PubMed]
  • Dubcovsky J, Luo MC, Zhong GY, Bransteitter R, Desai A, Kilian A, Kleinhofs A, Dvorák J. Genetic map of diploid wheat, Triticum monococcum L., and its comparison with maps of Hordeum vulgare L. Genetics. 1996 Jun;143(2):983–999. [PMC free article] [PubMed]
  • Dvorák J, Luo MC, Yang ZL. Restriction fragment length polymorphism and divergence in the genomic regions of high and low recombination in self-fertilizing and cross-fertilizing aegilops species. Genetics. 1998 Jan;148(1):423–434. [PMC free article] [PubMed]
  • Edwards KJ, Barker JH, Daly A, Jones C, Karp A. Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques. 1996 May;20(5):758–760. [PubMed]
  • Innan H, Terauchi R, Miyashita NT. Microsatellite polymorphism in natural populations of the wild plant Arabidopsis thaliana. Genetics. 1997 Aug;146(4):1441–1452. [PMC free article] [PubMed]
  • Künzel G, Korzun L, Meister A. Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics. 2000 Jan;154(1):397–412. [PMC free article] [PubMed]
  • Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier MH, Leroy P, Ganal MW. A microsatellite map of wheat. Genetics. 1998 Aug;149(4):2007–2023. [PMC free article] [PubMed]
  • Russell J, Fuller J, Young G, Thomas B, Taramino G, Macaulay M, Waugh R, Powell W. Discriminating between barley genotypes using microsatellite markers. Genome. 1997 Aug;40(4):442–450. [PubMed]
  • Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW. Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci U S A. 1984 Dec;81(24):8014–8018. [PMC free article] [PubMed]
  • Saghai Maroof MA, Biyashev RM, Yang GP, Zhang Q, Allard RW. Extraordinarily polymorphic microsatellite DNA in barley: species diversity, chromosomal locations, and population dynamics. Proc Natl Acad Sci U S A. 1994 Jun 7;91(12):5466–5470. [PMC free article] [PubMed]
  • Moore G, Abbo S, Cheung W, Foote T, Gale M, Koebner R, Leitch A, Leitch I, Money T, Stancombe P, et al. Key features of cereal genome organization as revealed by the use of cytosine methylation-sensitive restriction endonucleases. Genomics. 1993 Mar;15(3):472–482. [PubMed]
  • Moore G, Devos KM, Wang Z, Gale MD. Cereal genome evolution. Grasses, line up and form a circle. Curr Biol. 1995 Jul 1;5(7):737–739. [PubMed]
  • Morgante M, Rafalski A, Biddle P, Tingey S, Olivieri AM. Genetic mapping and variability of seven soybean simple sequence repeat loci. Genome. 1994 Oct;37(5):763–769. [PubMed]
  • Ostrander EA, Jong PM, Rine J, Duyk G. Construction of small-insert genomic DNA libraries highly enriched for microsatellite repeat sequences. Proc Natl Acad Sci U S A. 1992 Apr 15;89(8):3419–3423. [PMC free article] [PubMed]
  • Pearson WR. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol. 1990;183:63–98. [PubMed]
  • Ramsay L, Macaulay M, Cardle L, Morgante M, degli Ivanissevich S, Maestri E, Powell W, Waugh R. Intimate association of microsatellite repeats with retrotransposons and other dispersed repetitive elements in barley. Plant J. 1999 Feb;17(4):415–425. [PubMed]
  • Waugh R, Bonar N, Baird E, Thomas B, Graner A, Hayes P, Powell W. Homology of AFLP products in three mapping populations of barley. Mol Gen Genet. 1997 Jul;255(3):311–321. [PubMed]
  • Röder MS, Plaschke J, König SU, Börner A, Sorrells ME, Tanksley SD, Ganal MW. Abundance, variability and chromosomal location of microsatellites in wheat. Mol Gen Genet. 1995 Feb 6;246(3):327–333. [PubMed]

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