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. 2000 Dec;156(4):1997–2005. doi: 10.1093/genetics/156.4.1997

A simple sequence repeat-based linkage map of barley.

L Ramsay 1, M Macaulay 1, S degli Ivanissevich 1, K MacLean 1, L Cardle 1, J Fuller 1, K J Edwards 1, S Tuvesson 1, M Morgante 1, A Massari 1, E Maestri 1, N Marmiroli 1, T Sjakste 1, M Ganal 1, W Powell 1, R Waugh 1
PMCID: PMC1461369  PMID: 11102390

Abstract

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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  1. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389–3402. doi: 10.1093/nar/25.17.3389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Areshchenkova T., Ganal M. W. Long tomato microsatellites are predominantly associated with centromeric regions. Genome. 1999 Jun;42(3):536–544. [PubMed] [Google Scholar]
  3. Becker J., Heun M. Barley microsatellites: allele variation and mapping. Plant Mol Biol. 1995 Feb;27(4):835–845. doi: 10.1007/BF00020238. [DOI] [PubMed] [Google Scholar]
  4. Bennett M. D., Smith J. B. Nuclear dna amounts in angiosperms. Philos Trans R Soc Lond B Biol Sci. 1976 May 27;274(933):227–274. doi: 10.1098/rstb.1976.0044. [DOI] [PubMed] [Google Scholar]
  5. 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. doi: 10.1093/genetics/156.2.847. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Dubcovsky J., Luo M. C., Zhong G. Y., 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. doi: 10.1093/genetics/143.2.983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Dvorák J., Luo M. C., Yang Z. L. 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. doi: 10.1093/genetics/148.1.423. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Edwards K. J., Barker J. H., Daly A., Jones C., Karp A. Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques. 1996 May;20(5):758–760. doi: 10.2144/96205bm04. [DOI] [PubMed] [Google Scholar]
  9. Innan H., Terauchi R., Miyashita N. T. Microsatellite polymorphism in natural populations of the wild plant Arabidopsis thaliana. Genetics. 1997 Aug;146(4):1441–1452. doi: 10.1093/genetics/146.4.1441. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. 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. doi: 10.1093/genetics/154.1.397. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Moore G., Abbo S., Cheung W., Foote T., Gale M., Koebner R., Leitch A., Leitch I., Money T., Stancombe P. Key features of cereal genome organization as revealed by the use of cytosine methylation-sensitive restriction endonucleases. Genomics. 1993 Mar;15(3):472–482. doi: 10.1006/geno.1993.1097. [DOI] [PubMed] [Google Scholar]
  12. Moore G., Devos K. M., Wang Z., Gale M. D. Cereal genome evolution. Grasses, line up and form a circle. Curr Biol. 1995 Jul 1;5(7):737–739. doi: 10.1016/s0960-9822(95)00148-5. [DOI] [PubMed] [Google Scholar]
  13. Morgante M., Rafalski A., Biddle P., Tingey S., Olivieri A. M. Genetic mapping and variability of seven soybean simple sequence repeat loci. Genome. 1994 Oct;37(5):763–769. doi: 10.1139/g94-109. [DOI] [PubMed] [Google Scholar]
  14. Ostrander E. A., Jong P. M., 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. doi: 10.1073/pnas.89.8.3419. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Pearson W. R. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol. 1990;183:63–98. doi: 10.1016/0076-6879(90)83007-v. [DOI] [PubMed] [Google Scholar]
  16. 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. doi: 10.1046/j.1365-313x.1999.00392.x. [DOI] [PubMed] [Google Scholar]
  17. 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. doi: 10.1139/g97-059. [DOI] [PubMed] [Google Scholar]
  18. Röder M. S., Korzun V., Wendehake K., Plaschke J., Tixier M. H., Leroy P., Ganal M. W. A microsatellite map of wheat. Genetics. 1998 Aug;149(4):2007–2023. doi: 10.1093/genetics/149.4.2007. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Röder M. S., Plaschke J., König S. U., Börner A., Sorrells M. E., Tanksley S. D., Ganal M. W. Abundance, variability and chromosomal location of microsatellites in wheat. Mol Gen Genet. 1995 Feb 6;246(3):327–333. doi: 10.1007/BF00288605. [DOI] [PubMed] [Google Scholar]
  20. Saghai Maroof M. A., Biyashev R. M., Yang G. P., Zhang Q., Allard R. W. 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. doi: 10.1073/pnas.91.12.5466. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Saghai-Maroof M. A., Soliman K. M., Jorgensen R. A., Allard R. W. 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. doi: 10.1073/pnas.81.24.8014. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. 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. doi: 10.1007/s004380050502. [DOI] [PubMed] [Google Scholar]

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