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Genetics. Oct 2000; 156(2): 847–854.
PMCID: PMC1461288

Computational and experimental characterization of physically clustered simple sequence repeats in plants.

Abstract

The type and frequency of simple sequence repeats (SSRs) in plant genomes was investigated using the expanding quantity of DNA sequence data deposited in public databases. In Arabidopsis, 306 genomic DNA sequences longer than 10 kb and 36,199 EST sequences were searched for all possible mono- to pentanucleotide repeats. The average frequency of SSRs was one every 6.04 kb in genomic DNA, decreasing to one every 14 kb in ESTs. SSR frequency and type differed between coding, intronic, and intergenic DNA. Similar frequencies were found in other plant species. On the basis of these findings, an approach is proposed and demonstrated for the targeted isolation of single or multiple, physically clustered SSRs linked to any gene that has been mapped using low-copy DNA-based markers. The approach involves sample sequencing a small number of subclones of selected randomly sheared large insert DNA clones (e.g., BACs). It is shown to be both feasible and practicable, given the probability of fortuitously sequencing through an SSR. The approach is demonstrated in barley where sample sequencing 34 subclones of a single BAC selected by hybridization to the Big1 gene revealed three SSRs. These allowed Big1 to be located at the top of barley linkage group 6HS.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Akkaya MS, Bhagwat AA, Cregan PB. Length polymorphisms of simple sequence repeat DNA in soybean. Genetics. 1992 Dec;132(4):1131–1139. [PMC free article] [PubMed]
  • 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]
  • Antezana MA, Kreitman M. The nonrandom location of synonymous codons suggests that reading frame-independent forces have patterned codon preferences. J Mol Evol. 1999 Jul;49(1):36–43. [PubMed]
  • Bell CJ, Ecker JR. Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics. 1994 Jan 1;19(1):137–144. [PubMed]
  • Paglia GP, Olivieri AM, Morgante M. Towards second-generation STS (sequence-tagged sites) linkage maps in conifers: a genetic map of Norway spruce (Picea abies K.). Mol Gen Genet. 1998 Jun;258(5):466–478. [PubMed]
  • Bureau TE, Wessler SR. Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants. Plant Cell. 1994 Jun;6(6):907–916. [PMC free article] [PubMed]
  • Panaud O, Chen X, McCouch SR. Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet. 1996 Oct 16;252(5):597–607. [PubMed]
  • Chakraborty R, Stivers DN, Su B, Zhong Y, Budowle B. The utility of short tandem repeat loci beyond human identification: implications for development of new DNA typing systems. Electrophoresis. 1999 Jun;20(8):1682–1696. [PubMed]
  • Panstruga R, Büschges R, Piffanelli P, Schulze-Lefert P. A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome. Nucleic Acids Res. 1998 Feb 15;26(4):1056–1062. [PMC free article] [PubMed]
  • Cox R, Mirkin SM. Characteristic enrichment of DNA repeats in different genomes. Proc Natl Acad Sci U S A. 1997 May 13;94(10):5237–5242. [PMC free article] [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]
  • 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]
  • Dib C, Fauré S, Fizames C, Samson D, Drouot N, Vignal A, Millasseau P, Marc S, Hazan J, Seboun E, et al. A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature. 1996 Mar 14;380(6570):152–154. [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]
  • Dietrich WF, Miller J, Steen R, Merchant MA, Damron-Boles D, Husain Z, Dredge R, Daly MJ, Ingalls KA, O'Connor TJ. A comprehensive genetic map of the mouse genome. Nature. 1996 Mar 14;380(6570):149–152. [PubMed]
  • Echt CS, May-Marquardt P. Survey of microsatellite DNA in pine. Genome. 1997 Feb;40(1):9–17. [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]
  • Hamada H, Kakunaga T. Potential Z-DNA forming sequences are highly dispersed in the human genome. Nature. 1982 Jul 22;298(5872):396–398. [PubMed]
  • Lagercrantz U, Ellegren H, Andersson L. The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res. 1993 Mar 11;21(5):1111–1115. [PMC free article] [PubMed]
  • Stallings RL, Ford AF, Nelson D, Torney DC, Hildebrand CE, Moyzis RK. Evolution and distribution of (GT)n repetitive sequences in mammalian genomes. Genomics. 1991 Jul;10(3):807–815. [PubMed]
  • Sverdlov VE, Dukhanina OI, Hoebee B, Rapp JP. Linkage mapping of fifty-eight new rat microsatellite markers. Mamm Genome. 1998 Oct;9(10):816–821. [PubMed]
  • Weising K, Weigand F, Driesel AJ, Kahl G, Zischler H, Epplen JT. Polymorphic simple GATA/GACA repeats in plant genomes. Nucleic Acids Res. 1989 Dec 11;17(23):10128–10128. [PMC free article] [PubMed]
  • Manninen I, Schulman AH. BARE-1, a copia-like retroelement in barley (Hordeum vulgare L.). Plant Mol Biol. 1993 Aug;22(5):829–846. [PubMed]
  • Wu KS, Tanksley SD. Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet. 1993 Oct;241(1-2):225–235. [PubMed]
  • Milbourne D, Meyer RC, Collins AJ, Ramsay LD, Gebhardt C, Waugh R. Isolation, characterisation and mapping of simple sequence repeat loci in potato. Mol Gen Genet. 1998 Aug;259(3):233–245. [PubMed]
  • Zhao X, Kochert G. Characterization and genetic mapping of a short, highly repeated, interspersed DNA sequence from rice (Oryza sativa L.). Mol Gen Genet. 1992 Feb;231(3):353–359. [PubMed]
  • Morgante M, Olivieri AM. PCR-amplified microsatellites as markers in plant genetics. Plant J. 1993 Jan;3(1):175–182. [PubMed]

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