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Genetics. Nov 2003; 165(3): 1475–1488.
PMCID: PMC1462854

An analysis of microsatellite loci in Arabidopsis thaliana: mutational dynamics and application.

Abstract

Microsatellite loci are among the most commonly used molecular markers. These loci typically exhibit variation for allele frequency distribution within a species. However, the factors contributing to this variation are not well understood. To expand on the current knowledge of microsatellite evolution, 20 microsatellite loci were examined for 126 accessions of the flowering plant, Arabidopsis thaliana. Substantial variability in mutation pattern among loci was found, most of which cannot be explained by the assumptions of the traditional stepwise mutation model or infinite alleles model. Here it is shown that the degree of locus diversity is strongly correlated with the number of contiguous repeats, more so than with the total number of repeats. These findings support a strong role for repeat disruptions in stabilizing microsatellite loci by reducing the substrate for polymerase slippage and recombination. Results of cluster analyses are also presented, demonstrating the potential of microsatellite loci for resolving relationships among accessions of A. thaliana.

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Selected References

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  • Alonso-Blanco C, Koornneef M. Naturally occurring variation in Arabidopsis: an underexploited resource for plant genetics. Trends Plant Sci. 2000 Jan;5(1):22–29. [PubMed]
  • Bachtrog D, Agis M, Imhof M, Schlötterer C. Microsatellite variability differs between dinucleotide repeat motifs-evidence from Drosophila melanogaster. Mol Biol Evol. 2000 Sep;17(9):1277–1285. [PubMed]
  • Balloux François, Lugon-Moulin Nicolas. The estimation of population differentiation with microsatellite markers. Mol Ecol. 2002 Feb;11(2):155–165. [PubMed]
  • Barker GC. Microsatellite DNA: a tool for population genetic analysis. Trans R Soc Trop Med Hyg. 2002 Apr;96 (Suppl 1):S21–S24. [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]
  • Bergelson J, Stahl E, Dudek S, Kreitman M. Genetic variation within and among populations of Arabidopsis thaliana. Genetics. 1998 Mar;148(3):1311–1323. [PMC free article] [PubMed]
  • Borevitz Justin O, Liang David, Plouffe David, Chang Hur-Song, Zhu Tong, Weigel Detlef, Berry Charles C, Winzeler Elizabeth, Chory Joanne. Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res. 2003 Mar;13(3):513–523. [PMC free article] [PubMed]
  • Boutin-Ganache I, Raposo M, Raymond M, Deschepper CF. M13-tailed primers improve the readability and usability of microsatellite analyses performed with two different allele-sizing methods. Biotechniques. 2001 Jul;31(1):24–28. [PubMed]
  • Brohede Jesper, Primmer Craig R, Møller Anders, Ellegren Hans. Heterogeneity in the rate and pattern of germline mutation at individual microsatellite loci. Nucleic Acids Res. 2002 May 1;30(9):1997–2003. [PMC free article] [PubMed]
  • Casacuberta E, Puigdomènech P, Monfort A. Distribution of microsatellites in relation to coding sequences within the Arabidopsis thaliana genome. Plant Sci. 2000 Aug 8;157(1):97–104. [PubMed]
  • Chakraborty R, Kimmel M, Stivers DN, Davison LJ, Deka R. Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci. Proc Natl Acad Sci U S A. 1997 Feb 4;94(3):1041–1046. [PMC free article] [PubMed]
  • Clauss MJ, Cobban H, Mitchell-Olds T. Cross-species microsatellite markers for elucidating population genetic structure in Arabidopsis and Arabis (Brassicaeae). Mol Ecol. 2002 Mar;11(3):591–601. [PubMed]
  • Cornuet JM, Luikart G. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics. 1996 Dec;144(4):2001–2014. [PMC free article] [PubMed]
  • Cunniff C. Molecular mechanisms in neurologic disorders. Semin Pediatr Neurol. 2001 Sep;8(3):128–134. [PubMed]
  • Driscoll Carlos A, Menotti-Raymond Marilyn, Nelson George, Goldstein David, O'Brien Stephen J. Genomic microsatellites as evolutionary chronometers: a test in wild cats. Genome Res. 2002 Mar;12(3):414–423. [PMC free article] [PubMed]
  • Moriguchi Y, Iwata H, Ujino-Ihara T, Yoshimura K, Taira H, Tsumura Y. Development and characterization of microsatellite markers for Cryptomeria japonica D.Don. Theor Appl Genet. 2003 Feb;106(4):751–758. [PubMed]
  • Eckert Kristin A, Mowery Andrew, Hile Suzanne E. Misalignment-mediated DNA polymerase beta mutations: comparison of microsatellite and frame-shift error rates using a forward mutation assay. Biochemistry. 2002 Aug 20;41(33):10490–10498. [PubMed]
  • Nei M. Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci U S A. 1973 Dec;70(12):3321–3323. [PMC free article] [PubMed]
  • Ellegren H. Microsatellite mutations in the germline: implications for evolutionary inference. Trends Genet. 2000 Dec;16(12):551–558. [PubMed]
  • Noël L, Moores TL, van Der Biezen EA, Parniske M, Daniels MJ, Parker JE, Jones JD. Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis. Plant Cell. 1999 Nov;11(11):2099–2112. [PMC free article] [PubMed]
  • Noor MA, Kliman RM, Machado CA. Evolutionary history of microsatellites in the obscura group of Drosophila. Mol Biol Evol. 2001 Apr;18(4):551–556. [PubMed]
  • Ranum Laura P W, Day John W. Dominantly inherited, non-coding microsatellite expansion disorders. Curr Opin Genet Dev. 2002 Jun;12(3):266–271. [PubMed]
  • Estoup Arnaud, Jarne Philippe, Cornuet Jean-Marie. Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Mol Ecol. 2002 Sep;11(9):1591–1604. [PubMed]
  • Richard GF, Pâques F. Mini- and microsatellite expansions: the recombination connection. EMBO Rep. 2000 Aug;1(2):122–126. [PMC free article] [PubMed]
  • Rolfsmeier ML, Lahue RS. Stabilizing effects of interruptions on trinucleotide repeat expansions in Saccharomyces cerevisiae. Mol Cell Biol. 2000 Jan;20(1):173–180. [PMC free article] [PubMed]
  • Rubinsztein DC, Amos B, Cooper G. Microsatellite and trinucleotide-repeat evolution: evidence for mutational bias and different rates of evolution in different lineages. Philos Trans R Soc Lond B Biol Sci. 1999 Jun 29;354(1386):1095–1099. [PMC free article] [PubMed]
  • Gill P, Jeffreys AJ, Werrett DJ. Forensic application of DNA 'fingerprints'. Nature. 1985 Dec 12;318(6046):577–579. [PubMed]
  • Sakamoto T, Okamoto N. [Microsatellite linkage map of rainbow trout and its application for QTL analysis]. Tanpakushitsu Kakusan Koso. 2000 Dec;45(17 Suppl):2872–2879. [PubMed]
  • Grimaldi MC, Crouau-Roy B. Microsatellite allelic homoplasy due to variable flanking sequences. J Mol Evol. 1997 Mar;44(3):336–340. [PubMed]
  • Schug MD, Wetterstrand KA, Gaudette MS, Lim RH, Hutter CM, Aquadro CF. The distribution and frequency of microsatellite loci in Drosophila melanogaster. Mol Ecol. 1998 Jan;7(1):57–70. [PubMed]
  • Sharbel TF, Haubold B, Mitchell-Olds T. Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe. Mol Ecol. 2000 Dec;9(12):2109–2118. [PubMed]
  • Hauser MT, Harr B, Schlötterer C. Trichome distribution in Arabidopsis thaliana and its close relative Arabidopsis lyrata: molecular analysis of the candidate gene GLABROUS1. Mol Biol Evol. 2001 Sep;18(9):1754–1763. [PubMed]
  • Shriver MD, Jin L, Chakraborty R, Boerwinkle E. VNTR allele frequency distributions under the stepwise mutation model: a computer simulation approach. Genetics. 1993 Jul;134(3):983–993. [PMC free article] [PubMed]
  • Hile SE, Yan G, Eckert KA. Somatic mutation rates and specificities at TC/AG and GT/CA microsatellite sequences in nontumorigenic human lymphoblastoid cells. Cancer Res. 2000 Mar 15;60(6):1698–1703. [PubMed]
  • Sia EA, Kokoska RJ, Dominska M, Greenwell P, Petes TD. Microsatellite instability in yeast: dependence on repeat unit size and DNA mismatch repair genes. Mol Cell Biol. 1997 May;17(5):2851–2858. [PMC free article] [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]
  • Katti MV, Ranjekar PK, Gupta VS. Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol Biol Evol. 2001 Jul;18(7):1161–1167. [PubMed]
  • Thuillet Anne-Céline, Bru David, David Jacques, Roumet Pierre, Santoni Sylvain, Sourdille Pierre, Bataillon Thomas. Direct estimation of mutation rate for 10 microsatellite loci in durum wheat, Triticum turgidum (L.) Thell. ssp durum desf. Mol Biol Evol. 2002 Jan;19(1):122–125. [PubMed]
  • van Treuren R, Kuittinen H, Kärkkäinen K, Baena-Gonzalez E, Savolainen O. Evolution of microsatellites in Arabis petraea and Arabis lyrata, outcrossing relatives of Arabidopsis thaliana. Mol Biol Evol. 1997 Mar;14(3):220–229. [PubMed]
  • Litt M, Luty JA. A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet. 1989 Mar;44(3):397–401. [PMC free article] [PubMed]
  • Vigouroux Yves, Jaqueth Jennifer S, Matsuoka Yoshihiro, Smith Oscar S, Beavis William D, Smith J Stephen C, Doebley John. Rate and pattern of mutation at microsatellite loci in maize. Mol Biol Evol. 2002 Aug;19(8):1251–1260. [PubMed]
  • Lukowitz W, Gillmor CS, Scheible WR. Positional cloning in Arabidopsis. Why it feels good to have a genome initiative working for you. Plant Physiol. 2000 Jul;123(3):795–805. [PMC free article] [PubMed]
  • Vision TJ, Brown DG, Tanksley SD. The origins of genomic duplications in Arabidopsis. Science. 2000 Dec 15;290(5499):2114–2117. [PubMed]
  • Wierdl M, Dominska M, Petes TD. Microsatellite instability in yeast: dependence on the length of the microsatellite. Genetics. 1997 Jul;146(3):769–779. [PMC free article] [PubMed]
  • Matsuoka Y, Mitchell SE, Kresovich S, Goodman M, Doebley J. Microsatellites in Zea - variability, patterns of mutations, and use for evolutionary studies. Theor Appl Genet. 2002 Feb;104(2-3):436–450. [PubMed]
  • Zane L, Bargelloni L, Patarnello T. Strategies for microsatellite isolation: a review. Mol Ecol. 2002 Jan;11(1):1–16. [PubMed]
  • McCouch SR, Chen X, Panaud O, Temnykh S, Xu Y, Cho YG, Huang N, Ishii T, Blair M. Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Mol Biol. 1997 Sep;35(1-2):89–99. [PubMed]

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