Direct estimation of the mutation rate at dinucleotide microsatellite loci in Arabidopsis thaliana (Brassicaceae)

T. N. Marriage, S. Hudman, M. E. Mort, M. E. Orive, R. G. Shaw, J. K. Kelly

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The mutation rate at 54 perfect (uninterrupted) dinucleotide microsatellite loci is estimated by direct genotyping of 96 Arabidopsis thaliana mutation accumulation lines. The estimated rate differs significantly among motif types with the highest rate for AT repeats (2.03 × 10 -3 per allele per generation), intermediate for CT (3.31 × 10 -4), and lowest for CA (4.96 × 10 -5). The average mutation rate per generation for this sample of loci is 8.87 × 10 -4 (s.e.2.57 × 10 -4). There is a strong effect of initial repeat number, particularly for AT repeats, with mutation rate increasing with the length of the microsatellite locus in the progenitor line. Controlling for motif and initial repeat number, chromosome 4 exhibited an elevated mutation rate relative to other chromosomes. The great majority of mutations were gains or losses of a single repeat. Generally, the data are consistent with the stepwise mutation model of microsatellite evolution. Several lines exhibited multiple step changes from the progenitor sequence, but it is unclear whether these are multi-step mutations or multiple single-step mutations. A survey of dinucleotide repeats across the entire Arabidopsis genome indicates that AT repeats are most abundant, followed by CT, and CA.

Original languageEnglish (US)
Pages (from-to)310-317
Number of pages8
Issue number4
StatePublished - Oct 2009

Bibliographical note

Funding Information:
We thank J Gleason, S Macdonald, L Hileman, J Preston, J Mojica, and M Holder for comments on this paper. C Baer provided insightful criticism of an early draft. This research was supported by NIH grant GM073990 and NSF grant DEB-0543052 to JK Kelly, NSF grants DEB-9629457 and DEB-9981891 to RG Shaw, and NSF DEB-0108242 to M Orive. ME Mort acknowledges DEB-0344883. We thank S Macdonald and J Gleason for use of their laboratory equipment and Lisa Darmo for establishing the MA lines.


  • Arabidopsis
  • Dinucleotide repeats
  • Microsatellite
  • Mutation accumulation
  • Mutation rate


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