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

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

T N Marriage et al. Heredity (Edinb). 2009 Oct.

Abstract

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 x 10(-3) per allele per generation), intermediate for CT (3.31 x 10(-4)), and lowest for CA (4.96 x 10(-5)). The average mutation rate per generation for this sample of loci is 8.87 x 10(-4) (s.e.=2.57 x 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.

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Figures

Figure 1

Figure 1

The number of lines scored as mutant is given as a function of initial allele length.

References

    1. Akashi H. Distinguishing the effects of mutational biases and natural selection on DNA sequence variation. Genetics. 1997;147:1989–1991. -PMC -PubMed
    1. Bachtrog D, Agis M, Imhof M, Schlötterer C. Microsatellite variability differs between dinucleotide repeat motifs- Evidence from Drosophila melanogaster . Mol Biol Evol. 2000;17:1277–1285. -PubMed
    1. Bakker EG, Stahl A, Toomajian C, Nordborg M, Kreitman M, Bergelson J. Distribution of genetic variation within and among local populations of Arabidopsis thaliana over its species range. Mol Ecol. 2006;15:1405–1418. -PubMed
    1. Balloux F, Lugon-Moulin N. The estimation of population differentiation with microsatellite markers. Mol Ecol. 2002;11:155–165. -PubMed
    1. Benson G. Tandem repeats finder: A progroam to analyze DNA sequences. Nucleic Acids Res. 1999;27:573–580. -PMC -PubMed

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