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Estimating a nucleotide substitution rate for maize from polymorphism at a major domestication locus
Richard M Clark1, Simon Tavaré, John Doebley
1Laboratory of Genetics, University of Wisconsin, USA. richard.clark@tuebingen.mpg.de
Molecular Biology and Evolution
|August 5, 2005
Summary
Maize domestication provides insights into single nucleotide substitution rates. DNA methylation significantly impacts mutation rates, with specific sites showing much higher activity.
Area of Science:
- Genetics
- Evolutionary Biology
- Bioinformatics
Background:
- Maize (Zea mays ssp. mays) domestication from teosinte (Z. mays ssp. parviglumis) involved selection on genes like teosinte branched1 (tb1).
- Low sequence diversity in the intergenic region 5' to tb1 suggests recent fixation of haplotypes.
Purpose of the Study:
- To estimate the single nucleotide substitution rate in maize.
- To investigate the influence of DNA methylation on mutation patterns.
Main Methods:
- Utilizing genetic and archaeological data on maize domestication.
- Applying coalescent and mutation-based approaches to estimate substitution rates.
- Analyzing polymorphism patterns in the tb1 intergenic region.
Main Results:
- Nucleotide substitution rate estimates for the tb1 intergenic region are approximately 2.9-3.3 x 10^-8 substitutions per site per year.
- DNA methylation significantly affects mutation rates, with CG and CNG sites exhibiting rates nearly an order of magnitude higher.
- Excluding methylated sites reduces overall mutation rate estimates by 50%-60%.
Conclusions:
- The tb1 region provides a valuable resource for estimating maize mutation rates.
- DNA methylation is a major driver of mutation in maize, particularly at specific sequence contexts.
- Mutation rate estimates inform the timing of transposable element expansion in the maize genome, suggesting a recent expansion within the last million years.