Originally published as Genetics Published Articles Ahead of Print on October 11, 2005.

Genetics, Vol. 172, 569-577, January 2006, Copyright © 2006
doi:10.1534/genetics.105.049916

Variation in Mutation Dynamics Across the Maize Genome as a Function of Regional and Flanking Base Composition

Brian R. Morton^*,1, Irie V. Bi, Michael D. McMullen^, and Brandon S. Gaut

^* Department of Biological Sciences, Barnard College, Columbia University, New York, New York 10027, Department of Agronomy, Plant Sciences Unit, University of Missouri 65211, Columbia, Missouri, Plant Genetics Research Unit, USDA-ARS, Columbia, Missouri 65211 and Department of Ecology and Evolution, University of California, Irvine, California 92697

¹ Corresponding author: Department of Biological Sciences, Barnard College, Columbia University, 3009 Broadway, New York, NY 10027.
E-mail: bmorton{at}barnard.edu

We examine variation in mutation dynamics across a single genome (Zea mays ssp. mays) in relation to regional and flanking base composition using a data set of 10,472 SNPs generated by resequencing 1776 transcribed regions. We report several relationships between flanking base composition and mutation pattern. The A + T content of the two sites immediately flanking the mutation site is correlated with rate, transition bias, and GC AT pressure. We also observe a significant CpG effect, or increase in transition rate at CpG sites. At the regional level we find that the strength of the CpG effect is correlated with regional A + T content, ranging from a 1.7-fold increase in transition rate in relatively G + C-rich regions to a 2.6-fold increase in A + T-rich regions. We also observe a relationship between locus A + T content and GC AT pressure. This regional effect is in opposition to the influence of the two immediate neighbors in that GC AT pressure increases with increasing locus A + T content but decreases with increasing flanking base A + T content and may represent a relationship between genome location and mutation bias. The data indicate multiple context effects on mutations, resulting in significant variation in mutation dynamics across the genome.

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