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    Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition.

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    Date
    2006
    Author
    Morton, B.
    Vroh Bi, Irie
    McMullen, M.
    Gaut, B.
    Type
    Journal Article
    Metadata
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    Abstract
    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.
    https://doi.org/10.1534/genetics.105.049916
    Multi standard citation
    Permanent link to this item
    https://hdl.handle.net/20.500.12478/5505
    Digital Object Identifier (DOI)
    https://doi.org/10.1534/genetics.105.049916
    IITA Subjects
    Research Method; Genetic Improvement; Impact Assessment; Plant Diseases
    Agrovoc Terms
    Mutation; Genomes; Nucleotides
    Regions
    Acp; Africa; North America; South America; West Africa
    Countries
    United States; Colombia; Nigeria
    Collections
    • Journal and Journal Articles4136
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