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

dc.contributor.authorMorton, B.
dc.contributor.authorVroh Bi, Irie
dc.contributor.authorMcMullen, M.
dc.contributor.authorGaut, B.
dc.date.accessioned2019-12-04T11:31:26Z
dc.date.available2019-12-04T11:31:26Z
dc.date.issued2006
dc.identifier.citationMorton, B., Vroh Bi, I., McMullen, M. & Gaut, B. (2006). Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition. Genetics, 172(1), 569- 577.
dc.identifier.issn0016-6731
dc.identifier.urihttps://hdl.handle.net/20.500.12478/5505
dc.description.abstractWe 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.
dc.description.sponsorshipNational Science Foundation
dc.description.sponsorshipUnited States Department of Agriculture
dc.language.isoen
dc.subjectMutation
dc.subjectGenomes
dc.subjectNucleotides
dc.titleVariation in mutation dynamics across the maize genome as a function of regional and flanking base composition.
dc.typeJournal Article
dc.description.versionPeer Review
cg.contributor.affiliationColumbia University
cg.contributor.affiliationUniversity of Missouri
cg.contributor.affiliationInternational Institute of Tropical Agriculture
cg.contributor.affiliationUnited States Department of Agriculture
cg.contributor.affiliationUniversity of California
cg.coverage.regionAcp
cg.coverage.regionAfrica
cg.coverage.regionNorth America
cg.coverage.regionSouth America
cg.coverage.regionWest Africa
cg.coverage.countryUnited States
cg.coverage.countryColombia
cg.coverage.countryNigeria
cg.isijournalISI Journal
cg.authorship.typesCGIAR and advanced research institute
cg.iitasubjectResearch Method
cg.iitasubjectGenetic Improvement
cg.iitasubjectImpact Assessment
cg.iitasubjectPlant Diseases
cg.accessibilitystatusLimited Access
local.dspaceid103862
cg.identifier.doihttps://doi.org/10.1534/genetics.105.049916


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