|Broh Bi, Irie|
Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/4/2005
Publication Date: 1/2/2006
Citation: Morton, B.R., Broh Bi, I., McMullen, M.D., Gaut, B.S. 2006. An analysis of neighboring nucleotide effects on SNPs in nuclear DNA from maize (zea mays). Genetics. 172:569-577. Interpretive Summary: Although the genetic variability generated by mutation is the underlying material required for the progress made by plant breeders during crop improvement, very little is known about DNA sequence factors affecting mutation rates in plants. In this study we demonstrate a number of diverse neighboring sequence effects on mutation rates in corn. These effects include both specific nucleotide effects where mutations are believed to be linked to chemical nucleotide modifications and more general regional effects on mutation rates, such as different mutation rates in high AT vs. high GC regions. These results are important in that they provide scientists clues to understanding the mechanisms underlying gene mutation in plants.
Technical Abstract: The composition of neighboring nucleotides influences the pattern and rate of mutation in plant organelle DNA and in vertebrate nuclear DNA. Here we study the influence of context on mutations in nuclear DNA from a plant (maize; Zea mays ssp. mays) using a dataset of 10,472 SNPs generated by resequencing 1,776 transcribed regions of the genome. We report a significant CpG effect in which the rate of transition is increased 2.1-fold at CpG dinucleotides, most likely as a result of the deamination of methylated cytosines. The strength of this effect is correlated with regional composition, ranging from a 1.7-fold increase in relatively G+C-rich regions to a 2.6-fold increase in A+T-rich regions. In contrast, cytosines in other contexts that are known to be methylated in plant nuclear DNA show no evidence for increased transition rates. In addition to the CpG effect we observe several other relationships between local context and mutation pattern. Most noticeably, the A+T content of the two sites immediately flanking the mutation site is correlated with rate, transition bias and GC -> AT pressure, a result that is similar to what has been reported for maize chloroplast DNA. At a regional level we observe a relationship between locus A+T content and GC -> AT pressure. The data indicate multiple context effects on mutations in the maize nuclear genome.