Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition
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 mutati...
| Autores principales: | , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Oxford University Press
2006
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/100083 |
| _version_ | 1855537644474204160 |
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| author | Morton, B. Vroh Bi, Irie McMullen, M. Gaut, B. |
| author_browse | Gaut, B. McMullen, M. Morton, B. Vroh Bi, Irie |
| author_facet | Morton, B. Vroh Bi, Irie McMullen, M. Gaut, B. |
| author_sort | Morton, B. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace100083 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2006 |
| publishDateRange | 2006 |
| publishDateSort | 2006 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1000832024-08-27T10:36:59Z Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition Morton, B. Vroh Bi, Irie McMullen, M. Gaut, B. mutation genomes nucleotides 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. 2006-01-01 2019-03-03T05:55:17Z 2019-03-03T05:55:17Z Journal Article https://hdl.handle.net/10568/100083 en Limited Access Oxford University Press Morton, 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. |
| spellingShingle | mutation genomes nucleotides Morton, B. Vroh Bi, Irie McMullen, M. Gaut, B. Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition |
| title | Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition |
| title_full | Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition |
| title_fullStr | Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition |
| title_full_unstemmed | Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition |
| title_short | Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition |
| title_sort | variation in mutation dynamics across the maize genome as a function of regional and flanking base composition |
| topic | mutation genomes nucleotides |
| url | https://hdl.handle.net/10568/100083 |
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