Fine-Grained Analysis of Spontaneous Mutation Spectrum and Frequency in Arabidopsis thaliana
Mutations are the ultimate source of all genetic variation. However, few direct estimates of the contribution of mutation to molecular genetic variation are available. To address this issue, we first analyzed the rate and spectrum of mutations in the reference accession after 25 generations of singl...
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Published in | Genetics (Austin) Vol. 211; no. 2; pp. 703 - 714 |
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Main Authors | , , , , , , , |
Format | Journal Article |
Language | English |
Published |
United States
Genetics Society of America
01.02.2019
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Subjects | |
Online Access | Get full text |
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Summary: | Mutations are the ultimate source of all genetic variation. However, few direct estimates of the contribution of mutation to molecular genetic variation are available. To address this issue, we first analyzed the rate and spectrum of mutations in the
reference accession after 25 generations of single-seed descent. We then compared the mutation profile in these mutation accumulation (MA) lines against genetic variation observed in the 1001 Genomes Project. The estimated haploid single nucleotide mutation (SNM) rate for
is 6.95 × 10
(SE ± 2.68 × 10
) per site per generation, with SNMs having higher frequency in transposable elements (TEs) and centromeric regions. The estimated indel mutation rate is 1.30 × 10
(±1.07 × 10
) per site per generation, with deletions being more frequent and larger than insertions. Among the 1694 unique SNMs identified in the MA lines, the positions of 389 SNMs (23%) coincide with biallelic SNPs from the 1001 Genomes population, and in 289 (17%) cases the changes are identical. Of the 329 unique indels identified in the MA lines, 96 (29%) overlap with indels from the 1001 Genomes dataset, and 16 indels (5% of the total) are identical. These overlap frequencies are significantly higher than expected, suggesting that
mutations are not uniformly distributed and arise at polymorphic sites more frequently than assumed. These results suggest that high mutation rate potentially contributes to high polymorphism and low mutation rate to reduced polymorphism in natural populations providing insights of mutational inputs in generating natural genetic diversity. |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Present address: Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Austria. Present address: Department of Biology, Westfield State University, Westfield, MA 01086. |
ISSN: | 1943-2631 0016-6731 1943-2631 |
DOI: | 10.1534/genetics.118.301721 |