Dataset Information

Fine-Grained Analysis of Spontaneous Mutation Spectrum and Frequency in Arabidopsis thaliana.

ABSTRACT: 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 Arabidopsis thaliana 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 A. thaliana is 6.95 × 10-9 (SE ± 2.68 × 10-10) per site per generation, with SNMs having higher frequency in transposable elements (TEs) and centromeric regions. The estimated indel mutation rate is 1.30 × 10-9 (±1.07 × 10-10) 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 de novo 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.

SUBMITTER: Weng ML

PROVIDER: S-EPMC6366913 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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Publications

Fine-Grained Analysis of Spontaneous Mutation Spectrum and Frequency in <i>Arabidopsis thaliana</i>.

Weng Mao-Lun ML Becker Claude C Hildebrandt Julia J Neumann Manuela M Rutter Matthew T MT Shaw Ruth G RG Weigel Detlef D Fenster Charles B CB

Genetics 20181204 2

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 <i>Arabidopsis thaliana</i> 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 estimate ...[more]

PMID: 30514707

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Project description:Genetic variations are an important source of germplasm diversity, as it provides an allele resource that contributes to the development of new traits for plant breeding. Gamma rays have been widely used as a physical agent for mutation creation in plants, and their mutagenic effect has attracted extensive attention. However, few studies are available on the comprehensive mutation profile at both the large-scale phenotype mutation screening and whole-genome mutation scanning. In this study, biological effects on M1 generation, large-scale phenotype screening in M2 generation, as well as whole-genome re-sequencing of seven M3 phenotype-visible lines were carried out to comprehensively evaluate the mutagenic effects of gamma rays on Arabidopsis thaliana. A total of 417 plants with visible mutated phenotypes were isolated from 20,502 M2 plants, and the phenotypic mutation frequency of gamma rays was 2.03% in Arabidopsis thaliana. On average, there were 21.57 single-base substitutions (SBSs) and 11.57 small insertions and deletions (InDels) in each line. Single-base InDels accounts for 66.7% of the small InDels. The genomic mutation frequency was 2.78 × 10-10/bp/Gy. The ratio of transition/transversion was 1.60, and 64.28% of the C > T events exhibited the pyrimidine dinucleotide sequence; 69.14% of the small InDels were located in the sequence with 1 to 4 bp terminal microhomology that was used for DNA end rejoining, while SBSs were less dependent on terminal microhomology. Nine genes, on average, were predicted to suffer from functional alteration in each re-sequenced line. This indicated that a suitable mutation gene density was an advantage of gamma rays when trying to improve elite materials for one certain or a few traits. These results will aid the full understanding of the mutagenic effects and mechanisms of gamma rays and provide a basis for suitable mutagen selection and parameter design, which can further facilitate the development of more controlled mutagenesis methods for plant mutation breeding.

Dataset Information

Fine-Grained Analysis of Spontaneous Mutation Spectrum and Frequency in Arabidopsis thaliana.

Publications

Fine-Grained Analysis of Spontaneous Mutation Spectrum and Frequency in <i>Arabidopsis thaliana</i>.

Similar Datasets

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