The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

Abstract

To take complete advantage of information on within-species polymorphism and divergence from close relatives, one needs to know the rate and the molecular spectrum of spontaneous mutations. To this end, we have searched for de novo spontaneous mutations in the complete nuclear genomes of five Arabidopsis thaliana mutation accumulation lines that had been maintained by single-seed descent for 30 generations. We identified and validated 99 base substitutions and 17 small and large insertions and deletions. Our results imply a spontaneous mutation rate of 7 × 10−9 base substitutions per site per generation, the majority of which are G:C→A:T transitions. We explain this very biased spectrum of base substitution mutations as a result of two main processes: deamination of methylated cytosines and ultraviolet light–induced mutagenesis.

The effect of induced mutations on quantitative traits in Arabidopsis thaliana: Natural versus artificial conditions

“…First, the estimate of the number of mutations induced in coding regions, and hence potentially affecting fitness, was far greater than the number of mutations accumulated in the studies of spontaneous mutations (25 here via mutagenesis vs. four per line via spontaneous mutations in Ossowski et al., 2010 as determined by direct sequence). The increase in the number of mutations potentially affecting fitness increases the probability that a large magnitude deleterious mutation will affect the line (Camara et al., 2000) and lead to a genetic death (Crow, 1997, 2000; Muller, 1950); that is, if mutations that have a strong deleterious effect on fitness occur with some regularity, increasing the number of mutations increases the chance that a line will get one of these mutations, and it will swamp the effects of any slightly beneficial mutations, dragging the fitness of the line down.…”

“…While the spectrum of mutations due to EMS is similar to that from spontaneous mutation (Greene et al., 2003; Ossowski et al., 2010), EMS does not result in indels and is therefore only a subset of natural spontaneous mutations. It is possible that mutations resulting in indels may have a different distribution of effects on fitness than the point mutations induced by EMS.…”

“…Arabidopsis thaliana has about 28,000 loci (Redei & Koncz, 1992). This mutation rate resulted in an approximate threefold to fourfold greater number of nonsynonymous mutations in protein coding sequence as quantified from direct sequencing (Ossowski et al., 2010) of Columbia mutation accumulation lines representing 30 generations of spontaneous mutation accumulation (Ossowski et al., 2010). These sequenced lines represented a subset of the mutation accumulation lines tested for field performance (Rutter et al., 2010, 2012).…”

“…Although this approach does bias the spectrum of mutation types dependent on the mutagenizing agent, mutagenesis has the advantage of being much quicker than MA approaches based on spontaneous naturally occurring mutations. The spontaneous mutation rate is roughly one to four mutations per zygote in many of the model organisms studied (e.g., Ossowski et al., 2010). Because many more mutations can be induced in a single bout of mutagenesis, the cumulative effect of many mutations can be more readily quantified.…”

Direct mutation analysis by high-throughput sequencing: From germline to low-abundant, somatic variants

“…The reduced cost and higher throughput of MPS has led to the first genome-wide estimates for germline mutation rates and spectra in yeast[85], worms[86], plants[87], and flies[88]. The experiments, run on both 454 and Illumina machines, used accumulation lines, where inbred populations accumulated mutations over many generations.…”