Table 3. Examples of induced mutation types and frequency in food crops and plant model species evaluated via WGRS analyses.
FN, Fast neutron; NaN3-MNU, sodium azide-methyl-nitro urea; GR, gamma ray; SV, structural variant
| Plant (Assembled Genome Size)a | Mutagen | No. of Plants Analyzed | Mean Mutations/Plantb (per diploid genome) | Total Mutation Frequencyc (mutations per nucleotide site per experiment) | Reference |
|---|---|---|---|---|---|
| Rice (O. sativa; 375 Mb) | FN | 1,504 | 29 SNPs | [1.6 × 10−7] | Li et al., 2017 |
| 26 indels | |||||
| 3 translocations | |||||
| 3 inversion /duplications | |||||
| 61 total | |||||
| GR | 6 | 2,419 SNPs | [8.86 × 10−6] | Li et al., 2016 | |
| 452 Indels | |||||
| 69 SV | |||||
| 383 CNV | |||||
| 3,323 total | |||||
| Tissue culture | 2 | 114 SNPs | 1.86 × 10−7 | Tang et al., 2018 | |
| 36 indels | |||||
| 150 total | |||||
| Sorghum (Sorghum bicolor; 708 Mb) | EMS | 256 | 7,660 SNPs | [1.1 × 10−5] | Jiao et al., 2016 |
| Soybean (G. max; 978 Mb) | EMS | 12 | 12,796 SNPs | [1.3 × 10−5] | Tsuda et al., 2015 |
| 12,854 SNPs (Md) | |||||
| Tomato (S. lycopersicum; 950 Mb)d | EMS | 4 | 1348 SNPs | [1.4 × 10−6] | Shirasawa et al., 2016 |
| 17 indels | |||||
| 1,365 total | |||||
| GR | 3 | 137 SNPs | [1.9 × 10−7] | ||
| 40 indels | |||||
| 177 total | |||||
| L. japonica (472 Mb)d | EMS | 2 | 2,201 SNPs | [4.7 × 10−6] | Mohd-Yusoff et al., 2015 |
| Arabidopsis (135 Mb) | GR | 6 | 11 SNPs (8.5 Md) | 3.6 × 10−7 | Belfield et al., 2012 |
| 7 indels (6.5 Md) | |||||
| 18 total | |||||
| Tissue culture | 5 | 26 SNP (18 Md) | 4.2 × 10−7–24.2 × 10−7 | Jiang et al., 2011 | |
| 4 indels (5 Md) | |||||
| 30 total |
Assembled genome size is based on information from the EnsemblPlants database (http://plants.ensembl.org) unless otherwise noted.
The mean number of mutations per analyzed plant are either published values or were calculated based on total mutations observed across all plants divided by the number of plants analyzed. All plants listed are diploids and studies confirmed full (>90%) genomic coverage unless otherwise noted (see footnote c). For some studies, median values (Md) for numbers of mutations per plant were also calculated.
Total mutation frequency is based on published values or was calculated (numbers in brackets) by dividing total mutations per plant by the assembled genome size. As noted, total mutation frequency was not limited to a single type of mutation.
Average genome sequence coverage was <90% for tomato (86% coverage; 815 Mb) and L. japonica (67% coverage; 315 Mb); partial genomic coverage values were used to normalize the number of mutations per diploid genome and to calculate total mutation frequency.